1. SDS-PAGE can be used to determine: a) whether subunits in a protein complex a
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Question
1. SDS-PAGE can be used to determine:
a) whether subunits in a protein complex are identical or not.
b) the molecular mass of a native protein complex.
c) the overall charge on a polypeptide.
d) the molecular mass of denatured protein subunits.
e) none of the above.
2. A certain protein contains a relatively large number of arginine and lysine residues on its surface. Which of the following can be predicted about the purification of this protein if it were present in a buffer with a pH of 7?
a) The protein would elute very early during sizes-exclusion chromatography.
b) The protein would bind to an anion exchange resin.
c) The protein would bind to a cation exchange resin.
d) The protein would bind to a GST column.
e) The protein would migrate very quickly through SDS-PAGE.
3. Which of the following amino acids is LEAST likely to be found on the surface of a protein?
a) lysine
b) tryptophan
c) glutamine
d) serine
e) aspartate
4. Experiments on denaturation and renaturation in the enzyme ribonuclease (RNase) by Dr. Anfinsen have shown that:
a) Folding of denatured RNase into the native, active conformation, requires the input of energy in the form of heat.
b) The completely unfolded RNase enzyme, with all disufide bonds broken, is still enzymatically active as long as there is no urea present.
c) The primary amino acid sequence of RNase is sufficient to determine its specific tertiary structure.
d) The order of cysteines in RNase does not matter, as long as the correct weak interactions can form between the other amino acids as a result of urea removal.
e) Proteins cannot self-assemble into a functional conformation after they have been denatured.
5. Five DNA polymerases have been identified in the bacterium E. coli. Two of them (DNA polymerases IV and V) lack a 3'-5' exonuclease activity. What is the function of the 3'-5' exonuclease activity present in many DNA polymerases?
a) The 3'-5' exonuclease function allows the cell to generate dNMPs, which can be converted to dNTPs and then used for synthesis of essential DNA when nutrients are low
b) The 3'-5' exonuclease is a proofreading function, eliminating mismatched nucleotides incorrectly inserted into the growing DNA strand.
c) The 3'-5' exonuclease removes DNA and RNA primers.
d) The 3'-5' exonuclease creates blunt ends so ligase can join DNA fragments.
e) The 3'-5' exonuclease creates 3' extensions after double-strand breaks are detected, which in turn promote strand invasion as part of the double-strand break repair mechanism.
6. The term "semidiscontinuous DNA replication" indicates:
a) implementation of multiple replication forks.
b) the insertion of DNA to replace the RNA primers during lagging-strand synthesis.
c) the mechanisms of leading- (continuous) and lagging- (discontinuous) strand synthesis.
d) the mechanisms of leading- (discontinuous) and lagging- (continuous) strand synthesis.
e) the presence of several chromosomes that are replicated separately.
9. As DNA polymerase forms a new phosphodiester bond, all the following occur EXCEPT:
a) an amino acid residue accepts the H+ released from 3 1 hydroxyl of deoxyribose.
b) oxygen of 3 1 hydroxyl attacks a phosphoryl group of nucleoside triphosphate.
c) phosphate is displaced and protonated by an acidic amino acid residue.
d) hydrogen bonds between DNA strands help position nucleotides.
e) metal ions lower pKa within the active site to facilitate activation of the '3' O- nucleophile.
10. In the replication fork structure, the strand being synthesized
a) into the fork is the leading strand.
b) away from the fork is the leading strand.
c) in a discontinuous fashion is the leading strand.
d) in a continuous fashion is the lagging strand.
e) None of the answers is correct.
I I . At the POI I active site, the primer 3'-OH is deprotonated and the incoming dNTP is bound as the pyrophosphate leaving group departs. This mechanism is carried out by:
a) side chains of the conserved asparagine residues present at the site.
b) two magnesium ions and does not include any protein side chains at all.
c) magnesium, together with conserved asparagine side chains.
d) a water molecule that is deprotonated.
e) None of the above.
12. Which of the following proteins does NOT contain enzymatic activity?
a) Gyrase
b) DNA ligase
c) Single-strand binding protein (SSB)
d) DNA helicase
e) Primase
13. A biochemist is purifying a new DNA helicase encoded by a pathogenic virus. The enzyme acti vity is readily detected after the first several purification steps that generate fractions a, b, and c, each with successively greater purity. The researcher then puts fraction c on an ionexchange column, and this process generates two new fractions, d and d'. The helicase acti vity cannot be detected in either of the new fractions. However, when fractions d and d are mixed, the activity reappears. The most likely explanation for this is:
a) The helicase is present in both fractions; however, the low concentration results in no activity. Mixing the fractions yields a higher helicase concentration and then acti vity can be observed.
b) The helicase is present one fraction; however, it has additional peptide sequences that must be removed in order for the helicase to assume an active form. An enzyme in the second fraction activates the helicase via proteolytic cleavage.
c) The helicase is present in one fraction and another protein or macromolecule required for helicase activity is present in the other fraction.
d) The helicase is present in one fraction; however, the helicase requires ATP, which is present in the other fraction. When the fractions are mixed, the helicase becomes catalytic again.
e) All of the above are equally likely.
