test 1 questions Flashcards
1) The difference between a nucleoside and a nucleotide is: A) the presence of uracil. B) a phosphate group. C) a phosphodiester bond. D) a 2' —H group. E) methylated cytosine.
B
2) Which statement is CORRECT?
A) Both phosphodiester and glycosidic bonds in RNA and DNA are hydrolyzed in acid solution.
B) Both RNA and DNA are hydrolyzed in mild alkaline solution.
C) DNA is more unstable when dehydrated than when in solution
D) RNA is not hydrolyzed in mild alkaline solution.
E) Both A and B
A
3) Nucleotides are all weak acids.
FALSE
4) The nucleotide sequence of a polynucleotide chain is called the ________ structure.
primary
5) Which of the following does NOT describe the secondary structure of DNA as proposed by Watson and Crick?
A) The two strands of the double helix are stabilized by hydrogen-bonding between A and T and between G and C.
B) The two strands of the double helix run in opposite directions.
C) The distance between the 1’ carbons of the deoxyribose units is the same between the A-T and the G-C base pair.
D) The phosphate deoxyribose backbones of the helix are on the outside.
E) The base pairs are stacked on one other with their planes at 180o to the helix axis.
E
6) An important observation that assisted in the elucidation of the secondary structure of DNA was that the mole percent adenine was almost always the same as the mole percent of thymine. (T/F)
TRUE
7) The mode of replication of DNA is BEST described as ________.
semiconservative
8) Which of the following statements about nucleic acid secondary structure is FALSE?
A) The width of the major and minor grooves is more equal in the A-from of DNA than in the B-form.
B) Triple helices and G-quadruplexes can form at specific sequences in DNA.
C) DNA can form cruciform structures at palindromic sequences.
D) The A-form of DNA exists at high humidity, whereas the B-form exists at low humidity.
E) Some nucleic acids can form a zig-zag structure or Z form.
D
9) Supercoiled DNA has a lower mobility than relaxed DNA with the same number of base pairs when subjected to gel electrophoresis.
Answer: FALSE
10) Single-stranded RNA molecules can have extensive regions of intramolecular base pairing leading to defined secondary and tertiary structure.
Answer: TRUE
11) DNA in vivo is normally ________ supercoiled.
Answer: negatively
12) Calculate the superhelix density of a circular DNA molecule with 210 base pairs and two negative supercoils, assuming that there are 10.5 bp per turn of the double helix.
Answer: -0.1
13) Calculate the linking number in vivo for a plasmid that is 4200 bp in size if there is normally 1 negative supercoil in every 20 base pairs of a circular DNA. Assume there are 10.5 bp per turn of the double helix.
Answer: 190
14) Nucleic acids absorb light strongly in the ultraviolet region of the spectrum because they have ________ double-bond systems.
Answer: conjugated
15) The melting temperature of DNA ________ with increasing G plus C content.
Answer: increases
16) Expression of genetic information involves first ________ then ________.
Answer: transcription, translation
17) Restriction endonucleases are useful in gene cloning because:
A) they can cut DNA at specific sequences.
B) they can join DNA molecules that have been cut at specific sequences.
C) they all make cohesive ends when they cut DNA.
D) they all make 5’ phosphate extensions and recessed 3’ OH groups that can be rejoined by DNA ligase.
E) they can both cut and rejoin DNA molecules.
Answer: A
18) Viral genomes cannot be used as vectors for making recombinant DNA molecules.
Answer: FALSE
19) Dideoxynucleotide sequence analysis is a template-directed method that makes use of chain terminators that stop DNA synthesis because they lack a 2’OH group.
Answer: FALSE
20) Which of the following is a feature of X-diffraction?
A) Radiation passing through a structure will be scattered only if the structure contains repeating units.
B) Scattered radiation from repeating units in a structure will be weakened by interference.
C) Scattered radiation from repeating units in a structure will be strengthened by interference.
D) Short spacings in repeating structures will result in short spacings in diffraction patterns.
E) The wavelength of radiation used to generate diffraction patterns must be slightly longer than the spacings between the repeating units of the structure.
Answer: C
1) A bacterial genome is packaged into a nucleoid, which is organized mainly by:
A) interactions with protein.
