CH 20 DNA Replication and Repair

Although DNA damage is a cause of cancer, some cancer chemotherapies are based on drugs that damage DNA. For example, the drug carboplatin introduces a platinum ion that cross-links adjacent guanine residues in a DNA strand. These types of drugs induce ______ in the three dimensional structure of DNA, which_________ impact DNA metabolism.

kinks / will

Replication of the circular chromosome in E. coli begins when a protein called DnaA binds to the replication origin on the DNA. DnaA initiates replication only when the DNA that constitutes the DNA replication origin is _________ supercoiled, since this topology of DNA is______

negatively / easier to unwind

The incomplete removal of an RNA primer leaves ribonucleotides incorporated into DNA. Provide the order of the following enzyme activities that would be required to repair DNA containing a stretch of several ribonucleotides. Step 1: Step 2: Step 3: Step 4:

1- endoribonuclease 2- exonuclease 3- DNA polymerase 4 - DNA Ligase

DNA replication of the _________chromosome in E. coli begins when a protein called DnaA binds to the replication origin on the DNA. The replication origin likely to be richer in _________, thereby making it easier to separate the strands during replication.

circular / A:T

Based on your knowledge of replication proteins, DNA polymerase would have a _________ affinity for DNA when compared to single-strand binding protein (SSB); in terms of concentration, the cellular abundance of DNA polymerase would be ____________ than single-strand binding protein (SSB).

higher / lower

You have discovered a drug that inhibits the activity of the enzyme inorganic pyrophosphatase. This drug would ______ DNA synthesis?

inhibit

During DNA replication, the polymerase accidentally inserts an A opposite a C in the template strand. What type of mutation(s) could this cause in the DNA? A. Nonsense mutation. B. Missense mutation. C. Frame-shift mutation. D. Either A or B.

D. Either A or B.

Mutations do not occur randomly across the human genome; in fact, there is a higher incidence of nucleotide-substitution mutations near the 5ʹ ends of Okazaki fragments. These mutations likely occur because the 5ʹ ends of Okazaki fragments are synthesized by __________, which __________ have proofreading functions

DNA polymerase (alpha) / does not

A chemical mutagen converts C to U. What type of mutations could this cause in the DNA? A. None, since DNA does not contain uracil. B. Non-sense mutations. C. Mis-sense mutations. D. Frame-shift mutations. E. B or C is correct.

E. B or C is correct.

Which of the following statements is correct regarding telomerase?

It extends the template strand of DNA.

Which of the following is FALSE regarding plasmids found in bacterial cells? They are small, circular molecules of single-stranded DNA. They may confer antibiotic resistance on the cell. They may make the cell more virulent. They are part of the cell's genome.

They are small, circular molecules of single-stranded DNA.

Classify the following base changes as transitions or transversions: a. A → T: b. G → A: c. T → A: d. C → G: e. G → C: f. T → C:

a, c, d, e = transversion / b, f = transition

Which of the following conditions would favour the dissociation of histones from DNA without denaturing the DNA? a. A high concentration of NaCl. b. A high pH and a high temperature. c. A high temperature. d. A high pH. e. A high concentration of NaCl and a high pH.

a. A high concentration of NaCl.

Which of the following statements is most correct? a. DNA polymerase can only add a nucleotide to the free 3'-OH group of a base-paired polynucleotide. b. DNA polymerase can only add a nucleotide to the free 5'-OH group of a base-paired polynucleotide. c. DNA polymerase can only add pyrophosphate to the free 3'-OH group of a base-paired polynucleotide. d. DNA polymerase can only add a nucleotide to the free 3'-OH group of a polynucleotide that is not base-paired.

a. DNA polymerase can only add a nucleotide to the free 3'-OH group of a base-paired polynucleotide.

The "replisome" is the complex of proteins located at a replication fork. Which of the following is NOT required in a replisome in E. coli? a. DnaA. b. DNA gyrase. c. Primase. d. DNA ligase. e. Pol I.

a. DnaA.

