Chapter 2Mendels Breakthrough: Patterns, Particles, and Principles of Heredity Fill in the Blank 1.

A _______________________ is a sequence of nucleotides that are basic units of biological information. Ans: gene Difficulty: 1 2. _______________________ is the science of heredity and it seeks a precise explanation of the biological structures and mechanisms that determine what is inherited and how it is inherited. Ans: Genetics Difficulty: 1 3. _______________________ is the purposeful control over mating by choice of parents for the next generation. Ans: Artificial selection Difficulty: 1 4. _______________________ is the process whereby both egg and pollen come from the same plant. Ans: Self fertilization Difficulty: 1 5. _______________________ is a Mendelian law that states both alleles must separate during gamete formation. Ans: Law of segregation Difficulty: 1 6. ___________, _____________ and _____________ all were involved in the rediscovery of Mendel's research. Ans: Corens, deVaries, Tschermak Difficulty: 1 Describe below the meaning of each symbol. 7. _______________________ Ans: Normal male Difficulty: 1

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8. _______________________ Ans: Normal female Difficulty: 1 9. _______________________ Ans: Marriage Difficulty: 1 10. _______________________ Ans: Affected male Difficulty: 2 11. _______________________ Inherited trait expressed only when the controlling gene is homozygous. Ans: Recessive Difficulty: 2 12. ________________________ One contrasting form of a gene. Ans: Allele Difficulty: 2 13. ________________________ Symbol for the grandparents of a given individual. Ans: P2 Difficulty: 2 14. ________________________ The observable properties of an organism that are under genetic control. Ans: Phenotype Difficulty: 2 Multiple Choice

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15. A) B) C) D) E)

The first offspring from the parents are called: P. F1. F2. testcross. backcross. Ans: B Difficulty: 1 A _____________ is a cross between an unknown and a homozygous recessive. testcross dihybrid monohybrid backcross controlled Ans: A Difficulty: 1

16. A) B) C) D) E)

17. If an individual has 10 gene pairs, how many different gametes can be formed if three of the gene pairs are homozygous and the remaining 7 gene pairs are heterozygous? A) 49 B) 100 C) 128 D) 1024 E) 131,072 Ans: C Difficulty: 4 18. If the parents of a family already have two boys, what is the probability that the next two offspring will be girls? A) 1 B) 1/2 C) 1/3 D) 1/4 E) 1/8 Ans: D Difficulty: 2

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19. In some genetically engineered corn plants the dominant gene (BT) produces a protein that is lethal to certain flying insect pests that eat the corn plants. It was also found that the pollen could also cause death in some flying insects. If the corn plant is heterozygous for BT, what proportion of the pollen would carry the dominant gene? A) All pollen B) 1/2 C) 1/3 D) 1/4 E) 1/8 Ans: B Difficulty: 1 20. Suppose that in plants, smooth seeds (S) are dominant to wrinkle seeds (s) and tall plants (T) are dominant to short plants (t). A tall plant with smooth seeds was backcrossed to a parent that was short and wrinkle. What proportion of the progeny is expected to be heterozygous for tall and smooth? A) 1/2 B) 1/4 C) 1/8 D) 1/16 E) 0 Ans: B Difficulty: 2 21. Suppose that in plants, smooth seeds (S) are dominant to wrinkle seeds (s) and tall plants (T) are dominant to short plants (t). A tall plant with smooth seeds was backcrossed to a parent that was short and wrinkle. What proportion of the progeny is expected to be homozygous for short and wrinkle? A) 1/2 B) 1/4 C) 1/8 D) 1/16 E) 0 Ans: B Difficulty: 2

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22. Sickle cell anemia is a recessive trait in humans. In a cross between a father who has sickle cell anemia and a mother is heterozygous for the gene, what is the probability that their first three children will be normal? A) 1/4 B) 1/2 C) none D) 1/8 E) 1/16 will be albino Ans: D Difficulty: 2 23. The dominant trait, Huntington disease causes severe neural/brain damage at approximately age 40. A female whose mother has Huntington disease, marries a male whose parents are normal. It is not known if the female has the disease. What is the probability that their first-born will inherit the gene that causes Huntington disease? A) 25% B) 50% C) 75% D) 100% E) 0% Ans: A Difficulty: 1 24. In a monohybrid cross AA aa, how many homozygotes are found among the F2 offspring? A) one B) two C) three D) four E) five Ans: B Difficulty: 1 25. In a monohybrid cross AA aa, how many heterozygotes are found among the F2 offspring? A) one B) two C) three D) four E) five Ans: B Difficulty: 1

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26. In a dihybrid cross AAbb aaBB, how many homozygotes are found among the F2 offspring? A) one B) two C) three D) four E) five Ans: D Difficulty: 1 27. In a dihybrid cross AABB aabb, how many heterozygotes at both gene pairs are found among the F2 offspring? A) one B) two C) three D) four E) five Ans: D Difficulty: 1 28. In the dihybrid cross AaBb aabb, how many homozygotes are found among the F1 offspring? A) one B) two C) three D) four E) five Ans: A Difficulty: 1 29. In the dihybrid cross AaBb aabb, how many heterozygotes for both gene pairs are found among the F1 offspring? A) one B) two C) three D) four E) five Ans: A Difficulty: 1

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30. A) B) C) D) E)

Among the dihybrid crosses below, which will give a 1:1 ratio? AABB aabb AaBb AaBb AaBb aabb AaBB aaBB AAbb aaBB Ans: D Difficulty: 1 Among the dihybrid crosses below, which will give a 1:1:1:1 ratio? AABB aabb AaBb AaBb AaBb aabb AaBB aaBB AAbb aaBB Ans: B Difficulty: 1

31. A) B) C) D) E)

32. Assume that in guinea pigs, dark brown fur (B) is dominant to black fur (b). If you mate a heterozygous black guinea pig with a homozygous brown guinea pig, what proportion of the progeny will be black? A) none B) 1/4 C) 1/2 D) 3/4 E) all Ans: D Difficulty: 1 33. Assume that in guinea pigs, dark brown fur (B) is dominant to black fur (b). If you mate a homozygous black guinea pig with a homozygous brown guinea pig, what proportion of the progeny will be heterozygous? A) none B) 1/4 C) 1/2 D) 3/4 E) all Ans: C Difficulty: 1

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34. Assume that in guinea pigs, dark brown fur (B) is dominant to black fur (b). If you mate a black guinea pig with a homozygous brown guinea pig, what proportion of the progeny will be homozygous? A) none B) 1/4 C) 1/2 D) 3/4 E) all Ans: C Difficulty: 1 Matching Match the following terms with the best definition
a. b. c. d. e. self-fertilization cross fertilize monohybrid crosses artificial selection reciprocal crosses

35. ______ the purposeful control of mating by choice of parents for the next generation. Ans: d Difficulty: 1 36. ______ fertilization in which both egg and pollen come from the same plant, resulting in offspring with the same genetic traits as the single parent. Ans: a Difficulty: 1 37. ______ to brush the pollen from one plant onto the female organ of another plant, thereby creating offspring with the particular traits of the selected parent plants. Ans: b Difficulty: 1 38. ______ crosses in which the male and female traits are reversed, thereby controlling whether a particular trait is transmitted by the egg or the pollen. Ans: e Difficulty: 1

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39. A) B) C) D) E)

______ crosses between parents that differ in only one trait. self-fertilization cross fertilize monohybrid crosses artificial selection reciprocal crosses Ans: C Difficulty: 1

40. An allele that expresses its phenotype even when heterozygous with a recessive allele is termed: A) recessive B) recombinant C) dominant D) parental E) independant Ans: C Difficulty: 1 41. A) B) C) D) E) An alternative form of a single gene is known as a(n): parental dihybrid reciprocal allele recessive Ans: D Difficulty: 1

42. The diploid cell formed by the fertilization of the egg by the sperm during sexual reproduction is a(n): A) reciprocal B) zygote C) dihybrid D) gamete E) monohybrids Ans: B Difficulty: 1

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43. A phenotype reflecting a new combination of genes occurring during gamete formation is called: A) a recombinant type B) an independent assortment C) heterozygous D) homozygous E) a mutlihybrid cross Ans: A Difficulty: 1 44. A) B) C) D) E) The actual alleles present in an individual are called their: recombinant types zygote dominant allele allele genotype Ans: E Difficulty: 1

True or False 45. Mendel was the only botanist to work with large numbers of offspring, to count all offspring, subject his results to statistical analysis and then compare his results with predictions based on his models. Ans: False Difficulty: 2 46. The mating of parents with antagonistic traits produces hybrids. Ans: True Difficulty: 1 47. Mendel's law of segregation states that two alleles for each trait unite in a specific manner during gamete formation and therefore give rise to predictable observable traits. Ans: False Difficulty: 2 48. The Punnett square was introduced in 1906 by Reginald Punnett and provides a simple and convenient method of tracking possible combinations of gametes that might be produced in a given cross. Ans: True Difficulty: 1

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49. Using the product rule, one would calculate the probability of parents having six children who are all boys as ()6. Ans: True Difficulty: 1 50. The sum rule states that the probability of both of two mutually exclusive events occurring is the sum of their individual probabilities. Ans: False Difficulty: 3 (either, not both) 51. If you know the phenotype and the dominance relation of the alleles you can predict the genotype. Ans: True Difficulty: 1 52. An individual can be a heterozygote for one trait and a homozygote for another. Ans: True Difficulty: 1 53. A testcross is a cross between two heterozygotes. Ans: False Difficulty: 2 54. At fertilization, in the mating of dihybrids, four different kinds of eggs can combine with four different kinds of pollen, producing a total of 16 different genotypes. Ans: False Difficulty: 2 55. During gamete formation, different pairs of alleles segregate independently of each other. Ans: False Difficulty: 3 (not if linked) 56. If yellow and round phenotypes in peas are dominant, you know the genotype of all peas that are green and wrinkled. Ans: False Difficulty: 2 57. A pedigree is a family history of a specific trait shown for a minimum of three generations. Ans: True Difficulty: 1

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58. Several single-gene disorders are more common in some populations of people than others. Ans: True Difficulty: 1 59. A lethal disorder does not include the inheritance of traits that cause death in adulthood. Ans: False Difficulty: 2 60. The following symbols ~" Ans: True Difficulty: 1 " indicate a consanguineous mating.

61. Cross-fertilization is the same thing as reciprocal cross. Ans: False Difficulty: 2 62. The first filial generation is the offspring of parents. Ans: True Difficulty: 1 63. A zygote is a fertilized egg. Ans: False Difficulty: 1 64. A YY or yy genotype is called heterozygous. Ans: False Difficulty: 2 65. When Mendel repeated his pea experiments in bean, he found flowers that ranged from white to pale violet to purple. This is due to bean flower color being determined by more than one gene. Ans: True Difficulty: 1 Short Answer 66. In corn liguleless, (l1) is recessive to ligules (L1) and a green leaf (G) is dominant to the normal non-green (g). If a plant homozygous for liguleless and green leaves is crossed to one homozygous for non-green with ligules, predict the phenotypes and genotypes of the F1. Ans: Genotype Phenotype LlGg Ligules/Green Difficulty: 1

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67. If an F1 plant from the question above were test crossed, what would be the phenotypes and genotypes of the progeny? Ans: Genotype Phenotype LlGg/Ligules Green Llgg/Ligules non-green llGg/Liguless Green llgg/Liguless non-green Difficulty: 3 68. In corn liguleless, (l1) is recessive to ligules (L1) and a green leaf (G) is dominant to the normal non-green (g). If a plant homozygous for liguleless and green leaves is crossed to one homozygous for non-green with ligules predict the phenotypes and genotypes of the F2. Ans: Genotype Phenotype 1:LLGG/Ligules Green 2:LLGg/Ligules Green 2:LlGG/Ligules Green 4:LlGg/Ligules Green 1:LLgg/Ligules non-green 2:Llgg/Ligules non-green 1:llGG/Liguless Green 2:llGg/Liguless Green 1:llgg/Liguless non-green Difficulty: 3 69. In Drosophila, forked (fk) bristles are recessive to normal (fk+) and glassy eyes (gls) are recessive to wild (gls+). If a homozygous wild-type male is mated to a forked bristle, glassy eye female, predict the genotypes and phenotypes of the F1. Ans: Genotype Phenotype fk+fk gls+gls wildtype Difficulty: 1 70. If an F1 female from the cross in question 69. was backcrossed to its male parent, predict the genotypes and phenotypes of the offspring. Ans: Genotype Phenotype fk+fk+gls+gls+ Wild type fk+fk+gls+gls Wild type + + + fk fk gls gls Wild type fk+fk gls+gls Wild type Difficulty: 2

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71. In Drosophila, forked (fk) bristles are recessive to normal (fk+) and glassy eyes (gls) are recessive to wild (gls+). If a homozygous wild-type male is mated to a forked bristle, glassy eye female, predict the genotypes and phenotypes of the F2. Ans: Genotype Phenotype 1:fk+fk+ gls+gls+ Wild 2:fk+fk+ gls+gls Wild 2:fk+fk gls+gls+ Wild 4:fk+fk gls+gls Wild 1:fk+fk+ glsgls Glassy 2:fk+fk glsgls Glassy 1:fkfk gls+gls+ Forked 2:fkfk gls+gls Forked 1:fkfkglsgls Forked and Glassy Difficulty: 3 72. A rosy-eyed Drosophila was crossed with a forked Drosophila. The F1 were all wildtype while the F2 consisted of 306 wild-type, 94 rosy-eyed, 102 fork-bristled and 33 forked-bristled and rosy-eyed flies. Infer the genotypes of the parents. Ans: Both parents are homozygotes; AAbb aaBB. Difficulty: 2 73. In pecans, the outer shell may be thick (T) or thin (t). The shell of pecans is the pericarp. If you use the pollen from a homozygous thick shell to pollinate a thin shell tree, what shell type would form on the tree following the cross?

Ans: Genotype pp Difficulty: 3

Phenotype thin

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74. If you use the seed from the pecans of the above cross to produce an F2, what type of shells will form on the F1 plant?

Ans: Genotype Pp Difficulty: 3

Phenotype thick

75. After a cross between two corn plants, the F1 plants all had a dwarfed phenotype. The F2 consisted of 1,207 dwarf plants and 401 tall plants. Identify the phenotypes and genotypes of the two parents.

Ans: Parent A DD/dwarf Difficulty: 2

Parent B dd/tall

76. After a cross between two mice, the F1 offspring all had the same phenotype. The F2 consisted of 91 short tails and 29 normal tails. Identify the phenotypes and genotypes of the two parents plants.

Ans: Parent A SS/Short tails Difficulty: 2

Parent B ss/Long tails

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Below is a pedigree for a human trait. Shaded symbols are for individuals showing the trait. (A) Identify the mode of inheritance of the trait. (B) Apply the laws of probability and calculate the probability the offspring of the cousin marriage will have the trait.

77. Mode of inheritance Ans: Recessive Difficulty: 1 78. Prob. 1 6 Ans: 1/3 Difficulty: 4 79. Prob. 3 7 Ans: 1/6 Difficulty: 4

_________________

____________________

____________________

80. In some plants, a purple pigment is synthesized from a colorless precursor. In a cross between two plants, one purple and the other colorless produced an F1 that was purple. The F2 produced from the F1 had 775 purple, 200 Red and 65 colorless. What is the genotype of the parents?

Ans: The ratio is a 12:3:1; Parents: AABB aabb Difficulty: 3 81. Short hair in rabbits is governed by a dominant gene (l+) and long hair by its recessive allele (l). Black hair results from the action of the dominant gene (b+) and brown hair is from its allele (b). Give the genotypic and the corresponding phenotypic ratios of the F1 from a cross of a female rabbit with brown hair and male rabbit with long hair. This assumes female is homozygous for short hair and male is homozygous for black hair. Ans: Genotype Phenotype l+l b+b Difficulty: 1

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82. Short hair in rabbits is governed by a dominant gene (l+) and long hair by its recessive allele (l). Black hair results from the action of the dominant gene (b+) and brown hair is from its allele (b). Give the genotypic and the corresponding phenotypic ratios of the F2 from a cross of a female rabbit with brown hair and male rabbit with long hair. This assumes female is homozygous for short hair and male is homozygous for black hair. Ans: # Genotype Phenotype 1 l+l+ b+b+ Short Black 2 l+l b+b+ Short Black 2 l+l+ b+b Short Black 4 l+l b+b Short Black 1 l+l+ bb Short Brown 2 l+l bb Short Brown 1 ll b+b+ Long Black 2 ll b+b Long Black 1 llbb Long Brown Difficulty: 3 83. Stem color of tomato plants is known to be under the genetic control of at least one pair of alleles such that A- results in the production of anthocyanin pigment (purple stem). The recessive genotype aa lacks this pigment and hence is green. The production of two locules in the tomato fruit is controlled by the dominant allele M and multiple locules is determined by mm. Give the genotypic and phenotypic ratios of the F1 a cross between an inbred tomato plant that has a purple stem and fruit with two locules crossed to a tomato plant that have fruit with multiple locules and a green stem. Ans: Genotype Phenotype AaMm Purple & 2 locules Difficulty: 2

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84. Stem color of tomato plants is known to be under the genetic control of at least one pair of alleles such that A- results in the production of anthocyanin pigment (purple stem). The recessive genotype aa lacks this pigment and hence is green. The production of two locules in the tomato fruit is controlled by the dominant allele M and multiple locules is determined by mm. Give the genotypic and phenotypic ratios of the F2 from a cross between an inbred tomato plant that has a purple stem and fruit with two locules crossed to a tomato plant that have fruit with multiple locules and a green stem. Ans: # Genotype Phenotype 1 AAMM Purple, 2 locules 2 AaMM Purple, 2 locules 2 AAMm Purple, 2 locules 4 AaMm Purple, 2 locules 1 aaMM Green, 2 locules 2 aaMm Green, 2 locules 1 AAmm Purple, Multi loc 2 AAMm Purple, Multi loc 1 aamm Green, Multi loc Difficulty: 3 85. What does a diamond symbol in a pedigree indicate? Ans: sex unspecified Difficulty: 2 86. What is does a vertical pattern of inheritance in a pedigree likely indicate? Ans: rare dominant trait Difficulty: 2 87. Calculate the probability of the production of a homozygous recessive genotype for the following cross: AaBbccddEeFf AaBbCcddEeFf Ans: 1 Difficulty: 3 88. Calculate the probability of either all dominant or all recessive genotypes for the alleles A, B, E, and F in the following cross: AaBbccddEeFf AaBbCcddEeFf Ans: ( ) + ( ) Difficulty: 4 89. What are the four general themes that have arisen from Mendel's work? Ans: Variation, as expressed in alternative forms of a trait, is widespread in nature. Observable variation is essential for following inheritance of traits. Variation is not distributed by chance alone but is inherited according to the genetic tenet that like begets like. Mendel's laws apply to all sexually reproducing organisms. Difficulty: 4

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Diagram Problems What are the possible genotypes of persons 1, 2, 3 and 4?

90. Person 1 Ans: Aa Difficulty: 2 91. Person 2 Ans: Aa Difficulty: 2 92. Person 3 Ans: Aa Difficulty: 2 93. Person 4 Ans: aa Difficulty: 2 94. Below is a pedigree of a human genetic disease in which stricken individuals are solidcolored. Apply the laws of probability and calculate the probability the offspring of the cousin marriages a) 2 3 will have the disease.

Ans: The trait is a recessive trait: Difficulty: 2

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95. Below is a pedigree of a human genetic disease in which stricken individuals are solid colored. Apply the laws of probability and calculate the probability the offspring of the cousin marriages a) 1 4

Ans: The trait is a recessive trait; Difficulty: 1 Experimental Design and Interpretation of Data 96. A youngster has dozens of pet mice and asks you why their coat colors are so different. He explains that his favorite color is black with white patches and wonders how he can get more of them, yet his favorite mice are actually the nice white ones who are gentler than the active nippy black ones. You decide to give a simple genetics lesson. Help the youngster set up an artificial selection for nice, black mice with white spots, including an indication of expected results and an interpretation of the data. Ans: Breed male black mice with female white mice and male white mice with female black mice. Interbreed the offspring. Test all black mice with white spots for gentle behavior and breed the gentlest males to the gentlest females. If the genes for coat color and gentle behavior are unlinked, not closely linked, or not the same gene, this experimental design will result in the production of gentle mice that are black with white spots. If selection pressure is continued for numerous generations, the genes will become fixed in the population and gentle black mice with white spots will always result. Difficulty: 4 97. As an owner of an orchard you realize that the selective breeding of apple trees to produce the most beautiful red apples have left customers with a displeasure toward the now bland tasting beautiful apples. The results indicate what about the two traits? How would you as an orchard owner fix the problem for the long-term? Ans: The genes for taste and red color are not linked. To fix the beautiful, tasteless, apple problem, a rederivation of the apples is necessary. It will be necessary to cross the beautiful red apple tree with apples with outstanding taste. Each generation should be observed for taste and color with the most tasty and colorful being crossed to each other. As you might imagine, fixing the problem in your orchard will take a very long time. Difficulty: 4

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98. You are out on a nature walk up in the mountains and you find a pretty wild flower in the lower altitude that is short and bushy with small fragrant, bright purple flowers and in the higher altitude you find what seems to be the same plant yet it is tall and sparse with larger flowers of the same color and fragrance. a) Set up an experiment to test the hypothesis that the plants are different due to genetic but not environmental influences. b) Is it possible to tell if both genetic and environmental effects occur? Ans: a) Obtain several specimens from each location. Plant seeds of both types of plants in both low and high altitude locations. Observe the offspring. If the offspring look the same as their parental stock then the differences are simply genetic in nature. If the offspring look short and bushy with small fragrant, bright purple flowers in the lower altitude and tall and sparse with larger flowers of the same color and fragrance in the higher altitude then the differences are due to simple environmental influences. b) Yes, a combination of the traits would indicate that both environmental and genetic influences play a role in the differences you have identified. Difficulty: 3 99. You wish to know the genotype of some carrot plants that you have grown in your garden so that you might grow more of them. They have redish-orange flesh, are sweet in taste, long in root and short in leaf. Using classical genetic techniques how would you determine the genotype? Ans: You need to determine the recessive nature of each trait. Set up crosses between redish-orange, sweet tasting flesh, long in root and short in leaf and true orange, plain tasting, short in root and long in leaf to determine each dominant trait. Then create a tester plant that is recessive for all four traits. Cross your favorite carrot plants with the tester and observe the offspring. The traits shown in the offspring are indicative of the genotype of your original carrot plant. Difficulty: 4 100. You are talking to your father about your relatives and he shares with you that there is a late-onset disease that seems to run in his family. What could you do to determine your probability of having this late-onset disease? Ans: Create a pedigree of your family tree for the late-onset disease going back at least three but as many generations as possible. Based on your pedigree, you will need to determine whether the trait is recessive or dominant, autosomal or X-linked. Use the product rule to determine the probability of your having inherited the trait. Keep in mind that individuals not old enough to show the trait should be diagramed as unknowns on your pedigree and your probability of inheriting the disease may depend on whether that given individual has the trait. Difficulty: 2

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Chapter 3Extensions to Mendel: Complexities in Relating Genotype to Phenotype Fill in the Blank 1. The proportion of all copies of a gene in a population that are of a given allele type is called ________________________ __________________________. Ans: allele frequency Difficulty: 1 2. A wild-type allele is an allele designated by a superscript plus sign (+) whose frequency is greater than ________ percent. Ans: one Difficulty: 1 3. A gene with only one wild-type allele is called _______________________________. Ans: monomorphic Difficulty: 2 4. A ________________________ is a non-inherited change in phenotype arising from environmental affects that mimic the effect of a mutation in a gene. Ans: phenocopy Difficulty: 2 5. _________________________________ refers to traits determined by two or more factors, including multiple genes interacting with each other or one or more genes interacting with the environment. Ans: mulitfactorial Difficulty: 1 6. _______________________ genes produce a subtle, secondary effect on phenotype by altering the effect of the alleles of other genes. Ans: modifier Difficulty: 1 7. A ______________________________ trait or continuous trait is an inherited trait that exhibits many intermediate forms; determined by segregating alleles of many different genes whose interaction with each other and the environment produces the phenotype. Ans: quantitative Difficulty: 2 8. A phenomenon in which a single gene determines a number of distinct and seemingly unrelated characteristics is called __________________________. Ans: pleiotropy Difficulty: 1

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9. ____________________________ is the degree or intensity with which a particular genotype is expressed in a phenotype. Ans: expressivity Difficulty: 1 10. If all individuals carrying a dominant mutant gene show the mutant phenotype, the gene is said to show complete ___________________________. Ans: penetrance Difficulty: 1 Multiple Choice 11. The interaction between non-allelic genes that results in the expression of a phenotype is: A) epistasis. B) epigenetics. C) dominance. D) codominance. E) incomplete dominance. Ans: A Difficulty: 1 12. A) B) C) D) E) Which of the following diseases show pleiotropism? albinism muscular dystrophy colorblindness sickle cell anemia male pattern baldness Ans: D Difficulty: 1

13. A deviation from normal Mendelian ratios which may be resolved by counting and/or controlled crosses, is seen in which of the following terms? A) pleiotropy B) codominance C) incomplete dominance D) complete dominance E) penetrance and expressivity Ans: E Difficulty: 1

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14. A) B) C) D) E)

Which of the following ratios show incomplete dominance? 2:1 3:1 1:2:1 1:1 4:1 Ans: C Difficulty: 2 Which of the following ratios show codominance? 2:1 3:1 1:2:1 1:1 4:1 Ans: C Difficulty: 1 Which of the following ratios indicates a lethal gene? 2:1 3:1 1:2:1 1:1 4:1 Ans: A Difficulty: 2 A person who has type O blood has: anti-A antibodies. anti-B antibodies. anti-AB antibodies. both anti-A and -B antibodies. no surface antigens. Ans: D Difficulty: 2 If two or more forms of the same gene exist, the different forms are called: incomplete dominance. penetrance and expressivity. pleiotropic. multiple alleles. dihybrid. Ans: D Difficulty: 2

15. A) B) C) D) E)

16. A) B) C) D) E)

17. A) B) C) D) E)

18. A) B) C) D) E)

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19. A) B) C) D) E)

The blood groups A, B and O are: incomplete dominance. penetrance and expressivity. pleiotrophic. multiple alleles. dihybrid. Ans: D Difficulty: 1 The blood groups A, B and O show: complete dominance. recessive. codominance. a, b, and c none of the above Ans: D Difficulty: 2 Which of the following monohybrid ratios can describe incomplete and codominance? 2:1 3:1 1:3 1:2:1 4:1 Ans: D Difficulty: 1 Which of the following ratios demonstrate gene interaction? 2:1 3:1 1:2:1 9:3:4 1:3 Ans: D Difficulty: 1 A _____________ results whenever the nucleotide sequence is changed. phenotype genotype mutation trait character Ans: C Difficulty: 1

20. A) B) C) D) E)

21. A) B) C) D) E)

22. A) B) C) D) E)

23. A) B) C) D) E)

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24. When the same gene is related to respiratory problems and sterility, it can be described as: A) pleiotropy. B) codominance. C) incomplete dominance. D) complete dominance. E) penetrance and expressivity. Ans: A Difficulty: 1 25. A) B) C) D) E) Another name for a normal gene is: wild-type. pleiotropy. dominant. codominant. recessive. Ans: A Difficulty: 1 The genetic ratio 1:2:1 may indicate: complete dominance. codominance. epistasis. recessive lethal. b and c only Ans: B Difficulty: 1 The genetic ratio 3 : 1 may indicate: complete dominance. codominance. epistasis. incomplete dominance. b and c only Ans: A Difficulty: 1 The genetic ratio 2:1 may indicate: complete dominance. codominance. epistasis. recessive lethal. b and c only Ans: D Difficulty: 1

26. A) B) C) D) E)

27. A) B) C) D) E)

28. A) B) C) D) E)

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29. A) B) C) D) E)

The genetic ratio 9:7 may indicate: complete dominance. codominance. epistasis. recessive lethal. b and c only Ans: C Difficulty: 1 The genetic ratio 9:3:4 may indicate: complete dominance. codominance. epistasis. recessive lethal. b and c only Ans: C Difficulty: 1 Which of the following show independent assortment? 9:3:3:1 9:7 9:3:4 13:3 all of the above Ans: E Difficulty: 1

30. A) B) C) D) E)

31. A) B) C) D) E)

Matching Write the correct phase of epistasis, pleiotropy, complete dominance, recessive, incomplete dominance, or co-dominance for each question. 32. equal expression Ans: co-dominant Difficulty: 2 33. partial expression Ans: incomplete dominance Difficulty: 2 34. expressed in the heterozygous or homozygous conditions Ans: complete dominance Difficulty: 2

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35. blood type AB Ans: co-dominant Difficulty: 2 36. neither gene is fully expressed Ans: incomplete dominance Difficulty: 2 37. only expressed in the homozygous condition Ans: recessive Difficulty: 2 38. whenever the allele is present it is expressed Ans: dominant Difficulty: 2 39. gene interaction Ans: epistasis Difficulty: 2 40. a gene that has more than one effect Ans: pleiotrophic Difficulty: 2 41. blood type IAIO Ans: co-dominant Difficulty: 1 True or False 42. Multifactorial inheritance is when a phenotype arises as a result of the interaction of one or more genes with the environment and/or each other. Ans: True Difficulty: 1 43. The flower colors white, pink and red indicate codominant inheritance. Ans: False Difficulty: 2 44. When a late blooming pea and an early blooming pea are crossed and an intermediate phenotype occurs, this result would suggest incomplete dominant inheritance. Ans: False Difficulty: 2

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45. In codominance, F1 hybrids show the traits of both parents. Ans: True Difficulty: 1 46. Different alleles indicate unique genes. Ans: False Difficulty: 1 47. Mutations are the source of new alleles. Ans: True Difficulty: 1 48. A wild-type allele is any allele whose frequency is closest to 100%. Ans: False Difficulty: 2 49. A mutant allele is one that with a frequency less than 1%. Ans: True Difficulty: 2 50. Genes with more than one wild-type allele are termed polymorphic. Ans: True Difficulty: 2 51. The mouse agouti gene has one wild-type allele and several mutant alleles. Ans: True Difficulty: 2 52. The phenomenon of a single gene determining a number of distinct and seemingly unrelated characteristics is known as pleiotropy. Ans: True Difficulty: 1

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Short Answer 53. In corn three dominant genes are necessary for aleurone color. The genotype B__D__R is colored. Any homozygous recessive for one gene is colorless. Predict the genotypes and phenotypes of the offspring of the cross BbDdRr BbDdRr Ans: Phenotype: 27 colored; 37 colorless Ratio of Genotype 1 BBDDrr 2 BbDDrr 2 BBDdrr 4 BbDdrr 1 BBDDrr 2 BBDDrr 1 BBDDrr 2 BBDDrr 1 BBDDrr 2 BBDDRr 4 BBDdRr 4 BbDDRr 8 BbDdRr 2 BBddRr 4 BbddRr 2 bbDDRr 4 bbDdRr 2 bbddRr 1 BBDDRR 2 BbDDRR 2 BBDdRR 4 BbDdRR 1 bbDDRR 2 bbDdRR 1 BBddRR 2 bbDdRR 1 bbddRR Difficulty: 4

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54. In corn three dominant genes are necessary for aleurone color. The genotype B__D__R is colored. Any homozygous recessive for one gene is colorless. Predict the genotypes and phenotypes of the offspring of the cross BbDdRR BbDdRR Ans: Phenotype: 9 Color; 7 Colorless Ratio of Genotype_ 1 BBDDRR 2 BbDDRR 2 BBDdRR 4 BbDdRR 1 bbDDRR 2 bbDdRR 1 BBddRR 2 bbDdRR 1 bbddRR Difficulty: 3 55. In corn three dominant genes are necessary for aleurone color. The genotype B__D__R is colored. Any homozygous recessive for one gene is colorless. Predict the genotypes and phenotypes of the offspring of the cross BbDdRR BbDdrr Ans: Phenotype: 9 Color; 7 Colorless Ratio of Genotypes 1 BBDDRr 2 BBDdRr 2 BbDDRr 4 BbDdRr 1 BBddRr 2 BbddRr 1 bbDDRr 2 bbDdRr 1 bbddRr Difficulty: 4 56. In the rat the gene for the pigment (P) is dominant to no pigment (p). The gene for black (B) is dominant to the gene for cream (b). If a pigment gene (P) is absent, genes B and b are inoperative. Predict the genotypes and phenotypes of the F1 of a cross between a homozygous black rat and an albino homozygous for cream. Ans: Genotype Phenotype PpBb Black Difficulty: 1

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57. In the rat the gene for the pigment (P) is dominant to no pigment (p). The gene for black (B) is dominant to the gene for cream (b). If a pigment gene (P) is absent, genes B and b are inoperative. Predict the genotypes and phenotypes of the F2 of a cross between a homozygous black rat and an albino homozygous for cream. Ans: 9 Black; 3 cream; 4 colorless Genotype Phenotype 1 PPBB Black 2 PPBb Black 2 PpBB Black 4 PpBb Black 1 ppBB colorless 2 ppBb colorless 1 PPbb cream 2 Ppbb cream 1 ppbb colorless Difficulty: 2 58. In the common daisy the genes A and a, B and b represent two pairs of alleles acting on flower color. A and B are required for color. The alleles of these two genes show recessive epistasis. The two gene pairs together, thus show duplicate recessive epistasis. Predict the genotypes and phenotypes of the F1 of a cross between two colorless plants, one homozygous for A and the other homozygous for B. Ans: Genotype Phenotype AaBb Color Difficulty: 1 59. In the common daisy the genes A and a, B and b represent two pairs of alleles acting on flower color. A and B are required for color. The alleles of these two genes show recessive epistasis. The two gene pairs together, thus show duplicate recessive epistasis. Predict the genotypes and phenotypes of the F2 of a cross between two colorless plants, one homozygous for A and the other homozygous for B. Ans: 9 Black; 7 colorless Genotype Phenotype 1 AABB Color 2 AABb Color 2 AaBB Color 4 AaBb Color 1 aaBB colorless 2 aaBb colorless 1 AAbb colorless 2 Aabb colorless 1 aabb colorless Difficulty: 2

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Corn in Alabama and Tennessee were both found to produce colorless aleurone in corn seeds. When these two plants were crossed the resulting F1 had Purple Aleurone. When the F1 was crossed to produce and F2 the results were 270 purple and 210 Colorless aleurone. 60. What is the genotype of the F1 progeny? Ans: The F1 is a heterozygote; BbDd from parents BBdd and bbDD Difficulty: 1 61. What are the genotypes and corresponding phenotype of the F2? Ans: Genotype Phenotype 1 BBDD Color 2 BbDD Color 2 BBDd Color 4 BbDd Color 1 bbDD colorless 2 bbDd colorless 1 BBdd colorless 2 Bbdd colorless 1 bbdd colorless Difficulty: 3 62. Give the possible biosynthetic pathway for gene activity. Ans: A BSubstrate Intermediate Color aa BSubstrate xxxxxxxxx Colorless Abb Substrate Intermediate Colorless Difficulty: 3 63. In poultry, if a Black Longshank male with feathered shanks is crossed with a Buff Rock female with unfeathered shanks the F1 are all feathered and the F2 show 90 feathered to 6 unfeathered. Infer the genotypes of the parents. Ans: AABB aabb; The ratio is a 15:1 which is a dihybrid ratio; therefore the parents are homozygous and produce a heterozygous F1. Difficulty: 2 The following five mothers, (a) through (e), with given phenotypes, each produced one child whose phenotype is described as to blood group (A,B,O), M or N antigens, and Rh factor. For each child, select as the father one of the five males whose genotypes are given. (ii = Type O blood) [rr = rh- & R = rh+]

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64. Child of Mother (a) = Father ____________ Ans: 4 Difficulty: 3 65. Child of Mother (b) = Father _________ Ans: 3 Difficulty: 3 66. Child of Mother (c) = Father _________ Ans: 1 or 4 Difficulty: 3 67. Child of Mother (d) = Father _________ Ans: 2 or 5 Difficulty: 3 68. Child of Mother (e) = Father _________ Ans: 1 Difficulty: 3 100 Nicotiana plants were tested for self and cross sterility and were found to fall into groups which had the following relationships with respect to offspring: Male Parent

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Identify the allelic constitutions of EACH: 69. A ________________________ Ans: S1S2 Difficulty: 4 70. B ________________________ Ans: S3S4 Difficulty: 4 71. C ________________________ Ans: S3S5 Difficulty: 4 72. D ________________________ Ans: S2S5 Difficulty: 4 73. E ________________________ Ans: S1S4 Difficulty: 4 74. F ________________________ Ans: S2S3 Difficulty: 4 75. G ________________________ Ans: S2S4 Difficulty: 4 76. H ________________________ Ans: S1S3 Difficulty: 4 77. M ________________________ Ans: S1S5 Difficulty: 4

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78. R ________________________ Ans: S4S5 Difficulty: 4 These data represent the occurrence of the same gene in different mutants. It is sometimes referred to as complementation mapping. In the table, O indicates that both organisms are mutant for the same gene. The + indicates the mutants carry the mutation in different genes. The boxes on top of the lines indicate the mutants A through F. If the lines overlap then the two mutations are in the same gene. Use the data in the table to determine which boxes contain the appropriate mutation. Place the alphabet in the appropriate boxes on each line to show complementation (different genes) & non-complementation (same gene). Two answers have been provided: Mutants A and F are mutant in the same gene. Mutants A and F have a O in the table, therefore their lines should overlap.

79. Ans: B Difficulty: 3 80. Ans: D or E Difficulty: 81. Ans: C Difficulty: 82. Ans: D or E Difficulty:

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Genes A and B are required for color. If A or B are absent (a or b) the result is colorless. Give the genotypes and phenotypes for each F1 and F2 below.

83. Aabb aabb Ans: F1=Aabb/Colorless; F2= 1AAbb:2Aabb:1aabb/All colorless Difficulty: 2 84. aaBB aaBB Ans: F1=aaBb/Colorless; F2= 1aaBB:2aaBb:1aabb/All colorless Difficulty: 2 85. AAbb aabb Ans: 9 Color; 7 Colorless Genotype Phenotype F1=AaBb Color F2=1AABB Color 2AABb Color 2AaBB Color 4AaBb Color 1aaBB Colorless 1AAbb Colorless 2aaBb Colorless 2Aabb Colorless 1aabb Colorless Difficulty: 3 Coat color in a certain species of rabbit is governed by multiple alleles. The hierarchy with reference to dominance for these alleles are as follows: Colored (c+), Chinchilla, (cch), Himalayan (ch) and Albino (c). Give the phenotypes and ratios from the following crosses. 86. c+ c ch ch Ans: 1 normal; 1 himalayan Difficulty: 1 87. c+ c+ ch cch Ans: All normal Difficulty: 1

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88. c+ c ch c Ans: 2 normal; 1 himalayan; 1 albino Difficulty: 1 89. c c ch cch Ans: 1 himalayan; 1 chinchilla Difficulty: 1 90. c+ ch ch cch Ans: 2 normal; 2 himalayan Difficulty: 1 91. c+ cch ch cch Ans: 2 normal; 1 himalayan; 1 chinchilla Difficulty: 1 92. c c c+cch Ans: 2 normal; 2 chinchilla Difficulty: 1 93. In a certain breed of plants, dark green is determined by the dominant gene G and light green is determined by the recessive gene g. The heterozygote shows 75% penetrance and will look phenotypically light green. If the parental cross is GG gg; what phenotypes would be observed in a population of 400 F2 plants? Ans: 250 Dark Green; 150 light green Difficulty: 4 94. A man with blood type A, whose father was blood type O, married a woman of blood type B whose mother was blood type O. What are the possible blood types of their offspring? Ans: Blood Type A, B, AB and O are possible Difficulty: 1 95. What phenotypes and genotypes would you expect from the following cross. IB i rh+ rh+ IA i rh+ rhAns: IBIArh+rhAB positive IBIArh+rh+ AB negative + ii rh rh O positive ii rh+rh+ O negative Difficulty: 2

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96. Horses can be cremello (light cream color), chestnut (a brownish color) or palomino (golden color with white in the horse's tail and mane). Of these phenotypes, only palominos never breed true. From the results shown below, determine the mode of inheritance by assigning gene symbols and indicating which genotypes yield which phenotypes.

Ans: A) PP Pp / B) Difficulty: 2

pp Pp / C)

Pp Pp

Below is a pedigree for a human trait. Shaded symbols are for individuals showing the trait. (A) Identify the mode of inheritance of the trait Dominant or Recessive. (B) Apply the laws of probability and calculate the probability the offspring of the cousin marriage will have the trait.

97. mode of inheritance _________________ Ans: Dominant Difficulty: 1 98. probability of 2 7 ____________________ Ans: 1/2 Difficulty: 2 99. probability 3 5 ____________________ Ans: 2/3 Difficulty: 3

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100. probability 1 7 ____________________ Ans: 8/9 will have the trait Difficulty: 4 Experimental Design and Interpretation of Data 101. You have obtained an interesting flower for your garden from your neighbor. The neighbor has given you two pure lines of the plant, one with red flowers and one with yellow flowers. You decide to cross them and find that you obtain all orange flowers. The curious molecular geneticist in you decides to test two independent hypotheses: Hypothesis 1: Incomplete Dominance; Hypothesis 2: Recessive Epistasis. The first step in your test is to self the F1 orange plants, which you complete only to find that the results do not statistically distinguish the two hypotheses. a) What ratio of yellow, orange and red would you expect in the F2 population for each hypothesis and b) what crosses would you complete next to definitively test your two hypotheses? Ans: a) The expected phenotypic ratio for recessive epistasis is 9:3:4 and 1:2:1 for incomplete dominance. b) Cross the yellow F2 flowers with true breeding red flowers. If the hypothesis for incomplete dominance is correct, the yellow color will be determined by a single gene and all F2 yellow flowers will be homozygous recessive and give rise to only orange flowers in the F3 population [aa x AA = Aa]. However, if the hypothesis for recessive epistasis is correct, a cross of F2 yellow and true breeding red flowers will give rise to some red and some orange flowers [ Yyrr x yyRR = either yyRr or YyRr]. Difficulty: 4 102. Your nephew has asked for help with his science project that focuses on coat color determination in mice. He has obtained several mice of different colors from the lab of a generous researcher at the local university. The two of you set out to breed the mice together in a variety of crosses to determine how coat color is inherited. Your curious and intelligent nephew notices that the mice have a variety of different tail lengths that make them easier or more difficult to pick up by the tail. He asks you about this oddity and in your search for answers you call the scientist from whom he received the mice only to find out that he has never paid much attention to this trait before but that the mice are inbred strains maintained by a national animal provider. When you call the company they tell you that all the members of each strain look the same but that the differences between the strains have always existed. Based on this information, you now know how the different tail lengths occur. What do you tell your nephew? Ans: Tail length is genetically determined by a modifier gene (as opposed to a tail versus no tail) for which there are several alleles because the inbred mice always differ between strains. Difficulty: 4

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103. A friend of yours is a volunteer in the Peace Corps working in an area of the world that is extremely hot. Your friend has captured some interesting crme colored mice and adopted them as pets. When your friend returns to his home town in the northern Midwest in the U.S., he is surprised to find that his crme colored pet mice are now giving birth to babies that have dark brown ears and legs. Your friend knows that you are a genetics student and asks for your help to explain this phenomenon. Given that your friend is certain that no other mouse got into the cage to breed, what do you tell your friend about the genetics underlying his mouse results? Ans: The mouse coat color is affected by temperature. The genetic term that describes this phenomenon is phenocopy, a change in phenotype that mimics a mutation but arises from an environmental effect. Difficulty: 3 104. You are a judge in a civil trial where a young man is attempting to prove that he is the illegitimate child of a very wealthy man who has recently died. He wishes to be included in the distribution of his wealth. After considering all the testimony about how this person was conceived the key evidence seems to come down to two main facts. The wealthy man and the mother of the young man are both deaf but the young man is not. Therefore the lawyer of the family suggests that the wealthy man is not the father. The mother, wealthy man and young man all have O, MM, Rh- blood type at the phenotypic level but a genotyping screen indicates that the wealthy man is actually IAIA hh blood type. How do you interpret the evidence presented and how does it influence your decision in this legal case? Ans: The fact that the young man can hear is not evidence against his being the son of the wealthy man. Two deaf individuals can, via complementation, give rise to hearing offspring if the mutation they carry is on different genes (Hearing is a polygenic trait.). The blood type evidence is definitive in favor of the wealthy man not being the father of the young man. Although both putative parents and the son in question have O blood type, the wealthy man is genetically type A and phenotypically type O due to recessive homozygousity of the h allele which leads to Bombay phenotype; the protein to which the A sugar attaches is missing therefore making the wealthy man phenotypically type O. Any son of his would be highly likely to have A-antigen as the h allele is very rare in humans making homozygous recessive offspring extremely unlikely except in consanguinous matings. Difficulty: 4

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105. A science teacher is attempting to convince her class that alcoholism, which has long been known to be a disease of polygenic inheritance, really is partially genetically determined. You are asked to assist in the design of an experiment that will help show eighth graders genetic transmission of differences in alcohol drinking. You have been given outbred rats as your experimental model. Set up a quantitative experiment that would test the hypothesis that alcoholism, as determined by amount of alcohol drunk, is a quantitative trait. Ans: Set up a selective breeding experiment. Measure alcohol consumption per day for all rats. Breed the high drinking male rats with the high drinking females and the low drinking males with low drinking females. Test the offspring and do the same in subsequent generations. If the rats bred for high drinking continue to increase their drinking levels from generation to generation and the low drinkers decrease their drinking levels in the same, this is evidence that alcohol drinking is genetically determined. Your data will also show that the individual rats differ in consumption and when plotted together show a continuous distribution indicating a quantitative trait (more than one gene interactions, and interactions with the environment contribute to the alcohol drinking trait). Difficulty: 4

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Chapter 4The Chromosome Theory of Inheritance Fill in the Blank 1. The process of two consecutive cell divisions in the diploid progenitors of sex cells is called ______________________________. Ans: meiosis Difficulty: 1 2. _________________________ is the term that describes a single set of chromosomes. Ans: haploid Difficulty: 1 3. In _______________________ chromosomes, the centromere is closer to one end than to the middle. Ans: acrocentric Difficulty: 2 4. Chromosomes that match in size, shape and banding pattern are called _________________________________. Ans: homologs Difficulty: 2 5. A ____________________________ is an image of all the chromosomes of an organism cut from a micrograph, arranged based on staining pattern into pairs and, by convention, in decreasing size followed by sex chromosomes. Ans: karyotype Difficulty: 1 6. ______________________________ occurs when chromosomes fail to separate properly during meiosis. Ans: nondisjunction Difficulty: 2 7. The smaller diploid sister cell that results during meiosis I in females is called ______________________________. Ans: polar body Difficulty: 2 8. A ________________________ is an animal cell with two or more nuclei. Ans: syncytium Difficulty: 2

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9. A multinucleate plant tissue is called a _____________________________. Ans: coenocyte Difficulty: 2 10. The process of matching chromosomes becoming zipped together during the zygotene stage of prophase I is called ______________________________. Ans: synapsis Difficulty: 1 Multiple Choice 11. In Drosophila virilis, nuclei of somatic cells contain 12 chromosomes while nuclei of sperm cells contain only 6 chromosomes. What does n equal for this species? A) 3 B) 6 C) 12 D) 24 E) 6 or 12, depending on cell type Ans: B Difficulty: 1 12. The stage of mitosis when chromosomes condense to form rod-shaped structures visible under the microscope is called: A) interphase. B) prophase. C) metaphase. D) anaphase. E) telophase. Ans: B Difficulty: 1 13. The stage of mitosis when sister chromatids separate from each other and migrate to opposite poles of a cell is called: A) interphase. B) prophase. C) metaphase. D) anaphase. E) telophase. Ans: D Difficulty: 1

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14. During which of the following stages of the cell cycle would a chromosome consist of only a single chromatid? A) G1 B) G2 C) mitotic prophase D) mitotic metaphase E) all of the above Ans: A Difficulty: 1 15. A) B) C) D) Which of the following statements applies to homologous chromatids? They are attached to the same centromere They are genetically identical They segregate from each other at anaphase of mitosis They contain the same genes in the same order but may have different alleles of some genes E) More than one of the above statements applies to homologous chromatids Ans: D Difficulty: 2

16. Drosophila melanogaster has four pairs of chromosomes. Sperm from this species are formed by a meiotic process in which homologous chromosomes pair and segregate but do not undergo crossing over. How many genetically different kinds of sperm could be produced by a Drosophila melanogaster male? A) 4 B) 8 C) 16 D) 64 E) 256 Ans: C Difficulty: 3 17. Nondisjunction can occur at either the first or second division of meiosis. XYY individuals would most likely arise from nondisjunction at the ______ meiotic division in the ______. A) first, mother B) second, mother C) first, father D) second, father E) more than one of the above could give rise to XYY individuals Ans: D Difficulty: 3

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18. Nondisjunction can occur at either the first or second division of meiosis. XXY individuals could arise from nondisjunction at the ______ meiotic division in the ______. A) first, mother B) second, mother C) first, father D) second, father E) more than one of the above could give rise to XXY individuals Ans: E Difficulty: 3 19. Crossing over between homologous chromosomes occurs at which of the following stages of meiosis? A) S phase B) prophase I C) metaphase I D) anaphase I E) prophase II Ans: B Difficulty: 1 20. Humans have 22 pairs of autosomes plus one sex chromosome pair. How many autosomes are present in a normal human primary spermatocyte? A) 22 B) 23 C) 44 D) 45 E) 46 Ans: C Difficulty: 2 21. A) B) C) D) E) Premeiotic germ cells that divide mitotically in females are referred to as: primary oocytes. secondary oocytes. ootids. oogonia. ova. Ans: D Difficulty: 1

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22. A) B) C) D) E)

The cells in which meiosis occurs in males are referred to as: spermatocytes. spermatogonia. spermatids. oocytes. sperm. Ans: A Difficulty: 1 A chromosome with two arms of equal length is referred to as: acrocentric. homologous. telocentric. metazoan. metacentric. Ans: E Difficulty: 1

23. A) B) C) D) E)

24. At which of the following stages of meiosis would homologous chromosomes be paired? A) prophase of meiosis I B) prophase of meiosis II C) metaphase of meiosis I D) metaphase of meiosis II E) a and c are correct Ans: E Difficulty: 2 25. A) B) C) D) E) Which of the following events occurs during mitosis but not meiosis? Segregation of sister chromatids. Pairing of homologous chromosomes. Crossing-over between homologous chromosomes. Alignment of chromosomes on the metaphase plate. None of the above Ans: E Difficulty: 2

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26. The mitotic stage during which chromosomes begin attaching to spindle fibers and moving randomly and reversibly to the centrosomes is: A) prophase. B) prometaphase. C) metaphase. D) anaphase. E) telophase. Ans: B Difficulty: 1 27. If a geneticist were to closely examine the make-up of a single autosomal chromosome from one of your cells, that chromosome would be found to be: A) derived entirely from genes from just one of your grandparents. B) a mosaic of genes derived from your mother and father. C) a mosaic of genes derived from all four of your grandparents. D) a mosaic of genes derived from just two of your grandparents either your two grandfathers or your two grandmothers. E) a mosaic of genes derived from just two of your grandparents either your maternal grandparents, or your paternal grandparents. Ans: E Difficulty: 4 28. A) B) C) D) E) If you are a male, your X chromosome contains genes derived from: your paternal grandfather only. your maternal grandfather only. both your paternal and maternal grandfathers. both your paternal grandfather and grandmother. both your maternal grandfather and grandmother. Ans: E Difficulty: 4

29. The chromosomal structure to which spindle fibers attach during the mitotic divisions is referred to as a: A) chromatid. B) centrosome. C) kinetochore. D) metaphase plate. E) centromere. Ans: C Difficulty: 1

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30. Microtubules that attach to centrosomes but not chromosomes and that interdigitate with microtubules emanating from the centrosome at the opposite pole are known as: A) kinetochore microtubules. B) polar microtubules. C) astral microtubules. D) interdigitating microtubules. E) none of the above Ans: B Difficulty: 1 31. Mitosis results in _______ in chromosome number while meiosis results in ______ chromosome number. A) a doubling of, no change in B) no change in, no change in C) a reduction by half in, no change in D) no change in, a doubling of E) no change in, a reduction by half in Ans: E Difficulty: 2 32. A) B) C) D) E) Cells said to be in the G0 stage: have two chromatids per chromosome. are replicating their chromosomes. are about to enter the mitotic phase of the cell cycle. are in an extended G1 phase and no longer cycling. are dead. Ans: D Difficulty: 1

33. Cells in G2 stage of the cell cycle have ______ as cells of the same species in the G1 stage. A) twice as many chromosomes B) twice as many chromatids C) half as many chromatids D) the same number of chromatids E) half as many chromosomes Ans: A Difficulty: 1

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34. A cross between a white-eyed female fruit fly and a red-eyed male would generate which of the following types of progeny? A) Red-eyed females and white-eyed males. B) White-eyed females and red-eyed males. C) All red-eyed females and a 50:50 mixture of white-eyed and red-eyed males. D) All red-eyed males and a 50:50 mixture of white-eyed and red-eyed females. E) The result can not be predicted because it depends on whether the female is homozygous or heterozygous. Ans: A Difficulty: 2 35. A female fruit fly with singed bristles was mated with a male from a true-breeding wild type stock with long bristles. All of the F1 females had wild-type bristles and all of the F1 males had singed bristles. If the F1 flies are intercrossed, the expected ratio of long to singled bristles in the F2 flies is: A) 1:0 in both sexes (i.e. males and females will all have long bristles). B) 3:1 in both sexes. C) 3:1 in females, while all the males will have singed bristles. D) 1:1 in females, while all the males will have singed bristles. E) 1:1 in both sexes. Ans: E Difficulty: 2 36. Red-green color-blindness is controlled by an X chromosomal gene in humans. A normal man and woman whose fathers are both color-blind marry. What is the probability that their first child will be color-blind? A) 1/2 B) 1/4 C) 1/8 D) 1/3 E) 0 Ans: B Difficulty: 2 37. Hemophilia is caused by an X-linked mutation in humans. If a woman whose paternal uncle (father's brother) was a hemophiliac marries a man whose brother is also a hemophiliac, what is the probability of their first child having hemophilia (note: assume no other hemophilia in the pedigree and no hidden carriers). A) 0 B) 1/4 C) 1/2 D) 1/8 E) 1 Ans: A Difficulty: 3

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38. A white-eyed female fruit fly is mated to a red-eyed male. One of their progeny is a white-eyed female. What is the likely karyotype of this white-eyed daughter? A) XX B) XXY C) XO D) XXX E) XYY Ans: B Difficulty: 2 39. A white-eyed female fruit fly is mated to a red-eyed male. One of their progeny is a white-eyed female. This white-eyed daughter likely arose from nondisjunction of the sex chromosomes during _________ in the __________. A) meiosis I, mother B) meiosis II, mother C) meiosis I, father D) meiosis II, father E) meiosis I or II, mother Ans: E Difficulty: 3 40. A) B) C) D) E) Males with one copy of an X-linked gene are said to be _________ for that gene. homozygous heteroallelic heterozygous hemizygous deficient Ans: D Difficulty: 1

41. In chickens, it is the females that have two different sex chromosomes (Z and W) while the males have two Z chromosomes. A Z-linked gene controls the pattern of the feathers with the dominant B allele causing the barred pattern and the b allele causing non-barred feathers. From which of the following crosses would all of the daughters be of one type (barred or non-barred) and all of the sons the other type? A) barred females non-barred males B) non-barred females barred males C) non-barred females non-barred males D) barred females barred males E) more than one of the above Ans: A Difficulty: 4

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42. In Drosophila, the recessive allele for forked bristles is sex-linked, and the recessive allele for purple eyes is autosomal. The wild-type alleles are for straight bristles and red eyes, respectively. A female heterozygous for both pairs of alleles is mated with a male with forked bristles and purple eyes. What percentage of the daughters will have forked bristles and purple eyes? A) 100% B) 75% C) 50% D) 25% E) 0% Ans: D Difficulty: 3 43. In what proportion of a man's sperm will all 23 chromosomes have centromeres inherited from the same parent (either his mother or his father)? A) 1/2 B) (1/2)23 C) (1/2)46 D) (1/2)22 E) (1/4)46 Ans: D Difficulty: 4 44. Suppose you discover a new species of worm that exists in two forms slimy and nonslimy. You find that when slimy females are mated to non-slimy males the offspring consist of slimy males and non-slimy females, whereas when non-slimy females are mated with slimy males, the offspring of both sexes are all slimy. You would conclude that the _________ allele is dominant and that ________ are the heterogametic sex (the sex with two different sex chromosomes) in this species of worm. A) slimy, females B) slimy, males C) non-slimy, females D) non-slimy, males Ans: A Difficulty: 4 45. A) B) C) D) E) Which of the following is not a property of homologous chromosomes? They pair physically during prophase of meiosis I. They exchange genes by crossing over during meiosis. They carry alleles for the same genes at the same chromosomal position. They are attached to the same centromere during G2 of the cell cycle. They segregate to opposite poles at anaphase of meiosis I. Ans: D Difficulty: 2

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46. Suppose you discover a new variant in which mice have spiky fur instead of the usual soft fur. You notice that this trait seems only to be present in males. To investigate this pattern, you cross a spiky-fur male with a soft-fur female, and find that all of the F1 progeny of both sexes have soft fur. You then interbreed the F1 and observe that all of the F2 females have soft fur, but 1/4 of the F2 males have spiky fur. You conclude that: A) the spiky allele is an X-linked recessive. B) the spiky allele is Y-linked. C) the spiky allele is autosomal recessive with sex-limited expression. D) the spiky allele is an X-linked dominant. E) the spiky allele is an autosomal dominant with sex-limited expression. Ans: C Difficulty: 3 47. In fruit flies, brown eyes can be caused by the recessive mutations pn (prune), bw (brown) or ry (rosy), which are on the X chromosome, second chromosome and third chromosome, respectively. Wild-type alleles for all three genes must be present for eyes to be red. Suppose that two brown-eyed flies are crossed and their progeny consist of brown-eyed sons and red-eyed daughters. Which mutation is responsible for the brown eyes in the parental female? A) pn B) bw C) ry D) either bw or ry E) any of the three pn, bw or ry Ans: A Difficulty: 4 48. Color vision depends upon the dominant alleles of three genes the R gene and the G gene are both on the X chromosome, while the B gene is autosomal. Recessive mutations in any of the three genes can cause color-blindness. Suppose a colorblind man marries a colorblind woman and all of their offspring have normal vision. What is the genotype of the woman? A) RRGGbb B) RRggBB C) rrGGbb D) RRggBB or RRGGbb E) rrGGbb or rrggBB Ans: A Difficulty: 4

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49. A variable feature of some chromosomes in corn is the presence or absence of knobs at particular sites. Suppose that one member of each of two pairs of chromosomes in a corn plant has a knob. If this plant were crossed with a knobless plant, what percentage of the offspring is expected to be knobless? A) 100% B) 75% C) 50% D) 25% E) 0% Ans: D Difficulty: 3 50. What aspect of chromosome behavior most clearly accounts for Mendel's law of segregation? A) Movement of sister chromatids to opposite poles at anaphase II of meiosis. B) Movement of homologous chromosomes to opposite poles at anaphase I of meiosis. C) Crossing over between homologous chromosomes during prophase I of meiosis. D) Replication of chromosomes prior to meiosis. E) Independent alignment of different homologous pairs on the metaphase I spindle. Ans: B Difficulty: 2 51. What aspect of chromosome behavior most clearly accounts for Mendel's law of independent assortment? A) Movement of sister chromatids to opposite poles at anaphase II of meiosis. B) Movement of homologous chromosomes to opposite poles at anaphase I of meiosis. C) Crossing over between homologous chromosomes during prophase I of meiosis. D) Replication of chromosomes prior to meiosis. E) Independent alignment of different homologous pairs on the metaphase I spindle. Ans: E Difficulty: 2 52. Which aspect(s) of chromosome behavior is/are primarily responsible for the tremendous amount of genetic variability associated with sexual reproduction? A) Segregation of sister chromatids at anaphase II of meiosis. B) Segregation of homologous chromosomes at anaphase I of meiosis. C) Crossing over between homologous chromosomes during prophase I of meiosis. D) Independent alignment of different homologous pairs on the metaphase I spindle. E) Both c and d contribute to the generation of variability. Ans: E Difficulty: 2

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53. A) B) C) D) E)

Which sex chromosomes are limited to only one sex? X and Z X and W Y and Z Y and W X and Y Ans: D Difficulty: 1

54. In the following pedigree, the indicated trait is caused by what type of allele?

A) B) C) D) E)

autosomal recessive autosomal dominant X-linked recessive X-linked dominant Y-linked Ans: C Difficulty: 2

55. In the following pedigree, the indicated trait is caused by what type of allele?

A) B) C) D) E)

autosomal recessive autosomal dominant X-linked recessive X-linked dominant Y-linked Ans: D Difficulty: 2

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56. In the following pedigree, the indicated trait is caused by what type of allele?

