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Bio 344 Molecular Biology Final Exam Spring Semester (May 10) 2003
Name __________________________________ Soc. Sec. # ___________________________________
Answer the multiple choice questions (1-54) on the answer sheet; there is only one best answer for each

question (2.5 pts each). Answer the last 4 questions on the test itself (5 points each). Since the total
possible points is 155, there are 5 extra-credit points built in to the test.
The first 19 questions concern the last two weeks’ material.
1. The chloroplast genome encodes about how many genes?
a. 16
> b. 125
c. 3500
d. 160,000
2. True or false. There is a close correlation between genome size (in kbp) and complexity of organisms.
a. True > b. False
3. True or False. Yeast, even though it is a eukaryote has only ~ 40% more genes than E. coli.
>a. True b. False
4. The smallest genome known for a self-replicating, free living organism is
a. found in an archaeote
b. found in a prokaryote
c. 517 genes
d. a and c
> e. b and c
5. Integration of exogenous (external) DNA into the nuclear genome in mammalian cells usually involves
a. homologous recombination
> b. non-homologous recombination
c. similar sequences in the integrating DNA and in the genome target
d. both a and c
6. What is the function of the neo gene in a typical mammalian transformation vector?
a. makes cells susceptible to gangcyclovir
b. provides neomycin resistance to cells transformed by homologous recombination
c. provides neomycin resistance to cells transformed by non-homologous transformation
> d. both b and c
e. all of the above
7. True or False. In a knock-out mouse, a normal gene is replaced with a disrupted gene.
>a. True b. false
8. The first mouse generated in the process of making a knock-out mouse is usually
a. completely normal
b. homozygous for the KO gene in some cells, but not others
> c. heterozygous for the KO gene in some cells, but not others
d. none of the above
9. Crown galls on dicot plants
a. are caused by Agrobacterium tumefaciens
b. resemble tumors in showing uncontrolled growth
c. can occur on different tissues
d. produce opines
> e. all of the above
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10. The uncontrolled growth of crown galls is caused by
a. opines
b. altered auxin and cytokinin levels
c. genes on T-DNA
d. a and b
> e. b and c
11. True or false. DNA placed between the LB and RB of T-DNA is transferred to plant cells.
>a. True b. False
12. The vir gene products function to
a. transport AS into the bacterial cell
b. cut T-DNA at the LB and RB borders of one strand
c. transfer T-DNA to the plant cell
d. b and c
> e. all of the above
13. In the binary vector system for plant transformation, the foreign gene is placed on the plasmid
a. with the selectable marker gene
b. with the vir genes
c. between the LB and RB
d. a and b
> e. a and c
14. The uncontrolled growth of the Agrobacterium -induced tumor is caused by which genes
a. vir
b. aux A and aux B
c. cyt
> d. aux A, aux B and cyt genes
e. all of the above
15. Getting DNA into cells by generating transient pores in the cell membrane with high voltage pulses is
called
> a. electroporation
b. biolistics
c. electrocution
d. electrofusion
16. HIV codes for up to _______ different mRNAs, because of alternative splicing
a. 3
> b. 30
c. 300
d. 3000
17. The REV gene of HIV
a. is expressed early in infection
b. is expressed late in infection
c. promotes transport of unspliced (genomic) HIV RNA into the cytoplasm
> d. a and c
e. b and c
18. The TAT gene of HIV functions as a
> a. transcriptional activator of the LTR promoter
b. transcriptional activator of the TAT gene only
c. transcriptional activator of cellular defense genes
d. a and c
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19. TAT activates transcription by
a. binding to the TAR domain
b. binding to the nascent HIV RNA
c. promoting elongation by RNAP II
d. promoting phosphorylation of the CTD
> e. all of the above
The remaining questions, except #58, concern the material covered in exams 1-3.
