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Final Exam Practice Fall 2009 Biology 202 Drs. Bloom and Shemer
Your TA's name:

Please read ALL questions CAREFULLY before starting. Answer in as short a manner as possible--
writing down a lot of words won’t help.

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1) You have a partial diploid for the lac operon. The plasmid copy of the operon has a mutation
in the activator binding site, preventing the activator protein from binding to it. The
chromosomal copy has a mutation in the lacZ gene. When will functional beta-galactosidase
be produced? (choose all that apply)

a. glucose and lactose are both absent

b. glucose is present and lactose is absent

c. glucose is absent and lactose is present

d. glucose and lactose are both present

e. never

2) You are interested to screen a cDNA library obtained from human brain with a probe you
constructed based on a mouse gene. How would you generate such a cDNA library?

cDNA is made through reverse transcription of mRNA, using a polyT primer and a reverse
transcriptase. The cDNA is then ligated into a plasmid, and transformed into E. coli. Each
E. coli cell then divides into a colony, which contains a different cDNA. This library can
now be screened by the mouse DNA probe.

3) When transforming a hemoglobin gene into E.coli, I use a plasmid containing an antibiotic-
resistance gene. Why?

a. So the hemoglobin is immune to the antibiotic

b. So I can add antibiotic to the growth media and prevent cells without the insert in the
plasmid from growing

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c. So I can add antibiotic to the growth media and prevent cells without the plasmid
from growing

d. So that the colonies containing a plasmid will be blue, and those without a plasmid will be

white

4) During our “graduation project” in class, we mentioned that your friend isolated the eyeless
mutant in flies and cloned the eyeless gene, the first gene known to be involved in eye
development.

a. Today, after you learned about developmental genetics, you can guess that your friend took
a reverse/forward genetic approach (mark the right one and explain).

Forward. As no genes were known, she had to mutagenize the flies randomly and select
for the right phenotype

b. A new allele of eyeless has been isolated from flies. This mutant carries a gain-of-function
(gf) mutation in exon 3 of the eyeless gene. Assuming the eyeless gene is normally expressed
in the eye of the fly specifically in the R7 cell (one of more than 30 cells in the eye), it is most
likely that the mutated gene will be expressed:

a. specifically in the R7 cell

b. in all the eye cells

c. in all the cells of the fly

d. in none of the cells

Explain your answer:

The gf mutation in exon 3 should not affect the regulatory elements of the gene.
Therefore, it will be expressed just like WT. It might be localized at different sites as a
protein (e.g. Golgy instead of the plasma membrane), because of the GF mutation.

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5) What is common and what is different between dsRNAs and miRNAs?

Both are recognized and cleaved by Dicer to ~22bp. Both are then recognized by the RISC
complex and bind to endogenous mRNAs in the cytoplasm. Both are components of the
post-transcriptional regulatory machinery.

Differences: dsRNA: exogenous, exact matching with target mRNA, degradation of mRNA.
miRNA: endogenous, mismatches with target mRNA, translation inhibition of mRNA.

6) The genetic code is degenerate because

a. mRNA is rapidly degraded

b. the code is not universal among organisms

c. some amino acids have more than one codon

d. frameshift mutations are tolerated

e. stop codons may have corresponding tRNA molecules

7) When screening for mutants involved in programmed cell death, Horvitz and his students
isolated several mutant alleles of the gene ced-9. One of the allele was found to be a gain-of-
function allele.

a. What is the phenotype of the ced-9(gf) mutant?

No cell death

b. Would ced-9(gf) suppress the ced-1(lf) phenotype (the original engulfment mutant)?
Explain

Yes, no death = no corpses = no ectopic button-like cells

c. In a screen for suppressors of ced-9(gf), would it be possible to find ced-3 mutants? If it

is possible, would they be ced-3(lf) or ced-3(gf)?

Yes, ced-3(gf) would suppress ced-9(gf) as ced-3 is epistatic and ced-3 might kill cells
without being susceptible to ced-9 inhibition.

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8) The Retinoblastoma cancer disease is inherited in pedigrees as a

a. simple Mendelian dominant

b. simple Mendelian recessive

c. multifactorial trait

d. X-linked recessive

e. extranuclear trait

9) Oncogenes are ____________________ mutations because they improperly enhance the

expression of genes that promote cell proliferation or inhibit apoptosis.

Gain-of-function

10) The Rb gene acts in normal cells to inhibit the transcription factor E2F, which promotes the
entry of cell cycle to the S phase. A mutation in the gene encoding the E2F protein was found
to be associated with tumor progression. Would you expect this mutation to be a gain-of-
function or a loss-of-function mutation? Would that mutation be sufficient to cause cancer?

Gain-of-function, this will be an oncogene. While this mutation might be one of the
mutations leading to cancer, it is not sufficient to cause cancer, as cells need to acquire
more mutations (and as a result, more cancerous properties) in order to make
metastatic tumors.

