Nu Synthesis & Dna Replication

Front 1

only the ______ anomer sugar is observed in DNA

Back 1

β

Front 2

DNA synthesis always proceeds in the _____ to _____ direction

(parent strand is read in ___ to ___ direction)

Back 2

5' to 3'

parent read in 3' to 5' direction

Front 3

what is the correlation between # of DNA base pairs and # of chromosomes?

Back 3

↑ bp ≡ ↑ chromosomes

Front 4

what is the correlation between # of genes and # of chromosomes?

Back 4

no relationship

Front 5

What occurs in reverse transcription?

Back 5

Reverse transcriptase performs a three stage conversion of RNA into DNA (RNA virus)

1. synthesis of DNA complimentary to RNA (cDNA)
2. digestion of RNA
3. synthesis of 2nd strand of DNA

Front 6

exons


introns

Back 6

exons- the expressed sequences of a gene

introns- the intervening (non-expressed) sequences

Front 7

salvage pathway

Back 7

5-phosphoribose-1-PP (PRPP) + base −> nucleotide

Front 8

what drug is a potent inhibitor of Thymidylate synthase?

Back 8

prodrug Fluorouracil -> Fluorodeoxyuridylate

Front 9

Why was Prontosil screening successful?

Back 9

It was screened on mice, not on a plate. It would have failed in plate b/c it needs to be reduced to Sulfanilamide in the liver.

Sulfanilamide mimics the substrate PABA in the folate pathway.

Front 10

What is the function of Mg in DNA synthesis?

How many are needed and why?

Back 10

Mg neutralizes Pi, making a better leaving group and allowing nucleophiles to attack the phosphate of interest

Need 2 Mg++:

1. coordinates 3' -OH; increases acidity of proton and allows formation of nucleophillic alkoxide

2. coordinates dNTP phosphates neutralizing charge and providing scaffold for replacement reaction

Front 11

Which Watson-Crick base pairing is stronger and why?

Back 11

G-C bonds are stronger because they have 3 hydrogen bonds vs. A-T have 2

Front 12

exonuclease

Back 12

cuts a nucleotide off the end of DNA strand

Front 13

endonuclease

Back 13

cuts into the middle of a DNA strand to remove a nucleotide

Front 14

Okazaki fragments

Back 14

newly synthesized DNA segments on the lagging strand

- small fragments are part of the stepwise replication of the lagging strand. Followed by pol I removing the primer then ligase joining the strands together

Front 15

What is the mechanism of Topoisomerase I?

Does it use ATP?

Back 15

Topoisomerase I relaxes the DNA by using an active site Tyrosine to cause a nick in DNA, then holds close to be put back together after relaxing

- does not need ATP

Front 16

What is the mechanism of Topoisomerase II?

Does it use ATP?

Back 16

Topoisomerase II breaks both strands of DNA so another strand can pass through, then the strands are put back together

- needs ATP

- would like to have this for untangling a fine metal chain; could just pop a strand right out of a knot

Front 17

What is the replication rate of DNA polymerase III?

Back 17

500 nucleotides per second ( x2 strands → 1000/sec)

Front 18

Helicase:

What does it do?
How does it do it?
Does it use ATP?

Back 18

Helicase splits and opens a DNA strand for replication. AND it recruits the other enzymes needed for replication.

It spins and uses a ratchet mechanism (grab, pull, release) to slide along one of the strands. Conformational change of the 'ratchet' occurs with ATP binding and hydrolysis.

Yes, it uses ATP

Front 19

DnaB

Back 19

helicase

- the 'ratchet' that separates strands of DNA for replication

Front 20

What is the purpose of the RNA primer in DNA synthesis?

Is it accurate? Why/why not?

Back 20

DNA polymerase requires the primer to start

It is not very accurate. It does not need to be because it is temporary.

Front 21

What is the structure and mechanism of the 'sliding clamp' on DNA polymerase III

Back 21

1. Opened clamp attaches to lagging ssDNA
2. Lots of α-helices on inside project pos. charge (i.e. Arg) to lightly bind enough to stick but allow sliding

Front 22

What is the inhibitor of de novo Purine synthesis?

Back 22

allosteric regulation of Aspartate Transcarbamoylase by CTP

Front 23

What are the inhibitors of Pyrimidane Synthesis?

Back 23

1. IMP, AMP, & GMP inhibit formation of Phosphoribosylamine from Ribose 5-phosphate

2. AMP inhibits formation of Adenylosuccinate (AMP precursor) from IMP

3. GMP inhibits formation of Xanthylate (GMP precursor) from IMP

Front 24

DNA polymerase I

Back 24

erases primer and fills in gaps on lagging strand

Front 25

DNA polymerase II

Back 25

DNA repair

Front 26

primase

Back 26

synthesizes the RNA primer at the beginning of DNA replication

Front 27

DNA Polymerase III

Back 27

the workhorse of DNA replication

- quickly synthesizes the leading strand in one sequence
- synthesizes Okazaki fragments of the lagging strand

- many DNA pol III's include a proofreading mechanism which decreases errors by 100 fold

Front 28

Topoisomerase IV

Back 28

separates genomic DNA molecules after replication

Front 29

What drug is an inhibitor of Topoisomerase II

Back 29

Cipro

Front 30

Transition

Back 30

purine to purine or pyrimidine to pyrimidine mutation

Front 31

Transversion

Back 31

purine to pyrimidine or pyrimidine to purine mutation

Front 32

What does the 'finger domain' of DNA pol III do?

Back 32

binding of correct nuceotide triggers a conformation change that aligns the substrates and increases probability of reaction

incorporation of incorrect base leads to conformational change and base removal by exonuclease activity (hydrolysis of phosphodiester bond)

Front 33

In Watson-Crick base pairing, H-bonding is important for ____________, but less important for ____________

Back 33

H-bonding is important for duplex stability

polymerase just looks at shape, not at h-bonds

Front 34

How do bacterial and eukaryotic replication differ regarding concurrent replications?

Back 34

bacteria- one replication bubble

eukaryotes- many replication bubbles

Front 35

How does DNA replication know where to start?

Back 35

origins have a unique sequence structure "oriC" (a tandem array of 13-mer sequence) where DnaA binds then recruits the other enzymes

Front 36

How are the ends of DNA protected from degredation?

Back 36

telomerase adds short, repeat telomere sequences to the ends of chromosomes