lecture 11

Question 1

having more than one replication origin can

Answer 1

speed up reactions

Question 2

conservative model

Answer 2

completely new strand
parental strand remains the same

Question 3

how many replication forks at each origin?

Answer 3

two replication forks are formed at each replication origin

Question 4

How does the replication fork move?

Answer 4

DNA replication is bidirectional (each fork moves in opposite directions)

Dynamic movement— changes as replication occurs

Question 5

Raw materials needed for DNA replication (5)

Answer 5

-DNA template

-deoxyribonucleoside triphosphates (dNTPs)

-a protein complex involving the DNA polymerase enzyme

-DNA/RNA primer

-Mg^2+ ions (cofactor)

Question 6

polymerization starts from the —- end

Answer 6

5’ to 3’ end

(the complementary strand– NOT the template strand)

Question 7

DNA polymerase (enzyme) function

Answer 7

proofreading; checks for mistakes in nucleotide sequence during replication
–> cuts them and correct base pair is added

catalyzes the addition of nucleotide 3’ end of a growing nucleic acid

corrects its own mistakes

Question 8

what does DNA polymerase require in order to function

Answer 8

requires an existing 3’ end to function (can’t begin a new strand otherwise)

Question 9

exonuclease function

Answer 9

degrade nucleic acids from the end

Question 10

endonuclease function

Answer 10

cleave nucleic acids within a sequence
–> works like a backspace on a keyboard

Question 11

DNA polymerase corrects errors using a —- exonuclease (during proofreading)

Answer 11

3’ to 5’

Question 12

4 contributing factors to the accuracy of DNA polymerase

Answer 12

1. H bonding of complementary base pairs
2. DNA polymerase monitors the base-pairing before catalyzing the addition of the nucleotide
3. cells maintain roughly equal concentration of dNTPs
4. proofreading

Question 13

DNA polymerization sites

Answer 13

separate site for DNA polymerization (P) and error correcting (E)

Question 14

how does the E site work>

Answer 14

the incorrect nucleotide is pushed to site E when there is an error

Question 15

can DNA synthesize a new strand without a primer?

Answer 15

NO!!!

Question 16

primase proofreading ability?

Answer 16

Primase does not have a proofreading ability— but doesn’t matter bc primer will be removed anyways

Question 16

primase definition

Answer 16

an RNA polymerase that creates RNA primers using a DNA template

Question 17

how does primase work?
-how many does leading/lagging need?

Answer 17

adds nucleotides 5’ to 3’ (the strand being synthesized).
leading strand only needs one primer.
lagging strand needs many primers.

Question 18

Replication machine requires

Answer 18

coordination of several proteins

Question 18

DNA ligase

Answer 18

links the primers together!!!

-seals the gap between the two okazaki fragments during replication
-requires ATP
-happens during DNA repair phase

Question 19

3 proteins that the replication machine requires coordination of (and their function)

Answer 19

1. DNA helicase= pries the double stranded helix apart, requires ATP hydrolysis
2. Single-stranded DNA binding proteins= bind to a single stranded DNA, prevents them from reforming base pairs
3. DNA topoisomerases=relieves tension that builds up in the replicationm fork, creates nicks in the DNA

Question 20

sliding clamp keeps

Answer 20

DNA attached to DNA

Question 21

clamp loader locks

Answer 21

new clamps onto the DNA

Question 22

2 problems with primers

Answer 22

1. RNA primers are replaced w DNA except for the primers used at the very 5’ end of the newly synthesized strands
   –> not replaced bc DNA polymerase needs an nuc that already exists to add incoming dNTPs
2. the single stranded part can’t be filled in! vulnerable to degredation. DNA may get shorter and shorter each time

Question 23

What is the solution to the 2 primer problems?

Answer 23

telomerase!!!
telomeres attract enzymes (telomerase) which extend the length of the telomeres using an anti-internal RNA template

Question 24

Models of replication

Answer 24

Semiconservative
Dispersive
Conservative

Question 24

Semiconservative model

Answer 24

each daughter molecule has one parental

Question 25

Dispersive model

Answer 25

daughter molecules have patches of old and new DNA

Question 26

Conservative model

Answer 26

one completely new strand. parental strand remains the same/intact

Question 27

replication origins are rich in–?
opened up by –?

Answer 27

rich in A-Ts
opened up by initiator proteins (including helicase, SSB –single stranded binding proteins and topoisomerases)