B) being bound within a nuclear membrane.
C) supercoiling of the DNA.
D) having many attachment points to the cell membrane.
E) being wrapped around histone proteins.
Answer: C
2) Approximately how much of the human genome has a biological function? A) 90% B) 80% C) 60% D) 50% E) 40%
Answer: B
3) Heterochromatin is transcriptionally active.
Answer: FALSE
4) The human genome contains one gene for every protein that can be translated from the mRNA.
Answer: FALSE
5) The linker histone H1 has a high proportion of the following amino acid residue. A) Leucine B) Lysine C) Isoleucine D) Asparagine E) Histidine
Answer: B
6) In eukaryotic cells, chromosomes are organized into a DNA-protein complex known as chromatin.
Answer: TRUE
7) The post-translational modifications of histone proteins have functional roles in gene expression.
Answer: TRUE
8) The repeating unit of chromatin is known as the ________.
Answer: nucleosome
9) Nucleosomal core particles contain ________ bp of DNA wrapped around a histone octamer.
Answer: 146
10) If 10.4 bp of DNA represents a linear length of 3.4 nm, how long (in meters) would one copy of the human genome (~3 × 109 bp) be if all of the DNA was placed end to end in a linear fashion?
Answer: 0.98 m
11) Restriction-modification systems:
A) exist in all organisms as a protection against foreign DNA invasion.
B) include a site-specific exonuclease to degrade foreign DNA.
C) modify DNA by acetylation.
D) include a DNA methylase and an endonuclease.
E) include three types of endonuclease all of which cleave within a specific DNA target sequence.
Answer: D
12) The ________ activity associated with restriction-modification systems is able to flip out the target base from the DNA.
Answer: DNA methylase
13) Random variations among human genome sequences can result in gain or loss of ________ endonuclease cleavage sites.
Answer: restriction
14) Calculate the number of times a recognition site for a 4 bp restriction endonuclease is likely to occur in the diploid human genome
Answer: 2.4 × 10 7
15) Southern blotting and hybridization is a technique that uses specific probes to analyze:
A) restriction fragment length polymorphisms.
B) complex mixtures of any nucleic acid.
C) centromeres or telomeres on condensed chromosomes.
D) DNA fingerprints.
E) both A and D.
Answer: E
16) If a PCR reaction starts out with 20 double-stranded DNA targets, how many specific PCR products could be formed after 35 cycles of denaturation, annealing and extension.
Answer: 6.87 × 1011
1) Both type I or type II topoisomerases carry out their catalytic activity via a covalent phosphodiester intermediate between a phosphate group on the DNA and a tyrosine hydroxyl group on the enzyme.
Answer: TRUE
2) DNA gyrase is able to relax supercoils as well as introduce negative supercoils in DNA.
Answer: TRUE
3) The DNA polymerase reaction is a nucleophilic substitution facilitated by:
A) the 3’OH group being a weak nucleophile.
B) the 3’OH group being a strong nucleophile.
C) the pyrophosphate being a good leaving group.
D) the reaction being irreversible.
E) none of the above.
Answer: C
4) Which of the following statements about E. coli DNA polymerase I is FALSE?
A) It can copy a circular DNA template but cannot join the ends.
B) It can extend a gapped duplex from a 3’OH group and displace a preexisting 5’ end.
C) The 3’ exonuclease site is some distance from the polymerase active site.
D) It has 3’ exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.
E) It has 5’ exonuclease activity that resides in a small N-terminal fragment that can be cleaved off by limited proteolysis.
Answer: D
5) Which of the following statements about E. coli DNA replication is INCORRECT?
A) The β subunit of DNA polymerase III is the sliding clamp essential for processivity.
B) The clamp-loading complex uses exchange between ADP and ATP to eject the clamp loader and close the clamp.
C) Single-stranded DNA-binding protein promotes denaturation of DNA by lowering the melting temperature.
D) Helicases are multimeric proteins that bind preferentially to one strand and rely on ATP-hydrolysis to unwind the duplex.
E) Topoisomerases are responsible for relieving torsional stress ahead of the replication fork generated by unwinding the duplex.
Answer: B
6) The specificity of DNA polymerase activity is determined by the shapes of the substrate molecules as well as their ________ capacity.
