Biochem ch 28

mikebewo's version from 2015-05-19 23:20


Question Answer
All of the following are characteristic of replication of the E. coli circular chromosome EXCEPT:
a. replication is bi-directional. b. it initiates at a unique position called oriC.
c. torsional stress introduced in the duplex DNA is relieved by DNA gyrase.
d. the unwinding of the duplex DNA is driven by the translocation of the DNA polymerase.
e. replication forks move in opposite directions.
All are correct about DNA gyrase in E. coli EXCEPT:
a. It is a topoisomerase that hydrolyzes ATP during its reaction mechanism.
b. Its mechanism involves the breaking of a single phosphoester bond in one strand of dsDNA.
c. It works to remove positive supercoiling introduced by the DnaB protein (helicase).
d. It works to introduce negative supercoiling in DNA to overcome the torsion stress imposed upon unwinding.
e. All are true.
SSBs are:
a. substrates for DNA ligases.
b. supercoil stabilizing bodies.
c. single-stranded bodies called Okazaki fragments.
d. single-stranded DNA binding proteins that prevent re-annealing.
e. nucleases that hydrolyze single-stranded RNA primers.
Which of the following is NOT true regarding E. coli replication on the lagging strand?
a. is primarily carried out by DNA polymerase I.
b. synthesized discontinuously.
c. performed in a 5'→3' direction of synthesis
d. initially synthesized as Okazaki fragments
e. requires the enzymes primase and DNA ligase
All are characteristics of Okazaki fragments EXCEPT:
a. newly synthesized short lagging strand fragments.
b. synthesis performed in the 5'→3' direction.
c. initiated with an RNA primer.
d. about 20-30 nucleotides in length.
e. binds anti-parallel to the template strand.
E. coli DNA polymerase I has all of the following characteristics EXCEPT:
a. a 5'→3' exonuclease activity.
b. a 3'→5' exonuclease activity.
c. a 5'→3' DNA polymerase activity.
d. modest processivity (approximately 20 nucleotides).
e. does not require a primer for initiation.
The degree to which the enzyme remains associated with the template through successive cycles of nucleotide addition is referred to as:
a. processivity.
b. turn-over number.
c. progression.
d. semidiscontinuousness
e. dissociativity.
E. coli DNA polymerase I has ____ distinct catalytic active site(s) on its single polypeptide chain.
a. 1
b. 2
c. 3
d. 4
e. 5
3'-Exonuclease activity of DNA polymerase I of E. coli has all the characteristics EXCEPT:
a. is an "editor" of polymerase activity.
b. is opposite to the polymerase activity.
c. removes nucleotides that do not base pair at the 3'-end of the growing chain.
d. is relatively fast compared to the polymerase activity.
e. all are true.
All are properties of DNA polymerase III EXCEPT:
a. It is responsible for incorporating most of the nucleotides in the lagging strand.
b. It synthesizes most of the leading strand prior to aiding in the synthesis of the lagging strand.
c. It contains a 3' to 5' exonuclease activity.
d. It is a large protein complex containing more than five subunits.
e. Much greater processivity than DNA polymerase I.
A pair of β-subunits of DNA polymerase III form a ____ to tether the polymerase to the template thus increasing the ____ of the polymerase.
a. ligase; unwinding