A) B) C) D) E)

autosomal recessive autosomal dominant X-linked recessive X-linked dominant Y-linked Ans: B Difficulty: 2

57. In the following pedigree, the indicated trait is caused by what type of allele?

A) B) C) D) E)

autosomal recessive autosomal dominant X-linked recessive X-linked dominant Y-linked Ans: A Difficulty: 2

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58. In the following pedigree, the indicated trait is caused by what type of allele?

A) B) C) D) E)

autosomal recessive autosomal dominant X-linked recessive X-linked dominant Y-linked Ans: E Difficulty: 2

59. A female fruit fly with vermilion eyes and normal wings is crossed to a male with normal red eyes and cut wings. The F1 progeny consist of females with red eyes and normal wings, and males with vermilion eyes and normal wings. When the F1 progeny are interbred, the F2 consists of two types of females vermilion eyes, normal wings (1/2) and red eyes, normal wings (1/2), and two types of males vermilion eyes, normal wings (1/2) and red eyes, cut wings (1/2). Are the genes for eye-color and wingtype X-linked or autosomal? A) The eye-color gene is X-linked and the wing-type gene is autosomal. B) The eye-color gene is autosomal and the wing-type gene is X-linked. C) Both genes are X-linked. D) Both genes are autosomal. E) More than one of the above is consistent with the data. Ans: C Difficulty: 4 60. In fruit flies, an X-linked dominant mutation (N) causes Notch wings in heterozygous females but is lethal in hemizygous or homozygous condition. What ratio of offspring would be observed in a cross of a Notch female by a normal male? A) 1/3 Notch females, 1/3 normal females, 1/3 normal males B) 1/4 Notch females, 1/4 normal females, 1/4 Notch males, 1/4 normal males C) 1/2 Notch females, 1/2 normal males D) 1/2 normal females, 1/2 Notch males E) 2/3 Notch females, 1/3 normal males Ans: A Difficulty: 3

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61. The following is a list of mitotic events out of order. A) Chromosomes align on the midplate of the cell. B) Kinetochores begin attaching to spindle fibers. C) Nuclear membrane reforms, chromosomes decondense D) Chromosomes condense, centrosomes migrate to opposite sides of nucleus. E) Sister chromatids separate, move to opposite poles. What is the correct order of events? A) BDACE B) DABEC C) DBAEC D) ABDCE E) EDBAC Ans: C Difficulty: 2 62. Here is a list of meiotic events out of order. A) Segregation of homologous chromosomes to opposite poles. B) Segregation of sister chromatids to opposite poles. C) Alignment of homologous pairs on the midplate of the cell. D) Pairing and synapsis of homologous chromosomes. E) Condensation of chromosomes in a diploid nucleus. What is the correct order of events? A) CDEAB B) DCEBA C) EDCBA D) EDCAB E) DCABE Ans: D Difficulty: 2 63. A cell with three pairs of chromosomes has the genotype AaBbCc, such that each pair of alleles is on a different pair of chromosomes. If this cell were to undergo a meiotic division, how many genetically different types of gametes could be produced? A) 1 B) 3 C) 6 D) 8 E) 9 Ans: D Difficulty: 2

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64. A cell with three pairs of chromosomes has the genotype AaBbCc, such that each pair of alleles is on a different pair of chromosomes. If this cell were to undergo a mitotic division, how many genetically different types of gametes could be produced? A) 1 B) 3 C) 6 D) 8 E) 9 Ans: A Difficulty: 2 65. In humans, XO individuals are females with Turner's syndrome and XXY individuals are males with Klinefelter's syndrome. Which of the following events could not give rise to a Klinefelter's male? A) Nondisjunction at meiosis I in the mother. B) Nondisjunction at meiosis II in the mother. C) Nondisjunction at meiosis I in the father. D) Nondisjunction at meiosis II in the father. E) All of the above could give rise to a Klinefelter's male. Ans: D Difficulty: 3 66. In humans, XO individuals are females with Turner's syndrome and XXY individuals are males with Klinefelter's syndrome. Red-green color blindness is caused by an Xlinked recessive allele. Suppose a colorblind man and a normal woman with no family history of color-blindness married and had a daughter who was colorblind and had Turner's syndrome. Which event could have given rise to this offspring? A) Nondisjunction at meiosis I in the mother. B) Nondisjunction at meiosis II in the mother. C) Nondisjunction at meiosis I in the father. D) Nondisjunction at meiosis II in the father. E) Either a or b could give rise to such an offspring. Ans: E Difficulty: 3 67. A) B) C) D) E) Individuals with an XXY karyotype are ______ in humans and ______ in fruit flies. male, male male, female female, male female, female male, intersexual Ans: B Difficulty: 2

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68. In animal gametogenesis, a single primary spermatocyte generates ______ sperm, while a single primary oocyte generates ______ egg(s). A) 1, 4 B) 1, 1 C) 4, 2 D) 4, 1 E) 4, 4 Ans: D Difficulty: 1 Matching 69. Match the event with the appropriate stage of mitosis. 1. Sister chromatids separate and move to opposite poles. 2. Chromosomes begin attaching to spindle fibers. 3. Chromosomes decondense and nuclear membrane reforms. 4. Chromosomes condense and spindle forms. 5. Sister chromatids attached to opposite spindle poles. Ans: 1-b, 2-d, 3-e, 4-a, 5-c Difficulty: 2 a. prophase b. prometaphase c. metaphase d. anaphase e. telophase

70. Match the chromosomal event with the appropriate stage of meiosis. 1. Homologous chromosomes pair and cross over. a. prophase 3. Homologous chromosomes segregate to opposite poles. b. metaphase 3. Sister chromatids segregate to opposite poles. c. anaphase I 4. Pairs of chromosomes align on the spindle. d. metaphase II 5. Sister chromatids attach to opposite poles of spindle. e. anaphase II Ans: 1-a, 2-c, 3-e, 4-b, 5-d Difficulty: 2 71. Match the event with the cell division process in which it occurs. (Note: there can be more than one correct letter for each blank.) 1. Pairing of homologous chromosomes. a. meiosis I 2. Segregation of sister chromatids. b. meiosis II 3. Condensation and decondensation of chromosomes. c. mitosis 4. Segregation of homologous chromosomes. 5. Crossing over. Ans: 1-a, 2-b,c, 3-a,b,c, 4-a, 5-a Difficulty: 3

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72. Match the event with the type of cell in which it occurs during spermatogenesis. (Note: a cell type may be used more than once or not at all, but there is only one correct letter per blank.) 1. Homologous chromosomes pair and cross over. a. Spermatogonia 2. Sister chromatids segregate to opposite poles. b. Primary spermatocytes 3. Cells undergo morphogenetic changes. c. Secondary spermatocytes 4. Cells divide mitotically. d. Spermatids 5. Homologous chromosomes segregate to opposite poles. Ans: 1-b, 2-c, 3-d, 4-a, 5-b Difficulty: 2 73. Match the events with the appropriate stage of the cell cycle. 1. Chromosomes replicate. a. G1 2. Growth period between replication and division, each b. S phase chromosome has two sister chromatids. c. G2 3. Growth period between division and replication, each d. M phase chromosome has only one chromatid. e. G0 4. An extended interphase in non-cycling cells. 5. Cells divide; chromosomes undergo mitosis. Ans: 1-b,2-c,3-a,4-e,5-d Difficulty: 2 74. Match the genotype with the appropriate term and with the appropriate sex (put a, b or c, and M or F on each blank). Genotype Terms Sex 1. XwXw _____ a. homozygous M 2. Xw+Xw _____ b. heterozygous F 3. Xw+Y _____ c. hemizygous w 4. X O _____ 5. ZBZB _____ 6. ZbW _____ 7. ZBZb _____ Ans: 1-aF, 2-bF, 3-cM, 4-cM, 5-aM, 6-cF, 7-bM Difficulty: 3 75. Match the stage of oogenesis in humans with the appropriate numbers of chromosomes and chromatids. Stage of Oogenesis # of chromosomes # of chromatids 1. Primary oocytes _______ a. 23 d. 23 2. Secondary oocytes ______ b. 46 e. 46 3. Ootids ______ c. 92 f. 92 4. Ova _____ Ans: 1-bf, 2-ae, 3-ad, 4-ad Difficulty: 2

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True or False 76. Sister chromatids are identical chromosomes, duplicated during metaphase and still attached to each other. Ans: True Difficulty: 1 77. The nonsex chromosomes are called autosomes. Ans: True Difficulty: 1 78. A female that is XXO has Turner Syndrome. Ans: False Difficulty: 2 79. A chromatin-laden nucleus is quiescent. Ans: False Difficulty: 2 80. The period between cell cycles is called interphase. Ans: True Difficulty: 1 81. During the S and G2 stages of interphase, the centrosomes replicate, producing two centrosomes that remain in extremely close proximity. Ans: True Difficulty: 1 82. Chromosomes attach to these microtubules through linkage groups. Ans: False Difficulty: 1 83. Polar microtubules are short and unstable and extend out from the centrosome toward the cell's periphery. Ans: False Difficulty: 2 84. A somatic cell is a cell destined for a specialized role in the production of gametes. Ans: False Difficulty: 1

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85. During pachytene, structures called recombination nodules begin to appear along the synaptonemal complex, and an exchange of parts between nonsister chromatids occurs at these nodules. Ans: True Difficulty: 2 Short Answer 86. In humans, why is pattern baldness seen only in men? Ans: Pattern baldness is an example of sex-limited expression. It is caused by heterozygosity for an autosomal baldness gene, which when homozygous causes baldness in both sexes; in the heterozygous condition, pattern baldness is expressed only in males and is thus sex-limited. Difficulty: 2 87. Give examples of three different methods by which chromosomes can determine sex. Ans: XX females, XY males humans, fruit flies; XX females, XO males some moths and other insects; ZZ males, ZW females birds and butterflies. Difficulty: 2 88. What are the consequences of a mutation that disrupts cytokinesis for cells that are actively dividing? Ans: Mitosis without cytokinesis leads to multinucleate cells with multiple copies of each chromosome. Difficulty: 1 89. What is the major cause of Down's syndrome? Ans: Trisomy (three copies) of chromosome 21, which results from nondisjunction of chromosome 21 in meiosis of the mother (80% of cases) or father (20% of cases). Difficulty: 1 90. What is meant by the term checkpoint with respect to regulation of the cell cycle? Ans: A checkpoint is a moment when cell cycle progress can be stopped temporarily if a preceding step is not yet complete. Difficulty: 2 91. What was the evidence that led Walter Sutton to conclude that the X and Y chromosomes determine sex? Ans: Sutton studied the chromosomes of grasshoppers and showed that males always had one X and one Y while females always had two Xs. Difficulty: 2

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92. Bridges crossed white-eyed female and red-eyed male fruit flies and recovered rare exceptional white-eyed females and red-eyed males in addition to the usual red-eyed females and white-eyed males. How did Bridges' observations lend support to the chromosome theory of inheritance? Ans: Bridges showed that the exceptional flies also had exceptional karyotypes for the sex chromosomes (XO males and XXY females). So, a reversal in the normal pattern of transmission of a genetic trait is perfectly correlated with a mistake in the pattern of transmission of a particular pair of chromosomes (the sex chromosomes), such that the exceptional sons inherit their X (and their eye color) from their father, and the exceptional daughters inherit both of their Xs (and their eye color) from their mother, proving that the eye color gene must be on the X chromosome. Difficulty: 4 93. What are two important functions of meiosis? Ans: To reduce chromosome number by half in preparation for fertilization so that biparental inheritance does not lead to an increase in chromosome number; to generate offspring that differ genetically from their parents and from each other. Difficulty: 3 94. Why are recessive X-linked traits more commonly seen in men than in women? Ans: Because expression of an X-linked trait in a man requires only that he inherit one copy of the allele from his mother, whereas expression in females requires inheritance of two copies, one from each parent. Difficulty: 2 95. Why are dominant X-linked traits seen in women more commonly than in men? Ans: There are two reasons: 1) Any X chromosome is twice as likely to be present in a woman as a man because women have two X chromosomes and men have one; 2) many dominant mutations are recessive lethals, so that for many dominant X traits, men that inherit them die during development because of hemizogosity. Difficulty: 3

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Experimental Design and Interpretation of Data 96. In Drosophila, vestigial wings (vg) is a recessive autosomal mutant allele, and yellow body (y) is a recessive X-linked mutant allele. The wild-type alleles, vg+ and y+ control normal wings and dark-brown body color respectively. If a homozygous yellow, vestigial female is crossed to a normal male and the F1 offspring are interbred, what will be the phenotypes and ratios of the F1 and F2? Ans: F1 females: all brown body, normal wings males: all yellow body, normal wings F2 females and males: brown body, normal wings 3/8 brown body, vestigial wings 1/8 yellow body, normal wings 3/8 yellow body, vestigial wings 1/8 Difficulty: 4 97. In Drosophila, white eyes (w) and yellow body (y) are both recessive X-linked mutations. The wild type alleles, w+ and y+, control red eyes and dark body color, respectively. If a homozygous yellow body, red eyed female is crossed with a dark body, white-eyed male, and F1 progeny are interbred, what will the phenotypes and ratios of the F1 and F2 be? Ans: F1 females: all dark body, red eyes males: all yellow body, red eyes F2 females: yellow body, red eyes 1/2 dark body, red eyes 1/2 males: yellow body, red eyes 1/2 dark body, white eyes 1/2 Difficulty: 4 98. Suppose you discovered a new mutation in mice that caused a curved spine. You notice that this mutation is only seen in females. When curved-spine females are crossed with normal males, the progeny are always recovered in the ratio: 1/3 curved-spine females, 1/3 normal females, 1/3 normal males. Explain the genetic basis for this ratio. Ans: The gene is X-linked; the curved-spine allele is dominant to the normal allele in heterozygotes but causes lethality in hemizygous males. Difficulty: 4

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99. In crosses of white-eyed Drosophila females by red-eyed males, Bridges recovered white-eyed daughters and red-eyed sons at a rate of around one per 2,000 offspring. (Most of the offspring were white-eyed males and red-eyed females.) He hypothesized that these exceptional progeny resulted from nondisjunction of the X chromosomes in meiosis in the female. Why did he suspect that nondisjunction was occurring in the female parent? What types of progeny would result from nondisjunction in the male parent? Ans: XXY red-eyed females and XO white-eyed males, so male nondisjunction does not account for the observed exceptions. Difficulty: 3 100. In crosses of white-eyed Drosophila females by red-eyed males, Bridges recovered white-eyed daughters and red-eyed sons at a rate of around one per 2,000 offspring. (Most of the offspring were white-eyed males and red-eyed females.) He hypothesized that these exceptional progeny resulted from nondisjunction of the X chromosomes in meiosis in the female. What is the expected karyotype of the exceptional red-eyed males? Give two ways to test this predicted karyotype. Ans: XO, tests 1) examine nuclei for Y chromosome, 2) test males for fertility. Difficulty: 3

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Chapter 5Linkage, Recombination, and the Mapping of Genes on Chromosomes Fill in the Blank 1. Genes that travel together from one generation to the next more often than not exhibit _____________________ ______________________. Ans: genetic linkage Difficulty: 1 2. A probability test that measures goodness of fit between observed and predicted results is a __________ ________________ test. Ans: chi square test Difficulty: 1 3. A hypothesis that predicts no linkage between genes is called the ______________ hypothesis. Ans: null hypothesis Difficulty: 2 4. Genes that can serve points of reference on a chromosome are useful as genetic markers while cytologically visible abnormalities that also make it possible to keep track of chromosomes are called ________________________ markers. Ans: physical Difficulty: 1 5. The movement of chiasmata toward the end of a chromosome is called _____________________. Ans: teminalization Difficulty: 2 6. One percentage point of recombination, or recombination frequency, is a unit of measure called either centimorgan or ___________ _____________. Ans: map unit Difficulty: 1 7. Crossovers do not occur independently and the occurrence of one crossover reduces the likelihood of another occurring elsewhere on the chromosome this is called __________________________ __________________________. Ans: chromosomal interference Difficulty: 2 8. A tetrad that contains four recombinant class haploid cells is known as a ____________________ ditype. Ans: non-parental ditype Difficulty: 1

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9. A tetrad that carries four kinds of haploid cells: two different parental and two different recombinant class spores is referred to as ________________________. Ans: tetratype Difficulty: 1 10. Mistakes in mitosis during development often result in ______________________ organisms containing tissues of different genotypes. Ans: mosaic Difficulty: 1 Multiple Choice 11. The R/r and S/s genes are linked and 10 map units apart. In the cross Rs/rS rs/rs what fraction of the progeny will be RS/rs? A) 5% B) 10% C) 25% D) 40% E) 45% Ans: A Difficulty: 3 12. If the map distance between genes A and B is 10 map units and the map distance between genes B and C is 25 map units, what is the map distance between genes A and C? A) 15 map units B) 35 map units C) Either 15 map units or 35 map units, depending on the order of the genes. D) The map distance between A and C can not be predicted from these data. Ans: C Difficulty: 2

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13. In Drosophila, singed bristles (sn) and cut wings (ct) are both caused by recessive, Xlinked alleles. The wild type alleles (sn+ and ct+) are responsible for straight bristles and intact wings, respectively. A female homozygous for sn and ct+ is crossed to a sn+ct male. The F1 flies are interbred. The F2 males are distributed as follows: sn ct 13 sn ct+ 36 sn+ ct 39 sn+ ct+ 12 What is the map distance between sn and ct? A) 12 m.u. B) 13 m.u. C) 25 m.u. D) 50 m.u. E) 75 m.u. Ans: C Difficulty: 2 The following information applies to problems 14 & 15. In Drosophila, singed bristles (sn) and carnation eyes (car) are both caused by recessive, X-linked alleles. The wild-type alleles (sn+ and car+) are responsible for straight bristles and red eyes, respectively. A sn car female is mated to a sn+ car+ male and the F1 progeny are interbred. The F2 are distributed as follows: sn car 55 + sn car 45 sn+ car 45 sn+ car+ 55 200 14. What is the value of X2 for a test of the hypothesis that the sn and car genes are unlinked? A) 0.5 B) 1.0 C) 2.0 D) 0.4 E) 20 Ans: C Difficulty: 2

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15. A) B) C) D) E)

What is the p value from this test? (Pick the most accurate choice.) p>.5 .5>p>.1 p<.1 p<.05 p<.01 Ans: A Difficulty: 3

16. Suppose the L and M genes are on the same chromosome but separated by 100 map units. What fraction of the progeny from the cross LM/lm lm/lm would be Lm/lm? A) 10% B) 25% C) 50% D) 75% E) 100% Ans: B Difficulty: 3 17. The pairwise map distances for four linked genes are as follows: A-B = 22 m.u., B-C = 7 m.u., C-D = 9 m.u., B-D = 2 m.u., A-D = 20 m.u., A-C = 29 m.u. What is the order of these four genes? A) ABCD B) ADBC C) ABDC D) BADC E) CADB Ans: B Difficulty: 3 18. A) B) C) D) E) The zipper-like connection between paired homologs in early prophase is known as a: spindle fiber. synaptic junction. synaptonemal complex. chiasma. none of the above Ans: C Difficulty: 1

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19. The measured distance between genes D and E in a two point test cross is 50 map units. What does this mean in physical terms? A) D and E are on different pairs of chromosomes. B) D and E are linked and exactly 50 map units apart. C) D and E are linked and at least 50 map units apart. D) either a or b E) either a or c Ans: E Difficulty: 2 20. Dihybrid test crosses are made between each pairwise combination of the three genes O, P and Q with the following results: OoPp oopp PpQq ppqq OoQq ooqq OP 152 PQ 88 OQ 198 Op 348 Pq 415 Oq 289 oP 353 pQ 413 oQ 311 op 147 pq 84 oq 202 1000 1000 1000 2 You wish to use the test to determine whether the O and P genes are linked. Which set of data would you use? A) the first cross B) the second cross C) the third cross D) all three crosses E) the first and second crosses Ans: A Difficulty: 1 The following information applies to problems 21 & 22. In humans, the genes for red-green color blindness (R=normal, r=color-blind) and hemophilia A (H=normal, h=hemophilia) are both X-linked and only 3 map units apart. 21. Suppose a woman has four sons, and two are colorblind but have normal blood clotting and two have hemophilia but normal color vision. What is the probable genotype of the woman? A) HR/hr B) Hr/hr C) hr/hR D) Hr/hR E) HR/Hr Ans: D Difficulty: 3

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22. A woman whose mother is colorblind and whose father has hemophilia A is pregnant with a boy and wants to know the probability that he will have normal vision and blood clotting. What is the probability? A) .03 B) .15 C) .485 D) .47 E) .015 Ans: E Difficulty: 4 23. The R/r and S/s genes are linked and 10 map units apart. In the cross Rs/rS rs/rs what percentage of the progeny will be Rs/rs? A) 5% B) 10% C) 25% D) 40% E) 45% Ans: E Difficulty: 3 The following information applies to problems 24-27. In fruit flies, the recessive pr and cn mutations cause brown and bright-red eyes, respectively (wild-type flies have brick-red eyes). The double mutant pr cn combination has orange eyes. A female who has wild-type eyes is crossed to an orange-eyed male. Their progeny have the following distribution of eye colors: wild-type 8 brown 241 bright-red 239 orange 12 500 24. A) B) C) D) E) Which classes are the parental types? wild-type and orange brown and bright-red wild-type and brown bright-red and orange there is no way to determine this Ans: A Difficulty: 2

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25. A) B) C) D) E)

What is the genotype of the mother of these progeny? prcn/pr+cn+ pr+cn/pr+cn pr+cn/prcn+ prcn+/prcn+ prcn/prcn Ans: C Difficulty: 2

26. The mother of these progeny resulted from a cross between two flies from true breeding lines. What are the genotypes of these two lines? A) prprcn+cn+ and pr+pr+cncn B) pr+pr+cn+cn+ and prprcncn C) pr+prcn+cn and prprcncn D) pr+prcncn and prprcn+cn E) either a or b could be true Ans: A Difficulty: 2 27. A) B) C) D) E) What is the map distance between the pr and cn genes? 20 m.u. 2 m.u. 4 m.u. 46 m.u. 8 m.u. Ans: C Difficulty: 2

28. A dihybrid test cross is made between genes H and I. Four categories of offspring are produced: HI, Hi, hI, and hi. You wish to use the 2 test to test the hypothesis that the H and I genes are unlinked. How many degrees of freedom would there be in this test? A) 1 B) 2 C) 3 D) 4 E) 0 Ans: C Difficulty: 1

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29. A) B) C) D) E)

Which of the following processes can generate recombinant gametes? Segregation of alleles in a heterozygote. Crossing over between two linked heterozygous loci. Independent assortment of two unlinked heterozygous loci. b and c a, b and c Ans: D Difficulty: 2

30. Crossing over takes place in paired bivalents consisting of ______ chromatids, and involves _______ of the chromatids. A) 2, 2 B) 2, 4 C) 4, 2 D) 4, 4 E) 8, 4 Ans: C Difficulty: 2 31. In Drosophila, the genes y (yellow body) and car (carnation eyes) are located at opposite ends of the X chromosome. In doubly heterozygous females (y+ car+/y car), a single chiasma is observed somewhere along the X chromosome in 90% of the examined oocytes. No X chromosomes with multiple chiasmata are observed. What percentage of the male progeny from such a female would be recombinant for y and car? A) 5% B) 10% C) 45% D) 55% E) 90% Ans: C Difficulty: 4 32. Genes Q and R are 20 map units apart. If a plant of genotype QR/qr is selfed, what percentage of the progeny will be rs in phenotype? A) 4% B) 10% C) 16% D) 20% E) 40% Ans: C Difficulty: 4

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33. The map of a chromosome interval is Q 10 R 40 S. Which interval would likely show the higher ratio of double to single chiasmata? A) Q-R B) R-S C) The ratios would be the same in the two intervals. D) Two chiasmata never occur in the same interval. Ans: B Difficulty: 3 34. The map of a chromosome interval is A 10 B 40 C. From the cross Abc/aBC abc/abc, how many double crossovers would be expected out of 1000 progeny? A) 5 B) 10 C) 20 D) 40 E) 80 Ans: D Difficulty: 3 35. The cross Lpq/lPQ lpq/lpq is carried out, the L gene is found to be in the middle. What would be the genotypes of the double crossover gametes in this cross? A) LPQ and lpq B) LpQ and lPq C) lpQ and LPq D) Lpq and lPQ E) cannot be determined Ans: A Difficulty: 3 36. Suppose a three-point testcross was conducted involving the genes X, Y and Z. If the most abundant classes are XYz and xyZ and the rarest classes are xYZ and Xyz, which gene is in the middle? A) X B) Y C) Z D) cannot be determined Ans: B Difficulty: 2

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37. In Drosophila, the genes b, c and sp are linked and in the order given, the distances being b-c = 30 m.u. and c-sp = 20 m.u. These intervals exhibit 90% interference. How many double crossovers would be recovered in a three-point cross involving b, c and sp out of 1000 progeny? A) 3 B) 6 C) 54 D) 60 E) 600 Ans: B Difficulty: 4 38. A) B) C) D) E) In tetrad analysis, the criterion for linkage of two genes is: NPD = T. PD = T. PD = NPD. PD > NPD. PD > T. Ans: D Difficulty: 3 In tetrad analysis, NPD asci result from: independent assortment of unlinked genes. double crossovers between linked genes. single crossovers between linked genes. single crossovers between a gene and a centromere. a or b Ans: E Difficulty: 3 In tetrad analysis, second-division segregations result from: single crossovers between linked genes. double crossovers between linked genes. single crossovers between a gene and a centromere. independent assortment of unlinked genes. nondisjunction of homologs. Ans: C Difficulty: 2

39. A) B) C) D) E)

40. A) B) C) D) E)

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41. Tetrad analysis shows that crossing over occurs at the four-strand stage (i.e., after replication) because, when two genes are linked,: A) NPD > T B) T > NPD C) T > PD D) PD > NPD E) PD > T Ans: B Difficulty: 4 The following information applies to problems 42 & 43. Consider a pair of homologous chromosomes heterozygous for three genes (e.g. ABC/abc) during prophase I of meiosis. Let the sister chromatids of one homolog be numbered 1 and 2; and the sister chromatids of the other homolog be numbered 3 and 4. 42. A crossover that would result in genetic recombination (e.g., Abc or aBC) could involve which chromatids? A) 1 & 2 or 3 & 4 B) 1 & 3 or 2 & 4 C) 1 & 4 or 2 & 3 D) 1 & 3 or 1 & 4 or 2 & 3 or 2 & 4 E) any two of the four chromatids Ans: D Difficulty: 3 43. Assume a double crossover occurs in this pair of chromosomes that results in chromatids of the genotype AbC and aBc. If the first crossover (the one between A and B) involves chromatids 1 & 4, which chromatids could be involved in the second crossover? A) 1 & 2 or 3 & 4 B) 1 & 3 or 2 & 4 C) 1 & 4 or 2 & 3 D) 1 & 3 or 1 & 4 or 2 & 3 or 2 & 4 E) any two of the four chromatids Ans: D Difficulty: 4

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44. Sturtevant's detailed mapping studies of the X chromosome of Drosophila established what genetic principle? A) That genes are arranged in a linear order on the chromosomes. B) That genes are carried on chromosomes. C) That sex determination is controlled by the X and Y chromosomes. D) That segregation of an allelic gene pair is accompanied by disjunction of homologous chromosomes. E) That different pairs of chromosomes assort independently. Ans: A Difficulty: 2 45. The map of a chromosome is A 40 B 10 C 10 D 40 E. Suppose an investigator were to conduct two trihybrid crosses, cross 1: ACE/ace ace/ace and cross 2: BCD/bcd bcd/bcd with the purpose of comparing the levels of crossover interference between the two crosses. Which cross would be expected to have the higher coefficient of coincidence? A) cross 1 B) cross 2 C) Neither, the coefficient of coincidence is constant along a chromosome. D) There is no way to predict which cross would have the higher coefficient of coincidence. Ans: A Difficulty: 4 46. Suppose an individual is heterozygous for a pair of alleles (e.g. A/a). Under what conditions would a crossover in a somatic cell of this individual lead to a clone of cells homozygous for a? (Pick the most precise answer.) A) The crossover would have to occur between the A locus and the centromere and involve two homologous (non-sister) chromatids. B) The crossover would have to occur between the A locus and the end of the chromosome and involve two homologous (non-sister) chromatids. C) The crossover would have to occur on the same chromosome arm as the A locus and involve two homologous (non-sister) chromatids. D) The crossover would have to occur on the same chromosome as the A locus and involve two homologous (non-sister) chromatids. E) The crossover would have to occur between the A locus and the centromere and involve two sister chromatids (not homologous) chromatids. Ans: A Difficulty: 3

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47. Suppose an individual is heterozygous for two linked pairs of alleles on the same chromosome arm, Ab/aB such that the A locus is closer to the centromere than the B locus. Under what conditions would a crossover in a somatic cell generate a twin spot, i.e. two adjacent clones of cells, one clone homozygous for a and the other clone homozygous for b? A) The crossover would have to occur between the A locus and the centromere locus and involve two homologous (non-sister) chromatids. B) The crossover would have to occur between the A locus and the B locus locus and involve two homologous (non-sister) chromatids. C) The crossover would have to occur between the B locus and the end of the chromosome locus and involve two homologous (non-sister) chromatids. D) A double crossover would have to occur, with one crossover between the A locus and the centromere and a second crossover between the A and B loci locus and both crossovers would have to involve two homologous (non-sister) chromatids. E) No crossover in a somatic cell could generate a twin spot. Ans: A Difficulty: 4 48. A) B) C) D) E) Individuals heterozygous for the RB+ and RB- alleles can develop tumors as a result of: a mitotic crossover that leads to homozygosity for both RB+ and RB-. a somatic mutation in the RB+ allele that leads to homozygosity for RB-. a somatic mutation in the RB- allele that leads to homozygosity for RB+. the fact that RB- is dominant to RB+. a and b Ans: E Difficulty: 3

49. What happens physically during the process of crossing over? A) Two homologous chromatids break and rejoin at random sites along the chromosome. B) The genetic information on one chromatid is replaced by copying genetic information from a homologous chromatid without there being any physical exchange between the chromosomes. C) Two homologous chromatids break and rejoin at precisely the same site along the chromosome so that there is no loss or gain of material on either product. D) It is not known what occurs during crossing over. Ans: C Difficulty: 2

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50. Here is a list of events during meiosis I. It is not in the correct order. A) Homologous chromosomes are roughly aligned but not physically linked. B) Homologous chromosomes segregate to opposite poles. C) Homologous chromosomes are linked by synaptonemal complexes. D) Homologous chromosomes are linked by chiasmata. E) Chromosomes replicate. What is the correct order of these events? A) ACDBE B) AECDB C) EACDB D) EADCB E) CDABE Ans: C Difficulty: 3 51. Some of the larger human chromosomes typically contain multiple chiasmata during meiotic prophase. If you were to carefully study the distribution of these chiasmata, what would you find? A) Chiasmata are randomly distributed along chromosomes. B) All chromosome pairs have the same number of chiasmata. C) A single chromosome pair always has the same number of chiasmata in every meiotic cell. D) Chiasmata are spaced along a chromosome arm more regularly than would be expected by chance. E) Chiasmata are spaced more irregularly along a chromosome arm than would be expected by chance. Ans: D Difficulty: 4 Matching In a mating between haploid yeast cells of type a = his4/TRP1 type " = HIS4/trp1, a/" diploid offspring result. Match the appropriate ditype that results when these undergo meiosis with the genotypes shown: parental (PD), non-parental (NPD), or tetratype (T). 52. ______ his4/TRP1; his4/trp1; HIS4/trp1; HIS4/TRP1 Ans: PD Difficulty: 1 53. ______ his4/TRP1; his4/TRP1; HIS4/trp1; HIS4/trp1 Ans: T Difficulty: 1

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54. ______ his4/trp1; his4/trp1; HIS4/TRP1;HIS4/TRP Ans: NPD Difficulty: 1 55. ______ HIS4/trp1; HIS4/TRP1; his4/TRP1; his4/trp1 Ans: T Difficulty: 1 56. ______ HIS4/trp1; HIS4/trp1; his4/TRP1; his4/TRP1 Ans: PD Difficulty: 1 Match the following results of offspring in an ordered octad with the appropriate segregation pattern: first-division (1) or second division (2). 57. ______ ws; ws; ws; ws; ws+; ws+; ws+; ws+ Ans: 1 Difficulty: 1 58. ______ ws; ws; ws+; ws+; ws; ws; ws+; ws+ Ans: 2 Difficulty: 1 59. ______ ws; ws; ws; ws; ws+; ws+; ws; ws Ans: 1 Difficulty: 1 60. ______ ws+; ws+; ws+; ws+; ws; ws; ws; ws Ans: 2 Difficulty: 1 61. ______ ws+; ws+; ws; ws; ws+; ws+; ws; ws Ans: 2 Difficulty: 1 True or False 62. Recombination due to crossing over occurs only rarely in mitosis. Ans: True Difficulty: 1

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63. Two genes are considered linked when F2 progeny more commonly show the recombinant genotype. Ans: False Difficulty: 1 64. When considering the chi-square test, a p-value of 0.05 is often considered significant but is actually an arbitrary assignment of significance. Ans: True Difficulty: 2 65. Chiasmata are structures of cross over between sister chromatids of homologous chromosomes. Ans: False Difficulty: 1 66. Chiasmata can be seen through a light microscope and are sites of recombination. Ans: True Difficulty: 1 67. Three-point crosses are more tedious and less accurate than two-point crosses. Ans: False Difficulty: 1 68. Chromosomal interference is not uniform and may significantly vary within a region of a single chromosome. Ans: True Difficulty: 2 69. Genetic mapping distance calculated for a chromosome is directly related to physical distance along that chromosome. Ans: False Difficulty: 2 70. Genes chained together by linkage relationships are known collectively as a linkage group. Ans: True Difficulty: 2 71. Ascospores are haploid cells that can germinate, replicate by mitosis, and survive as haploid individuals. Ans: True Difficulty: 1

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Short Answer 72. C. Stern studied recombination between two homologous X chromosomes in Drosophila in which one chromosome had two cytologically visible abnormalities at opposite ends. What did he find? Ans: Crossover products determined genetically were also recombinant for the cytological markers, indicating that genetic recombination involves physical exchange between homologs. Difficulty: 3 73. What is a chiasma? Ans: The cytological manifestation of a crossover. Difficulty: 1 74. When setting up crosses to determine map distances, why do geneticists prefer to cross the hybrid individuals to individuals homozygous for the recessive alleles in the cross? Ans: Because the recessive alleles from the tester parent will allow the alleles from the other parent to be revealed, so that all genotypes will be apparent from the phenotypes in the progeny. Difficulty: 1 75. What is a testcross? Ans: A cross in which one parent is homozygous for the recessive alleles. Difficulty: 1 76. What feature of meiosis in fungi such as Neurospora makes them especially suitable for the analysis of recombination? Ans: All of the products of a single meiosis remain packaged together in an ascus. Difficulty: 2 77. What use is genetic mapping? Give one example where it has been of value to society. Ans: The cystic fibrosis gene was cloned by a positional method that first required detailed mapping. Cloning has led to some therapeutic interventions and holds hope for a cure. Difficulty: 1 78. Why does the formula for the map distance between a gene and the centromere count only half of the second division segregations? Ans: Because in each second division segregation ascus only four of the eight spores result from a crossover between the gene and the centromere. Difficulty: 3

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79. Why does the formula for map distance between the two outside genes in a 3-point testcross count the double crossovers twice whereas the formula for the distance between an outside gene and the middle gene counts the double crossovers only once? Ans: Because a double crossover is two single crossovers, one in one interval and one in the other. Since the distance between the outside genes includes both intervals, each crossover must be counted. Difficulty: 2 80. When mapping three genes, why do geneticists prefer to do one three-point cross rather than three two-point crosses? Give two reasons. Ans: 1. Three point crosses can establish gene order unambiguously. 2. Three point crosses account for double crossovers as well as single crossovers and so estimate map distances more accurately. 3. Three point crosses allow calculation of interference parameters. Difficulty: 2 Experimental Design and Interpretation of Data In Drosophila, the genes y, f and v are all X-linked. y f v females are crossed to wild-type males and the F1 females are test-crossed. The F2 are distributed as follows: y f v 3210 yf+ 72 y + v 1024 y + + 678 +fv 690 + f + 1044 ++v 60 + + + 3222 10,000 81. Determine the linkage arrangement of these three genes and calculate the map distances. Ans: y v f; y-v = 15 m.u., v-f = 22 m.u.; y-f = 37 m.u. Difficulty: 3 82. Calculate the coefficient of coincidence. Ans: c.c. = 0.4. Difficulty: 3 83. State what a coefficient of coincidence of 0.5 would mean. Ans: Half as many double crossovers were observed as would have been expected if crossovers in the two intervals were independent. Difficulty: 3

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84. Map distances between each pair of three linked genes L, M and N are measured by two point test crosses and determined to be: L-M = 20 cM, M-N = 25 cM, and L-N = 38 cM. Explain why the measured distance between the two farthest apart genes is not equal to the sum of the two shorter distances. Ans: The two point cross between L and N does not count the events in which crossovers occurred both between L and M and between M and N, but these are counted separately in the two smaller distances. Difficulty: 2 Dihybrid test crosses are made between each pairwise combination of the three genes C, D and E with the following results: CD 222 CE 48 DE 198 Cd 280 Ce 455 De 289 cD 280 cE 445 dE 311 cd 218 ce 52 de 202 1000 1000 1000 85. Which are the recombinant classes in these three crosses? Ans: CD and cd, CE and ce, DE and de Difficulty: 2 86. Give the genotypes of the dihybrids in these three crosses, showing linkage arrangements. Ans: Cd/cD, Ce/cE, and De/dD. Difficulty: 3 87. Draw the map for these three genes, indicating the order and the lengths of the intervals in map units. Ans: CED; C-E = 10 m.u., D-E = 40 m.u., C-D = 44 m.u. Difficulty: 3 88. What can you say about crossover interference based on this data set? Ans: Nothing, interference can be measured only in a 3-point cross. Difficulty: 2 89. Why do the map distances not add up? Ans: Because the C-D distance does not include the double crossovers. Difficulty: 2

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Females heterozygous for the recessive second chromosome mutations pn, px and sp are mated to a male homozygous for all three mutations. The offspring are as follows: px sp cn 1,410 px sp + 3,498 px + cn 1 px + + 11 + sp cn 8 + sp + 0 + + cn 3,483 +++ 1,489 10,000 90. What is the genotype of the females that gave rise to these progeny? Ans: px sp cn+/px+ sp+ cn Difficulty: 3 91. Using the two point cross method, what are the distances among these three genes? Ans: px-sp = .2 m.u., px-cn = 30 m.u., cn-sp = 30.18 m.u. Difficulty: 3 92. Using the three point cross method, determine which gene is in the middle (which has to be flipped). Ans: px. Difficulty: 3 93. Which method provides more confidence as to the correct order of the genes? Ans: The 3-point method gives an unambiguous order because single crossovers can be distinguished from double crossovers. The 2-point method is less reliable because the difference between 30.0 and 30.18 is too small to provide a certain distinction. Difficulty: 2 94. Calculate the coefficient of coincidence and comment on its meaning. Ans: c.c.= 1/6 = .16; 6 double crossovers were expected but only one was observed, so interference is quite strong. Difficulty: 4 95. 50 map units is the maximum measurable map distance between two genes in a twopoint cross, yet some human chromosomes are over 200 map units in length. Explain this discrepancy. Ans: Two point crosses do not count multiple crossovers, which is why 50 map units is the most that can be measured. But a 200 map unit chromosome has an average of four crossovers per meiosis. Difficulty: 2

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In peas, tall (T) is dominant to short (t), red flowers (R) is dominant to white flowers (r), and wide leaves (W) is dominant to narrow (w). A tall, red, wide plant is crossed to a short, white, narrow plant and the progeny are as follows: tall red wide tall white wide short red wide short white wide 381 122 118 379 1000

96. What is the genotype of the tall, red, wide parent? Ans: TtRrWW. Difficulty: 4 97. Give the linkage arrangements. Ans: T/t and R/r are linked and 24 map units apart. Linkage of W/w unknown. Difficulty: 3 98. A strain of Neurospora with the genotype MN is crossed with a strain that is mn. Half the progeny are MN and half are mn. Explain these results. Ans: Genes M and N are completely linked, so that no recombinants are produced. Difficulty: 3 A dihybrid test cross is made between the genes C and D with the following results: CcDc ccdd CD 222 Cd 280 cD 280 cd 218 1000 99. You wish to test the hypothesis that the C and D genes are unlinked. What are the expected values for each class on the assumption that the genes are unlinked? Ans: 250 for each. Difficulty: 2 100. Calculate 2 to test the hypothesis that the C and D genes are unlinked. Ans: X2 = 14.4. Difficulty: 3

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101. Determine the degrees of freedom and calculate the p value. Ans: df = 3; p < .01. Difficulty: 2 102. State what this p value means. Ans: There is less than 1 chance in 100 that deviations from expected this large or larger could have been generated by chance, or, more simply, there is less than 1 chance in 100 that the C and D genes are unlinked. Difficulty: 3 103. What would the outcome of this test have been if only 100 progeny had been counted and the same proportions observed? Ans: X2 would have been between 1.0 and 2.0, so p would have been much greater than .05; we would not have been able to rule out the hypothesis of no linkage. Difficulty: 4 104. A female mouse from a true-breeding wild-type strain was crossed to a male mouse with apricot eyes (ap) and grey body (gy). The F1 mice were wild-type for both traits. When the F1 were interbred, the F2 were distributed as follows (200 total): Females: all wild type Males: wild type 91 apricot 11 grey 9 apricot, grey 89 Explain these results. Ans: ap and gy are X-linked and 10 map units apart. Difficulty: 2 Suppose the map for a particular human chromosome interval is: a-1-b-1-c-1-d-1-e-1-f, where the numbers indicate map distances. 105. In a man heterozygous for all six genes, what fraction of his sperm would be recombinant in the a-f interval? Ans: 5%. Difficulty: 3 106. In a man of the genotype ABCDEF/abcdef, what event would give rise to a sperm with the genotype abcdeF? Ans: A crossover between the E/e and F/f loci. Difficulty: 2

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In Neurospora the cross AB ab was made and 100 asci were scored:

107. Which classes are the PDs, NPDs & Ts? Ans: PD I & IV; NPD VI, VII; T - II, III & V. Difficulty: 2 108. Which class(es) are second division segregations? Ans: For A III, IV, V and VI; for B II, IV, V, and VI. Difficulty: 2 109. What is the map of these genes and any linked centromere(s)? Ans: A-cent-B; A-cent = 22; cent-B = 14; A-B = 32. Difficulty: 3 110. How do we know that crossing-over is reciprocal? Ans: Because when a recombinant spore class is present in an ascus, the reciprocal recombinant class is generally present as well. Difficulty: 3

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Chapter 6DNA: How The Molecules of Heredity Carries, Replicates, and Recombines Information Fill in the Blank 1. The full chemical name of DNA is _________________. Ans: deoxyribonucleic acid Difficulty: 2 2. The protein, ________, is needed to lay down a segment of RNA complementary to the DNA before replication can begin. Ans: primase Difficulty: 2 3. An origin of replication generally has _______ (how many?) replication forks. Ans: two Difficulty: 2 4. The discontinuous lagging strand on a replication fork consists of _________ fragments that are later ligated together to form one strand of DNA. Ans: Okazaki Difficulty: 2 5. The E. coli chromosome contains _____ (how many?) origin(s) of replication? Ans: one Difficulty: 3 6. A prokaryote lacks a __________ membrane. Ans: nuclear Difficulty: 2 7. Recombination is probably always initiated by _______ of DNA. Ans: nicking Difficulty: 3 8. The _________ strand is synthesized continuously during DNA replication. Ans: leading Difficulty: 2 9. A _____________ enzyme recognizes a specific DNA sequence and is able to cleave the DNA generating either blunt or sticky ends of the DNA. Ans: restriction Difficulty: 1

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10. A virus that infects bacterial cells is called a _____________. Ans: bacteriophage Difficulty: 2 11. The genetic material of some viruses such as X174 and M13 is ____________. Ans: single-stranded DNA Difficulty: 3 12. The genetic material of the viruses that cause polio and AIDS is ________. Ans: RNA Difficulty: 3 13. Topoisomerase _________ supercoils by nicking the DNA. Ans: relaxes Difficulty: 2 14. In E. coli, recombination begins at _____ sites where recBCD nicks and displaces a strand. Ans: chi Difficulty: 2 Multiple Choice 15. A) B) C) D) E) Which of the following is not true of DNA? It is acidic. It contains deoxyribose. It is found in cell nuclei. It contains phosphate. It contains proteins. Ans: E Difficulty: 2 The molecule of heredity is: RNA. DNA. protein. carbohydrate. none of the above Ans: B Difficulty: 1

16. A) B) C) D) E)

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17. A) B) C) D) E)

The four subunits which compose DNA are called: phosphodiesters. proteins. nucleotides. nucleosides. polymers. Ans: C Difficulty: 2 DNA is localized mainly in the: cell membrane. endoplasmic reticulum. vacuoles. chromosomes. none of the above Ans: D Difficulty: 2 Each nucleotide of DNA is made up of: a deoxyribose sugar. a nitrogenous base. a phosphate. a and b only. all of the above Ans: E Difficulty: 2 The polarity of DNA synthesis is: 5'3'. 3'5'. 5'2'. 2'5'. none of the above Ans: A Difficulty: 1

18. A) B) C) D) E)

19. A) B) C) D) E)

20. A) B) C) D) E)

21. In the Hershey and Chase experiment designed to determine the molecule of heredity, what was radiolabeled with 35S? A) protein B) DNA C) RNA D) rRNA E) none of the above Ans: A Difficulty: 2

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22. A) B) C) D) E)

The ratio of _____ is 1:1. guanine to adenine adenine to thymine cytosine to adenine uracil to cytosine none of the above Ans: B Difficulty: 2

23. X-ray data showed that the spacing between repeating units along the axis of the DNA helix is: A) 2.0 angstroms. B) 3.4 angstroms. C) 20 angstroms. D) 34 angstroms. E) none of the above Ans: B Difficulty: 3 24. A) B) C) D) E) X-ray data showed that the DNA helix undergoes one complete turn every: 2.0 angstroms. 3.4 angstroms. 20 angstroms. 34 angstroms. none of the above Ans: D Difficulty: 3

25. ________ bonds are responsible for the chemical affinity between A and T (or G and C) nucleotides. A) Ionic B) Covalent C) Hydrogen D) Electro-ionic E) none of the above Ans: C Difficulty: 2

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26. _______ -form DNA spirals to the right and is the major form of naturally occurring DNA molecules. A) A B) B C) D D) Y E) Z Ans: B Difficulty: 2 27. A) B) C) D) E) The nucleotide that is present in RNA but not DNA is: thymine. uracil. adenine. cytosine. guanosine. Ans: B Difficulty: 1 DNA replication occurs through a _________process. conservative semiconservative dispersive transferal none of the above Ans: B Difficulty: 2

28. A) B) C) D) E)

29. During complementary base pairing, enzymes join the base's nucleotide to the preceding nucleotide by a __________bond. A) hydrogen B) ionic C) phosphodiester D) electrostatic E) none of the above Ans: C Difficulty: 2

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30. A) B) C) D) E)

During early interphase the state of the DNA can be described as: a single continuous linear double helix. a double helix replicated semiconservatively. a double helix replicated conservatively. single-stranded DNA. none of the above Ans: A Difficulty: 4 During the S phase of interphase, the state of the DNA can be described as: a single continuous linear double helix. a double helix replicated semiconservatively. a double helix replicated conservatively. a triple helix replicated semiconservatively. none of the above Ans: B Difficulty: 4

31. A) B) C) D) E)

32. The step in DNA replication in which the replication proteins open up the double helix and prepare for complementary base pairing is called: A) initiation. B) elongation. C) termination. D) translation. E) translocation. Ans: A Difficulty: 2 33. The step in DNA replication in which the proteins connect the correct sequence of nucleotides into a continuous new strand is called: A) initiation. B) elongation. C) termination. D) translation. E) translocation. Ans: B Difficulty: 2

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34. The step in DNA replication in which two replication forks moving in opposite directions may meet is called: A) initiation. B) elongation. C) termination. D) translation. E) translocation. Ans: C Difficulty: 2 35. A) B) C) D) E) The group of enzymes able to relax supercoils in DNA is called: primases. helicases. topoisomerases. telomeres. ligases. Ans: C Difficulty: 2 How many replication forks depart from an origin of replication? one two three four none of the above Ans: B Difficulty: 2 The protein that progressively unwinds DNA ahead of each replication fork is called: primase. helicase. topoisomerase. telomerase. ligase. Ans: B Difficulty: 2 In eukaryotic cells, replication proceeds from ____ origin(s) of replication. no one two several many Ans: E Difficulty: 3

36. A) B) C) D) E)

37. A) B) C) D) E)

38. A) B) C) D) E)

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39. Eukaryotic chromosomes have evolved special structures at the ends of chromosomes to ensure the replication of the two ends of linear chromosomes. These structures are called: A) methylases. B) capping proteins. C) ligases. D) telomeres. E) single-stranded biding proteins. Ans: D Difficulty: 2 40. Which of the following is not involved in ensuring the accuracy of a cell's genetic information? A) redundancy B) repair enzymes C) precision of replication machinery D) DNA polymerase proofreading mechanism E) restriction endonucleases Ans: E Difficulty: 3 41. A) B) C) D) E) The process of _________ is extremely important in generating genetic diversity. translation transcription recombination transformation none of the above Ans: C Difficulty: 2

42. Any deviation from the expected 2:2 segregation of parental alleles that results from recombination is known as: A) allelic exchange. B) gene conversion. C) crossing over. D) recombination. E) DNA replication. Ans: B Difficulty: 3

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43. A) B) C) D) E)

Recombination occurs during meiotic ________. anaphase interphase prophase metaphase none of the above Ans: C Difficulty: 3 Recombination involves the breakage and reunion of DNA molecules from: homologous nonsister chromatids. homologous sister chromatids. heterologous nonsister chromatids. heterologous sister chromatids. none of the above Ans: A Difficulty: 2 The nicking of DNA that initiates recombination during mitosis may be due to all but: instruction from normal cell-cycle program. X-rays. chemical damage. physical damage. radiation. Ans: A Difficulty: 3

44. A) B) C) D) E)

45. A) B) C) D) E)

46. What radiolabeled substance did Hershey and Chase use to label the protein component of the bacteriophage in their study to determine whether protein or DNA was necessary for phage production? A) nitrogen B) carbon C) sulfur D) phosphorous E) iodide Ans: C Difficulty: 2

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47. If 35% of the bases in a region of the mouse genome are cytosine, what percentage in that region are adenine? A) 15% B) 20% C) 30% D) 35% E) none of the above Ans: A Difficulty: 3 48. A) B) C) D) E) The complementary sequence of 5' AATTCGCTTA 3' is: 5' AATTCGCTTA 3'. 3' AATTCGCTTA 5'. 5' TAACGCTTAA 3'. 5' TAAGCGAATT 3'. 3' TAAGCGAATT 5'. Ans: D Difficulty: 2

49. Two strains of S. cerevisae (yeast) are crossed. One has the genotype ABC and the other abc. Five sets of the resultant tetrads are noted below. In which set did a gene conversion event occur? A) abc, aBc, AbC, aBC B) abc, abc, ABC, ABC C) aBc, aBc, AbC, AbC D) abC, abc, ABc, ABC E) Abc, Abc, aBC, aBC Ans: A Difficulty: 4 50. Without __________ regions on the DNA during recombination, gene conversion could not occur. A) homoduplex B) heteroduplex C) homotriplex D) heterotriplex E) none of the above Ans: B Difficulty: 2

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51. Occasionally, a loss of function mutation may occur in the telomerase enzyme in a cell. What is likely to be the result of this mutation on the DNA in the cell over the course of several rounds of mitosis? A) Chromosome length will gradually increase. B) Chromosome length will gradually decrease. C) Chromosome length will stay constant. D) Chromosomes will fail to dissociate after replication. E) None of the above Ans: B Difficulty: 3 52. Bacterial DNA is resistant to degradation by its own restriction enzymes through the protection of: A) methylases. B) recombinases. C) topoisomerases. D) ligases. E) primases. Ans: A Difficulty: 2 53. Hershey and Chase relied on ________ to physically separate the infected bacterial cells from the phage ghosts. A) radioactivity B) gel filtration C) ion exchange D) centrifugation E) none of the above Ans: D Difficulty: 3 54. Meselson and Stahl relied on equilibrium density gradient centrifugation in a _______ solution to resolve the DNA containing 14N from the DNA containing 15N. A) radiolabeled phosphate B) calcium chloride C) radiolabeled nitrogen D) sodium acetate E) cesium chloride Ans: E Difficulty: 3

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Matching Match the scientist with their contribution to understanding more about DNA a. early recombination models b. transformation c. semiconservative replication d. x-ray structure of DNA e. revised recombination models f. basic structure of DNA g. DNA = molecule of heredity h. discovery of nuclein i. nucleotide ratios in DNA j. famous phage blender experiment 55. ___ Watson and Crick Ans: f Difficulty: 3 56. ___ Chargaff Ans: i Difficulty: 3 57. ___ Franklin and Wilkins Ans: d Difficulty: 3 58. ___ Griffith Ans: b Difficulty: 3 59. ___ Hershey and Chase Ans: j Difficulty: 3 60. ___ Miescher Ans: h Difficulty: 3 61. ___ Meselson and Stahl Ans: c Difficulty: 3 62. ___ Holliday Ans: a Difficulty: 3

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63. ___ Meselson and Radding Ans: e Difficulty: 3 64. ___ Avery, MacLeod and McCarty Ans: g Difficulty: 3 Diagram Matching (Match the region or item on the diagram with the correct term from the list below)

65. ___ lagging strand Ans: c Difficulty: 2 66. ___ leading strand Ans: d Difficulty: 2 67. ___ origin Ans: a Difficulty: 2 68. ___ RNA primer Ans: e Difficulty: 2 69. ___ Okazaki fragment Ans: f Difficulty: 2

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70. ___ helicase Ans: g Difficulty: 2 71. ___ polymerase Ans: b Difficulty: 2 True or False 72. A phosphodiester bond joins one nucleotide together in the DNA polymer. Ans: True Difficulty: 1 73. Prokaryotes have a circular chromosome surrounded by a nuclear membrane. Ans: False Difficulty: 1 74. Transformation in bacteria results from the uptake of foreign DNA. Ans: True Difficulty: 1 75. DNA is highly negatively charged throughout the molecule and therefore has no polarity. Ans: False Difficulty: 1 76. A region of DNA 100 bp in length has the potential to be represented by 4100 unique sequences. Ans: True Difficulty: 1 77. Viruses use only DNA as their genetic material. Ans: False Difficulty: 1 78. Restriction enzymes are molecular weapons which cut DNA that bacteria use in their fight to protect themselves from DNA viruses. Ans: True Difficulty: 1 79. Human DNA is replicated in a conservative manner. Ans: False Difficulty: 1

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80. In DNA replication, new DNA is produced in a continuous bi-directional fashion. Ans: False Difficulty: 1 81. DNA topoisomerase supercoils DNA to get it out of the way of DNA polymerase. Ans: False Difficulty: 2 82. Accuracy of replication is enhanced by the redundancy of DNA, enzymatic repair of damaged DNA and the remarkable precision of the cellular replication machinery. Ans: True Difficulty: 1 83. A 2:2 segregation of parental alleles is known as gene conversion. Ans: False Difficulty: 2 84. Recombination events are limited to only hot spots along a chromosome. Ans: False Difficulty: 1 85. Gene conversion in which a small segment of information from one homologous chromosome transfers to the other can give rise to an unequal yield of two different alleles. Ans: True Difficulty: 2 86. Alternative resolutions of the Holliday intermediate are responsible for whether or not crossing over or gene conversion occurs. Ans: True Difficulty: 2 Short Answer 87. Draw the complementary strand to the one shown below. Be sure to note polarity. 5' CATAGCCTTA 3' Ans: 5' TAAGGCTATG 3' Difficulty: 2

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88. The enzyme HindIII cleaves DNA between the two adenine bases in the specific sequence seen below. Indicate where the cuts would occur on each strand of the DNA below. Indicate what type of DNA ends result from this cleavage. 5' AAGCTT 3' 3' TTCGAA 5' Ans: 5'A AGCT T 3' 3'TTCGA A 5' sticky or cohesive ends Difficulty: 2 89. Briefly describe the role of an initiator protein in DNA replication. Ans: The initiator protein is the first protein to bind to the origin of replication and attracts helicase which is able to unwind the region surrounding the originthe first step in initiation of DNA replication. Difficulty: 3 90. During the DNA replication process, RNA primers are removed and replaced with DNA. Briefly state why it is important that this RNA be replaced with DNA. Ans: RNA is more unstable than DNA (it may be easily degraded). DNA must also be present so that the next round of replication may proceed. Difficulty: 4 91. Why are DNA molecules considered redundant? Ans: Either strand of the double helix can specify the sequence of the other. Difficulty: 2 92. The Holliday model of recombination has been modified and is now called the consensus model, which is now consistent with current research. What are the five properties of recombination, as they are now understood? Ans: 1. homologs physically break, exchange parts, and rejoin 2. breakage and repair create reciprocal products of recombination 3. recombination events can occur anywhere along the DNA molecule 4. the exchange is precise, there is no gain or loss of nucleotides 5. gene conversion can give rise to an unequal yield of two different alleles Difficulty: 4

