Chapter 28

Question 1

DNA Helicases

Answer 1

Enzymes responsible for forcibly separating the DNA strands and unwinding the parental duplex

Question 2

Single Stranded DNA Binding Proteins (SSB)

Answer 2

Prevents the strands from reassociating and protect the strands from enzymatic cleavage

Question 3

DNA Topoisomerases

Answer 3

Enzymes that are responsible for removing positive and negative supercoils that form as a result of overwinding by transiently cleaving one or both strands of DNA

Question 4

Ciprofloxacin

Answer 4

MOA: Inhibits bacterial DNA gyrase (type II DNA topoisomerase)

Results: Inhibition of bacterial DNA synthesis, eukaryotes do not have DNA gyrase therefore does not interfere with the patient’s own cells

Question 5

RNA Primer

Answer 5

DNA polymerase cannot initiate synthesis without it, the free 3’-OH primer acts as the 1st acceptor of a dNTP from the polymerase. Only one needed for the leading strand and multiple needed for the lagging (Okazaki fragments)

Question 6

Types of Polymerase (E. coli)

Answer 6

Pol I, II, and V function primarily in DNA repair. DNA Pol III is involved in elongation

Question 7

DNA Gyrase (E. coli)

Answer 7

Unwinds DNA

Question 8

DnaA Prokaryotes

Answer 8

Initiation factor; origin-binding protein

Question 9

DnaB

Answer 9

5’ to 3’ helicase

Question 10

DnaC

Answer 10

DnaB chaperone; loading DnaB on DNA

Question 11

Primase (DnaG) Prokaryotes

Answer 11

Synthesis of RNA primer

Question 12

DNA ligase

Answer 12

Covalently links Okazaki fragments

Question 13

Tus

Answer 13

Termination

Question 14

Polymerase alpha (Eukaryotes)

Answer 14

Contains primase, initiates DNA synthesis

Question 15

Polymerase beta (Eukaryotes)

Answer 15

Repair

Question 16

Polymerase gamma (Eukaryotes)

Answer 16

Replicates mitochondrial DNA

Question 17

Polymerase delta (Eukaryotes)

Answer 17

Elongates Okazaki fragments of the lagging strand

Question 18

Polymerase epsilon (Eukaryotes)

Answer 18

Elongates the leading strand

Question 19

RNA primers are removed by what enzymes?

Answer 19

Rnase H and flap endonuclease-1 (FEN1)

Question 20

Telomeres

Answer 20

Complex of noncoding DNA plus proteins located at the end of linear eukaryotic chromosomes that form protective caps

Question 21

Telomerase

Answer 21

Maintains telomeric length in germ, stem, and cancer cells

Question 22

How does telomerase work?

Answer 22

Elongates the already longer 3’ end of the DNA with a “AAGGTT” sequence, then adds the reverse compliment RNA primer, then DNA pol alpha goes to work to fill in the gaps of the 5’ end

Question 23

North to South Cleavage

Answer 23

Splice recombinant heteroduplex

Question 24

East to West

Answer 24

Patch Recombinant heteroduplex

Question 25

RecBCD enzyme complex

Answer 25

Intiaties recombination

Question 26

RecA protein

Answer 26

Binds ssDNA

Question 27

RuvA, RuvB, RuvC proteins

Answer 27

Drive branch migration and process Holliday junction

Question 28

BRCA1 protein

Answer 28

Functions in the regulation of the cell cycle response to DNA damage

Question 29

BRCA2 protein

Answer 29

Participates in pathway for DNA repair by HR

Question 30

Transposable Elements

Answer 30

A repetitive DNA sequence that can enzymatically change its position within in the genome

Question 31

Class I TEs

Answer 31

Retrotransposons (copy and paste)

Question 32

Class II TEs

Answer 32

DNA Transposons (cut and paste)

Question 33

Melanomas

Answer 33

Develop from exposure from the sun, causes pyrimidine dimers to form in the DNA (Thymine Dimers). Mutations may result from non- repair of dimers.

Question 34

Benzo[a]pyrene

Answer 34

A carcinogen, binds to the P53 gene segment of DNA leading to lung cancer. Upon oxidation, it covalently binds to guanine residues in DNA, interrupting G-C pairs and producing distortions

Question 35

3 Common Steps of DNA Repair

Answer 35

1. Excision
2. Repair
3. Ligation

Question 36

Nucleotide Excision Repair (NER)

Answer 36

Identifies pyrimidine dimer or an adduct, specific endonucleases nick both sides of the damaged strand, and the gap is filled with polymerase and ligated.

Question 37

Base Excision Repair (BER)

Answer 37

Removes abnormal bases by using specific glycosylases that cleave the faulty base from the backbone. AP endonuclease recognizes the site of the missing base and nicking the 5’ side of the backbone. Deoxyribose phosphate lyase finishes the job by removing the nicked backbone, allowing for DNA polymerase and ligase to repair.

Question 38

Mismatch Repair

Answer 38

Used when base pairs are mismatched. Mut proteins are used to identify the parent strand via methylation. The daughter strand is then nicked by an endonuclease, and repaired by DNA polymerase and ligase

Question 39

Homologous Recombination

Answer 39

Used when there is a double stranded break. Holliday junction

Question 40

Non-Homologous Recombination

Answer 40

Ku protein is used to ligate the two broken ends together, loss of DNA can lead to mutations.

Question 41

Transcription-Coupled Repair

Answer 41

This pathway is used when RNA polymerase discovers an error in the DNA. The same repair system as NER is used.

Question 42

Xeroderma pigmentosum

Answer 42

A deficiency in the NER pathway, leading to extreme consequences when an individual is exposed to UV radiation. Cannot be exposed.

Question 43

Cockayne Syndrome

Answer 43

An autosomal recessive disorder that is linked to defects in NER and TCR. Results in the inability to repair mutated DNA which can lead to symptoms like premature aging, impaired development of the nervous system, and sensitivity to UV irradiation.

Question 44

Burkitt’s Lymphoma

Answer 44

A lymphoma cancer that is characterized by the translocation and deregulation of the c-myc on chromosome 8. Ultimately leads to deregulation of cell cycle control. One of the fastest growing malignancies in humans.

Question 45

Origin of Replication Difference in Prokaryotes vs Eukaryotes

Answer 45

Eukaryotes have multiple origins while prokaryotes only have one