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Chapter 28 DNA Replication, Repair and Recombination

Matching Questions
Use the following to answer questions 1-10:
Choose the correct answer from the list below. Not all of the answers will be used.
a) helicases
b) Type I
c) Type II
d) Ames
e) telomeres
f) unwound
g) Z-DNA
h) A-DNA
i) linking
j) template
k) Holliday
l) Okazaki
1 ____________ A left-handed double helix.
Ans: g
Section: 28.1
2 The ____________ number is the number of times a DNA strand winds around the helix when it
is constrained.
Ans: i
Section: 28.2
3 The strands of DNA must be ____________ for replication.
Ans: f
Section: 28.2
4 Type of topoisomerase that does not require ATP is ____________.
Ans: b
Section: 28.2
5 Type of topoisomerase that can introduce supercoils is ____________.
Ans: c
Section: 28.2
6 DNA can serve as a ____________ to direct synthesis of the complementary strand of DNA or
RNA.
Ans: j

Chapter 28 DNA Replication. Ans: pyrimidine dimers Section: 28.3 9 The ends of chromosomes are called ____________. Ans: l Section: 28. the RNA primer pieces are removed by __________________. Ans: d Section: 28.2 14 The primer for DNA synthesis is an RNA molecule formed by the enzyme _______________.5 Fill in the Blank Questions 11 The Watson and Crick model of DNA is called __________-DNA Ans: B Section: 28.1 12 The tertiary structures in DNA are created by the process known as ______________.5 2 . Ans: supercoiling Section: 28.000 Section: 28. Ans: leading Section: 28.3 7 The small DNA pieces observed during DNA replication are called ____________ fragments. Ans: II .2 13 Type ________ topoisomerase introduces negative supercoils in DNA while type ________ topoisomerase relaxes supercoil structures. Ans: DNA polymerase I Section: 28. Ans: a Section: 28. Ans: e Section: 28. Ans: 10. I Section: 28.4 17 During DNA replication.3 8 Proteins that use ATP to melt the DNA at specific sites are called ____________.3 15 The DNA strand that is replicated continuously is known as the _____________ strand.3 16 DNA polymerase III is approximately ________________ times faster than DNA polymerase I. Ans: primase Section: 28.4 10 An assay used to determine carcinogenic potential is the ____________ test. Repair and Recombination Section: 28.4 18 UV light causes damage to DNA by forming __________________.

Ans: D Section: 28. b.49 Multiple Choice Questions 21 The observed error rate in DNA replication is A) 1 per 106 nucleotides. genetic skin disease. B) When the backbone of one strand is cleaved. 23 Which of the following is (are) true? A) Naturally occurring DNA usually has negative supercoiling. D) E) 3' → 3' direction.2 24 The mechanism by which type II topoisomerase relaxes DNA includes which of the following? A) The OH of tyr 723 attacks a phosphate group on one DNA strand. E) a. caused by a mutation in components of the human nucleotideexcision-repair pathway is called ___________________. Repair and Recombination 3 19 The human.2 25 What is DNA gyrase? A) a bacterial topoisomerase II B) a bacterial topoisomerase I C) a bacterial helicase Ans: A Section: 28. None of the above.5 20 ________________ are intermediates in recombination pathways composed of four polynucleotide chains in a cross-like structure. and c. C) 1 per 1010 nucleotides. B) Forms with same linking number can be interconverted without cleavage.2 26 Replication moves from A) 5' → 3' direction.6 and Figure 28. B) 3' → 5' direction. C) The twist value rarely changes in naturally occurring DNA. D) E) All of the above. Ans: xeroderma pigmentosum Section: 28. the DNA rotates. C) ATP binds. D) E) All of the above None of the above. . leading to a conformation change.2 D) E) 1 per 1015 nucleotides. none of the above. Ans: D Section: 28.Chapter 28 DNA Replication. Ans: C Section: Introduction 22 What is the formula for linking? A) Lk = Wr − Tw B) Lk = Wr + Tw C) Tw = Wr + Lk Ans: B Section: 28. E) a. D) a and b. C) 5' → 5' direction. and c. Ans: Holliday junctions Section: 28. b. none of the above. D) a and b. B) 1 per 104 nucleotides.

3 29 One function of the two metal cations that are required by DNA polymerases is A) to stabilize the negative charge of the transition state.3 27 What is true about DNA polymerases? A) There are five structural classes. Repair and Recombination Ans: A Section: 28.3 28 How is replication specificity dictated? A) formation of proper hydrogen bonds B) Enzyme interactions with the DNA act as a “ruler” to determine if the properly spaced base pair has been formed. Ans: A Section: 28.3 30 How can the leading and lagging strands be synthesized in a coordinated fashion? A) Specific enzymes control the size of the DNA opening. E) None of the above. B) to bind ATP. E) a. C) the insertion of one or more bases in the DNA.4 32 Common types of mutations include A) the mismatch of bases in the DNA. D) All of the above. Ans: C Section: 28. C) Pol III is a dimeric holoenzyme. D) a and b. C) The bond is broken and reformed to ensure its accurate placement at each base pair. E) a. B) All have finger and thumb domains that wrap around the DNA. B) the deletion of one or more bases in the DNA.4 31 The free end of the eukaryotic chromosome is thought to form a unique DNA structure that allows for complete replication. which requires metal cofactors. E) none of the above. C) supercoiled loop. and the looped lagging strand allows the enzyme to proceed in the same direction with each strand. B) large duplex loop. and c. Ans: B Section: 28. B) Lagging-strand binding proteins inhibit leading-strand replication if the strands become disproportionate in size. 4 . This structure involves a G-rich repeating sequence and forms a A) replication fork. D) b and c. D) displacement loop E) none of the above.Chapter 28 DNA Replication. C) All catalyze the same reaction. Ans: D Section: 28. Ans: E Section: 28. b. C) to complex with a tyr residue in the active site. b. and c. D) a and c.

