Biotech: Nucleic Acids - DNA Synthesis (slides 22-30)

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1

this enzyme is responsible for forming the phosphodiester bonds by catalyzing the attack for the 3'-OH group onto the 5'-PPP group of the incoming nucleotides

DNA polymerase

2

what is the nucleophile in DNA synthesis?

3'-OH

3

what is the leaving group in DNA synthesis?

pyrophosphate

4

the incoming ___ in DNA synthesis is dictated based upon what is in the template strand

nucleophile

5

2 requirements of DNA polymerase:

1) template
2) primer

6

a primer is a piece of nucleic acid which has a free ____ group

3'-OH

7

a ___ is a piece of nucleic acid which has a free 3'-OH group

primer

8

in DNA replication, the primer is ___

RNA

9

DNA ___ the template from 3' to 5' and ____ from 5' to 3'

reads, synthesizes

10

what requires both a template and a primer?

DNA polymerase

11

the level of accuracy of DNA replication is accomplished by 3 mechanisms:
1. the correct geometry and hydrogen bonding of the ___ ___
2. ___ of the DNA Pol
3. DNA ____ enzymes

base pairs, proofreading, repair

12

the ability for some DNA Pol to go back and correct their mistakes

proofreading

13

proofreading is accomplished by a special activity of DNA Pol termed 3' to 5' _____

exonuclease

14

_____ enzymes catalyze the removal of nucleotides from DNA

exonuclease

15

exonuclease cleaves a phosphodiester bond from this end first

3' (since DNA is synthesized from 5' to 3', it makes sense that the exonuclease would start deleting from 3' to 5')

16

proteins that unwind DS (double stranded) DNA ahead of the replication fork

helicase(s)

17

helicases require ___ because they need energy to break bonds (since they unwind DNA)

ATP

18

responsible for supercoiling of DNA, they release the strain caused by DNA unwinding

topoisomerase(s)

19

stabilize unwound DNA

SS (single strand) DNA binding protein

20

synthesizes the RNA primers for DNA replication

primase(s)

21

primases are particularly active in ___ strand synthesis

lagging (b/c each of the Okazaki fragments require their own primer)

22

used in lagging strand synthesis to link 2 Okazaki fragments together

DNA ligases

23

do DNA ligases require ATP?

yes

24

these are used to keep DNA Pol attached to DNA to make Pol processive

sliding clamps

25

these are used to place sliding clamps onto DNA

clamp loaders

26

DNA Pol is ____, meaning that it can continually synthesize DNA without falling off and having to start over

processive

27

slide 27 shows the process of leading strand synthesis with all the enzymes

...

28

in lagging strand DNA synthesis, DNA is synthesized until it hits the previous Okazaki fragment where ___ ___ falls off, goes backwards and binds to the new ___ and begins synthesis again from 5' to 3' until it hits the previous Okazaki fragment

DNA polymerase, primer

29

the breaks between the Okazaki fragments are called ___

nicks

30

this enzyme binds to the nick in the lagging strand and cleaves the RNA primer and adds DNA to fill in the gap (but they are still not linked)

DNA Polymerase I

31

DNA Polymerase I has 5' to 3' ___ activity specific to RNA

exonuclease

32

once DNA Polymerase I removes the RNA primer and replaces it with DNA, ___ ___ can form a phosphodiester bond between the 2 strands of DNA making a continuous strand of DNA in the lagging strand

DNA ligase

33

DNA repair is only possible because of the two ___ strands of DNA which makes it obvious of what the nucleotide should be

complementary

34

T/F: SS DNA has repair mechanisms

false (it only has one strand so there is no complementary strand to read from)

35

once a ___ passes into the next generation, it can never be repaired

mutation

36

can a mutation that passes into the next generation be repaired?

no

37

4 types of repair pathways:

1) mismatch repair
2) base excision repair
3) nucleotide excision repair
4) direct repair

38

this repair pathway is used to fix an error from the DNA Pol when the wrong base goes into DNA and proofreading doesn't catch it

mismatch repair

39

this repair pathway is used to remove faulty bases such as those produced by deamination

base excision repair

40

this repair pathway is used to remove damage due to large distortions in DNA

nucleotide excision repair

41

this repair pathway is used to remove damage to DNA without cleaving the nucleotide involved

direct repair