DNA & Replication

Question 1

Nucleoside

Answer 1

5C sugar bonded to a nitrogenous base

Question 2

Nucleotide

Answer 2

Nucleoside + 1 to 3 phosphates attached

Question 3

Which histone protein stabilizes the nucleosome?

Answer 3

H1

Question 4

DNA coiled around histone protein

Answer 4

Nucleosome

Question 5

DNA and its associated histones

Answer 5

Chromatin

Question 6

Dense, transcriptionally silent DNA

Answer 6

Heterochromatin

Question 7

Less dense, transcriptionally active DNA

Answer 7

Euchromatin

Question 8

Telomeres contain a high content of what two nucleotides? Why?

Answer 8

GC, to prevent DNA from unraveling

Question 9

How many origins of replication in Eukaryotes vs. Prokaryotes?

Answer 9

Euk - multiple per chromosome

Pro - one per chromosome

Question 10

Enzyme responsible for unwinding DNA during replication

Answer 10

Helicase

Question 11

Stabilize unwound template strands to prevent reannealing or degradation

Answer 11

SSB’s (single stranded binding proteins)

Question 12

Enzyme responsible for the synthesis of short RNA primer in 5’ –> 3’ direction to start replication on each strand

Answer 12

Primase

Question 13

Enzyme responsible for actual synthesis of new DNA strands

Answer 13

DNA Polymerase

Question 14

What DNA pol is used in eukaryotes vs. prokaryotes?

Answer 14

Euk - DNA pol alpha, sigma, and epsilon

Pro- DNA pol III

Question 15

What is the enzyme responsible for removing primers in prokaryotes, and what type of activity does it exhibit?

Answer 15

DNA polymerase I (5’ to 3’ exonuclease)

Question 16

What is the enzyme responsible for removing RNA primers in eukaryotes, and what type of activity does it exhibit?

Answer 16

RNase H (5’ to 3’ exonuclease)

Question 17

What polymerases fill in the gaps left behind when RNA primers are removed in eukaryotes and prokaryotes?

Answer 17

Euk - DNA pol sigma

Pro - DNA pol I

Question 18

What enzyme is responsible for joining of Okazaki fragments?

Answer 18

DNA ligase

Question 19

What enzyme is responsible for removal of positive supercoils ahead of advancing replication forks?

Answer 19

DNA topoisomerases (DNA gyrase)

Question 20

Enzyme responsible for synthesis of telomeres?

Answer 20

Telomerase

Question 21

Proto-oncogenes

Answer 21

name given to oncogenes before mutation

Question 22

What kind of proteins do oncogenes primarily encode?

Answer 22

Cell-cycle related proteins

Question 23

Name of genes that code for proteins that reduce cell cycling or promote DNA repair

Answer 23

Tumor suppressor genes

Question 24

T/F: tumor suppressor genes can also lead to cancer

Answer 24

True

Question 25

What enzyme is responsible for proofreading?

Answer 25

DNA polymerase

Question 26

During proofreading activity, how does DNA polymerase discriminate between the parent and daughter strands?

Answer 26

By level of methylation: parent strand has existed for longer time period and thus is more heavily methylated

Question 27

DNA composed of nucleotides from two different sources

Answer 27

Recombinant DNA

Question 28

What is the name of the enzyme machinery (and the genes that encode these enzymes) in the G2 phase of cell cycle which detects and removes errors introduced in replication that were missed during S phase of cell cycle?

Answer 28

Mismatch repair genes = MSH2 and MLH1 in eukaryotes and MutS and MutL in prokaryotes

Question 29

What kind of damage does UV light cause in DNA?

Answer 29

induces formation of dimers between Thymine residues which interferes with DNA replication and normal gene expression and disorts the DNA double helix

Question 30

How is DNA damage induced by UV light repaired?

Answer 30

Nucleotide excision repair (NER) mechanism which uses an excision endonuclease along with DNA polymerase and DNA ligase to cut-and-patch Thymine dimers

Question 31

Thermal energy absorption leads to what kind of DNA damage?

Answer 31

Cytosine deamination and conversion to Uracil

Question 32

What kind of damage does base-excision repair fix and how?

Answer 32

Fixes nondeforming DNA lesions (such as cytosine deamination) by removing affected base & leaving behind an AP site which is recognized by an AP endonuclease that functions to remove and replace affected base