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93. What are the eight steps of recombination (crossing over)? Ans: 1. the DNA strand is nicked 2. helicase unwinds the DNA and whisker displacement occurs 3. first strand invasion occurs 4. second strand invasion occurs 5. the D-loop is degraded and the gaps are repaired and ends are ligated 6. branch migration lengthens the heteroduplex region 7. chromatid rotation forms a Holliday intermediate 8. endonucleases cut the strands and the chromatids are resolved. Difficulty: 4 94. How is it possible for an individual to be XX male or XY female? Ans: An illegitimate recombination event can take place between the X and Y chromosomes. The result is a Y chromosome that lacks the SRY region or an X that has gained it. Difficulty: 3 95. How does mismatch repair lead to gene conversion? Ans: Repair can proceed in two ways, correction of the incorrect strand or change of the correct strand to the incorrect sequence. Difficulty: 3 96. What is a heteroduplex region? Ans: The segment that is located between the annealed break points of recombination is called heteroduplex because one strand is maternal and one is paternal and mismatch may be present. Difficulty: 3 Experimental Design and Interpretation of Data 97. An illegitimate recombination event can take place between the human X and Y chromosomes. The result may be a sperm with a Y chromosome which lacks SRY (the sex-determining region). Fertilization of an egg by this particular sperm would yield what type of individual. State both genotype and phenotype. Ans: XY individual that develops as a female. Difficulty: 3

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98. A circular 5.0 kb piece of DNA is cut with a restriction enzyme, EcoRI, which cleaves the DNA twice. One fragment is 3.0 kb, while the other is 2.0 kb. When the same 5.0 kb piece of DNA is cleaved with HindIII, only one cut is made. Briefly describe how you would determine whether the HindIII site resides in the 3.0 kb EcoRI fragment or in the 2.0 kb EcoRI fragment. (Assume that the HindIII site is at least 500 bp away from each of the EcoRI sites.) Ans: A double digest with both EcoRI and HindIII would determine which EcoRI fragment is further cleaved with HindIII. Difficulty: 4 99. Griffith found that smooth (S) forms of S. pneumoniae have a polysaccharide capsule and rough (R) forms do not. Only S forms cause infection. Briefly describe how Griffith demonstrated transformation using live R form and heat killed S form bacteria. Ans: SHK does not yield infection Rlive does not yield infection SHK+Rlive = infection, R has been transformed by S. Difficulty: 2 100. When Meselson and Stahl performed the experiment that showed that replication is a semiconservative process, they utilized E. coli, and various isotopes of nitrogen (15N and 14N). Explain briefly what their results would have been if DNA replicated conservatively. Ans: Following centrifugation, the first generation of replication would yield 2 bands 15 N and 14N (no hybrid). The second generation would again result in the same pattern with no hybrid pattern ever revealed. Difficulty: 4 101. You are a researcher at a new Biotech company. You have been asked to devise a scheme to use bacteria to produce protein X, which has been found important in cancer treatment in humans. Protein X is not a native bacterial protein. Briefly describe your scheme. Ans: The X gene is cloned into an appropriate plasmid through the use of restriction enzymes and ligase. The plasmid is then introduced into a bacterial host and the cells should produce protein X (as long as it is not toxic to the host). Difficulty: 3 102. Design an experiment that utilizes suggestive physical evident to test the hypothesis that during recombination DNA molecules break and rejoin. Ans: Bacteriophage previously grown in either heavy or light isotopes of nitrogen or carbon can be used to track breakage by infection of bacteria and subsequent CsCl gradient centrifugation. Banding at densities intermediate to the control heavy and light phage DNA indicates the occurrence of breakage and rejoining. Difficulty: 4

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103. Viruses may have RNA, ssDNA or dsDNA as their molecule of heredity. Design an experiment that would allow you to test an unknown virus and determine which it carried. Ans: Grow bacteria infected with virus in the presence of radioactive uracil. Isolated genetic material from phage will be radioactive if they are an RNA containing virus. Double stranded versus single stranded DNA can be resolved by the ability to undergo digestion with restriction enzymes. Difficulty: 4

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Chapter 7Anatomy and Function of a Gene: Dissection Through Mutation Fill in the Blank 1. A ______________________ allele is one whose frequency is greater than 1% in a natural population. Ans: wild-type Difficulty: 1 2. ______________________ are heritable changes in base sequence that can affect phenotype. Ans: mutations Difficulty: 1 3. A ____________ is a specific protein-encoding segment of DNA composed of a distinctive set of nucleotide pairs. Ans: gene Difficulty: 1 4. A mutation that changes a wild-type allele of a gene to a different allele is called a ____________ mutation. Ans: forward Difficulty: 2 5. A ________________ mutation causes a novel allele to be converted back to a wildtype allele. Ans: reverse Difficulty: 2 6. An ____________________ is a type of mutation where a segment of a chromosome is rotated 180. Ans: inversion Difficulty: 1 7. A mound of genetically identical bacteria derived from a single bacterium is called a __________________. Ans: colony Difficulty: 1 8. Any physical or chemical agent that increases the rate of mutation above the spontaneous rate is a _________________________. Ans: mutagen Difficulty: 1

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9. A collection of mutations that do not complement each other is known as a __________________ ____________________. Ans: complementation group Difficulty: 3 10. A cell that can synthesize all its needed molecules for growth from minimal media is ________________________. Ans: prototrophic Difficulty: 3 11. The end of a polypeptide that contains a free amino group that is not connected to another amino acid is called the ____________________________. Ans: N-terminus Difficulty: 1 12. When a protein is exposed to heat, extremes of pH, or molecules such as urea or mercaptoethanol it unfolds and is said to be _________________________. Ans: denatured Difficulty: 2 13. The three-dimensional structure of a protein consisting of two of more polypeptide chains is called _______________________structure. Ans: quaternary Difficulty: 2 14. A ____________________ mutation produces either much less of a protein or a protein with very weak but detectible function. Ans: hypomorphic Difficulty: 3 15. ___________________________ results when one wild-type allele does not provide enough gene product to produce the wild-type phenotype. Ans: haploinsufficiency Difficulty: 2 Multiple Choice 16. A) B) C) D) E) The term mutation refers to: only changes in the DNA that result in new phenotypes. only changes in the DNA that result in novel proteins. any change in the DNA of a cell. a heritable change in the DNA of a cell. any change in the cell that changes its survival chances. Ans: D Difficulty: 2

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17. A) B) C) D) E)

A heritable change in DNA base sequence is called a: forward mutation. reversion. substitution. deletion. mutation. Ans: E Difficulty: 1 Replacing a thymine nucleotide with a guanine is an example of a: translocation. transition. transversion. forward mutation. reversion or reverse mutation. Ans: C Difficulty: 1 Replacing an adenine nucleotide with a guanine is an example of a: translocation. transition. transversion. forward mutation. reversion or reverse mutation. Ans: B Difficulty: 1

18. A) B) C) D) E)

19. A) B) C) D) E)

20. Assume that a wild-type sequence is 5'AGCCTAC3'. Indicate the sequence that might be produced by a transversion. A) 5'AGTCTAC3' B) 5'AGCCGCCGCCGCCTAC3' C) 5'AGCCCAC3' D) 5'ATCCTAC3' E) 5'AGCCTGC3' Ans: D Difficulty: 3

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21. A mutation in which parts of two nonhomologous chromosomes change places is called a: A) translocation. B) transition. C) transversion. D) insertion. E) deletion. Ans: A Difficulty: 1 22. A) B) C) D) E) Indicate the statement that is most accurate regarding mutations. Most mutations alter protein structure and phenotype. Only those mutations that alter protein structure will alter phenotype. Mutations altering a region that does not code for a protein may alter phenotype. All mutations that alter protein structure will alter phenotype. All altered phenotypes result from altered proteins. Ans: C Difficulty: 3

23. Assume that the mutation rate for a given gene is 510-6 mutations per gene per generation. For that gene how many mutations would be expected if 10 million sperm are examined? A) none B) 510-6 C) 5 D) 50 E) 500 Ans: D Difficulty: 3 24. A) B) C) D) E) Which type of mutation is least likely to revert? deletion transition transversion insertion all are equally likely Ans: A Difficulty: 2

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25. Consider the following results. When 50 million sperm were examined for a specific mutation, 100 mutations were found. Indicate the mutation rate for that gene. A) 510-6 B) 5010-6 C) 210-6 D) 210-5 E) 510-5 Ans: C Difficulty: 2 26. Assume that a researcher set out to duplicate the Luria-Delbruck fluctuation experiment. This researcher planted twenty small flasks with bacteria from the same colony and let them grow overnight. The next morning the researcher noticed that all but one of the flasks had come open and were ruined. Not wishing to redo the experiment the researcher took bacteria samples from the one remaining intact flask and placed them on twenty phage plates. What results would you expect to see when the twenty phage plates are examined, and how would these results compare with those of the original LuriaDelbruck fluctuation experiment? A) Identical to the Luria-Delbruck results, namely different numbers of resistant colonies. B) Identical to the Luria-Delbruck results, namely identical numbers of resistant colonies. C) Not like the Luria-Delbruck results, namely different numbers of resistant colonies. D) Not like the Luria-Delbruck results, namely identical numbers of resistant colonies. E) Identical to the Luria-Delbruck results, namely no resistant colonies. Ans: D Difficulty: 4 27. A) B) C) D) E) The results of the Luria-Delbruck fluctuation experiment indicated that: bacteria are naturally resistant to phage. a low level of any bacteria population are naturally resistant to phage. bacteria become resistant to phage by mutation when exposed to phage. bacteria become resistant to phage by random spontaneous mutation. the phage mutate to produce large plaques with sharp edges. Ans: D Difficulty: 2

28. A) B) C) D)

In the Luria-Delbruck fluctuation experiment, the bacteria + phage plates showed: all plates had some resistant colonies, some had very many. some plates had no resistant colonies, a few plates had very many resistant colonies. all plates had the same number of resistant colonies. some plates had no resistant colonies, the plates that had resistant colonies all had the same number of resistant colonies. E) phage caused mutations to occur in some of the plates but not in others. Ans: B Difficulty: 3

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29. A) B) C) D) E)

The hydrolysis of a purine base from the deoxyribose-phosphate backbone is called: depurination. deamination. replica plating. excision repair. deletion. Ans: A Difficulty: 1

30. Assume that in the organism under study the DNA polymerase has an error rate of 1 mistake in every 106 bases copied. However, the overall mutation rate is much lower. This is most likely because: A) the polymerase is more careful in replicating regions where genes exist. B) repair mechanisms correct errors made by the polymerase. C) not all mutations can be detected easily. D) the DNA polymerase has no proofreading function. E) mutations do not occur if mutagens are not present. Ans: B Difficulty: 2 31. A) B) C) D) E) Excision repair corrects DNA by: removing a double-stranded fragment of damaged DNA. detecting, removing, and replacing a single stranded fragment of damaged DNA. excising the incorrect base from a nucleotide. removing extraneous groups such as methyl or oxygen added by mutagens. correcting A=T to C=G transitions. Ans: B Difficulty: 1 Thymine dimers are caused by: X-rays. free radicals such as oxygen. EMS or NSG. depurination. UV light. Ans: E Difficulty: 1

32. A) B) C) D) E)

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33. A) B) C) D) E)

UV light is a mutagen that can cause: depurination. deamination. alkylation. thymine dimers. oxidation. Ans: D Difficulty: 1

34. The genetic condition xeroderma pigmentosum, which can lead to skin cancer, results from: A) inability to correct UV induced dimers. B) inability to process phenylamine. C) inability to produce functional hemoglobin. D) inability to correct transitions. E) breaks in the X chromosome. Ans: A Difficulty: 2 35. The bacterial repair system that corrects mismatched bases after polymerization is able to discriminate between the old and newly made DNA strands because: A) the new strand will contain the incorrect base if a mismatch occurs. B) older DNA is more likely to contain errors. C) older DNA contains methyl groups at specific sequences. D) newer DNA contains methyl groups at specific sequences. E) the DNA polymerase is attached to the new strand. Ans: C Difficulty: 2 36. The consequence to a bacterial cell of a mutation that inactivated the enzyme that methylates the A of the sequence GATC in newly made DNA would be: A) failure to carry out replication. B) failure to correct thymine dimers. C) failure to distinguish old and new DNA during mismatch repair. D) inactivation of certain metabolic genes. E) decrease in the mutation rate. Ans: C Difficulty: 3

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37. A) B) C) D) E)

Unequal crossing over results in: an exchange between nonhomologous chromosomes. a loss of genetic material. a repair of UV-induced damage. a production of eggs containing Y chromosomes. a creation of deletions and duplications. Ans: E Difficulty: 2

38. The heritable disorder fragile X syndrome, a major cause of mental retardation, is caused by: A) production of enzymes that break the phosphate backbone. B) UV light. C) X-rays. D) presence of an extra X chromosome in the sperm or egg. E) duplication of multiple three-nucleotide repeats. Ans: E Difficulty: 2 39. If a man shows the premutation allele for fragile X syndrome, what is the probability that he will pass it on to his son? A) 100% B) 75% C) 50% D) 25% E) 0% Ans: E Difficulty: 2 40. The duplication of the triplet sequence CGG resulting in elongation or breakage of the X chromosome is termed: A) Barr-eyed. B) Huntington's disease. C) unequal crossing over. D) fragile X syndrome. E) Rhys syndrome. Ans: D Difficulty: 1

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41. Genes on the X chromosome of mammals and Drosophila are particularly suitable for genetic study because: A) males have only one X and most genes behave as haploids. B) females have only one X and most genes behave as haploids. C) the X chromosome is large and many more genes are located there. D) when present as Barr bodies they are exposed for electron microscopic examination. E) they behave as diploids in females. Ans: A Difficulty: 2 42. If a base analog such as 5-Bromouracil is used as a mutagen, how many generations will be required to mutate the codon for proline (CCC) into the codon for alanine (GCC)? A) one generation B) two generations C) three generations D) at lease two, but perhaps more due to chance E) it will not occur Ans: E Difficulty: 3 43. A) B) C) D) E) Base analogs differ from other classes of mutagen in that they: only alter bases. can only cause transversions. only work during DNA replication or repair. can only cause forward mutations, nor reversions. will not function in bacterial cells. Ans: C Difficulty: 2 Intercalating agents such as acridine orange function as mutagens to: promote transitions. remove amine groups. attach to purines causing distortions. add ethyl or methyl groups. fit between stacked bases and disrupt replication. Ans: E Difficulty: 2

44. A) B) C) D) E)

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45. A) B) C) D) E)

Alkylating agents such as ethylmethane sulfate (EMS) function as mutagens to: promote deletions and insertions. remove amine groups. add oxygen free radicals to bases. add ethyl or methyl groups. fit between stacked bases and disrupt replication. Ans: D Difficulty: 2 In the Ames test for mutagenicity: auxotrophic bacteria are converted to prototrophs which survive. prototrophic bacteria are converted to auxotrophs which survive. cells are treated with mutagen and only those with no mutations survive. cells are treated with excess amino acids, killing cells that carry mutations. rat liver enzymes protect cells from mutation. Ans: A Difficulty: 3

46. A) B) C) D) E)

47. In the Ames test for mutagenicity, rat liver enzymes are included with the compound under test because: A) bacterial cell walls must be treated to permit uptake of the compounds. B) rat liver enzymes increase the sensitivity of the bacteria to mutagens. C) rat liver enzymes kill mutant cells and allow colonies to form. D) rat liver enzymes may modify or break down some compounds. E) the mutant strain of bacteria requires rat liver enzymes to digest nutrients for growth. Ans: D Difficulty: 2 48. Assume that a new low-calorie sweetener is developed. The structure is novel and is tested with the Ames test for mutagenicity. The following results are obtained: Sample Number of his+ revertent colonies distilled water 2 distilled water + rat liver enzymes 3 sweetener 6 sweetener + rat liver enzymes 65 What conclusion is most consistent with this data? A) The sweetener is not mutagenic. B) Rat liver enzymes are highly mutagenic. C) The sweetener is not mutagenic but can be converted into strong mutagens. D) The sweetener is mutagenic and can be converted into strong mutagens. E) The sweetener and its conversion products are equally mutagenic. Ans: C Difficulty: 3

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49. A) B) C) D) E)

The Ames test for mutagenicity is useful to identify potential carcinogens because: since bacteria do not get cancer they can survive lethal carcinogens. mutagens that affect bacterial DNA are likely to cause human mutation. bacteria thrive on substances that could cause cancer in humans. the same genes that cause cancer in humans can be mutated in bacteria. liver enzymes alter the bacteria so they will behave like mammal cells. Ans: B Difficulty: 2 The size of the human genome in base-pairs is about: 210 million 100,000 2.75 106 2.75 109 2.75 1010 Ans: D Difficulty: 1 A complementation group is: a group of mutations that produce the same phenotype. a group of mutations that are in the same gene and complement each other. a group of mutations that are in the same gene and do not complement each other. a group of mutations in two different genes that complement each other. a group of mutations in two different genes that do not complement each other. Ans: C Difficulty: 3

50. A) B) C) D) E)

51. A) B) C) D) E)

52. Choose the statement that is most correct regarding the rII- strain of T4 that Benzer studied. A) Produces smaller plaques than wild type. B) Produces smaller plaques, grows in E. coli K(), not in E. coli B. C) Produces larger plaques, grows in E. coli K(), not in E. coli B. D) Produces larger plaques, grows in E. coli B, not in E. coli K(). E) Produces larger plaques, grows in both E. coli K() and in E. coli B. Ans: D Difficulty: 3 53. A) B) C) D) E) A plaque is: a colony of bacteria growing on a plate. a colony of bacteria that contain phage within them. a region on a plate where living bacteria survive phage infection. an area on a plate containing live phage-resistant bacteria. an area on a plate containing phage and dead or destroyed bacteria. Ans: E Difficulty: 1

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54. Shown below are the results of a series of coinfections using T4 rII- strains similar to those employed by Benzer. Each strain contains a different deletion mutation. Ability to produce wild-type progeny phage is indicated by (+), (o) indicates no wild-type progeny. A B C D E A o + o + + B + o + o o C o + o + + D o o + o + E + o + + o A) CADBE B) ACBDE C) ABCDE D) BEDCA E) CEADB Ans: A Difficulty: 3 55. Shown below are the results of a series of coinfections using T4 rII- strains similar to those employed by Benzer. Each strain contains a different deletion mutation. Ability to produce wild-type progeny phage is indicated by (+), (o) indicates no wild-type progeny. A B C D E A o o + o + B o o + o + C + + o o o D o + o o + E + + o + o Indicate the order that is most consistent with these data. A) CADBE B) ACBDE C) BADCE D) BEDCA E) CEADB Ans: C Difficulty: 3

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56. Choose the statement that best distinguishes a complementation test and a recombination analysis when examining mutations in phage. A) Both tests require two different mutations. B) Recombination can only occur between two genes. C) Complementation results can be seen immediately, recombination requires a second infection. D) Recombination results can be seen immediately, complementation requires a second infection. E) Recombination can distinguish one gene with two alleles from two different genes. Ans: C Difficulty: 3 57. Shown below are the deletion maps of a series of rII- mutations. The deleted region is indicated as (......) and the intact region as ______. 1 _____(..........)____________________ 2 _________________(..........)________ 3 (.........)__________________________ 4 ________________________(..............) 5 ___________(...........)______________ A series of point mutations A-E is used in a coinfection experiment. Shown below are the results of those coinfections. Ability to produce wild-type progeny phage is indicated by (+), (o) indicates no wild-type progeny. 1 2 3 4 5 A + + o + + B + + + + + C + + + o + D + + + + o E + o + + + Indicate the order that is most consistent with these data. A) CADBE B) ACBDE C) BADCE D) ABDEC E) CEADB Ans: D Difficulty: 4

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58. Shown below are the deletion maps of a series of rII- mutations. The deleted region is indicated as (......) and the intact region as ______. 1 ___________(...........)_______________ 2 _________________(...........)_________ 3 (.....................)_______________ ______ 4 ________________________(................) 5 _____(..........)______________________ A series of point mutations A-E is used in a coinfection experiment. Shown below are the results of those coinfections. Ability to produce wild-type progeny phage is indicated by (+), (o) indicates no wild type progeny. 1 2 3 4 5 A + o + + + B o + + + + C + + + o + D + + o + + E + + o + o Indicate the order that is most consistent with these data. A) CADBE B) DEBAC C) BADCE D) ABDEC E) CEADB Ans: B Difficulty: 3

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59. Shown below are the deletion maps of a series of rII- mutations. The deleted region is indicated as (......) and the intact region as ______. Note that strain 5 carries two different deletions. 1 ___________(...........)_______________ 2 _________________(...........)_________ 3 (.....................)_______________ ______ 4 ________________________(................) 5 _____(..........)________________(.........) A series of point mutations A-E is used in a coinfection experiment. Shown below are the results of those coinfections. Ability to produce wild-type progeny phage is indicated by (+), (o) indicates no wild type progeny. 1 2 3 4 5 A + + o + o B + o + + + C + + o + + D o + + + + E + + + o o Indicate the order that is most consistent with these data. A) CADBE B) DEBAC C) BADCE D) ABDEC E) CEADB Ans: A Difficulty: 4 60. Indicate the correct order for one round of infection by bacteriophage T4. 1. Lysis of host cell. 2. Phage proteins and DNA synthesized, host DNA degraded. 3. Assembly of phage within host cell. 4. Phage body enters host cell. 5. Phage injects DNA into host cell. A) 4, 2, 3, 1 B) 1, 2, 3, 4, 5 C) 5, 1, 2, 3, D) 5, 2, 3, 1 E) 4, 5, 3, 1 Ans: D Difficulty: 2

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61. A) B) C) D) E)

How many progeny phage are released when a single E. coli cell is lysed by phage T4? between 1 and 10 between 10 and 100 between 100 and 1,000 about 10,000 about 100,000 Ans: C Difficulty: 1

62. Indicate which of the following is least important in doing a complementation test with coinfection of phage T4. A) Ensuring that sufficient phage of both strains are present. B) Recovering phage from the plaques after growth and lysis. C) Counting the plaques that are produced on E. coli K(). D) Control using both mutations in cis configuration and a wild type. E) All the above steps are essential for the experiment. Ans: C Difficulty: 3 63. Assume that a researcher is studying coat color in voles. Three strains of white vole have been isolated: milky, blanc, and weiss. White is a recessive trait in each strain. Homozygous white voles are obtained for each strain. Consider the following crosses: milky blanc = all white progeny milky weiss = all brown (wild-type vole color) blanc weiss = all brown (wild-type vole color) The conclusion most consistent with these results is: A) all three strains have mutations in the same gene. B) all three strains have mutations in different genes. C) milky and blanc have mutations on the same gene, weiss has a mutation in a different gene. D) milky and weiss have mutations on the same gene, blanc has a mutation in a different gene. E) weiss and blanc have mutations on the same gene, milky has a mutation in a different gene. Ans: C Difficulty: 3

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64. Assume a researcher is studying the rII locus of phage T4. Three rII- strains are obtained: A, B, and C. When coinfections are performed in E. coli strain K() the following results are obtained: A B = plaques form A C = plaques form B C = no plaques form The conclusion most consistent with these data is: A) A, B, and C carry mutations in three different genes. B) A and B carry mutations in the same gene, C is on a different gene. C) A and C carry mutations in the same gene, B is on a different gene. D) B and C carry mutations in the same gene, A is on a different gene. E) A, B, and C carry mutations in the same gene. Ans: D Difficulty: 3 65. Assume a researcher is studying the rII locus of phage T4. Four rII- strains are obtained: A, B, C and D. When coinfections are performed in E. coli strain K() the following results are obtained: A B = lysis A C = lysis B C = no lysis B D = no lysis C D = no lysis In a second experiment, coinfections are performed in E. coli strain B. When progeny phage are examined for their ability to form plaques in E. coli strain K(), the following results are obtained: A B = plaques B C = plaques C D = plaques B D = no plaques The conclusion most consistent with these data is: A) A carries a mutation in one gene, B, C and D are on a different gene, C and D both carry the same mutation. B) A and B carry mutations in the same gene, C and D are on a different gene. C) A carries a mutation in one gene, B, C and D are on a different gene, B and C both carry the same mutation. D) A carries a mutation in one gene, B, C and D are on a different gene, B and D both carry the same mutation. E) A, B, C and D carry mutations in the same gene. Ans: D Difficulty: 4

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66. Choose the statement that is most accurate concerning biochemical pathways. A) All enzymes in the pathway catalyze the same reaction. B) If an enzyme in a pathway is inactive, adding excessive amounts of its substrate will restore the normal phenotype. C) If an enzyme in a pathway is inactive, adding excessive amounts of its product will restore the normal phenotype. D) If the enzyme that catalyzes the final step in a pathway is inactive all the other enzymes will be inactivated as well. E) If the first enzyme in a pathway is inactivated, adding the final product will not restore the normal phenotype. Ans: C Difficulty: 2 67. Assume 7 different strains of fly have been isolated, each shows a recessive white eye trait. Crosses are performed as follows; (w) indicates white-eyed progeny, (R) indicates wild-type red eyes.

A) B) C) D) E)

Based on these crosses, how many different genes are present? only one gene with several different alleles 2 3 4 7 Ans: C Difficulty: 3

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68. Assume 8 different strains of fly have been isolated, each shows a recessive white eye trait. Crosses are performed as follows; (w) indicates white-eyed progeny, (R) indicates wild-type red eyes.

A) B) C) D) E)

Based on these crosses, how many different genes are present and what strains have mutations in the same gene as does strain A? 2, B, E, and H 3, B and C 3, B, C, and H 3, B, E, and H 4, B and H Ans: D Difficulty: 4

69. In the human genetic disorder alkaptonuria, urine turns black because of the presence of homogentisic acid in individuals with the trait. This is due to: A) the presence of large amounts of homogentisic acid in the diet. B) failure of individuals with alkaptonuria to manufacture enzymes involved in the synthesis of homogentisic acid. C) failure of wild-type individuals to manufacture enzymes involved in the synthesis of homogentisic acid. D) failure of the kidneys to remove homogentisic acid from the urine. E) failure of individuals with alkaptonuria to manufacture enzymes involved in the breakdown of homogentisic acid. Ans: E Difficulty: 2

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70. Consider the pathway for the synthesis of the amino acid arginine in Neurospora: ARG-E ARG-F ARG-H ornithine citrulline argininosuccinate arginine Mutant strains of Neurospora are grown in minimal media supplements as follows. Each mutant strain carries only a single mutation. Growth is shown by (+), no growth is shown by (o). Supplements mutant nothing ornitihine citrulline argininoarginine strain succinate a o o o + + b o o + + + c o o o o + Indicate the correct strain / defective gene pairing. A) strain a / ARG-F B) strain a / ARG-H C) strain b / ARG-F D) strain c / ARG-E E) strain c / ARG-F Ans: A Difficulty: 3 71. Consider the pathway for the synthesis of the amino acid arginine in Neurospora: ARG-E ARG-F ARG-H ornithine citrulline argininosuccinate arginine Mutant strains of Neurospora are grown in minimal media supplements as follows. Strains may carry more than one mutation. Growth is shown by (+) no growth is shown by (o). Supplements mutant nothing ornitihine citrulline argininoarginine strain succinate a o o o o + Indicate the most accurate statement regarding strain A. A) There is a mutation in ARG-H, if citrulline accumulates, ARG-F is also defective. B) There is a mutation in ARG-H, if ornithine accumulates, ARG-F is also defective. C) There is a mutation in ARG-H, if argininosuccinate accumulates, ARG-F is also defective. D) There is a mutation in ARG-H, if citrulline accumulates, ARG-E is also defective. E) There is a mutation in ARG-E, if citrulline accumulates, ARG-F is also defective. Ans: A Difficulty: 4

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72. Consider the pathway for the synthesis of the amino acid arginine in Neurospora: ARG-E ARG-F ARG-H ornithine citrulline argininosuccinate arginine Mutant strains of Neurospora are grown in minimal media supplements as follows. The strains may carry more than one mutation. Growth is shown by (+) no growth is shown by (o). Supplements mutant nothing ornitihine citrulline argininoarginine strain succinate a o o o + + b o o o + + Strain (a) accumulates citrulline, strain b does not. Indicate the statement that is most correct regarding these two strains. A) Strain a has a mutation in ARG-E only. B) Strain b has only one mutation. C) Strain a has mutations in ARG-F and ARG-H. D) Strain a has mutations in ARG-E, ARG-F and ARG-H. E) Strain a has a mutation in ARG-H only. Ans: E Difficulty: 4 73. A) B) C) D) E) Indicate the false statement regarding amino acids. Every amino acid contains a carboxyl group. The side chain or R group differs for each amino acid. Amino acids are joined together by peptide bonds. The end of the polypeptide termed the N terminus contains a free amino group. All the above statements are correct. Ans: E Difficulty: 1 Indicate the false statement regarding amino acids. Several amino acids linked together are termed an oligopeptide. Amino acids are linked by peptide bonds that join two amino groups together. The C terminus of a polypeptide chain contains a free carboxylic acid group. Two amino acids joined together is termed a dipeptide. All the above statements are correct. Ans: B Difficulty: 2

74. A) B) C) D) E)

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75. A) B) C) D) E)

Choose the condition below that does not involve a defect in an enzyme pathway. alkaptonuria albinism sickle-cell anemia phenylketonuria (PKU) all of the above involve a defect in an enzyme pathway Ans: C Difficulty: 2

76. Choose the interaction listed below that is not involved in maintaining tertiary structure in protein molecules. A) covalent bond B) hydrogen bond C) hydrophobic/hydrophilic interactions D) ionic interactions E) all of the above may be involved in maintaining protein tertiary structure Ans: E Difficulty: 1 77. A) B) C) D) E) The condition sickle-cell anemia is due to: the insertion of an amino acid. the deletion of an amino acid. substitution of an amino acid. failure to synthesize a hemoglobin molecule. unequal recombination resulting in the deletion of the -chain hemoglobin gene. Ans: C Difficulty: 2 Choose the statement below that is not true regarding sickle-cell anemia. Individuals who are heterozygous for the sickle cell allele can not make hemoglobin. The sickle-cell hemoglobin molecule contains an amino acid substitution. The hemoglobin molecules of an individual with sickle cell anemia clump together. The red blood cells of an individual with sickle cell anemia distort and elongate. All of the above are true regarding sickle cell anemia. Ans: A Difficulty: 2

78. A) B) C) D) E)

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79. Though sickle-cell anemia is frequently lethal for individuals who are homozygous for the sickle cell allele, natural selection seems to have maintained that allele in certain geographic locations. A likely explanation for this observation is: A) the forward mutation rate to sickle-cell is much higher in those regions. B) individuals with sickle-cell anemia live longer and have more children. C) reversion from sickle-cell to wild type is prevented in some populations. D) individuals who are heterozygous for the sickle-cell allele are protected from malaria. E) only certain populations have been tested for the presence of the sickle cell allele. Ans: D Difficulty: 2 80. The structure of a polypeptide that is characterized by a three dimensional shape with a characteristic geometry at local regions maintained by hydrogen bonds is: A) primary structure. B) secondary structure. C) tertiary structure. D) quaternary structure. E) both tertiary and quaternary structure. Ans: B Difficulty: 1 81. The structure of a protein that involves the interaction between two distinct polypeptide chains is: A) primary structure. B) secondary structure. C) tertiary structure. D) quaternary structure. E) both primary and secondary structure. Ans: B Difficulty: 1 82. Assume that a certain strain of bacteria carries a mutation that causes it to die at high temperature (37 C), but grows normally at cooler temperatures. This mutation is termed: A) recessive. B) deletion. C) biochemical pathway mutant. D) conditional lethal that grows under restrictive conditions. E) conditional lethal that dies under restrictive conditions. Ans: E Difficulty: 2

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83. A) B) C) D) E)

Mutations that abolish the function encoded by the wild-type allele are known as: null mutations. hypomorphic mutations. hypermorphic mutations. conditional mutations. neomorphic mutations. Ans: A Difficulty: 1 A neomorphic mutation results in an allele that: produces no gene product. produces a nonfunctional gene product. produces novel proteins or cause inappropriate expression resulting in a new phenotype. produces proteins that aggregate with wild-type subunits, inactivating them. produces an altered protein that results in a wild-type phenotype. Ans: C Difficulty: 2

84. A) B) C) D) E)

85. Assume that a transition mutation results in an amino acid substitution in the resulting polypeptide. What level of protein structure might be affected as a result? A) primary structure B) secondary structure C) tertiary structure D) quaternary structure E) all levels might be affected by a single amino acid substitution Ans: E Difficulty: 2 86. A) B) C) D) E) The photoreceptor protein rhodopsin: is found in cone cells and is sensitive to weak light at many wavelengths. is found in rod cells and is sensitive to weak light at many wavelengths. is found in cone cells and is responsible for blue and green color vision. is found in rod cells and is responsible for blue and green color vision. is missing in individuals who exhibit red-green colorblindness. Ans: B Difficulty: 2 Examination of the rhodopsin gene family provides evidence for gene evolution by: duplication and divergence. accumulation of random mutations. convergent evolution. spontaneous generation. drift. Ans: A Difficulty: 1

87. A) B) C) D) E)

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88. A) B) C) D) E)

Red-green color blindness is more common in males than females because: the red pigment gene is on the X chromosome, the green is on an autosome. the green pigment gene is on the X chromosome, the red is on an autosome. rhodopsin gene is on the X chromosome. both the red and the green pigment genes are on the X chromosome. both the red and the green pigment genes are on an autosome. Ans: D Difficulty: 2

89. Consider the gene for color in a particular flower. Three alleles exist: dark blue, white, and sky. Flowers homozygous for each allele produce the characteristic color. In heterozygotes, incomplete dominance occurs and intermediate colors are seen in a natural population. How many different color phenotypes are possible with these three alleles? A) 9 B) 2 C) 4 D) 6 E) 8 Ans: D Difficulty: 2 90. The appearance of a novel phenotype resulting from the substitution of a single base pair might be due to: A) change in the amino acid sequence only. B) change in the amount of protein expressed. C) alteration in a gene that codes for a nontranslated RNA. D) change in the developmental time or location at which a gene is expressed. E) all of the above are possible consequences of a single base pair substitution. Ans: E Difficulty: 2

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91. Assume that a series of compounds has been discovered in Neurospora. Compounds AF appear to be members of an enzyme pathway. Several mutations have been identified and strains 1-4 each contain a single mutation. Shown below are 5 possible pathways. Choose the pathway that best fits the data presented. [growth in minimal media with supplements is shown by (+), no growth is shown by (o)] media supplement strain A B C D E F 1 o o o + o o 2 o o o o o + 3 o o o o + + 4 o o + o o o A) A B C D E F B) A B C F E D C) A B C D EF D) A B C D EF E) A B C D EF Ans: E Difficulty: 4 92. Assume that a series of compounds has been discovered in Neurospora. Compounds AF appear to be members of an enzyme pathway. Several mutations have been identified and strains 1-4 each contains a single mutation. Shown below are 5 possible pathways. Choose the pathway that best fits the data presented. [growth in minimal media with supplements is shown by (+), no growth is shown by (o)] media supplement strain A B C D E F 1 o o o + + + 2 o o o o + + 3 o o o o + o 4 o o + + + + A) A B C D E F B) A B C F D E C) F B C D A E D) A B C D F E E) A B F E C D Ans: D Difficulty: 3

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93. A) B) C) D) E)

The term fecundity refers to: ability to live a long life. ability to survive in several different conditions. ability to transcribe DNA. ability to produce offspring. ability to metabolize several different sugar molecules. Ans: D Difficulty: 2

94. Assume that for a given gene a mutation creates an allele that functions as a dominant negative. The gene codes for a protein that forms a trimer within the cell. If at least one of the subunits has the mutant structure the entire protein is inactivated. For a heterozygous individual, what percent of the trimers present in the cell will be inactive? A) 100% B) 25% C) 50% D) 6.25% E) 12.5% Ans: E Difficulty: 3 95. A neomorphic dominant mutation in the Antennapedia (Antp) gene of Drosophila causes: A) kinks to form in their tails. B) shortened tails. C) total loss of color vision. D) failure to assemble microtubules during mitosis. E) growth of leg from the head region. Ans: E Difficulty: 2 Matching Match the following descriptions with the terms that best fit a) auxotrophic b) prototrophic c) null mutation d) inversion e) transposable element f) intercalators g) complementation h) dominant negative mutation i) cistron j) reverse mutation

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96. ______ mutant allele is mutated to wild-type Ans: j Difficulty: 1 97. ______ capable of growth on minimal media Ans: b Difficulty: 2 98. ______ complementation group identified by cis-trans test Ans: i Difficulty: 2 99. ______ grows on minimal media only if supplemented Ans: a Difficulty: 1 100. ______ flat planar molecules that sandwich between DNA bases Ans: f Difficulty: 1 101. ______ 180B rotation of a segment of a DNA molecule Ans: d Difficulty: 1 102. ______ when a mutant subunit of a multimer blocks the activity of the subunits produced by normal alleles Ans: h Difficulty: 2 103. ______ mutation that abolishes the function of a protein Ans: c Difficulty: 1 104. ______ all DNA segments that move about in a genome, regardless of mechanism Ans: e Difficulty: 2 105. ______ when alleles on each of two homologs make up for a defect in the other chromosome, generating enough of both gene products to yield a wild-type phenotype. Ans: g Difficulty: 2

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True or False 106. Methyl-directed mismatch repair corrects mistakes in replication by methylating the new daughter strand and thus being able to distinguish it from the parental DNA strand. Ans: False Difficulty: 2 107. Base analogs similar to the normal nitrogenous bases of DNA can be incorporated during replication often causing substitutions in the next round of replication. Ans: True Difficulty: 2 108. The Food and Drug Administration assesses whether an agent is mutagenic by first screening it in an Ames Test and then subsequently in rodents. Ans: True Difficulty: 1 109. A cistron is any complementation group identified by the cis-trans test and is synonymous with a gene. Ans: True Difficulty: 2 110. A hot spot is a region of DNA resistant to mutations. Ans: False Difficulty: 1 111. A mutation in a single gene that codes for a protein in a biochemical pathway often leads to auxotrophy for the end product of that pathway. Ans: False Difficulty: 1 112. A missense mutation is one that creates a premature stop codon. Ans: False Difficulty: 1 113. The secondary structure of a protein is its overall three-dimensional structure. Ans: False Difficulty: 1 114. Only multimeric proteins have quaternary structure. Ans: True Difficulty: 1

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115. Ectopic expression is when a protein is produced outside of its normal place or time. Ans: True Difficulty: 2 Short Answer 116. Distinguish between neomorphic, hypomorphic, and hypermorphic mutations. Ans: A hypomorphic mutation produces either much less of a protein or a protein with very weak but detectible function while a hypermorphic mutation does the opposite; it gives rise to more wild-type protein or the same amount of a more efficient protein. Neomorphic mutations are ones that simply result in a new phenotype. Difficulty: 3 117. What is a null mutation? Ans: Null mutations abolish the function of a protein. Difficulty: 2 118. Geneticists have detected mutations affecting vision that result in blue cone monochromacy. What is this and how does it occur? Ans: Blue cone monochromacy is an X-linked genetic disorder that affects the function of red and green cones, which results in red/green colorblindness. Seven different deletion mutations have been identified that result in blue cone monochromacy. Difficulty: 3 119. How is DNA altered by hydrolysis, radiation, UV light, and oxidation respectively? Ans: DNA hydrolysis of A or G bases results in depurination and the DNA strand has a continuous sugar backbone but an unspecified base where the depurination occurred. X-irradiation breaks the sugar backbone while UV light induces thymidine dimerization. Oxygen free radicals oxidize bases into analogs that do not hydrogen bond properly in the DNA double strand. During replication, mismatch pairing ends up creating a base change resulting in mutation. Difficulty: 4 120. What mutation occurs in the genetic disease xeroderma pigmentosa and what are the consequences? Ans: Individuals with the disease xeroderma pigmentosa have a mutation in excision repair, which results in a lack of enzymatic ability to recognize and repair thymidine dimers. Difficulty: 2

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Experimental Design and Interpretation of Data 121. What two hypotheses are tested in the Luria-Delbruck fluctuation test? Ans: Hypothesis 1: Resistance is a physiological response Hypothesis 2: Resistance arises from random mutation Difficulty: 2 122. What technique would you use to test the hypothesis that multiple drug resistant bacterium exist in a heterogenous population? Ans: Replica plating on each of the drugs to be screened will indicate the drug resistance of individual bacteria within the population. Difficulty: 2 123. Chemical X has just been screened using the Ames test. A total of 5000 bacteria were tested against 0.001 mM, 1 mM, 0.1M and 1M concentrations for which 4, 1, 0, and 200 colonies grew respectively. Control plate of minimal media supplemented with histidine had 5000 colonies while minimal media alone had only two. Interpret these data. Ans: The control plate supplemented with histidine has 5000 colonies which indicates the total number of bacteria present in the sample. The control plate with no histidine has 2 colonies indicating that the natural rate of his- reversion is 2/5000. Only the high concentration of 1M chemical X caused a his- reversion at a rate significantly higher than control indicating the chemical X is a mutagen only at high levels. Difficulty: 3 124. The local pet store received several shipments of albino ferrets. You choose two males and two females as pets; one breeding pair from the same litter, one from two different litters. When your ferret's litters are born, one has normally pigmented offspring. State which offspring are albino and which are pigmented and explain why. Ans: The breeding pair from the same litter would have albino offspring (they would carry a mutation in the same gene) while the breeding pair with the unrelated male and female could have pigmented offspring if each had a mutation in different genes involved in pigmentation. The two unrelated albino ferret's mutations complemented each other's genetic deficiency leading to pigmented offspring. Difficulty: 3

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Chapter 8Gene Expression: The Flow of Genetic Information from DNA via RNA to Protein Fill in the Blank 1. The usual flow of genetic information within a cell or organism is often called the " __________ ___________" of Molecular Biology. Ans: Central Dogma Difficulty: 1 2. There are ______ total possible codons. Of these, the codon _______ is recognized by a ribosome as the initiator codon. Ans: 64; AUG Difficulty: 3 3. There are _______ stop (nonsense) codons recognized by ribosomes. The sequences of these codons are _______, ________, and ________. Ans: 3; UAA, UAG, UGA Difficulty: 3 4. ____________ is the process of making RNA from a DNA template, where ____________ is the process of making protein by reading the mRNA code. Ans: transcription; translation Difficulty: 2 5. A ____________ is a change in the DNA sequence of an organism. A ____________ ___________ is a change in the DNA that does not change the structure of the protein product. Ans: mutation; silent mutation Difficulty: 3 6. Splicing of eukaryotic RNA molecules removes the _____________ and links together the __________ within the genetic sequence. Ans: introns; exons Difficulty: 2 7. ___________ _____________ is the small roundworm that is the first organism of its kind to be completely mapped genetically. Ans: Caenorhabditis elegans Difficulty: 3 8. If a base is inserted into or deleted from a DNA sequence, a _____________ mutation will occur. Ans: frameshift Difficulty: 2

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9. A ribosome has two "slots" where codons and tRNA molecules fit. The names for these areas within the ribosome/mRNA/tRNA complex forms are the ____________ site and the _____________ site. Ans: peptidyl; aminoacyl Difficulty: 4 10. _________________ mutations usually cause a change in the amino acid sequence by changing the "meaning" of a specific codon. Ans: missense Difficulty: 2 11. Processing of eukaryotic RNA usually adds a ____________ cap and a ____________ tail. Ans: methyl-group; poly-A Difficulty: 4 12. The three steps of transcription (in order) are ___________, ____________, and ____________. Ans: initiation; elongation; termination Difficulty: 3 13. ____________ splicing of RNA molecules can lead to the variability needed in the genetic sequences for antibody molecules to allow for them to recognize a vast number of antigens. Ans: alternative Difficulty: 4 14. The enzyme _________________________ "recharges" tRNA molecules, while the enzyme ______________________ catalyzes the formation of peptide bonds between amino acids during translation. Ans: aminoacyl-tRNA synthetase; peptidyl transferase Difficulty: 4 15. Reverse transcription is a genetic process that is unique to HIV and other viruses that are grouped in the __________________ family. Ans: retrovirus Difficulty: 2

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Multiple Choice 16. In the usual flow of genetic information (often called the Central Dogma), which of the following best represents the expression of genes? A) Protein - RNA - DNA B) DNA - RNA - Protein C) RNA - DNA - Protein D) DNA -Protein - RNA Ans: B Difficulty: 1 17. A) B) C) D) The cellular organelle responsible for protein synthesis is the: nucleus. mitochondria. centrioles. ribosome. Ans: D Difficulty: 2 The scientists credited with postulating the basis for the Genetic Code are: Hershey and Chase. Griffith and Avery. Watson and Crick. Cohen and Boyer. Ans: C Difficulty: 3 A codon is: a three base sequence of mRNA that codes for an amino acid. a three base sequence of rRNA that codes for an amino acid. a three base sequence of tRNA that codes for an amino acid. a three base sequence of DNA that codes for an amino acid. Ans: A Difficulty: 1 Which of these is NOT a character of the genetic code? There are the same number of codons as there are amino acids. The code is used by nearly every living organism. Some amino acids have multiple codons. The code is degenerate. Ans: A Difficulty: 2

18. A) B) C) D)

19. A) B) C) D)

20. A) B) C) D)

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21. Charles Yanofsky helped decipher the genetic code working with the _____ biosynthesis genes in _______. A) leucine; Salmonella enteritidis B) phenylalanine; Klebsiella pneumoniae C) tryptophan; Escherichia coli D) glycine; Serratia marcescens Ans: C Difficulty: 3 22. A sequence of DNA that reads: 5' ATGCCTGAATCAGCTTTA 3' should code for ____ amino acids after all steps of conversion into protein are complete. A) 5 B) 6 C) 7 D) 8 Ans: B Difficulty: 4 23. How many DIFFERENT amino acids could be coded for using the synthetic mRNA sequence of (5' UGCUGCUGC 3')? A) 0 B) 1 C) 2 D) 3 Ans: D Difficulty: 4 24. A) B) C) D) There are ______________ usually found in the genetic code. 3 start codons and 1 stop codon 2 start codons and 2 stop codons 1 start codon and 3 stop codons 0 start codons and 4 stop codons Ans: C Difficulty: 2

25. The pattern or sequence in which a molecule of mRNA is deciphered by a ribosome is called the: A) synthesis platform. B) code degeneration. C) peptide transition. D) reading frame. Ans: D Difficulty: 3

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26. A) B) C) D)

Which of these terms is NOT used as a nickname for a stop codon? emerald amber opal ochre Ans: A Difficulty: 3 Nonsense codons are: codons that code for multiple amino acids. codons that code for no amino acids. codons that can be read forward or backward. start codons. Ans: B Difficulty: 2 Which of these is NOT a step in transcription? replication initiation termination elongation Ans: A Difficulty: 3 Splicing of transcripts normally occurs only in: both prokaryotes and eukaryotes. only prokaryotes. only eukaryotes. mitochondria, as they have their own DNA. Ans: C Difficulty: 1 The sequences within mRNA that are spliced out (removed) are called: extremes. exons. inclusions. introns. Ans: D Difficulty: 1

27. A) B) C) D)

28. A) B) C) D)

29. A) B) C) D)

30. A) B) C) D)

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31. A) B) C) D)

The (expressed) sequences within mRNA that code for gene products are called: extremes. exons. inclusions. introns. Ans: B Difficulty: 1 The retroviruses, including HIV, are unique because they do: reverse replication. reverse transcription. reverse splicing. reverse translation. Ans: B Difficulty: 2 A typical example of a genetic system that employs RNA splicing is: the genes that code for the segments in an earthworm. the genes responsible for making antibodies in humans. the HIV virus genes. the genes that enable RNA splicing. Ans: B Difficulty: 4 Experiments that are done outside a living cell are describe by the Latin term: in vino. in vito. in vivo. in vitro. Ans: D Difficulty: 2 Experiments that are done inside a living cell are describe by the Latin term: in vino. in vito. in vivo. in vitro. Ans: C Difficulty: 2

32. A) B) C) D)

33. A) B) C) D)

34. A) B) C) D)

35. A) B) C) D)

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36. A) B) C) D)

The enzyme that makes RNA from a DNA template is: RNA-dependent DNA polymerase. DNA-dependent DNA polymerase. DNA-dependent RNA polymerase. RNA-dependent RNA polymerase. Ans: C Difficulty: 3

37. Transcription occurs in the ________ and translation occurs in the __________ of EUKARYOTIC cells. A) nucleus; cytoplasm B) cytoplasm; nucleus C) nucleus; nucleus D) cytoplasm; cytoplasm Ans: A Difficulty: 3 38. Transcription occurs in the ________ and translation occurs in the __________ of PROKARYOTIC cells. A) nucleus; cytoplasm B) cytoplasm; nucleus C) nucleus; nucleus D) cytoplasm; cytoplasm Ans: D Difficulty: 3 39. A) B) C) D) Which of the following statements is true under ordinary conditions? DNA and RNA last only for a short time within a cell. DNA lasts forever within a cell while RNA only lasts a short time. RNA lasts forever within a cell while DNA only lasts a short time. RNA and DNA both last forever within a cell. Ans: B Difficulty: 3

40. In the modification of eukaryotic mRNA, a cap consisting of a/an _________ and a tail consisting of _______ are usually added to the transcript. A) acetyl group; multiple cytosines B) multiple guanines; methyl group C) multiple thymines; acetyl group D) methyl group; multiple adenines Ans: D Difficulty: 3

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41. RNA polymerase binds to a sequence called a/an ______________ before beginning transcription. A) promoter B) operator C) structural gene D) replication origin Ans: A Difficulty: 2 42. A) B) C) D) Ribosomes are composed of: tRNA and protein. mRNA and protein. rRNA and protein. only proteins folded together. Ans: C Difficulty: 2

43. A tRNA molecule looks like a compact ____ when it is folded into its functional configuration. A) G B) L C) C D) P Ans: B Difficulty: 1 44. A) B) C) D) Aminoacyl-tRNA Synthetase is the enzyme that: folds tRNA molecules into their proper configuration. causes tRNA molecules to bind to the aminoacyl site of a ribosome. produces tRNA by reading DNA molecules. adds the appropriate amino acid to an uncharged tRNA. Ans: D Difficulty: 3

45. Which enzyme forms peptide bonds between adjacent amino acids during polypeptide synthesis? A) RNA polymerase B) phosphotransferase C) peptidyl transferase D) ribonuclease Ans: C Difficulty: 2

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46. A) B) C) D)

A bacterial (prokaryotic) ribosome is composed of ______ subunits. 20S & 40S 30S & 50S 40S & 60S 50S & 70S Ans: B Difficulty: 3 An anticodon is a physical component of a/an _______ molecule. tRNA mRNA rRNA DNA Ans: A Difficulty: 1 Which of these processes are coupled (linked) in prokaryotes but NOT in eukaryotes? transcription and translation replication and transcription replication and translation replication, transcription, and translation are not separate in prokaryotes Ans: A Difficulty: 2

47. A) B) C) D)

48. A) B) C) D)

49. A mutation that is characterized by a change in the DNA sequence, but no change in the resulting protein sequence, is called a: A) frameshift mutation. B) missense mutation. C) silent mutation. D) nonsense mutation. Ans: C Difficulty: 2 50. A mutation that changes a codon sequence, and subsequently changes the amino acid that should have been placed at that point in the polypeptide chain, is called a: A) frameshift mutation. B) missense mutation. C) silent mutation. D) nonsense mutation. Ans: B Difficulty: 2

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51. A mutation that changes a codon that originally coded for an amino acid into a stop codon is called a: A) frameshift mutation. B) missense mutation. C) silent mutation. D) nonsense mutation. Ans: D Difficulty: 2 52. A mutation that occurs when a base is inserted into or deleted from a DNA sequence, completely altering an entire amino acid sequence, is called a: A) frameshift mutation. B) missense mutation. C) silent mutation. D) nonsense mutation. Ans: A Difficulty: 2 53. A) B) C) D) Drugs like AZT, ddC, or ddI work against the AIDS virus because they: destroy viral proteins. prevent the formation of viral mRNA. block the action of viral tRNA. look like nitrogenous bases and block viral reverse transcriptase. Ans: D Difficulty: 3

54. A tRNA that recognizes a nonsense codon, and inserts an amino acid where protein synthesis should have stopped, is called a: A) nonsense tRNA. B) suppressor tRNA. C) revertant tRNA. D) excision tRNA. Ans: B Difficulty: 3 55. Protein synthesis begins with the amino acid ___________, as its codon is the one used as the start codon by nearly all organisms. A) methionine B) arginine C) cysteine D) leucine Ans: A Difficulty: 2

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Matching Match the following terms with the descriptions that best fit (each term will be used once)

56. ____ Anticodon Ans: r Difficulty: 2 57. ____ Codon Ans: g Difficulty: 2 58. ____ Exon Ans: p Difficulty: 1 59. ____ Genetic Code Ans: d Difficulty: 3 60. ____ Initiation Codon Ans: k Difficulty: 3 61. ____ Intron Ans: o Difficulty: 1

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62. ____ Messenger RNA Ans: b Difficulty: 2 63. ____ Nonsense Codon Ans: j Difficulty: 3 64. ____ Post-translational Modification Ans: t Difficulty: 3 65. ____ Promoter Ans: m Difficulty: 3 66. ____ Reading Frame Ans: h Difficulty: 3 67. ____ Reverse Transcription Ans: n Difficulty: 2 68. ____ Ribosomal RNA Ans: s Difficulty: 2 69. ____ Ribosome Ans: c Difficulty: 2 70. ____ RNA Polymerase Ans: l Difficulty: 1 71. ____ Splicesome Ans: q Difficulty: 2 72. ____ Template Strand Ans: i Difficulty: 3

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73. ____ Transcription Ans: a Difficulty: 1 74. ____ Transfer RNA Ans: e Difficulty: 2 75. ____ Translation Ans: f Difficulty: 1 True or False 76. The restoration of gene function by one mutation canceling another in the same gene is known as intragenic suppression. Ans: True Difficulty: 2 77. Frameshift mutations occur when the number of bases inserted or deleted is not a multiple of three. Ans: True Difficulty: 1 78. In vitro translation allows the determination of protein sequence. Ans: False Difficulty: 1 79. The template and RNA-like DNA strand are equivalent. Ans: False Difficulty: 1 80. Nonsense codon and stop codon are synonymous. Ans: True Difficulty: 2 81. The genetic code is absolutely universal. Ans: False Difficulty: 2 82. Except in reverse transcription, RNA is synthesized in a 3' to 5' fashion. Ans: False Difficulty: 2

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83. Capping enzyme and methyl transferases are needed to add a 5' cap on mRNA. Ans: True Difficulty: 1 84. Exons are excised from mRNA. Ans: False Difficulty: 1 85. In most splice donor sites a G U dinucleotide sequence is flanked by a couple of 5' and 3' purine bases. Ans: True Difficulty: 2 86. rRNA carries an anticodon which it the complementary sequence to the mRNA codon that specifies a particular amino acid. Ans: False Difficulty: 2 Short Answer 87. The Genetic Code is described as being nearly universal, degenerate, and nonoverlapping. Briefly describe what each of these properties refers to. Ans: The code is nearly universalNearly all organisms use the same codons to specify the amino acids found to correspond to the mRNA sequence. To date, only a few organisms (such as Archaebacteria) and some organelles (such as mitochondria) DO NOT use the codons the same way. The code is degenerateSome amino acids are coded for by more than one codon. Though there are 64 possible codons, only 61 are used for coding purposes. There are only 20 amino acids found in living organisms' proteins, so there are many more codons than are necessary. The code is nonoverlappingEash codon can code for only one amino acid. For example, if a synthetic mRNA sequence of 5' UUUUUU 3' is added to the end of a transcript, only the amino acid phenylalanine will be added for those codons, showing that 5' UUU 3' codes only for phenylanine. Difficulty: 3

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88. Describe the process of splicing in eukaryotic RNA molecules. Ans: RNA processing is unique to eukaryotes. When the original transcript molecule is synthesized, several non-expressed sequences, called "introns," must be removed and the expressed sequences, or "exons," must be linked together in order before the transcript can be used as an mRNA. Ribonucleases make cuts at the opposing ends of introns, the "splicesome" (intron unit) is removed. The 3' end of the first exon is linked to the 5' end of the second exon. This process is done along the entire sequence of the original transcript until all introns have been removed. Difficulty: 2 89. Briefly describe the events of transcription in a living cell. Ans: The DNA helix surrounding the location of a gene is unwound, and the strands of DNA are separated. RNA polymerase binds to the promoter region of the DNA, and shortly downstream from the promoter, polymerase begins matching complementary RNA nucleotides to the template sequence of the DNA. RNA synthesis continues in the 5' to 3' direction until a termination sequence is reached. At that point, RNA polymerase dissociates from the DNA, the newly-synthesized RNA is released, and the DNA helix reforms. Difficulty: 3 90. Outline the steps of translation in prokaryotes. Ans: The 30S subunit of a ribosome binds to the ribosome binding site of a messenger RNA molecule. A 50S subunit then joins with the other parts to complete the ribosome-mRNA complex. The ribosome "scans" the mRNA for the first 5' AUG 3' initiator codon. When the first AUG is found, a tRNA molecule matches its anticodon to the initiator codon, and fills in the peptidyl (P) site within the ribosome. A second tRNA brings in the next amino acid, filling the aminoacyl (A) site of the inside of the ribosome. The enzyme peptidyl transferase catalyzes the formation of a peptide bond between the amino acids. tRNA #1 is released to the cytoplasm, and the ribosome shifts one codon downstream. A third tRNA brings in the next amino acid, and the steps repeat themselves until all codons have been read. When the ribosome finds a non-sense codon, the entire complex dissociates and the newly-synthesized protein is free to perform its function. Difficulty: 4

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91. Describe how the "wobble" theory applies to protein synthesis. Ans: In the genetic code, all but two amino acids have multiple codons that code for their placement into proteins through translation. Though there are 61 possible coding codons, organisms will not have 61 tRNA molecules. Some tRNA molecules will effectively bind to codons even though their anticodon is not a perfect match. This "wobble effect" usually happens at the 3' position of a codon. An example is the insertion of phenylalanine into a polypeptide. Both codons UUU and UUC code for phenylalanine. If an single tRNA is able to bind to the codon UUPyrimidine, only one tRNa would be needed to bind for inserting phenylalanine into a growing polypeptide. Difficulty: 3 92. How does compartmentalization of transcription and translation lead to differences between prokaryotes and eukaryotes? Ans: Eukaryotes have a nucleus and therefore transcription and translation are separated. In prokaryotes, translation occurs concurrent with transcription. Difficulty: 2 93. Why are the genes for rRNA, tRNA and snRNAs transcribed but not translated? Ans: These molecules are RNA species not proteins so these genes do not need to be translated. Difficulty: 2 94. Describe nonsense suppression. Ans: A mutation in a tRNA gene allows for an amino acid to be incorporated into a growing polypeptide rather than stopping at a stop codon created by a mutation. Therefore,one mutation suppresses the other (the mutant stop is over-ridden). Difficulty: 2 95. What does reverse transcripase do? Ans: Reverse transcriptase is an enzyme that transcribes RNA into DNA. Difficulty: 2 96. What is alternative splicing and how does it occur? Ans: Introns are removed from eukaryotic mRNAs and exons are spliced together. In some genes, splicing is regulated and under certain circumstances some splicing signals are ignored resulting in changes to the primary transcript and ultimately the production of more than one polypeptide from a given gene. Difficulty: 3