b. sliding clamp; processivity
c. primer binding; primase activity
d. loop of DNA; direction
e. none are true
Removal of RNA primer and replacement with DNA is carried out by:
a. DNA polymerase I.
b. DNA gyrase.
c. DNA polymerase III.
d. DNA ligase.
e. primerase.
The termination of DNA replication in E. coli occurs when ____ protein binds the ____ locus on the DNA and acts as a ____.
a. tag; oriC; helicase
b. ter; tag; polymerase
c. DnaC; DnaG; gyrase
d. Tus; Ter; contrahelicase
e. SSB; primer; RNA polymerase
Eukaryotic cells have replication regions called ____ that occur every ____ kbp and the units of replication are called ____.
a. replicons; 2-5; replication forks
b. replication factories; 5-10; replicons
c. replicators; 3-300; replicons
d. replication forks; 5-50; replicators
e. none are true
Progression through the cell cycle for eukaryotic cells is regulated through a series of ____ that depend on ____, produced at one phase and degraded at another, that bind ____ which regulate specific proteins by phosphorylation.
a. checkpoints; cyclins; cyclin dependent protein kinases (CDKs)
b. cyclins; phosphorylation; protein kinases
c. phosphorylations; cyclins; protein kinases
d. CDKs; cyclins; protein kinases
e. none are true
The principal DNA polymerase in eukaryotic leading strand DNA replication is:
a. DNA polymerase α (alpha).
b. DNA polymerase β (beta).
c. DNA polymerase γ (gamma).
d. DNA polymerase δ (delta).
e. DNA polymerase ε (epsilon).
An RNA-dependent DNA polymerase that carries the RNA template with it to synthesize repeats at the 3'-ends of chromosomes is called:
a. DNA ligase.
b. telomerase.
c. DNA polymerase γ (gamma).
d. topoisomerase.
e. DNA polymerase β (beta).
All are characteristic of retroviruses EXCEPT:
a. uses viral DNA as a template.
b. reverse transcriptase is required to produce dsDNA for insertion into host genome
c. the viral RNA genome is degraded prior to complete synthesis of dsDNA
d. reverse transcriptase is often error-prone causing viruses to mutate quickly
e. genome can lie dormant for years as a provirus in the host chromosome.
Reverse transcriptases possess all of the following activities EXCEPT:
a. RNA-directed DNA polymerase activity.
b. RNase H activity.
c. ssDNA-directed DNA polymerase activity.
d. dsDNA-directed DNA polymerase activity.
e. all are true.
AZT (3'-azido-2',3'-dideoxythymidine) is a drug that gets incorporated into growing viral DNA and blocks the activity of:
a. DNA ligase.
b. DNA polymerase β (beta).
c. DNA polymerase α (alpha).
d. reverse transcriptase.
e. none of the above.
Compared to their parents, progeny may have new combinations of traits because of:
a. reverse transcriptase.
b. cyclin dependent protein kinase.
c. genetic recombination.
d. processivity.
e. all are true.
Prions are defined as:
a. ions with an inappropriate number of protons.
b. ions about to form.
c. ionic proteins that bind DNA.
d. proteinaceous infectious particles.
e. particle ions that bind proteins.
All of the following are true of prion diseases include all EXCEPT:
a. they include "mad cow disease".
b. they are genetic and infectious.
c. their occurrence may be sporadic.
d. they are dominantly inherited.
e. all are true.
The correct sequence for homologous recombination steps is:

