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LS3 MIDTERM I EXAM

INSTR: L. JOHNSON Jan. 31, 2014
NAME:_________________________________
(last) (first)
I.D. #__________________________________

TA ___________________________________

Test Form A


INSTRUCTIONS
This exam is 8 pages long. Before starting make sure you have all the pages.

Using a number 2 pencil, on the front of your scantron fill in the Instructor (Johnson), Class
(LS3), Hour (11:00)
Write and Bubble in your UID, your last name and first name.

On the back of your scantron Write and Bubble in your UID and Test Form (see above).

Each question below is worth 2.5 points.






















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1. Most infections are caused by either viruses or bacteria. Prions can also
cause disease
a) but differ from viruses because they do not contain a genome.
b) but differ from viruses because they propagate by inducing a normal
cellular protein to misfold.
c) but are similar to sickle cell anemia in that the misfolded protein
aggregates
d) All of the above.
2. In the Hershey-Chase experiment what would happen if the
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S-T2-infected
cells were centrifuged before they were blended?
a) Most of the
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S would be found in the supernatent.
b) Most of the
35
S would be found in the pellet.
c) The
35
S would be split evenly between the supernatent and the pellet.
d) There is no way of knowling.
3. Suppose you have recently isolated a human virus and analyzed its genome.
You find that its nucleic acid content is 30% G, 20% A, 20% U and 30% C.
What can you deduce about the genome structure?
a) double-stranded DNA
b) single-stranded DNA
c) double-stranded RNA
d) single-stranded RNA
4. Weak interactions hold DNA strands together in a B-form double helix that
contains 10.5 bases pairs per 34 A
O
turn. Which of the following does not
contribute to the stability of DNA?
a) sodium ion concentration
b) temperature
c) pH
d) aqueous environment
e) All of the above contribute to the stability of the helix.
5. What is the appropriate abbreviation for the following compound?

a) ADP
b) UDP
c) GDP
d) CDP





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6. In a pulse-chase experiment, what is the point of the chase?
a) to allow time for macromolecular synthesis
b) to allow break-down of macromolecules
c) to allow movement of labeled macromolecules
d) to allow time for radioactive decay
7. Secondary structure in proteins refers to
a) one-dimensional sequence of amino acids
b) two-dimensional diagram of protein folding
c) second level of protein structure
8. Which of the following amino acids have side chains that cannot form
hydrogen bonds?
a) tyrosine
b) aspartate
c) glutamine
d) glycine
9. Some amino acid substitutions in proteins have no effect because the amino
acids have similar properties. Which of the following would you expect to
have no effect?
a) D to N
b) I to L
c) E to Q
d) A to T
e) R to C
10. Glycine and proline are considered special amino acids because
a) glycine is more flexible and proline is less flexible than other amino
acids
b) glycine has no side chain and proline has an extra long side chain
c) glycine and proline are more flexible than other amino acids
11. The DNA double helix and a protein alpha helix are similar in that
a) hydrophobic stacking plays an important role in stability
b) hydrogen bonding is perpendicular to the axis of the helix
c) the DNA bases and amino acid side chains are involved in hydrogen
bonding
d) they both are right handed helices
e) All of the above.
12. The DNA double helix and a beta-sheet in proteins are similar in that
a) hydrogen bonding occurs between two strands
b) interactions between the two backbones is critical for stability
c) they are always antiparallel
d) the DNA bases and amino acid side chains are important for stabilit
13. The alpha helix is more rigid than a DNA double helix because
a) the hydrogen bonds are perpendicular to the axis of the helix
b) the hydrogen bonds are parallel to the axis of the helix
c) the peptide bond is planar
d) the peptide bond is more stable than the phosphodiester bond

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14. Which of the following is not true about the tertiary structure of a protein?
a) A high percentage of the polypeptide is found in alpha helix or beta
sheet conformation.
b) All hydrophobic residues are buried inside.
c) All H-bond donors and acceptors are involved in H-bonds.
d) It is the lowest energy state.
e) All of the above are true.
15. An independently folding region of a protein is called a
a) functional domain
b) structural domain
c) motif
16. Non-specific DNA binding proteins generally bind to DNA through
a) ionic interactions between amino acid side chains and the
phosphodiester backbone
b) hydrogen bonding between amino acid side chains and the
phosphodiester backbone
c) hydrophobic stacking between amino acids side chains and bases
d) A and B
e) All of the above.
17. Starting with a 600 bp plasmid and with 5 negative superhelical turns
(assume 10 bp/turn). What are the values of L, T and W?
a) 60, 55, 5
b) 55, 60, -5
c) 55, 60, 5
d) 60, 55, -5
18. Now, referring to the plasmid described above, suppose you add enough
ethidium bromide to completely relax the plasmid. What are the values of L,
T and W now?
a) 60, 60, 0
b) 55, 55, 0
19. Suppose instead of adding ethidium bromide to relax the plasmid, you add
topoisomerase. What are the values of L, T, W (start with plasmid containing
supercoils above)?
a) 60, 60, 0
b) 55, 55, 0
20. Nucleosomes
a) compact DNA in prokaryotes and eukaryotes.
b) have two copies each of H1, H2, H3 and H4
c) have N-terminal tails that can get post-translationally modified
d) a and b
e) All of the above





