final DNA replication problems

Question 1

what do adaptor proteins do

Answer 1

help hold other proteins together

Question 2

what are gene regulatory proteins

Answer 2

transcription factors that play a key role in defining the level of transcription

Question 3

what are clathrin coat proteins important for

Answer 3

forming vesicles as they bud off from membrane - identify the origin membranes of the vesicle so it can be targeted properly

Question 4

what are the 3 main error-correcting mechanisms to achieve high fidelity of DNA replication

Answer 4

5’-3’ polymerization, 3’-5’ exonucleolytic proofreading, strand-directed mismatch repair

Question 5

what prevents extension by the polymerase

Answer 5

lack of base-pairing by a mismatched nucleotide

Question 6

why can DNA polymerase only extend a base-paired primer

Answer 6

there is a dependence of perfect base-pairing of -1 base (last nucleotide in chain)

Question 7

why does DNA replication need a RNA primer

Answer 7

it provides a 3’ paired nucleotide bc DNA polymerases can only add onto existing strands of DNA

Question 8

what does a RNA primer provide

Answer 8

a 3’ paired nucleotide for the polymerase to recognize in order to start a chain

Question 9

what happens to DNA without perfect base pairing

Answer 9

DNA will not add another nucleotide

Question 10

what happens to exonuclease when mismatch occurs

Answer 10

exonuclease removes any nucleotides until there is a clean basepair at the 3’ end, then DNA polymerase can add a new nucleotide

Question 11

what is a newly synthesized, mismatched pair recognized by

Answer 11

the presence of an unsealed nick

Question 12

how can you distinguish between a newly synthesized strand and the original strand

Answer 12

the original is unbroken because it has Okazaki fragments sealed with DNA ligase and the newly synthesized is broken

Question 13

how is a mis-incorporated nucleotide fixed (aka mutation)

Answer 13

second cut in new strand is made, then the stretch of DNA is removed, then gap is filled by DNA polymerase and sealed with DNA ligase

Question 14

what are the three ways that somatic DNA can be damaged

Answer 14

• oxidation of nucleotides
• hydrolysis cleavage of base away from sugar/groups away from base
• methylation of nucleotides that can typically happen bc of chemicals to damage DNA

Question 15

what are the common forms of DNA damage and how are they generated

Answer 15

depurination and deamination, by hydrolysis reactions

Question 16

what is depurination

Answer 16

removal of base from sugar - removes purines (G, A)

Question 17

what is deamination

Answer 17

removal of amine groups from base to change identity of base

Question 18

how does DNA glycosylation recognize individual damaged bases and remove them

Answer 18

base flipping - can be flipped out from double helix because they don’t pair properly

Question 19

what is base excision repair

Answer 19

fixes excised bases - results in the surgical removal of the damaged base followed by DNA synthesis and ligation

Question 20

what is a translesion polymerase

Answer 20

can replicate damaged DNA

Question 21

why do translesion polymerase added nucleotides not follow Watson-Crick base pairing

Answer 21

allows it to jump over a few nucleotides and save the rest of the genome

Question 22

what are the two ways double-stranded breaks can be repaired

Answer 22

non-homologous end joining and homologous recombination

Question 23

what does non-homologous end joining do

Answer 23

seals ends back together

ends of DNA will be trimmed back to be blunt ends and will be ligated together with DNA ligase

Question 24

what does homologous recombination do

Answer 24

chews it back to get gap; ends of broken chromosome will invade and make pairing with sister chromatid. will use sequence of it as template for reconstructing sequence that has been lost, then can be resealed back up together