BCH3020 Tutorial Questions and Answers

DNA structure, replication and repair

March 20, 2004

1. Which of the following statements about the double-helical structure of DNA are
correct?
(a) It has adenine paired with thymine and cytosine paired with guanine.
(b) It can assume many different forms including A-DNA, B-DNA and Z-DNA.
(c) In B-DNA, all the hydrogen-bonded base pairs lie in a plane perpendicular to
the helix axis.
(d) It can be deformed by both smooth bends and kinks.
(e) It is rigid and static.

C is incorrect because of local variations. The H-bonded base pairs are often
twisted and tilted out of the plane that is perpendicular to the helical axis.

2. A-DNA exists in low relative humidity. Since such arid conditions presumably
never occur in the cell, what is the significance of the structure of this DNA?

ds-RNA, RNA-DNA hybrids and some short regions of ds-DNA have structures
like that of A-DNA. Knowing the helical structure of A-DNA helps us to
understand other similar helices that are of physiological importance.

3. Match the following features to A-, B- and Z-DNA.

(a) Phosphates in the backbone are zigzagged.
(b) Formation is favored by negative supercoiling.
(c) Has a relatively wide and deep major groove.
(d) Has a right-handed helix.
(e) Has 10.4 base pairs per turn.
(f) Has a structure similar to that of double-stranded RNA.

A-DNA: d, f; B-DNA: c,d,e; Z-DNA a,b. Answer b is correct for Z-DNA because
the conversion of B-DNA to Z-DNA requires the complete unwinding of the
right-handed helix to form the left-handed one. Negative supercoiling promotes
unwinding of the right-handed helix.

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4. The topological features of circular DNA may affect which of the following?
(a) The electrophoretic mobility of the DNA.
(b) The sedimentation properties of the DNA.
(c) Its affinities toward proteins that bind to the DNA.
(d) The susceptibility of the strands of the DNA to unwinding.
(e) The susceptibility of the DNA to the action of DNA ligase.
a, b, c, d. For answer e, supercoiling has nothing to do with DNA ligase.

5. What are the differences between topoisomerase I and II?

Type I topoisomerase catalyzes the relaxation of supercoiled DNA, a

thermodynamically favorable process. Type II topoisomerase utilizes free
energy from ATP hydrolysis to add negative supercoils to DNA.

6. Which of the following statements about DNA polymerase I are correct?

(a) It adds deoxyribonucleotide units to the 3’hydroxyl of a primer.
(b) It uses the template strand to select which deoxyribonucleoide unit to add to
the growing DNA chain.
(c) It contains a 3’ to 5’ nuclease that cleaves phosphodiester bonds to yield
3’dNMPs and 3’-phosphate-terminated DNA.
(d) It contains two nuclease activities in the same polypeptide chain that contains
the polymerase active site.
(e) It can be cleaved with a protease into two fragments, each of which has a
nuclease activity.

a, b, d, e. The 3’ to 5’ exonuclease action generates a 5’-dNMP from the

3’-hydroxyl of the DNA, leaving a 3’-hydroxyl group on the residual DNA.

7. Which of the following statements about DNA replication in E. coli are correct?
(a) It occurs at a replication fork.
(b) It starts at a unique locus on the chromosome.
(c) It proceeds with one replication fork per replicating molecule.
(d) It involves discontinuous synthesis on the leading strand.
(e) It uses RNA transiently as a template.

a, b, e. C is incorrect because E. coli has two replication forks, as it synthesizes

the DNA bidirectionally from the unique OriC locus.

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8. Why is RNA synthesis essential to DNA synthesis in E. coli?

DNA polymerases cannot make DNA de novo. Instead, they need an RNA
primer.