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21. Transcription
a) involves the polymerization of nucleotides.
b) takes place in the nucleus in eukaryotic cells.
c) is catalyzed by RNA polymerase.
d) results in the synthesis of single-stranded RNA
e) All of the above
22. In prokaryotes, promoter
a) refers to the region upstream of a gene that is bound by RNA
polymerase
b) contains the transcription initiation site
c) is found on one strand of the DNA
d) a and b
e) All of the above.
23. Which of the following is not characteristic of the bacterial genome?
a) Genes are located far from one another.
b) Multiple genes can be transcribed together into a single RNA
molecule.
c) Genes can be oriented in either direction.
d) Genes are not disrupted by intervening sequences.
24. Topoisomerase I
a) cleaves one strand of the DNA.
b) action results in a change in the linking number.
c) retains the energy associated with the phosphodiester bond through a
covalent bond between a tyrosine and a phosphate in DNA
d) a and c
e) All of the above.
25. Which of the following is not true about prokaryotic transcription?
a) The 5 end of the RNA is always a monophosphate.
b) The transcription bubble is about 12-14 nucleotides long.
c) Formation of RNA from nucleoside triphosphates is an energetically
favorable reaction.
d) Sigma factor is required for promoter recognition
e) All of the above are true.
26. RNA synthesis involves
a) the 3 OH attack on the alpha phosphate of a nucleoside triphosphate
b) the 5 OH attack on the alpha phosphate of a nucleoside triphosphate
c) the release of phosphate
d) the release of H2O
27. During enzyme catalysis, the free energy of _________________ is lowered.
a) the substrates
b) the transition state
c) the products
d) the reaction
e) None of the above.


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28. Consider the diagram above, where the lines represents a DNA and the
arrows restriction enzyme cut sites. You do a Southern blot (shown on right)
using DNA from two different individuals (1 and 2) and use the indicated
probe. What can you say about individual 1 with respect to the disease?
a) He is not a carrier.
b) He is a carrier.
c) He has the disease.
29. What can you say about individual 2?
a) He is not a carrier.
b) He is a carrier.
c) He has the disease.
30. How does acetylation of lysines differ from methylation?
a) acetylation neutralizes the charge, methylation does not.
b) methylation neutralizes the charge, acetylation does not.
c) only one acetyl group can be added, but more than one methyl can be
added.
d) a and c
e) b and c
31. During transcription the supercoiling that forms in front of the polymerase is
a) negative supercoiling
b) positive supercoiling
32. Only rNTPs act as substrates (not rNDPs or rNMPs). Why do you suppose
that is?
a) They fit the best in the active site.
b) It is more energetically favorable.
c) It just evolved that way.
d) NTPs are at higher concentrations in the cell.
33. The coding strand in DNA
a) is the same sequence as the mRNA
b) is the complementary sequence to the mRNA
c) can be either one since genes can go in either direction



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34. Consensus sequences are determined by comparing many sequences and
determining the most favorable base at each position. Consider the five
sequences below and determine the consensus sequence:
5 AATTGCCA 3
5 AAATGACA 3
5 GCTTCACA 3
5 AATCGATA 3
5 AATTGACA 3
a) 5 AATTCACA 3
b) 5AATTGACA 3
c) 5AATCGACA 3
d) 5AATTGCCA 3
35. The influenza virus, which causes the flu, is a single-stranded RNA virus whose
genome is composed of eight RNAs. After infection of respiratory cells these
RNAs are used first to synthesize a complementary RNA and then translated into
a protein. Would the influenza genome be equivalent to the coding or template
strand of the a DNA molecule?
a) coding strand
b) template strand
36. Viruses, such as the influenza virus, that have single-stranded RNA genomes
mutate at a higher rate than viruses with double-stranded DNA genomes. Which
of the following might explain this high rate of mutagenesis?
a. RNA is less stable than DNA due to the presence of the 2OH
b. Synthesis of RNA is more prone to error than DNA.
c. Being a single-stranded genome, errors not immediately
detected will be passed on to the progeny viruses
d. b and c
e. All of the above.
37. The influenza virus can infect birds (avian), pigs (swine) and humans (as well as
other mammals). If pigs or birds are infected with human influenza as well as
avian or swine influenza, new strains can be generated rapidly. This gives rise to
pandemics where there is no immunity to the new virus. Why do you suppose a
virus having a segmented genome might give rise to new strains of virus more
rapidly than a non-segmented genome?
a) Having the genome in eight different segments allows each one to
accumulate mutations at a faster rate.
b) It allows the mixing of genes from different viruses in one generation.
c) The genes encoding the surface proteins could be exchanged
between the viruses causing a complete change in antigenic
properties.
d) b and c




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38. Given the DNA sequence shown below and the transcription is going from right
to left, what is the sequence of the RNA synthesized?
5 -------------CTGA--------------3
3 -------------GACT--------------5
a) pppCTGA
b) pppGACT
c) pppTCAG
d) pppAGTC
39. The dissociation constant of a protein-ligand complex tells you
a) the protein concentration at which it is found 50% complexed with ligand
b) the salt concentration at which the protein-ligand complex is stably formed
c) the ligand concentration at which the protein is found 50% complexed
with ligand
40. What do you feel has been most helpful in learning the material weve covered so
far this quarter? (youll get 2.5 pts for any answer given below, Id just like some
feedback).
a) Mastering Biology
b) Online Quizzes
c) Clicker questions
d) Discussion sections
e) text