Bacteria, which do not contain duplicate chromosomes, have no need for the mechanism of general recombination. a. False b. True

a. False

DNA polymerase I (Pol I) is E. coli's primary DNA replicase. a. False b. True

a. False

Okazaki fragments are synthesized in the 3' -> 5' direction. a. False b. True

a. False

Recombination in E. coli occurs when the RecA protein binds as a dimer to a strand of DNA. a. False b. True

a. False

The UvrABC endonuclease repair system is specific for the repair of pyrimidine dimers. a. False b. True

a. False

The ends of eukaryotic chromosomes typically have 5' extensions called telomeres. a. False b. True

a. False

A circular, covalently-closed molecule of duplex DNA consists of 2000 base pairs. In solution this DNA molecule is found in a relaxed state. What are the values of the Linking number (L), the Twist (T) and the Writhe (W) associated with this molecule in this state? (Assume 10 base pairs/turn of the B-DNA helix). a. L = 200; T = 200; W = 0 b. L = 20; T = 20; W = 10 c. L = 200; T = 200; W = 10 d. L = 20; T = 20; W = 0

a. L = 200; T = 200; W = 0

Which statement about the tertiary structure of eukaryotic DNA is FALSE? a. The electrostatic interactions between DNA and histones have a lower bond energy than hydrogen bonds. b. Histones contain a high proportion of positively-charged amino acids. c. Each molecule of DNA is far longer than the dimensions of the nucleus, and so it must be packed tightly to fit in. d. The beads on a string form of chromatin contains both nucleosomes and linker DNA.

a. The electrostatic interactions between DNA and histones have a lower bond energy than hydrogen bonds.

In eukaryotic DNA, 5-methylcytosine (5-mC) may be found in place of cytosine in the DNA double helix. Which of the following is 5-mC? a. The molecule in the middle. b. The molecule on the right. c. The molecule on the left.

a. The molecule in the middle.

What tumor suppressor gene is mutated in nearly 50% of all human tumors? a. p53 b. Ras c. BRCA1 d. BRCA2

a. p53

The enzyme telomerase, which repairs the ends of eukaryotic chromosomes, is which of the following: a. A DNA-directed RNA polymerase. b. An RNA-directed DNA polymerase. c. A DNA-directed DNA polymerase. d. An RNA-directed RNA polymerase.

b. An RNA-directed DNA polymerase.

If one strand of a double-stranded DNA helix has the sequence 5'-ACGTAACC-3', which of the following accurately denotes the sequence of the complementary region on the other strand? a. TGCATTGG b. GGTTACGT c. ACGTAACC d. CCAATGCA

b. GGTTACGT

Why cannot O^6-methylguanine-DNA methyltransferase be strictly classified as an enzyme? a. It becomes inactivated after several cycles due to oxidation of its active site Cys residue. b. It becomes inactivated after one reaction due to transfer of a methyl group to its active site Cys residue. c. It becomes inactivated after one reaction due to transfer of a purine base to its active site Cys residue. d. Its rate of catalysis is very low.

b. It becomes inactivated after one reaction due to transfer of a methyl group to its active site Cys residue.

Naturally-occurring DNA in a cell is most commonly found in which of the following states? a. Relaxed helix b. Negatively supercoiled c. Positively supercoiled

b. Negatively supercoiled

Which, if any, of the following enzyme activities is NOT involved in the initiation of replication in E. coli? a. Topoisomerase. b. RNA polymerase, helicase, and topoisomerase activates are all required. c. RNA polymerase. d. Helicase.

b. RNA polymerase, helicase, and topoisomerase activates are all required.

Why does DNA contain thymine (T) instead of uracil (U)? a. Because T does not undergo spontaneous deamination. b. So the cell can recognize U that is produced by spontaneous deamination. c. Because T is easier to synthesize than U. d. Because the spontaneous deamination of C to U is mutagenic.

b. So the cell can recognize U that is produced by spontaneous deamination.

