DNA Replication

Question 1

DNA replication is ____ and ______

Answer 1

Bidirectional (goes either way from origin of rep)

Semiconservative (one conserved parental strand, one newly synth daughter strand)

Question 2

DNA synthesis ALWAYS proceeds in _____ direction

Answer 2

5’ to 3’

Question 3

Leading strand has ______ replication, lagging strand has ______replication

Answer 3

continuous

discontinuous

Question 4

origin of replication

Answer 4

AT rich sequences recognized by origin binding proteins
Bacterial: 1
Eukaryotic: multiple

Question 5

DNA polymerase does what?

Answer 5

Synthesizes DNA strand 5’ to 3’ direction.

Question 6

Replication forks

Answer 6

Site where DNA synthesis is occurring.

Question 7

Origin binding proteins

Answer 7

They recognize and bind to origin of replication (AT rich sequences)

Question 8

Helix unwinds _____ of replication fork by _____

Answer 8

ahead

helicases

Question 9

What can hold DNA in single stranded conformation?

Answer 9

single-strand binding proteins
(Protects ssDNA from nucleases)
RPA: humans
SSB: bacteria

Question 10

What problems must be overcome by DNA Pol in order to copy DNA?

Answer 10

1. Unwinding (can’t melt strands to separate them)
2. Primer: DNA Pol CANNOT initiate a new strand, it can only elongate an existing primer.
3. Polarity (Strands have opposite polarity, but DNA Pol starts at 3’ end to make strands 5’-3’)

Question 11

topoisomerase

Answer 11

Moves ahead of replication fork to prevent supercoiling by breaking and rejoining DNA backbone.
DNA gyrase is in prokaryotes (inhibited by quinolones)
Topo II makes double stranded breaks

Question 12

Characteristics of replication origins

Answer 12

1. unique segments w/ multiple short repeats
2. rich in AT base pairs
3. recognized by multimeric origin binding proteins

Question 13

primase

Answer 13

enzyme that catalyzes a reaction that copies the parental strand to form RNA primer (which has about 10 nucleosides)

Question 14

DNA polymerase

Answer 14

Adds deoxyribonucleotides to 3’ hydroxyls of RNA primer and to ends of growing DNA strand

Question 15

Two DNA polymerases that carry out DNA rep?

Answer 15

DNA Pol I

DNA Pol III

Question 16

DNA Pol I

Answer 16

1. “clean up” in DNA replic/repair.(3’ to 5’ exonuclease activity for proofreading)
2. Also removes RNA primer from DNA by using 5’ to 3’ exonuclease activity
3. 5’ to 3’ DNA Pol activity (needs 3’ OH primer and DNA template strand)

Question 17

DNA Pol III

Answer 17

MAJOR replicative enzyme b/c it has clamp which keeps it attached to DNA over long dist. High processivity.

Question 18

DNA ligase

Answer 18

JOINS Okazaki fragments, catalyzes formation of phosphodiester bonds b/t 3’ OH and 5’ phosphate group b/t two polynucleotide chains.

Question 19

Cofactor for ligase in eukaryotes and prokaryotes?

Answer 19

ATP for euk

NAD+ for pro

Question 20

Sliding clamp for euk and prok

Answer 20

PCNA for eukaryotic DNA Pol δ
Beta subunit for prokaryotic DNA pol III
(Clamp increases processivity of DNA pol)

Question 21

Leading and lagging strands are synthesized concurrently via ______

Answer 21

looping of the lagging strand (solves polarity issue)

Question 22

What does DNA Pol use to increase accuracy?

Answer 22

Discrim b/t correct and incorrect nucleotides by:
-ability to form hydrogen bonds (specifies correct pairing b/t complimentary bases
-Common geometry (AT, CG required to fit in active site of polymerase)
10^4-10^5 correct additions

Question 23

Proofreading by DNA pol

Answer 23

increases accuracy to correct additions for every million to 100 million nucleotides
3’ to 5’ exonuclease activity of DNA Pol I AND DNA Pol III

Question 24

Sliding Clamp on Euk and Prok

Answer 24

Prok: Beta clamp
Euk: Lagging strand: delta clamp, leading strand E (epsilon) clamp

Question 25

Retroviral replication require conversion of _____ to ____ by _____

Answer 25

ssRNA to dsDNA by reverse transcriptase (reverse transcription)

Question 26

Telomerase

Answer 26

RNA-dependent DNA Pol that maintains chromosomal ends by copying telomeric repeat sequences from RNA template.

• Repressed in normal cells
• De-repressed in cancer cells (and stem cells), normal cell death is NOT triggered–>tumor growth

Question 27

End replication problem refers to which strand?

Answer 27

Lagging, because it needs RNA primer to begin synth of each lagging strand. But @ end, there is nothing for it to attach to. Last section can’t be synthesized. Telomeres get shorter and shorter.