DNA replication

Question 1

DNA replication is ________ and __________

Answer 1

semi-conservative

bidirectional

Question 2

Origin of replication

Answer 2

• sequence specific site recognized by replication proteins

- hundreds of origins per chromosome in euk (only 1 in prok)

Question 3

Replication fork

Answer 3

where DNA helicases have unwound the double helix and the replication machinery sits and synthesizes complementary strands

Question 4

Origin binding proteins

Answer 4

• Recognize replication origin

- Proteins bind to origin and become part of the complex, also recruits Polymerase

Question 5

Helicase

Answer 5

enzymes that catalyze the breaking of H-bonds between base pairs and the subsequent ‘unwinding’ of the helix.

Question 6

Single-Stranded Binding Proteins

Answer 6

bind to the melted strands of original DNA to prevent them from re-annealing or getting attacked by nucleases

Question 7

Primase

Answer 7

Enzyme that catalyzes the addition of the RNA primer to begin replication
(RNA primer required for DNA pol)

Question 8

DNA polymerase I (3 different activities)

Answer 8

Removes RNA primer, replace with DNA

1) 5’–>3’ exonuclease activity: removes RNA primer
2) 3’–>5’ exonuclease activity: proof-reading
3) 5’–>3’ DNA synthesis: fills gap once RNA is removed

Question 9

_________ is distributive and falls on and off the DNA easily and _______ is processive

Answer 9

DNA polymerase I

DNA polymerase III

Question 10

DNA Polymerase III (2 activities)

Answer 10

• Elongation of DNA from RNA primer
• uses sliding clamp (processive)
• multi-protein complex

1) 5’–>3’ DNA synthesis
2) 3’–>5’ Exonuclease activity (proofreading)

Question 11

DNA polymerase III determines the correct base to input based on ________ and _________

Answer 11

H-bonds and geometry

Question 12

DNA ligase

Answer 12

• enzyme responsible for sealing Okazaki fragments together once the RNA primers have been replaced by Pol I
• Uses cofactors (ATP-euk, NAD+ - prok)

Question 13

Sliding clamp

Answer 13

• Holds on to DNA and allows DNA pol III to hold on to DNA strongly, but enables it to move
• PCNA (euk), Beta clamp (prok)

Question 14

Telomere

Answer 14

• sequence at the ends of chromosomes, consisting of a large number of repeating segments
• gets consistently shorter with every chromosome replication

Question 15

Dysteratosis congenita

Answer 15

telomere shortening syndrome

Question 16

Topoisomerase/gyrase

Answer 16

• Enzyme responsible for relieving torsional strain in the DNA helix in the region ahead of the replication fork
• Does so by breaking and rejoining dsDNA
• topogyrase for prok

Question 17

Exonucleases

Answer 17

chews from the end

Question 18

Endonuclease

Answer 18

cuts within a DNA strand - breaks phosphodiester bond between sugar and phosphate

Question 19

DNA polymerase requires that the deoxyribonucleotide to have a _________ group for phosphodiester bond synthesis

Answer 19

3 hydroxy group

Question 20

DNA synthesis requires a ______ and proceeds in the _______ direction

Answer 20

RNA primer

Proceeds in the 5’–>3’ direction

Question 21

Errors in replication are corrected by the __________ activity of the DNA polymerase

Answer 21

3’–>5’ exonuclease proofreading

Question 22

7 Steps of DNA synthesis on leading strand

Answer 22

1) origin binding proteins bint to origin
2) DNA melted apart by helicases
3) Topoisomerase relieves tension ahead of replication fork
4) ssbinding proteins protect unwound ssDNA
5) RNA primer synthesized by RNA primase
6) Pol III elongats DNA from RNA primer, complementary to leading strand
7) New and old strands annealed

Question 23

DNA synthesis on lagging strand (5 steps - after DNA unwound)

Answer 23

1) primase attaches RNA primer to lagging strand segment
2) Pol III elongates DNA from RNA primer back a short ways, forming an Okazaki fragment
3) RNA primer removed and replaced with DNA by Pol I
4) Fragments sealed together with DNA ligase
5) new and old strands annealed

Question 24

In eukaryotes: DNA pol E synthesizes on the _________ strand and DNA pol d synthesizes on the _______ strand

Answer 24

leading

lagging

Question 25

In Prokaryotes: DNA pol III synthesizes leading and lagging strands concurrently via ___________ in the _________ polymerase complexes

Answer 25

looping of the lagging strand

2 core

Question 26

End replication problem

Answer 26

progressive shortening of chromosomal ends during rounds of DNA replication

Question 27

Telomerase

Answer 27

• Reverse transcriptase that uses RNA template to copy DNA repeats onto the ends of telomeres
• can be a target for treating cancer

Question 28

AZT

Answer 28

targets reverse transcriptase

Question 29

Acyclovir

Answer 29

targets viral DNA polymerase

Question 30

Quinolones

Answer 30

targets bacterial DNA gyrase