What determines the size of Okazaki fragments synthesized by E. coli DNA polymerase III (Pol III)? a. The size of the looped lagging strand template. b. The relative sites of the RNA primers. c. The rate of DNA synthesis of the leading strand. d. The rate of DNA synthesis of the lagging strand.

b. The relative sites of the RNA primers.

Which of the following best explains the term "tertiary structure of DNA?" a. Chromatin. b. Beads on a string. c. Chromosomes. d. Double helix. e. Nucleosomes.

c. Chromosomes.

Why is 0.5 M NaCl effective at dissociating histones from DNA in a sample of chromatin? a. Histones are more soluble in 0.5 M NaCl than in a solution with DNA. b. Histones are bound to DNA by hydrogen bonds, which can be disrupted by 0.5 M NaCl. c. Histones are bound to DNA by ion pairs, which can be disrupted by 0.5 M NaCl. d. Histones are bound to DNA by dipole-dipole interactions, which can be disrupted by 0.5 M NaCl.

c. Histones are bound to DNA by ion pairs, which can be disrupted by 0.5 M NaCl.

Which of the following statements about topoisomerases is FALSE? a. Type II topoisomerases can increase writhe because they use ATP in their reaction mechanism. b. Type I topoisomerases use a tyrosine side chain in their active site to catalyze a nucleophilic attack. c. In the reaction catalyzed by type I topoisomerases, the enzyme changes conformation to provide the energy required to change the linking number of the DNA. d. Type I topoisomerases do not use ATP in their reaction mechanism. e. Type I AND type II topoisomerases can both increase or decrease L.

c. In the reaction catalyzed by type I topoisomerases, the enzyme changes conformation to provide the energy required to change the linking number of the DNA.

Which of the following does NOT apply to the reaction catalyzed by a DNA polymerase? a. It is a phosphoryl group transfer reaction. b. It is facilitated by the hydrolysis of a pyrophosphate group. c. It is a biosynthetic (anabolic) reaction and so has a positive free energy change (delta G). d. It requires an abundant supply of deoxynucleoside triphosphates. e. It involves a nucleophilic attack by an -OH group.

c. It is a biosynthetic (anabolic) reaction and so has a positive free energy change (delta G).

Human cells infected by HIV increase the expression of SAMDH1, a phosphohydrolase that removes triphosphate groups from dNTP substrates. Explain how SAMDH1 inhibits HIV replication. a. For this reaction, the rates are in units of M2/s, so the rate of this reaction is +360 M2 s-1. b. For this reaction, the rates are in units of M/s, so the rate of this reaction is +720 M s-1. c. Removing the triphosphates depletes the pool of substrates for RNA transcriptase. d. For this reaction, the rates are in units of M/s, so the rate of this reaction is +360 M s-1. e. Removing the triphosphates depletes the pool of substrates for DNA polymerase. f. For this reaction, the rates are in units of M2/s, so the rate of this reaction is -720 M2 s-1. g. The newly formed nucleosides serve as inhibitors for RNA transcriptase. h. The newly formed nucleosides serve as inhibitors for DNA polymerase.

c. Removing the triphosphates depletes the pool of substrates for RNA transcriptase.

Which of the following is plausible as a molecular basis for the carcinogenesis? a. Activating p53 b. Activating the tumor suppressor gene c. Silencing the tumor suppressor gene d. Regulating apoptosis e. Regulating DNA repair

c. Silencing the tumor suppressor gene

Read the following statements carefully and determine which are true and which are false.1. Single-stranded nucleic acids such as RNA can form complex, 3-D, folded structures.2. RNA does not contain uracil.3. Translation is carried out by an enzyme called RNA polymerase. a. All three statements are true. b. 1 & 2 are true, and 3 is false. c. All three statements are false. d. 1 is true, and 2 & 3 are false. e. 1 & 3 are false, and 2 is true.

d. 1 is true, and 2 & 3 are false.

