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Flashcards in DNA Replication And Repair Deck (39):
1

What does inactivating dam methylase do?

Blocks expression of virulence genes by salmonella and prevents disease development. Can block gut-colonizing bacteria.

2

What is AZT?

Anti-AIDS pyrimidine analog

3

Acyclovir

Purine analog used to treat herpes

4

What is dactinomycin?

Anti-cancer drug that intercalates into minor groove of DNA double helix, interferes with DNA and RNA synthesis

5

Topoisomerase I

-does not require ATP, cuts 1 strand of DNA, removes negative and positive supercoils

6

Topoisomerase II

-ATP dependent, DNA gyrase (bacterial) can introduce - supercoils into relaxed DNA

7

Quinolone Drugs

Novobiocin, nalidixic acid, cipro
-block DNA gyrase activity, halt bacterial DNA synthesis

8

Camptothecin

-anticancer drug that targets topo I

9

Adriamycin and etoposide

Anti cancer drugs that target topo II

10

How many bp in a nucleosome core? How many in spacer?

~140
~20-80

11

Bacterial replication initiation

______induces melting of AT rich origin, ___ dependent

______ (helicase) uses ATP to force strands apart

SSB bind

+ supercoiling ahead of fork due to strand separation

_____ (topo II) removes + supercoils

_____ removes negative supercoils behind

_____ synthesizes primer

-DNA-A induces melting of AT rich origin, ATP dependent
-DNAB (helicase) uses ATP to force strands apart
-SSB bind
-+ supercoiling ahead of fork due to strand separation
-DNA GYRASE (topo II) removes + supercoils
-TOPO I removes negative supercoils behind
-PRIMASE synthesizes primer

12

DNA Polymerase III

-DNA chain elongation in bacteria, leading and lagging strands
-has 3'-->5' exonuclease activity for proofreading

13

DNA Polymerase I

-prokaryotic
-3'-->5' exonuclease activity
-5'-->3' exonuclease activity
-primer removal, gap synthesis
-repair

14

DNA Polymerase II

-prokaryotic
-repair
-3'-->5' exonuclease activity

15

Gemcitabine

-analog of deoxycytidine
-pancreatic cancer treatment

16

DNA Pol Alpha

Eukaryotic
-contains primase activity, synthesizes hybrid RNA/DNA primers
-primer synthesis on leading and lagging strands
-NO exonuclease activity

17

DNA Pol Beta

Eukaryotic
-BER
-no exonuclease activity

18

DNA Pol Gamma

-mitochondrial DNA replication, 3'-->5' exonuclease activity

19

DNA Pol Delta

-eukaryotic
-Associates with PCNA to elongate lagging strand
-displaces 5' ends of primers from Okazaki frags, when are then degraded by FEN1 and other nucleases
-3'-->5' exonuclease activity
-DNA repair (MMR and NER)

20

DNA Pol Epsilon

-Associates with PCNA to elongate leading strand
-DNA repair (MMR and NER)
-3'--->5' exonuclease activity

21

Telomeres and Telomerase

-G rich
-telomerase is ribonucleoprotein complex with reverse transcriptase activity (hTERT)
-synthesizes DNA using RNA subunit as template
-RNA dependent DNA transcriptase
-adds to 3' ends of chromosomes

22

Dyskeratosis congenita

-reduced telomerase activity
-affects precursor cells in highly proliferative tissues: hair, mouth, intestines, skin, alveoli, testes, bone marrow.
-pts generally die of bone marrow failure

23

Hutchinson-Gilford Progeria

-accelerated telomere shortening

24

MMR Pathway

-strand specificity provided by _________
Recognition of mutation
-_______ for mismatches
-_______ for insertions/deletions
_____/______ endonuclease cleaves newly synthesized strand on either side of mismatch
_______ and _____ remove DNA from newly synthesized strand
DNA pol ____/_____ w. _____ fill gap
DNA ligase

-Mutations in _____ or _____ account for 90% of pts with Lynch Syndrome

-strand specificity provided by METHYLATION
Recognition of mutation
-MSH2/6 for mismatches
-MSH2/3 for insertions/deletions
MLH1/PMS2 endonuclease cleaves newly synthesized strand on either side of mismatch
HELICASE and EXONUCLEASE remove DNA from newly synthesized strand
DNA pol DELTA/EPSILON w. PCNA fill gap
DNA ligase

-Mutations in MSH2 or MLH1 account for 90% of pts with Lynch Syndrome

25

BER Pathway

-_______ recognizes damage, cuts N-glycosidic bond
-_______ releases base
-________________ cuts backbone at this position
-_____________________ removes residue
-DNA pol _____ (_) fills gap
-DNA ligase

-fixes cytosine-->uracil, depurination, alkylation, oxidation
-DNA GLYCOSYLASE recognizes damage, cuts N-glycosidic bond
-HELICASE releases base
-AP ENDONUCLEASE cuts backbone at this position
-DEOXYRIBOPHOSPHATE LYASE removes residue
-DNA pol BETA (I) fills gap
-DNA ligase

26

Adenomatous colorectal polyposis (FAP)