increased bases per turn. but twisted like propeller blades. the bases are not coplanar. Ans: This is a structure of antiparallel chains that twist in a left-handed screw. and the base pairs per turn slightly greater. B) alkylating agent. D) E) all of the above. it is wider and shorter. C) suppressor mutants. D) E) all of the above.1 39 Describe Z-DNA. . Section: 28. none of the above. with the phosphates and sugars on the outside. in simple terms.5 D) E) all of the above. like B-DNA. Repair and Recombination 5 D) b and c. The bases are found on the inside of the helix. Frequently. The phosphates are zigzagged.1 37 Compare A. Ans: A-DNA is a more dehydrated form. and placement of the bases. Ans: E Section: 28. E) a. It is a right-hand helix of antiparallel strands. Ans: DNA consists of two chains of polynucleotides. C) ligate single-strand breaks.5 34 Afflatoxin B1 is an example of a(n) A) intercalating chemical. can vary. Ans: A Section: 28. Ans: B Section: 28. Ans: B Section: 28. Short-Answer Questions 36 Describe. and large pitch. with a long rise. B) trinucleotide expansion. B) remove damaged bases. but running in opposite directions in a right-handed helical form around a central axis. It is the narrowest helix. The bases are held together by hydrogen bonds: adenine and thymine by two hydrogen bonds. observed at lower humidity.Chapter 28 DNA Replication. paired via hydrogen bonds. and guanine and cytosine by three hydrogen bonds.1 38 What did x-ray analysis of crystallized DNA indicate? Ans: These studies indicted that deviations from the “B” structure are common. b. and c. C) base analog. However. the hallmarks of DNA structure.5 35 Photolysase functions to A) repair pyrimidine dimers. Section: 28. none of the above. In A-DNA the pitch is smaller. none of the above.5 33 Huntington disease is caused by A) pyrimidine dimers. The bases are perpendicular to the axis. The rotation of the helix. and the base pairs are tilted and less perpendicular to the central axis.and B-DNA. Section: 28. The major groove is flatter. and the minor groove is very deep.

2) A segment of DNA is passed through the break.5 47 Name the types of DNA repair.3 43 What is a processive polymerase enzyme versus a distributive polymerase enzyme? Ans: Processive enzymes catalyze multiple reactions without dropping the polymer substrate. Section: 28.4 45 How are single-stranded regions of DNA maintained? Ans: Single-stranded binding proteins (SSB) bind to the single-stranded regions of DNA.1 40 Describe the three-step process of topoisomerases I types. Section: 28. It can only seal a break in a double-strand piece of DNA. Some helicases appear to be monomers. 3) The DNA break is resealed.2 41 How are breaks sealed in discontinuous DNA formed during replication? Ans: DNA ligase is the enzyme that seals the breaks by creating a phosphodiester bond between a 3' hydroxyl group and a 5' phosphate at the end of the other piece. base-excision repair. .4 46 Describe the consequences of incorrect DNA replication or DNA damage. where NAD + serves as the AMP donor.4 44 How is the processivity of DNA polymerase III accomplished? Ans: The structure of the enzyme complex allows the reaction processivity. Section: 28. Repair and Recombination 6 Section: 28.3 42 What is known about helicases by comparison of amino acid sequences? Ans: There are numerous helicases. which forms a ring around the DNA polymer. Ans: 1) One or both strands of DNA must be cleaved. It normally uses the energy provided by ATP. categorized in groups.Chapter 28 DNA Replication. Section: 28. while others are oligomers. Section: 28. Section: 28.5 48 Why is thymine used in DNA instead of uracil? Ans: The methyl group on thymine allows it to be unique from deaminated cytosine. Ans: The types include direct repair. Some of these are the ATP-binding sites.1 and Table 28. In contrast. and nucleotide-excision repair. except in bacteria. and blockage of DNA replication. A specific subunit leaves enough space for the newly assembled DNA to be formed properly. The enzyme is a large complex. Section: 28. and acts as a sliding DNA clamp. Section: 28. Ans: The most serious consequences are cell death. The changes in DNA can also be inherited and passed on to future generations. cell transformation. a distributive enzyme releases the polymer between successive steps. and comparisons indicate about seven common regions. others are the clefts between domains that are critical to the conformational change observed during action.

Section: 28.Chapter 28 DNA Replication. and is a fairly common event.5 49 What does the phrase “recombination of genetic material” refer to? Ans: Two daughter molecules are formed by the exchange of genetic material between two parent molecules. D-loop. The uracil is recognized as foreign and is repaired.6 7 . a member of the AAA ATPase family. Section: 28. Repair and Recombination Deamination of cytosine forms uracil.6 50 What role does the protein RecA play in recombination? Ans: RecA. promotes the formation of the displacement loop. Section: 28. This process is often called strand invasion.