DNA

Question 1

Avery, McCloud, and McCarty

Answer 1

Described DNA as the genetic material.

DNA isolated from virulent bacteria transformed live nonvirulent bacteria > mouse death

Question 2

Chargaff’s Rules

Answer 2

Purines=Pyrimidines

%G=%C & %A=%T

Purine/Pyrimidine ratio is different in DNA from different organisms

Question 3

What does DNA melting mean?

Answer 3

Temperature that separates 50% of the DNA double strand.

Question 4

What factors effect melting temperature?

Answer 4

1. Salt concentration (higher concentration increases Tm)
2. Extremes of pH (effect ionization states of groups on bases)
3. Chain length
4. Number of GC residues

Question 5

Origin binding proteins

Answer 5

Recognize replication origin, bind and open DNA forming a small bubble

Question 6

What is the cofactor for ligase in eukaryotes/prokaryotes?

Answer 6

ATP/NAD+

Question 7

What is PCNA?

Answer 7

Sliding clamp for eukaryotic DNA Pol

Question 8

How does DNA polymerase discriminate between correct and incorrect nucleotides?

Answer 8

Hydrogen bonds

Common geometry

Question 9

What polymerase has 5’-3’ exonuclease activity?

Answer 9

DNA Pol 1

Question 10

What polymerases has a sliding clamp?

Answer 10

DNA Pol 3

Question 11

What are the ways a nucleotide base can be damaged?

Answer 11

Depurination; alkylation; deamination; pyrimidine dimers; oxidative damage

Question 12

What are the types of DNA repair?

Answer 12

Direct reversal; excision; tolerance/bypass; strand break repair

Question 13

DNA ligase repair

Answer 13

Reversal of a specific type of single stranded DNA break

Question 14

Photolyase

Answer 14

Reversal of UV caused base damage

Question 15

MGMT

Answer 15

Reversal of base alkylation

Question 16

BER

Answer 16

Repairs base damages that do not distort the DNA using base specific glycosylases

Question 17

NER

Answer 17

Repairs base damages that distort the DNA

Question 18

MMR

Answer 18

Removes misincorporated nucleotides during DNA replication

Question 19

What are the steps common to all 3 excision repair mechanisms?

Answer 19

1. Recognition
2. Endonuclease cutting of phosphodiester backbone
3. Nuclease removal of DNA fragment
4. DNA polymerase mediated synthesis
5. DNA ligase

Question 20

Regarding BER, once a glycosylase recognizes a specific modified base, what happens?

Answer 20

Leaves an AP site