Genomic stability and tumorigenesis (L12)

Question 1

What does Topoisomerase do and what are the differences b/w Topoisomerase I and II?

Answer 1

Topoisomerase prevents overwinding in DNA.

I cleaves one strand via a tyrosine residue w/o using ATP

II cleaves both strands using ATP and induces negative supercoiling.

Question 2

Name an inhibitor of each Topoisomerase I and II.

What are they used for?

Answer 2

Camptothecin inhibits Top. I by preventing re-ligation of the nicked DNA strand;

Etoposide inhibits Top. II by preventing religation of DNA double strand.

They are used for lung, ovarian, testicular/breast, and prostate cancer.

Question 3

Why does ciprofloxacin, used to treat infections, not affect the human cells?

Answer 3

Ciprofloxacin inhibits DNA gyrase which is a topoisomerase found ONLY in prokaryotes.

Question 4

Name 4 topoisomerase II inhibitors used for bacterial infections (like urinary and respiratory).

Answer 4

1. Novobiocin (blocks ATP binding)
2. Nalidixic acid (DNA gyrase)
3. Ciprofloxacin (DNA gyrase)
4. Norfloxacin (DNA gyrase)

Question 5

Describe the process of priming for DNAP in E. coli.

Answer 5

Primase synthesizes an RNA primer that anneals to a single strand of DNA, DNAP III will come and new DNA for the rest of that strand.

DNAP I will alter remove the RNAP and DNA ligase will fill in that last little gap.

Question 6

Primase is a ___ Dependent ___ polymerase.

DNAP III is a ___ dependent ___ polymerase.

Telomerase is a ___ dependent ___ polymerase.

Answer 6

DNA; RNA

DNA; DNA

RNA; DNA

Question 7

What does DNA ligase do in DNA replication?

Answer 7

Joins okazaki fragments together.

Question 8

What AA is in the active site for DNA ligase?

Answer 8

Lysine

Question 9

What are the functions of the 3 main bacterial polymerases and in which direction do they have EXOnuclease activity?

Answer 9

DNAP I: fills gap after RNA primer removal, removes RNA primer w/ RNaseH, DNA repair; exonuclease 5’>3’ AND 3’>5’

DNAP II: DNA repair; exonuclease 3’>5’

DNAP III: Replication (synthesis of DNA); exonuclease 3’>5’

Question 10

In eukaryotes, how does the origin of replication differ?

Which is the main DNAP for eukaryotes and what exonuclease activity does it have?

Answer 10

there are several point of origins, each of which have bi-directional synthesis (which is semi-conservative).

DNAP delta has 3’>5’ exonuclease activity

Question 11

What are the 4 phases of the cell cycle and what happens in each one?

Answer 11

G1: growth and metabolism

S: DNA replication

G2: Preparation for cell division

M: Mitosis

(G₀):Non dividing stage

Question 12

What do telomerases do?

Answer 12

They extend the 3’ overhang using a built in RNA sequence as a template to synthesize new DNA nucleotides 5’>3’, then DNAP can come and fill in the important overhang sequence

Question 13

How does doxorubicin work?

Answer 13

It is an anticancer drug that intercalates b/w stacked bp’s thus inhibiting DNA replication and transcription

Question 14

How does 5-Fluorouracil work?

Answer 14

It is an analog of U or T, and is converted in the body to 5-FdUMP, which binds tightly to thymidylate synthase (the enzyme that synthesizes dUMP>dTMP). Thus Thymine nu’s can’t be generated for DNA synthesis.

Question 15

How does acycloguanosine work?

Answer 15

It is an anti-viral drug that imitates guanosine and is incorporated into DNA which halts replication b/c it can’t be paired with anything.

Question 16

Describe the effect of mutagenic tautomers.

Answer 16

The imino tautomer of Adenine can pair w/ Cytosine, eventally leading to a transition from A-T to C-G.

NOTE: Tautomer forms of bases are rare but still occasionally happen (99:1 equilibrium ratio of normal to tautomeric form).

Question 17

What happens when you treat DNA w/ nitrous acid?

Answer 17

It converts Adenine to Hypoxanthine which pairs to cytosine, inducing a transition from A-T to G-C

Question 18

Nitrosamine, a dietary mutagen metabolites methylate guanine (which will pair to Thymine).

Name 4 places it is found.

Answer 18

1. Latex products (eg balloons)
2. nitrite in food products after entering stomach
3. fryed foods (enhanced from high temp)
4. pickling-salt (a preservative in Japan)

Question 19

What is ethidium bromide and how is it a mutagen?

Answer 19

It is an acridine dye and induces FRAMESHIFT mutations by intercalating into the DNA, leading to the incoroporation of an additional base.

Question 20

Benzo[a]pyrene is not carcinogenic until____.

Where is a common place it is found?

Answer 20

Until it is oxidized w/in cells. It is found w/ the burning of tobacco which will coat the airways and lungs.

Question 21

What is the difference in effect b/w UV light and ionizing radiation?

Answer 21

UV causes pyrimidine dimers, ionizing radiation causes double strand breaks.

Question 22

How do melanomas appear?

Answer 22

They are dark brown growths that result from nonrepair of pyrimidine dimers caused by UV light.

Question 23

What’s the difference b/w base and nucleotide excision repair?

Answer 23

Base excision repair replaced one BASE by using glycosylase to cleave the glycosidic bond.

Nucleotide excision repair removes several NUCLEOTIDES at once and uses DNAP to fill in the gap and ligase to bind it.

Question 24

Describe Burkitt’s lymphoma.

Answer 24

MYC, a proto-oncogene, is translocated from chromosome 8 to the immunoglobin heavy chain gene locus on chromosome 14. Thus, the MYC gene will be heavily transcribed in B cells resulting in enhanced cell proliferation, commonly leading to many neuroblastomas.

Question 25

Xeroderma pigmentosum is a result of a defect in ____

Answer 25

the nucleotide excision repair mechanism, so thymine dimers are not repaired efficiently.

Question 26

A defect in mismatch repair proteins can lead to

Answer 26

Hereditary Nonpolyposis Colorectal Cancer