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BIOLOGY 221
EXAM 2 FOR 2017
KEY
This is a provisional key.

Regrades are only allowed with a typed written statement of why you think your answer is
correct and must be submitted by Tuesday, Nov 14th by the end of class. Hand in to a TA
or Dr. Bonini.

Please note that when your exam is re-graded, then the entire exam is re-graded, so you
may get additional points, but may also get points taken off.

When you write an answer, the entire answer must be considered. Only exams in pen
without correction tape or white out may be considered for re-grading.
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1. (7 pts) Which of the following are true and which are false about RNA?
Circle the right answer.

a. rRNAs never contain introns T or F

b. The polyA tail of an mRNA is required for ribosome recognition

T or F

c. tRNAs contain modified bases T or F

d. mRNAs in general have a shorter half life than rRNAs T or F

e. Prokaryotic mRNAs have a homogenous size T or F

f. tRNAs have additional sequence added beyond that encoded in the gene, but it is only
added at the 3’end.

T or F

g. DNA and RNA are both very stable nucleic acids T or F

2. (2 pts) Prokaryotic mRNAs are often multigenic, but this is rarely observed in eukaryotic
mRNAs. What differences between prokaryotic and eukaryotic translation reflect this difference
in mRNA organization.

Circle all of the correct answers.

A. The ribosomes of eukaryotes are larger than those of prokaryotes, allowing prokaryotes
to have more efficient and faster protein translation.
B. Prokaryotes organize genes in operons whereas eukaryotes use operators.
C. Prokaryotes use a sequence-specific recognition for protein translation initiation.
D. Eukaryotes have a nucleus, devoid of chromatin, whereas prokaryotes do not have a
nuclear compartment.
E. Prokaryotes organize gene transcription in Christmas tree structures, which is not seen
in eukaryotes.
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3. Niremberg was the first to crack the genetic code by using a synthetic RNA, incubating with
cellular extract, and then examining the amino acid that was produced.
(9 pts)

List the polypeptides that will be produced from the following synthetic RNAs

A. Poly(GGG)?

Poly-glycine

GGG-GGG-GGG

B. Poly(GGC)?

Poly-glycine
Poly-alanine
Poly-arginine

The three possible ribosome frames are:

GGC-GGC-GGC
GCG-GCG-GCG
CGG-CGG-CGG

C. If you performed an experiment like Niremberg did, by incubating the RNA of B above in
a test tube with E. coli extract and with radioactively-labelled glycine amino acid, what
are all polypeptides you would detect being synthesized?

Only poly-glycine

Although all peptides will be made, only radioactive 1 will be detectable by Niremberg’s method.
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Multiple Choice (2 pts each):

4. Which statement best describes the role of the Poly-A tail?

A) The tail is required only for the stability of the mRNA

B) The tail is required for the ribosome to recognize the start site for translation
C) The tail is required for mRNA stability and for nuclear export
D) The tail is not required
E) The tail is required for tRNA function

5. In a DNA strand, a phosphate connects a 3’ carbon atom in one deoxyribose to:

A) a base in an adjacent nucleotide

B) a base in the same nucleotide
C) a 3’carbon in an adjacent deoxyribose
D) a 5’carbon in an adjacent deoxyribose
E) a 2’carbon in an adjacent deoxyribose.

6. In the experiment of Avery, McLeod and McCarty, the addition of Rnase and protease to the
S cell extract:

A) Allowed the conversion of type S into type R bacteria

B) Prevented the conversion of type S into type R bacteria
C) Allowed the conversion of type R into type S bacteria.
D) Prevented the conversion of type R into type S bacteria.
E) None of the above.

7. If an E coli chromosome has fired it’s origin of replication, how many replication forks are
present?
A) One fork
B) Two forks
C) Six forks (the original and two additional forks after the progeny origins fire)
D) Three forks (the central fork, and the two regions where DNA replication is proceeding).
E) None; prokaryotic replication does not use replication forks because it is a circular
chromosome.

8. You have identified an aminoacyl-tRNA synthetase that is mutated such that it recognizes
tRNA with an anti-codon for phenylalanine, but binds glycine at its amino acid binding site.
What effect might this have on translation?

A. No effect; each tRNA binds specifically to its cognate amino acid independent of
aminoacyl-tRNA synthetase.
B. Translation will be slower, because this enzyme will not function at all and the cell will
depend on the tRNA and aminoacyl-tRNA synthetases that exhibit the other
phenylalanine-encoding codons and wobble base pairing to translate phenylalanine.
C. Translation will stop, because this enzyme is non-functional and the translation
machinery will stop each time it reaches the codon for phenylalanine and there is no
tRNA to “read” it.
D. The tRNA will become “charged” with glycine instead of phenylalanine, so translation will
go on at the same rate but with glycine in many of the places where phenylalanine
should be.
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9. Cairns did a genetics experiment to test the significance of the enzyme that Kornberg isolated
biochemically.

