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Discussion Section __________________

MCDB 101A Fall 2021

Section 200
Thursday, October 21st 2021
Midterm 1 Version X

20 Multiple Choice - 3 points each – 60 points total

6 Short answer - 6 – 10 points – 40 points total

1. Select the best answer possible

2. In your scantron, mark the version of the exam
3. Write your name, perm number and discussion section in this page as well as in the short answers pages
4. Write as legible as possible
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Discussion Section __________________

0 A B C Ans Question
1 20 6 9 A Which protein is required for theta replication but NOT by rolling circle?
a. Dna A / DNA B / Gyrase
b. Primase
c. Ligase
d. ssbp’s
e. All listed proteins are needed in both processes

2 10 8 3 B Two strains of T2 phage with different combination of alleles for the

genes r (related to colony size) and h (related to host specificity)
were plated on a mixture of E.coli B and B/2. The counts for all the
phenotypes observed are shown in the table below. Which of the
following were the parental genotypes?
a. h+r+ and hr
b. h+r and hr+
c. h+r and h+r
d. h+r+ and hr+
e. none of the above are correct

3 3 9 4 A This genetic map shows the deletions (marked by

letters) found in a phage’s genome. Select the
recombination table that matches the map:

4 19 2 14 A Below are the trans test results between 6 point mutations at the T4
rII locus. Based on this table, select the answer that contains the
correct number of genes as well as the mutation grouping per gene.
Genes are separated by backslashes
a. 3 genes, BE/ACF/D
b. 3 genes, ACD/BE/F
c. 2 genes, BEF/ACD
d. 2 genes, ACF/BDE
e. 4 genes, AC/B/D/A
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5 4 4 12 C In the graph shown from the Okazaki experiment, what is represented
by the rising peak observed approximately at the middle of the tube
(relative distance from top of tube =2)?
a. the individual okazaki fragments
b. the elongating leading strand
c. the okazaki fragments being joined by the ligase
d. the accumulation of fragments due to the lack of ligase activity
e. the accumulation of RNA primers due to the lack of ligase activity

6 17 3 18 A What would have been the consequence of under-blending during the Hershey & Chase
experiment?
a. a higher percentage of S35 would have been observed in the pellet
b. a higher percentage of S35 would have been observed in the supernatant
c. a higher percentage of P32 would have been observed in the pellet
d. a higher percentage of P32 would have been observed in the supernatant
e. none of the listed options

7 13 14 17 A Which of the following statements correctly describes the interaction between DNA and the
protein described?
a. the sigma factor of RNA polymerase binds to the promoter region of a gene during
transcription
b. Dna A binds to the 13 bp repeats of the ori C site during replication initiation
c. DNA B binds to the 9 bp repeats of the ori C site during replication initiation
d. the DNA polymerase I beta subunits associate in a ring-like structure during replication
elongation
e. the DNA polymerase I alpha subunits associate to the DNA template strand during replication

8 12 13 7 A Two DNA plasmids have a linking number of 100 and the same number of positive supercoils.
Plasmid A is composed of Z DNA while plasmid B is composed of B DNA. Which molecule has
more base pairs?
a. Plasmid A
b. Plasmid B
c. They are the same size
d. More information is needed to answer this question

9 14 15 2 E Which of the data tables below matches the metabolic pathway

shown? Metabolites are indicated by letters and mutants are
indicated by numbers.
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E. None of these

10 6 5 16 E Auxotrophic mutants…
a. can result from mutations in genes encoding enzymes
b. can result from mutations in genes encoding metabolite transporters
c. can result from mutations in genes encoding gene expression regulators
d. can survive in minimal media without any supplement
e. more than one option is correct

11 5 7 15 C According to Chargaff rules, which of the following statements must be true?

a. A single stranded RNA virus that contains 28% Adenine must also contain 44% G+C
b. The ratio of guanines/adenines in any nucleic acid must always be 1
c. If a single stranded DNA, the A+G/T+C ratio = 0.2, the A+G/T+C ratio in the complementary
strand is 5
d. The A+G/T+C ratio varies across the genomes of different animal species
e. More than one statement is true

12 18 17 13 Null When comparing the DNA Topoisomerase I (Topo I) and Topoisomerase II (Topo II), which of
the following statements are TRUE?
a. Topo I cuts both strands of DNA while passing another segment of the dsDNA molecule
through the break while Topo II cuts one strand only
b. Topo I is associated with positive supercoiling while Topo II is associated with negative
supercoiling
c. Theta replication requires the function of Topo II ahead of the replication fork to relieve the
negative supercoiling caused by the expansion of the bubble
d. Topo II, but not topo I, is capable of creating phosphodiester bonds to rejoin the broken
strands of DNA
e. Lack of Topo II function is associated with hyper negative supercoiling, causing RNA pol
stalling

13 7 19 11 C Which of the following statements is consistent with the

DNA melting curve graph of two DNA fragments? Uppercase
letters refer to the two DNA molecules, and the lower case
letters refer to points on the graph. Both DNA molecules are
the same length.

a. Molecule A requires more energy to melt than molecule B

b. p and r refer to the point when DNA is almost completely
single stranded
c. Molecule A has a higher A+T/G+C ratio than molecule B
d. Molecule A has a higher concentration of A and G than
molecule B
e. Molecule B has a higher concentration of A and T than molecule A