11) What was the main evidence that showed the bead theory was wrong when it came to “the
gene is a fundamental unit of structure”?

Crossovers can take place within a gene between two fragments of phage DNA (Benzer’s
experiments)

12) Which of the following features of a protein structure is most directly determined by the
genetic code?

a. Its shape

b. Its secondary structure

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c. Its catalytic or structural role

d. Its amino acid sequence

e. Its subunit composition (quaternary structure)

13) You are studying a very short protein-encoding gene whose sequence is
shown below. The region of sequence shown is from the transcriptional start site to the
transcriptional stop site. The gene’s one small intron is shown for you in bold.

a. Which strand is used as a template in transcription, the upper strand or the lower strand?
The upper strand. The only strand that has a start codon (5’-ATG-3’, bolded and
underlined above) is the bottom strand, so the bottom strand must look like the mRNA.
This means that the upper strand is the one that is used as a template.

b. How many amino acids long would the protein product of this gene be?

8 amino acids. The mRNA looks like this after splicing the intron out:
5’-GUACGAUCGAAUCGGAAUGCGACUAGAUCGAGGGAAUAGCUAGUACGUAG-3’
The AUG encodes methionine, the first amino acid. You then have seven other codons that
code for amino acids until the stop codon.

1st codon: AUG

2nd codon: CGA
3rd codon: CUA
4th codon: GAU
5th codon: CGA
6th codon: GGG
7th codon: AAU
8th codon: AGC
stop codon: UAG

c. What is the amino acid that would be on the C-terminus end of the protein produced from this
gene?
Serine (ser). The last codon of this gene is the 8th codon: AGC. If you look up AGC on the
codon table, it codes for serine.

14) A flower that is true breeding for white petals is crossed with a flower that is true breeding for red
petals. All of the F1 plants had white petals. When the F1 individuals were crossed the F2 plants
showed the following phenotypes:

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White 245

Red 61

Pink 19

a. What were the genotypes of the true breeding parents? (Use symbols that we can easily
distinguish as dominant or recessive.)

White: ______________ AA; bb

Red: ________________aa; BB

b. What are the possible genotypes for the F2 generation? (Use the same symbols that you used in
part a.)

White: _________________A -; B – or A -; bb

Red: __________________ aa; B -

Pink: __________________aa; bb

Note: In part a. the white and red genotypes can be switched which is fine if they follow that
through in part b.

15) Explain why dideoxy nucleotides are useful in Sanger DNA sequencing. Why is it important to use
correctly titrated, amounts of dideoxynucleotides in the dideoxy method of DNA sequencing? In
other words what happens if there is too much dideoxynucleotide in a reaction mixture?

Dideoxynucleotides lack a 3' OH group, which is essential for attachment of the next nucleotide in
a growing DNA strand. Therefore, incorporation of a dideoxynucleotide terminates further
synthesis of the strand.

The use of a small amount in a sequence reaction ensures that a set of fragments is produced that
each terminate at all possible sites. If there is too much ddN, then the chains terminate
prematurely and only short “reads” are produced.

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16) 8. Compare and contrast the DNA code versus the “histone” code.

DNA code:

Three base nonoverlapping code.

Encodes the potential for 64 amino acids (because of wobble, only 20 amino acids).

The Code specifies protein sequence and is read-out by translation machinery.

Genetically transmitted.

HISTONE code:

Post-translational modification of charged amino acids on histone tails.

Encodes an unlimited potential (many charged amino acids that can be acetylated,
phosphorylated, methylated, ubiquitinated).

The histone code specifies chromatin structure and contributes to active vs. inactive chromatin
states.

Epigenetic transmission.

17) The eyes of a certain mutant Drosophila have a rough texture due to abnormal facet
structure. Three of the mutants that produce approximately the same phenotype (mimics) are
sex-linked recessives; roughest (rst), rugose (rg) and roughex (rux). The loci of these genes in
terms of their distances from the end of the X chromosome are 2, 11, and 15 map units,
respectively. A) From test crossing wild-type females of genotype rst + rux/+ rg +, predict
the number of wild-type and rough-eyed progeny flies expected from 20, 000 progeny.
Assume no interference. B) approximately how many rough-eyed flies are expected for every
wild-type individual. C) If the females of part a were of the genotype rst, rg rux / + + + what
would be the approximate ratio of wild-type:rough-eyed progeny?

ANS: a) only double crossover will give wt progeny, so 9% (11-2) x 4% (15-11) = .36 =
36/10000 are double xovers. Half are wt, half are rough.

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36 rough, 19 964 wt

B) 1:555

c) no crossover 50 wt/ 50 rough.

But single crossover give rise to rough and rough progeny.

So this is 4% plus 9% = 13%

So 87 % noncrossover

13 % crossover

87 (non crossover progeny) 44 wt , 43 rough 13 (crossover progeny) all rough

Final answer 43+13 = 56 rough, 44 wt (we’ll take 57 rough, 43 wt as well)