9. Match the left column with the right column.

(a) Replication fork
(b) Ori C
(c) Lagging strand
(d) Leading strand
(e) Okazaki fragments
(f) DnaB helicase
(g) ss binding protein
(h) DNA gyrase
(i) Primase
(j) DNA polymerase III
(k) εsubunit of poly III
(l) DNA polymerase I
(m) DNA ligase
(1) Synthesis direction is opposite that of
replication fork movement
(2) Unwinds strands at the origin of replication in
association with dnaA and dnaC proteins
(3) Is synthesized continuously
(4) Synthesizes most of DNA
(5) Is synthesized discontinuously
(6) Relieves positive supercoiling
(7) Is the locus of DNAunwinding
(8) Hydrolyzes ATP to reduce the linking number
of DNA
(9) Binds dnaA, dnaB, and dnaC proteins
(10) Fills in gaps where RNA existed
(11) Is the point of initiation of synthesis
(12) Joins lagging strand pieces to each other
(13) Contains a 5’ to 3’ exonuclease that removes
RNA primers
(14) Is an RNA polymerase
(15) Performs ‘proofreading’ on most of the DNA
synthesized
(16) Stabilizes unwound DNA
(17) Uses NAD to form phosphodiester bonds

(a) 7; (b) 7, 9, 11; (c) 1, 5; (d) 3; (e) 1; 5-individual fragment is synthesized

continuously, but the different fragments are synthesized one after another; (f) 2;
(g) 16; (h) 6, 8; (i) 14; (j) 4; (k) 15; (l) 1-because it is used to fill up the gaps of the
lagging strand, 10, 13; (m) 12, 17.

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(10) Which of the following nucleotide substitutions are transition mutations and
which are transversion mutations?
(a) G to A
(b) A to C
(c) C to T
(d) T to G

a, c - transition mutation. b, d – transversion mutation.

(11) How could the tautomerization of a keto group on a guanine residue in DNA to
the enol form lead to a mutation?

The rare enol tautomer of G could base-pair with a T in the template to allow its
incorporation into a growing DNA strand during replication. If the
proofreading process missed this erroneous incorporation, the resulting daughter
DNA duplex would contain a G.T base pair. During next round of replication,
the T would direct the incorporation of an A into its complementary daughter
strand. The final result would be the substitution of an A.T base pair for the
original G.C. base pair.

(12) Match the left column with the right column.

(a) 5-bromouracil
(b) 2-aminopurine
(c) Hydroxylamine
(d) Acridines
(e) Nitrous acid
(f) Ultraviolet light
(1) Transversion
(2) Transition
(3) Insertion or deletion
(4) Trnaslational frameshift
(5) Block in replication

(a) 2, (b) 2, (c) 2, (d) 3, 4, (f) 5. None of these mutagens commonly cause
transversions.

(13) What property of DNA allows the repair of some residues damaged through the
action of mutagens?

DNA is double-stranded. Therefore, damage to one strand can be repaired

using the other strand as the template.

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(14) How does the repair machinery of E. coli identify a DNA strand that has recently
misincorporated a noncomplementary nucleotide during replication in order to
repair it?

The parental strand has its GATC sequences methylated by a sequence-specific

DNA methylase (dam methylase). The methyl groups serve as tags to direct the
MUT repair enzymes to cut the newly synthesized unmethylated strand, which
contains the wrong nucleotide, and remove the mispaired nucleotide and a
variable number of neighboring nucleotides. DNA repair synthesis then
replaces these nucleotides to form a corrected strand, and DNA ligase joins to
form intact DNA.

(15) Given that T requires more energy to synthesize than U, and A pairs equally well
with U or T, why does DNA contain A-T base pairs instead of A-U base pair?

C spontaneously deaminates to form U in DNA. This change would lead to a

mutation during replication. The methyl group on T distinguishes it from
undesirable uracils formed by deamination.

(16) Explain how mutations in genes encoding proteins likely to be involved in DNA
repair, such as those defective in xeroderma pigmentosum and hereditary
nonpolyposis colorectal cancer, may contribute to the onset of cancer.

If DNA repair is defective, mutation on DNA will accumulate. As a result, genes

regulating cellular proliferation may go wrong, causing cancer.

Questions and answers are extracted from Student Companion for Stryer’s
Biochemistry.