3. Drug targets, DNA repair & disorders

Question 1

Polymerase I

Answer 1

used in removal of RNA primer (5’ -3’ exonuclease activity)
filling the gap by DNA repair (5’-3’ polymerase activity)
proof reading activity (3’-5’ exonuclease activity)

Question 2

Polymerase II

Answer 2

usually in DNA repair

Question 3

Polymerase III

Answer 3

Required for DNA replication (replicates bacterial DNA)

Question 4

Type I topoisomerase (both form covalent intermediates with DNA)

Answer 4

Make nicks in one DNA strands

can relieve supercoiling

Question 5

Type II topoisomerase (both form covalent intermediates with DNA)

Answer 5

make nicks in both DNA strands

can relieve supercoiling and untangle linked DNA helices

Question 6

Examples of Topoisimerase inhibitors

Answer 6

Camptothecin - topo I inhibitor

Doxorubicin - topo II inhibitor

Question 7

ciprofloxacin

Answer 7

bacterial-specific topo DNA gyrase inhibitor

Question 8

mechanism of antimicrobial action

Answer 8

interfere with function of nucleic acid
most often used against viruses
effective against rapidly dividing cancer cells
distort shapes of nucleic acid and replication, transcription or translation

Question 9

Telomere

Answer 9

DNA/protein structure that caps the ends of chromosomes

Question 10

Telomerase

Answer 10

The enzyme that replicates telomere DNA (reverse transcriptase activity)

Question 11

what damage does alkylation cause

Answer 11

adds alkyl group to the H-bond of G or T, resulting in G-T mispairing

Question 12

what damage does UV radiation cause

Answer 12

UV rays result in formation of pyrimidine dimers (CPDs)

Question 13

what damage do Gamma and x-rays cause

Answer 13

form highly reactive free radicals that attack DNA - alter bases, break strands

Question 14

Modes of DNA repair mechanism

Answer 14

1. direct reversal - photolyase

2. Excision repair (damged DNA is removed and replaced) - base excision repair(BER) and nucleotide excision repair (NER)

Question 15

what enzyme is used in a base excision repair

Answer 15

DNA glycosylase (easy repair)

Question 16

example of a DNA repair enzyme in base excision repair

Answer 16

DNA polymerase I

Question 17

Steps in base excision

Answer 17

DNA pol I fills in missing nucleotide
Base is removed, remains apurinic or apyrimidic
AP endonuclease cuts
Phosphodiesterase removes the AP sugar phos
Pol I performs repair synthesis

Question 18

Different step in nucleotide excision

Answer 18

damaged DNA is removed as an oligonucleotide of 12-13

Question 19

what enzyme fills in missing nucleotides in NER

Answer 19

DNA polymerase I

Question 20

what is the most dangerous form of DNA damage

Answer 20

double stranded DNA break

Question 21

2 ways eukaryotes deal with dsDNA

Answer 21

Homologous recombination

Nonhomologous end-joining (NHEJ)

Question 22

Describe non-homologous end joining

Answer 22

-Requires Ku and DNA-PKcs (binds at DNA ends) - lets ends find regions of microhomology.
-2 DNA-PK complexes phosphorylate each other and activates i) catalytic subunit to dissociate
ii)DNA helices activity of Ku to unwind DNA ends.
-Extra flaps of DNA removed, gaps fills, ends permanently ligated
NB there has to be microbiology for non-homologous to take place

Question 23

Mismatch repair in eukaryotes

Answer 23

recognizes the parental strand by methylated A in GATC sequence, corrects the progeny strand

Question 24

Recombination Repair

Answer 24

repaired by the recombining of a damaged DNA strand with a normal DNA strand to solve the problem

Question 25

Disease caused from failure of Nucleotide Excision Repair

Answer 25

Xeroderma Pigmentosum

Question 26

Disease caused by defect in mismatch repair

Answer 26

Hereditary Nonpolyposis Colorectal Cancer (HNPCC)