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Experimental Design and Interpretation of Data 97. You are a graduate student working for a mentor whose research is top secret. You are asked to complete in vitro translation experiments using top-secret cell cultures to determine a genetic code for what you believe are cells isolated from extraterrestrial life. Given that you have determined that the nucleotides in the DNA are the same as on earth but the cells contain 10 unique amino acids, describe how you would definitively determine the genetic code of the extraterrestrial cells. Ans: Mutation analysis would determine size of a codon and the code itself could be cracked by using short, synthetic RNA molecules in an in vitro translation system. A single radioactive amino acid would be added to a tRNA so that each amino acid could be tested separately. The tRNA with charged radiolabeled amino acid, plus a single codon would be mixed with lysate containing ribosomes. The mixture would then be poured through a filter where the ribosome + tRNA would be too large to pass through. Whenever the filter contains radioactivity, that codon codes for the radiolabeled amino acid being tested. You need to test all ten amino acids for all combinations of codons to determine the complete genetic code. Difficulty: 4 98. What are silent, missense and nonsense mutations? Compared to control wild-type samples how would each mutation affect the outcome of Northern and Western analyses? Ans: Silent mutations are gene mutations that have no consequences at the phenotypic level. A missense mutation changes a codon so that it codes for a different amino acid while a nonsense mutation results in the conversion of a coding codon to a stop codon or vice versa. The size of the bands on a Northern blot would not change (a change in stop for translation does not change the size of the RNA). It is unlikely that intensity would change either unless the coding region had some unknown effect on regulation. On a Western blot, silent and missense mutations would show no change in size however, a nonsense mutation would likely either increase or decrease the size of the protein. Difficulty: 3

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99. Hypothetically speaking, a particular protein named GOTEAM is 1,000 amino acids and is known to be involved in the phenotype, avid football fan. Some individuals have been genotyped and were found to have a deletion of 2 nucleotides near the 5' end of the GOTEAM gene. Other individuals have been found to have a deletion of 99 bases in the same region. What is the length of GOTEAM gene?_______________ Which mutation do you think would be more likely to be the most deleterious to the GOTEAM phenotype? Ans: The coding region of GOTEAM is 3,000 base pairs in length. The 2 bp deletion would most likely be more deleterious because it will change the reading frame of the gene while the 99 bp deletion is a multiple of 3 and the protein will essentially be missing a 33 amino acid regiondepending on its involvement in the function of the protein, it could be unimportant or relatively important. Difficulty: 4 100. In your studies of an unusual prokaryotic organism, you have cloned and sequenced an interesting gene and the protein that it codes. Although you have sequenced the gene several times, the start codon is always read as GTG instead of ATG. How do you interpret this result? Ans: The prokaryotic organism from which you cloned your gene has an alternative start site; GTG instead of ATG. Difficulty: 3

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Chapter 9Deconstructing the Genome: DNA at High Resolution Fill in the Blank 1. Sickle cell anemia is caused by a mutation in the _______________________ gene. Ans: -globin Difficulty: 1 2. AvaI (CPyCGPuG, Py stands for pyrimidine, Pu for purine) will cut DNA approximately every _________ bp. Ans: 1024 Difficulty: 3 3. A stored collection of DNA fragments in vectors is called a __________________. Ans: library Difficulty: 1 4. A short single-stranded piece of DNA that is labeled and used in hybridization experiments is called a ____________________. Ans: probe Difficulty: 1 5. _________________ techniques are based on the natural propensity of complementary single-stranded molecule to form stable double helices. Ans: hybridization Difficulty: 1 6. Vectors that contain plasmid-derived selectable markers and two segments of phage are called ________________________. Ans: cosmids Difficulty: 1 7. A __________________________ enzyme recognizes a specific sequence of bases anywhere within the genome and then severs two covalent bonds in the sugar-phosphate backbone at particular positions within or near that sequence. Ans: restriction Difficulty: 1 8. Minute circles of dsDNA called ___________________ can gain access to and replicate, independently of the endogenous chromosome, within many kinds of bacterial cells. Ans: plasmid Difficulty: 1

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9. A specialized vector that allows production of transcript and polypeptide is called an _________________________ vector. Ans: expression Difficulty: 1 10. ___________________________ are used as chain terminators in the Sanger DNA sequencing process. Ans: dideoxynucleotides Difficulty: 2 Multiple Choice 11. The technique of primer walking begins with a vector-based primer. This is used to obtain DNA sequence for one end of a long insert. The partial sequence of the insert is used to: A) find restriction enzymes that can be used to cut the insert for shotgun sequencing. B) pinpoint the location of the insert within the vector. C) make primers so the rest of the insert can be amplified by PCR for cloning. D) synthesize a probe for Southern blotting to identify the insert in genomic DNA. E) design a new primer that will sequence into the next unknown section of the insert. Ans: E Difficulty: 2 12. A) B) C) D) E) What is the reason for partial digestion of genomic DNA with restriction enzymes? Generating blunt ends, when only enzymes that leave sticky ends are available. Generating sticky ends, when only enzymes that leave blunt ends are available. Cutting only one strand of a restriction site, leaving a nick instead of a break. Producing fragments that are slightly shorter than a complete digest would produce. Producing fragments that are slightly longer than a complete digest would produce. Ans: E Difficulty: 1 Which of the following is an example of a recombinant DNA molecule? A PCR-amplified fragment. A single-stranded RNA hybridized to a single-stranded DNA. A genomic fragment of human DNA ligated to a bacterial plasmid vector. A chromosome in a bacterial cell. A bacterial plasmid cut with a restriction enzyme. Ans: C Difficulty: 1

13. A) B) C) D) E)

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14. The diagram shows the products from enzymatic extension sequencing. What is the sequence of the template strand (5' to 3' left to right)? A) GACCGCT B) TCGCCAG C) AGCGGTC D) CTGGCGA Ans: C Difficulty: 3 15. Figure 1 shows the products from enzymatic extension sequencing. If a primer is designed to hybridize to the template strand for PCR amplification, what will its last 4 bases be (5' to 3', left to right)? A) GCGA B) CTGG C) CCGA D) CGCT E) TCGC Ans: D Difficulty: 4 16. A) B) C) D) E) One of the reasons that PCR is useful in diagnosis of HIV is because it: detects antibodies against the virus. interferes with viral replication, causing the virus to become latent. automatically determines the sequence, as well as the presence of the viral genome. detects an infection at an earlier stage than the current standard test. detects both viral DNA and viral proteins. Ans: D Difficulty: 1

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17. A) B) C) D) E)

PCR cannot be successfully performed without: at least 100 starting DNA molecules. at least some sequence information about the region to be amplified. a cDNA version of the region to be amplified. a section of at least 100 kb to amplify. an undamaged, non-degraded DNA sample. Ans: B Difficulty: 2 What information CANNOT be determined from the DNA sequence of a cDNA clone? exon sequences sequence of the promoter similarity to previously identified sequences amino acid sequence of the encoded polypeptides sequence of the spliced mRNA transcript Ans: B Difficulty: 2

18. A) B) C) D) E)

19. In Sanger (enzymatic extension) sequencing, what causes DNA synthesis to terminate at a specific base? A) Chemicals that cleave DNA after particular bases. B) Fluorescent chemicals. C) Nucleotide triphosphates that lack a base. D) Nucleotide triphosphates that lack a hydroxyl. E) Nucleosides that lack a 5' phosphate. Ans: D Difficulty: 2 20. What technique is used to separate DNA molecules that are the size of whole chromosomes? A) PCR B) Southern blotting C) hybridization D) transformation E) pulsed field gel electrophoresis Ans: E Difficulty: 1

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21. In gel electrophoresis of DNA, fragments move at different rates because they have different: A) charge densities. B) sizes. C) base sequences. D) amino acid compositions. E) electrical strengths. Ans: B Difficulty: 1 22. The recognition sites for the restriction enzymes BamHI, XbaI and BglII are G^GATCC, T^CTAGA and A^GATCT, respectively. Which enzymes leave compatible ends that can be ligated together? A) All of these enzymes leave ends that are compatible with ends generated by the others. B) None of the enzymes produce compatible ends. C) Only BamHI and BglII fragments are compatible. D) Only BamHI and XbaI fragments are compatible. E) Only BglII and XbaI fragments are compatible. Ans: C Difficulty: 3 23. A genomic library is made for an organism with a haploid genome of 5 107 bp. If the fragments are approximately 20 kb each, how many clones would be screened to ensure a 95% probability of a particular locus being represented at least once? A) 1.25 106 B) 5 106 C) 5 105 D) 2.5 105 E) 1.25 104 Ans: E Difficulty: 4 24. A) B) C) D) E) What charge does DNA have, and what gives it this charge? positive, from the phosphates positive, from the bases negative, from the phosphates negative, from the bases negative, from the ribose Ans: C Difficulty: 2

Table 9.1

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restriction enzyme 1. BglII 2. EcoRV 3. PvuI 4. SacII 5. SmaI

recognition site A^GATCT GAT^ATC CGAT^CG CCGC^GG CCC^GGG

25. From table 9.1, which combination of enzymes leaves ends that can, theoretically, be ligated together? A) 1 and 2 B) 1 and 3 C) 2 and 3 D) 2 and 5 E) 4 and 5 Ans: D Difficulty: 2 26. From table 9.1, which restriction enzyme leaves an end that could be a substrate for a polymerase? A) 1 B) 2 C) 3 D) 4 E) 5 Ans: A Difficulty: 3 27. T4 phage DNA polymerase has 2 activities. One is polymerization. The other is 3' to 5' exonuclease activity against 3' overhangs, which are sticky ends that have a singlestranded region at the 3' end of one of the strands. The enzyme converts sticky ends to blunt. DNA fragments cut with the enzymes in the above table are incubated with T4 polymerase and all 4 nucleotide triphosphates. Which statement is TRUE about how the fragments will be affected? A) The exonuclease activity will blunt the BglII ends. B) The exonuclease activity will blunt both the BglII ends and the PvuI ends. C) The exonuclease activity will blunt both the PvuI and SacII ends. D) The polymerase activity will blunt both the BglII and PvuI ends. E) The polymerase activity will blunt both the PvuI and SacII ends. Ans: C Difficulty: 4

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28. An EcoRV (GAT^ATC) fragment that contains a promoter, is ligated to a SmaI (CCC^GGG) fragment that contains most of a protein-coding gene. What is the probability that the newly introduced ATG will be in frame with the protein encoded in the SmaI fragment? A) 1 in 2 B) 1 in 3 C) 1 in 4 D) 1 in 6 E) 1 in 9 Ans: B Difficulty: 2 Table 9.2 restriction enzyme AvaI SalI TaqI XhoI

recognition site C^PyCGPuG (Py stands for pyrimidine, Pu for purine) G^TCGAC T^CGA C^TCGAG

29. Use table 9.2 for enzyme recognition sites. A plasmid is cut with SalI, and combined with genomic DNA digested with XhoI. In those plasmids with a genomic fragment, the SalI-XhoI junction can be cut with: A) SalI only. B) XhoI only. C) both original enzymes. D) either SalI or TaqI. E) TaqI only. Ans: E Difficulty: 2 30. A) B) C) D) E) What proportion of AvaI sites will also be XhoI sites? 1 in 2 1 in 3 1 in 4 1 in 5 1 in 6 Ans: C Difficulty: 2

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31. A) B) C) D) E)

What percentage of AvaI sites will be compatible with SalI sites? 15% 25% 30% 50% 75% Ans: B Difficulty: 2 An AvaI fragment is ligated to a SalI fragment. The junction can be cut with: XhoI or SalI, but not AvaI. XhoI or AvaI, but not SalI. SalI or AvaI, but not XhoI. all three enzymes: SalI, AvaI or XhoI. none of the three enzymes: SalI, AvaI or XhoI. Ans: E Difficulty: 3

32. A) B) C) D) E)

33. Approximately how many fragments would you predict if the haploid human genome was cut with AvaI? A) 3 105 B) 3 106 C) 3 107 D) 7.5 105 E) 7.5 106 Ans: B Difficulty: 4 34. In a human genomic DNA library made by complete SalI (G^TCGAC) digestion, approximately how many clones constitute a genomic equivalent? A) 12,000,000 B) 700,000 C) 150,000 D) 46,000 E) 15,000 Ans: B Difficulty: 3

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35. A) B) C) D) E)

PCR is used to: generate DNA fragments for genomic libraries. generate DNA fragments for cDNA libraries. determine the sequence of a DNA fragment by the Maxam-Gilbert procedure. amplify minute quantities of a DNA fragment. replicate recombinant plasmids. Ans: D Difficulty: 1 Restriction enzymes were named because they restrict: the capacity for viral growth. the growth of the bacteria that produces them. bacterial translation. bacterial transformation. bacterial transcription. Ans: A Difficulty: 2

36. A) B) C) D) E)

37. Which of the following would not have its gene represented in a cDNA library from red blood cell precursors? A) -globin B) a glycolysis enzyme C) a ribosomal protein D) an rRNA E) a DNA polymerase subunit Ans: D Difficulty: 3 38. A) B) C) D) E) DNA molecules are separated by pulsed field gel electrophoresis when they are: going to be sequenced by the Maxam-Gilbert procedure. going to be sequenced by the Sanger (enzymatic) procedure. too long to be separated by standard agarose gels. too short to be separated by standard agarose gels. are single-stranded. Ans: C Difficulty: 2

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39. If DNA had 5 different bases, a restriction enzyme with a 4-base recognition sequence would cut DNA approximately every: A) 125 bp. B) 256 bp. C) 425 bp. D) 625 bp. E) 1056 bp. Ans: D Difficulty: 3 40. If DNA had 5 different bases, approximately how many fragments would result from cutting a 1 Mb piece of DNA with a 4-base cutter? A) 125 B) 320 C) 625 D) 1050 E) 1600 Ans: E Difficulty: 3 41. Two DNA fragments are separated by electrophoresis. How is the fragment that traveled farther different from the other fragment? A) It is longer. B) It is shorter. C) It is more negatively charged. D) It has blunt ends. E) It has sticky ends. Ans: B Difficulty: 2 42. A) B) C) D) E) Which of the following would be found in a cDNA library, but not a genomic library? centromeres replication origins promoters exons introns Ans: D Difficulty: 2

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43. A) B) C) D) E)

A genomic library is a: collection of DNA fragments from an organism, inserted into vectors. collection of restriction enzymes that make regularly spaced cuts in a genome. series of DNA fragments generated by chemical cleavage, used to determine sequence. set of genes that can be inserted into vectors to confer antibiotic resistance. collection of mRNA molecules cloned into vectors. Ans: A Difficulty: 1 The lacZ gene is sometimes included in a cloning vector. What does it encode? A restriction enzyme that cuts the vector while it is in transformed cells. A blue pigment that identifies any cell that has been transformed. An enzyme that converts RNA to DNA. An enzyme that confers antibiotic resistance. A detectable enzyme that is not produced if the gene is interrupted by an insert. Ans: E Difficulty: 3

44. A) B) C) D) E)

45. A plasmid has tetr and lacZ genes for tetracycline resistance and -galactosidase, respectively. There is a single EcoRI site within lacZ, and a single Hind III site within tetr. The EcoRI-HindIII cut plasmid is combined with a DNA fragment with compatible ends. Cells that contain the plasmid with the insert will be: A) tetracycline resistant and blue if grown on X-gal. B) tetracycline sensitive and blue if grown on X-gal. C) tetracycline resistant and white if grown on X-gal. D) tetracycline sensitive and white if grown on X-gal. Ans: D Difficulty: 3 46. Genomic DNA is isolated from bacteria. After a long digestion with a 6-base cutting enzyme that recognizes the sequence GAATTC, the DNA is not cut. The genome is 4 Mb, so there should be approximately 1,000 sites in the DNA. What is the most likely explanation? A) There are no G's in the genome. B) There are no A's in the genome. C) The bacterium methylated the DNA, because it produces the 6-base cutting enzyme. D) All the recognition sites are in genes, and the enzyme will not cut in genes. E) All the recognition sites are in promoters and regulatory sequences, and the enzyme cuts only in genes. Ans: C Difficulty: 3

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47. A 6-base cutting enzyme should cut every 4kb, on average. Approximately how many sites are in the human genome (for simplicity, use 4 million kb as the size of the human genome)? A) 100 B) 1,000 C) 10,000 D) 100,000 E) 1,000,000 Ans: E Difficulty: 2 48. The basic problem in isolating/cloning a human gene is that the genome contains __________ of base pairs, and a gene is usually several __________ base pairs in length. A) trillions, million B) trillions, thousand C) billions, million D) billions, thousand E) millions, hundred Ans: D Difficulty: 2 49. A) B) C) D) E) What is the function of the ampr gene in a vector? It is a restriction enzyme recognition site. It is a selectable marker. It is the origin of replication. It makes the enzyme -galactosidase if it is intact, indicating vectors without inserts. It is required for packing into viral shells. Ans: B Difficulty: 2

50. A circular DNA of 1 kb length is cut with a restriction enzyme whose precise recognition sequence is not known. The digest yields 4 fragments of approximately equal size. What is the most likely conclusion from these data? A) The enzyme is a 4-base cutter. B) The enzyme is a 6-base cutter. C) The enzyme is an 8-base cutter. D) The enzyme leaves blunt ends. E) This was a partial digest. Ans: A Difficulty: 3

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51. A) B) C) D) E)

Which choice is NOT a characteristic of a plasmid used as a cloning vector? Confers a detectable property on a host cell. Can be purified away from the host cell's genome. Replicates independently. Replicates itself and the inserted DNA. Methylated to protect from digestion by host cell restriction enzymes. Ans: E Difficulty: 2

52. Where do restriction enzymes come from, and what is their normal physiological function? A) Phage produces them, and they replicate viral DNA. B) Phage produces them and they confer antibiotic resistance. C) They are yeast DNA replication enzymes. D) Bacteria produce them to protect against viral invasion. E) They are bacterial DNA replication enzymes. Ans: D Difficulty: 2 53. A) B) C) D) E) How do bacteria protect their own DNA from the restriction enzymes they produce? Their DNA never contains the recognition site. Ligase connects their DNA as soon as it is cut. Digestion is blocked by -CH3 groups added to recognition sequences in their DNA. Phosphate groups added to the recognition sequences in their DNA block digestion. Restriction enzymes are blocked from entry into the nucleus. Ans: C Difficulty: 3

54. If the restriction enyzme EcoRI cuts a linear 19 kb piece of DNA into fragments of 1, 3, 6 and 9 kb, what size fragment (in kb), would NOT be possible from a partial digest? A) 12 B) 10 C) 7 D) 5 E) 4 Ans: D Difficulty: 2

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55. A) B) C) D) E)

A restriction enzyme with a recognition site of 10 bp cuts an average of every: 410 bp. 104 bp. 210 bp. 102 bp. 24 bp. Ans: A Difficulty: 2

56. A restriction enzyme with a recognition site of CCNNGG (where N is any base) cuts an average of every: A) 16 bp. B) 250 bp. C) 400 bp. D) 4 kb. E) 65 kb. Ans: B Difficulty: 2 57. A) B) C) D) E) Reverse transcriptase is an enzyme made by: red blood cells. phage . retroviruses. yeast. E. coli. Ans: C Difficulty: 1 Which vector is appropriate for cloning an insert of 1 Mb? phage vector YAC cDNA cosmid ampr plasmid Ans: B Difficulty: 1

58. A) B) C) D) E)

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59. A 16 kb linear DNA is cut with EcoRI and BamHI. The EcoRI digest yields fragments of 2, 6 and 8 kb. The BamHI digest yields fragments of 5 and 11 kb. An EcoRI-BamHI double digest yields 2, 3, 5 and 6 kb fragments. The map of this DNA has: A) 3 EcoRI sites and 2 BamHI sites. B) 3 BamHI sites and 2 EcoRI sites. C) 2 EcoRI sites and 2 Bam HI sites. D) 2 EcoRI sites and 1 BamHI site. E) 1 EcoRI site and 2 Bam HI sites. Ans: D Difficulty: 1 60. A 16 kb linear DNA is cut with EcoRI and BamHI. The EcoRI digest yields fragments of 2, 6 and 8 kb. The BamHI digest yields fragments of 5 and 11 kb. An EcoRI-BamHI double digest yields 2, 3, 5 and 6 kb fragments. If the 3 kb fragment from the double digest is used as the probe in a Southern blot of the EcoRI digest, to which fragment(s) will it hybridize? A) 2 kb B) 6 kb C) 8 kb D) 2 and 6 kb E) 6 and 8 kb Ans: C Difficulty: 4 61. A 10 kb linear DNA is cut with EcoRI and HindIII. The EcoRI digest yields fragments of 2 and 8 kb. The HindIII digest yields fragments of 3 and 7 kb. What are the possible fragments (in kb) from an EcoRI-HindIII double digest? A) 1, 3, 6 or 1, 4, 5 B) 1, 4, 5 or 1, 2, 7 C) 1, 4, 5, or 2, 3, 5 D) 1, 2, 7 or 1, 3, 6 E) 1, 2, 7 or 2, 3, 5 Ans: E Difficulty: 3 Table 9.3 restriction enzyme BamHI BstBI BglII

recognition site (5' to 3') G^GATCC TT^CGAA A^GATCT

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62. A) B) C) D) E)

Digestion with BstBI (TT^CGAA) leaves: blunt ends. sticky ends with the single-stranded sequence 5' CGAA 3'. sticky ends with the single-stranded sequence 5' CG 3'. sticky ends with the single-stranded sequence 5' AAGC 3'. sticky ends with the single-stranded sequence 5' GC 3'. Ans: C Difficulty: 4

63. In 3 separate reactions, DNA is cut with the 3 enzymes as in table (9.3). Do the fragments have complementary ends that can be ligated together? A) Fragments from the BamHI and BstBI digests can ligate to each other. B) Fragments from the BamHI and BglII digests can ligate to each other. C) Fragments from the BstBI and BglII digests can ligate to each other. D) All the ends are complementary, so all the fragments can ligate to each other. E) None of the fragments have complementary ends, so none will ligate to each other. Ans: B Difficulty: 3 64. A) B) C) D) E) Approximately how many bp between BstBI recognition sites (TT^CGAA)? 65,000 4,000 1,000 250 100 Ans: B Difficulty: 2

65. DNA with the following sequence was cut with BstBI (TT^CGAA) and cloned into a vector. What is the sequence of the peptide that is encoded within the BstBI-BstBI fragment? 5' ACCTTTCGAACTGATGGAAGAGTGTCACTGACTGGTTCGAAAAT 3' A) lys-leu-gly-gln-ser B) thr-phe-arg-thr-asp C) met-his-cys-glu-lys D) met-lys-leu-gly-gln E) met-glu-glu-cys-his Ans: E Difficulty: 3

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66. Approximately how many times is BamHI (G^GATCC) expected to cut a 5kb piece of DNA? A) 1 B) 4 C) 10 D) 65 E) 250 Ans: A Difficulty: 2 67. The partial amino acid sequence of a protein is: met-cys-tyr-trp-gln. A mixture of oligonucleotides containing all possible codons for each amino acid is generated. How many different oligonucleotides in the mixture? A) 8 B) 16 C) 32 D) 64 E) 128 Ans: A Difficulty: 4 68. When bacterial transformants containing a library are transferred to nitrocellulose filters and screened, one of the steps is treatment with an alkaline solution. What does this do? A) Attaches the library DNA to the nitrocellulose. B) Promotes hybridization between the probe and complementary inserts. C) Labels the DNA so it can be visualized. D) Stimulates DNA replication, to increase the plasmid copy number. E) Lyses the cells and denatures the released DNA. Ans: E Difficulty: 2 69. A) B) C) D) E) In references to the -globin locus or -globin locus, the term locus me a duplicated, ancestral gene. a chromosome region with a cluster of related globin protein genes. an -, or a -globin protein with a single amino acid change. the location, in this case red blood cells, where a mutant phenotype is manifested. a geographical region where a genetic disease like sickle cell anemia is common. Ans: B Difficulty: 1

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70. A) B) C) D) E)

How are the genes in the -globin locus different from each other? They use different template strands for transcription. They are expressed at different times in development. They have different evolutionary origins, from different ancestral genes. They are dispersed on different chromosomes. Some are expressed in all cells, some are expressed only in red blood cells. Ans: B Difficulty: 1 Pseudogenes are evidence for: gene duplications. the existence of integrated viruses, or proviruses. the importance of TATA boxes in eukaryotic promoters. the importance of the order of the globin genes in dictating their expression. diseases that result from deletions in the -globin genes. Ans: A Difficulty: 2

71. A) B) C) D) E)

72. Which statements are true? 1. In thalassemias, globin proteins are produced, but contain a point mutation. 2. In sickle cell anemia, globin proteins are produced, but contain a point mutation. 3. Sickle cell anemia is caused by a mutation in the -globin gene. 4. Sickle cell anemia is caused by a mutation in the -globin gene. A) 1, 2 B) 1, 3 C) 2, 3 D) 1, 4 E) 2, 4 Ans: C Difficulty: 1 73. A) B) C) D) E) In cosmids, what is the function of the cos sites? origins of replication restriction enzyme recognition sites allow packaging into viral shells selectable markers encode enzymes that allow detection of insert-containing recombinant molecules Ans: C Difficulty: 2

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74. If a single DNA molecule is amplified by PCR, how many DNA molecules will there be after 6 cycles? A) 6 B) 12 C) 24 D) 64 E) 86 Ans: D Difficulty: 3 75. Which mutation in the -globin gene could, in theory, be detected with a genomic clone but not with a cDNA clone? A) A point mutation that changes a single amino acid. B) A mutation that prevents removal of one intron. C) A promoter mutation that prevents transcription. D) A 10 bp deletion in an exon. E) A frameshift mutation. Ans: C Difficulty: 2

Figure 2 above shows a series of restriction digests of a circular plasmid. lane 1 2 3 4 5 6 7 8 enzyme(s) BamHI EcoRI HindIII SalI BamHI and EcoRI BamHI and HindIII BamHI and SalI EcoRI and SalI

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76. Referring to figure 2, if the plasmid is cut with EcoRI and HindIII, which size fragment is NOT a possibility? A) 0.5 B) 1 C) 7 D) 7.5 E) 9 Ans: E Difficulty: 3 77. A) B) C) D) E) Which technique is required to generate a restriction map? electrophoresis partial digestion with restriction enzymes hybridization to a synthetic oligonucleotide probe selection of recombinant bacteria by antibiotic resistance transformation Ans: A Difficulty: 1

Matching Match the technique with one or more applications a. DNA fingerprinting b. analyzing trace amounts of degraded, ancient DNA c. making a cDNA library d. identifying a gene in genomic DNA, if sequence is unknown, but a probe is available 78. Southern blotting Ans: a, d Difficulty: 2 79. reverse transcription of mRNA to DNA Ans: c Difficulty: 2 80. PCR Ans: a, b Difficulty: 2 Match the technique with one or more applications
a. b. c. d. identifying sequences complementary to a probe separation of large DNA molecules introducing recombinant DNA into hostcells using synthetic oligonucleotide primers to direct the PCR amplification of a DNA fragment

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81. pulsed-field electrophoresis Ans: b Difficulty: 1 82. hybridization Ans: a, d Difficulty: 1 83. transformation Ans: c Difficulty: 1 True or False 84. The genetically determined molecular composition of hemoglobin changes several times during development including changing from embroyic, to fetal, to adult hemoglogin. Ans: True Difficulty: 1 85. Hybridization is the covalent binding together of two complementary DNA strands. Ans: False Difficulty: 2 86. All diploid human cells contain two nearly identical sets of 3 billion base pairs of DNA, that when unwound, would extend 200 km. Ans: True Difficulty: 1 87. Size of the recognition site and base composition of the genome effect fragment length produced by restriction enzymes. Ans: True Difficulty: 1 88. The average length of a human chromosome is 130,000,000 bp. Ans: True Difficulty: 1 89. Probability of a six-base restriction enzyme site existing in a stretch of DNA is (1/6)4. Ans: False Difficulty: 2 90. The formation of a recombinant DNA molecule occurs through the cutting and splicing together of a vector and a fragment of DNA from another origin. Ans: True Difficulty: 1

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91. Anitbiotic resistance genes are often used as selectable markers in vectors. Ans: True Difficulty: 1 92. The genomic equivalent of a library is determined by multiplying the number of clones on a plate by the size of the average insert. Ans: False Difficulty: 2 93. PCR makes millions of perfect copies of the DNA being amplified. Ans: False Difficulty: 2 Short Answer 94. Refer to Figure 2. If the 1 kb EcoRI site is used as a probe in a Southern blot of the gel, to what will it in hybridize in lane 7? Ans: the 9 kb fragment Difficulty: 3 95. From the information in Figure 2, what size fragments would result from a triple digest with BamHI, EcoRI and SalI? Ans: 1, 3, 5, 6.5 Difficulty: 4 96. What are the largest capacity vectors that are currently available? Ans: yeast artificial chromosomes (YAC) Difficulty: 1 97. List two reasons that partial digests are performed on genomic DNA when producing fragments for a library. Ans: 1. To obtain fragments of intermediate length (e.g. between a 6-base, and 8-base cutter) 2. So genes that contain recognition sites within their coding regions might be obtained intact and uninterrupted. Difficulty: 4 98. List two advantages of cDNA libraries over genomic libraries. Ans: 1. Only expressed coding sequences are represented 2. Introns, non-coding and repetitive sequences are usually not included 3. They are tissue-specific, with highly expressed sequences represented more often 4. Obtained clones can be ligated to promoters for expression in bacteria. Difficulty: 2

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99. List the components of a Sanger (enzymatic extension) sequencing reaction. Ans: template DNA, primer, nucleotide triphosphates, fluorescently labeled dideoxynucleotide triphosphate, DNA polymerase. Difficulty: 3 100. What enzyme is used to generate DNA from RNA transcripts, for cDNA libraries? Ans: reverse transcriptase, or RNA dependent DNA polymerase. Difficulty: 1 Experimental Design and Interpretation of Data 101. The restriction enzyme EcoRI cuts a linear 19 kb piece of DNA into fragments of 1, 3, 6 and 9 kb. How many EcoRI sites are there in the 19 kb piece of DNA? Ans: 3 Difficulty: 1 102. A genomic library for an organism with a haploid genome of 5 107 bp has fragments of approximately 20 kb. How many clones represent a single genomic equivalent? Ans: 2500 Difficulty: 3 103. The partial amino acid sequence of a protein is met-cys-tyr-trp-gln. Write the sequence of the DNA probe that would hybridize to the template strand of the gene for this protein (if more than one base is possible at a given position, use / to indicate the mixture of bases). Ans: 5' ATG TGT/C TAT/C TGG CAA/G 3' Difficulty: 3 104. You wish to produce an abundance of protein for a gene you have just recently cloned from genomic DNA. How would you do this? Ans: Isolate mRNA, reverse transcribe and create a cDNA library using an expression vector. Probe the library with your genomic clone and use the expression vector to produce your protein in large quantities for purification and further study. Keep in mind that the expression vector needs to be compatible with the organism in which you need to produce your protein. In many cases, prokaryotes can not properly produce eukaryotic proteins which may require production in a more expensive but more appropriate system. Difficulty: 4

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Chapter 10Reconstructing the Genome Through Genetic and Molecular Analysis Fill in the Blank 1. RFLP analysis requires a ___________ complementary to an RFLP of interest. Ans: probe Difficulty: 2 2. FISH is the acronym for ________________________. Ans: Fluorescent in situ hybridization Difficulty: 2 3. Karyotype analysis has a resolution of about _____ kb. Ans: 5,000 Difficulty: 3 4. A ________________ is the entire collection of chromosomes in an organism. Ans: genome Difficulty: 1 5. The __________________ refers to all mRNAs expressed in a single cell or cell type. Ans: transcriptome Difficulty: 3 6. _________________ genes arise by duplication and often constitute a gene family. Ans: paralogous Difficulty: 3 7. A _______________ map is a constellation of overlapping DNA fragments that are ordered and oriented and span each of the chromosomes in a given genome. Ans: physical Difficulty: 2 8. The method of using the ends of unconnected contigs as probes to retrieve clones that extend into an unmapped region is known as ________________________. Ans: chromosome walking Difficulty: 3 9. SINES and LINES are ________________-derived repeats. Ans: transposon Difficulty: 4

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10. Processed __________________ are inactive copies of protein-coding genes and small structural RNAs that lack introns and regulatory sequences. Ans: pseudogenes Difficulty: 4 11. Chromosomal regions of a megabase or more of DNA without an identifiable gene is known as a _____________________. Ans: gene desert Difficulty: 1 12. ________________ gene transfer is the direct transfer of genes from one species in the germ line of another species. Ans: lateral Difficulty: 2 13. Of the two sexes in humans,_________ appear to have a higher mutation rate than _____________. Ans: males, females Difficulty: 2 14. ___________ is a recent technique used for quantification of the transcriptome including very rare transcripts. Ans: MPSS massively parallel signature sequence Difficulty: 3 15. A technique that uses ICATs and is called _______________ permits researchers to analyze the changing patterns of protein expression in two different cellular states. Ans: isotope analysis Difficulty: 3 Multiple Choice 16. A) B) C) D) E) An organism's genome is: the sequence of its genes for brain cells. the sequence of its genes for the heart. the DNA content of its sex chromosomes. the DNA content of its mitochondrial genes. the DNA content and sequence of all of an organisms genes. Ans: E Difficulty: 3

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17. A) B) C) D) E)

The human genome contains approximately how many microsatellites? one million one hundred thousand ten thousand one thousand one hundred Ans: B Difficulty: 3 Which is not true of DNA arrays? Thousands of DNA fragments of known sequence are attached to microchip. The attached fragments may contain allelic variants. Fragments from a test single stranded DNA sample may hybridize to DNA on the chip. In case of a match, the computer will express this fact. This method is too advanced to be applied at this time. Ans: E Difficulty: 3

18. A) B) C) D) E)

19. Genomics is: A) the branch of biology that studies genes. B) the branch of biology that develops and applies mapping, sequencing and computational tools. C) the branch of biology that studies model organisms. D) the branch of biology that studies Mendelian inheritance patterns. Ans: B Difficulty: 1 20. A) B) C) D) E) STSs are: microsatellite sequences. generally highly polymorphic. unique markers along the chromosome. a and b b and c Ans: E Difficulty: 1

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21. Over six thousand STSs markers have been placed on the human map and they are on average about 0.5 103 kbp apart. If 30,000 markers were available, what would be the average distance between markers? A) 10 kb B) 50 kb C) 100 kb D) 200 kb E) 500 kb Ans: C Difficulty: 2 22. A) B) C) D) FISH analysis is useful for: determining the order of DNA fragments in a YAC. determining the pattern of expression of a cloned gene. determining the chromosomal location of a gene. determining the map order of two closely linked genes. Ans: C Difficulty: 2 A contig is: a map of genetic markers that separated by less than 1cM. a map showing the order of cloned bits of DNA. unique DNA sequences that serve as molecular markers. sets of two or more partially overlapping cloned DNA fragments. Ans: D Difficulty: 2

23. A) B) C) D)

24. Sequence conservation among mammals allow researchers to: A) screen YACs made from human DNA for coding regions by hybridization to human DNA. B) screen YACs made from human DNA for coding regions by hybridization to mouse DNA. C) disregard introns or noncoding regions. D) disregard related genes. Ans: B Difficulty: 3 25. A) B) C) D) E) Model organisms: allow the discovery of similar pathways. allow the discovery of genes that are conserved across evolutionary time. allow the discovery of every human gene. a, b, and c a and b Ans: E Difficulty: 4

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26. Below are several steps involved in FISH. From the choices available, pick the order of steps that would be successful. 1. Fix chromosomes and denature the DNA. 2. Arrest cells in metaphase. 3. Take a picture using ultraviolet light. 4. Drop cells onto microscope slide to open the cells. 5. Label a DNA probe bound to fluorescent dye. 6. Hybridize the DNA probe to the chromosomes. A) Order 1, 2, 3, 4, 5, 6 B) Order 4, 2, 1, 6, 5, 3 C) Order 2, 1, 4, 3, 5, 6 D) Order 2, 4, 1, 5, 6, 3 Ans: D Difficulty: 4 27. A) B) C) D) Karyotypic analysis is: used for high resolution mapping. used for locating cloned genes on particular parts of a chromosome. used for direct analysis of DNA. used for restriction mapping. Ans: B Difficulty: 2 The study of polypeptide motifs allows researchers: to determine which amino acids are found together. to discern possible biochemical properties of a protein. to detect expression patterns. to detect the cellular location of the polypeptide. Ans: B Difficulty: 2

28. A) B) C) D)

29. Homology: A) between two protein sequences suggests that the genes encoding them derive from a single ancestral gene. B) can be 90%. C) is indicated by similarity in the coding region. D) a, b, and c E) a and b Ans: D Difficulty: 3

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30. A) B) C) D) E)

What DNA sequence information is not present in a cDNA? the promoter the introns the exons the 3' untranslated region a and b Ans: E Difficulty: 2

31. If you find a helix-loop-helix motif, what function might you postulate for this polypeptide? A) secreted polypeptide B) mitochondrial polypeptide C) nuclear polypeptide D) Golgi polypeptide Ans: C Difficulty: 2 32. A) B) C) D) If you find a zinc-finger motif, what function might you postulate for this polypeptide? signal transduction growth hormone receptor transcription factor cytoskeletal component Ans: C Difficulty: 2

33. Gene therapy is possible for some genes in humans at present. Which of the following are potential problems? A) large size of genes B) identifying the responsible gene C) random integration of transforming DNA D) tissue-specific gene expression E) all of the above F) a, b, and d Ans: F Difficulty: 3 34. A) B) C) D) E) The location of a gene on the Y chromosome could be identified by: Northern analysis FISH genomic Southern analysis a and b b and c Ans: E Difficulty: 3

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35. A) B) C) D)

Chromosome walking: will allow one to move from one chromosome to another. will allow one to move from one clone to another. requires FISH. will allow one to define the fine details of each clone. Ans: B Difficulty: 2

36. If you wanted to study a cell cycle control gene, which model organism would be best suited? A) E. coli B) S. cerevisiae C) C. elegans D) M. musculus Ans: B Difficulty: 37. If you wanted to study a gene involved in apotosis, which model organism would be best suited? A) E. coli B) S. cerevisiae C) C. elegans D) M. musculus Ans: C Difficulty: 2 38. If you wanted to study a gene involved in rod cells in the retina, which model organism would be best suited? A) E. coli B) S. cerevisae C) D. melanogaster D) M. musculus Ans: D Difficulty: 2 39. A) B) C) D) Stem cells are useful targets for gene therapy because: they are easily found. they are nondividing. they are dividing and able to differentiate. they are accessible. Ans: C Difficulty: 3

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40. The Human Genome Project has six distinct objectives. Which of the following is NOT one. A) to generate capital for the United States government. B) to generate physical, genetic, and sequence maps of the human genome. C) to sequence the genomes of a variety of organisms. D) to consider the ethical, social, and legal challenges posed by genomic information. Ans: A Difficulty: 2 41. A) B) C) D) The most common method for genotyping allelic SSRs is by: Southern analysis FISH PCR and gel electrophoresis Sequencing Ans: C Difficulty: 3

42. A method of using the ends of unconnected contigs as probes to further map a genome is called: A) sequence analysis B) FISH C) YAC D) overlap analysis E) chromosome walking Ans: E Difficulty: 2 43. A method of analysis that uses a pattern of restriction fragments sizes to compare regions of gemomic DNA. A) RFLP B) DNA fingerprinting C) Northern analysis D) PCR Ans: B Difficulty: 3 44. Mapping strategies often utilize the PCR of unique sites in the genome which are polymorphic and whose sequence is known. These sequences are best called: A) SSRs B) SNPs C) STSs D) SSCP Ans: D Difficulty: 3

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45. A) B) C) D)

The highest resolution map of a genome can best be generated from: haplotype mapping linkage mapping sequence analysis FISH Ans: C Difficulty: 1

46. Random generation of overlapping insert fragments from large clones for the purpose of sequence analysis is termed: A) digestion B) shotgun C) minimal D) maximal Ans: B Difficulty: 1 47. A) B) C) D) Which of the following are dissimilar between mouse and man: synteny karyotype orthologous order genes Ans: B Difficulty: 3 There are estimated to be how many genes in the human genome: 40,000-60,000 4,000-6,000 100,000 200,000 3 4 million Ans: A Difficulty: 3 Genome sequencing projects have and will continue to: expedite gene-finding and gene-function analyses. enhance studies on evolution. increase the number of known genetic polymorphisms. all of the above. Ans: D Difficulty: 1

48. A) B) C) D)

49. A) B) C) D)

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50. A) B) C) D) E) F)

Noncoding RNAs include: tRNAs rRNAs snoRNAs snRNAs all of the above. only a, b, and c. Ans: E Difficulty: 1 Genes encode: noncoding RNAs proteins both a and c Ans: C Difficulty: 2

51. A) B) C)

52. Protein analysis has shown that humans and worms have approximately how much proteome homology: A) 10% B) 43% C) 80% D) 2% Ans: B Difficulty: 3 53. A) B) C) D) Repeat sequences constitute how much of the human genome: 98% 50% 1% 5% Ans: B Difficulty: 2 Which of the following is not one of the five classes of repeat sequences: segmental duplications pseudogenes DNA coding for 5' UTRs transposon sequences Ans: C Difficulty: 2

54. A) B) C) D)

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55. A) B) C) D)

Transposon-derived repeats constitute how much of the human's genome: 0.5% 2% 45% 97% Ans: C Difficulty: 2

56. A gene considered to generate the upper limit of known splice variants might have how many: A) 500-1000 B) 5-10 C) 100-200 D) 10,000 20,000 Ans: A Difficulty: 3 57. Which of the following is not one of the four classes of transposon-derived repeat sequences: A) LINES B) SINES C) DNA transposons D) Long terminal repeat transposons E) pseudogenes Ans: E Difficulty: 3 58. Which of the following is not considered a distinct type of organization within a genome: A) presence of gene families B) junk DNA C) gene-rich regions D) gene deserts Ans: B Difficulty: 3 59. A) B) C) Which of the following is not true: human race differences are distinguishable by genotype and phenotype. the human population encompasses a number of different races. sequence analysis has found that there is more genotypic variation within a race than between races. Ans: A Difficulty: 2

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60. A) B) C) D)

Which of the following is not a method for measuring mRNA levels: DNA microarray sequence analysis oligonucleotides array Northern analysis Ans: B Difficulty: 1 The population of mRNA expressed in a single cell or cell type is called: transcriptome genome proteome spliceosome Ans: A Difficulty: 1

61. A) B) C) D)

62. Deleterious mutations in which of the following genes leads to a 70% predisposition toward breast cancer: A) p53 B) CFTR C) BRCA1 D) EGF Ans: C Difficulty: 2 63. A) B) C) A mass spectrometer is used to: quantify mRNA levels. determine sequence of DNA. following ionization and transfer to a vacuum, a molecule's mass can be determined by migration in an electric field. Ans: C Difficulty: 1

64. Which of the following is a technique used to quantitatively define a transcriptome including very rare transcripts: A) SAGE B) PAGE C) microarray analysis D) MPSS Ans: D Difficulty: 3

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Matching Match the best term with the appropriate definition a. heterochromatic DNA b. homologous genes c. paralogous genes d. orthologous genes e. sequence tag sites (STSs) f. genome g. proteome h. transcriptome i. DNA fingerprint j. syntenic block 65. ______ genes similar in two different species that arose from a common ancestor. Ans: d Difficulty: 2 66. ______ population of mRNAs expressed. Ans: h Difficulty: 2 67. ______ genomic DNA that is not clonable with current technology. Ans: a Difficulty: 2 68. ______ population of proteins present. Ans: g Difficulty: 1 69. ______ DNA pattern of restriction fragment sizes. Ans: i Difficulty: 1 70. ______ two genes with enough similarity to be considered evolutionarily related. Ans: b Difficulty: 2 71. ______ genomic blocks of chromosomal sequence with similarities in genes and orthologous order between two species. Ans: b Difficulty: 2

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72. ______ entire collection of chromosomes in an organism. Ans: f Difficulty: 1 73. ______ genes that arise by duplication within a specie. Ans: c Difficulty: 2 74. ______ short DNA sequences that are readily located and amplified by PCR and that identify unique physical genomic locations. Ans: e Difficulty: 2 True or False 75. We have a very good idea of what 95% of human DNA is doing. Ans: False Difficulty: 2 76. A probe is unnecessary for detecting RFLPs. Ans: False Difficulty: 2 77. For RFLPs to be of use in following the inheritance of a gene, they must be inside the gene. Ans: False Difficulty: 4 78. For an RFLP to be useful to follow a gene of interest, it must be closely linked to a gene. Ans: True Difficulty: 3 79. For an RFLP to be useful to follow the inheritance of a gene, it need not be on the same chromosome. Ans: False Difficulty: 2 80. Discovery science is used to identify all the elements of a biological system rather than to test a specific hypothesis. Ans: True Difficulty: 1

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81. Having sequenced the human genome, we now know that junk DNA does not play an important role in the genome. Ans: True Difficulty: 1 82. Heterochromatic DNA is DNA that is easy to clone. Ans: False Difficulty: 2 83. The human genome is 200 times larger that the yeast genome and 200 times smaller than that of Amoeba dubia. Ans: True Difficulty: 2 84. Some DNA sequences may be repeated 10,000 times within a genome. Ans: True Difficulty: 3 85. In humans, 1cM = 1 Mb, whereas in mice, 1 cM = 2 Mb for linkage versus physical map distances. Ans: True Difficulty: 3 86. Once considered junk DNA, transposon-derived repeats have given rise to at least 47 different human genes. Ans: True Difficulty: 4 87. A low GC content is a hallmark of a gene-rich region in humans. Ans: False Difficulty: 3 88. About half of all olfactory receptor genes are pseudogenes. Ans: True Difficulty: 3 89. The presence of genes with very large introns often leads to regions of gene deserts within a genome. Ans: True Difficulty: 2

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Short Answer 90. What is a cDNA microarray? Ans: A DNA microarray is a chip to which thousands of short DNA sequences, oligonucleotides, are attached. A matching DNA probe to one of the oligos attached to the microchip will generate a signal that is detected by computer. This method opens the way of surveying tens of thousands of cloned or PCR-produced fragments for complementarity with one of the microchip oligos. Difficulty: 2 91. What is the difference between ESTs and STSs? Ans: An EST is an expressed sequence tag and a STS is a sequence tagged site. ESTs are the 3' end of an expressed gene, often an unknown gene, while sequence tagged sites are sites whose location and sequence are known and can be used as markers in gene mapping. Difficulty: 2 92. Changes in the way science is completed have resulted from the sequencing of whole genomes. List two most significant changes? Ans: 1) Systems biology involving the analysis of genomes is now often completed in a non-hypothesis driven manner. 2) The medical practice has changed and now includes the use of predictive and preventative analysis and treatment rather than just treatment of symptoms. Difficulty: 2 93. What is the difference between SNPs and SSRs? Ans: SNPs are single nucleotide polymorphisms, a difference in a single base, and SSRs are simple sequence repeats, short regions of a repeated sequence, usually about 2-5 bp. Both are used for large-scale linkage mapping. Difficulty: 2 94. What are YACs and BACs? Ans: Yeast and Bacterial Artificial Chromosomes. They are used in library construction and physical mapping. Difficulty: 2 95. What is FISH and in FISH karyotype analysis, what stage of mitosis is needed for mapping a gene? Ans: Fluorescent in situ hybridization. Mapping can only be completed when whole chromosomes can be seen: during metaphase. Difficulty: 2

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96. What is meant by hierarchical shotgun sequencing strategy? Ans: Hierarchical shotgun sequencing strategy was used by the publicly funded Human Genome Project to produce a draft of the human genome. This multi-step approach involves the generation of a BAC library, a map of the minimal overlapping clones for each chromosome, sequence analysis of small cloned fragments of the BACs, and reassembly of the sequence for each individual chromosome. Celera used a whole genome shotgun approach rather than an individual chromosome approach, which did not require the construction of a physical map. Difficulty: 2 97. What is Yeast Two-Hybrid and what would you use it for? Ans: Yeast two-hybrid is a method for the detection of protein-protein interactions. A gene of interest is subcloned into a yeast-expression vector as a fusion to the DNA-binding domain of Gal4. This yeast clone is then mated to a library of yeast cells that contain genes fused to the Gal4 activator domain. If in a diploid cell, the Gal4 binding domain comes into contact with the activation domain through the contact of a protein-protein interaction via the fusion proteins this interaction will activate the genes under Gal4 control and thus allow selection for the proteinprotein interaction such as through histidine auxotrophy. Difficulty: 2

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Experimental Design and Interpretation of Data A YAC with a 157 kb insert is partially digested with a single restriction enzyme and the resulting restriction fragments are cloned into a cosmid vector. The restriction patterns of the inserted fragments in seven unique cosmids are shown below. (The YAC arms are not subcloned.)

98. What size fragments are adjacent to the 25 kb fragment? Ans: 27 kb, 25 kb Difficulty: 4 99. What size fragments are adjacent to the 13 kb fragment? Ans: 5 kb, 20 kb Difficulty: 4 100. What size fragments are adjacent to the 12 kb fragment? Ans: 10 kb, 27 kb Difficulty: 4 101. How many restriction enzyme recognition sites are present in this insert? Ans: 10 Difficulty: 4

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Chapter 11The Direct Detection of Genotype Distinguishes Individual Genomes Fill in the Blank 1. From a single cell removed from the embryo of Cfcf parents to produce a high copy number DNA fragment with the CF mutation, the _________ technique was used. Ans: PCR Difficulty: 2 2. For the ____________ technique, two short single strand DNA sequences called ____________ complementary to the CF gene are needed. Ans: PCR, primers Difficulty: 1 3. When it is possible to follow the segregation of one or more alternative alleles at a particular locus with DNA probes or PCR-based analyses, researchers consider the locus ______________. Ans: polymorphic Difficulty: 2 4. The approximate number of microsatellites in the human genome is _________________. Ans: 100,000 Difficulty: 2 5. In minisatellites the number of bases (in the boxcar) is ____________. Ans: 10-40 Difficulty: 3 6. A contraction of phrases from haploid genotype _____________. Ans: haplotype Difficulty: 1 7. The units used for a genetic map are __________; the units used for a physical map are ____________. Ans: centimorgan(cM); kilobasepairs (kbp) Difficulty: 2 8. Mutant alleles that show only a predisposition toward a mutant or disease phenotype show ________________. Ans: incomplete penetrance Difficulty: 2

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9. Traits that arise in the absence of a mutant genotype because of an environmental treatment are known as ____________________. Ans: phenocopies Difficulty: 2 10. Different combinations of alleles at multiple loci that result in measurable differences in phenotype are known as ______________________ loci. Ans: quantitative trait Difficulty: 2 11. An _____________ is one of two or more alternative DNA sequences found at a locus, either coding or noncoding, in different homologs of the same chromosome. Ans: allele Difficulty: 1 12. _________________ protocols can produce a quick snapshot of a combination of genomic features that can identify an individual. Ans: genotype Difficulty: 1 13. Short oligonucleotides of 18-24 bases that can hybridize to only one of the two alleles at a SNP locus under appropriate conditions are known as _______________________________________. Ans: ASO allele specific oligonucleotides Difficulty: 2 14. A piece of foreign DNA that has been inserted into an organism's genome through experimental manipulation of early-stage embryos or germ cells is called a _________________________. Ans: transgene Difficulty: 2 Multiple Choice 15. A) B) C) D) E) If the parents are Cfcf, the chance that any future child will be Cfcf is: 1/1. 1/3. 1/4. 1/2. 0. Ans: D Difficulty: 1

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16. If a PCR amplified sample hybridizes with two allele specific probes, one normal and one mutant sequence, a carrier is identified if: A) both samples give a signal. B) neither sample gives a signal. C) only the mutant probe gives a signal. D) only the non-mutant probe gives a signal. E) none of the above Ans: A Difficulty: 2 17. A) B) C) D) E) Molecular geneticists equate an allele with: only transcribed genes. only non-transcribed DNA. any DNA site that is different among genomes. any DNA site that is different among coding genomes. any DNA site that is different among non-coding genomes. Ans: C Difficulty: 3

18. When the 250 kb region that encompass the Cf gene is sequenced in two CfCf individuals, it is found that on the average the following number of base sequences is different between them. A) 0 B) less than 100 C) 350 D) 700 E) 1,000 Ans: D Difficulty: 4 19. For a gene or a locus to be considered polymorphic it must satisfy the following two conditions: A) must be present in all males and females. B) must be present in two or more sequence variations in at least 10% of the population. C) must be present in two or more sequence variations in at least 1% of the population. D) must be present in two or more sequence variations in at least 10% of children since not all may reach adulthood. E) must be present in two or more sequence variations in at least 1% of children since not all may reach adulthood. Ans: C Difficulty: 4

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20. When two haploid genomes are compared, about how many base sequence differences can be found in the non-coding DNA? A) 3.4 billion B) 3.4 million C) 340 thousand D) 34 thousand E) 3.4 thousand Ans: B Difficulty: 3 21. A) B) C) D) E) Which is the most frequent cause of DNA polymorphism? single base differences duplications inversions translocations ploidy Ans: A Difficulty: 1 In microsatellites, one, two or three base sequences are tandemly repeated about: one million times. one hundred thousand times. one thousand times. two hundred times. 15-100 times. Ans: E Difficulty: 2 The human genome contains approximately how many microsatellites? one million one hundred thousand ten thousand one thousand one hundred Ans: B Difficulty: 3 Which of the following is the main source of variation in microsatellites? chemicals in water chemicals in food ultraviolet light background radiation faulty DNA replication Ans: E Difficulty: 3

22. A) B) C) D) E)

23. A) B) C) D) E)

24. A) B) C) D) E)

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25. A) B) C)

Microsatellites compared to coding genes show: more variation. less variation. about the same variation. Ans: A Difficulty: 2 Deletions, duplications and insertions have the following number of bases. 1 10 100 1000 from one to megabase Ans: E Difficulty: 3 Deletions, and duplications are most often caused by: ultraviolet light. ionizing radiation. unequal crossing over. all of the above. b and c only Ans: E Difficulty: 3 Restriction sites provide substrates for: DNA endonucleases. enzymes that cut double stranded DNA. enzymes which cut the ends of DNA. a and b only b and c only Ans: D Difficulty: 3 Three sequential restriction sites will produce how many fragments? 3 2 1 Ans: B Difficulty: 1

26. A) B) C) D) E)

27. A) B) C) D) E)

28. A) B) C) D) E)

29. A) B) C)

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30. If the middle of three sequential restriction sites undergoes mutation, how many fragments will be expected? A) 3 B) 2 C) 1 Ans: C Difficulty: 1 31. A) B) C) D) E) Allele-specific probes are: dependent on PCR. should be 20 or less bases long. should be around 50 bases long. a and b a and c Ans: D Difficulty: 4

32. Lack of strong hybridization by an allele specific probe of about 20 bases to DNA to be tested detects: A) a normal, unchanged sequence. B) a polymorphic sequence. C) the probe is too short. D) the probe is too long. E) inappropriate protocol. Ans: D Difficulty: 4 33. A) B) C) D) E) The strength of holding of a probe and the DNA to be tested together depends on: length of the probe. temperature chosen during hybridization. ionic strength of post-hybridization washes. a and b a, b and c Ans: E Difficulty: 3 With the microsatellite analysis feature, all of the following apply except: must know the sequence of flanking markers. must know the sequence of the repeat units in the microsatellite. polymorhism is a matter of DNA size. electrophoresis. PCR. Ans: B Difficulty: 2

34. A) B) C) D) E)

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35. A) B) C) D) E)

Huntington disease is caused by: a closely linked marker allele. less than 34 CAG repeats. base-pair substitution. recessive allele. 42 or more CAG repeats. Ans: E Difficulty: 4 Positional cloning requires: knowledge about the function of a gene. knowledge about the expression pattern of a gene. knowledge about the map location of a gene. knowledge about the sequence of a gene. Ans: C Difficulty: 3

36. A) B) C) D)

37. Below are several steps involved in positional cloning. From the choices available, pick the order of steps that would be successful. 1. Examining Northerns for candidate genes in specific tissues. 2. Obtaining DNA or cells from members of a family with an inherited disease. 3. Obtain a molecular marker that fails to recombine with the disease gene. 4. Examine sequences of possible exons. 5. Perform linkage analysis with known markers to determine linkage to a chromosome arm. A) Order 1, 2, 3, 4, 5 B) Order 3, 2, 1, 4, 5 C) Order 5, 3, 4, 1, 2 D) Order 2, 5, 3, 1, 4 Ans: B Difficulty: 3 38. A) B) C) D) Phenocopies of genetic diseases can arise: from environmental stimuli in adulthood. from environmental stimuli in utero. from genetic alterations. a, b, and c Ans: B Difficulty: 2

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39. A) B) C) D) E)

Quantitative traits can be distinguished by: being measurable. being influenced by multiple genes. not having genetic causes. a and c a and b Ans: E Difficulty: 1 Incomplete penetrance: can vary from trait to trait. is observed when the mutant genotype does not result in a mutant phenotype. is only observed for late-onset diseases. a and b a and c Ans: D Difficulty: 3

40. A) B) C) D) E)

41. If the chance a person being polymorphic for a particular microsatellite is 50%, what is the chance that a person is polymorphic for four unlinked microsatellite loci? A) 75% B) 50% C) 25% D) 6.25% Ans: D Difficulty: 4 42. A) B) C) D) SNP is the acronym for: simple Northern probe. single nucleotide polymorphism. sample in situ probe. simple nucleotide probe. Ans: B Difficulty: 1

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43. Below are several steps involved in Northern blots. From the choices available, pick the order of steps that would be successful. 1. Blot the RNA from the gel to a filter. 2. Purify the RNA. 3. Separate the RNA by size in an electrical field in an agarose gel. 4. Expose the filter to a labeled probe to allow hybridization. 5. Develop the film. 6. Perform autoradiography. A) Order 1, 2, 3, 4, 5, 6 B) Order 2, 3, 6, 4, 1, 5 C) Order 2, 3, 1, 4, 6, 5 D) Order 2, 3, 4, 1, 6, 5 Ans: C Difficulty: 4 44. A) B) C) D) E) Predisposition to breast cancer results from mutations: in multiple genes. in BRCA1 that show 50% penetrance. and from environmental causes. a and b a and c Ans: D Difficulty: 3 Identification of candidate genes: can use a possible tissue specificity of expression. can use evolutionary conservation of coding sequences. can use short open reading frames. a and b a and c Ans: D Difficulty: 2 A transgene: can be used to create new mutant organisms. is a piece of foreign DNA that is inserted into the genome of an organism. can be used to determine if a candidate gene is responsible for a disease phenotype. a, b and c a and c Ans: D Difficulty: 4

45. A) B) C) D) E)

46. A) B) C) D) E)

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47. A) B) C) D) E)

The sequence of DNA is useful for: finding differences between individuals. finding information about protein function. finding protein motifs. duplicated genes. all of the above Ans: E Difficulty: 3 To find a gene that is responsible for a mutant or disease phenotype, the researcher will: sequence the entire contig. use Northern blots to find tissue-specific gene expression. pick out regions of conserved sequence by hybridization. look for mutations. a, b, and c b, c, and d Ans: F Difficulty: 3

48. A) B) C) D) E) F)

49. Mapping a disease gene requires: A) large families with DNA and pedigrees. B) large numbers of mapped physical markers with complete genomic coverage and small families with DNA and pedigrees. C) small numbers of mapped markers and small families with DNA and pedigrees. D) a or b E) a or c Ans: D Difficulty: 2 50. If a human disease gene is within 5 cM of a physical marker, then it is approximately within: A) 5 kb B) 50 kb C) 5,000 kb D) 50,000 kb Ans: C Difficulty: 4

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51. A) B) C) D) E)

If a gene is thought to be a possible disease gene, one can: sequence alleles from affected and unaffected family members. examine the expression pattern of the gene. make a transgenic mouse, if an appropriate mouse mutation is known. all of the above a and c Ans: D Difficulty: 3

52. Thalidomide was a common treatment for morning sickness in the 1950s. Children born to mothers given this drug showed the phenotypes of a genetic disease known as phocomelia, which involves shortened limbs. This may represent: A) incomplete dominance. B) genetic heterogeneity. C) penetrance. D) phenocopy. Ans: D Difficulty: 2 Matching Match the terms with the definition that best fits. a) allele b) DNA polymorphism c) anonymous locus d) microsatellite e) minisatellite f) transgene g) phenocopy h) QTL i) haplotype j) linkage disequilibruim 53. ______ the existence of two or more genetically different classes in the same interbreeding population. Ans: b Difficulty: 1 54. ______ a large DNA element composed of numerous repeats of a 10-40 base pair segment. Ans: e Difficulty: 1

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55. ______ loci that control the expression of continuous traits. Ans: h Difficulty: 1 56. ______ the non-random distribution into the gametes of a population of the alleles of genes that reside on the same chromosome. Ans: j Difficulty: 2 57. ______ A segment of DNA of unknown gene content that has been localized to a specific site on a chromosome. Ans: c Difficulty: 1 58. ______ specific combination of linked alleles in a cluster of related genes. Ans: i Difficulty: 1 59. ______ any piece of DNA that has been experimentally inserted into an organism while in the embryonic or germ cell stage. Ans: f Difficulty: 1 60. ______ alternative form of a single gene. Ans: a Difficulty: 1 61. ______ a non-heritable change in phenotype arising from environmental agents that mimic the effects of a mutation in a gene. Ans: g Difficulty: 1 62. ______ DNA element composed of 15-100 tandem repeats of 1- 2- or 3-base sequences. Ans: d Difficulty: 1 True or False 63. If a couple has a child who suffers from cystic fibrosis both parents must be a carriers. Ans: True Difficulty: 1

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64. Modern geneticists define an allele as any DNA site difference among genomes. Ans: True Difficulty: 3 65. If DNA is isolated from two healthy individuals, it is very likely that their DNA sequence will be identical. Ans: False Difficulty: 2 66. All DNA sequence changes in the Cf gene lead to the disease called cystic fibrosis. Ans: False Difficulty: 3 67. Two members of homologous chromosomes from one individual show less sequence differences than two of the same homologous chromosomes from two individuals. Ans: False Difficulty: 4 68. Microsatellites tend to be highly conserved, that is, once made they stay the same. Ans: False Difficulty: 2 69. DNA polymerase stutter is a main source of variation in microsatellites. Ans: True Difficulty: 4 70. The genetic role of minisatellites is well known. Ans: False Difficulty: 1 71. Misalignment during synapsis is a source of additional number of repeats in minisatellites. Ans: True Difficulty: 3 72. The material deleted from one homologous chromosome can be material for duplication in a homologous chromosome. Ans: True Difficulty: 1 73. Restriction sites refer to a specific DNA sequence recognized by a specific endonuclease. Ans: True Difficulty: 1

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74. DNA fingerprinting established that Anna Anderson was the same as Grand Duchess Anastasia. Ans: False Difficulty: 1 75. The DNA fingerprints of monozygotic twins are identical. Ans: True Difficulty: 2 76. A gene is simply a coding locus. Ans: True Difficulty: 2 77. Sequence variation is about 1 per 1000 bases for any two individuals. Ans: True Difficulty: 2 78. Nearly all SNPs are biallelic. Ans: True Difficulty: 1 79. DNA fingerprints identify polymorphisms in microsatellites and can be used to identify family relationships between old skeletal material and living individuals. Ans: True Difficulty: 2 80. LOD score analysis is a statistical approach used to discover whether an unknown locus is linked to a marker locus of known chromosomal location. Ans: True Difficulty: 2 81. QTL is the acronym for qualitative trait loci. Ans: True Difficulty: 2 82. Haplotype association in humans allows high-resolution gene mapping. Ans: True Difficulty: 2

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Short Answer 83. The parents of the two available embryos, one CfCf and the other Cfcf, chose to have both placed in the womb. Using the carrier embryo increased their chance of having a child, but they were willing to pass on a harmful allele to satisfy their own desire to procreate. What would you have done in their place? Ans: As a person familiar with genetic disease, I would have used the CfCf embryo, only. As a layperson I would have done what the parents did in the textbook case study. Difficulty: 2 84. Compare and contrast the definition of an allele by Mendel, Morgan and other classical geneticists to the definition offered by current geneticists. Ans: Mendel and Morgan identified the existence of alleles if there were two or more phenotypes associated with a gene. Current geneticists equipped with molecular genetic tools define an allele as any DNA sequence difference between the DNA in homologous chromosomes. Difficulty: 2 85. Define a locus in a classic sense and define it in a modern sense. How are the two definitions similar and different? Ans: In the Mendel, Morgan or classic sense, a coding gene and its allele(s) were associated with a location in a chromosome (a locus or prular loci). In current, modern, use, a locus is any place in the genome where there is a base difference between DNA of homologous chromosomes. Difficulty: 2 86. If the recognition sequence for EcoR1 is 3 kb, 5 kb and 12 kb from the beginning of a cloned fragment, what DNA fragments would be expected and what kind of probe might be most useful? Ans: Expected fragments would be 2 and 7 kb. A probe has complementary to flanking the 5 kb recognition site. Difficulty: 2

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Experimental Design and Interpretation of Data A pure-breeding tomato with large fruit size (100 grams) is crossed to a pure-breeding tomato with small fruit size (20 grams). The F1 generation has intermediate sized fruit (60 grams). A plant from the F1 generation is crossed to the parent with small fruit size. The following data is collected among the progeny of this cross.