DNA replication requires Kornberg’s enzyme. Did Cairn’s study show that DNA replication
required Kornberg’s enzyme? Circle the right answer.
(1 pt)
Yes or No

What did Cairns screen for when he did his experiments? Circle all of the correct answers.
(4 pts)
A) He screened for E coli mutants that would be temperature-sensitive viable.
B) He screened for E coli mutants that would grow at high temperature (37C).
C) He screened for E coli mutants that did not have DNA polymerase activity at high
temperature (37C).
D) He screened for E coli mutants that would grow at low temperature (30C).
E) He screened for E coli mutants that would have DNA polymerase activity at low
temperature (30C).

When Cairns tested his mutants for the function of Kornberg’s enzyme, what did he test for?
Circle all the correct answers.
(4pts)
A) He tested for temperature-sensitive DNA polymerase activity.
B) He tested for the ability to purify DNA polymerase protein.
C) He tested for growth at low temperature (30C).
D) He tested for growth at high temperature (37C).
E) He tested for lack of DNA polymerase activity at high temperature (37C).

10. (3 pts) We have discussed a number of elements of a gene, including

A) The transcription start site 


B) The TATA box
C) Transcription factor binding sites in the promoter.
D) Exons
E) Introns
F) enhancer elements

A. Of these (A-F), which are transcribed as pre-mRNA?

A,D, E (F could also be in intron)

B. Which can encode the protein product? D

C. Which are required to regulate and transcribe the gene? B,C,F

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11. (8 pts) For the following lac operon partial diploids, fill in the table below with whether on
colonies grown on IPTG plates, the synthesis of the lacZ mRNA will be constitutive, inducible or
uninducible, and whether the phenotype will be lac+ or lac- (specifically, able to utilize lactose
on the bacterial plate or not).

GENOTYPE lacZ mRNA synthesis Lac phenotype

(constitutive, inducible, (lac+ or lac-)
uninducible)

A. I-P+O+Z+Y+/I+P+O+Z+Y+ Inducible Lac+

B. I+P+OCZ+Y+/I+P+O+Z-Y+ Constitutive Lac+

C. ISP+O+Z+Y+/I+P+O+Z+Y+ Uninducible Lac-

D. I+P+OCZ-Y+/ISP-O+Z+Y+ Constitutive* Lac-

*Is cannot bind Oc because Oc is mutant, so Is has no effect on Oc operon copy. The other
operon copy is dead (no promoter). mRNA of Oc operon is being synthesized constitutively, but
it is lacZ- (mutant) so no functional protein.

12. If an E coli colony is blue on an X-gal plate, is the lac operon on or off? Circle an answer.
(1 pt)

ON or OFF

13. Adenylate cyclase mutants of E coli cannot make cAMP. If you grow this E coli strain on X-
gal plates with IPTG, will the colonies be white or blue? Circle an answer.
(1 pt)
WHITE or BLUE
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14. Below is an origin of replication on a chromosome. The sequence in region 1 is shown.

(12 pts total–4 pts each)

Region 1: 5’...CTGACTGACA...3’
3’...GACTGACTGT...5’

A. Within region 1 indicate above, which strand will be the template for leading strand DNA
replication, the top or the bottom? Circle your answer.

TOP or BOTTOM

B. If we assume that a lagging strand fragment is made from region 1, what will be its
sequence? Circle all the right answers.

5’...CTGACTGACA...3’

3’...GACTGACTGT...5’

5’...GACTGACTGT...3’

3’...CTGACTGACA...5’

C. You are studying DNA replication in an E coli mutant that has defective DNA
polymerase III. In vitro experiments using the mutant DNA polymerase give an error rate
of 10-3 compared to the expected 10-6 rate. Which of the following activities is likely to
be missing compared to normal polymerase? Circle all that apply.

5’-to-3’ polymerase 3’-to-5’ exonuclease

5’-to-3’ exonuclease 3’-to-5’ polymerase

5’-to-3’ recombinase 3’-to-5’ recombinase

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15. (4 pts)
Below is a schematic of a molecule that inserts a tryptophan in protein synthesis.

A. This schematic represents a tRNA

B. On the schematic, fill in the nucleotides of the anticodon.

5’ C C A 3’
Key here is to know that the amino acid is added to the 3’ end. So the codon being recognized
is 5’-UGG-3’, by the anti-codon in the tRNA of 3’-ACC-5’. Anticodon must be properly oriented,
given the amino acid on the 3’end.
16. In Crick and colleagues studies, they used the phenotype of mutants in a gene of
bacteriophage of bacteria to deduce the number of DNA bp required for the genetic code.
Answer the following questions below.