14 1 1 5 A The fact that the genetic code is non-overlaping is demonstrated in the fact that
a. a single base pair substitution mutation can only alter a single amino acid in a given sequence
b. codons must contain 3 nucleotides
c. a given aminoacid can be encoded by more than one codon
d. for some codons, only the first two nucleotides are needed
e. different species have an overabundance of a particular codon for a given amino acid
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15 16 20 1 D The following DNA sequence transcribes a very short protein. Which of the two strands is the
TEMPLATE strand for this protein? How many amino acids would the protein have once it is
translated?

a. Bottom strand; 5 amino acids

b. Top strand; 6 amino acids
c. Bottom strand; 4 amino acids
d. Top strand; 5 amino acids
e. Both strands can be the template; two peptides are formed (5 and 6 amino acids)

16 9 11 6 C A deletion mutation that spans over the Shine-Dalgarno sequence of gene A is likely to
interfere with...
a. The ability of the mutant bacteria to carry out theta replication
b. The ability of the mutant bacteria to carry out rolling cycle replication
c. The ability of the mutant bacteria to initiate translation of protein A
d. The ability of the mutant bacteria to initiate transcription of gene A
e. The ability of the mutant bacteria to terminate transcription of gene A

17 8 18 10 B In a similar experiment to Nirenberg’s you introduce an mRNA with a repeating codon to an in

vitro protein system that does not require a start codon. As a result, you obtain a mixture of
two peptides: a poly-Ile (Ile-Ile-Ile…) and a poly-Asn (Asn-Asn-Asn…). Which of the following
sequences could have yielded those peptides?
a. 5’- AUCAUCAUC...-3’
b. 5’- AUAAUAAUA... -3’
c. 5’- AUUAUUAUU...-3’
d. 5’-AACAACAACA...-3’
e. None of these sequences could have yielded those peptides.
18 2 12 20 D What is likely the consequence of not using the DNA phosphatase after restriction enzyme
digestion of the plasmid during cloning?
a. A low 260/280 ratio will be observed during the DNA quantification
b. The sticky ends of the gene will not match the blunt ends of the digested plasmid
c. A smaller number of cells will be subject to transformation
d. The ends of the plasmid could reclose without incorporating the DNA fragment of interest.
e. The proteins from the cell lysate will not precipitate, making the sample impossible to purify

19 15 16 8 E An alien organism has DNA composed of 2 instead of 4 different nucleotides. Its proteins are
composed of 16 amino acids. What would be its minimal codon size? Write down the number
of nucleotides per codon without any units
a. 1
b. 2
c. 3
d. 4
e. 5

20 11 10 19 B After plasmid purification, having a low 260 to 280 absorbance ratio is an indication of…
a. A low concentration of single stranded DNA vs double stranded DNA
b. High levels of protein contamination
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c. A low efficiency of plasmid transformation
d. A low concentration of DNA vs RNA
e. A high concentration of single stranded DNA vs double stranded DNA
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Short Answer

21. What experimental results would have made Hershey and Chase conclude that proteins were the molecule
responsible to transmit genetic information? In a few sentences describe this hypothetical results and their
interpretation. (6 points)

The results would have shown that the culture of the phage grown with radioactive sulfur (S35) would display the
majority of the radioactivity in the pellet and not in the supernatant (2 points), whereas the phage culture with
radioactive phosphorous (P32) would have displayed the majority of the radioactivity in the supernatant and not the
pellet (2points). This would have meant that the protein was entering the cytoplasm of the bacteria to carry the genetic
information into the cell and therefore that it was the genetic material (2 points)

22. Using a diagram, represent the DNA bands that would have been observed if the Meselson and Stahl experiment
would have been conducted in media containing the N14 isotope first, then the bacteria were switched to N15
containing media for one cycle and switched once more to N14 media for the second cycle. In your diagram, represent
the bands observed from all 3 DNA extractions and label the composition of DNA within the bands. (6 points)

2 points per tube, 1 point for bands, 1 point for composition

23. A temperature sensitive mutation that affects only the epsilon domain of DNA polymerase III is placed at the non-
permissive temperature. Which DNA pol III activity is affected by this mutation? What would be the consequence of this
mutation? (6 points)

This mutation will affect the proofreading capability of DNA pol III (3 points) and the end result would be an increased
rate of mutations (3 points)

24. To make a cis test for two rII mutants, you coinfected mutants rIIa and rIIb, extract the lysate, and do two 10X serial
dilutions of the solution and plate 0.5 mL of this solution on a plate with E. coli B. You obtain 200 plaques. Separately,
you do one 10X serial dilution of the original lysate and plate 0.5 mL of this solution in E coli strain K and obtain 40
plaques. What is the map distance between mutants (in map units)? Show your work (8 points)
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25. Two phages, (genotypes eqs, +++) were crossed. The percentages of plaques observed per phenotype are given in
the following table. Determine the relative order, recombination frequencies and the map distances in between the
three markers. Show your work including all calculations and the diagram of the crosses (10 points)
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26. You repeat the Nirenberg and Matthaei experiments to figure out the genetic code, by placing all the necessary
components for in vitro translation (enzymes, ATP, aminoacids, etc) plus different molecules of RNA. On tube 1 you add
a poly A (aaa...aaa) and obtain poly-Lysine. On tube 2 you add a 50/50 mixture of poly a and poly c (ccc...ccc) and obtain
Poly Lysine and Poly Proline. On tube 3 you add a 50/50 mixture of poly a and poly u (uuu...uuu) and get no peptide.
likely explanation for the result on tube 3? (4 points)

The two mRNAs in tube 3 are complementary to one another and therefore bound to each other. This prevented their
transcription.