87. What type of inheritance pattern do these data suggests? Ans: quantitative trait loci Difficulty: 2 88. Assume that there are equally contributing loci that produce this phenotype, how many loci are likely to be involved? Ans: 4 Difficulty: 4 89. How many different genotypes would be found among the plants that produce 30-gram tomatoes? Ans: 4 Difficulty: 4 90. How many different genotypes would be found among the plants that produce 40-gram tomatoes? Ans: 6 Difficulty: 4 91. If two F1 plants were crossed to each other and the fruit sizes among the F2 progeny were examined, how many phenotypic classes would be observed? Ans: 9 Difficulty: 4 92. If two F1 plants were crossed to each other and the fruit sizes among the F2 progeny were examined, what fraction of the plants would produce fruits of 100 grams? Ans: 1/64 Difficulty: 4

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93. How many alleles are involved in the determination of fruit size based on these parents? Ans: 8 Difficulty: 4 Allele specific oligonucleotides (ASO) can be used to determine the different alleles present in a DNA sample. Single sperm, which have completed meiosis, can be used for a polymerase chain reaction (PCR). The amplified DNA is then spotted to filters and hybridized with probes that recognize single nucleotide differences. Four primers (called A, B, D, and E) were used to amplify DNA samples and ASO probes were used to determine the allele present (Either allele 1 or 2). X indicates the allele is present and indicates the allele is not present.

94. Which loci are heterozygous? Ans: A, D, E Difficulty: 4 95. Which loci are linked? Ans: A, D, E Difficulty: 4 96. What genotypes are likely to have been contributed by this male's parents? Ans: A1 B1 D1 E2 and A2 B1 D2 E1 Difficulty: 4 97. What is an estimate of the map distance between the three pairs of linked genes? Ans: A-D = 25.3 cM, A-E = 10.6 cM, D-E = 35.9 cM Difficulty: 3 98. What feature would distinguish a Y-linked gene if you used PCR-amplified ASO markers in sperm? Ans: Allele in only 1/2 of the sperm Difficulty: 3 99. What feature would distinguish an X-linked gene if you used PCR-amplified ASO markers in sperm? Ans: Allele in only 1/2 of the sperm Difficulty: 3

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Quantitative trait loci can be examined using pure-breeding parents and measuring a particular trait. If each allele makes an equal contribution to the phenotype, then the number of loci can be discerned. Bristle length in Drosophila behaves as a quantitative trait. If one parent has bristles of 30 nm and a second fly has bristles of 10 nm, then the F1 will have bristles of 20 nm. If the F1 flies are crossed to produce the F2 generation, the following classes of flies are observed. Number of F2 Flies Length of bristles 10 10 40 15 60 20 40 25 10 30 100. How many different genotypes would be found among the flies with 10 nm bristles? Ans: 1 Difficulty: 4 101. How many different genotypes would be found among the flies with 30 nm bristles? Ans: 1 Difficulty: 4 102. How many different genotypes would be found among the flies with 15 or 25 nm bristles? Ans: 2 Difficulty: 4 103. How many loci are affecting this trait? Ans: 2 Difficulty: 4 104. If one wanted to find a physical marker that was linked to genes affecting bristle length, which flies would be most useful? Ans: 10 nm or 30 nm Difficulty: 4

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Chapter 12The Eukaryotic Chromosome: An Organelle for Packaging and Managing DNA Fill in the Blank 1. In many human tumor cells, abnormal activation of the _________________ gene seems to bestow the capacity to divide indefinitely. Ans: telomerase Difficulty: 2 2. Specialized elements that ensure the accurate duplication and segregation of chromosomes include telomeres, origins of replication, and _________________. Ans: centromeres Difficulty: 2 3. The components of eukaryotic chromosomes include DNA, _________________, and nonhistone proteins. Ans: histones Difficulty: 2 4. _________________ is the generic term for any complex of DNA and protein found in a cell's nucleus. Ans: Chromatin Difficulty: 2 5. The most rudimentary DNA packaging unit which involves four types of histones is the _________________. Ans: nucleosome Difficulty: 2 6. The largest class of nonhistone proteins foster or regulate _________________ and RNA processing during gene expression. Ans: transcription Difficulty: 2 7. Packaging into nucleosomes condenses naked DNA about _________________. Ans: 7-fold Difficulty: 3 8. Two small acrocentric chromosomes in the great apes fused to form _________________ chromosome 2 in humans. Ans: metacentric Difficulty: 2

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9. The duplication of chromosomal DNA depends on origins of replication and ________________. Ans: telomeres Difficulty: 2 10. In a typical human cell, DNA polymerase replicates about _________________ nucleotides per second. Ans: 50 Difficulty: 2 11. The DNA running both ways from one origin of replication to the endpoints where it merges with DNA from adjoining replication forks is called a replication unit, or _________________. Ans: replicon Difficulty: 3 12. The telomeres of all mammals and most of the other higher animals contain the same repetitive DNA sequence. The bases in this sequence are _________________. Ans: TTAGGG Difficulty: 3 13. Even though telomeres normally carry no genes, they contain essential information for the duplication, segregation, and stability of _________________. Ans: chromosomes Difficulty: 2 14. The _________________ of eukaryotic chromosomes assure their precise distribution during cell division. Ans: centromeres Difficulty: 2 15. Centromeres are contained within blocks of repetitive, simple noncoding sequences known as _________________ DNAs. Ans: satellite Difficulty: 2 16. The _________________ is the specialized structure composed of DNA and proteins that is the site at which chromosomes attach to the spindle fibers. Ans: kinetochore Difficulty: 2 17. Cells express their genes mainly during _________________ when the chromosomes have decondensed, or decompacted. Ans: interphase Difficulty: 2

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18. When viewed under the light microscope, certain regions of chromosomes that have been stained with certain DNA-binding chemicals appear lighter than others. These regions are called _________________. Ans: euchromatin Difficulty: 2 19. Chromosomal regions that remain condensed in heterochromatin at most times in all cells are known as _________________ heterochromatin. Ans: constitutive Difficulty: 2 20. Regions of chromosomes that are heterochromatic in some cells and euchromatic in other cells of the same organism are known as _________________ heterochromatin. Ans: facultative Difficulty: 2 21. Inactive X chromosomes that appear in interphase cells as darkly stained heterochromatin masses are called _________________. Ans: Barr bodies Difficulty: 2 22. Drosophila salivary glands contain giant chromosomes called _________________ chromosomes consisting of many identical chromatids lying in parallel register. Ans: polytene Difficulty: 2 23. The centromeres of polytene chromosomes fuse to form a dense heterochromatic mass known as the _________________. Ans: chromocenter Difficulty: 2 24. When observing the interphase nucleus of a eukaryotic cell, a certain large sphereshaped structure may be seen clearly. This structure is called the _________________. Ans: nucleolus Difficulty: 2

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Multiple Choice 25. The enzyme that some organisms use to replicate DNA at the 5' ends of chromosomes is called: A) DNA polymerase. B) telomerase. C) DNA ligase. D) replicase. Ans: B Difficulty: 1 26. A) B) C) D) Which of the following is not usually seen when a cell loses telomerase activity? Telomeres shorten slightly with each cell division. After 30-50 divisions cells show signs of senescence and then die. In the immune system certain capacity for protection is gradually lost. Many normal somatic cells gain the ability to divide indefinitely. Ans: D Difficulty: 2

27. The chromosome can be considered a dynamic organelle for _______________ of DNA. A) expression B) segregation C) replication D) packaging E) all of the above Ans: E Difficulty: 1 28. A) B) C) D) E) The components of a chromosome include one long DNA molecule and: phospholipids. proteins. carbohydrates. steroids. RNA. Ans: B Difficulty: 1 By weight, chromatin consists roughly of: 1/3 DNA, 1/3 histones, & 1/3 nonhistones. 1/3 DNA, 2/3 acidic proteins. 1/3 DNA, 1/3 histones, & 1/3 basic proteins. 1/4 DNA, 1/4 RNA, 1/4 histones, 1/4 nonhistones. Ans: A Difficulty: 2

29. A) B) C) D)

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30. A) B) C) D) E)

Histones and DNA have a strong attraction for each other because: DNA is positively charged and histones are negatively charged. both DNA and proteins are hydrophobic. DNA is negatively charged and histones are positively charged. like substances share common charges. none of the above Ans: C Difficulty: 2 Which of the following is not a role ascribed to nonhistone proteins found in chromatin? structural replication chromosome segregation nucleosome packers Ans: D Difficulty: 2

31. A) B) C) D)

32. Histones appear to have a singular role in the packaging of DNA. The nonhistone proteins in chromatin have which of the following functions? A) different functions for different tissues, such as tissue-specific transcription factors B) activity at different moments in the life cycle C) centromere function activity D) all of the above Ans: D Difficulty: 1 33. A) B) C) D) The first level of compaction of DNA consists of: DNA winding around histones to form small nucleosomes. tight coiling of DNA with nucleosomes into higher order structures. high level compaction into metaphase-type chromosomes. histone, DNA, and nonhistone covalent bonding. Ans: A Difficulty: 1

34. An electron micrograph of chromatin, which looks like a bead on a string, allows measurement of structural dimensions. The beads appear to have a diameter of about ________ and the string a diameter of about ________ . A) 20, 100 B) 20, 0.1 C) 100, 20 D) 120, 100 Ans: C Difficulty: 2

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35. Nucleosomal chromatin with a diameter of 100 supercoils into a 300 superhelix. The histone that appears to be responsible for this compaction is: A) H4. B) H3. C) H2. D) H1. Ans: D Difficulty: 2 36. In DNA, the 300 fiber is formed into structural loops. Responsibility for this function appears to lie with: A) histone H4. B) nucleosomase. C) histone H1. D) certain nonhistone proteins. Ans: D Difficulty: 1 37. At what stage of mitosis do we first see a chromosome that is compacted 250-fold over the 40-fold compacted 300 fiber? A) prophase B) metaphase C) anaphase D) telophase E) never achieves this level of compaction Ans: B Difficulty: 1 38. Which of the following is not a piece of evidence that supports the radial loop-scaffold model of DNA packaging? A) Histone-depleted metaphase chromosomes still maintain their X-like shapes. B) Electron micrographs of whole-mounted mitotic chromosomes show loops of chromatin at the periphery of the chromosomes. C) Topoisomerase II assists in 100 packaging. D) Special, irregularly spaced repetitive base sequences associate with nonhistone proteins to define the chromatin loops. E) All of the above are such evidence. Ans: C Difficulty: 3

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39. The total compaction of DNA as seen in metaphase chromosomes is approximately ______ fold. A) 10,000 B) 50,000 C) 100,000 D) 40 Ans: A Difficulty: 2 40. Technique of preparing mitotic chromosomes involves a staining procedure using Giemsa stain. One variation of this technique allows low-resolution of chromosome bands while a second variation allows a high-resolution. At low resolution we can see about _________ bands while at high-resolution we see about _______. A) 300, 2,000 B) 300, 1,000 C) 100, 2,000 D) 100, 1,000 Ans: A Difficulty: 2 41. A) B) C) D) Chromosome banding patterns can be used for which of the following? Analyze chromosomal differences between species. Locate genes. Reveal the cause of certain genetic diseases. All of the above Ans: D Difficulty: 1

42. If one looks at the chromosome banding pattern of certain primates it can be seen that humans and another primate have banding patterns nearly identical on 13 of the chromosomes. This primate is the: A) gorilla B) chimpanzee C) orangutan D) baboon Ans: B Difficulty: 1

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43. In the medical literature can be found a case history of a young boy with defects in four X-linked traits. When looking at the banding patterns in his karyotype, which of the following can be seen that apparently explains the situation? A) A duplication near the centromere. B) Loss of all interband regions. C) Deletion of a small white band between two darker bands. D) A fusion of two small chromosomes to form the number two chromosome. Ans: C Difficulty: 3 44. A) B) C) D) With regard to the typical human cell, which of the following appears to be true? There is only one origin of replication. There are multiple origins of replication that function consecutively. There are multiple origins of replication that function simultaneously. Replication is not understood well enough to postulate on replication origins. Ans: C Difficulty: 3 In mammalian cells, replication proceeds: unidirectionally. bidirectionally. unidirectionally from many origins. bidirectionally from only one origin. Ans: B Difficulty: 2

45. A) B) C) D)

46. The 10,000 origins of replication in mammalian cells suggests that concerning origin of replication there is: A) at least one per loop of DNA. B) probably one every other loop of DNA. C) a random distribution across the genome. D) a precise pattern of distribution relative to other replication points. Ans: A Difficulty: 2 47. Yeast research with autonomously replicating sequences (ARS), along with digestion of chromatin with DNase I, have led scientists to determine that: A) DNA is not protected inside a nucleosome. B) ARSs are really plasmids. C) RSs bond irreversibly to replication enzymes. D) origins of replication are accessible regions of DNA devoid of nucleosomes. Ans: D Difficulty: 3

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48. A) B) C) D)

Which of the following is not true about DNA polymerase? It cannot begin the 5' end of a new strand without a primer. It can only travel in the 5'-to-3' direction. It can reconstruct the 3' end of each newly made DNA strand. It can replace RNA primer with DNA at the 5' end. Ans: D Difficulty: 2 Which of the following are properties of telomeres? Consist of special repetitive DNA sequences. Prevent the loss of DNA through incomplete replication. Cap the ends of each chromosome. Number of repeats varies with cell type. All of the above Ans: E Difficulty: 1

49. A) B) C) D) E)

50. Telomeres appear to function in at least two ways during the replication of chromosomes. One way is to provide a primer for DNA polymerase. The second is to: A) allow the chromosome to shorten each generation to speed up replication. B) attract telomerase. C) permit the hairpin turn at the end to be cleaved. D) all of the above E) none of the above Ans: B Difficulty: 1 51. The two chromatids of each replicated chromosome must separate from one another and segregate during: A) mitosis. B) meiosis I. C) meiosis II. D) both a and b E) both a and c Ans: E Difficulty: 2 52. A) B) C) D) E) In DNA, most satellite sequences are found in: chromosome arms. telomeres. centromeres. spaces around the dark bands. none of the above Ans: C Difficulty: 1

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53. One of the functions of a centromere is to contribute to proper chromosome segregation. The other function is to: A) hold sister chromatids together. B) ensure that proper chromosome arm length is maintained. C) allow easy karyotyping. D) develop meiotic chromosome replication. E) all of the above Ans: A Difficulty: 2 54. A) B) C) D) During mitosis, kinetochores develop during: telophase. anaphase. metaphase. prophase. Ans: D Difficulty: 1 In yeast chromosomes, centromeres: help distinguish one chromosome from another. are closely related in sequence. are only 10-15 bp long. play various roles in chromosome segregation. Ans: B Difficulty: 2 In higher eukaryotes, kinetochores attach to: one spindle fiber. one spindle fiber on each side. multiple spindle fibers. multiple repeating structural subunits. Ans: C Difficulty: 2

55. A) B) C) D)

56. A) B) C) D)

57. The single-celled yeast, Saccharomyces cerevisiae, was the organism of choice as raw material for constructing artificial chromosomes because of all the following except: A) it is easy to manipulate. B) it is unicellular. C) its genetic machinery is similar to the one in higher organisms. D) its origins of replication have been defined as discrete, small segments of DNA. Ans: B Difficulty: 3

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58. A) B) C) D) E)

A yeast artificial chromosome (YAC) usually consists of: a yeast centromere. a yeast origin of replication. telomere sequences. suitable selectable markers. all of the above Ans: E Difficulty: 1

59. Which of the following appears to be true concerning yeast artificial chromosomes (YACs) and segregation errors during cell division? A) 11,000 bp YACs show 50% errors. B) 55,000 bp YACs show 1.5% errors. C) >100,000 bp YACs show 0.3% errors. D) all of the above are true Ans: D Difficulty: 2 60. Even though not well understood, certain chromosome features, known as _________, restrict DNA unwinding to specific regions and prevent decompaction from spreading beyond a certain point. A) rosettes B) telomerases C) nucleosomes D) boundary elements Ans: D Difficulty: 2 61. A) B) C) D) Many, but not all, DNase hypersensitive (DH) sites are found: at the 5' ends of genes to be transcribed by the cell. in and near nucleosomes. near histone-rich regions. all of the above Ans: A Difficulty: 2

62. Which of the following is true concerning the location of DNase hypersensitive (DH) sites in higher organisms? A) In red blood cells the DH site is at the 5' end of the gene for hemoglobin. B) In muscle cells the DH site exposes myoglobin. C) In a type of white blood cell DH sites are at the 5' ends of the genes for antibodies. D) In nerve cells DH sites expose the genes for neurotransmitters. E) All of the above Ans: E Difficulty: 2

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63. From DNA research, sites of transcription and therefore most of the genes along the length of the chromosome appear to be found in: A) heterochromatin. B) euchromatin. C) constitutive heterochromatin. D) centromeric regions. Ans: B Difficulty: 1 64. When a chromosomal rearrangement such as an inversion occurs placing a known gene into or next to a heterochromatic region, the gene's expression: A) will turn on. B) may be amplified. C) may cease. D) none of the above Ans: C Difficulty: 1 65. In the position effect variegation of red and white eye color in Drosophila, eyes are produced: A) one red and one white. B) red or white depending on which gene is dominant. C) with every other eye facet red or white. D) with varying sizes and positions of red and white patches. E) none of the above Ans: D Difficulty: 2 66. A) B) C) D) E) In which of the following cases will a Barr body be seen? XX XY XO XXY both a and d Ans: E Difficulty: 2

67. During development, an XX female embryo will form one of the X chromosomes in each cell into a Barr body. This usually occurs: A) about two weeks after zygote formation. B) by the end of the first trimester. C) at the 16-cell stage. D) in the X that is the most recessive. Ans: A Difficulty: 2

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68. Drosophila polytene chromosomes go through 10 rounds of replication without undergoing mitosis. The resulting sister chromatids will consist of ________ double helixes. A) 2,048 B) 1,024 C) twice as many D) 10 times as many Ans: B Difficulty: 2 69. Drosophila chromosomes contain bands that range in size from 3 kb to more than 150 kb. These bands total about ________. A) 5,000 B) 2,048 C) 2,500 D) 4,000 Ans: A Difficulty: 2 70. At certain times, a region of the polytene chromosome may swell to form a large, diffuse structure called a: A) lampbrush. B) centromere. C) chromocenter. D) chromosomal puff. Ans: D Difficulty: 1 71. A) B) C) D) E) The nucleolus consists of: long loops of DNA from several chromosomes. ribosomal RNA (rRNA) genes. growing rRNA transcripts. completed transcripts from arrays of rRNA genes. all of the above Ans: E Difficulty: 2

72. Certain reversible changes in chromatin structure allow a variety of chromosome functions. These include: A) coordinated compaction for segregation and transport. B) universal unwinding for replication. C) selective unwinding for gene expression. D) all of the above Ans: D Difficulty: 2

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Matching Match the following terms with the definition that best fits. a) telomer b) nucleosome c) replicon d) kinetochore e) constitutive heterochromatin f) facultive heterochromatin g) Barr bodies h) chromocenter i) chromosomal puff j) nucleolar organizer 73. ______ centromere Ans: d Difficulty: 1 74. ______ a short tandomly repeated G-C rich DNA sequence near the end of chromosomes. Ans: a Difficulty: 2 75. ______ a genetic element that behaves as an autonomous unit during DNA replication. Ans: c Difficulty: 2 76. ______ the chromosomal region that contains the ribosomal RNA genes. Ans: j Difficulty: 2 77. ______ made of repetitious DNA that is late to replicate and is transcriptionally inactive. Ans: e Difficulty: 2 78. ______ inactivated chromosomal DNA. Ans: f Difficulty: 2 79. ______ a localized swelling of a specific region of a polytene chromosome due to localized synthesis of DNA or RNA. Ans: i Difficulty: 2

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80. ______ a beadlike structure of eukaryotic chromosomes, consisting of a core of eight histone molecules wrapped by a DNA segment about 150 base pairs in length and separated by linker DNA. Ans: b Difficulty: 2 81. ______ a condensed single X chromosome seen in the nuclei of somatic cells of female mammals. Ans: g Difficulty: 2 82. ______ a formation in polytene chromosomes where heterochromatic segments near the centromere adhere to one another. Ans: h Difficulty: 2 True or False 83. The linear chromosomes of eukaryotic cells terminate at both ends in protective caps called telomeres. Ans: True Difficulty: 1 84. During metaphase of mitosis the chromosomes look like a tangled mass of grainy string scattered throughout the nucleus. Ans: False Difficulty: 1 85. Chemical and physical analysis of chromosomes within a cell has shown us that a chromosome contains several long linear molecules of DNA. Ans: False Difficulty: 1 86. That histones have changed so little throughout evolution underscores the importance of their contribution to chromatin structure. Ans: True Difficulty: 2 87. Nucleosomes are evenly spaced along a chromosome, but they do not have a welldefined arrangement along the chromatin. Ans: False Difficulty: 2

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88. At this time the loops and scaffold concept of higher level chromatin packaging remains a hypothesis. Ans: True Difficulty: 2 89. It appears that chromosome bands produced by staining embody discrete differences in base composition over long distances. Ans: False Difficulty: 2 90. It is possible to use chromosome bands to assist in location of genes. Ans: True Difficulty: 1 91. In all placental mammals, the diploid genome carries roughly 6 billion base pairs, but is packaged into different numbers of chromosomes with different banding patterns. Ans: True Difficulty: 2 92. It appears that all origins of replication are active during all mitotic divisions that create an organism. Ans: False Difficulty: 2 93. While duplicating an entire chromosome, DNA polymerase cannot begin the 5' end of a new strand without a primer. Ans: True Difficulty: 2 94. Telomeres prevent the transcription of genes brought into their vicinity. Ans: True Difficulty: 1 95. Telomerase is an enzyme that consists of a protein portion in association with RNA. Ans: True Difficulty: 1 96. If removal of a DNA sequence disrupts chromosome segregation and reinsertion of the same sequence restores stable transmission, the sequence must lie outside the centromere. Ans: False Difficulty: 2

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97. To build a yeast artificial chromosome (YAC), scientists must insert parts of the yeast into a plasmid. Ans: True Difficulty: 2 98. Yeast artificial chromosomes (YACs) that are more than 100,000 bp long show a frequency of segregation errors nearly identical to that of natural yeast chromosomes. Ans: False Difficulty: 1 99. When looking for the relationship between chromosome banding and number of genes per band in polytene chromosomes, one finds a direct one-to-one relationship. Ans: False Difficulty: 2 Short Answer 100. Describe how researchers learned from physical and chemical studies that each chromosome within a cell nucleus contains one long linear molecule of DNA. Ans: In one study researchers used the base analog 5-bromodeoxyuridine to label newly synthesized DNA in metaphase chromosomes consisting of two sister chromatids. The two chromatids stained in a fashion consistent with the idea that each chromatid contains one long double helix of DNA produced by a semiconservative mode of replication. In a second study, they placed chromosomal DNA between two cylinders, stretched the DNA by rotating one of the cylinders, and measured the DNA's rate of recoil. Shorter molecules recoil faster than longer ones. When they applied this measure to the DNA in a Drosophila chromosome, the length of the DNA molecule was sufficient to account for the entire DNA in a single chromosome. It is also possible to use pulsed gel electrophoresis to separate the DNA molecules of a relatively small genome by size; with the yeast genome, the number and sizes of the separated DNA molecules correspond to the number and sizes expected if each chromosome contains a single DNA molecule. Difficulty: 4

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101. Discuss how a nucleosome is constructed from DNA and histone proteins. Ans: On an electron micrograph of chromatin, the chromatin fibers resemble beads on a string, with the beads having a diameter of about 100, and the string a diameter of about 20, which is just DNA. Student may sketch a figure similar to a text figure and explain how DNA wraps around histone cores to form the chromatin fiber's observed beads-on-a-string structure. Each bead is a nucleosome containing about 160 bp of DNA wrapped around a core of 8 histones 2 each of H2A, H2B, H3, and H4 (student sketch may show the arrangement). The 160 bp wrap twice around the core octamer and 40 bp form linker DNA to connect nucleosomes. Histone H1 lies outside the core and appears to associate with DNA where it enters and leaves the nucleosome. Difficulty: 4 102. Describe the ways in which telomeres are critical to chromosome function. Ans: Telomeres prevent chromosomal shortening during replication that could dismantle vital genes nucleotide by nucleotide. They also maintain the integrity of the chromosomal ends. Broken chromosomes without telomeres are recognized as defective by the cellular DNA repair machinery. The repair machinery will frequently put the broken ends back together. Sometimes the unprotected broken ends are repaired incorrectly and may result in chromosome fusion or the chromosome may be degraded entirely. Both fusion and degradation upset proper chromosome number and function. Difficulty: 4 103. Ignoring the detailed description of how DNA polymerase functions, discuss the roles that proteins play in reproducing chromatin structure. Ans: Student may comment on the role of DNA polymerase and DNA ligase. Before DNA synthesis can occur, the chromatin fiber must unwind. Next, as DNA replication proceeds, newly formed DNA must associate with histones, either preexisting histones or recently synthesized ones that have just made their way to the nucleus. The synthesis and transport of histones must be coordinated with DNA synthesis since the nascent DNA becomes incorporated into nucleosomes within minutes of its formation. Finally, the nucleosomal DNA must interact in specific ways with a variety of proteins to compact in the same pattern as before. Student may also write about the different pattern seen in differentiating cells that allows expression of different genes. Difficulty: 4

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104. Describe the process of nucleosome decompaction that allows the transcription of RNA. Ans: Because RNA polymerase is much larger than the nucleosomes in the 300 fiber some loosening of individual nucleosomes must occur at the beginning of genes. Some of the nonhistone proteins known as transcription factors carry out this task by unwinding nucleosomes and dislodging histones from DNA at the 5' end of genes where transcription will begin. The nucleosome-free regions are now decompacted enough for RNA polymerase and other transcription factors to have access to the DNA and thus allow recognition of promoter regions and initiate gene expression. Difficulty: 4 105. Discuss how research on position effect variegation has been used to help identify the molecules involved in heterochromatin formation. Ans: Geneticists have used various procedures involving position effect variegation to identify the molecules involved in heterochromatin formation. In one procedure, they obtained mutations that either enhance the amount of variegation produced by genes positioned near heterochromatin, or diminish the amount of variegation. Enhancement reflects gene inactivation in more cells; diminishment reflects gene inactivation in fewer cells. Using molecular cloning, researchers later isolated several of the genes that had mutated, and raised antibodies against the mutant protein products of these genes. In this way, they discovered that at least some of the genes influencing heterochromatin formation encode DNA-binding proteins that localize selectively to the heterochromatin. Difficulty: 4 106. Describe the relationship between chromatin structure and gene function in eukaryotic chromosomes. Ans: Student may mention and describe position effect variegation and Barr body formation as specialized cases of the relationship between chromatin structure and gene function. The compaction of chromosomes makes DNA inaccessible to the proteins that initiate gene expression. This compaction is greatest at metaphase and anaphase, which curtails most gene transcription at these times. On the other hand decompaction precedes gene expression. The opening up and closing off of chromosomal areas depends on a dynamic network of DNA-protein interactions, which modifies the density of chromatin packaging to appropriate levels for genetic function and passage through the cell cycle. Once established, the chromatin structure that determines a gene's expression is stably transmitted to daughter cells. Difficulty: 4

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Experimental Design and Interpretation of Data 107. You examine cells with a microscope and detect that there are two Barr bodies present in each cell. What is most likely the genotype of the cells? Ans: XXX Difficulty: 4 108. You are on vacation in a remote tropical region and discover what appears to be an unusual bacterial colony but it might also be a clump of small eukaryotic organisms. You think you may have discovered a new specie and therefore bring the animal back in a plastic baggie placed on ice from your cooler. Of course, your new life form is dead by the time you arrive back in the lab but the debris can tell you a lot. Based on DNA structure, how can you tell whether or not your find is eukaryotic or prokaryotic? Ans: Several answers are possible and include digesting the DNA with DNase and determining if regular multiples of about 200 bp result (from protection by eukaryotic nucleosome formation). DNA associated proteins could be isolated and differences could indicate if the new organism was prokaryotic or eukaryotic. Difficulty: 4 109. Manipulation of Yeast Artificial Chromosomes (YAC) can be used to test hypotheses about eukaryotic chromosomal structure. What is a YAC and how would you use it to test the hypothesis that there is a minimum length requirement for proper chromosomal function? Ans: A YAC is a bacterial plasmid with a yeast centromere, origin of replication, telemetric sequences and usually a selectable marker gene inserted. Varying lengths of DNA could be inserted into a plasmid and tested for normal chromosomal function. In this manner, it had been determined that a minimum of about 100,000 bp is necessary for normal chromosomal function. Difficulty: 4

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Chapter 13Chromosomal Rearrangements and Changes in Chromosome Number Reshape Eukaryote Genomes Fill in the Blank 1. Events that reshape genomes by reorganizing the DNA sequences within one or more chromosomes are known as ____________________. Ans: rearrangements Difficulty: 2 2. ____________________, duplications, inversions, translocations, and movements of transposable elements are all types of rearrangements of chromosomal material. Ans: Deletions Difficulty: 2 3. Very large deletions are visible at the relatively low resolution of a __________________, showing up as the loss of one or more bands from a chromosome. Ans: karyotype Difficulty: 2 4. Changes in gene ____________________, the number of times a given gene is present in the cell nucleus, can create a genetic imbalance. Ans: dosage Difficulty: 3 5. An unpaired bulge of one member of a homologous pair of chromosomes during prophase of meiosis I is known as a ____________________. Ans: deletion loop Difficulty: 3 6. A recessive mutation in the mouse that prevents homozygous animals from walking in a straight line is known as the ____________________ gene. Ans: shaker-1 Difficulty: 3 7. When repeats of a region lie adjacent to each other they are called ____________________ duplications. Ans: tandem Difficulty: 2 8. Inversions that include the centromere are termed ____________________. Ans: pericentric Difficulty: 2

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9. Inversions that exclude the centromere are termed ____________________. Ans: paracentric Difficulty: 2 10. A crossover product that lacks a centromere is known as a(n) ____________________fragment. Ans: acentric Difficulty: 2 11. The type of large-scale mutation in which parts of two different chromosomes trade places is a ____________________ translocation. Ans: reciprocal Difficulty: 2 12. ____________________ is the enzyme that catalyzes transposition. Ans: Transposase Difficulty: 2 13. Organisms with four copies of a particular chromosome (2n+2) are ________________. Ans: tetrasomic Difficulty: 3 14. Down syndrome is also known as ____________________. Ans: trisomy 21 Difficulty: 2 15. If a tetraploid derives all of its chromosome sets from the same species, we call this kind of polyploid a(n) ____________________. Ans: autopolyploid Difficulty: 3 Multiple Choice 16. A) B) C) D) E) Which of the following are considered chromosomal rearrangements? inversions duplications deletions translocations all of the above Ans: E Difficulty: 1

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17. A) B) C) D) E)

Which of the following removes material from the genome? inversions duplications deletions translocations none of the above Ans: C Difficulty: 1 Which of the following adds material to the genome? inversions duplications deletions translocations none of the above Ans: B Difficulty: 1

18. A) B) C) D) E)

19. The type of chromosomal rearrangement which reorganizes the DNA sequence within one chromosome is known as a(n): A) inversion B) duplication C) deletion D) translocation E) none of the above Ans: A Difficulty: 2 20. In general, which of the following usually has a greater chance of lethality than the others? A) inversion B) duplication C) deletion D) translocation E) all have an equal chance Ans: C Difficulty: 2

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21. Sometimes a piece of one chromosome attaches to another chromosome. This is known as a(n): A) inversion B) duplication C) deletion D) translocation E) none of the above Ans: D Difficulty: 1 22. Sometimes a part of the genome moves from chromosome to chromosome. This is known generally as a(n): A) inversion B) duplication C) deletion D) translocation E) transposable element Ans: E Difficulty: 2 23. Rearrangements and changes in chromosome number may affect gene activity or gene transmission by altering the ________________________ of certain genes in a cell. A) position B) order C) number D) all of the above Ans: D Difficulty: 2 24. A) B) C) Karyotypes generally remain constant within a species because: rearrangements occur frequently. changes in chromosome number occur infrequently. genetic instabilities produced by genomic changes usually are at a selective disadvantage. D) genetic imbalances are often at a selective advantage. Ans: C Difficulty: 2 Despite selection against chromosomal variations: related species almost always have the same karyotype. related species almost always have a different karyotype. closely related species diverge by many chromosomal rearrangements. distantly related species diverge by only a few chromosomal rearrangements. Ans: B Difficulty: 2

25. A) B) C) D)

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26. In higher organisms, using genetic analysis is usually difficult to distinguish small deletions in one gene from: A) heterozygotes. B) small duplications. C) monosomies. D) point mutations. Ans: D Difficulty: 1 27. For an organism to survive a deletion of more than a few genes, it must carry a nondeleted homolog of the deleted chromosome. This is known as: A) a deletion heterozygote. B) a deletion homozygote. C) dosage compensation. D) a triplolethal chromosome. Ans: A Difficulty: 2 28. Individuals born heterozygotes for certain deletions have a greatly increased risk of losing both copies of certain genes and developing cancer. One such disease is: A) triplolethal. B) scarlet eyes. C) retinoblastoma. D) cataracts. Ans: C Difficulty: 1 29. During the pairing of homologs in prophase of meiosis I, the region of a normal, nondeleted chromosome that has nothing with which to recombine forms a so-called: A) inversion loop. B) deletion heterozygote. C) crossover suppressor. D) deletion loop. Ans: D Difficulty: 2 30. Using Drosophila polytene chromosomes and small deletions, geneticists have been able to: A) map the shaker-1 gene in Drosophila. B) assign genes to regions of one or two polytene chromosome bands. C) assign genes to regions of 100kb or less of DNA. D) all of the above Ans: D Difficulty: 2

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31. Which of the following molecular techniques could a scientist use to help locate genes on cloned fragments of DNA with deletion mutants? A) In situ hybridization B) Crossover analysis C) Southern blot analysis D) all of the above E) both a and c Ans: E Difficulty: 3 32. A) B) C) D) Duplications arise by: chromosomal breakage and faulty repair. unequal crossing over. errors in replication. all of the above Ans: D Difficulty: 1

33. During the pairing of homologs in prophase of meiosis I, the region of a chromosome bearing extra copies of a particular chromosomal region that has nothing with which to recombine forms a so-called: A) inversion loop. B) deletion heterozygote. C) duplication loop. D) deletion loop. Ans: C Difficulty: 2 34. An inversion may result from: A) a half-circle rotation of a chromosomal region following two double-strand breaks in a chromosome's DNA. B) the action of a transposable element. C) a crossover between DNA sequences present in two positions on the same chromosome in inverted orientation. D) all of the above E) none of the above Ans: D Difficulty: 2

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35. A) B) C) D)

Inversions may be hard to detect because they: never visibly change chromosome banding patterns. increase recombination in heterozygotes. do not usually cause an abnormal phenotype. normally are removed immediately in natural populations. Ans: C Difficulty: 3 Which of the following does not happen when an intragenic inversion occurs? One part of the gene is relocated to a distant region of the chromosome. One part of the gene stays at its original site. Homozygotes for the inversion do not survive. The gene's function is not disrupted. Ans: D Difficulty: 3

36. A) B) C) D)

37. When a crossover occurs within the inversion loop of a pericentric inversion each recombinant chromatid will have: A) a single centromere. B) a duplication of one region. C) a deletion different from the one of duplication. D) all of the above Ans: D Difficulty: 2 38. Robertsonian translocations result from which of the following? A) Breaks at or near the centromeres of two acrocentric chromosomes followed by the reciprocal exchange of broken parts. B) A part of one chromosome becomes attached to a non-homologous chromosome. C) Unequal crossing over during meiosis. D) The fusion of two small chromosomes end-to-end such that a double centromere occurs. Ans: A Difficulty: 2 39. A) B) C) D) Which of the following does not usually show a problem during meiosis? translocation heterozygotes translocation homozygotes paracentric inversion pericentric inversion Ans: B Difficulty: 1

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40. Of the following segregation patterns, which one is most likely to result in a normal zygote? A) alternate B) adjacent-1 C) adjacent-2 D) nondisjunction Ans: A Difficulty: 2 41. A) B) C) D) The condition of semisterility is most closely associated with: chromosomal duplications. pericentric inversions. translocation heterozygotes. translocation homozygotes. Ans: C Difficulty: 2 Translocations can help: determine linkage groups. aid in the diagnosis and treatment of certain cancers. map important genes. all of the above Ans: D Difficulty: 1 Down Syndrome can result from: three copies of chromosome 21. a translocation of a part of chromosome 21. a reciprocal translocation between any two autosomes. a and b a, b, and c Ans: D Difficulty: 2 Which of the following do translocations and inversions not have in common? don't alter the amount of DNA in the genome ability to alter gene function use of inversion loops during crossing over catalysts of speciation Ans: C Difficulty: 2

42. A) B) C) D)

43. A) B) C) D) E)

44. A) B) C) D)

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45. A transposition is considered a cytologically invisible sequence rearrangement. With which of the following does it share this property? A) small deletion B) large duplication C) inversion D) translocation Ans: A Difficulty: 2 46. A) B) C) D) Barbara McClintock is most closely associated with which of the following? The initial discovery of genetic transposition. The discovery of transposable elements in corn. The mutation rate in translocation heterozygotes. The demonstration of the presence of transposable elements in polytene chromosomes. Ans: B Difficulty: 1

47. Transposable elements have many things in common. Which of the following is not a usual characteristic of them? A) Typically smaller than 50 bp. B) May be present in a genome from one to thousands of times. C) Are found only in a select group of organisms. D) Need not be sequences that do something for the organism. Ans: A Difficulty: 3 48. Retroposons and retro-viruses have structural parallels. Which of the following also shares structural parallels with them? A) tRNA B) DS-DNA C) rRNA D) mRNA Ans: D Difficulty: 2 49. Which of the following is a possible effect that a transposable element may have on a gene? A) Shift the reading frame. B) Diminish the efficiency of splicing. C) Provide a transcription stop signal. D) all of the above Ans: D Difficulty: 2

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50. A) B) C) D)

Which of the following is not an aneuploidy? monosomy tetraploid trisomy tetrasomy Ans: B Difficulty: 1

51. The most common human aneuploidy is trisomy 21, Down syndrome. All of the effects listed below may be seen in this syndrome except: A) death always by age 25. B) mental retardation. C) skeletal abnormalities. D) heart defects. E) increased susceptibility to infection. Ans: A Difficulty: 2 52. A) B) C) D) E) Which of the following sex chromosome aneuploidies is not usually seen in live births? XO XXY YO XXX None of the above Ans: C Difficulty: 2

53. Turner syndrome, XO, is a sex chromosome aneuploidy. Of the effects listed below, which one is not usually seen in this syndrome? A) unusually short stature B) infertility C) skeletal abnormalities D) unusually long limbs Ans: D Difficulty: 2 54. In Drosophila, a gynandromorph, which is composed of equal parts male and female tissue, results from: A) an XX female losing one X chromosome during the first mitotic division after fertilization. B) an egg carrying an X chromosome fertilized by a Y-carrying sperm. C) a normal egg fertilized by both an X-carrying sperm and a Y-carrying sperm. D) the fusion of a female embryo with a male embryo. Ans: A Difficulty: 3

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55. A) B) C) D)

Which of the following is not an example of a euploid condition? triploidy diploidy Down syndrome tetraploidy Ans: C Difficulty: 1 Triploid organisms usually result from: the union of haploid and diploid gametes. unequal disjunction during embryogenesis. propagation of fused cell lines. fusion of three gametes simultaneously. Ans: A Difficulty: 2

56. A) B) C) D)

57. During mitosis, if the chromosomes in a diploid tissue fail to separate after replication, the resulting daughter cells will be: A) monoploid. B) tetrasomic. C) triploid. D) tetraploid. Ans: D Difficulty: 2 58. Hybrids in which the chromosome sets come from two distinct, though related, species are known as: A) autopolyploids. B) allopolyploids. C) amphiploids. D) bivalents. Ans: B Difficulty: 2 59. The genus Triticale is a new genus of the various allopolyploid hybrids between wheat and rye. Some of the members of this genus show agricultural promise because: A) wheat has a high yield. B) rye adapts well to unfavorable environments. C) wheat has a high level of protein. D) rye has a high level of lysine. E) all of the above Ans: E Difficulty: 2

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60. A) B) C) D)

Which of the following rarely, if ever, results in a positive force for evolution? polyploidy allopolyploidy trisomy amphidiploidy Ans: C Difficulty: 2

Matching Match the following descriptions with the terms below a. inversion b. duplication c. deletion d. translocation e. transposable element 61. A piece of genetic material that moves from place to place in the genome. Ans: e Difficulty: 2 62. A change in the genome whereby new material is added to the genome. Ans: b Difficulty: 1 63. A change in the genetic material where a DNA sequence changes direction. Ans: a Difficulty: 1 64. A decrease of genetic material in the genome. Ans: c Difficulty: 1 65. A piece of chromosome attaches to another chromosome. Ans: d Difficulty: 2 Match the following descriptions with the terms below a. retroposon b. transposon c. transposable element d. transposase

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66. Any DNA segment that moves about in the genome. Ans: c Difficulty: 3 67. Moves in the genome with the aid of an RNA intermediate. Ans: a Difficulty: 2 68. Moves DNA directly. Ans: b Difficulty: 3 69. An enzyme that catalyzes a transposition event. Ans: d Difficulty: 1 True or False 70. When comparing mouse and human Giemsa-stained karyotypes, we see no conservation of banding patterns. Ans: True Difficulty: 2 71. Karyotypes generally remain constant within a species because rearrangements and changes in chromosome number occur infrequently. Ans: False Difficulty: 3 72. Changes in chromosome number include aneuploidy, monoploidy, polyploidy, and duplications. Ans: False Difficulty: 2 73. Deletion may arise from errors in replication, from faulty meiotic or mitotic recombination, and from exposure to X-rays. Ans: True Difficulty: 2 74. Homozygosity for a deletion is often, but not always, lethal. Ans: True Difficulty: 2 75. Recessive mutations can often be covered by deletions in heterozygotes. Ans: True Difficulty: 2

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76. Most duplications have no obvious phenotypic consequences and can be detected only by cytological or molecular means. Ans: False Difficulty: 2 77. Duplication of chromosomal segments rarely has an effect on the evolution of genomes. Ans: True Difficulty: 2 78. Crossing-over within an inversion loop produces aberrant recombinant chromatids. Ans: False Difficulty: 3 79. Reciprocal translocations are usually phenotypically abnormal because they have neither lost nor gained genetic material. Ans: True Difficulty: 1 80. A hallmark of transposons is that their ends are inverted repeats of each other. Ans: False Difficulty: 3 81. The mouse genome has high synteny with the human genome since about 170 DNA blocks are simply rearranged between the two genomes. Ans: True Difficulty: 2 82. Euploid cells contain only incomplete sets of chromosomes. Ans: False Difficulty: 2 83. Down syndrome is an example of triploidy. Ans: False Difficulty: 2 84. Genetic imbalance results from polyploidy. Ans: False Difficulty: 1 85. An acentric fragment is an inversion cross-over product lacking a centromere. Ans: True Difficulty: 1

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Short Answer 86. Explain how data from the linkage groups of the mouse can be used as a resource for assessing human linkage groups. Ans: Because virtually all genes cloned from the mouse genome are conserved in the human genome and vice versa, it is possible to construct linkage maps for the two genomes from the same set of markers. Comparisons of the mouse and human linkage groups allow one to see a picture somewhere between complete correspondence and unrelatedness. Genes closely linked in the mouse tend to be closely linked in humans, but genes that are less tightly linked in one species tend not to be linked at all in the other. This shows that even though mice and humans diverged about 65 million years ago, the DNA sequences in many regions are very similar. Difficulty: 4 87. Explain the differences between chromosomal rearrangements and changes in chromosome number. Cite at least one example of each. Ans: Chromosomal rearrangements reorganize the DNA sequences within one or more chromosomes. Changes in chromosome number involve losses or gains of entire chromosomes or sets of chromosomes. (Student may cite as an example of rearrangements: deletion, duplication, inversion, translocation, and transposable elements. For changes in chromosome number student may cite an aneuploidy such as a monosomy or trisomy, monoploidy, or polyploidy.) Difficulty: 4 88. Describe how an inversion heterozygote can reduce the number of recombinant progeny. Ans: When inversion heterozygotes have chromosomes pair up during meiosis, an inversion loop is formed to allow the tightest possible alignment of homologous regions. This always produces aberrant recombinant chromatids. Two inversion cases are possible pericentric and paracentric. In a pericentric crossover within the inversion loop each recombinant will carry a duplication of one region and a deletion of another. This abnormal dosage of some genes will result in abnormal gametes and if they fertilize normal gametes, zygotes may die because of genetic imbalance. In a paracentric crossover within the inversion loop the recombinant chromatids will be unbalanced in both gene dosage and centromere number. (Student may then explain how centromere number can result in genetically unbalanced gametes such as what acentric and dicentric chromatids would produce.) Difficulty: 4

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89. Discuss the several effects that translocations and inversions have in common. Ans: Both translocations and inversions change genomic position without affecting the total amount of DNA. If a breakpoint of either one is within a gene, the gene function may be altered or lost. Both types may produce genetically imbalanced gametes that may negatively affect a zygote or developing embryo. (Student may explain at this point the differences between how the imbalanced gametes are produced.) Because both reduce viable progeny and heterozygotes, they may play a role in speciation and evolution. Difficulty: 4 90. Explain the possible effects that a transposable element may have on a gene. Ans: Insertion of a transposable element near or within a gene can affect gene expression and alter phenotype. For example, a B type hemophilia occurs after insertion of Alu into the gene encoding clotting factor IX. Secondly, the effect of insertion depends on what the element is and where the insertion point is. If insertion is into a protein-coding exon, the reading frame may shift or a stop codon may be introduced. Insertion into an intron may lower the efficiency of splicing, which may result in removal from the transcript that could lower production of a normal polypeptide. A stop signal could also affect genes downstream. Upstream insertion into a regulatory gene could affect gene function in various ways also. Difficulty: 4 91. Explain the mechanism by which aneuploidy occurs. Ans: Aneuploidy occurs because of meiotic nondisjunction either in meiosis I or meiosis II. In meiosis I if homologs do not separate all gametes produced will contain an error. Two of the gametes will contain both homologs and two will contain neither. When fertilization of a normal gamete occurs by either of these abnormal gametes, aneuploidy results. Half of the zygotes will be trisomic and half will be monosomic. Meiotic nondisjunction during meiosis II will produce two normal and two abnormal gametes. If fertilization occurs with either of the abnormal gametes, aneuploid zygotes are produced. Difficulty: 4 92. Discuss why triploid organisms are almost always sterile. Ans: (Student may explain how triploids occur.) Triploids are almost always sterile because meiosis produces mostly unbalanced gametes. During the first meiotic division in a triploid germ cell, three sets of chromosomes must segregate into two daughter cells. Most likely one daughter will end up with two chromosomes and the other will have only one of any one set of homologs. Some cells will have two of some chromosomes and the normal one of others. Many combinations of incorrect number of chromosomes will occur with very little chance of the normal amount. Most gametes will be aberrant and will have a reduced chance of producing viable offspring. Difficulty: 4

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93. Discuss how deletions and duplications may contribute to evolution. Ans: General examples of how chromosomal rearrangements might contribute to evolution: Deletions a small deletion that moves a coding sequence of one gene next to a promoter or other regulatory element of an adjacent gene may, rarely, allow expression of a protein at a novel time in development or in a novel tissue. If the new time or place of expression is advantageous to the organism, it might become established in the genome. Duplications a duplication will provide at least two copies of a gene. If one copy maintains the original function, the other could conceivably acquire a new function that would probably be related to the original function. Many examples can be seen in higher plants and animals. (Students may also write about the evolutionary contributions of the other chromosomal rearrangements and might even mention the role of changes in chromosome number.) Difficulty: 4 94. Why do inversions act as cross-over suppressors? Ans: Inversions act as cross-over suppressors because only progeny that do not recombine within an inversion loop will survive. Difficulty: 4 95. What is a balancer chromosome? Ans: A balancer chromosome is a special chromosome often created by the use of Xrays for the purpose of genetic manipulation; these chromosomes often carry multiple, overlapping inversions that enable researchers to follow them through crosses, and a recessive lethal mutation that prevents the survival of homozygotes. Difficulty: 4 96. What is the difference between alternate and an adjacent-1 segregation or an adjacent-2 segregation pattern? Ans: An alternate segregation pattern results in balanced chromosomes while adjacent 1or 2 patterns yield chromosomes that are unbalanced. Difficulty: 4

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Experimental Design and Interpretation of Data 97. We now know that several organisms have a high degree of synteny at the genomic level. You wish to test the hypothesis that the laboratory mouse and human share genomic similarities. What tests would you complete and given that we now know that the mouse and human genomes are highly syntenic, what results would you expect? Ans: Karyotype analysis can be used to test the hypothesis of genomic similarities however, only animals that have high homology will show similar banding patterns. Therefore, FISH (fluorescence in situ hybridization) would be a more useful technique to determine synteny. The mouse and human genomes are similar in that approximately 170 similar fragments an average length of about 18 Mb are simply rearranged (this is not visible in a karyotype). Difficulty: 4 98. You are mapping traits in your favorite organism but unbeknownst to you, your laboratory model organism contains a rare deletion. How will your mapping results be affected? Ans: The mapping distance will appear smaller than the actual physical distance in the wild-type organism. Difficulty: 4 99. You have discovered an altered phenotype and cloned the gene responsible. However, the gene you cloned appears to have an unusual sequence in it. In order to determine the chromosomal location of your new gene, you perform FISH, using only the unusual sequence, on several animals. To your surprise, the FISH results suggest that each animal contains the gene on a different chromosome. How would you interpret your results. Ans: The unusual sequence is a transposon and your new phenotype arose via the disruption of its gene by the transposon. Difficulty: 4 100. You are a master gardener and your favorite tomato plant is very sensitive to a pesticide called DEADBUG. You wish to make your special tomato plants resistant to the pesticide which you spray on other bushes in your garden. Using microbial techniques give sufficient and complete details of how you would do this (include ploidy status). Ans: Haploid pollen grains are cold treated and plated on agar plates. The resulting embryoids are treated with hormone in liquid culture and eventually grown as a monoploid plant. The plant is treated with a mutagen to induce mutations that can result in insensitivity to the pesticide. Somatic cells are removed from the treated plant and plated on agar containing DEADBUG. Only cells resistant to DEADBUG will grow. Again the embryoid is hormone treated and grown into a resistant monoploid plant. Treatment with colchicine will allow duplication of chromosomes without separation resulting in a normal diploid plant. Difficulty: 4

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Chapter 14The Prokaryotic Chromosome: Genetic Analysis In Bacteria Fill in the Blank 1. The three major evolutionary lineages of living organisms are __________, __________, and __________. Ans: bacteria, archea, eukaryotes Difficulty: 1 2. Of the three major evolutionary lineages of living organisms, __________ and __________ are much more similar to each other than either of them are to __________. Ans: bacteria, archea, eukaryotes Difficulty: 1 3. Unchecked growth of E. coli cells would generate a mass of bacteria equal to the mass of the earth in __________ days. Ans: two Difficulty: 2 4. A(n) __________ is unable to grow on __________ medium without at least one added nutrient. Ans: auxotroph, minimal Difficulty: 2 5. The process of spontaneous uptake of DNA from the surrounding medium is known as __________ __________, while the process of __________ __________ requires laboratory procedures that make cell walls and membranes permeable to DNA. Ans: natural transformation, artificial transformation Difficulty: 2 6. The process by which N. gonorrhoeae obtained penicillin resistance is an example of __________ __________. Ans: natural transformation Difficulty: 2 7. IS elements on F plasmids allow homologous recombination between an F plasmid and the E. coli chromosome to create a(n) __________ bacterium. Ans: Hfr Difficulty: 1 8. Conjugation can produce recombinant cells only if an __________ number of crossovers occurs. Ans: even Difficulty: 3