A. What were the bacteriophage and the gene that they used for their studies?
(2 pt)
a. Bacteriophage: T4

b. Gene: rIIB

B. To recombine the suppressor mutations away from the FC0 mutation, what did they
have to co-infect the E coli bacteria with?
(2 pt)
A) The FC0 phage
B) The suppressor mutation
C) Wild type
D) A new phage mutant.
E) Bacterial strain K.

C. When they recombined two suppressor mutations in one bacteriophage genome, was
the recombinant wild type or mutant? Circle an answer.
(2 pts)
WILD TYPE or MUTANT
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Some multiple choice questions regarding the ends of the chromosomes. Circle all the right
answers.
(2 pts each)

17. DNA polymerases cannot replicate

A) the 5’end of circular chromosomes

B) the 3’end of circular chromosomes
C) the 5’end of linear chromosomes
D) the 3’end of linear chromosomes [The 3’end of the chromosome being copied cannot be
replicated because it requires a 5’-3’ RNA primer for replication of the chromosome]
E) both the 5’end and 3’end of linear chromosomes

18. Telomerase is unique because it contains

A) A DNA molecule
B) An RNA molecule
C) Different RNA molecules
D) Different DNA molecules
E) Both DNA and RNA molecules

19. Which of the following best describes the function of telomerase at the telomere?

A) It makes special primers that do not need to be removed

B) It synthesizes new DNA without the use of a template
C) It adds new DNA to both strands of the telomere overhang.
D) It adds new DNA to the shorter strand of the telomere overhang.
E) It adds new DNA to the longer strand of the telomere overhang.

20. Telomeres consist of direct repeat sequences of DNA

A) True
B) False
C) It is not possible to know the sequence.
D) Telomeres consist of RNA sequence.

21. In the absence of telomerase activity, chromosomes are shortened slightly after every round
of replication.

A) True
B) False
C) Only true in those cells with telomerase.
D) Only true in somatic cells with telomerase.
E) Not possible to determine.
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22. A bacterial inducible operon, similar to the lac operon, contains three genes R, T and S
that are involved in the regulation of transcription.
One of these genes is the operator, one is a regulatory protein, and one is a structural enzyme.
In the table below, “+” indicates that the structural enzyme is synthesized, and “-“ indicates that
it is not produced.
(12 pts)

Using the information provided, determine which gene is the operator, which gene produces the
regulatory protein, and which gene produces the enzyme.

Genotype Enzyme synthesis with Enzyme synthesis with

inducer present inducer absent
R +S +T + + —

R -S + T + — —

R + S -T + + +

R +S +T - + +

R-S+T+/R+S-T- + +

R+S-T+/R-S+T- + +

R+S+T-/R-S-T+ + —

Operator: S

Regulatory protein: T

Enzyme: R

R+S+T+ shows how gene acts. No inducer, it’s off. Inducer it’s on.
R-S+T+, No enzyme synthesized even though induced. R=enzyme
R+S-T+, not responsive to inducer. Acts like an operator mutant or regulatory protein mutant.
R+S+T-, not response to inducer. Acts like operator or regulatory protein mutant.

So S and T are the operator and regulatory protein. Given this, need to work through the other
combinations to figure out which of S or T can act in trans (regulatory protein), and which acts
only in cis (operator).

R+S+T-/R-S-T+ shows that T+ can act on T- copy of the operon to restore function, indicating
that T is the trans-acting regulatory protein.
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23. One property of position effect variegation is that heterochromatin can spread over more
than 1000 kb of previously euchromatic chromatin. A rearrangment in fruit flies allows you to
investigate whether this process can skip over genes as it spreads along the chromosome.
The rearrangement below has brought both the white+ gene and the roughest+ gene near
heterochromatin.

Wild type flies with both w+ and rst+ alleles have red eyes and a smooth eye surface. Flies
mutant for these two genes have white eyes and rough-surfaced eyes.

You examine male flies with the re-arrangment for the presence of variegated sectors in their
eyes. You do see sectors in the fly eyes.
(6 pts)

A. What is the apparent genotype of white+ and roughest+ genes in those sectors that are
white and smooth? Circle all the correct answers.

A) w+, rst-
B) w+, rst+
C) w-, rst-
D) w-, rst+
The question is asking what the genotype appears to be based on phenotype.
Sectors that are white have the apparent genotype of w-, sectors that are smooth have the
apparent genotype of rst+.

B. What is the genotype of white+ and roughest+ genes in those sectors that are red and
rough? Circle all the correct answers.

A) w+, rst-
B) w+, rst+
C) w-, rst-
D) w-, rst+

As seen above, the genotype is always w+, rst+. The loss of gene activity is due to
heterochromatin spreading due to altered position of the genes in the genome, and due to
actual mutation of the gene function.