Which enzyme is used to join bits of DNA?
Answer: B
Correct answer: DNA ligase
DNA ligase forms the phosphodiester bond that closes a nick between two adjacent fragments. It is what joins Okazaki fragments in the cell, and what joins an insert to a vector in cloning. Polymerase extends a chain from a primer; endonucleases and primases cut and prime respectively.
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The melting of 40-45 bp at the oriC site of E. coli requires
Answer: A
Correct answer: DnaA + ATP + HU
Melting the AT-rich 13-mer repeats at oriC is the initiation step, and it needs only three things: DnaA charged with ATP, which binds the 9-mer boxes and bends the DNA, and the histone-like HU protein, which helps that bending. DnaB, the helicase, is loaded afterwards by DnaC to extend the opening, and Pol III arrives later still.
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The nicks or gaps between Okazaki fragments are eventually sealed by
Answer: B
Correct answer: DNA ligase
Once the RNA primer of each Okazaki fragment has been removed and the gap filled by polymerase, one phosphodiester bond is still missing. DNA ligase forms it, joining the fragments into a continuous strand. Gyrase manages supercoiling and polymerase extends chains; neither can close a nick.
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DNA unwinding is done by ____________
Answer: B
Correct answer: Helicase
Helicase uses the energy of ATP to break the hydrogen bonds between the paired bases and travel along the duplex, separating the two strands so each can be copied. Single-strand binding proteins then keep them apart, and topoisomerases handle the supercoiling that results.
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What is the origin of replication?
Answer: A
Correct answer: Particular site at which DNA replication starts
The origin is a defined sequence at which the initiator protein binds and the duplex is first opened - oriC in E. coli. It is not a random point: the site is AT-rich, so it takes less energy to melt, and it carries the repeats the initiator recognises.
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Reverse transcriptase produces
Answer: D
Correct answer: DNA from RNA
Reverse transcriptase makes DNA using an RNA template - the reverse of the usual flow of information, which is what gives retroviruses their name. It is also the enzyme behind cDNA synthesis in the laboratory.
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Which of the following proteins is NOT involved in opening a replication bubble?
Answer: D
Correct answer: ligase
Opening the bubble takes three kinds of protein: helicase to break the base pairs, single-strand binding protein to keep the separated strands from re-annealing, and topoisomerase to relieve the supercoiling that unwinding forces ahead of the fork. Ligase plays no part in opening - it comes later, sealing the nicks between Okazaki fragments.
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When DNA polymerase is in contact with guanine in the parental strand, what does it add to the growing daughter strand?
Answer: B
Correct answer: Cytosine
Base pairing is fixed by hydrogen bonding: G pairs with C through three hydrogen bonds, and A with T through two. So a guanine on the template directs the insertion of a cytosine. Uracil belongs to RNA, not DNA.
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In DNA replication, one new strand is synthesized complementary to an old (parent) strand and is referred as
Answer: B
Correct answer: semiconservative
Because each daughter duplex keeps one parental strand and gains one new one, half of each product is “conserved” from the parent - hence semi-conservative. Antiparallel describes the opposite orientation of the two strands, and discontinuous the way the lagging strand is made; neither is the name for this pattern of inheritance.
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Which of the following is used to determine the appropriate stringency (Wallace rule)?
Answer: C
Correct answer: Tm = 4 x (No.of G:C base pair) + 2 x (No.of A:T base pair)
The Wallace rule for short oligonucleotides weights each base pair by the number of hydrogen bonds it makes - three for G:C, two for A:T - giving
\[ T_m = 4(G+C) + 2(A+T) \]in degrees Celsius. The heavier weight goes to G:C, which is the trap in the alternatives. The rule is a rough guide, reliable only for probes of roughly 14-20 bases.
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