Answer: hydrogen-bonding
7) Evidence supporting E.coli DNA polymerase III having the major role in nucleotide incorporation during replication includes:
A) DNA polymerase III has a high Vmax.
B) There are ten or fewer molecules of enzyme per cell.
C) Replication is blocked at high temperatures in temperature sensitive mutants with a thermolabile form of DNA polymerase III.
D) A point mutation can inactivate DNA pol III and inhibit replication.
E) All of the above.
Answer: E
8) E. coli DNA polymerase III makes extensive contacts with the ________ in duplex DNA.
Answer: minor groove
9) A null mutant in the ________ activity of DNA polymerase I will be defective in DNA replication because it will be unable to carry out primer removal.
Answer: 5’-exonuclease OR 5’-exonucleolytic
10) Okazaki fragments are initiated with ________ primers by a primase enzyme.
Answer: RNA, or ribonucleic acid
11) DNA ligase can join Okazaki fragments after activation by ________ of a lysine residue in the active site.
Answer: adenylation
12) E. coli DNA polymerase I in vitro requires a template and primer, which must always be separate nucleic acids.
Answer: FALSE
13) The individual proteins of the E. coli replisome complex dissociate and reassociate in a dynamic manner.
Answer: TRUE
14) The replicative E. coli DNA polymerase is a symmetrical dimer, with each part of the dimer being responsible for replicating one strand of the DNA duplex.
Answer: FALSE
15) Which of the following is NOT a requirement of E. coli DNA ligase?
A) A nick in the DNA strand must have a 3’ OH group.
B) A nick in the DNA strand must have a 5’ phosphate group.
C) The nucleotides being linked must be adjacent in the duplex structure.
D) The nucleotides being linked must be properly based-paired.
E) ATP
Answer: E
16) Which of the following statement about eukaryotic DNA replication is INCORRECT?
A) Only one DNA polymerase is required to propagate a replication fork.
B) The same polymerase in humans is involved in proofreading and primer removal as well as lagging strand elongation.
C) The main DNA polymerase that elongates the leading strand has an intrinsic processivity factor.
D) Eukaryotes require two enzymes to remove RNA primers.
E) Chromatin must be dismantled in advance of replication forks and reassembled on daughter strands after the fork has passed through.
Answer: A
17) The initiation of DNA replication in E. coli can occur anywhere on the genome that has repeat sequence elements and requires the interaction of DnaA proteins that results in stretching and bending of DNA causing tension that leads to local unwinding.
Answer: FALSE
18) 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 repeat cycles.
E) all of the above.
Answer: D
19) Replication of linear genomes is problematic because primer removal at the ________ leaves a gap in the duplex.
Answer: 5’-end
20) Fidelity of DNA replication is determined solely by the 3’ exonucleolytic proofreading activity of the DNA polymerase.
Answer: FALSE
21) A single-stranded RNA virus makes a DNA copy of itself by the use of a viral multifunctional enzyme called ________.
Answer: reverse transcriptase
1) O6-methylguanine has a high probability of base pairing with thymine to result in a post replication mutation from a GC base pair to: A) TA. B) AT. C) CG. D) GT. E) TC.
Answer: B
2) The only function of Uracil-DNA N-glycosylase is to remove dUMP residues in DNA that have been arisen by deamination of cytosine.
Answer: FALSE
3) Which of the following types of DNA damage cannot be repaired by base excision repair? A) Depurination B) Cytosine deamination C) Thymine dimer D) Single-strand break E) Base oxidation
Answer: C
4) Nucleotide excision repair:
A) involves a multisubunit enzyme.
B) preferentially repairs genes that are being actively transcribed.
C) involves making nicks on either side of a DNA lesion.
D) uses helicase, polymerase and ligase to repair the DNA.
E) all of the above.
Answer: E
5) Photoreactivation using DNA photolyase is responsible for direct repair of thymine dimers in all organisms.
Answer: FALSE
6) ________ and bulky adducts on DNA can be repaired using the nucleotide excision repair process.
Answer: Thymine dimers
7) The direct DNA repair enzymes DNA photolyase and O6-alkyguanine alkytransferase are unusual in that they are ________ after one catalytic cycle.
Answer: inactivated