14. The function of DNA ligase is to:
a) facilitate base pairing between single stranded molecules of DNA.
b) catalyze the formation of hydrogen bonds between adjacent nucleotides.
c) unwind the double-stranded DNA prior to replication.
d) catalyze the formation of covalent bonds between adjacent nucleotides.
e) keep the single strands of DNA apart during replication.
15. What is accomplished when ATP is hydrolyzed by DnaA?
a) Allows formation of the oriC/DnaA complex
b) Allows DnaA to unwind DNA
c) Inacti vates the DnaA for replication initiation
d) Removes DnaA at termination of replication
e) Helps bind DnaB helicase to the clamp
16. What is accomplished when ATP is hydrolyzed by DnaC?
a) Allows formation of the oriC/DnaB complex
b) Helps release DnaB helicase as it is loaded onto the DNA
c) Helps bind DnaB helicase to the [3 clamp
d) Removes DnaC at termination of repl ication
e) Removes DnaA at termination of replication
17. When a replication error is detected:
a) the tilispaired nucleotide is removed by a condensation reaction, releasing a water.
b) the mispaired 3' terminus frays by four nucleotides to allow it to be inserted into the 3 1 -5' exonuclease site.
c) the —OH group on a tyrosine acts as a nucleophile to remove the incorrect base.
d) the 5 1 -3' exonuclease site uses acidic amino acids to catalyze nucleotide removal.
e) all of the above are correct.
1 8. Universal features of DNA polymerases include:
a) 5'-3' exonuclease function.
b) Formation of an 'closed' conformation of the polymerase when the template-nucleotide base pair is correct.
c) Use of a single magnesium ion to orient reacting molecules and assist in dissipation of the negative charge that develops during nucleotidyl transfer.
d) Alignment of conserved residues in the active site for attack of the DNA primer by the 3'OH on the incoming nucleotide.
e) Continuous unbinding and rebinding of the polymerase to the DNA template as each nucleotide is added.
19. Which of the following is FALSE of the trombone model of replication?
a) As Okazaki fragments are extended by POI Ill , the loop in the DNA template grows.
b) Once an Okazaki fragment is completed, the (3 clamp is ejected.
c) A loop is formed in one strand of the template DNA to allow 5 1-3' synthesis of the lagging strand.
d) When a new [3 clamp is loaded, primase is triggered to synthesize a primer.
e) Binding of the polymerase core to a new primer/template complex occurs after loading of the (3 clamp.
20. What function does helicase perform during replication?
a) It stabilizes the negative charge of the transition state.
b) It utilizes ATP to power DNA strand separation.
c) It adds negative supercoils to DNA.
d) Both A and C are correct.
e) None of the above.
21 . The clamp loader loads the sliding clamp onto the DNA. Review the steps listed below. Which step would come SECOND?
a) ATP binds to the y (gamma) subunits, which undergo a conformation change.
b) Double-stranded DNA passes through the ß clamp.
c) They (gamma) — p clamp —ATP complex binds primed DNA.
d) Y (gamma) subunits bind to and open the clamp.
e) Single-stranded DNA passes through the side of the ß clamp loader gap.
22. Which of the following describes the approximate chromosomal location of the termination of replication in bacteria?
a) Termination occurs at oriC once the replication fork has advanced the entire length of the chromosome.
b) Termination occurs at a location one-quarter around the chromosome.
c) Termination occurs at a location halfway around the chromosome.
d) Termination occurs at random locations where replication forks collide.
e) Termination occurs at the first Ter site encountered by the replication fork.
23. Eukaryotic DNA replication initiates replication at multiple origins of replication simultaneously. How is eukaryotic replication initiated to ensure simultaneous initiation at multiple origins?
a) A Pre-replication complex (preRC) is formed at all hemimethylated origins.
b) The Pre-replication complex (preRC) forms in Go phase.
c) Cyclin-dependent protein kinase (CDK) enzymes are active during formation of PreReplication Complex (preRC).
d) Cyclin-dependent protein kinase (CDK) enzymes activate the Pre-RC to allow for coordinated activation of replication once other replication factors associate to form the Replication Complex (RC).
e) None of these answers is correct.
24. Eukaryotes solve the problem of replicating the ends of their linear chromosomes by:
a) terminal redundancy whereby each end of the chromosome is duplicated allowing recombination.
b) using a protein as a primer.
c) by covalently linking the two strands at each end of the linear chromosome to form a circle.
d) enzyme activity that uses an RNA template and reverse transcription in a series of repeating cycles.
e) all of the above.
25. Why is primase required for replication?
a) DNA polymerases cannot begin DNA synthesis without a primer containing a free 3 OH.
b) DNA polymerases can only begin DNA synthesis if they are stimulated by dimerization with a primase subunit.
c) Primase is required to recruit helicase to the site of DNA synthesis.
d) Primase is required for proofreading DNA during replication.
e) Primase is required for removal of RNA primers during replication.
Explanation / Answer
1. SDS-PAGE can be used to determine:
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