What does this image show? a. A complex of histones. b. Chromatin. c. A DNA double helix. d. A nucleosome. e. A histone.

d. A nucleosome.

How might the UV radiation in the sun impact DNA, thereby leading to cancer? a. The sun's UV radiation in sunlight can cause DNA mutations b. The DNA damage caused by sunlight can halt DNA replication c. The DNA damage caused by sunlight can halt DNA transcription d. All of the above e. None of the above

d. All of the above

What is a common cause of cancer? a. Inherited genetic variations b. Environmental factors c. Random mutations d. All of the above e. None of the above

d. All of the above

Which of the following is true of reverse transcriptase? a. It includes 3' exonuclease activity. b. It is a DNA-directed RNA polymerase. c. It has a lower binding affinity for AZT than normal cellular DNA polymerases. d. It incorporates mutations into the viral genome at a high rate.

d. It incorporates mutations into the viral genome at a high rate.

Which of the following describes the semidiscontinuous replication of DNA? a. The leading strand is synthesized in the 5' -> 3' direction first. Upon completion, the lagging strand is synthesized, in pieces, in the 3' -> 5' direction. b. The leading strand is synthesized in the 5' -> 3' direction first. Upon completion, the lagging strand is synthesized, in pieces, in the 5' -> 3' direction. c. The leading strand is synthesized in the 5' -> 3' direction, while the lagging strand is synthesized, in pieces, in the 3' -> 5' direction. d. The leading strand is synthesized in the 5' -> 3' direction, while the lagging strand is synthesized, in pieces, in the 5' -> 3' direction.

d. The leading strand is synthesized in the 5' -> 3' direction, while the lagging strand is synthesized, in pieces, in the 5' -> 3' direction.

Which of the following statements about type I topoisomerases is FALSE? a. Type I topoisomerases are found in both prokaryotes and eukaryotes. b. Their reaction mechanism involves nucleophilic attack by an active site tyrosine residue at a phosphate group in a phosphodiester bond. c. During the reaction mechanism, type I topoisomerases switch between closed and open conformations. d. They can only decrease writhe (W) and therefore, they can only reduce the linking number of DNA.

d. They can only decrease writhe (W) and therefore, they can only reduce the linking number of DNA.

The multiple hit hypothesis suggests that inheriting a defective gene for the retinoblastoma protein, BRCA1, or p53 _______ guarantee that an individual will develop cancer.

does not

Read the following statements carefully and determine which are true and which are false. i) The energy required to synthesize nucleic acids comes from the nucleotide building blocks themselves. ii) The "groove" in the structure of double-stranded DNA allows binding interactions between proteins and particular base sequences. iii) In double-stranded DNA, the two strands are wound around one another in a right-handed helix. a. i) & iii) are false, and ii) is true. b. i) is false, and ii) & iii) are true. c. i) & ii) are true, and iii) is false. d. All three statements are false. e. All three statements are true.

e. All three statements are true.

Which of the following ingredients of replication is NOT essential in PCR? a. A primer b. dNTPs c. DNA polymerase d. A template e. DNA ligase

e. DNA ligase

Which of the following statements about proofreading in DNA polymerases is TRUE? a. Proofreading is, specifically, a 3' endonuclease activity. b. Proofreading occurs in all DNA polymerases. c. Proofreading occurs in the same active site as polymerization. d. Proofreading enhances the processivity of DNA polymerases. e. Proofreading is a hydrolysis reaction.

e. Proofreading is a hydrolysis reaction.

Read the following three statements carefully and determine which are true and which are false.i) Nucleic acids are synthesized in the 3' - 5' direction.ii) The sugar-phosphate groups which form the "backbone" of the DNA double-helix are located on the outside of the helix because they are polar.iii) RNA polymerase "reads" a template strand by running along it in a 5' - 3' direction. a. i) is false, and ii) & iii) are true. b. All three statements are false. c. All three statements are true. d. i) & ii) are true, and iii) is false. e. i) & iii) are false, and ii) is true

e. i) & iii) are false, and ii) is true