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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
Q

BER Pathway

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

Adenomatous colorectal polyposis (FAP)

A
  • autosomal recessive

- biallelic mutations in DNA glycosylase MYH gane

27
Q

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
A
  • 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
Q

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
A
  • 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
Q

Benzo[a]pyrene

A

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

30
Q

Cockayne Syndorme (CS)

A
  • 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
Q

Cisplatin

A
  • chemo drug
  • forms bulky intra-strand adducts with DNA
  • treats testicular cancer
  • tumor cells deficient in NER are sensitive to this drug
32
Q

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
A
  • 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
Q

Ataxia Oculomotor Apraxia (AOA1)

A
  • 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
Q

Things that cause DSBs

A 
Ionizing radiation
Oxidizing agents (bleomycin)
Topo inhibitors (camptothecin)
Aflatoxins in moldy peanuts 
Mechanical stress
35
Q

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
A
  • 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
Q

Homologous Repair

A
  • 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
Q

Chemo drugs that induce DSBs

A

Bleomycin, anthracyclines, topo inhibitors

38
Q

Ataxia Telangiectasia

A
  • 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
Q

Werner’s Syndrome

A
  • 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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