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9. Bacteria can exchange genetic information between different strains through __________, __________, and __________. Ans: transformation, conjugation, transduction Difficulty: 1 10. The endosymbiont theory proposes that __________ and __________ in eukaryotes originated when free-living bacteria were engulfed by primitive nucleated cells. Ans: mitochondria, chloroplasts Difficulty: 1 11. DNA replication in E. coli begins at __________ and proceeds __________ around the circular genome to the terminator region. Ans: oriC, bidirectionally Difficulty: 2 12. In __________ transduction, phages can package any part of the donor genome. __________ transduction is a property of lysogenic bacteriophages, which can package only host genes adjacent to the integrated prophage genome. Ans: generalized, specialized Difficulty: 2 13. Although bacterial cells are haploid, F' plasmids carrying bacterial genes can create specific regions of __________ __________. Ans: partial diploidy Difficulty: 2 14. The behavior of seeking out or avoiding chemicals is known as __________. Ans: chemotaxis Difficulty: 1 15. During chemotaxis, the one-second, one-way movement is called a __________ __________; the abrupt reorienting movement is a __________. Ans: straight run, tumble Difficulty: 2 16. Bacteria move up or down a concentration gradient by executing a __________ __________ __________ in which the time spent in a __________ __________ is longer after the addition of __________ and shorter after the addition of __________. Ans: biased random walk, straight run, attractant, repellent Difficulty: 3

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Multiple Choice 17. Which of the following is a bacterial disease common among sexually active individuals. A) gonorrhea B) Haemopilus infections C) pneumonia D) pancreatis E) jaundice Ans: A Difficulty: 1 18. Which of the following is an infection in newborn infants when born to mother with gonorrhea. A) pneumonia B) brain lesions C) eye infection D) heart disease E) tendon inflammation Ans: C Difficulty: 1 19. A) B) C) D) E) ________ are small circular pieces of DNA frequently found in bacteria. Transposons Insertion sequences Plasmids Bacteriophage Centromere Ans: C Difficulty: 1

20. Penicillin works by inhibiting an enzyme involved in synthesis of cell walls in bacteria. Mutations result in changes in the amino acid sequence of the enzyme so that it no longer binds penicillin and cells are no longer inhibited. What will happen to a cell with this mutation if no penicillin is present in the growth environment? A) Nothing, it will not be selected and will remain a very minor component of the microflora. B) Mutant bacterium will come to dominant the population. C) Mutant bacterium will not grow normally. D) Mutant bacterium will not form a normal cell wall. E) None of these will happen. Ans: B Difficulty: 2

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21. Another mutation for penicillin resistance is in an enzyme called a -lactamase. Penicillin is a -lactam. Changes in the amino acid composition of the enzyme result in it being able to degrade penicillin so it can't inhibit cell wall synthesis. What will happen to a cell with this mutation if penicillin is present in the environment? A) Nothing, it will not be selected and will remain a very minor component of the microflora. B) Mutant bacterium will come to dominant the population. C) Mutant bacterium will not grow normally. D) Mutant bacterium will not form a normal cell wall. E) None of these will happen. Ans: B Difficulty: 2 22. We isolate nine different mutants unable to make histidine. They map in different locations, by genetics means we can show there are nine different genes in the pathway. How many enzymes can we anticipate finding in this pathway? A) 1 B) 3 C) 6 D) 9 E) 12 Ans: D Difficulty: 1 23. A bacterium is found that is resistant to the antibiotic gentimycin. The bacterium was isolated in a hospital where patients were routinely given gentimycin for a variety of infections. What was the selective pressure driving development of this resistant population? A) Presence of gentimycin in the environment. B) High mutation rate for the bacterium. C) Growth situation for the bacterium. D) Patients not receiving antibiotic provided source of bacteria. E) None of the above Ans: A Difficulty: 1 24. A) B) C) D) E) The bacterial chromosome is: circular. covalently closed. 1 strand DNA. contains mobile sequences. all of the above. Ans: E Difficulty: 1

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25. Organisms that lack a nuclear membrane and have no membrane-enclosed organelles are termed: A) bacteria. B) archaea. C) prokaryotes. D) eukaryotes. E) none of the above Ans: C Difficulty: 1 26. Bacterial numbers in the large intestine can exceed 1012 /gm in feces. There are perhaps a half dozen species that predominate this flora and hundreds that play a very small role. The bacteria grow and die, often lyse releasing DNA into the environment. What protects viable bacteria from this DNA? A) Largely impermeable cytoplasmic membrane. B) Capsule composed of polysaccharide surrounding the cell. C) Restriction endonucleases in the cells that degrade foreign DNA. D) Nucleases excreted by bacteria to degrade DNA into sugar and the bases. E) None of the above Ans: C Difficulty: 2 27. We spread 109 bacteria on a plate with 25 g streptomycin/ml media. We get four colonies to grow. These colonies include bacteria that are: A) wild type. B) resistant to streptomycin. C) resistant to all antibiotics. D) able to grow in unusual circumstance. E) none of the above Ans: B Difficulty: 1 28. We grow up the streptomycin resistant (Strr) cells to 109 and plate them on medium with 25 g/ml gentimycin. We get six colonies to grow. These cells should be: A) Strr. B) Gen r. C) Strr Gen r. D) wild type. E) none of the above. Ans: C Difficulty: 3

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29. We plate bacteria out on a plate covered with a normally virulent bacteriophage. Two colonies form. These bacteria in the colonies are now: A) phage resistant. B) phage sensitive. C) wild type. D) all of the above E) none of the above Ans: A Difficulty: 1 30. How many plantings would it take to make a bacterium resistant to streptomycin, gentimycin and a bacteriophage? A) 1 B) 2 C) 3 D) 4 E) 5 Ans: C Difficulty: 2 31. If resistance to streptomycin occurs about one in 109 cells (one amino acid gets changed in one ribosomal protein), resistance to gentimycin occurs about one in 109 cells, how often could you get double mutants, one that was mutated in both functions? A) 109 B) 1018 (109 109) C) 1 D) cannot estimate E) none of the above Ans: B Difficulty: 2 32. The Ames test for carcinogens uses his- mutants of S. typhimurium. Carcinogens are mutagens, and cause mutations. These mutants can be reverted, made to be his+ with common mutagens. We spread 108 bacteria on a plate and then add the putative mutagen/carcinogen on a piece of filter paper and count the colonies around the filter paper. Lots of colonies mean lots of mutations, an effective mutagen. We test two chemicals, A and B. One g/ml A causes 14 colonies to appear, one g B causes 96 colonies to form. Which is the most potent mutagen? A) A B) B C) A or B D) none of the above E) both A and B Ans: B Difficulty: 3

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33. A) B) C) D) E)

A strain of E. coli is trp- his- lac-. Which medium would this bacterium grow on? lactose + histidine + tryptophan glucose + histidine + tryptophan maltose + histidine + tryptophan minimal glucose, no histidine, no tryptophan b and c Ans: B Difficulty: 2

34. What must an ORF contain to indicate that it codes for a protein? A) Shine Delgarno sequence immediately upstream from the first codon to bind the ribosomes to start translation. B) Met codon, first amino acid. C) A stop codon, to indicate the end of the protein. D) A sequence indicative of a real protein, not simply poly phenylalanine. E) All of the above Ans: E Difficulty: 2 35. Transposons are like insertion sequences but include a gene that confers selective advantage to the bacterium, resistance to an antibiotic or to a heavy metal. Tn10 confers resistance to tetracycline. We can isolate a Trp- mutant of E. coli by introducing a vector for Tn10 (a plasmid that won't replicate in E. coli, a bacteriophage with the transposon), growing for many generations and plating out on medium with tetracycline. This will select the Tetr mutants, presumably from the transposon. Then the Tetr mutants can be tested for their ability to grow with and without tryptophan. We have introduced Tn10 into wild type E. coli and want to select mutants unable to use lactose. We can do this by plating the cells on: A) tetracycline. B) tetracycline + lactose. C) tetracycline + glycerol + X-gal. D) tetracycline + glucose. E) tetracycline + maltose. Ans: C Difficulty: 3 36. E. coli DNA introduced into S. typhimurium occasionally undergoes recombination, but this is very rare. Why is this so rare? A) Restriction endonuclease in S. typhimurium degrade the E. coli DNA. B) The DNA is dissimilar enough to make recombination less likely. C) Some genes in E. coli are not found in S. typhimurium. D) A region found in E. coli is simply absent from S. typhimurium. E) All of these are good explanations. Ans: E Difficulty: 2

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37. We run a cross Hfr A+B+C+D+E+ F-A-B-C-D-E-. After 5 minutes we get F-B+, after 10 minutes F-B+D+, after 15 minutes F-B+D+E+, after 20 minutes, F-B+D+E+A+, after 25 minutes F-B+D+E+A+C+. The gene order is: A) ABCDE. B) BDEAC. C) BDACE. D) EDCAB. E) EAEDB. Ans: B Difficulty: 3 38. We run a cross Hfr A+B+C+D+E+ F-A-B-C-D-E-. We count numbers of colonies with each trait in the F- recombinants. We get 122 B+ 102 C+ 88 E+, 65 D+, 45 A+, 14 C+. What is the gene order (this is called mapping by frequency)? A) ABCDE B) EDCBA C) AEBCD D) BCEDAC E) AEDCB Ans: D Difficulty: 3 39. In the A region, we also find genes M and K. With transduction we run a cross: P1 (wild type) A-M-K-. We get 63 A+K+, 11 M+K+, and 33 M+K+. What is the gene order for these three markers? A) AMK B) AKM C) AMK D) MKA E) cannot determine Ans: D Difficulty: 3 40. In artificial transformation in E. coli, we add lots of calcium to the DNA. Why is this done? A) To inactivate any nucleases secreted by the cell. B) To act as a counter ion for the - charges on DNA. C) To keep RNA from hybridizing with DNA. D) To keep the DNA single stranded. E) None of the above Ans: B Difficulty: 2

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41. We have a mutant strain, A-B-. If these mutants revert, return to wild type (happens lots with missense mutations, wrong amino acid) 1 10-7, what is the probability of having both genes revert? A) 1 10-7 B) 1 10-7 1 10-7 = 10-14 C) 1 10-3 D) 1 10-6 E) cannot determine Ans: B Difficulty: 2 42. We grow two bacteria together in a rich, undefined medium. One is A-B-, one is C-D-. We grow to 109 cells/ml. We find about 1,000 cells will grow on minimal medium, that is are A+B+C+D+. What must have happened? A) A-B- reverted B) C+D+ reverted C) genetic exchange occurred D) any of these could have occurred E) cannot determine Ans: C Difficulty: 1 43. We grow the cells together with DNAase present. We still find the A+B+C+D+. Which mechanism do we know is not occurring? A) transduction B) transformation C) conjugation D) mitosis E) meiosis Ans: B Difficulty: 1 44. We grow the cells together with a 0.44 m filter separating the cells. We don't find the A+B+C+D+. Which mechanism is probably involved in this genetic exchange? A) transduction B) transformation C) conjugation D) mitosis E) meiosis Ans: C Difficulty: 1

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45. We've got an Hfr strain with the plasmid inserted near the trp (tryptophan) locus. We run a cross of this Hfr strain with a F- trp- strain. We isolate a trp+ strain that can readily donate this trait to other trp- strains. No other traits are transferred. What has happened? A) generated a F'trp plasmid B) typical Hfr mating C) transduction occurs D) transformation occurs E) cannot determine from this information Ans: A Difficulty: 2 46. By transduction we run a cross between A+B+C+ and A- B-C-. We run the cross and get 179 A+B+C+, 173 A-B-C-, 52 A-B+C+, 46 A+B-C-, 22 A-B+C-, 4 A+B+C- and 2 A-B-C+. What is the gene order for these three genes (this is a classical three point cross)? A) ABC B) ACB C) BAC D) CBA E) none of the above Ans: B Difficulty: 4 47. Bacteriophage normally integrates in a region called int. It is possible to isolate mutants that lack this site. In these mutants the phage will integrate at random at any point in the chromosome. And like the wild type situation, occasionally when it excises from the genome, it carries adjacent genes. Thus a with nearly any gene can be isolated. We have made a phage lysate in a int mutant. We take the lysate and infect a trp- mutant with the lysate. We pick one colony that grows on minimal medium. What has happened? A) A with trp attached has infected the cell. B) We have a revertant. C) Conjugation with wild type bacteria has occurred. D) Transformation with wild type bacteria has occurred. E) None of the above Ans: A Difficulty: 2

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48. We are working with wild type . We prepare a lysate on wild type cells and infect a gal- strain and get a few colonies that grow on minimal galactose. What has happened? A) generate a dgal phage B) isolated a revertant C) conjugation D) transformation E) none of the above Ans: A Difficulty: 1 49. Transposon mutagenesis generates what act like deletion mutants. The function is completely lost. The transposon has jumped into the middle of the gene and it is no longer functional. A student has a mutant bacterium that is resistant to penicillin, it makes a -lactamase that recognizes penicillin and cuts it. He infects this cell with Tn5. He finds a cell that is now resistant to kanamycin (the antibiotic carried by Tn5) but is no longer resistant to penicillin. What has happened? A) Transposon alter bacterial metabolism. B) Transposon alters how bacterium makes cell walls. C) Transposon hopped into the gene for the -lactamase. D) Transposon carries information for penicillin resistance in another form. E) cannot determine Ans: C Difficulty: 2 50. We have isolated 15 mutant bacteria unable to use maltose. All 15 mutations map in the same region by conjugation. We have tested the mutant for two enzymes in maltose metabolism and find at least one of the mutants lacks one of the enzymes, other mutants lack the other. What does this suggest? A) Lots of enzymes in maltose metabolism. B) All the genes for maltose metabolism are in a cluster, could be one operon. C) There are genes scattered all over, we've simply found one set of mutants. D) Maltose transport is very complex, these are transport mutants. E) None of the above Ans: B Difficulty: 2

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51. We have determined that two genes are two minutes apart by mating and co-transduce about 10% of the time with phage P1. We introduce a plasmid with an insertion sequence in it. After many generations, we find the two genes are now three minutes apart and no longer co-transduce at any frequency. What can we conclude? A) Insertion sequence has inserted between the genes. B) DNA has migrated to location between the genes and recombined. C) An unidentified gene has mutated preventing co-transduction. D) DNA has a loop between the genes that alters its ability to recombine. E) Cannot determine Ans: A Difficulty: 2 52. We are interested in how a bacterium handles osmotic stress. We mutagenize with a transposon, isolate the antibiotic resistant mutants and replica plate looking for bacteria no longer able to grow in medium with 0.4 M NaCl (can't handle osmotic stress). How can we clone this mutation? A) Use a hybridization probe using a gene in E. coli known to be involved in osmoregulation. B) Use an immunological probe using a protein from E. coli known to be made when cells are osmotically stressed. C) Use a hybridization probe using Tn5 DNA. D) Use a genetic complementation probe, make a gene library form the mutant and test the genes in wild type bacteria. E) None of the above Ans: C Difficulty: 3 53. The bacteriophage Mu is a transposon, 44 kb long with inverted repeats at either end, a transposase gene. It replicates by jumping from one gene to another in the genome of the bacteria. With each jump it induces a mutation. We introduce Mu into E. coli and get a Lac- mutant. How can we determine if this was induced by Mu? A) Clone the gene, sequence, and look for Mu DNA sequences. B) Clone the gene, introduce the plasmid with the cloned gene to another host and see if any mutants. C) Make a gene library and probe the library with Mu DNA and with lac DNA and see if the same fragment binds both pieces of DNA. D) Run an Hfr conjugal cross and see if genes to either side of lacT are a minute further apart. E) All of these approaches would work. Ans: E Difficulty: 3

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54. There are promiscuous plasmids, plasmids that can be interchanged between very different bacteria. These often pick up transposons carrying antibiotic resistance. We are in a hospital that has an outbreak of a variety of bacteria carrying resistance to streptomycin, gentamycin, and penicillin. How could we determine how this was occurring? A) Test all the resistant bacteria for a plasmid. B) See if the same plasmid could be isolated from all resistant bacteria. C) See if the plasmid isolated from the bacteria conferred restance to a test bacterium. D) With restriction mapping, see if the plasmid seemed to contain transposons known to carry resistance to these antibiotics. E) All of these would be good approaches. Ans: E Difficulty: 3 55. Resistance to streptomycin occurs about once in 109 cells in E. coli. Resistance to penicillin occurs about once in 108. How often would a spontaneous double mutant occur? A) Once in 109 B) Once in 108 C) Once in 1017 D) Once in 1072 E) Cannot determine Ans: C Difficulty: 2 56. We want to isolate mutants temperature sensitive for utilization of glucose. What kind of mutagen should we use? A) transposon B) uv to cause deletions C) nitrous acid to cause missense mutations D) frame shift mutagens E) none of the above Ans: C Difficulty: 2

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57. There are protozoa that engulf cyanobacteria (photosynthetic bacteria) and maintain a given number of the cyanobacteria even when they divide. The protozoa divide only after the cyanobacteria have doubled their number. The cyanobacteria excrete glucose that the protozoa consume. This is a good example of: A) parasitism by protozoa. B) example of how protozoa consume particulate food. C) establishment of an endosymbiotic relationship. D) symbiosis between two microorganisms. E) none of the above Ans: C Difficulty: 1 58. What would happen if a transposon were to jump into the origin of the bacteria genome? A) Transposon would be replicated like the genome. B) Transposon would jump to another location. C) Transposon would inactivate the origin, no DNA replication possible. D) Transposon would express its genes constituitively. E) None of the above Ans: C Difficulty: 1 59. Bacteria like E. coli do not normally take up foreign DNA, they do not have the proteins required to bring the DNA into the cell. We get around this with special washing procedures, with electroporation. These treatments probably affect which aspect of the cell? A) The cell wall, open it to permit DNA to pass through. B) The cytoplasmic membrane, alter it to permit DNA to pass through. C) The nucleases in the cell, inactivate them. D) Inactive RNA polymerase so genes don't get expressed as it happens. E) None of the above Ans: B Difficulty: 2 60. Two bacteria grow together. One appears to donate DNA to the other. One of the bacteria contains a bacteriophage that is normally quiescent but occasionally forms a plaque. What sort of genetic exchange is occurring? A) transformation B) conjugation C) transduction D) electroporation E) none of the above Ans: C Difficulty: 1

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61. We think we might have an insertion sequence in a gene causing a mutation. We know the sequence of insertion sequence. How could we determine if the mutation is caused by an insertion sequence? A) Clone the gene and sequence. B) Clone the gene and probe with insertion sequence DNA. C) Make PCR mers and see if a ds DNA product is made by the cloned gene. D) Carry out transduction of adjacent genes and see if they are further apart. E) All of the above Ans: E Difficulty: 3 62. We want to isolate a temperature sensitive DNA polymerase, at 30o the enzyme works, at 40o it doesn't. What sort of mutagen should be used? A) Screen for spontaneous missense mutations. B) Use a missense mutagen like nitrous acid. C) Introduce a transposon. D) Clone the gene and introduce an insertion sequence. E) None of the above Ans: B Difficulty: 1 63. Bacteriophage proliferate in the host cell and then lyse the cell when they have perhaps 100 new phage. How many phage could be produced from a culture with 109 bacteria? A) 109 B) 1010 C) 1011 D) 1012 E) 1013 Ans: C Difficulty: 2 64. We have isolated a mutation in E. coli that makes the bacterium unable to grow with high osmolarity. How can we map this gene, the first step? A) conjugation B) transformation C) transduction D) transposon mutagenesis E) none of the above Ans: A Difficulty: 1

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65. Which technique is used to make a copy of the colonies on a petri plate? One plate can be analyzed by a destructive method and the other retained to have the cells for future use. A) penicillin selection B) replica plating C) bifurcated plating D) none of the above Ans: B Difficulty: 1 66. Early in the history of bacterial genetics, it was found that mutations in a pathway usually mapped in the same region (certainly the same region by conjugation). These clusters of genes were called operons. How would individual genes in each operon be mapped to determine the gene order? A) transduction B) transformation C) high resolution conjugation D) a and b E) b and c Ans: D Difficulty: 1 67. A) B) C) D) How do you isolate a bacterial mutant resistant to streptomycin? Plate bacteria on agar medium containing streptomycin. Replicate plate on regular medium and medium with streptomycin. Grow cells to mid log phase, add streptomycin and penicillin. Grow cells to late stationary phase, add streptomycin, measure respiration in representative colonies. E) none of the above Ans: A Difficulty: 1

68. Rhizobia are bacteria that live symbiotically in the roots of leguminous plants. It has been proposed that some enzymes in the bacteria were derived from the plant. What mechanism would most likely have been involved in this? A) transduction B) transformation C) conjugation D) cannot determine Ans: B Difficulty: 2

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69. Many years ago Frederick Griffith isolated a mutant of Streptococcus pneumoniae that was not pathogenic. It did not make a polysaccharide capsule surrounding the cell. Griffith showed that he could mix dead pathogenic cells with live non-pathogenic cells and isolate pathogenic cells. Oswald Avery went on to determine which chemical in the dead cells conferred pathogenicity back to the live mutant cells? A) polysaccharide B) phospholipids C) protein D) RNA E) DNA Ans: E Difficulty: 1 70. We have three genes A, B and C. By transformation we find that A and C cotransform about 5% of the time. B and C cotransform about 5% of the time. A and B never cotransform. How would this be diagrammed? A) A........C......B B) ACB C) ABC D) A..........B........C E) none of the above Ans: A Difficulty: 1 Matching 71. Match the following taxonomic groups with their appropriate characteristics. a. bacteria 1. circular genome b. archaea 2. lack membrane-bound organelles c. eukaryotes 3. contain nuclear membrane 4. haploid 5. most live in extreme environments Ans: a. 1, 2, 4; b. 1, 2, 4, 5; c. 3 Difficulty: 2

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72. Match each item in the left column with the single most appropriate item in the right column. Each number should be used only once. a. auxotroph 1. requires cell-to-cell contact b. conjugation 2. capable of taking up DNA c. Hfr 3. uptake of DNA from external medium d. transduction 4. requires at least one nutrient for growth e. F' 5. F factor that has picked up a piece of the bacterial genome f. transformation 6. E. coli strain with F factor integrated into bacterial genome g. competent 7. requires virus Ans: a. 4; b. 1; c. 6; d. 7; e. 5; f. 3; g. 2 Difficulty: 2 73. Match each item in the left column with the single most appropriate item in the right column. Each number should be used only once. a. Hfr strain 1. created through an error in excision b. merozygote 2. partial diploid in which the two gene copies are identical c. F' plasmid 3. partial diploid carrying different alleles of the same gene d. heterogenote 4. created through an integration event Ans: a. 4; b. 2; c. 1; d. 3 Difficulty: 2 74. Match the experiment to the appropriate medium onto which you would spread cells from a lac-strs E. coli culture to: a. select for Lac+ cells 1. rich medium + X-Gal b. screen for Lac+ cells 2. rich medium + streptomycin c. select for Strr cells 3. minimal medium + glucose + r d. select for Lac Str 4. minimal medium + lactose 5. minimal medium + streptomycin + lactose Ans: a. 4; b. 1; c. 2; d. 5 Difficulty: 3 75. Match each item in the left column with the single most appropriate item in the right column. Each number should be used only once. a. virulent 1. bacterial cell that contains an integrated phage genome b. prophage 2. phage that always enters lytic cycle after infecting host c. lysogenic 3. cycle in which phage DNA integrates into host chromosome d. lysogen 4. cycle in which phage multiply rapidly and kill the cell e. temperate 5. the integration of viral DNA into the host chromosome f. lysogeny 6. integrated phage genome g. lytic 7. phage that can enter either lytic or lysogenic cycle Ans: a. 2; b. 6; c. 3; d. 1; e. 7; f. 5; g. 4 Difficulty: 3

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76. Match each item in the left column with the single most appropriate item in the right column. Each number should be used only once. a. specialized transduction 1. the simultaneous transduction of two or more b. generalized transduction bacterial marker genes c. cotransformation 2. property of lysogenic phages, which can package only d. cotransduction host genes adjacent to the integrated prophage genome 3. the simultaneous transformation of two or more bacterial marker genes 4. the ability of certain phages to transduce any gene in the bacterial genome Ans: a. 2; b. 4; c. 3; d. 1 Difficulty: 2 77. Match each item in the left column with the single most appropriate item in the right column. Each number should be used once and only once. a. pilus 1. contains bacterial chromosome b. insertion sequence 2. group of 107-108 bacterial cells that are genetically identical c. nucleoid body 3. appendage by which a donor cell contacts a recipient cell d. capsule 4. small, circular, double-stranded, piece of e. episome extrachromosomal DNA f. plasmid 5. thick, mucus-like coating around some bacterial cells g. colony 6. small, transposable elements that allow integration of F plasmid into host chromosome through homologous recombination 7. plasmid that can integrate into host chromosome Ans: a. 3; b. 6; c. 1; d. 5; e. 7; f. 4; g. 2 Difficulty: 2 78. Match the type of mutant in the left column with the appropriate isolation method or methods in the right column. a. auxotroph 1. screen r b. streptomycin 2. selection c. mutant bacteria that form shiny colonies 3. screen or selection d. temp-sensitive lethal e. lacf. streptomycins g. lac+ h. resistance to infection by T1 phage Ans: a. 1; b. 2; c. 1; d. 1; e. 1; f. 1; g. 3; h. 2 Difficulty: 3

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True or False 79. Bacteria have a single circular chromosome of dsDNA. Ans: True Difficulty: 1 80. An open reading frame is a long stretch of DNA that codes for amino acids uninterrupted by a stop codon. Ans: True Difficulty: 1 81. IS elements are plasmids that insert new phenotypes to bacteria. Ans: False Difficulty: 2 82. Small circular dsDNA molecules carrying non-essential genes, called plasmids, may exist as multiple copies in some bacteria. Ans: True Difficulty: 1 83. A transductant is a bacteria that has been the recipient of donor DNA from a bacteriophage. Ans: True Difficulty: 1 84. Electroporation is the use of high voltage and high salt to force foreign DNA into bacteria. Ans: False Difficulty: 2 85. A plasmid that can integrate into the host bacterial genome is called an episome. Ans: True Difficulty: 1 86. Mating between bacteria can be disrupted using a kitchen blender. Ans: True Difficulty: 2 87. The lysogenic cycle of phage production results in bacterial cell lysis. Ans: False Difficulty: 1 88. An integrated copy of a temperate bacteriophage is called a prophage. Ans: True Difficulty: 1

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Short Answer 89. Describe five types of mutants that can be observed in bacteria. Ans: Mutations affecting colony morphology; mutations conferring resistance to antibiotics or bacteriophages; auxotrophic mutations; metabolic mutations (affecting ability to break down and utilize complicated chemicals in the environment); and mutations in essential genes. Difficulty: 3 90. Since a mutation in an essential gene prevents a colony from growing, how would a bacteriologist study such a strain? Ans: Use a conditional lethal mutation such as a temperature-sensitive mutation. Difficulty: 4 91. Explain why different Hfr cells can have F plasmids integrated at different sites. Ans: Hfr cells are created when F plasmids integrate into the bacterial genome. F plasmids contain insertion sequences (IS sequences). The bacterial genome also contains IS sites, found at various positions along the bacterial chromosome. F plasmids can integrate at any of these bacterial IS sites through homologous recombination, resulting in Hfr strains with F plasmids integrated at different sites. Difficulty: 3 92. Explain the difference between the F-, F+, Hfr, and F' designations. Ans: An F- cell has no F plasmid, an F+ cell does have an F plasmid, an Hfr cell has an integrated F plasmid, and an F' cell has an F plasmid that has picked up a piece of the bacterial genome. Difficulty: 2 93. Plasmids are small, circular pieces of DNA that some bacteria carry in addition to their own chromosome. Plasmids may include genes that benefit the bacterial host under certain conditions. Describe what some of these genes may be. Ans: One important group of plasmids (the F plasmids) carry genes that promote conjugative gene transfer between two bacteria. Other beneficial genes include genes that protect their hosts against toxic metals, genes that allow bacteria to metabolize petroleum products, genes that contribute to pathogenicity, and genes encoding resistance to antibiotics to name just a few. Difficulty: 3

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94. Describe the difference between generalized and specialized transduction. Ans: Transduction is a form of gene transfer in bacteria that depends on the packaging of bacterial donor DNA in the protein coat of a bacteriophage. In generalized transduction, phages can package any part of the donor genome. Specialized transduction is a property of lysogenic bacteriophages, which can package only host genes adjacent to the integrated prophage genome. Difficulty: 3 95. Describe the difference between selection and screen with respect to mutant isolation methods. Ans: A selection uses conditions in which only the desired mutant will grow (e.g. selection for resistance to an antibiotic by growing the cells on plates containing the antibiotic). A screen requires the examination of each colony in a population for its phenotype (e.g. to screen for colonies with different morphological characteristics). Difficulty: 3 96. Describe how to screen for bacteria that have lost their ability to carry out chemotaxis. Ans: Inoculate bacteria onto center of a wet nutrient plate. Bacteria will multiply and motile bacteria will swarm out to edges of plate in concentric circles, with the leading edge moving toward the unused nutrient supply. After motile cells have swarmed, pick cells from the center of the plate. These are the cells that could not chemotax to unused nutrient supply. Difficulty: 3 97. What type of processes could be defective in a mutant unable to carry out chemotaxis? Ans: Some might be defective in making flagella (flagellum mutants); some in turning the flagella (motor mutants); others in coordinating the behavior of flagella (signal transduction mutants); and still others in detecting gradients of chemicals (receptor mutants). Difficulty: 3

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Experimental Design and Interpretation of Data 98. In the original interrupted mating experiment performed by Wollman and Jacob, they mated HfrH strs thr+ azir tonr lac+ gal+ cells to F- strr thr- azis tons lac- gal- cells, disrupted mating pairs at 1 minute intervals and plated the exconjugants on plates containing streptomycin and lacking threonine. a. Why did they choose that type of medium to plate on? b. In order for the above experiment to work, what must be true about the location of the thr gene? Ans: a. They used plates containing streptomycin and lacking threonine to select for cells that had undergone conjugation. Donor cells are killed by streptomycin and recipient cells cannot grow without threonine. b. The thr gene must be close to the F plasmid integration site in that particular strain and thus is one of the first genes transferred during the interrupted mating experiment. Difficulty: 4 99. A P1 generalized transducing lysate from a wild-type strain is used to infect a leu-thrara- recipient strain. When ara+ transductants are selected, 47% of the ara+ also carry leu+ and 2% of the ara+ transductants also carry thr+. When leu+ transductants are selected, 50% also carry ara+, but none also carry thr+. What is the order of the three genes? Ans: The order is leu ara thr (ara closer to leu than to thr). The leu and thr genes were not co-transduced but ara and thr were co-transduced at low frequency, so they must be closer together than leu and thr. Difficulty: 3 100. Describe how you would screen for Arg- cells arising from a wild-type culture of E. coli. Ans: To increase frequency of mutation, first expose wild-type culture to a mutagen. Then plate mutagenized cells onto minimal plates containing arginine. After colonies have grown up, replica plate onto minimal plates without arginine. Note position of cells that grow on first set of plates, but not the second set. Those are the Arg- mutants. Difficulty: 3

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101. Through the use of different Hfr strains (H, 1, 2, and 3) that have the F factor inserted into the chromosome at different points and in different directions, interrupted-mating experiments can provide the order of genes in the E. coli genome. The linear order of transfer of markers is shown below for four Hfr strains. Using this data, construct a physical map of the E. coli chromosome. HfrH thi gly his gal pur lac Hfr1 pro lac pur gal his gly Hfr2 lac pur gal his gly thi Hfr3 gal his gly thi thr pro Ans: The E. coli chromosome is circular, and the order of markers is: thi gly his gal pur lac pro thr. Difficulty: 2 102. In an Hfr X F- cross, azir enters as the first marker, but the order of the other markers is unknown. If the Hfr is wild-type and the F- is auxotrophic for each marker in the experiment, what is the order of the markers in a cross where azir recombinants are selected if 61% are lac+, 27% are gal+, 89% are tonr, and 1% are trp+? Ans: The order of the markers used in this experiment is: azir, tonr, lac+, gal+, trp+. Difficulty: 3

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103. A cross is made between an Hfr strain that is met+arg+gly+ and an F- strain that is metarg-gly-. Interrupted-mating experiments show that gly+ enters the recipient last, so the gly+ recombinants are selected on minimal plates supplemented with methionine and arginine. These recombinants are then tested for the presence of the met+ and arg+ alleles. The following numbers of colonies are found for each genotype: gly+met+arg+ 420 + + gly met arg 11 gly+met-arg+ 0 + gly met arg 49 a. Why was glycine (gly) left out of the selection medium? b. What is the gene order? c. What are the map distances in recombination units? Ans: a. Glycine was left out to allow for selection of gly+ recombinants because gly is the last marker to enter the recipient in this mapping experiment. This ensures that all loci being mapped in the cross have already entered each recombinant that is analyzed. b. Because we know that gly enters the cell last, there are only two possible orders to consider: arg-met-gly and met-arg-gly. Because the gly+metarg+ recombinant did not show up in this experiment, we can conclude that it required a quadruple crossover event, indicating that the order of genes must be arg-met-gly. c. To determine map distance between two genes, count the number of crossover events that occur between them. Recombination events between arg and met will result in a Gly+Met+Arg- phenotype (remember, all cells were selected first as gly+ recombinants). Thus, the distance between arg and met is 11/480 = 2.3 map units. Similarly, the map distance between met and gly is 49/480 = 10.2 map units. Difficulty: 4

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104. A generalized transducing phage is used to transduce an a-b-c-d-e- recipient strain of E. coli with an a+b+c+d+e+ donor. The recipient culture is plated on various media indicated in the second column of the table below, with the results shown in the third column. (Note that "a-" indicates a requirement for A as a nutrient, etc.) Experiment Compounds added Presence (+) or Number to minimal medium absence (-) of colonies 1 CDE 2 BDE + 3 BCE 4 BCD 5 ADE 6 ACE + 7 ACD + 8 ABE 9 ABD 10 ABC a. What genotype is being selected for in each experiment above? b. Which of the above markers can be cotransduced? c. What can you conclude about the linkage and order of the five genes? Ans: a. Experiment 1 is selecting for a+b+ recombinants, experiment 2 for a+c+, 3 for a+d+, then a+e+, b+c+, b+d+, b+e+, c+d+, c+e+, and d+e+ in experiment 10. b. The markers that can be cotransduced are a and c, b and d, and b and e. c. b, d, and e are relatively close to each other, with b in the middle. a and c are close to each other, but far from b, d, and e. Difficulty: 3

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Chapter 15The Chromosomes of Organelles Outside the Nucleus Exhibit Non-Mendelian Patterns of Inheritance Fill in the Blank 1. When maternal and paternal gametes do not contribute equally to the inheritance of a trait, we call this mode of inheritance ______________________________________. Ans: non-mendelian Difficulty: 1 2. In general, the genome of which organelles is larger mammalian mitochondrion or higher plant chloroplast? ______________________________________ Ans: chloroplast Difficulty: 2 3. Because they do not carry all the genes they need to function and reproduce, and because they need molecules encoded by nuclear genes, chloroplasts and mitochondria are considered ________________________. Ans: semiautonomous Difficulty: 1 4. In the 1970s, Lynn Margulis and others proposed that today's chloroplasts and mitochondria descended from prokaryotic ancestors in a theory called the ________________________________. Ans: endosymbiont theory Difficulty: 1 5. Allan Wilson and coworkers proposed all human mtDNA's today trace their ancestry to a single mtDNA present in some distant ancestor. They call this human ancestor ________________________. Ans: mitochondrial Eve Difficulty: 1 6. If mtDNA sequences suggest a mitochondrial Eve because of strict maternal inheritance, what type of human DNA sequences might show strict paternal inheritance and point to DNA Adam? ______________________________________ Ans: Y-chromosome sequences Difficulty: 3 7. In contrast with most nuclear DNA sequences, many mtDNA, cpDNA, and human Y chromosomes all show what mode of transmission? ______________________________________ Ans: uniparental inheritance Difficulty: 2

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8. Reciprocal crosses of green and variegated geraniums show what mode of transmission of the organelles responsible for variegation? ______________________________________ Ans: biparental inheritance Difficulty: 2 9. A device used to inject microscopic DNA-coated metal particles into cells is called a ______________________________________. Ans: gene gun Difficulty: 1 10. A burst of mitochondrial activity increases the temperature in the bloom of the ______________________________________. Ans: voodoo lily Difficulty: 1 11. The chlorophyll, the light-absorbing molecules, and the proteins of the photosynthetic electron transport system are located in the ______________________________________. Ans: thylakoid membranes Difficulty: 1 12. Cells that carry a mixture of organelle genomes are referred to as _______________________. Ans: heteroplasmic Difficulty: 1 13. The single mitochondrion of the protozoan Trypanosoma is known as a ____________________. Ans: kinetoplast Difficulty: 2 14. The process that converts pre-mRNAs to mature mRNAs is called _______________________. Ans: RNA editing Difficulty: 1 15. In trypanosome mitochondria, the workbench where RNA editing takes places is called a ______________________________________. Ans: editosome Difficulty: 2

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16. Evidence suggests that the women carrying the ancestral mtDNA for today's humans lived in sub-Saharan Africa roughly how many years ago? ______________________________________ Ans: 200,000 years ago Difficulty: Multiple Choice 17. A) B) C) D) Traits showing non-Mendelian extranuclear inheritance are inherited: always from the mother. always from the father. always both parents. depending on species, inheritance could be from mother, father, or both parents. Ans: D Difficulty: 2

18. With traits showing maternal inheritance, such as leaf variegation in four o'clocks, reciprocal crosses usually: A) yield the same results. B) yield different results. C) yield result which can seldom be predicted. D) eliminate the need for sexual reproduction. Ans: B Difficulty: 1 19. When eukaryotic cells are stained with DNA-specific dyes and viewed under the light microscope, DNA molecules are revealed: A) in the nucleus. B) in the matrix of the mitochondrion. C) in the stroma of chloroplasts. D) in all theses places: nucleus, mitochondrion, and chloroplast. Ans: D Difficulty: 1 20. A) B) C) D) The molecules used in a chloroplast to carry out photosynthesis: all are encoded by chloroplast DNA. some are encoded by chloroplast DNA, other by nuclear DNA. all are encoded by nuclear DNA. some are encoded in nuclear DNA and some in mitochondrial DNA. Ans: B Difficulty: 2

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21. A) B) C) D) E)

Which process(es) take place in the mitochondrion? Krebs cycle Calvin cycle oxidative phosphorylation of ADP to ATP both Krebs cycle and oxidative phosphorylation of ADP to ATP both Calvin cycle and oxidative phosphorylation of ADP to ATP Ans: D Difficulty: 2 A chloroplast URF is best described as: a cpDNA coding sequence with product of unknown function. a cpDNA intron, interrupting chloroplast coding sequences. a chloroplast operon, including several structural genes. an extraterrestrial sequence occurring as a symbiont. Ans: A Difficulty: 1

22. A) B) C) D)

23. Based on rRNA coding sequences in mtDNA, cpDNA, and bacterial DNA, it has been suggested that many mitochondrial genomes may be derived from a common ancestor of: A) chloroplasts. B) cyanobacteria. C) gram-negative non-sulfur purple bacteria. D) prochlorophyte bacteria. Ans: C Difficulty: 2 24. Based on rRNA coding sequences in mtDNA, cpDNA, and bacterial DNA, it has been suggested that modern chloroplast genomes may be derived from: A) mitochondria. B) cyanobacteria. C) gram-negative non-sulfur purple bacteria. D) chemautotrophic thermophilic bacteria. Ans: B Difficulty: 2 25. Which of the following is not accurate with regard to organelle genomes? A) mtDNA and cpDNA are usually organized into nucleosomes by histones. B) Mitochondrial translation is often inhibited by bacterial antibiotics (e.g., chloramphenicol). C) Like bacteria, mitochondria use N-formyl methionine and tRNAfmet in translation. D) All of the above are accurate. Ans: A Difficulty: 3

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26. A) B) C) D)

Molecular evidence suggests that DNA sequences may have been transferred between: mtDNA and nuclear DNA. cpDNA and mtDNA. different cpDNA molecules. evidence suggests all of the above have occurred. Ans: D Difficulty: 4

27. Which sequences would be most similar to the prevailing mtDNA sequences in today's human populations? A) mtDNA in mitochondrial Eve B) Neanderthal mtDNA C) mtDNA from a 4,000-year-old Egyptian mummy D) Chimpanzee mtDNA Ans: C Difficulty: 3 28. Which type of DNA sequences might be studied to help reunite displaced children with their families? A) mtDNA sequences B) cpDNA sequences C) Y-chromosome sequences D) highly conserved nuclear sequences Ans: A Difficulty: 2 29. Which type of DNA sequences might be studied to help determine the identity of a particular variety of a cultivated crop? A) mtDNA sequences B) cpDNA sequences C) Y-chromosome sequences D) highly conserved nuclear sequences Ans: B Difficulty: 2 30. A) B) C) D) Variegated four o'clock leaves have white patches among the green areas due to: a mtDNA mutation which blocks electron transport. a cpDNA mutation which incapacitates proteins essential for photosynthesis. a nuclear DNA mutation, which leads to mosaicism. both b and c Ans: B Difficulty: 1

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31. Xenopus borealis eggs are fertilized with sperm from a Xenopus laevis. In various tests, the mtDNA of the F1 hybrids is probed with mtDNA from both parental species. Which result is most likely? A) Only probe from X. borealis hybridizes with the F1 DNA. B) Only probe from X. laevis hybridizes with the F1 DNA. C) Probes from both X. borealis and X. laevis hybridize with the F1 DNA, but X. borealis probe hybridizes more efficiently. D) Probes from both X. borealis and X. laevis hybridize with the F1 DNA, but X. laevis probe hybridizes more efficiently. Ans: C Difficulty: 4 32. If the above study were repeated with Xenopus laevis eggs and Xenopus borealis sperm, what result would be most likely? A) Only probe from X. borealis hybridizes with the F1 DNA. B) Only probe from X. laevis hybridizes with the F1 DNA. C) Probes from both X. borealis and X. laevis hybridize with the F1 DNA, but X. borealis probe hybridizes more efficiently. D) Probes from both X. borealis and X. laevis hybridize with the F1 DNA, but X. laevis probe hybridizes more efficiently. Ans: D Difficulty: 2 33. A) B) C) D) Which of the genes is encoded by a chloroplast DNA sequence? The yellow 1 mutant in Chlamydomonas. Rubisco large subunit. Mating type in Chlamydomonas. The NADH dehydrogenase gene responsible for LHON. Ans: B Difficulty: 2

34. Consider the following cross between different Chlamydomonas mating types: yellow-1+ / streptomycin-resistant yellow-1- / streptomycin-sensitive Which of the following ratios might be observed in the resulting haploid progeny? A) (2) yellow-1+/streptomycin-resistant : (2) yellow-1/streptomycin-resistant B) (2) yellow-1+/streptomycin-resistant : (2) yellow-1/streptomycin-sensitive C) (4) yellow-1+/streptomycin-resistant : (0) yellow-1/streptomycin-resistant D) (1) yellow-1+ : (1) yellow-1 : (2) streptomycin-resistant : (0) / streptomycin-sensitive Ans: A Difficulty: 4

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35. A) B) C) D)

Which of the following statements is correct with respect to mitochondrial genes? They are transmitted, largely intact, from parent to offspring. Their inheritance shows Mendel's principle of segregation. Their inheritance shows Mendel's principle of independent assortment. All of the above Ans: A Difficulty: 3

36. After a cross between cells of two genetically different yeast strains, a number of diploid cells are formed during a period of vegetative growth. Which of the following is(are) correct regarding marker genes from the two parent strains, when observed in cells shortly after hybridization? A) Mitochondrial genetic markers from both parents are present. B) Nuclear genetic markers from both parents are present. C) Both mitochondrial and nuclear markers from both parents are present. D) Mitochondrial and nuclear markers from only one parent are observed. Ans: C Difficulty: 3 37. In the same cross between yeast strains as above, which would be correct regarding colonies from diploid cells after several generations of vegetative growth following hybridization? A) A colony shows mitochondrial genetic marker of one parental strain, but not both. B) Nuclear genetic markers from both parents are present in all colonies. C) Both mitochondrial and nuclear markers from only one parent are observed. D) a and b Ans: D Difficulty: 3 38. A) B) C) D) A researcher hopes that, after being shot with a gene gun, a plant cell will: die. incorporate foreign DNA into its nucleus. mutate to a new genotype. show uniparental inheritance. Ans: B Difficulty: 1 A homoplasmic cell carries: a mixture of organelle genomes. only one type of organelle DNA. only one mitochondrion. two identical nuclei. Ans: B Difficulty: 1

39. A) B) C) D)

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40. A) B) C) D)

A parasitic protozoan like Trypanosoma or Leishmania might have its mtDNA in: many mitochondria. a kinetoplast. minicircles and maxicircles. b and c Ans: D Difficulty: 3 Inhibitors of bacterial translation, such as chloramphenicol and erythromycin, generally: are inhibitors of eukaryotic cytoplasmic protein synthesis. are inhibitors of mitochondrial protein synthesis. have no effect on mitochondrial protein synthesis. a and c Ans: B Difficulty: 3 cpDNA-encoded proteins include: RNA polymerase. RNA polymerase and translation factors. RNA polymerase. translation factors, and ribosomal proteins. none of the above Ans: C Difficulty: 2 The codon UGA specifies: stop in the universal genetic code. the amino acid tryptophan in human mtDNA. formyl-methionine in mtDNA. a and b Ans: D Difficulty: 3 Which of the following has been associated with aging in humans? Loss of mitochondria. 5kb and 7.4kb deletions in mtDNA of heart cells. Loss of cytochrome oxidase c genes. All of the above Ans: B Difficulty: 2

41. A) B) C) D)

42. A) B) C) D)

43. A) B) C) D)

44. A) B) C) D)

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45. A) B) C) D)

Which of the following has been associated with Alzheimer's Disease? Loss of mitochondria. 5kb and 7.4kb deletions in mtDNA of heart cells. Mutations in cytochrome oxidase c genes in brain cells. All of the above Ans: C Difficulty: 2 The genomes of organelles inherited in a biparental fashion show: mitotic segregation. meiotic segregation. blending inheritance. Mendelian inheritance. Ans: A Difficulty: 3

46. A) B) C) D)

Matching Match the item with the correct answer below a. leaf variegation b. petite colonies c. NADP d. NAD e. Rubisco LSU f. Rubisco SSU 47. encoded by nuclear gene Ans: f Difficulty: 2 48. chloroplast dinucleotide Ans: c Difficulty: 1 49. maternal-chloroplast inherited Ans: a Difficulty: 2 50. encoded by chloroplast gene Ans: e Difficulty: 2 51. mitochondrion dinucleotide Ans: d Difficulty: 1

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52. due to mitochondrial mutation Ans: b Difficulty: 2 Match the item with the correct answer below a. resistant to chloramphenicol b. petite mutant yeast cells c. mutant mtDNA tRNALys d. a mutant nuclear gene in Chlamydomonas e. mutant mitochondrial electron transport enzyme f. a mating type among haploid yeast cells 53. MERFF Ans: c Difficulty: 1 54. LHON Ans: e Difficulty: 1 55. Cr Ans: a Difficulty: 1 56. rho Ans: b Difficulty: 1 57. MATa Ans: f Difficulty: 1 58. yellow 1 Ans: d Difficulty: 1 Match the item with the correct answer below a. a unicellular alga b. a frog c. a liverwort d. a parasitic protozoan e. a variegated geranium f. brewer's yeast

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59. Plasmodium falciparum Ans: d Difficulty: 1 60. Chlamydomonas reinhartii Ans: a Difficulty: 1 61. Pelargonium zonale Ans: e Difficulty: 1 62. Saccharomyces cerevisiae Ans: f Difficulty: 1 63. Marchantia polymorpha Ans: c Difficulty: 1 64. Xenopus laevis Ans: b Difficulty: 1 Match the item with the correct answer below a. 0.5kb - 2.5kb b. 16.5kb c. 21kb - 31kb d. 55kDa e. 186kb f. 120kb - 217 kb 65. human mitochondrial genome Ans: b Difficulty: 2 66. Marchantia mitochondrial genome Ans: e Difficulty: 2 67. Rubisco LSU size Ans: d Difficulty: 2

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68. chloroplast genomes Ans: f Difficulty: 2 69. kinetoplast minicircle Ans: a Difficulty: 2 70. kinetoplast maxicircle Ans: c Difficulty: 2 True or False 71. Genomes of organelles are inherited exactly as nuclear chromosomes. Ans: False Difficulty: 2 72. Most mitochondrial genomes are linear dsDNA molecules. Ans: False Difficulty: 2 73. Human mitochondrial DNA contains tightly packed genes without introns. Ans: True Difficulty: 1 74. Yeast have a larger mitochondrial genome and unlike human mtDNA genes, yeast mtDNA code for genes with introns. Ans: True Difficulty: 1 75. Plant mitochondrial genomes are smaller than animal mitochondrial genomes. Ans: False Difficulty: 2 76. The universal code of DNA also applies to mtDNA. Ans: False Difficulty: 2 77. RNA editing can occur in mitochondrial transcripts and is the addition and/or deletion of uracils and/or cytosines, which results in codon changes from the original DNA. Ans: True Difficulty: 1

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78. Mitochondrial DNA has an approximately 10-fold higher rate of mutation compared to nuclear DNA. Ans: True Difficulty: 1 79. In uniparental inheritance, transmission is usually maternal. Ans: True Difficulty: 1 80. Heteroplasmic cells lead to earlier appearance of mitochondrial-inherited disease compared to homoplasmic cells. Ans: False Difficulty: 2 81. The proportion of mutant mtDNAs and the tissue in which they reside influence phenotype. Ans: True Difficulty: 1 82. Mutations in mtDNA are often caused by free-radical damage, which results from oxidative phosphorylation. Ans: True Difficulty: 1 83. Oxidative phosphorylation decreases with age. Ans: True Difficulty: 1 84. Mitochondria in brain cells of patients with symptoms of Alzheimer's disease have unusually high energy metabolism. Ans: False Difficulty: 2 85. Mitochondria and chloroplasts are considered to be semiautonomous. Ans: True Difficulty: 1 Short Answer 86. Why does organelle DNA often have a buoyant density different from the cell's nuclear DNA? Ans: Different base composition; different AT:GC ratio. Difficulty: 3

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87. What is an explanation of the observation that mtDNA evolves almost ten times more rapidly than nuclear DNA in the same species? Ans: More errors in replication and less efficient repair mechanism. Difficulty: 3 88. Why is the mode of transmission of streptomycin resistance in Chlamydomonas said to be uniparental inheritance rather than maternal inheritance? Ans: Chlamydomonas is isogamous, gametes are neither egg nor sperm. Difficulty: 2 89. Is the so-called universal genetic code truly universal? Why or why not? Ans: No. There are several different codon assignments in mitochondria, for example. Difficulty: 3 90. Why do scientists believe the COXII gene transferred from the mtDNA to the nuclear genome, via an RNA intermediate, in some plants? Ans: The mtDNA COXII pseudogene has an intron, which the nuclear sequence lacks. Difficulty: 4 91. Why might the brain cells show abnormally low energy metabolism in individuals with Alzheimer's Disease? Ans: Defective mitochondrial cytochrome oxidase genes may reduce energy metabolism. Difficulty: 2 92. How does mtDNA variation provide evidence that modern humans emerged in Africa? Ans: More sequence differences among Africans, due to longer time to accumulate mutations. Difficulty: 4 93. The Endosymbiont hypothesis posited by Lynn Margulis in the 1970's is now considered a theory. What molecular evidence strongly supports the hypothesis to the point where it is now accepted as a theory? Ans: 1. both mitochondria and chloroplasts have their own DNA, which replicates independently of the nuclear genome. 2. like the DNA of bacteria, mtDNA and cpDNA are not organized into nucleosomes by histones. 3. mitochondrial genomes use N-formyl methionine as the start amino acid. 4. inhibitors of bacterial translation also inhibit mitochondrial translation. Difficulty: 3

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94. Explain how mitochondrial traits are inherited. Ans: Mitochondrial traits are inherited in a non-Mendelian fashion. Because mitochodria are not separated like chromosomes in cell division, equal segregation is not seen. Also mitochondria are usually maternally inherited in diploids, but can be paternal or biparentially inherited in some cases. Difficulty: 2 95. What is RNA editing? Ans: RNA editing is a molecular mechanism by which pre-mRNA is converted to mature mRNA through the unusual insertion and/or deletion of either uracils or cytosines. Without the editing the message does not correctly code for the protein produced. In other words, the DNA contains only bits and pieces of the actual gene which is added to or clipped prior to translation. Difficulty: 3 Experimental Design and Interpretation of Data 96. A scientist studies matings between yeast cells of the grande and petite forms; after sporulation, what types of yeast colonies will result from the spores produced, and in what proportions? Ans: 4 grande: 0 petite. Difficulty: 2 97. Why might a researcher attach a gene encoding a green fluorescent protein to a DNA sequence before transforming a cell's mtDNA? Ans: To confirm successful transformation by detecting fluorescence in the target. Difficulty: 2 98. Identical twins arise from a single zygote. One twin has symptoms of MERFF but the other twin does not show the disorder. Explain how this might happen. Ans: Unequal distribution of mitochondria during initial cell division and development. Difficulty: 3 99. Mom 1 and Mom 2 both show a hypothetical mitochondrial-related phenotype and neither Father is effected. Both families have four kids. The kids of family 1 are all affected but only half of the kids of family 2 show the phenotype. Interpret this result with respect to the genotype of Moms 1 and 2. Ans: Mom 1 is homoplasmic and Mom 2 is heteroplasmic for the hypothetical phenotype. Difficulty: 2

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100. Statistical calculations and assumptions regarding mutation rates are utilized in evolutionary biology. Two hypotheses exist regarding the evolution of humans. One, called the replacement theory, hypothesizes that man existed in parallel to other hominid species and simply out-competed them to exist today. The second hypothesis is that modern man is a direct descendent of Neanderthal man but that by random genetic loss or negative selection large sequence discrepancies exist between the species. What discovery and experiment is needed to test these two mutually exclusive hypotheses? Ans: The discovery and testing of a North African Neanderthal mtDNA. Analysis of Cro-Magnon mitochondrial DNA could also be supportive of one or the other hypothesis. Difficulty: 3

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Chapter 16Gene Regulation in Prokaryotes Fill in the Blank 1. The names of the two individuals winning the Nobel Prize for discovering the lac operon were __________________ and ___________________. Ans: Jacob, Monod Difficulty: 1 2. Mutations in either of two sites will produce a constitutive phenotype. These two sites are ____________ or ______________. Ans: Repressor, Operator Difficulty: 2 3. The process by which a specific molecule stimulates the synthesis of a given protein is called _________________. Ans: Induction Difficulty: 1 4. A regulator that physically blocks the DNA binding site of RNA polymerase is called a _______________ regulator. Ans: Negative Difficulty: 1 5. A genetic unit that consists of several genes coding for proteins, an operator (o) and a promoter (p) is termed an _____________. Ans: operon Difficulty: 1 6. Walter Gilbert purified the lac repressor and showed that it actually has two sites for binding. These two distinct binding sites are _________________ and ___________________. Ans: Lactose binding, DNA binding Difficulty: 2 7. A protein coding gene whose expression in the cell can be quantifiable by sensitive and reliable techniques of protein detection and therefore used to determine the specific conditions that induce the expression of any other gene is called a _________________________. Ans: reporter gene Difficulty: 3 8. Cascades of ___________ factors allow for the global regulation of multiple gene sets. Ans: sigma Difficulty: 3

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9. The most critical step in the regulation of most bacterial genes is the binding of _______________________ to the _____________________. Ans: RNA polymerase, promoter Difficulty: 2 10. Jacob and Monod found that most of the Lac- mutations they obtained could be mapped into two genes, ____________and _____________. Ans: lac Z, lac Y Difficulty: 1 11. Proteins such as the lac repressor that undergo reversible changes in conformation (shape) when bound to other molecules are called _____________ proteins. Ans: allosteric Difficulty: 3 12. The process by which glucose, even in the presence of lactose, will repress the lac operon is called _________________ repression. Ans: catabolite Difficulty: 2 13. Regulation of the lac operon depends on at least two proteins: ________________, a negative regulator, and _____________, a positive regulator. Ans: repressor, CAP Difficulty: 2 14. The so-called LacI repressor family of proteins has a common DNA binding motif called a ________________________ motif. Ans: helix turn helix Difficulty: 1 15. The presence of _______________ of the enzymes in a catabolic process that breaks down complex substances into smaller units usually regulates transcription of the genes for the enzymes. Ans: substrate Difficulty: 1 16. The presence of the _______________ usually regulates anabolic pathways that build or synthesize more complex molecules. Ans: end product Difficulty: 1 17. The __________ subunit of RNA polymerase is necessary for initiation of transcription at a promoter, but is not necessary for elongation. Ans: sigma Difficulty: 2

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18. Molecules responsible for stimulating the synthesis of a specific protein, are called ______________. Ans: inducers Difficulty: 1 19. The actual site of binding of RNA polymerase in order to initiate transcription is ________________. Ans: promoter Difficulty: 1 20. The term that describes the end product of a biosynthetic pathway in its role in regulation of transcription of the genes is __________________. Ans: corepressor Difficulty: 1 Multiple Choice 21. A) B) C) D) What would be the phenotype of a mutation that altered lac promoter function? constitutive inducible permanently repressed none of the above Ans: A Difficulty: 2 A common DNA structural feature involved in gene regulatory systems is: supercoiling of DNA. looping of the DNA. unwinding of the double helix. coiling into Z-DNA. Ans: B Difficulty: 1

22. A) B) C) D)

23. How do negative regulators such as the lac repressor prevent RNA polymerase from initiating transcription? A) By blocking passage of the polymerase through the operator. B) By forming a loop in the operator that restricts the passage of the polymerase. C) By physically blocking the DNA binding site of RNA polymerase. D) By binding to the polymerase thus preventing its binding. Ans: C Difficulty: 3

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24. A) B) C) D)

How do positive regulators stimulate initiation of transcription by RNA polymerase? By allowing passage of the polymerase through the operator. By binding to the polymerase and increase its ability to initiate transcription. By causing the helix to unwind in the operator allowing easier initiation. By making the transcription start site more exposed to the polymerase. Ans: B Difficulty: 2

25. Catabolic pathways that break down complex substances into more usable units are usually regulated by the: A) end products of the pathway. B) substrate of an enzyme in the pathway. C) other metabolites that are limiting. D) none of the above Ans: B Difficulty: 1 26. Anabolic pathways involved in the synthesis of essential molecules are usually regulated by: A) end product of the pathway. B) substrate of the pathway. C) other metabolites that are limiting. D) none of the above Ans: A Difficulty: 1 27. Which statement is true regarding global gene regulation in bacteria? A) Sigma factors are not involved in gene regulation, just attachment of the polymerase to the promoter. B) Alternative sigma factors recognizing different promoters carry out global gene regulation. C) E. coli cells devote more energy to the production of ribosomes during stress so that global gene regulation can occur. D) All promoters are recognized by all sigma factors. Ans: B Difficulty: 3 28. In the genotype presented below, what will the expression phenotype for galactosidase be (I+p+ocZ-Y-A+/I+p+o+Z-Y+A-)? A) inductive B) consitiutive C) absent D) lethal Ans: B Difficulty: 2