20. Which of the following are common elements (or features) of RNA structure
a. Watson-Crick type base pairs
b. stem-loops
c. A-form helices
d. a and b
> e. all of the above
21. DNA replication at an origin (Ori) is
a. bidirectional in prokaryotic cells
b. bidirectional (mostly) in eukaryotic cells
c. unidirectional in mammalian mitochondria
d. both a and b
> e. all of the above
22. True or false. Reverse transcriptase, discovered by H. Temin and D. Baltimore, is not a DNA
polymerase.
a. True >b. False
23. True or false. All known DNA polymerases synthesize DNA by adding nucleotides to the 3' end of a
pre-existing polymer chain.
>a. True b. False
24. The enzyme that synthesizes the RNA primer for the Okazaki fragments is
a. DNA Pol I
> b. primase
c. primerase
c. RNA Pol I
e. helicase
25. The polymerase that is absolutely required (i.e., null mutants don’t replicate DNA or divide) for DNA
replication in E. coli is
a. Pol I
b. Pol II
> c. Pol III
26. The beta clamp is very important for DNA replication as it
a. unwinds DNA ahead of the fork
b. clamps the beta subunit of the Pol III core onto the DNA template
> c. clamps the alpha subunit of the Pol III core onto the DNA template
d. clamps primase onto the DNA template
27. The initiation of replication at the major origin in E. coli (Ori C) starts with
> a. dnaA binding to the four 9-mers
b. dnaB binding to the four 9-mers
c. dnaA binding to the 13-mers
d. dnaC binding to the four 9-mers
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28. The core of the nucleosome contains
a. histones H2A, H2B, H3 and H4
b. histones H1, H2A, H2B, H3, and H4
c. ~145 bp of DNA
d. a and b
> e. a and c
29. Which of the following is the best order of sequential, increasing condensation (packing) of DNA
a. nucleosomes –> solenoid –> 30 nm fiber –> Loops on scaffold –> heterochromatin
b. euchromatin –> solenoid –> 30 nm fiber –> nucleosomes
c. nucleosomes –> 30 nm fibers –> euchromatin –> heterochromatin
> d. nucleosomes –> 30 nm fibers –> solenoid –> Loops on scaffold
30. True or false. Histones inhibit transcription by making it hard for proteins to bind to the promoter.
> a. True b. False
31. In homologous DNA recombination via the Holliday model, the Holliday junction
a. is a 4-stranded structure
b. is generated by cutting, exchanging and rejoining (intermolecularly) homologous strands