-autosomal recessive
-biallelic mutations in DNA glycosylase MYH gane

27

GG-NER

-________ recognized by _________
-previous proteins recruit _________ (____/____ and _____) which make SS incisions 5' and 3' the lesion
-ATP dependent ______ (____/____/____) releases damaged oligomer
-DNA pol _____/_____/I/PCNA fills gap
-DNA ligase

-HELICAL DISTORTIONS recognized by XPA/C/E
-previous proteins recruit EXCINUCLEASES (XPF/ERCC1 and XPG) which make SS incisions 5' and 3' the lesion
-ATP dependent HELICASE (TFIIH/XPB/XPD) releases damaged oligomer
-DNA pol DELTA/EPSILON/I/PCNA fills gap
-DNA ligase

28

TC-NER

-___/____ recognize ____________, displace it from lesion site, recruit ____/____, _____ and others
-_____/_/_____ cleave and release damaged oligomer
-DNA pol _____/_____/_____ fills gap
-DNA ligase
-transcription can resume

-CSA/CSB recognize STALLED RNA POL II, displace it from lesion site, recruit XPA/XPC, TFIIH and others
-XPA/C/TFIIH cleave and release damaged oligomer
-DNA pol DELTA/EPSILON/PCNA fills gap
-DNA ligase
-transcription can resume

29

Benzo[a]pyrene

-carcinogen from cig smoke, when oxidized, compounds covalently bind to DNA, interrupt normal H-bonding, distort helix, cause frameshifts

30

Cockayne Syndorme (CS)

-TC-NER defect
-mutations in CSA/CSB
-growth and mental retardation, neuro deficiencies, demyelination
-Sun sensitive but no increase of skin cancer (b.c. Transcription does not resume after RNA pol is blocked and the damaged transcriptionally active cells likely undergo apoptosis)

31

Cisplatin

-chemo drug
-forms bulky intra-strand adducts with DNA
-treats testicular cancer
-tumor cells deficient in NER are sensitive to this drug

32

SSB Repair Pathway

-______ recognizes SS breaks
-______ serves as scaffold to recruit vvv
-_________, which is involved with 3' and 5' end processing to restore proper 3'-OH and 5'-phosphate moieties so that vvv
-DNA pol ____ can insert missing NT
-DNA ligase

-usually fixes oxidative loss of NT and damages termini of SS
-PARP1 recognizes SS breaks
-XRCC1 serves as scaffold to recruit vvv
-APRATAXIN, which is involved with 3' and 5' end processing to restore proper 3'-OH and 5'-phosphate moieties so that vvv
-DNA pol BETA can insert missing NT
-DNA ligase

33

Ataxia Oculomotor Apraxia (AOA1)

-autosomal recessive
-lacks non-neurological features of AT such as immunodeficiency and telengiectasias
-cerebellar atrophy, ataxia, late axonal peripheral neuropathy, oculomotor apraxia, cognitive impairment, hypercholsterolemia, hypoalbuminemia, involuntary movements
-APTX mutated, it's hydrolase and transferase activities for end processing are compromised

34

Things that cause DSBs

Ionizing radiation
Oxidizing agents (bleomycin)
Topo inhibitors (camptothecin)
Aflatoxins in moldy peanuts
Mechanical stress

35

NHEJ Repair

-Broken DNA sensors _____/__ heterodimer bind DNA ends to facilitate alignment and recruitment of ________ to the ends
-Frayed ends removed by ________ or _____________
-Repair done by DNA Pol __ and _______
-DNA ligase XRCC4/ligase IV
-____ helicase involved somewhere

-major pathway in DSB repair
-does not require sequence homology
-error prone, leads to accumulation of random mutations and chromosomal translocations

-Broken DNA sensors KU70/80 heterodimer bind DNA ends to facilitate alignment and recruitment of DNA-DEPENDENT KINASE CATALYTIC SUBUNIT (DNA-PKcs) to the ends
-Frayed ends removed by ARTEMIS or FEN1 NUCLEASES
-Repair done by DNA Pol MU and LAMBDA
-DNA ligase XRCC4/ligase IV
-WRN helicase involved somewhere

36

Homologous Repair

-non mutagenic, uses highly homologous DNA
-restricted to S and G2, when sister chromatid is present
-RAD52 binds DNA ends, helps mediate DNA-DNA interactions
-Recombinase RAD51 searches for sequence homology, aligns strands
-RAD50, MRE11, RAD54, RPA, BRCA2 promote replication, single-strand invasion; undamages chromosome is template, repair has no change in DNA sequence
-BRCA1/2 major roles in homolog recombination by associating with RAD51 and regulating it's activity

37

Chemo drugs that induce DSBs

Bleomycin, anthracyclines, topo inhibitors

38

Ataxia Telangiectasia

-autosomal recessive
-hypersensitivity to ionizing radiation
-mutation in ATM protein, which is normally activated by DSBs to signal check pt to slow cell cycle and repair
-also responds to breaks in DNA during B and T cell development
-AT pts more likely to develop lymphoid cancer

39

Werner's Syndrome

-ReQ helicase mutation
-progeria
-normal development until 3rd decade
-lack of pubertal growth spurt
-high pitched voice, flat feet
-increased incidence of cancers
-telomere shortening, chromosome rearrangements, telomere fusions