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29. In the genotype presented below, what will the expression phenotype for -galactoside permease be (I+p+ocZ-Y-A+/I+p+o+Z-Y+A-)? A) constitutive B) inductive C) absent D) lethal Ans: B Difficulty: 2 30. In the genotype presented below, what will the expression phenotype for thiogalactoside transacetylase be (I+p+ocZ-Y-A+/I+p+o+Z-Y+A-)? A) constitutive B) inductive C) absent D) lethal Ans: A Difficulty: 2 31. Why is glucose involved in the catabolite repression of the lactose operon? A) It has nothing to do with regulation of the lactose operon. B) It is produced by the enzymatic breakdown of lactose, its presence thereby signifying the presence of lactose in the cell. C) It is also a substrate for -galactosidase. D) Its presence in the cell increases the amount of lac represor in the cell. Ans: B Difficulty: 4 32. A common amino acid motif found in many of the polypeptides that function as repressors is: A) Leucine zipper motif. B) Zinc finger motif. C) Helix turn helix motif. D) Helix loop helix motif. Ans: C Difficulty: 1

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33. How does tryptophan, the end product of the trp operon, function in the regulation of the operon? A) It binds to the repressor preventing it from binding to DNA thus allowing transcription of the operon. B) It binds to the repressor and only then can the repressor bind to DNA allowing transcription of the operon. C) It binds directly to DNA and inhibits transcription of the operon. D) It binds to the repressor and only then can this complex bind to DNA preventing transcription of the operon. Ans: D Difficulty: 2 34. What term describes a second level of regulation of the trp operon that occurs in TrpRmutants suggesting that it is repressor independent? A) modulation B) derepression C) attenuation D) amplification Ans: C Difficulty: 2 35. In E. coli, the heat shock response, switching off the synthesis of some proteins and switching on of different proteins, is mediated by: A) inactivation of certain repressor proteins by elevated temperature. B) denaturing of DNA in the promoters in the genes of heat sensitive proteins. C) synthesis of alternative sigma factors at high temperatures, which then regulate transcription of heat shock genes. D) increasing the promoter affinity of already existing polymerase sigma factors at high temperatures. Ans: C Difficulty: 2 36. How are complex processes such as sporulation, synthesis of flagella, and nitrogen fixation that require the transcription of multiple sets of genes regulated in bacteria? A) Multiple operons are simultaneously induced. B) Cascades of sigma factors synthesized in a temporal order, allow the turning on of successive sets of genes. C) The end product of one operon is used as an inducer of the next operon in sequence. D) There are single operons consisting of many genes for each of these processes. Ans: B Difficulty: 3

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37. How does phage T7 differentially control the transcription of its early and late genes? A) It has two RNA polymerases, each specific for either early or late genes. B) The early and late genes have promoters that specify their timing of transcription. C) The phage uses the E. coli polymerase to transcribe the early genes, and its own polymerase to transcribe the late genes. D) Products of the early genes are actually the inducers of the late genes. Ans: C Difficulty: 2 38. A) B) C) D) As a general principle of gene regulation through operons regulatory genes encode: trans-acting proteins that interact with cis-acting DNA elements. cis-acting proteins that interact with cis-acting DNA elements. cis-acting proteins that interact with trans-acting DNA elements. trans-acting proteins that interact with trans-acting DNA elements. Ans: A Difficulty: 2

39. In the trp operon, attenuation occurs through the recognition of two Trp codons in the leader sequence. What would happen if these two codons were mutated to stop codons? A) This operon will be insensitive to attenuation by tryptophan. B) The structural genes will be transcribed in the presence or absence of tryptophan. C) The tryptophan biosynthetic enzymes will be synthesized. D) None of these results will take place. E) All of these results will take place. Ans: E Difficulty: 4 40. Which partial diploid strain will produce -galactosidase constitutively, and maintain normal induction of the permease and transacetylase? A) I+ocZ+Y-A-/I+o+Z-Y+A+ B) I+o+Z+Y+A+/I+o+Z-Y+A+ C) I+ocZ-Y+A+/I+ocZ-Y+A+ D) I+ocZ+Y+A+/I+ocZ-Y+A+ Ans: A Difficulty: 4

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41. Initiation of transcription by RNA polymerase involved the binding of which of the following subunits to the core enzyme? A) delta B) sigma C) gamma D) alpha E) zeta Ans: B Difficulty: 2 42. A) B) C) D) E) The transition from transcriptional initiation to elongation involves: binding of sigma factor release of sigma factor release of RNA polymerase from DNA binding of RNA polymerase to DNA binding of rho factor Ans: B Difficulty: 2

43. Proteins that undergo reversible changes in conformation when bound to another molecule are called: A) reversible peptides B) allosteric proteins C) inducer proteins D) repressor proteins E) allostatic proteins Ans: B Difficulty: 3 44. A single DNA unit that enables the simultaneous regulation of more than one gene in response to environmental changes is called: A) promoter B) operator C) regulator D) inducer E) operon Ans: E Difficulty: 2 45. A) B) C) DNA sites can act: only in cis only in trans either in trans or in cis Ans: A Difficulty: 2

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46. A) B) C) D) E)

The scientists who proposed the operon theory were: Monod and Jacob Watson and Crick Hardy and Weinberg Darwin and Mendel Hershey and Chase Ans: A Difficulty: 1

47. A philosophic rule that states, The simplest, most economical explanation is preferable to a more complex one. is: A) Monod and Jacob's rule B) Watson and Crick's rule C) Occam's razor D) operon theory Ans: C Difficulty: 3 48. A) B) C) D) E) A reporter gene is: a protein encoding gene whose expression is easily quantifiable. often fused to another protein to access its activity. often fused to another genes' regulatory region to determine control. all of the above. none of the above. Ans: B Difficulty: 2 The sigma factor that mediates a global heat shock response in E. coli is: sigma 70 sigma 32 sigma 34 sigma 72 sigma 36 Ans: B Difficulty: 1 In the regulation of the trp operon, tryptophan acts as a: repressor attenuator activator corepressor operator Ans: D Difficulty: 3

49. A) B) C) D) E)

50. A) B) C) D) E)

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Matching Match the following terms with the best definition a) inducer b) repressor c) in trans d) in cis e) 70 f) 24 g) 32 h) microarray i) rho factor j) promoter 51. ______ the action of a DNA region that affects the activity of genes on the same chromosome. Ans: d Difficulty: 2 52. ______ an effector molecule that causes the cell to produce larger amounts of the enzymes involved in its metabolism. Ans: a Difficulty: 1 53. ______ normal housekeeping sigma factor. Ans: e Difficulty: 1 54. ______ the action of a DNA element that encodes a diffusible product that can influence the activity of other genes. Ans: c Difficulty: 2 55. ______ an alternative sigma factor that mediates the global response to heat shock. Ans: g Difficulty: 2 56. ______ a region on a DNA molecule to which RNA polymerase binds and initiates transcription. Ans: j Difficulty: 1

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57. ______ an oligomeric protein that attaches to certain DNA sites in order to assist in termination of transcription. Ans: i Difficulty: 3 58. ______ a protein that binds to an operator locus and blocks transcription of that operon. Ans: b Difficulty: 1 59. ______ a technique that can measure relative changes in transcription between two samples. Ans: h Difficulty: 2 60. ______ an alternative sigma factor always present. Ans: f Difficulty: 2 True or False 61. Because there is no nuclear membrane in prokaryotes, transcription and translation from a single gene can be taking place at the same. Ans: True Difficulty: 1 62. Negative regulation of gene expression usually takes place through enhancement of RNA polymerase activity. Ans: False Difficulty: 1 63. Positive regulators actually physically bind to RNA polymerase and enhance the enzyme's ability to initiate transcription. Ans: True Difficulty: 1 64. The concept that proteins bind to DNA and regulate transcription holds true for both positive as well as negative regulation of gene expression. Ans: True Difficulty: 1 65. Attenuation of gene expression is unique to prokaryotes, because it requires translation of a leader sequence at the same time transcription is taking place. Ans: True Difficulty: 1

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66. A chaperone protein is used to aid in the transport of other proteins across cellular membranes. Ans: False Difficulty: 2 67. Bacteriophage T7 promotors are recognized by both E. coli RNA polymerase as well as T7- specific RNA polymerase. Ans: True Difficulty: 3 68. An underlying principle of prokaryotic gene regulation is that it occurs through the binding of regulatory proteins to specific DNA sequences. Ans: True Difficulty: 1 69. There is only one site on the operator to which the lac repressor binds. Ans: False Difficulty: 2 70. In the trp operon, the protein repressor alone cannot bind to the operator to be a negative regulator. Ans: True Difficulty: 1 71. The mechanisms of gene regulation discovered in E. coli are not found in most other prokaryotes. Ans: False Difficulty: 2 72. In prokaryotes, the primary point of gene regulation occurs by either blocking or enhancing transcription. Ans: True Difficulty: 1 73. The occurrence of constitutive mutations of all three of the lactose utilizing enzymes indicates that their synthesis is regulated together, probably by another gene. Ans: True Difficulty: 1 74. Many of the DNA sequences to which negative or positive regulatory proteins bind have the same sequence on both strands of DNA reading in the 5'-3' direction. Ans: False Difficulty: 2

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75. In the operon model of gene regulation, transcription is shut off by the binding of the repressor to the promoter. Ans: False Difficulty: 1 76. Both inducers and corepressors lead to allostearic alterations in the repressor molecule. Ans: True Difficulty: 2 77. The presence of a diffusable gene product (protein) is a requirement for genes to act in trans. Ans: True Difficulty: 3 78. A distinguishing feature of control of gene expression in prokaryotes is that transcription and translation occur completely independently of each other. Ans: False Difficulty: 2 79. Attenuation of the trp operon requires the presence of tryptophanyl-tRNAtrp. Ans: True Difficulty: 3 80. In a repressible operon, the repressor alone can bind to the operator and shut down transcription. Ans: False Difficulty: 2 Short Answer 81. Describe the conditions for maximum induction of the lactose operon. Ans: This would be in a medium containing lactose, but lacking glucose. Under these conditions, the repressor binds inducer and becomes unable to bind to the operator, while CAP complexed with cAMP binds to a site near the promoter to assist RNA polymerase in the initiation of transcription. Difficulty: 3 82. Describe the two binding domains on the lac repressor protein. Ans: The repressor has two distinct binding domains, one for the operator and one for the inducer. Difficulty: 2

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83. Why is the lactose operon not induced in the presence of both lactose and glucose? Ans: Glucose acts in catabolite repression of the operon, even in the presence of lactose. Difficulty: 3 84. Describe the molecular subunit structure of the lac repressor, and explain what enables it to bind to the operator. Ans: The lac repressor protein is a tetramer of four LacI-encoded subunits, with each subunit containing an inducer-binding domain as well as a domain that recognizes and binds to DNA at the operator. Binding of the repressor to two sites in the operator simultaneously, causes a loop in the DNA of the operator to form, thus restricting binding of polymerase to the operator. Difficulty: 4 85. What is the unique feature about the base sequence of the lac operator to which the lac repressor binds? Ans: The lac repressor binds to a region of the operator with rotational symmetry, that is a similarity of sequence on the two strands when read in the 5'-3' directions, similar to a palindrome but not a perfect palindrome. Difficulty: 3 86. In the example of the lac operon, and most operons, what is the significance of a polycistronic message? Ans: This allows the coordinate expression of several functionally related genes. Difficulty: 2 87. Briefly describe the three classes of genes which must be sequentially induced in Rhizobium in order to bring about a functioning nitrogen-fixing nodule in a leguminous plant. Ans: nod genes that elicit the early steps of nodule formation, fix genes that contribute to the development and metabolism of bacteroids, and are essential to nitrogen fixation, and nif genes that encode the polypeptide subunits of the nitrogenase complex. Difficulty: 2 88. Distinguish between positive and negative regulation of transcription. Ans: Negative regulation involves the inhibition of RNA polymerase activity by physically blocking the DNA binding site of RNA polymerase, and positive regulation involves the enhancement of RNA polymerase activity by establishing a contact with RNA polymerase that enhances the enzyme's ability to initiate transcription. Difficulty: 2

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89. Explain how three enzymes appear simultaneously when lactose is introduced into a bacterial culture medium as the sole carbon source. Ans: These three enzymes are translated from a continuous polycistrontic message transcribed from all three genes. Difficulty: 2 90. How does the operator function in the regulation of an operon? Ans: Binding of the repressor to the operator site, blocks the promoter. Specifically, binding of the repressor to the operator keeps RNA polymerase from recognizing the promoter. Difficulty: 2 91. Explain how the CAP protein functions as a positive regulator of the lac operon. Ans: A small nucleotide known as cAMP binds to a protein called cAMP activator protein or CAP. The binding of cAMP to CAP enables CAP to bind to DNA in the regulatory region of the lac operator, and this DNA binding of CAP increass the ability of RNA polymerase to transcribe lac genes. Difficulty: 3 92. What are the two roles glucose plays in lac gene transcription? Ans: Glucose functions to reduce the level of cAMP, and also inhibits the cellular uptake of lactose. Difficulty: 2 93. What is the role of the subunit of RNA polymerase in transcription? Ans: The sigma subunit binds to RNA polymerase allowing it to bind to specific DNA sequences at the promoter. Difficulty: 2 94. What are the three enzymes in the lactose operon and what is their enzymatic function? Ans: -galactosidase splits lactose into glucose and galactose, -galactoside permease transports lactose in the medium into the E. coli cell and transacetylase that adds an acetyl group to lactose and other galactosides. Difficulty: 1 95. Explain the terms, trans acting, and cis acting elements. Ans: Elements that act in trans can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell. Elements that act in cis can only influence the expression of adjacent genes on the same DNA molecule. Difficulty: 2

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Experimental Design and Interpretation of Data 96. Will the production of normal -galactosidase be constitutive, inductive, or absent for each of the following genotypes: (A) I+p+o+Z +Y +A +, (B) I-p+o+Z +Y+A +, (C) I+p+ocZY+A +, (D) I+p+o+Z -Y +A+. Ans: (A) inductive, (B) constitutive, (C) absent, (D) absent. Difficulty: 2 97. Explain how the presence or absence of the amino acid tryptophan attenuates the transcription of the genes in the trp operon. Ans: This addresses attenuation or control of gene expression by premature termination of transcription. There are about 140 bases upstream from the first trp gene. This is called a leader sequence. There is a short open reading frame in the leader containing 14 codons, two of which code for trp. When tryptophan is present, the ribosome moves quickly past the trp codons and proceeds to the end of the leader's codons, allowing formation of the stem-loop 3-4 structure which causes the termination of transcription and thereby attenuation of trp-gene expression. In the absence of tryptophan, the ribosome stalls at the two trp codons in the RNA leader and a 2-3 stem-loop forms which prevents the formation of the 3-4 stemloop allowing transcription to proceed through the leader into the structural genes. Difficulty: 4 98. What would be the phenotype of a mutation in the CAP protein gene and why? Ans: A mutation in the CAP protein would probably be a low-level inducible phenotype, due to the fact that the CAP-cAMP complex would not function as a positive regulator assisting the Polymerase in initiation of transcription. Difficulty: 3 99. More than 20 different DNA-binding proteins in bacteria are similar to the LacI repressor, creating the LacI repressor family of proteins. Why do they all not bind at the lac operator, and repress the lac operon? Ans: Each of the LacI repressor proteins recognizes a slightly different operator DNA sequence, thus allowing them to only act on specific genes. Difficulty: 2 100. What was the advantage to Jacob and Monod by selecting lactose utilization in E. coli in order to discover the operon concept in gene regulation? Ans: The advantage of this lactose utilization system in E. coli allows the ability to grow very large populations of bacteria in order to isolate rare mutants. Difficulty: 2

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Chapter 17Gene Regulation in Eukaryotes Fill in the Blank 1. ______________________ are encoded by DNA distant from the gene being regulated, and often function as DNA-binding proteins. Ans: Trans-acting factors (transcription factors) Difficulty: 1 2. ______________________ are DNA sequences, often found near the 5' end of the regulated gene, to which proteins bind, thus regulating the transcription of the gene. Ans: Cis-acting elements Difficulty: 1 3. Trans-acting factors that function to increase the level of expression of a gene are termed ___________________________. Ans: transcriptional activators Difficulty: 2 4. Trans-acting factors that function to decrease the level of expression of a gene are termed ___________________________. Ans: transcriptional repressors Difficulty: 2 5. The mechanism of transcriptional repression in which trans-acting repressor proteins bind to an activator protein, thus preventing the activator from activating transcription is termed __________________. Repressors that function using this mechanism mediate their effect by binding to either the ________________________ domain or _________________________ domain of the activator protein. Ans: quenching, Transcriptional activation, DNA-binding Difficulty: 3 6. A single strand of nucleotides that is complementary to an mRNA is termed a(n) ___________________ sequence. Ans: antisense Difficulty: 2 7. Numerator and denominator elements regulate sex-determination in Drosophila. If the ratio of numerator homodimers to numerator/denominator heterodimers is high, the ________________ gene will be expressed, generating a fly with ___________________ sexual characteristics. Ans: sxl, female Difficulty: 3

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8. ______________________ is a small protein that is covalently attached to polypeptides in long chains, targeting the tagged peptide for degradation. The large, multienzyme complex that functions to degrade these tagged polypeptides is termed a ___________________. Ans: ubiquitin, proteosome Difficulty: 3 Multiple Choice 9. A) B) C) D) E) Transcription in prokaryotes and eukaryotes is similar in that: transcriptional machinery controls compaction and decompaction of chromatin. the mRNA produced can undergo alternative splicing. both prokaryotic and eukaryotic proteins have identical affinities for DNA. both are contained within the cell nucleus. both are regulated by attachment of proteins to DNA adjacent to the gene being transcribed. Ans: E Difficulty: 3 Most decisions controlling the amount of gene product synthesized are made during: termination of replication. transport of mRNA to the cytoplasm. initiation of transcription. alternative splicing. regulation of translation. Ans: C Difficulty: 2 Zinc-finger peptide motifs are responsible for what aspect of protein function? kinase activity DNA binding mRNA splicing DNA replication methylation Ans: B Difficulty: 2

10. A) B) C) D) E)

11. A) B) C) D) E)

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12. DNA sequences that serve as binding sites for proteins regulating transcription and are often found adjacent to a gene are said to be: A) cross-reacting. B) cis-acting. C) trans-acting. D) origins of transcription. E) transcription factors. Ans: B Difficulty: 2 13. The __________________________ is the cis-acting DNA sequence that serves as the binding site for RNA polymerase. A) promoter B) terminator C) enhancer D) regulator E) initiator Ans: A Difficulty: 1 14. ______________ are cis-acting DNA sequences that often function at a distance from the gene they are regulating. A) Promoter elements B) Terminator elements C) Enhancer elements D) Regulator elements E) Initiator elements Ans: C Difficulty: 2 15. A cis-acting DNA sequence that modulates the basal rate of transcription of a gene is termed a(n): A) repressor. B) activator. C) promoter. D) enhancer. E) initiator. Ans: D Difficulty: 2

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16. In generating a reporter construct to study gene regulation, the reporter gene introduced replaces: A) -galactosidase. B) a random region of DNA. C) the cis-acting regulatory DNA sequence. D) X-gal. E) the coding region of the gene being studied. Ans: E Difficulty: 3 17. Mutations altering the amount of protein synthesized from a reporter construct occur most often in which of the following sequences of DNA? A) The reporter gene. B) Cis-acting DNA elements. C) X-gal coding sequence. D) RNA polymerase II gene. E) none of the above Ans: B Difficulty: 3 18. A) B) C) D) E) Mutations introduced into reporter constructs are used to study: the DNA sequences that are important for regulating gene expression levels. the effects on cell function of expression of heterologous proteins. colorimetric assays. protein-protein interactions. Western blots. Ans: A Difficulty: 2

19. The gene products encoded by trans-acting elements perform their function by: A) associating with regulatory sequences distant from the gene from which they were transcribed. B) regulating the expression of the gene from which they were transcribed. C) the association of nucleotides with the elongating RNA transcript. D) physically associating with DNA polymerase. E) regulating the activity of telomerase. Ans: A Difficulty: 2

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20. A) B) C) D) E)

Trans-acting proteins that influence transcription are commonly referred to as: DNA polymerases. tumor suppressors. enhancers. transcription factors. promoter elements. Ans: D Difficulty: 1 RNA polymerase I synthesizes _________ using a DNA template. dsRNA mRNA tRNA snRNA rRNA Ans: E Difficulty: 2 The transcription and processing of rRNA molecules takes place in: the cytoplasm. Golgi bodies. the nucleolus. the nuclear envelope. ribosomes. Ans: C Difficulty: 1 tRNA molecules are transcribed by: DNA pol I. DNA pol II. DNA pol III. RNA pol I. RNA pol II. RNA pol III. Ans: F Difficulty: 2 The promoter of nearly all eukaryotic genes contains a(n): RNA polymerase binding region. TATA box. initiation site. b and c only a, b and c Ans: E Difficulty: 2

21. A) B) C) D) E)

22. A) B) C) D) E)

23. A) B) C) D) E) F)

24. A) B) C) D) E)

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25. A) B) C) D) E)

Which of the following is not true of enhancer DNA sequences? They contain the TATA box regulatory element. They retain function if their nucleotide sequence is inverted. They can be more than 10 kilobases from the gene they regulate. They may increase or decrease gene transcription levels. They may contain multiple regulatory elements. Ans: A Difficulty: 3

26. A transcription factor that increases initiation of transcription by associating with an enhancer element is termed a(n): A) initiator. B) activator. C) repressor. D) enhancer. E) super-repressor. Ans: B Difficulty: 2 27. A) B) C) D) E) The primary function of basal transcription factors is to: repress transcription initiation of a particular gene. assist in associating RNA polymerase with the promoter element. increase transcription by binding enhancer sequences. activate RNA synthesis at origins of replication. regulate activity of DNA polymerase II. Ans: B Difficulty: 2

28. _____________ are basal transcription factors that associate with TBP to assist in initiating transcription from eukaryotic class II genes. A) TATAs B) DNA- BPs C) TAFs D) Jun and Fos E) Sxl and string Ans: C Difficulty: 2

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29. _______________ motifs function to promote the DNA-binding activity of many transcriptional activator proteins. A) ABP B) Zinc finger C) Basolateral D) Leucine zipper E) Medial cleft Ans: B Difficulty: 2 30. A) B) C) D) E) Proteins that consist of two identical polypeptide subunits are classified as: monomers. oligomers. heterodimers. homodimers. diplomers. Ans: D Difficulty: 2 The leucine zipper motif functions to: mediate the physical association of two polypeptides. anchor transcriptional activator proteins to enhancer sequences. release leucines from misfolded transcription factors. integrate leucines and isoleucines into newly translated transcriptional activators. open up proteins after transcription. Ans: A Difficulty: 3

31. A) B) C) D) E)

32. _________________ are transcription factors that decrease transcriptional activity by associating with specific enhancer elements or activator proteins. A) Deregulators B) Depleters C) Regulators D) Repressors E) TBPs Ans: D Difficulty: 2

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33. Which of the following is not a mechanism employed by repressor proteins to decrease transcription of a specific gene? A) The repressor associates with a promoter element, blocking RNA polymerase from binding promoter element. B) The repressor binds to the activation domain of an activator, eliminating its ability to increase transcription. C) The repressor binds to DNA-binding domain of an activator, eliminating its ability to associate with enhancer. D) The repressor binds to a DNA sequence in an enhancer, eliminating access to sequence by activator. E) The repressor binds to RNA polymerase II, blocking its ability to associate with promoter element. Ans: E Difficulty: 4 34. A) B) C) D) E) The Myc transcription factor functions to increase transcription in specific cell types by: associating with Ras to form heterodimers. forming Myc-Myc homodimers. associating with Max for form heterodimers. dissociating with Fos-Jun heterodimers. enhancing formation of Max-Max homodimers. Ans: C Difficulty: 3 The Myc protein is synthesized only in cells that are: in G0. virally infected. proliferating. cancerous. dormant. Ans: C Difficulty: 3

35. A) B) C) D) E)

36. Which of the following protein dimers are unable to associate with a DNA enhancer element? A) Jun/Jun B) Fos/Jun C) Max/Max D) Myc/Myc E) Myc/Max Ans: D Difficulty: 4

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37. Why do Max/Max homodimers convert to Myc/Max heterodimers in the presence of Myc protein? A) Myc has a higher affinity for Max than Max has for Max. B) Myc more tightly associates with DNA, thus recruiting Max monomers to the enhancer. C) The enhancer element being regulated only associates with Myc/Max heterodimers. D) Max is rapidly degraded in the presence of Myc. E) Myc/Myc homodimers are rapidly degraded in the presence of Max. Ans: A Difficulty: 4 38. Mutations in the GAL80 gene in yeast result in the continuous expression of the GAL1, GAL7, and GAL10 genes, even in the absence of galactose. This genetic evidence suggests that the GAL80 gene product acts as a(n): A) transcriptional repressor. B) promoter element. C) enhancer element. D) transcriptional activator. E) RNA polymerase. Ans: A Difficulty: 4 39. A(n) _____________________ is a cis-acting DNA sequence that functions to regulate a cluster of two or more related genes. A) TBP B) promoter element C) transcriptional activator D) derepressor E) locus control region Ans: E Difficulty: 2 40. A locus control region (LCR) associated with its complete transcription factor complex is referred to as a(n): A) transcriptosome. B) regulosome. C) nucleosome. D) enhanceosome. E) spliceosome. Ans: D Difficulty: 2

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41. Eukaryotic cells are able to carefully regulate precise levels of transcription in specific genes encoding structural proteins through: A) complex enhancer elements that can associate with multiple activator and repressor proteins. B) production of different types of RNA polymerase. C) regulation of the expression of many different transcription factors. D) a and c E) a, b, and c Ans: D Difficulty: 3 42. The ________________ is the repeating structural unit of chromatin, consisting of approximately 200 base pairs of DNA and associated histone proteins. A) transcriptosome B) regulosome C) nucleosome D) enhanceosome E) spliceosome Ans: C Difficulty: 1 43. A) B) C) D) E) The association of DNA with histones to form chromatin affects transcription by: increasing basal transcription rates. decreasing basal transcription rates. increasing transcription of a few genes, while not influencing most others. decreasing transcription of a few genes, while not influencing most others. increasing transcription of some genes and decreasing transcription of others. Ans: B Difficulty: 2 Regions of DNA are most sensitive to DNAase digestion when: they are free of histones. they are maintained as chromatin. the nuclei in which they are contained enter prophase. a cell is in G0. found at a recombination hotspot. Ans: A Difficulty: 2

44. A) B) C) D) E)

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45. A) B) C) D) E)

The DNAase enzyme can be used in assays to identify regions of DNA that are: unable to undergo transcription. associated with DNA polymerase. unable to undergo replication. of the Z-DNA form. free of associated proteins. Ans: E Difficulty: 3 Hypercondensation of heterochromatin results in: hyperactivation of transcription. suppression of progression through metaphase. DNA replication. transcriptional silencing. none of the above Ans: D Difficulty: 2

46. A) B) C) D) E)

47. DNA regions that are transcriptionally silenced by hypercondensation have often undergone a modification of their cytosine residues termed: A) hyperoxidation. B) methylation. C) dephosphorylation. D) phosphorylation. E) integration. Ans: B Difficulty: 2 48. A) B) C) D) E) In yeast, the SIR protein complex physically interacts with histones H3 and H4 to cause: mRNA folding. transcriptional silencing. transcriptional activation. basal transcription. initiation of replication. Ans: B Difficulty: 3

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49. _______________ is used to describe a situation in which a gene's expression pattern is dependent upon the parent from which is was inherited. A) Genomic imprinting B) Spermatogenesis C) Heterodimerization D) Homodimerization E) Gender-specific RNA stability Ans: A Difficulty: 2 50. A variation that does not involve a change in DNA sequence but can be passed from one generation to another is a(n): A) enhancer trap. B) replication origin. C) Mendelian enhancer. D) mutant chromosome. E) epigenetic condition. Ans: E Difficulty: 3 51. In Drosophila females, Sxl protein associates with RNA transcribed from the ________________ gene, altering its splicing pattern. A) sax B) max C) sxl D) myc E) SIR Ans: C Difficulty: 4 52. A) B) C) D) E) Loss of the poly-A tail associated with eukaryotic mRNAs results in: rapid translation of the transcript. elongation of the transcript. decreased translation initiation on the transcript. rapid degradation of the transcript. the addition of a new polyA sequence to the transcript. Ans: D Difficulty: 2

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53. A) B) C) D) E)

The half-life of an mRNA transcript can be increased by: increasing RNA polymerase activity. decreasing the rate at which the transcript is synthesized. increasing the length of the polyA tail on the transcript. decreasing RNA polymerase activity. increasing the translation rate on the transcript. Ans: C Difficulty: 3

54. A change in nucleotide sequence that occurs after transcription and RNA splicing is termed: A) mRNA polishing. B) post-translational modification. C) methylation. D) mRNA editing. E) polymerase mutagenesis. Ans: D Difficulty: 2 55. Which of the following is not a mechanism for post-translational modification controlling gene function? A) ubiquitination B) methylation C) phosphorylation D) dephosphorylation E) all are post-translational modifications Ans: B Difficulty: 4 56. A) B) C) D) E) Recessive mutations in the sxl gene in Drosophila are lethal in XX females because: sxl functions as a repressor of a male-specific dosage of compensation genes. recessive mutations indicate an increase in sxl activity. these mutations are the result of a loss of both X chromosomes. sxl is required for transcription of male-specific genes. recessive mutations are always lethal. Ans: A Difficulty: 3

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57. ___________________ are short sequences of DNA of a predetermined sequence that are synthesized in vitro. A) Northern blots B) cDNAs C) Exotranscripts D) Ribonucleases E) Oligonucleotides Ans: E Difficulty: 2 58. Which of the following is not a difficulty encountered by molecular biologist attempting to develop oligonucleotide therapies from treatment of cancer? A) The oligonucleotides are much larger than antibodies and proteins. B) Oligonucleotides of differing lengths are effective against different genes. C) Short oligonucleotides are often complementary to more than one gene. D) Oligonucleotides may adversely affect critical internal organs. E) Oligonucleotides have decreasing specificity as the number of nucleotides they contain decreases. Ans: A Difficulty: 4 Matching In the problem below, match each of the enzymes with the protein function a. Synthesizes tRNAs and other small RNA molecules. b. Post-translationally modifies proteins by phosphorylating specific amino acids. c. Digests DNA molecules. d. Digests RNA in DNA/RNA hybrid molecules. e. Generates RNA molecules that become functional components of ribosomes. f. Modifies cytosines in CG dinucleotides, often resulting in transcriptional silencing. g. Generates long ribonucleotide sequences composed only of adenines for attachment to 3' ends of many mRNAs. h. Synthesizes RNA molecules that encode polypeptide sequences. 59. Ribonuclease H Ans: d Difficulty: 2 60. Poly-A polymerase Ans: g Difficulty: 2 61. Kinase Ans: b Difficulty: 2

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62. RNA polymerase I Ans: e Difficulty: 1 63. RNA polymerase II Ans: h Difficulty: 1 64. RNA polymerase III Ans: a Difficulty: 1 65. DNAase Ans: c Difficulty: 2 66. Methylase Ans: f Difficulty: 3 Match each of the proteins with the correct protein function a. Becomes covalently bound to specific proteins, thus targeting those proteins for destruction. b. Binds to specific enhancer elements to control mating type in yeast. c. Functions in association with other proteins to control gene expression by regulating chromatin structure. d. Forms homodimers that bind specific enhancers to repress transcription in terminally differentiated cells. e. Activates transcription of galactose metabolizing genes in yeast. f. Assists in binding of RNA polymerase II to promoter elements. g. Marker protein that fluoresces green when exposed to specific wavelengths of light. h. Represses expression of yeast galactose metabolizing genes by quenching a transcriptional activator protein. 67. Gal4 Ans: e Difficulty: 3 68. TBP Ans: f Difficulty: 2 69. Ubiquitin Ans: a Difficulty: 2

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70. 2 repressor Ans: b Difficulty: 3 71. GFP Ans: g Difficulty: 1 72. Max Ans: d Difficulty: 3 73. Gal80 Ans: h Difficulty: 3 74. SWI Ans: c Difficulty: 4 True or False 75. cis-acting elements are DNA sequences that serve as attachment sites for DNA-binding proteins that regulate the initiation of transcription. Ans: True Difficulty: 1 76. Trans-acting elements are genes located somewhere other than at the target gene and encode proteins that regulate another gene. Ans: True Difficulty: 1 77. RNA polymerase III transcribes all protein-encoding genes. Ans: False Difficulty: 2 78. Enhancers are regulatory sites that are next to the promoter. Ans: False Difficulty: 2 79. Basal transcription factors bind to the promoters of all protein-encoding genes. Ans: True Difficulty: 1

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80. In repressor quenching, a repressor protein binds directly to an activator protein. Ans: True Difficulty: 1 81. The max gene is expressed at all times. Ans: True Difficulty: 1 82. A locus control region acts in cis at a long distance. Ans: True Difficulty: 1 83. One function of chromatin is to increase transcription to a high basal level. Ans: False Difficulty: 2 84. Genomic imprinting is an example of epigenetic alteration of DNA. Ans: True Difficulty: 1 Short Answer 85. All somatic cells in an individual have the same genetic content. Yet different cell types have different functions. What allows two cells with identical DNA content to function differently? Ans: Although DNA content is identical, different genes are expressed in different cells. Difficulty: 2 86. Reporter constructs are used to identify and characterize DNA sequences that regulate the expression levels of specific genes. What two DNA sequences are linked together to generate a reporter construct? Ans: Cis-acting regulatory sequences from the gene being studied, and DNA sequence encoding the reporter gene product. Difficulty: 3 87. Unlike prokaryotes, eukaryotes have three RNA polymerases. What are they and what does each do? Ans: RNA polymerase I, II, and III are responsible for transcription of rRNA, mRNA, and tRNA and other small RNAs respectively. Difficulty: 2

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88. Each eukaryotic class II gene contains two kinds of essential DNA sequences. What are they? Ans: All eukaryotic class II genes contain promoter and enhancer regions. Difficulty: 3 89. What is an enhancesome? Ans: The term enhancesome is used to describe a multimeric complex of proteins and other small molecules associated with an enhancer element. Difficulty: 3 90. How does a Locus Control Region regulate a cluster of genes? Ans: Like an enhancer, the LCR functions by binding to transcription factors with activation domains. Unlike most enhancers, however, the LCR-transcription factor complex interacts sequentially with other transcriptions factors at cis-regulatory regions that are directly adjacent to each gene in the cluster. Difficulty: 4 91. How does chromatin structure regulate gene transcription? Ans: Basic chromatin structure keeps eukaryotic transcription at a relatively low level. Remodeling of chromatin can either completely silence or activate regional transcription. Hypercondensed regions are silenced. Remodeling proteins can cause specific nucleosomes to unravel and expose promoter regions in specific cells at specific times, which allows activation of some genes. Difficulty: 3 92. Why is genomic imprinting considered an epigenetic alteration? Ans: The methylation of CG dinucleotides within an imprinted region prevent RNA polymerase from gaining access to the DNA and although the region is affected for the life of the organism, the change is not encoded in the DNA and it is thus epigenetic, (outside the genes, but inherited). Difficulty: 4 Experimental Design and Interpretation of Data 93. You are studying a brain region specific mouse gene. You have cloned and sequenced the gene but wish to identify the DNA sequences that direct the regional specificity. Describe an experimental technique that would allow you to test this. Ans: You could clone the upstream region, 5'UTR, introns and 3'UTR individually into reporter constructs and make transgenic mice. The DNA segment responsible for the regulation of regional expression would allow reporter gene transcription in the brain region of interest while the other DNA sequences would not. Difficulty: 4

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94. Describe the results you would expect on Northern and Western analyses if a hypothetical gene was up-regulated at the transcriptional level in response to the presence of zinc. How would your results differ if zinc acted to reduce the turn-over of the protein? Ans: In the presence of zinc, Northern analysis would show more mRNA (a darker band) for the gene in comparison to controls without zinc. Western analysis should also detect more protein present in the presence of zinc if no other regulation changes occurred. In the latter case where zinc was known to effect protein turnover, there should be no difference in band intensity between control and zinc treated sample on the Northern blot but an increase in protein detected on the Western blot. Difficulty: 3 95. You have cloned and sequenced a new mouse gene and wish to know whether chromatin structure may effect its transcription. You DNase treat and then run Southern analysis. In the mouse strain with hypothetical phenotype A you detect your gene but it is not detected in DNase treated samples from the mouse strain with phenotype B. What do you suspect as the cause? Ans: The detection of your gene on a Southern blot indicates that the genomic DNA for your gene was protected by nucleosomes from DNase digestion and would therefore be inactive.Conversely, when the gene is not detected on Southern analysis following DNase digestion, the gene is not protected by chromatin structure and should therefore be active in vivo. Difficulty: 4 96. Gene A is maternally imprinted while Gene B is paternally imprinted. A Mom with Genes A and B imprinted and a Dad with an imprinted Gene A have a daughter and a son. The children then marry individuals known not to be imprinted for either gene. What is the imprint status of the daughter and son respectively? If each marriage results in the birth of a daughter and a son, what would you expect the imprint status of genes A and B for the grandchildren. Ans: Mom is imprinted for Gene A and B but only passes on an imprinted Gene A (to all her children). The Dad is imprinted for Gene A but since this is a maternally imprinted gene, he does not pass any imprint to his children. Therefore, all four children inherit an imprinted Gene A and a Gene B that is not imprinted. The children of the daughter will be the only grandchildren with imprinting and then only on Gene A. The grandsons are not imprinted for either Gene A or B. Difficulty: 4

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Chapter 18Cell-Cycle Regulation and the Genetics of Cancer Fill in the Blank 1. Mutations in the RB gene have been linked to inheritance between generation of some types of cancers. A mutation in RB is dominant for _____________________ cancer in individuals, while a mutation in RB is recessive for ___________________ cancer in individual cells. Ans: susceptibility to, expression of (or progression to) Difficulty: 3 2. Researchers have isolated cell-cycle-defective, temperature sensitive mutants in which a protein needed for cell division functions normally at a _____________________ temperature but loses function at a higher ______________________ temperature. Ans: permissive, restrictive Difficulty: 3 3. An enzyme converts a ___________________________ to a _______________________ . Ans: substrate, product Difficulty: 3 4. _________________________________ kinases control the cell cycle by phosphorylating other proteins. Ans: cyclin-dependent Difficulty: 3 5. An arrest in the cell cycle for repair is called a ____________________. Ans: check point Difficulty: 3 6. An increase from the normal two copies to hundreds of copies of a given gene indicates gene ________________________ has occurred. Ans: amplification Difficulty: 3 7. During ____________________, or programmed cell death, DNA is degraded and the nucleus condenses in a response to the presence of DNA damage. Ans: apoptosis Difficulty: 3 8. _________________ factors are extracellular hormones and cell-bound signals that stimulate or inhibit cell proliferation. Ans: growth Difficulty: 3

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9. Mutant alleles that act dominantly with respect to a cancer phenotype are called _________________. Ans: oncogenes Difficulty: 3 Multiple Choice 10. A) B) C) D) E) DNA replication occurs during ______ of the cell cycle. prophase G1 phase S phase G2 phase mitosis Ans: C Difficulty: 1 Which of the following does not occur during mitosis? Segregation of sister chromatids. Duplication of chromosomal DNA. Condensation of chromosomes. Nuclear envelope breakdown. Attachment of chromosomes to mitotic spindle. Ans: B Difficulty: 2

11. A) B) C) D) E)

12. The yeast Saccharomyces cerevisiae is particularly useful for genetic analysis of cell cycle control because: A) it is prokaryotic, allowing it to divide rapidly. B) mutant yeast cells form cancerous tumors. C) reproduction by budding allows easy identification of stage in cell cycle. D) all cells in a culture remain at the same stage of the cell cycle. E) yeast cells lack G1 and G2 stages. Ans: C Difficulty: 3 13. The yeast Saccharomyces cerevisiae reproduces _______________, allowing easy determination of the cell cycle stage in which a cell is found. A) ambiguously B) by fission C) sexually D) amorphously E) by budding Ans: E Difficulty: 1

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14. In the cell cycle of Saccharomyces cerevisiae, the appearance of a bud on the surface of a cell indicates that the cell: A) is entering M phase. B) has a mutation in a gene regulating G2M transition. C) is haploid. D) has a mutation in a gene regulating G2S transition. E) reaching the end of G1 phase. Ans: E Difficulty: 2 15. The temperature at which a cell with a temperature-sensitive mutation is unable to survive is considered the ___________ temperature. A) restrictive B) mutant C) dissociative D) permissive E) alternative Ans: A Difficulty: 1 16. The cells in a population of yeast cells in which all members of the population have a temperature-sensitive mutation in the same gene involved in cell cycle progression will appear _________ when shifted to the restrictive temperature. A) to vary in morphology B) as clumps of lysed cells C) to adhere to each other D) uniform in size and shape E) arrested in all stages of the cell cycle Ans: D Difficulty: 3 17. The ________ gene controls progression through start at the end of G1 in the cell cycle. A) CDK B) RAS C) CDC28 D) RAD9 E) DCC Ans: C Difficulty: 3

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18. A) B) C) D) E)

Enzymes that covalently link phosphate groups to their substrates are termed: kinases. phosphatases. cyclins. phosphatase inhibitors. ligases. Ans: A Difficulty: 2

19. CDKs, such as CDC28, require the assistance of ____________ to carry out their enzymatic activity. A) restriction enzymes B) proteases C) nucleases D) growth factors E) cyclins Ans: E Difficulty: 2 20. ________________ are proteins that form a structural scaffold on the inner surface of the nuclear membrane. A) Mitotic tubules B) Nuclear lamins C) Chromatin fibrils D) CDKs E) Histones Ans: B Difficulty: 2 21. A) B) C) D) E) The solubility of nuclear lamins is regulated by the _____________ of lamin proteins. length phosphorylation state kinase activity molecular weight condensation Ans: B Difficulty: 3

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22. The retinoblastoma (Rb) protein regulates progression into S phase by regulating ___________ activity. A) cyclin D B) p53 C) CDK4 D) E2F E) CDC28 Ans: D Difficulty: 3 23. A) B) C) D) E) The activity of Rb is regulated by: its phosphorylation state. cyclin A. E2F. its polyA tail. its level of methylation. Ans: A Difficulty: 2 The ____________ checkpoint is disrupted by mutations that alter p53 function. G0-to-G1 G1-to-S S-to-G2 G2-to-M M-to-G1 Ans: B Difficulty: 3 Which of the following is not likely to result form the loss of functional p53? The appearance of homogenously staining regions on chromosomes. Increases propensity to arrest in G1. Alterations in the G1 to S checkpoint. An increase in gene amplification in affected cells. Generation of fragments of chromosomal DNA lacking telomeres and centromeres. Ans: B Difficulty: 3 A programmed cell change that results in cell death is referred to as: apoptosis. G1 regulation. post-translational control. cancer. metastasis. Ans: A Difficulty: 2

24. A) B) C) D) E)

25. A) B) C) D) E)

26. A) B) C) D) E)

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27. Damage to DNA that takes place during DNA replication results in arrest of normal cells at the _______________ checkpoint. A) G0-to-G1 B) G1-to-S C) S-to-G2 D) G2-to-M E) M-to-G1 Ans: D Difficulty: 4 28. The cell-cycle checkpoint that occurs during mitosis causes nuclear division to pause until: A) DNA replication is complete. B) sister chromatids have separated. C) cytokinesis occurs. D) telophase begins. E) all chromosomes have attached to the mitotic spindle. Ans: E Difficulty: 3 29. CDKs associate with cyclins at specific stages of the cell cycle. The CDK subunit is responsible for phosphorylating a substrate protein, while the cyclin is responsible for: A) progression into G0. B) degradation of the CDK after phosphorylation. C) ubiquitin function. D) dephosphorylating Rb. E) determining which specific proteins will be phosphorylated. Ans: E Difficulty: 3 30. Which of the following is not a common consequence of mutations that eliminate cellcycle checkpoints? A) Increased DNA damage B) Decreased frequency of cell division C) Polyploidy D) Aneuploidy E) Increased chromosome loss Ans: B Difficulty: 3

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31. Molecules that function to stimulate or inhibit cell division are collectively referred to as: A) transcription factors. B) polymerases. C) kinases. D) growth factors. E) checkpoints. Ans: D Difficulty: 2 32. _______________________ are proteins that span the plasma membrane and transmit signals from outside the cell into the cytoplasm. A) Receptors B) Transcription factors C) Growth factors D) Nucleosomes E) Polymerases Ans: A Difficulty: 2 33. A) B) C) D) E) Cytoplasmic proteins that relay signals inside the cell are referred to as: growth factors. signal transducers. receptors. transcription factors. polymerases. Ans: B Difficulty: 2 In its active form, the RAS protein is associated with: DNA. ATP. GTP. RNA. GDP. Ans: C Difficulty: 3

34. A) B) C) D) E)

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35. The generation of a cancerous cell requires mutations in ____________ of that cell's genes. A) none B) one C) two D) 5-10 E) more than 100 Ans: D Difficulty: 1 36. All cells in a cancerous tumor arise from a single mutant precursor cell, meaning that the cells in the tumor are: A) sporadic. B) spastic. C) benign. D) divisionary. E) clonal. Ans: E Difficulty: 3 37. A) B) C) D) E) Which of the following statements regarding cancer is true? All cancers are genetic. All cancers are sporadic. All cancers run in families. None of the above a, b, and c Ans: A Difficulty: 2

38. ______________________ are mutant forms of normal genes that act dominantly to predispose a cell to a cancerous phenotype. A) Polymerases B) Oncogenes C) Activators D) Tumor suppressors E) Proto-oncogenes Ans: B Difficulty: 2

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39. Genes whose mutant alleles can function in a recessive manner to predispose cells to cancerous growth are referred to as: A) polymerases. B) oncogenes. C) activators. D) tumor suppressors. E) proto-oncogenes. Ans: D Difficulty: 1 40. The human papilloma virus (HPV) carries a gene that functions as an oncogene by inactivating the p53 protein. The fact that the loss of p53 function is oncogenic suggests that: A) p53 normally functions to prevent uncontrolled cell division. B) The HPV protein is encoded by a tumor suppressor gene. C) p53 gene expression is upregulated by the HPV protein. D) The HPV protein functions at origins of replication on DNA. E) p53 is a proto-oncogene. Ans: A Difficulty: 4 41. A) B) C) D) E) Some oncogenic forms of the RAS protein are oncogenic because they are unable to: convert GDP to dGDP. associate with GTP. release ATP. hydrolyze GTP to GDP. convert ADP to ATP. Ans: D Difficulty: 4

42. Genes encoding which of the following protein types do not function as oncogenes when mutated? A) transmembrane receptors B) transcription factors C) signal transmitters D) growth factors E) tumor suppressors Ans: E Difficulty: 3

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43. A) B) C) D) E)

Normal alleles of tumor suppressor genes function to encode proteins that: promote transition from G1-to-S. can slow the rate of cell division. increase the rate of mutagenesis. activate oncogenes. associate with growth factors at the cell surface. Ans: B Difficulty: 1

44. Tumor cells removed from an individual with retinoblastoma are _________________ for a deletion of the RB gene. A) homozygous B) heterologous C) hemizygous D) heterozygous E) endozygous Ans: A Difficulty: 2 45. Which of the following does not function to reduce the likelihood of a cell becoming cancerous? A) Alternative splicing within the nucleus B) Mismatch repair enzymes C) Proofreading ability of DNA polymerases D) Cell cycle checkpoints E) Tumor suppressor genes Ans: A Difficulty: 3 46. A) B) C) D) E) Cells that have migrated from a tumor and invaded a distant tissue are said to have: acclimated. metastasized. mutagenized. carcinogized. capacitated. Ans: B Difficulty: 1

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47. Glioblastoma multiforme (GBM) is an aggressive cancer caused by alterations in _________________ in the brain. A) arteries B) neurons C) glial cells D) mitochondria E) lymphocytes Ans: C Difficulty: 1 48. A) B) C) D) E) Glioblastoma multiforme (GBM) results from mutations in genes encoding: proto-oncogenes. tumor suppressors. cell cycle inhibitors. a and c a, b, and c Ans: E Difficulty: 2

49. Alterations in the activity of cyclin-dependent kinases can affect the _____________ cell cycle checkpoint. A) G1-to-S B) S-to-G2 C) G2-to-M D) a or c only E) a, b, or c Ans: D Difficulty: 1 50. _____________________ are enzymes that function to promote or inhibit cell cycle progression by phosphorylating specific substrates. A) Cyclins B) Growth factors C) Mutagens D) Cyclic phosphatases E) Cyclin dependent kinases Ans: E Difficulty: 2

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51. ______________________ are proteins that assist in regulating cell cycle progression and are often rapidly degraded at specific times in the cell cycle. A) Cyclins B) Growth factors C) Mutagens D) Receptors E) Cyclin dependent kinases Ans: A Difficulty: 2 52. Cyclin dependent kinases require _______________________ to catalyze phosphorylation of appropriate substrate proteins. A) cyclins B) growth factors C) mutagens D) receptors E) aneuploidy Ans: A Difficulty: 2 53. A) B) C) D) E) Genetic testing for cancer can: identify individuals that are resistant to cancer. indicate increased risk for certain cancers. predict the age of cancer onset in an individual. eliminate the possibility that an individual will develop cancer. none of the above Ans: B Difficulty: 1 Which of the following functions to regulate the G2-to-M transition? cyclin A cyclin B cyclin C cyclin D cyclin E Ans: B Difficulty: 3

54. A) B) C) D) E)

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55. In Saccharomyces cerevisiae, the _________________ protein inhibits progression of the cell cycle into mitosis in response to DNA damage. A) p53 B) RAD9 C) Rb D) E2F E) CDK Ans: B Difficulty: 2 56. Proteins produced from tumor suppressor genes function as _____________________ regulators of cell cycle progression. A) proto-oncogenic B) positive C) mutant D) non-functional E) negative Ans: E Difficulty: 2 57. Oncogenes found in viral genome often cause _____________________ when incorporated into eukaryotic cells. A) cell death B) arrest in G0 C) increased cell proliferation D) arrest at the G2-to-M checkpoint E) apoptosis Ans: C Difficulty: 1 58. One characteristic of cancer is unregulated cell proliferation. A second characteristic of cancer cells is: A) the synthesis of additional copies of DNA polymerase. B) arrest in G0. C) the failure to expand clonally. D) apoptosis. E) the ability to migrate to distant tissues. Ans: E Difficulty: 2

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59. The point in the cell cycle at which a cell is committed to progression from G1 phase into S phase is termed: A) M. B) CDC28. C) G0. D) Start. E) Ontogeny. Ans: D Difficulty: 2 Matching Using the cell stages listed, indicate the stage in the cell cycle in which each event occurs in eukaryotic cells a. G0 b. G1 c. G2 d. M e. S 60. Cyclin A association with CDKs. Ans: e Difficulty: 3 61. Formation of CDK4/cyclin D complexes. Ans: b Difficulty: 2 62. DNA replication. Ans: e Difficulty: 1 63. Initial bud formation in Saccharomyces cerevisiae. Ans: b Difficulty: 2 64. Preparation for nuclear division. Ans: c Difficulty: 1 65. Chromosome segregation. Ans: d Difficulty: 1

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66. Preparation for duplication of DNA. Ans: b Difficulty: 2 67. Lamin dephosphorylation. Ans: d Difficulty: 3 68. Chromosome condensation. Ans: d Difficulty: 2 69. Cell cycle arrest in S. cerevisiae CDC28 mutants. Ans: b Difficulty: 2 70. Repair of DNA damaged by single-strand nicking. Ans: b Difficulty: 3 71. Formation of CDK2/cyclin E complexes. Ans: b Difficulty: 4 72. Phosphorylation of Rb protein. Ans: b Difficulty: 3 73. Formation of CDC2/cyclin B complexes. Ans: c Difficulty: 4 True or False 74. The cell cycle has four phases, G, S1, S2, and M. Ans: False Difficulty: 2 75. Of the approximately 300 cell types, some, once terminally differentiated, never divide again even if life continues for nearly a century. Ans: True Difficulty: 1

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76. The S phase is when sister chromosomes segregate into daughter cells. Ans: False Difficulty: 2 77. A temperature sensitive screen is completed by treating cells with mutagen, replica plating, and then selecting for growth in permissive and restrictive temperatures. Ans: True Difficulty: 1 78. Cyclin-dependent kinases together with cyclins control the timing of cell-cycle events. Ans: True Difficulty: 1 79. Cell-cycle check points are arrests to the cell cycle in which the integrity of the genome and cell-cycle machinery are checked prior to continuing to the next cell-cycle stage. Ans: True Difficulty: 1 80. As cells begin DNA replication in the S phase, cyclin A is degraded and cyclins D and E are synthesized. Ans: False Difficulty: 2 81. An enzyme that removes a phosphate group from proteins is called a phosphatase. Ans: True Difficulty: 1 82. DNA damage activates the p53 transcription factor, which in turn induces expression of the p21 gene. Ans: True Difficulty: 1 83. DNA damage in normal cells only rarely leads to apoptosis. Ans: False Difficulty: 2 Short Answer 84. The cells in a cancerous tumor are described as being clonal. What does this mean? Ans: All cells in the tumor are descendants of a single precursor cell. Difficulty: 2

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85. Cell-surface receptors function to transmit signals from the outside of the cell into the cytoplasm. Name the three protein domains that are responsible for receptors to accomplish this signal transmission. Ans: Signal-binding site, transmembrane domain, and intracellular signal transmission domain. Difficulty: 3 86. You have generated a novel mutation in a strain of S. cerevisiae, and you designate this mutation CDC90 because the mutated gene appears to encode a protein that functions in regulating cell cycle progression. Interested in studying the CDC90 mutation further, you obtain a CDC28 mutant yeast strain from a colleague and observe that the CDC90 and CDC28 mutant strains exhibit different phenotypes. How could you determine if one of these mutations functions upstream from the other in controlling progression of yeast cells through the cell cycle? Ans: Generate a mutant yeast strain that contains both the CDC28 and CDC90 mutations and perform epistatic analysis. If the double mutant has the phenotype of one of the mutations, then that mutation is epistatic and is upstream in the pathway. Difficulty: 4 87. Name two mechanisms by which a retrovirus carrying a proto-oncogene can convert to proto-oncogene to an oncogene. Ans: A mutation can occur in the viral genome that alters the sequence of the protooncogene itself, thus generating an oncogene. Or, the proto-oncogene can be inserted adjacent to a strong promoter, resulting in overexpression of the gene. Difficulty: 3 Define (Provide a two- or three- sentence definition or description of the following terms or genes) 88. Proto-oncogene Ans: Normal gene regulating cell proliferation that can become an oncogene when mutated. Difficulty: 2 89. Apoptosis Ans: Programmed cell death in which the cell coordinates its own DNA degradation and nuclear condensation. Difficulty: 3 90. CDK Ans: Cyclin-dependent kinase. A family of proteins that phosphorylate specific substrates in response to a cell-cycle dependent association with specific cyclins. Difficulty: 2

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91. Signal transduction Ans: The relaying of a signal through the cytoplasm to the nucleus in order to mediate a cellular response to an extracellular signal. Difficulty: 3 92. Oncogene Ans: Mutant allele of a proto-oncogene that acts dominantly to promote a cancerous phenotype. Difficulty: 2 93. RB Ans: Retinoblastoma tumor suppressor gene. Unphosphorylated form of Rb gene product inhibits a transcription factor required for DNA replication, while phosphorylation of Rb allows progression into S-phase. Difficulty: 2 94. Astrocyte Ans: Glial cell that provides support for neurons in the brain. Multiple mutations in astrocytes often result in the generation of cancerous brain tumors referred to as astrocytomas. Difficulty: 4 95. Tumor suppressor gene Ans: Encodes gene products that inhibit unregulated cell division. Mutant tumor suppressor alleles function recessively in promotion of a cancerous phenotype in a cell. Difficulty: 2 96. Growth factor Ans: Molecule that affects cell proliferation. Generally, growth factors stimulate proliferation by associating with receptor proteins on the affected cell. Difficulty: 2 97. Glioblastoma multiforme Ans: The most malignant form of brain cancer, resulting from multiple mutations in genes regulating proliferation in a glial cell. Difficulty: 3

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Experimental Design and Interpretation of Data 98. A patient presents with cancer tumors in several organs. You genotype for several genes often related to the causation of cancer and find that cells from each disparate tumor have the same genotype for all of the genes tested. How do you interpret this data? Ans: The results are highly suggestive that the cells are clonal, arising from a single cell, and metastasized to the different organs found to contain cancerous tumors whose cells are genetically identical for those genes tested. Difficulty: 4 99. You wish to determine which genes are aberrantly expressed in a certain type of cancer. How would you measure a possible transcription difference on a genomic level between the cancer cells and normal cells? Ans: Isolate tumor cells and normal cells and perform microarray analysis using chips that contain the entire human genome. Differences in expression are detected by red/green fluorescence indicating up and down regulation of tumor cells compared to normal control cells. Difficulty: 4 100. You have identified a mutation in Gene X that appears along with mutations in three other genes to cause an increased likelihood for a certain cancer. Develop an assay to test patients for the polymorphism in Gene X. Ans: Utilize sequence information to determine differences in restriction enzyme sites between the wild-type and the mutant alleles. Using an enzyme that cuts one but not the other you can complete Southern analysis on digested DNA from each and look for one versus two bands. Alternatively you can design PCR primers and directly detect the bands by gel electrophoresis. Difficulty: 4 101. Using yeast, you wish to test the hypothesis that two new temperature-sensitive mutations you have isolated are involved in different steps of the cell cycle. Describe the experimental setup necessary to do so. Ans: Test each single mutant for cell cycle arrests as well as a double mutant (Epistasis experiment) containing both mutations. The phenotype of the double mutant will be the same as one of the two single mutants. This will represent the gene involved in the earlier of the two steps in the cell cycle. Difficulty: 4

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Chapter 19Using Genetics to Study Development Fill in the Blank 1. Cells ________________ from each other during embryonic development to form hundreds of different cell types. Ans: differentiate Difficulty: 2 2. In humans, TDF encoded by the SRY gene is involved in _______ determination. Ans: sex Difficulty: 2 3. When a loss-of-function mutation has a dominant effect it is termed_______________. Ans: dominant negative Difficulty: 2 4. An experimental strategy the uses dsRNA to deplete proteins products in a cell is called ___________. Ans: RNAi Difficulty: 3 5. __________________ gene expression is when a gene is expressed at an abnormal time or place. Ans: ectopic Difficulty: 3 6. The production of as many different mutants with related phenotypes as possible in an attempt to identify all the genes relevant to a process is called _____________________. Ans: saturation mutagenesis Difficulty: 3 7. ___________________ genes perform the same function and only one or the other is needed for the production of the wild-type phenotype. Ans: redundant Difficulty: 3 8. A mutation in one gene that compensates for or counteracts the effects of a mutation in another gene is known as a ___________________ mutation. Ans: suppressor Difficulty: 3

