week 4

Question 1

BACTERIAL DNA REPLICATION: where do initiator proteins bind to?

Answer 1

Bind to origin (AT rich sequence), requires ATP, they denature the sequence a little

Question 2

BACTERIAL DNA REPLICATION: what do initiator proteins do?

Answer 2

help helicase bind

Question 3

BACTERIAL DNA REPLICATION: how many types of helicase exist?

Answer 3

two

Question 4

BACTERIAL DNA REPLICATION: in which direction does the predominant helicase move?

Answer 4

5’-3’ along the LAGGING strand template

Question 5

BACTERIAL DNA REPLICATION: does helicase require atp?

Answer 5

yes

Question 6

BACTERIAL DNA REPLICATION: how many subunits does helicase have

Answer 6

6 (has quaternary structure)

Question 7

BACTERIAL DNA REPLICATION: what do single-strand binding proteins do?

Answer 7

1. separate DNA strands by binding ssDNA
2. Prevents strands from H-bonding (also prevents hair pins or loops—H-bonding w/n a strand—until replication can occur

Question 8

BACTERIAL DNA REPLICATION: What does DnA polymerase require in order to begin?

Answer 8

A bound primer (~10 nucleotides long, with a free 3’ OH bp to the template)

Question 9

BACTERIAL DNA REPLICATION: what is the purpose of primase?

Answer 9

synthesize an RNA primer

Question 10

BACTERIAL DNA REPLICATION: What direction does primase proceed in?

Answer 10

reads 3’-5’ along template strand

Question 11

BACTERIAL DNA REPLICATION: why is DNApol used at all?

Answer 11

cell doesn’t like to have duplexes very long (RNA and DNA bound), DNApol is very efficient and quick but just can’t start w/o primer which can start a new sequence just from template and raw materials

Question 12

BACTERIAL DNA REPLICATION: helicase + primase =

Answer 12

primosome

Question 13

BACTERIAL DNA REPLICATION: what does the sliding clamp do?

Answer 13

ring shaped protein that doesn’t impede function of DNAPol but hods it on tightly enough so it won’t fall off and DNAPol doesn’t have to bind very tightly (get slowed down and needs to be able to release template strand at certain points)

Question 14

BACTERIAL DNA REPLICATION: How doe the removal of RNA primers work

Answer 14

DNA repair system is responsible for removal of the RNA primer and replacing it with correctly matched DNA sequence, Repair polymerase uses original template DNA to guide replacement of RNA primer with DNA

Question 15

BACTERIAL DNA REPLICATION: how are the Okazaki fragments on the lagging strand linked together

Answer 15

ligase seals the nick after RNA primers are removed and replaced w correctly match DNA sequence
NOTE: not a gap, there are no nucleotides missing

Question 16

BACTERIAL DNA REPLICATION: leading strand is synthesized _________ from _______________ primer (s)

Answer 16

continuously, single RNA

Question 17

BACTERIAL DNA REPLICATION: Lagging strand is synthesized _____________ from _____________ primer(s)

Answer 17

discontinuously, multiple

Question 18

BACTERIAL DNA REPLICATION: Okazaki fragments:________ + ___________

Answer 18

RNA primer + DNA

Question 19

DNA synthesis proceeds in which direction?

Answer 19

5’-3’

Question 20

What problem does DNA topoisomerase solve?

Answer 20

as helicase unwinds DNA, supercoiling and torsional strain increases, this is a problem in circular chromosomes and large linear euk chromosomes

Question 21

Why is the shortening of the 5’ end of the daughter DNA a potential problem? How does this problem arise?

Answer 21

there could be a loss of sequence information. RNA primer cannot bind to the very end

Question 22

for which strand is the shortening of the 5’ end a concern?

Answer 22

Lagging

Question 23

How does telomerase solve the problem of the shortening of the 5’ end?

Answer 23

telomerase binds to an RNA template and generates G-rich, repetitive sequences on the 3’ end of the parental template.

Question 24

In certain circumstances cancer cells can reactivate _____________ (which is usually not abundant in somatic cells)and the cancer cells can add more _______ which help the cell to ___________ indefinitely

Answer 24

telomerase, telomeres, replicate

Question 25

what does the 3’-5’ exonuclease do?

Answer 25

removes misincorporated nucleotides and leaves a 3’OH so that a correct nucleotide can come in and DNAPol can keep adding nucleotides

Question 26

nucleases can digest ____________, exonucleases can remove ___________

Answer 26

nucleotides, nucleotides from the ends of strands

Question 27

how is strand directed mismatch repair initiated?

Answer 27

the detection of distortion in the geometry of the double helix generated by mismatched base pairs

Question 28

What are the two mismatch proofreading proteins?

Answer 28

MutS and MutL

Question 29

what are the functions of MutS and MutL?

Answer 29

MutS scans for distortions, MutL scans for nicks to know which is the new DNA strand

Question 30

what are four mains ways DNA can be damaged after synthesis?

Answer 30

oxidation, radiation, heat, chemicals

Question 31

what is a pyrimidine dimer and why is it bad

Answer 31

Occurs through damage to DNA, covalent bonds b/w bases CT CC or TT, it is a problem because DNAPol or RNAPol cannot get around it

Question 32

what are two examples of spontaneous damage to DNA

Answer 32

depurination (remove sugar phosphate prom purine base)
deamination (remove NH2 group from uracil)

Question 33

what are the two general mechanisms of DNA repair (not proofreading)

Answer 33

1. base excision repair (endonuclease removes one nucleotide and DNAPol replaces with correct one)
2. nucleotide excision repair (multiple nucleotides removed—separation of strands by DNA helicase— and replaced by DNAPol)