A. ligation.
B. branch migration and strand exchange.
C. nicking.
D. EW or NS cleavage, resolution and re-ligation.
E. strand invasion.

a. B, C, E, A, D
b. C, B, E, D, A
c. D, C, B, A, E
d. C, E, A, B, D
e. C, A, B, E, D
In general recombination in E. coli, the protein that binds ssDNA forming a nucleoprotein filament capable of strand invasion and homologous pairing is:
a. RecA.
b. RuvB.
c. RuvC.
d. RuvA.
e. RecBCD complex.
All are true for the DNA strand-exchange reaction EXCEPT:
a. ATP-dependent.
b. catalyzed by RecA protein.
c. requires DNA polymerase I.
d. complex has 3'-terminal ssDNA affinity for other DNA termini.
e. results in branch migration.
RuvA, RuvB, and RuvC are involved in all EXCEPT:
a. processing Holliday junctions into recombination products.
b. aiding strand invasions of the 3'-ssDNA into homologous DNA duplexes.
c. Holliday junction-specific helicase complex.
d. dissociates the RecA filament and catalyzes branch migration.
e. all are true.
All are characteristics of transposons EXCEPT:
a. segments of DNA moved non-enzymatically in the genome.
b. unstable location within genome.
c. range in size from hundreds of bps to 8 kbp.
d. the smallest transposons are called insertion sequences.
e. a major force in evolution.
Mutations in BACA1 and BACA2 genes causes increased likelihood of ____ because BACA1 protein functions in regulation of the cell cycle in response to ____, and BACA2 protein participates in DNA repair by ____.
a. breast and ovarian cancer; DNA damage control; homologous recombination
b. breast and ovarian cancer; homologous recombination; DNA damage control
c. uterine cancer; transposition; homologous recombination
d. genetic recombination; transposition; homologous recombination
e. none are true
When the methyl-directed repair system detects a mismatch in dsDNA it:
a. corrects the DNA strand that is methylated by removal of a single base and replacing with the correct one
b. corrects the DNA strand that is methylated by removal of a sting of nucleotides and replacing with correctly matched nucleotides
c. corrects the DNA strand that is not methylated by removal of a single base and replacing with the correct one
d. corrects the DNA strand that is not methylated by removal of a sting of nucleotides and replacing with correctly matched nucleotides
e. none of the above.
____ promotes the formation of covalent bonds between ____ thymine residues in a DNA strand creating a ____ ring called a thymidine dimer.
a. Visible light; adjacent; cyclohexyl
b. Visible light; nearby; cyclobutyl
c. UV light; adjacent; cyclobutyl
d. UV light; nearby; cyclohexyl
e. IR light; adjacent; cyclobutyl
The repair of cyclobutane pyrimidine dimers involves bacterial ____ and the cofactors ____ and ____.
a. DNA methylase; S-adenosyl methionine; ATP
b. DNA carboxylase; CoA; CoQ
c. DNA polymerase I; flavin; TPP
d. photolyase; flavin; NADH
e. photolyase; flavin; pterin
In base-excision repair, the first enzyme in the sequence is ____ creating a(n) ____ site.
a. DNA polymerase III; ligase binding
b. DNA glycosylase; apurinic or apyrimidinic
c. DNA polymerase I; apurinic or apyrimidinic
d. DNA ligase; polymerase III binding
e. AP endonuclease; ligase binding
All are characteristics of mammalian nucleotide excision repair EXCEPT:
a. sugar-phosphate backbone is cut in two places
b. the region of DNA excised is generally 27-29 bases in length
c. resulting gap is filled in by DNA polymerase β
d. DNA backbone is closed with DNA ligase
e. all are true
Together with ____, ____ provide(s) for genetic variability within species and, ultimately, the evolution of new species.
a. DNA repair; DNA glycosylase
b. DNA glycosylase; recombination
c. recombination; mutations
d. mutations; DNA glycosylase
e. DNA repair; mutations
A transition mutation would be replacing A by:
a. T.
b. C.
c. U.
d. G.
e. either T or C
A transversion mutation would be replacing T by:
a. A.
b. C.
c. U.
d. G.
e. either A or G.
Mutations in DNA may result from all of the following EXCEPT:
a. spontaneous mutations due to errors in replication.
b. physical insults on the cell, such as UV light.
c. errors in transcription.
d. chemical mutagens.
e. introduction of a base analog into DNA.
When the thymine analog, 5-bromouracil, incorporates into DNA normally occupied by thymine, what type of mutation can occur?
a. T-A to A-T, only.
b. T-A to C-G, only.
c. C-G to T-A, only.
d. both b and c are correct.
e. a, b, and c are correct.
Misincorporation of all subsequent amino acids results from ____ mutations.
a. chemical
b. base shift
c. frameshift
d. transition
e. all are true
Nitrous acid causes the oxidative deamination of cytosine producing uracil. What point mutation is the logical result?
a. C-G to A-T, only
b. C-G to T-A, only
c. C-G to G-C, only
d. both a and b are correct
e. a, b and c are correct
What type of mutation most likely results from the alkylation of the oxygen on position 6 of guanine base producing O6-methylguanine?
a. deletion
b. insertion
c. transition
d. transversion
e. frameshift
B-cells, T-cells, and macrophages are cell types capable of ____ as a mechanism of producing ____ essential to the immune response.
a. replication rearrangement; antibodies
b. complimentarity modification; antigens
c. DNA replication; genes
d. DNA rearrangement; antibodies
e. All are true
The vast diversity of immunoglobulin sequences is explained by:
a. DNA rearrangement
b. large sections of DNA devoted to immunoglobulin formation
c. susceptibility of the immunoglobulin genes to mutation
d. sensitivity of formed immunoglobulin proteins to environmental factors
e. all of the above
____ provides a mechanism for generating a variety of protein isoforms of immunoglobulins from a limited number of genes.
a. Genetic recombination
b. Replication licensing
c. DNA polymerase
d. DNA rearrangement
e. All are true

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