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9. A mutation that intensifies the effects of a first mutation is called an _____________ mutation. Ans: enhancer Difficulty: 3 10. The phenomenon of _________________________ arises when an individual simultaneously heterozygous for two genes exhibits an abnormal developmental phenotype that does not occur in individuals that are heterozygous for either mutation alone. Ans: nonallelic noncomplementation Difficulty: 4 11. A ______________________ is a common motif in proteins with developmental significance. Ans: homeodomain Difficulty: 3 12. ________________ are genetic mosaics in which the cells of different genotype come from two different individuals. Ans: chimeras Difficulty: 2 13. A protein tagged with GFP is an example of a _____________ protein. Ans: fusion Difficulty: 2 14. Development requires progressive changes in _____________________. Ans: gene expression Difficulty: 2 15. ____________________ are molecules whose concentration determines the developmental fate of a cell. Ans: morphogens Difficulty: 2 Multiple Choice 16. A) B) C) D) Which of the following is not a taboo on the use of humans in genetics studies. phenotypic analysis. experimental manipulation of affected individuals. forced matings. deliberate production of mutants. Ans: A Difficulty: 1

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17. A) B) C)

Evolution has had what effect on development in various organisms: varying. conservation of many genes and genetic pathways. none. Ans: B Difficulty: 1 Mutations that disrupt the earliest stages of human development almost always cause: no effect.. polydactyly. spontaneous abortion. disruption of the segmented body plan. Ans: C Difficulty: 2 Development occurs properly due to gene expression: at the right time. in the right place. in the right amount. all of the above. Ans: D Difficulty: 1 Cellular lineage in C. elegans is discerned by: gene tagging genotyping staining microscopy Ans: D Difficulty: 2 If you wanted to study cellular linage, which model organism would be best suited? E. coli S. cerevisiae C. elegans M. musculus Ans: C Difficulty: 3

18. A) B) C) D)

19. A) B) C) D)

20. A) B) C) D)

21. A) B) C) D)

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22. Which of the following model organisms would be easiest to study recessive mutations using complementation analysis: A) S. cerevisiae B) C. elegans C) M. musculus Ans: B Difficulty: 3 23. Which of the following model organisms would best be used to complete quantitative trait loci analysis for traits related to development of physical size: A) E. coli B) S. cerevisiae C) C. elegans D) M. musculus Ans: A Difficulty: 2 24. The Aniridia gene in humans is involved in eye formation. Although eye development is very different in flies, this gene is highly conserved. What is its homolog in Drosophila: A) ey B) Pax-6 C) noeye D) ommatidia Ans: A Difficulty: 2 25. A) B) C) D) How is sexual differentiation different in Drosophila than in hum Drosphila differentiate based on a cascade of splicing factors. Drosphila differentiate based on a transcription factor produced by the SRY gene. Drosphila differentiate based on temperature. Drosphila differentiate based on maternal imprinting. Ans: A Difficulty: 2 A loss-of function mutation that depends on special circumstances: null hypomorphic conditional dominant-negative Ans: C Difficulty: 2

26. A) B) C) D)

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27. A) B) C) D)

A loss-of-function mutation is best described as a: conditional hypomorphic null dominant-negative Ans: C Difficulty: 1 An unusual loss-of-function mutation that is not recessive: null hypomorphic conditional dominant-negative Ans: D Difficulty: 2 A partial loss-of-function mutation: null hypomorphic conditional dominant-negative Ans: B Difficulty: 3

28. A) B) C) D)

29. A) B) C) D)

30. What type of mutation is particularly useful to researchers who wish to study a gene's effect on development when a natural loss-of function mutation has not yet been isolated: A) haploinsufficient B) hypomorphic C) conditional D) dominant-negative Ans: D Difficulty: 4 31. What is the most significant advantage to using RNAi to study development: A) geneticists have only been able to identify a subset of the genes involved in development. B) genetic studies on a single gene can be completed without the creation or isolation of new mutant organisms. C) RNA is easy to isolate. D) RNAi causes phenotypes not typical of in vivo development. Ans: B Difficulty: 3

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32. A) B) C) D)

RNAi: depletes protein products of genes. uses dsRNA to trigger the degradation of mRNA. is used to create a functional knock-out. all of the above. Ans: D Difficulty: 3 Results from RNAi studies are most likely to vary due to: varying amount of cellular uptake of dsDNA. its nonheritable characteristic. different levels of starting mRNA. issues related to fertilization. Ans: A Difficulty: 3 What technique would be used to best study a phenocopy: RNAi transgene isolation of mutations QTL mapping analysis Ans: A Difficulty: 3

33. A) B) C) D)

34. A) B) C) D)

35. Mutations that result in a new phenotype for a gene through the production of too much protein are best described by the term: A) conditional B) permissive C) hypomorphic D) gain-of-function Ans: D Difficulty: 1 36. A) B) C) D) Gain-of-function alleles are usually: null conditional recessive dominant Ans: D Difficulty: 2

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37. A) B) C) D)

The expression of a gene at an abnormal place or time is called: epistasis ectopic epigenetic expressivity Ans: B Difficulty: 2 Gain-of-function mutations might involve which of the following: deletion of a promoter region. constitutive activation of an enzyme. a synonymous mutation. none of the above. Ans: B Difficulty: 3

38. A) B) C) D)

39. A) B) C)

What is the most common cause of rare spontaneous ectopic gene expression: insertion mutation. deletion mutation. a mutation at the chromosomal level which moves the gene next to a new regulatory element. D) none of the above. Ans: C Difficulty: 2

40. The deliberate production of as many different mutants with related phenotypes as possible in an attempt to identify all the genes relevant to a process, such as development, is called: A) overexpression mutagenesis B) artificial mutagenesis C) redundant mutagenesis D) saturation mutagenesis Ans: D Difficulty: 2 41. Saturation mutagenesis coupled with complementation analysis allows the determination of: A) identification of a gene's identity. B) purification of a protein involved in a pathway. C) mapping of the controlling promoter. D) the general complexity of a biological process. Ans: D Difficulty: 3

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42. Saturation mutagenesis would not be likely be helpful in the identification of which of the following: A) redundant genes B) haploinsufficient proteins C) recessive alleles D) complementation groups Ans: A Difficulty: 2 43. Which of the following could be most useful in the study of development through overexpression or misexpression screens in Drosophila: A) bacterial plasmid. B) transposable elements containing a specific promoter region. C) gene replacement by homologous recombination. D) YACs. Ans: B Difficulty: 3 44. What is the term for when an individual dies due to double homozygosity for two usually non-lethal mutations: A) suppressor mutation B) enhancer mutation C) synthetic lethality D) nonallelic complementation Ans: C Difficulty: 2 45. What is the term for when an individual shows a new phenotype due to double heterozygosity for two mutations that does not appear for either mutation alone: A) suppressor mutation B) enhancer mutation C) synthetic lethality D) nonallelic complementation Ans: D Difficulty: 2 46. A) B) C) D) When a second mutation intensifies the effects of another mutation it is called what: suppressor mutation enhancer mutation synthetic lethality nonallelic complementation Ans: B Difficulty: 2

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47. A mutation in one gene that compensates for or counteracts the effects of a mutation in another gene is known as a: A) suppressor mutation B) enhancer mutation C) synthetic lethality D) nonallelic complementation Ans: A Difficulty: 2 48. A) B) C) D) An example of ectopic gene expression is: achondroplastic dwarfism. lack of eye development. abnormal vulvar shape. legs instead of antennae. Ans: D Difficulty: 3

49. A single amino acid substitution in the FGFR3 protein, results in constitutive activation of the kinase domain and causes which of the following phenotype: A) achondroplastic dwarfism. B) lack of eye development. C) abnormal vulvar shape. D) legs instead of antennae. Ans: A Difficulty: 3 50. A) B) C) D) The presence of a homeodomain in a protein suggests what about its function: it has kinase activity. it is a membrane bound receptor. it is a secreted protein. it is a transcription factor. Ans: D Difficulty: 1

51. What technique would you use to best determine when and in what cells of a given tissue a specific gene is expressed: A) Northern analysis B) in situ hybridization C) RT-PCR D) Southern analysis Ans: B Difficulty: 2

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52. A) B) C) D)

How would you best follow the developmental timing of a given protein in vivo: in situ hybridization. Western blotting. using a GFP-fusion protein transgenic organism. microarray analysis. Ans: C Difficulty: 2 What does a homeodomain do: acts as a receptor. has kinase activity. it binds to specific DNA sequences. none of the above. Ans: C Difficulty: 2

53. A) B) C) D)

54. With respect to interpretation of mutation screens involving the order of epistatic gene action in development, it is important to take which of the following into consideration: A) whether the mutations are gain-of-function or loss-of-function. B) whether the mutations are enhancers or suppressors. C) whether the mutations are a result of single or multiple nucleotide changes. D) a and b but not c. E) a and c but not b. F) all of the above. G) none of the above. Ans: D Difficulty: 3 55. Screening for maternal-effect mutations would involve looking for which of the following: A) unusual phenotypes in female progeny. B) embryos that are all obviously developmentally arrested. C) asymmetric mutations. D) eggs that can not be fertilized. Ans: B Difficulty: 2 56. Cells that provide large amounts of mRNA and proteins for deposition into the egg are called: A) doctor cells B) nurse cells C) helper cells D) bicoid cells Ans: B Difficulty: 1

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57. A) B) C) D)

A molecule whose concentration determines the developmental fate of a cell is called: monomorphic a juxtacrine protein a signaling molecule a morphogen Ans: D Difficulty: 1

58. Signaling factors that complete cell-to-cell communication in the form of direct contact are called: A) juxacrine factors. B) paracrine factors. C) endocrine factors. D) all of the above. Ans: A Difficulty: 2 59. Ligands that circulate throughout the body and signal developmental differentiation are called: A) juxacrine factors. B) paracrine factors. C) endocrine factors. D) all of the above. Ans: C Difficulty: 2 60. A ligand secreted from a cell to a nearby cell that signals developmental differentiation is called: A) juxacrine factor. B) paracrine factor. C) endocrine factor. D) all of the above. Ans: B Difficulty: 2

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Matching Match the definitions with the term that best fits a. haploinsufficiency b. nonallelic noncomplementation c. synthetic lethality d. somatic cell e. stem cell f. germ cell g. neuroblast h. juxacrine i. paracrine j. endocrine 61. ______ specialized cells that incorporate into reproductive organs and produce gametes. Ans: f Difficulty: 1 62. ______ neural stem cell. Ans: g Difficulty: 1 63. ______ a cell that upon division gives rise to cells that can go through different differentiation pathways. Ans: e Difficulty: 1 64. ______ direct contact, cell-to-cell communication signaling. Ans: h Difficulty: 2 65. ______ any cell in an organism except gametes and their precursor cells. Ans: d Difficulty: 2 66. ______ ligands secreted by one cell signal another. Ans: i Difficulty: 2 67. ______ A situation of inviability resulting from a double mutation of two genes that are not individually lethal. Ans: c Difficulty: 3

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68. ______ ligands or hormones that circulate in the blood and affect tissues far from the cells that produced them. Ans: j Difficulty: 2 69. ______ the phenomenon of heterozygosity for two genes giving rise to a novel phenotype that neither alone when heterozygous produces. Ans: b Difficulty: 3 70. ______ a gene that can not promote wild-type function in only a single copy. Ans: a Difficulty: 2 True or False 71. A cloned organism will always be genotypically and phenotypically identical to the individual from which it was cloned. Ans: False Difficulty: 2 72. Presinilin is a protease that cleaves the Notch protein, which is involved in the regulation of cell-fate-specific target genes. Ans: True Difficulty: 2 73. Neural stem cells are called neuroblasts, which divide and form a daughter neuroblast and a ganglion mother cell; the latter give rise to neurons. Ans: True Difficulty: 2 74. Prospero is a protein that is involved in the lack of differentiation of neuroblasts. Ans: False Difficulty: 2 75. Although stem cells can continue dividing indefinitely, half of the cells they give rise to can differentiate into a variety of different cell types. Ans: True Difficulty: 2 76. Maternal and zygotic genes affect early development. Ans: True Difficulty: 2

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77. Bicoid is a maternal-effect mutation that results in larvae with two heads. Ans: False Difficulty: 1 78. A nurse cell produces large amounts of mRNA and proteins for deposit into the Drosphila egg. Ans: True Difficulty: 2 79. Development requires progressive changes in gene expression. Ans: True Difficulty: 2 80. Developmental regulation occurs mostly at the level of mRNA stability. Ans: False Difficulty: 1 81. The green fluorescent protein gene is often joined to genes of interest thus producing a fusion protein that is easily followed in vivo. Ans: True Difficulty: 2 82. When and in what tissue a gene is expressed can be determined by in situ hybridization. Ans: True Difficulty: 2 83. RNA in situ hybridization is an easier method of detecting gene regulation than by following the gene's protein by immunohistochemistry. Ans: False Difficulty: 3 84. The homeodomain is a common DNA-binding domain in many transcription factors that regulate development. Ans: True Difficulty: 2 85. Both suppressor and enhancer mutations modify the phenotype caused by mutations in another gene. Ans: True Difficulty: 2

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Short Answer 86. How do cells which all contain identical genetic information differentiate into myriad cell types and ultimately undergo the miracle of development from an embryo into a child? Ans: Gene regulation controls the timing, location and amount of transcript necessary for cells to divide, change shape, specialize and interact in highly reproducible ways. Difficulty: 2 87. Model organisms are useful for the study of developmental genetics because significant ethical limitations restrict studies in humans. Discuss some taboos to research in humans. Ans: Several aspects of research necessary to study development are unethical to complete in humans such as the deliberate production of mutations, the experimental manipulation of affected individuals, and forced matings between individuals with various abnormalities. Difficulty: 2 88. What three characteristics of value to geneticists do model organisms share? Ans: Ease of cultivation, rapid reproduction, and small size. Difficulty: 3 89. What advantages in particular do yeast provide with respect to the study of eukaryotes? Ans: Yeast are single celled eukaryotes having both haploid and diploid states, which make identification of mutations easier. Difficulty: 2 90. What properties of C. elegans make it a most useful model organism? Ans: C. elegans is a transparent round worm with an invariant number of cells in the adult. The female is a hermaphrodite. Difficulty: 2 91. What gene controls eye development and to what degree is it evolutionary conserved? Ans: The ey, Pax-6 and Aniridia genes control eye development in Drosophila, mice and man respectively. They are highly conserved which is surprising given the distinct phenotypic differences in eyes between these organisms. Difficulty: 3

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92. Although many aspects of development are highly conserved, distinct divergences exist. How are Drosophila and man different with respect to sexual determination? Ans: Sex determination in Drosophila involves a cascade of splicing factors while human sex is determined by the presence of testis-determining factor, encoded by the SRY gene on the Y chromosome. TDF is a transcription factor that regulates other important genes involved in sexual differentiation. Difficulty: 3 93. What is the difference between null, hypomorphic, and conditional mutations? Ans: A null mutation is one that completely lacks the normal function of the protein. A hypomorphic mutation is one with a partial lack-of-function. Conditional mutations are ones that cause a loss-of-function only under certain circumstances (permissive conditions). Difficulty: 2 94. What is a dominant-negative mutation? Ans: A dominant negative mutation is one where the loss-of-function is dominant rather than recessive as is usual for loss-of-function mutions. Difficulty: 2 95. What is the molecular basis of haploinsufficiency? Ans: The molecular basis of haploinsufficiency is that one wild-type allele does not produce sufficient protein to function and show the wild-type phenotype. Difficulty: 2 Experimental Design and Interpretation of Data 96. You are a very lucky scientist. You observe that an interesting mutant phenotype has arisen in your cell culture. A clonal kidney cell line has what appears to be a patch of muscle cells growing in it. (This suggests that the cell began from a single mutant cell.) You wish to test the hypothesis that gene expression changes result in a change in morphology. How would you test your hypothesis? Ans: To test the hypothesis that gene expression changes are involved in the muscle phenotype, you could carefully isolate the dividing cells of both phenotypes and complete a microarray analysis. Most labs now have access to a reasonably complete clone set of human genes. Hybridization of cDNA from the two cell types mRNA against each other would identify differences and generate new hypotheses regarding developmental differentiation. Control muscle cells versus the newly formed muscles cells would need to be included in your experiment in order to identify the difference between genes giving rise to muscle cells and genes that maintain the muscle cell phenotype. Difficulty: 4

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97. Due to ethical considerations development is studied in model organisms. How do you use genetic information gained from other species to isolate the human genes involved in development? Ans: You can use genes cloned in other organisms to find homologs in the human genome. This has been made considerably easier with the publication of the human genome sequence. Difficulty: 3 98. The sister of a friend of yours and her husband wishing to have children but having no luck seek a renown molecular geneticist's (MD, PhD) advice. Your friend said her sister was quite upset yesterday because her so called quack doctor told her that she was genetically a man but due to a mutation in an SRY gene she looks like a woman. Your friend knows that you are a biology major (your friend is an artist) and asks you to explain how a man can be a women. Focus your explanation on the effects of SRY on sexual development. Ans: You could assure your friend that her sister is indeed a woman, although genetically she has a Y chromosome. Because sex is determined developmentally, due to the SRY mutation her sister did not produce testisdetermining factor, the protein made from the SRY gene, and as a consequence she did not undergo cellular differentiation to a male phenotype. Therefore, she is phenotypically female but unable to reproduce. Difficulty: 3 99. How can hypomorphic mutations help tease out pleiotropic effects in development? Ans: Since hypomorphic mutations are a partial loss-of-function, they often allow survival of a homozygous lethal mutation and pleiotropic effects are uncovered. Difficulty: 3 100. What kind of mutation would be most helpful to test a hypothesis regarding the timing of developmental stages? Ans: When testing the effects of a protein on developmental timing, it is often beneficial to isolate conditional mutants so that the gene can be turned off and turned on by utilizing conditions that are specifically restrictive and permissive. Difficulty: 4

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Chapter 20The Genetic Analysis of Populations and How They Evolve Fill in the Blank 1. Genetic variation that affects the organism's characteristics is the basis for ______ selection. Ans: natural Difficulty: 1 2. Wild-type and heterozygous individuals of a ________ disease show normal phenotypes. Ans: recessive Difficulty: 1 3. Changes in gene frequencies within populations are termed __________. Ans: microevolution Difficulty: 1 4. New species formation through slow changes in the existing organisms which take very long periods of time is called as ____________. Ans: macroevolution Difficulty: 1 5. _________ for a given environment increases as the likelihood of survival and reproduction of a certain type of organism increases. Ans: fitness Difficulty: 2 6. A large part of the variation in a naturally occurring population can be largely accounted by ________ alone. Ans: mutation Difficulty: 2 7. If the likelihood that an individual will grow into an adult does not depend on the genotype, then the allele frequencies in the adults should be the same as in their _______. Ans: gametes Difficulty: 2 8. The binomial equation representing the ______-_________ proportions is p2 + 2pq +q2 = 1. Ans: Hardy-Weinberg Difficulty: 2

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9. _______ frequencies do not change from generation to generation in a population at Hardy-Weinberg equilibrium. Ans: Allele Difficulty: 1 10. A single generation of selection will eliminate a lethal ________ allele from the population. Ans: dominant Difficulty: 2 11. Allele frequency is affected by mutation and selection in ________ directions. Ans: opposing Difficulty: 2 12. New diseases emerge in human populations as a consequence of new _________. Ans: mutations Difficulty: 2 13. _______ relatedness of two individuals is the average fraction of common alleles at all gene loci that the individuals share because they inherited them from a common ancestor. Ans: genetic Difficulty: 3 14. The heritability of a trait _________ as the proportion of environmental variation increases. Ans: decreases Difficulty: 2 15. The strength of selection and the heritability of a trait directly determine the trait's rate of ________ in each generation. Ans: evolution Difficulty: 2 Multiple Choice 16. A) B) C) D) E) A population is a group of individuals of a species which: interbreed. reside in the same area. inhabit the same space at the same time. only b and c are true a, b, and c are true Ans: E Difficulty: 1

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17. A) B) C) D) E)

The sum total of all alleles carried in all members of a population is called its: gene pool. genome. ploidy. polygenic sum. polymorphism. Ans: A Difficulty: 1 Microevolution is defined as: a process that includes new species formation. changes in the frequency of alleles within a population. evolution of microorganisms. interactions between species. all of the above Ans: B Difficulty: 1 Macroevolution is defined as: evolution that occurs over geologic time. process by which new species emerge from existing species. the consequence of extended periods of microevolution. the origin of new species by mutation and natural selection. all of the above Ans: E Difficulty: 2 Population genetics provides answers for all of the following questions except: what is the frequency of genetic disease in a population? what fraction of the phenotypic variation in a trait is the result of genetic variation? what alleles are most likely to mutate? given certain quantifiable variables, how long is a disease likely to persist? how rapidly can a disease gain a foothold in a population? Ans: C Difficulty: 3 Which of the following is not one of the assumptions of the Hardy-Weinberg law ? The population is very large. There is non-random mating within the population. Mutations in the alleles do not occur. No migration occurs into or out of the population. The ability of all genotypes for survival and reproduction is the same. Ans: B Difficulty: 2

18. A) B) C) D) E)

19. A) B) C) D) E)

20. A) B) C) D) E)

21. A) B) C) D) E)

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22. A) B) C) D) E)

Hardy-Weinberg equilibrium in populations is defined as conditions which produce: only heterozygotes. many lethal alleles. genetic drift. constant allele frequencies which do not change from generation to generation. all of the above Ans: D Difficulty: 2

23. The heterozygote genotype frequency term for a gene with two alternate alleles A (frequency p) and a (frequency q) in the Hardy-Weinberg equation is: A) p2. B) q2. C) 2pq. D) (p+q)2. E) p+q. Ans: C Difficulty: 1 24. If in a population of 1 million people, 100 albinos (homozygous recessives, aa) were found, how many normal (homozygous dominants, AA) individuals will be found in the next generation under equilibrium conditions? A) 19,800 B) 100,000 C) 980,010 D) 999,900 E) 100 Ans: C Difficulty: 4 25. In humans, brachydactyly is a dominant condition. Six thousand four hundred people in a population of 10,000 show the disease (1,600 are BB, 4,800 are Bb) and 3,600 are normal phenotypes (bb). The frequency of the b allele is: A) 0.6. B) 0.4. C) 0.36. D) 0.48. E) 0.16. Ans: A Difficulty: 3

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26. The frequency of the Hemoglobin A allele is 0.9. The heterozygote with the recessive allele, s, show resistance to the malarial parasite. What is the frequency of the heterozygote for the pair As? A) 0.81 B) 0.1 C) 0.01 D) 0.18 E) 0.09 Ans: D Difficulty: 3 27. The genotypic frequency of inheriting autosomal recessive condition, phenylketonuria, is 1 in 3,600 people. The frequency of the normal allele is: A) 0.0167. B) 0.9833. C) 0.0328. D) 0.00286. E) 3,599. Ans: B Difficulty: 4 28. A) B) C) D) E) Which of the following is not generally true about conditions of natural populations? Size is not always very large. Individuals do not mate at random. New mutations do occur. There is migration in and out of the population. Different genotypes have the same fitness. Ans: E Difficulty: 1 Fitness is described as: an individual's ability to survive to adulthood. an individual's ability to reproduce. the effect of the particular genotype which cannot always be predicted. a, b, and c are true. only a, and b are true. Ans: D Difficulty: 1

29. A) B) C) D) E)

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30. Changes in allele frequency in conditions of either natural or artificial selection depends on: A) allele frequencies themselves. B) relative fitness related to viability. C) reproductive abilities of the different phenotypes. D) a, and b only. E) a, b, and c. Ans: D Difficulty: 1 31. Many human recessive genetic diseases are maintained despite continuing selection against them because: A) heterozygotes have a higher fitness than either homozygote. B) the recessive alleles mutate to dominant type. C) there is no inheritance for the recessive allele. D) the dominant allele frequency remain the same over generations. E) none of the above. Ans: A Difficulty: 1 32. A) B) C) D) E) A disease which has been studied in great detail for heterozygote superiority is: brachydactyly. sickle cell disease. insulin-dependent diabetes. albinism. tuberculosis. Ans: B Difficulty: 1

33. If African populations have a relative fitness of the wild type genotype of 0.8, and that of the heterozygote of 1.0, then the relative advantage in fitness of the heterozygotes would be: A) 0.8. B) 0.08. C) 0.16. D) 0.28. E) 1.25. Ans: E Difficulty: 2

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34. A) B) C) D) E)

Mutations arise from: DNA damage due to environmental agents. from errors in replication. from errors in transmission of genetic information in cell division. only a and b. a, b, and c. Ans: E Difficulty: 1 Frequency of disease alleles is influenced by: heterozygous advantage. mutation. time of onset of disease. selection. all of the above. Ans: E Difficulty: 1

35. A) B) C) D) E)

36. Unpredictable, chance fluctuation in allele frequency that have a neutral effect on fitness is called: A) founder effect. B) selection. C) genetic drift. D) mutation. E) inbreeding. Ans: C Difficulty: 1 37. A) B) C) D) E) The process in which rare alleles increase in frequency in a new population is known as: gene flow. genetic drift. founder effect. inbreeding. selection. Ans: C Difficulty: 2 Diseases persist because: changes in allele frequency tend toward evolutionary equilibrium. mutation balances selection. the alleles become dominant. only a and b. a, b, and c. Ans: D Difficulty: 2

38. A) B) C) D) E)

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39. A) B) C) D) E)

The factors contributing to the antibiotic resistance of bacterial pathogens are: patient noncompliance with drug treatments. strong selection imposed by antibiotic increases the rate of evolution in each generation. plasmids provide a means for the genetic exchange of resistance genes. only b and c. a, b and c. Ans: E Difficulty: 1

40. Development of Insulin-dependent diabetes is associated with how many separate regions of the human genome? A) 12 B) 10 C) 8 D) 6 E) 4 Ans: A Difficulty: 1 41. A) B) C) D) E) Multifactorial traits: are affected by both genetic and environmental factors. are continuous. vary over a continuous range of measurements. are affected by environmental factors such as penetrance and expressivity. all of the above. Ans: E Difficulty: 2 The total phenotype variance (VP) is: the sum of genetic variance (VG) and environmental variance (VE). the difference between VG and VE. not dependent on VG. not dependent on VE. always constant. Ans: A Difficulty: 2 Heritability is defined as: VG . VP . VE . VG/VP. VP/VG. Ans: D Difficulty: 3

42. A) B) C) D) E)

43. A) B) C) D) E)

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44. A) B) C) D) E)

The total genetic relatedness of two siblings is: 2. 1. 0.5. 0.2. none of the above. Ans: C Difficulty: 2 Which of the following is not true about monozygotic twins. They share all alleles at all loci. They have a genetic relatedness of 0.5. They have a genetic relatedness of 1. They come from the joining of a single egg with a single sperm cell. They are the result of a split of the zygote after fertilization. Ans: B Difficulty: 1 Recent heritability studies on twins show that there is a genetic component to: memory. extroversion. verbal reasoning. a, b, and c. only a and b. Ans: D Difficulty: 1 The response to selection, R, is equal to: the heritability (h2) of a trait. the strength (S) of selection. the difference between h2 and S. S/h2. h2S. Ans: E Difficulty: 2

45. A) B) C) D) E)

46. A) B) C) D) E)

47. A) B) C) D) E)

48. A number of interacting genes produce quantitative inheritance. The transmission of these genes can be seen in the phenotypical pattern of: A) discontinuous distribution of discrete phenotypes. B) continuous variation in phenotypic expression. C) strict dominance and recessiveness. D) all of the above. E) only a and b. Ans: B Difficulty: 2

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49. A cross between a tall and a short pea plant produced intermediate height in the F1 generation. When the F1s were crossed plants of the original parental heights and plants with a range of heights in between the extremes were produced. The mode of inheritance is described as: A) multifactorial. B) independent assortment. C) incomplete dominance. D) codominance. E) segregation. Ans: A Difficulty: 1 50. A) B) C) D) E) Multifactorial inheritance is observed in phenotypes which show typically: only one discrete type. two extremes. a bell shaped distribution. a higher mutation rate. all of the above. Ans: C Difficulty: 1 Continuous traits are: due to sex-linked genes only. due to autosomal genes only. qualitative in nature. quantifiable in measurements. result of test-crosses only. Ans: D Difficulty: 1 In addition to genetic factors, environmental factors influence the inheritance of: metabolic diseases. recessive diseases. dominant diseases. sex-linked diseases. polygenic traits. Ans: E Difficulty: 2

51. A) B) C) D) E)

52. A) B) C) D) E)

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53. Brown insects living in a dark background survived in a ratio of 90/120, while the same insects in a lighter background survived in a ratio of 30/120. The ratio of relative fitness of the insects in dark to lighter background is: A) 1 : 0.333. B) 0.75 : 0.25. C) 90 : 120. D) 3 : 1. E) none of the above. Ans: A Difficulty: 4 54. If the relative fitness of genotypes MM, MN, NN are 0.8, 1.0, and 0.2 respectively, the expected equilibrium frequency of N is: A) 0.8. B) 1.0. C) 0.2. D) 1.25. E) 4.0. Ans: C Difficulty: 4 55. A) B) C) D) E) Twins made from two individual zygotes (dizygotic twins): are related genetically as the monozygotic twins. share 0% genetic similarities. are similar in 100% of genetic sequences. are related genetically as non-twin siblings. are similar to parents. Ans: D Difficulty: 2 An increase in fitness is described as: migrating to a new environment. successful adaptation. being successful in producing many offspring. exhibiting new traits. mutating to a dominant trait. Ans: B Difficulty: 2

56. A) B) C) D) E)

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57. The frequencies of ABO blood groups in a certain population are: A=0.22, B=0.44, AB=0.18, and O=0.16. The frequency of the O allele in the population is: A) 0.469. B) 0.663. C) 0.424. D) 1.0. E) 0.4. Ans: E Difficulty: 3 58. Under special circumstances, migration does not change allele frequencies. If the allele frequencies of a dominant and recessive allele are both 0.5, then migration of which of the following will not change the frequencies of the alleles? A) homozygous recessive individuals B) haploid individuals C) diploid individuals D) heterozygous individuals E) homozygous dominant individuals Ans: D Difficulty: 3 Matching Match the following terms with the best definition a. genetic drift b. adaptation c. natural selection d. fitness e. polymorphism 59. The presence of many alleles of a gene in a population. Ans: e Difficulty: 2 60. Genetic contributions of an individual to succeeding generations. Ans: d Difficulty: 2 61. Change in structure, behavior or physiology that promotes the likelihood of the organism's survival in a specific environment. Ans: b Difficulty: 2

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62. The suitability of at least one genotype at every generation in varied environmental conditions. Ans: c Difficulty: 2 63. Chance, random change in the frequency of an allele at a locus. Ans: a Difficulty: 2 Match the following terms with the best definition a. heterozygous advantage b. response to selection c. population d. gene pool e. founder effect f. heritability 64. All alleles carried in all members of population. Ans: d Difficulty: 2 65. A group of interbreeding individuals of the same species. Ans: c Difficulty: 2 66. Occurs when a few individuals separate from a larger population and establish a new one that coexists with the original population. Ans: e Difficulty: 2 67. The proportion of total phenotypic variance ascribable to genetic variance. Ans: f Difficulty: 2 68. The property that maintains many recessive genetic diseases despite continuous selection against them. Ans: a Difficulty: 2 69. The term which takes into account both the strength of selection, and the heritability of a trait. It is also the amount of evolution. Ans: b Difficulty: 2

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True or False 70. The definition of allele frequency is the proportion of all copies of a given gene in a population that are of a specific allele type with the total gene number equal to two times the number of individuals in the population. Ans: True Difficulty: 1 71. Derivations of the Hardy-Weinberg law depends on five assumptions regarding the nature of the population in question, including that there is no migration into or out of the population. Ans: True Difficulty: 1 72. The binomial Hardy-Weinberg equation is represented by p2 + p2q2 + q2 = 1. Ans: False Difficulty: 2 73. A population that achieves genotype frequencies of p2, 2pq, and q2 in just one generation and remains at these frequencies, is said to be in Hardy-Weinberg equilibrium. Ans: True Difficulty: 1 74. Macroevolution is the drastic change of allele frequency in a population in a single generation. Ans: False Difficulty: 2 75. Fitness is the term that geneticists use to describe an individual's relative ability to survive and transmit genes to the next generation. Ans: True Difficulty: 1 76. Heterozygous advantage to a disease state is sometimes responsible for the retention of recessive genes that otherwise reduce fitness under normal conditions. Ans: True Difficulty: 1 77. Genetic drift has a predictable effect on evolution which scientists can easily calculate. Ans: False Difficulty: 2

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78. The founder effect may lead to a higher incidence of certain alleles than seen in large diverse populations. Ans: True Difficulty: 1 79. The evolution of drug resistance in bacteria results from several factors including, short generation time, large populations which ensure incidence of mutations, strong selection by drug and the variety of ways by which bacteria can acquire new genetic diversity. Ans: True Difficulty: 1 80. Selection for resistance in the presence of pesticides is the only factor that influences the rate of resistance among pest populations. Ans: False Difficulty: 2 81. Complex traits that are multifactorial are continuous. They are also called quantitative traits because they vary over a continuous range of measurement. Ans: True Difficulty: 1 82. Heritability is the proportion of total phenotypic variance due to genetic variance. Ans: True Difficulty: 1 83. One way scientists attempt to control confounds due to environmental variability is to cross-foster. Ans: True Difficulty: 1 84. When a trait has a large heritability, it is primarily genetically determined and thus, unaffected by the environment. Ans: False Difficulty: 2 Short Answer 85. What is migration? How does it affect Hardy-Weinberg equilibrium? Ans: Migration is the movement of individuals from one population to another. It results in a change in the frequency of each population. This change translates into allele frequencies which are no longer constant from generation to generation as predicted by the Hardy-Weinberg equilibrium. Difficulty: 2

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86. What is genetic drift? Is it dependent on the size of the population? Ans: Chance fluctuation in allele frequency is called genetic drift. It affects small populations because the loss of a single individual of a given genotype will drastically alter the gene frequencies of the remainder of the population. Difficulty: 3 87. How does the founder effect dictate the genetic composition of the new population? Ans: The founders of a new population are the sole source of alleles of a given gene. Therefore the genetic composition is entirely dependent on the allele types of the founders which typically interbreed within themselves and tend to conserve the alleles found in the originators. Difficulty: 2 88. What is selection? How does it alter allele frequencies? Ans: Selection is the process by which individual organisms are selected for survival and reproduction. The offspring contain the parental genetic information. The more successful organisms will leave more offspring and hence more of their genes and hence alleles of the parental types in the generations to come. Difficulty: 3 89. Explain QTLs. Ans: They refer to the genes which control the expression of quantitative traits. They are shorthand for quantitative trait loci. Difficulty: 1 90. Relate genetic variance (VG) and phenotypic variance (VP) to heritability. Ans: Heritability h2 = VG/VP. Difficulty: 2 91. What are the components of phenotypic variance? Ans: VP = VG + environmental variance. Difficulty: 3 92. Define a population in genetic terms? Ans: A population is a group of interbreeding individuals of the same species that inhabit the space at the same time. Difficulty: 1 93. What is the difference between phenotype frequency, genotype frequency and allele frequency? Ans: Phenotype and genotype frequency are the proportion of individuals in a population that show a particular phenotype or have a particular genotype respectively while allele frequency is the proportion of all copies of a gene in a population that are of a given allele type. Difficulty: 2

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94. Derivation of the Hardy-Weinberg law depends on what five assumptions? Ans: 1. The population includes a very large, virtually infinite number of individuals. 2. The individuals mate at random. 3. No new mutations appear in the gene pool. 4. There is no migration into or out of the population. 5. There are no genotypedependent differences in the ability to survive to reproductive age and transmit genes to the next generation. Difficulty: 3 95. What is the difference between natural and artificial selection? Ans: Natural selection is the progressive elimination of individuals whose fitness is low and the reproduction of individuals with highest fitness. Artificial selection is similar to natural selection in that low fitness individuals can be selected against but in this case matings are controlled and desired selection is deliberate. Difficulty: 2 96. List five forces that change the frequency of an allele in a population and discuss why the elimination of a deleterious recessive allele is nearly impossible. Ans: Allele frequency is altered by genetic drift, migration, mutation, natural selection, and nonrandom mating. Elimination of a deleterious recessive allele is nearly impossible because in the heterozygous state there is no negative selection against it so it commonly remains an uncommon allele in a population. Also, for some alleles there is heterozygous advantage which will contribute to selection for a deleterious recessive allele. Difficulty: 4 Experimental Design and Interpretation of Data 97. How would studies on monozygotic and dizygotic twins help in the understanding of genetic basis of behavior in humans? Ans: The degree to which variation in human behavior is determined by genetic inheritance can be studied by observing monozygotic twins under the same and different environmental conditions. Dizygotic twins on the other hand if grown in similar environments like the same household can yield valuable insights into the effect of heredity on behavioral characteristics. Difficulty: 3 98. How can a value of 1.0 for h2 can be interpreted? Ans: It means that almost all of the phenotypic variation is due to inheritance. Difficulty: 4 99. Explain why a population carries more genetic diversity than an individual? Ans: In the case of multiple alleles such as the ABO blood group system the greatest number of alleles an individual can carry is 2 while many can be carried by the population. Difficulty: 4

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100. A gene in a natural population of prairie dogs has three alleles, which can be determined by electrophoretic analysis following PCR amplification. The respective bands are 170, 200, and 230 base pairs in size. You have genotyped 1,000 animals and found the following frequencies for the six different genotypes: 170/170=0.06, 200/200=0.58, 230/230=0.04, 170/200=0.20, 170/230=0.02, 200/230=0.10. What are the allele frequencies? Is the population in Hardy-Weinberg Equilibrium? Ans: f(170)= 0.06 + (0.20) + (0.02) = 0.17 f(200)= 0.58 + (0.20) + (0.10) = 0.73 f(230)= 0.04 + (0.02) + (0.10) = 0.10 (p + q + r)2 = p2 + q2 + r2 + 2pq + 2pr + 2qr = 0.03 + 0.53 + 0.01 + 0.25 + 0.03 + 0.15 This is not what is observed therefore, the population is NOT in equilibrium. Difficulty: 4

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Chapter 21Evolution at the Molecular Level Fill in the Blank 1. Charles Darwin published his theory of evolution in his book called __________________in 1859. Ans: The Origin of Species Difficulty: 1 2. One of the cornerstones of Darwin's theory of evolution known as the process of _____________, states that some variant traits confer on some individuals a greater chance of surviving and reproducing while other traits reduce fitness. Ans: natural selection Difficulty: 1 3. Darwin understood that inheritance was a factor in evolution but his understanding of this process was limited because he did not read Mendel's paper, entitled_______________________, which was published in 1866. Ans: Experiments on Plant Hybrids Difficulty: 2 4. The populations of T and B lymphocytes that circulate throughout vertebrate blood and tissues have the genetic ability to synthesize a great variety of ___________________________________, which are protein molecules that can recognize non-self antigens from self antigens. Ans: cell surface immune receptors Difficulty: 2 5. The HIV viral genome experiences rapid mutation and subsequent evolution due to the replicative infidelity of the enzyme ________________________________ which converts viral RNA into double stranded ________ in infected cells. Ans: reverse transcriptase, cDNA Difficulty: 2 6. The fatal consequences of untreated HIV infection result from the rapid accumulation of billions of mutant virus strains in an infected individual which subsequently out paces the ability of the hosts _________________________________ to control. Ans: immune system Difficulty: 2

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7. The three basic components of molecular evolution are ___________________________ to produce genetic variants, ____________________________ of a favored subset of variants and the ______________________________ of the favored variants in a population over many generations. Ans: diversification, selection, amplification Difficulty: 3 8. All living cells capable of reproduction utilize ________________ as the genetic material while non-living viruses can have _________________________ genomes. Ans: DNA, DNA or RNA Difficulty: 2 9. Some RNA molecules have been identified as being capable of carrying out enzymatic reactions involving intron removal and are known as __________________, a term denoted by the discoverers T. Cech et al. Ans: ribozymes Difficulty: 2 10. In a primordial world, a major disadvantage to having RNA serve as the repository of genetic information is the molecules susceptibility to _______________ and ____________________ hydrolysis. Ans: chemical, enzymatic Difficulty: 3 11. Mutations which are selectively neutral either survive or are eliminated from populations by the process of _____________________ which results primarily of chance events during reproduction. Ans: genetic drift Difficulty: 2 12. An advantageous allele becomes _________________________ when it becomes present in more than 99 percent of the sum total of the loci present in a population. Ans: fixed Difficulty: 2 13. Genome size in eukaryotes has increased primarily by the processes of ___________________ and ________________________ of DNA sequences as new DNA arises from pre-existing sequences. Ans: duplication, diversification Difficulty: 3

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14. Duplications of chromosomal DNA sequences can naturally arise via two mechanisms called ______________, a type of chromosomal aberration, and ___________________, which is a form of illegitimate recombination. Ans: transposition, unequal crossing over Difficulty: 3 15. The existence of pseudogenes that have string of polyadenylic acid residues at their 3' end is indicative of integration of a cDNA copy of an RNA transcript produced by the action of the enzyme ________________________________ which is encoded by ________________________ sequences present in the genome. Ans: reverse transcriptase, retroviral Difficulty: 3 16. Transposition is defined as the movement of a ___________________________ copy of a chromosomal DNA sequence to a location on another non homologous chromosome. Ans: duplicated Difficulty: 2 17. Normal meiotic crossing over occurs during the ______________________ stage of prophase I and is mediated by a cytological structure called the ________________________. Ans: pachytene, synaptonemal complex Difficulty: 3 18. In Drosophila, the normal non-Bar eye, Bar eye, and Ultrabar phenotypes result from ____________________ and the Bar eye phenotype results from _______ copies of the Bar eye locus. Ans: Unequal crossing over, two Difficulty: 4 19. Non functional copies of normally expressed genes called _________________________ arise via random genetic drift and accumulate mutations at a faster rate than functional coding or regulatory sequences. Ans: pseudogenes Difficulty: 2 20. A duplicated copy of an ancestral vertebrate beta globin gene gave rise to an oxygen storage protein called ___________________ which is normally expressed in _____________________ tissue and is functionally monomeric. Ans: myoglobin, muscle Difficulty: 3

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21. The two types of T-cell receptors, called ____________ and _____________, are encoded by three gene families and the generation of T-cell receptor diversity is similar to the process that generates antibody diversity except that ________________________________ does not occur. Ans: alpha/beta, gamma/delta, somatic hypermutation Difficulty: 3 22. The _______________ portion of the human beta T-cell receptor has been duplicated and translocated to chromosome 9 and contains __________ V gene segments and one functional _________________________ gene. Ans: 3', 7, transposition Difficulty: 3 Multiple Choice Select all that apply 23. Triple drug therapy to arrest HIV infection is designed to specifically inhibit: a. DNA polymerases b. reverse transcriptase c. proteases d. endonucleases e. peptidyl transferase Ans: b, c Difficulty: 2 24. A small subset of immune cells called ________________ can persist long past the initial immune response in humans. They arise during the T and B cell clonal expansion and proliferation in response to antigen stimulation. a. effector cells b. CD4 cells c. memory cells d. macrophages e. T-helper cells Ans: c Difficulty: 2

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25. The Burgess Shale, which contains the earliest representation of all the phyla in current existence, was deposited around ___________________ years ago. a. 1.4 million b. 2.3 billion c. 1 billion d. 700 million e. 4.2 billion Ans: d Difficulty: 2 26. It is believed that the mass extinction which led to the dinosaurs demise around 65 million years ago was the result of a large asteroid impact near present day: a. Iceland b. Hawaii c. Siberia d. Manitoba e. Yucatan Ans: e Difficulty: 1 27. In an ideal primordial RNA world, multi functional RNA molecules would be required to have which of the following properties? a. fold into three dimensional structures with enzymatic capabilities b. carry out selective self replication c. synthesize double stranded DNA d. phosphorylate proteins e. encode genetic information in a four letter digital alphabet Ans: a, b, e Difficulty: 3 28. The genomes of humans and chimpanzees are about 99 percent similar yet many evolutionary biologists believe that most of the apparent phenotypic differences between the two species involve a. several large chromosomal deletions b. changes in regulatory DNA sequences c. changes in DNA regulatory and developmental protein factors d. transposition e. minor chromosomal rearrangements Ans: b, c, e Difficulty: 4

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29. Silent (synonymous) nucleotide substitutions in codons involve the ___________ nucleotide position in the codon which is based on the ________________ hypothesis involving codon and anticodon base pairing during translation. a. 3'-third, Lyon b. 3'-third, wobble c. 5'-first, hydrogen bonding d. 5'-first, wobble e. second, Ohno Ans: b Difficulty: 3 30. Mutations which result in the replacement of a serine amino acid with a glycine residue, which are both hydrophobic amino acids, is considered a _________________________ amino acid substitution because the chance may have little effect on the normal function of a particular protein. a. synonymous b. conservative c. non-conservative d. favorable e. neutralized Ans: b Difficulty: 2 31. Nucleotide or amino acid substitutions that have no apparent effect on an organism's phenotype, function, or development are considered _______________________ mutations. a. neutral b. conservative c. advantageous d. non-coding e. reverse Ans: a Difficulty: 2 32. Human heterozygotes for sickle cell anemia are selectively more fit than the normal homozygotes and considerably more fit than individuals homozygous for the sickle cell allele. This enhanced fitness of the heterozygotes is known as: a. adaptive value b. reproductive fitness c. heterozygous advantage d. hybrid vigor e. genetic drift Ans: c Difficulty: 2

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33. The beta globin gene superfamily has three major components located on three separate chromosomes in humans, they are the beta globin gene family, the ______________________ gene family and the myoglobin gene. a. alpha globin b. Hba-ps4 c. gamma globin d. delta globin e. leghemoglobin Ans: a Difficulty: 2 34. In humans, the two functional adult alpha globin genes: a. encode 8 different types of alpha globin chains. b. encode proteins that form heterodimers in hemoglobin. c. each have three very long introns. d. encode identical polypeptide products. e. are conserved by concerted evolution. Ans: d, e Difficulty: 4 35. The Hba-ps3 and Hba-ps4 pseudogenes which are located on mouse chromosomes 15 and 17 respectively are unlinked from the three principle globin gene families and thus considered: a. orphons. b. transposable elements. c. retrotransposons. d. SINES. e. LINES. Ans: a Difficulty: 2 36. Hox proteins have in common the functional capacity to: a. transcribe target genes. b. reduce gene expression in developmental genes. c. function as DNA binding transcription factors. d. transpose as a group. e. function as epistatic regulators of 3' Hox genes. Ans: c, e Difficulty: 3

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37. The ancestral Hox gene family, which arose ________________ years ago, consisted of _______ related genes that encode protein products that regulate the expression of other genes. a. 100 million, 8 b. 1 billion, 5 c. 65 million, 6 d. 600 million, 5 e. 100,000, 8 Ans: d Difficulty: 3 38. LINE, SINE, and retroviral DNA sequences are considered by many evolutionary biologists to be: a. selfish DNA. b. selectively neutral. c. middle repetitive DNA sequences. d. unique sequence DNA. e. copied by the action of reverse transcriptase. Ans: a, c, e Difficulty: 2 39. SINE elements are evolutionarily related to: a. signal recognition particle scRNA sequences. b. tRNA sequences. c. snRNP RNA species. d. rRNA. e. mRNA. Ans: a, b Difficulty: 4 40. LINE and SINE sequences evolve by the processes of episodic amplification and: a. exon shuffling. b. RNA splicing. c. sequence degradation. d. concerted evolution. e. gene conversion. Ans: c Difficulty: 2

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41. Homologous LINE and SINE elements in close proximity on the same chromosome can increase the rate of: a. gene expression. b. mutation. c. unequal crossing over. d. deletions. e. duplications. Ans: c, e Difficulty: 3 42. Satellite DNA contains DNA sequence subsets that are useful for DNA fingerprinting because of the inherent high level of polymorphisms that occur in their loci and include which of the following components? a. microsatellite sequences b. minisatellite sequences c. telomeric satellite sequences d. centromeric satellite sequences e. all of the above Ans: e Difficulty: 3 43. The human ________________ sequence is a noncoding 171 bp motif present in tandem arrays in a 1 mb region of human centomeres. a. deltoid b. orphon c. alphoid d. microsatellite e. pseudogene Ans: c Difficulty: 2 44. Telemeric repeated DNA sequences contain a hexomeric repeating unit containing a _______________ sequence motif. a. TTAGGG b. GGGAAA c. TTTAGG d. TTTGGG e. TGATGC Ans: a Difficulty: 2

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45. A 100 residue amino acid sequence called the ______________________________ is common to all members of the immunoglobulin gene superfamily. a. variable domain b. constant domain c. immunoglobulin homology unit d. immunoglobulin binding site e. beta-2 microglobulin domain Ans: c Difficulty: 2 46. The unique tertiary structure of the immunoglobulin fold permits it to: a. resist proteolysis. b. display a great diversity of recognition sites. c. retains its three dimensional structure. d. form trimeric molecules with other immunoglobulin folds. e. none of the above. Ans: a, b, c Difficulty: 4 47. The immunoglobulin supergene family contains three different types of homology units called variable (V), ___________________, and homology (H). a. constant (C) b. joining (J) c. diversity (D) d. CD4 (C) e. CEA (C) Ans: a Difficulty: 2 48. The principle evolutionary mechanism that gave rise to the diverse immunoglobulin supergene family was: a. gene conversion. b. exon shuffling. c. genetic drift. d. concerted evolution. e. transposition. Ans: b Difficulty: 2

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49. The immunoglobulin gene families encode specific antigen receptor classes called: a. T cell receptors. b. antibodies. c. beta-2 microglobulin. d. MHC molecules. e. a, b, and d above. Ans: e Difficulty: 2 50. Members of the immunoglobulin gene superfamily which carry out functions different from vertebrate immune recognition include: a. beta-2 microglobulin. b. carcinoembryonic antigen. c. contactin. d. almagam. e. MAG. Ans: b, c, d, e Difficulty: 3 51. Class I MHC molecules which are composed of a _____________________ chain and a beta microglobulin chain, typically present __________________________ to T cytotoxic cells. a. light, pathogens b. heavy, peptide fragments c. light, native proteins d. heavy, T-cell receptors e. heavy, light chains Ans: b Difficulty: 3 52. An immune response has three basic components, it is highly specific, selects for increased adaptivity, and: a. has mutability. b. has memory. c. evolved rapidly by gene duplication. d. is maintained by concerted evolution. e. secretes antibody. Ans: b Difficulty: 2

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53. A diagram depicting evolutionary history of a gene is called a: a. node. b. branch diagram. c. phylogenetic tree. d. molecular clock. Ans: c Difficulty: 1 Matching Match the following terms with the best definition a. Kingdom b. Hardy-Weinberg equilibrium c. Burgess Shale d. eukarya e. Phylum f. alpha helix g. nucleus h. First cellular life i. RNA secondary structure j. A,U,C,G k. prokaryotes l. archaea m. intramembrane system n. punctuated equilibrium o. North Pole, Australia 54. RNA alphabet Ans: j Difficulty: 1 55. complimentary base pairing in single stranded RNA molecules Ans: i Difficulty: 3 56. 3.5 billion years ago Ans: h Difficulty: 1 57. living representatives of the earliest life forms Ans: l Difficulty: 2

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58. compact genomes Ans: k Difficulty: 2 59. originated about 1.4 billion years ago Ans: d Difficulty: 1 60. the most universal feature of eukaryotic cells Ans: m Difficulty: 4 61. fossil evidence of the explosion of metazoan life forms Ans: c Difficulty: 2 62. taxonomic level based on body plan Ans: e Difficulty: 3 63. short bursts of rapid evolution Ans: n Difficulty: 2 Match the following terms with the best definition a. C. Elegans b. class I MHC genes c. D. Melanogaster d. M. Perutz e. nodes f. Gene superfamily g. Multigene family h. Simple sequence repeats i. branches j. Alu sequences k. Tissue Plasminogen Activator l. fibronectin m. human beta globin gene cluster n. RRNA, tRNA, and histone genes o. L. Pauling 64. examined hemoglobin and cytochrome c protein sequences Ans: o Difficulty: 1

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65. in phylogenetic trees, taxonomic unit are designated as Ans: e Difficulty: 2 66. (n)2, (n)3, (n)4, (n)5, etc. Ans: h Difficulty: 3 67. the first metazoan species whose complete genome has been sequenced Ans: a Difficulty: 2 68. 3'-locus control region Ans: m Difficulty: 3 69. Kringle, Growth Factor, and Finger Ans: k Difficulty: 3 70. A set of linked genes descended by duplication and divergence Ans: g Difficulty: 2 71. Arose by gene conversion from 38 donor pseudogenes to a small set of functional genes Ans: b Difficulty: 4 72. Conserved by one way gene conversion events within a species but can differ in consensus sequence between different species Ans: n Difficulty: 3 73. Human globin genes Ans: f Difficulty: 2 True or False 74. Darwin was the first to propose that species could undergo evolution. Ans: False Difficulty: 2

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75. HIV genome has a high rate of mutation, about 1 in 50 nucleotides per replication. Ans: False Difficulty: 2 76. Ribozymes are RNA molecules that act as enzymes. Ans: True Difficulty: 1 77. Metazoans are multicellular animals. Ans: True Difficulty: 1 78. Punctuated equilibrium of evolution is the tendency of evolution to proceed through long periods of stasis followed by short explosive periods of change. Ans: True Difficulty: 1 79. Humans diverged from chimpanzees about 6 billion years ago. Ans: False Difficulty: 2 80. Based on DNA genotyping, Neanderthal man was determined not to be a direct ancestor of modern man. Ans: True Difficulty: 1 81. Species-specific differences in phenotype are most likely due to differences in gene expression rather than mutations within genes. Ans: True Difficulty: 1 82. Nonsynonymous mutations have no effect on the amino acid encoded. Ans: False Difficulty: 2 83. There is evidence that synonymous mutations can be deleterious or favorable based on availability of tRNA and their various synthetases. Ans: True Difficulty: 1 84. Most extremely rare mutations that have deleterious effects become fixed in a population. Ans: False Difficulty: 2

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85. Duplications increase genome size and occur through transposition and unequal crossing-over. Ans: True Difficulty: 1 86. Phylogenetic trees have nodes and branches; branches represent taxonomic units while nodes represent the relationship of these units. Ans: False Difficulty: 2 87. Gene conversion outcome of unequal crossing-over allows the transfer of information from one gene to another. Ans: True Difficulty: 1 88. Concerted evolution allows changes in single genetic elements to spread across a complete set of genes in a gene family. Ans: True Difficulty: 1 Short Answer 89. Affinity maturation in which the immune response adaptively increases the fit between antibody and antigen binding during B cell proliferation and differentiation is the result of what underlying mechanism and how does it occur? Ans: Somatic Hypermutation is responsible for causing 10 - 15 mutations in V region immunoglobulin DNA sequences during the immune response in B-cells. Mutations that increase the binding affinity of antibody to antigen will be selectively amplified for clonal expansion. Difficulty: 4 90. What are the five primary processes that account for the generation of antibody diversity? Ans: Germline diversity, Combinatorial joining, junctional diversity, somatic hypermutation, and the joining of light and heavy immunoglobulin chains. Difficulty: 3 91. What was the key evolutionary event in the evolution of the T-cell receptor gene family and how might it have occurred? Ans: The key events were the acquisition of the ability to rearrange DNA gene segments via insertion of a transposable element into the 3' region of an ancestral beta (T-cell receptor family) gene segment followed by gene duplication, divergence, and adaptation. Difficulty: 3

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92. What are the most interesting features of the human beta T-cell receptor family? Ans: The 700 kb T-cell receptor gene family on chromosome 7 in humans contains 45 functional V beta gene segments, 19 pseudogene segments, 2 clusters containing 1 D segment and 5 - 6 functional J gene segments in 7 genomic modules, and LINE and Alu repetitive sequence elements occupying about 36 percent of the total DNA. Difficulty: 4 93. What are three unique features of the Burgess Shale fossils? Ans: The fossils have a great variety of basic body plans, the evolution of these body plans occurred in a very short evolutionary time frame of about 10 - 20 million years, and all the phyla present today came into existence during this Cambrian explosion of metazoan life forms. Difficulty: 4 94. Catastrophic evolution has occurred a number of times during the evolution of life forms on earth and has resulted in great changes in species numbers and dominance. If a large asteroid struck the earth today what would be the effects of an oceanic impact and what might be the consequences? Ans: An asteroid impact into the sea would drastically alter earths climate and ecosystem integrity for years following the event. Massive tidal waves, fires, acid rain, and atmospheric dust clouds would kill most organisms outright followed by a great reduction in photosynthesis which would greatly impact both the aquatic and terrestrial food chains. Mass extinctions would occur in the now toxic environment heated by gasses and fires followed by deep cold. Could we be among the species that are sufficiently adaptive or opportunistic to survive? Difficulty: 4 95. Once life in cellular form emerged, living organisms evolved into three distinct domains (kingdoms). What are they? Ans: archaea, bacteria, and eukarya. Difficulty: 2 96. In evolutionary terms, what is punctuated equilibrium? Ans: The tendency of evolution to proceed through long periods of stasis (lack of change) followed by short periods of considerable change. Difficulty: 2

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Experimental Design and Interpretation of Data 97. What evolutionary conclusions can be drawn from a comparison of the human and mouse beta T-cell receptor gene complexes? Ans: DNA sequence analysis has revealed that very different repetitive DNA sequences are spread throughout the region between both species. The general organization of the genes has been evolutionarily conserved. Trypsinogen genes are associated within the segments of both species but have been considerably more amplified in the mouse while the human segments have experienced an enhanced amplification of V beta T-cell genes. Difficulty: 4 98. What three key requirements would be expected of a molecule capable of self replication in the earliest proto cells? Ans: The ancestral molecule may have been RNA which could have preceded DNA as the repository of genetic information. The requirements for such a molecule in the primordial RNA world would have to be: To encode genetic information in a digital alphabet containing four RNA letters, assume variable three dimensional structures capable of self replication and directing other cellular reactions, and to expand the population of successful molecules and processes through selective adaptation. Difficulty: 4 99. Scientist have determined that chimpanzee and human genomes are approximately 99% similar with nearly identical karyotypes yet remarkable differences exist in phenotypic expression. Interpret this data. Ans: The data suggests that developmental expression of genes leads to significant differences between chimps and humans rather than absolute differences in protein coding regions of the two genomes. Difficulty: 3 100. Two hypothetical populations of animals exist, one is immense covering a large continent and the other rather small which occupies an area the size of Chicago, IL. Predict the effect of each population's size on its genetic drift. Ans: The smaller the population, the more rapidly genetic drift effects it. Difficulty: 3

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