DNA replication

Question 1

How is the structure of the double helix described?

Answer 1

right handed helix

Question 2

What is a nucleoside vs a nucleotide

Answer 2

nucleoside = base and the sugar
nucleotide = base, sugar and a phosphate

Question 3

Name the 5 nucleotides (UCATG)

Answer 3

adenosine
cytidine
guanosine
thymidine
uridine

Question 4

Name for base + ribose sugar

Answer 4

ribonucleic acid

Question 5

what is an NTP

Answer 5

nucleotide triphosphate

Question 6

what is a dNTP

Answer 6

deoxynucleotide triphosphate

Question 7

what are the purines?

Answer 7

adenine and guanine
larger structure with two rings

Question 8

what are the pyrimidines?

Answer 8

cytosine and thymine and uracil

Question 9

how does the numbering of carbons work for the sugars

Answer 9

1 starts at the carbon attached to the base

Question 10

how are DNA/RNA molecules polar?

Answer 10

5’ end is negative due to PO4^3-
3’ end has hydroxyl group where the O is delta negative and H is delta plus

Question 11

how does polymerisation work

Answer 11

new base added to 3’ end of chain via phosphodiester bond

Question 12

how are the bases arranged in the double helix

Answer 12

stacked up and pointing the same way

Question 13

how is DNA replication initiated?

Answer 13

RNA primers (later replaced with DNA)
DNA cannot be synthesised de novo

Question 14

DNA primase role

Answer 14

assembles as catalyses the synthesis of short RNA primers from NTPs on the DNA template

Question 15

structure of incoming dNTP being added to newly synthesised strand

Answer 15

deoxyribonucleoside triphosphate
PPPi on 5’ carbon

Question 16

how is DNA replication discontinuous

Answer 16

leading and lagging strands
lagging strand is synthesised discontinuously forming okazaki fragments that each start with an RNA primer

Question 17

what are single stranded binding proteins

Answer 17

proteins that prevent ssDNA from base pairing with the other template strand

Question 18

what is the sliding clamp

Answer 18

complex of proteins that keeps DNA polymerase from falling off the strand
it is assembled at the replication fork by a clamp-loader complex
it ensures efficient replication

Question 19

which enzyme joins up discontinuities where RNA primers were

Answer 19

DNA ligase

Question 20

why does DNA supercoiling occur

Answer 20

DNA is under tension as the replication form forms so it coils up in front of the fork
liable to break

Question 21

how is DNA tension solved

Answer 21

supercoiling relieves some tension
topoisomerases relieve the tension by cutting the DNA and allowing it to unwind
allows DNA to rotate freely

Question 22

2 types of topoisomerases

Answer 22

one makes a single strand cut
other makes a double strand cut

Question 23

risk of double stranded cuts

Answer 23

chromosomal translocation

Question 24

proof reading mechanism

Answer 24

proof reading function in the DNA polymerase
mismatch of nucleotides causes a discontinuity
in the active site where there is a base mismatch, the whole strand gets pushed from the polymerase domain into the proof reading domain where there is an exonuclease active site that snips off the last added nucleotide
strand flipped back to polymerase domain