c. is generated by the action of recBCD, recA, SSB and DNA ligase
d. b and c
> e. all of the above
32. RecA is a remarkable enzyme that
a. binds both double-stranded (DS) and single-stranded (SS) DNA
b. is an ATPase
c. catalyzes the exchange of 1 strand in a DS DNA with a homologous SS
d. a and c
> e. all of the above
33. Variegation or sectoring in maize is often caused by
a. DNA methylation
b. spatial gene regulation
c. transposable elements
d. genetic changes in somatic cells
> e. both c and d
34. The protein responsible for binding the -10,-35 elements of an E. coli promoter such as the lac
promoter is
a. beta
b. alpha
c. TBP
> d. sigma
e. none of the above
35. True or false. E. coli has only one RNA polymerase core.
>a. True b. False
36. Rho functions
a. to terminate transcription of certain operons
b. to terminate translation at Stop codons
c. as a helicase
> d. a and c
e. b and c
37. Affinity labeling of the E. coli RNAP with an ATP analogue revealed the active site to be on
a. alpha
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b. sigma
> c. beta
d. beta’
38. Activation of the lac operon by CAP
a. is mediated by cGMP
> b. is induced by low glucose outside of the cell
c. requires binding of CAP downstream of the classical lac operator sequence
d. involves binding of CAP to the beta’ subunit of the RNAP core
39. In the DMS footprinting assay
a. DMS cleaves DNA at purines
b. DMS methylates DNA at purines
c. binding of a protein to the DNA protects it (i.e., DNA) from DMS
d. both a and c
> e. both b and c
40. A circadian clock regulates transcription globally in Synechococcus. Which of the following are
characteristics of circadian rhythms
a. they peak once every 24 hours
b. they continue on schedule in constant conditions
c. the peak is always at the same time of day, regardless of the light-dark cycle
> d. both a and b
e. all of the above
41. Which of the following is true regarding the mitochondrial RNA polymerase
a. its core is made up of 4 subunits
b. it is encoded in the organelle in animals
> c. it resembles the RNAP in some phage
d. it recognizes -10,-35 promoters
e. it is inhibited by rifampicin
42. The rRNA genes of the nucleus are transcribed by which RNA polymerase
> a. Pol I
b. Pol II
c. Pol III
d. primase
43. All 3 major nuclear RNAP share which of the following features
a. all have 10-14 subunits
b. all have several subunits in common
c. all have 2 very large subunits
> d. all of the above
44. Which of the following cis-acting motifs is not a component of RNAP II promoters
a. TATA box
b. initiation region
c. upstream element
d. downstream element
> e. Core
45. Which of the following is not true of enhancers
a. stimulate transcription
b. orientation independent
c. position independent
d. can be found in introns
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> e. none of the above (all can describe enhancers)
46. The DABpolF complex, which can stably bind to class II promoters and can be formed in vitro with
purified factors and RNAP II, contains which of the following
a. TFIID
b. TFIIA
c. TFIIB
d. TFIIF
> e. all of the above
47. True or False. The TATA-box binding protein is required by all 3 nuclear RNAPs.
>a. True b. False
48. Which of the following is not true concerning the CAP of cytoplasmic mRNAs
a. it is composed of a methylated guanosine nucleotide
b. it enhances translation
c. it enhances splicing of the first intron for some pre-mRNAs
d. it is added mainly by a guanylyl transferase
> e. none of the above (all describe the CAP)
49. The greatest translation of a chimeric luciferase mRNA in electroporated plant protoplasts occurred
when the chimeric mRNA contained
a. a CAP but no poly A tail
b. a poly A tail but no CAP
> c. both a CAP and poly A tail
d. none of the above (plants don’t translate luciferase mRNAs)
50. Both phases of polyadenylation require
a. CPSF
b. poly A binding protein
> c. poly A polymerase
d. b and c
51. Self-splicing introns are found in which of the following intron classes
a. group I
b. group II
c. tRNA
> d. a and b
e. all of the above
52. The first step of splicing by a group I intron requires
a. ATP
b. an internal A
> c. GTP
53. Which of the following is not found in the “activated form of the spliceosome”
a. pre-mRNA
> b. U1
c. U6
d. U2
54. RNA editing in several systems involves conversion of Cs to Us. What enzyme(s) probably do the
chemistry required for this transition
a. endonuclease + ligase
b. endonuclease + terminal cytidine transferase
> c. cytosine deaminase
d. cytosine methylase
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55. RNAi is being touted as an important new tool in molecular biology. What is it used for? What is the
biological significance of RNAi?
RNAi is being used to knock down expression of specific genes in order to determine their function.
RNAi probably evolved as a mechanism to control viruses, particularly RNA viruses, and possibly
retrotransposons. It looks like it is also being adapted by cells to control certain genes at the RNA level
using microRNAs.
56. The mammalian reticulocyte has played an important role in our understanding of translational
initiation and regulation. What are reticulocytes? What proteins do they mainly produce? How do you
get
them? How do you use them?
Reticulocytes are precursors to erythrocytes (red bood cells). The mainly synthesize hemoglobin. They
can be collected in large quantities from the serum of rabbits made anemic by injecting
phenylhydrazine.
They can be lysed and a cell-free extract prepared that is very active in synthesizing proteins in response
to added mRNA.
57. What is the composition of the E. coli ribosome?
Please see slide in the translation 3 lecture.
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58. Describe how you get a completely transgenic, homozygous knock-out (KO) mouse from the
chimeric
mouse generated in the first phase of making a completely KOed mouse.
Please see slides on producing transgenic mice.