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Biochemistry > DNA Replication And Repair > Flashcards

DNA Replication And Repair Flashcards

1
Q

What does inactivating dam methylase do?

A

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

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2
Q

What is AZT?

A

Anti-AIDS pyrimidine analog

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3
Q

Acyclovir

A

Purine analog used to treat herpes

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4
Q

What is dactinomycin?

A

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

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5
Q

Topoisomerase I

A

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

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6
Q

Topoisomerase II

A

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

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7
Q

Quinolone Drugs

A

Novobiocin, nalidixic acid, cipro

-block DNA gyrase activity, halt bacterial DNA synthesis

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8
Q

Camptothecin

A

-anticancer drug that targets topo I

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9
Q

Adriamycin and etoposide

A

Anti cancer drugs that target topo II

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10
Q

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

A

~140

~20-80

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11
Q

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

A
  • 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
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12
Q

DNA Polymerase III

A
  • DNA chain elongation in bacteria, leading and lagging strands
  • has 3’–>5’ exonuclease activity for proofreading
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13
Q

DNA Polymerase I

A
  • prokaryotic
  • 3’–>5’ exonuclease activity
  • 5’–>3’ exonuclease activity
  • primer removal, gap synthesis
  • repair
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14
Q

DNA Polymerase II

A
  • prokaryotic
  • repair
  • 3’–>5’ exonuclease activity
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15
Q

Gemcitabine

A
  • analog of deoxycytidine

- pancreatic cancer treatment

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16
Q

DNA Pol Alpha

A

Eukaryotic

  • contains primase activity, synthesizes hybrid RNA/DNA primers
  • primer synthesis on leading and lagging strands
  • NO exonuclease activity
17
Q

DNA Pol Beta

A

Eukaryotic

  • BER
  • no exonuclease activity
18
Q

DNA Pol Gamma

A

-mitochondrial DNA replication, 3’–>5’ exonuclease activity

19
Q

DNA Pol Delta

A
  • 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
Q

DNA Pol Epsilon

A
  • Associates with PCNA to elongate leading strand
  • DNA repair (MMR and NER)
  • 3’—>5’ exonuclease activity
21
Q

Telomeres and Telomerase

A
  • 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
Q

Dyskeratosis congenita

A
  • 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
Q

Hutchinson-Gilford Progeria

A

-accelerated telomere shortening

24
Q

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

A

-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

Biochemistry (35 decks)

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