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M2M unit 1 > DNA Replication and Repair > Flashcards

DNA Replication and Repair Flashcards

1
Q

anti miRNA

A

singled stranded, chemicaly modified ASO bind to miRNA to block activity. miR-122 miRNA is therapy for HepC virus.

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2
Q

Components of a NT

A

nitrogenenous base attached on 1’ of ribose ring ribose phosphate group attached to 5’ carbon of ribose

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3
Q

Base Excision Repair

A

repairs those missed by NER, and that do not distort DNA

1) modified base recognized by DNA glysoylase which hydrlyzes glycosidic bond (base and sugar) to yield a-basic site.
2) AP site specific endonuclease cleaves Sugar phosphate backboke from 5’ to AP site
3) a different endonuclease cleaves Sp backbone from 3’ to AP site
4) DNA pol fills in gap and nick is sealed by ligase

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4
Q

Methylation of Adenine

A

this is done in bacterial cells and is used as an identifyer for DNA older strands

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5
Q

how are small RNAs delivered?

A

1) put them inside lipid nanoparticle with an external lipid layer that targets a particular region, where it is then take up in a lysocome and ssRNA comes in contact with mRNA 2) chemically modified so they do’t get degraded and have glycol-conjugate that is specific 3) virus expresses gene and makes RNA that folds back on itself.

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6
Q

how do Streomyces that make puromycin protect themselves?

A

they also make an enzyme that inactivates antibiotic in the bacteria itself. modifies the part of puromycin that is involved in the covalent attachment of polypeptide chain, rendering it inactive.

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7
Q

DNA Pol I vs DNA Pol III

A

1: distributive - dissociates easily replaces RNA primers Exonuclease 5’ to 3’ 3: processive both have Pol 5’ to 3’ and exonuclease 3’ to 5’

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8
Q

Cockayne syndrome

A

super hypersensitivity, premature aging, mutation in transcription NER

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9
Q

RNAi

A

endogenous gene silencing mechanism by siRNA and miRNA ds RNA induce translational inhibition or degradation of mRNA containing partially complimentary sequences.

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10
Q

When does Loss of Heterozygosity Occur?

A

Mis-regulation of HR use of other chromosomal homolog as template instead of sister chromatid

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11
Q

Nucleotide Excision Repair

A

Removes lesions that distort DNA structure \ block DNA and RNA pol movement ex: thymine dimers, DNA adducts Recognition of damage is by multi-protein complex, but all other steps are the same as BER

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12
Q

Rag Recombinase

A

initiates DS breaks in NHEJ to create antibody diversity

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13
Q

Steps NHEJ with Ku

A

1) Ku recognizes ds break and binds to protect form exonuclease 2) Ku recruits DNA-PKcs which autophosphorylates to attract ARTEMIS to remove DNA damage 3) polymerase fills in gap 4) Ligase 4 seals

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14
Q

Camptothecin

A

chemo drug targets topoisomerase

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15
Q

Dicer

A

ribonuclease of RNAse III that cleaves dsRNA into miRNA

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16
Q

How are DS breaks sensed?

A

PIKKs 1) ATM and ATR

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17
Q

How does BRCA1 promote HR?

A

phosphorylated by ATM and ATR to recruit to DS break. Depends on activated by CDK, when present, this pushes towards HR.

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18
Q

Dideoxyinosine

A

DDI inhibits DNA synthesis by the reverse transcriptase enzyme HIV medication Chain terminal mimic of nucleotide

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19
Q

What methods are for direct reversal of Damaged bases?

A

1) ssDNA break reversal by ligase
2) reversal of UV damage by photolyase
3) reversal of base alkylation (O6 methyltransferase MGMT)

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20
Q

what happens with imperfect match of miRNA?

A

transcriptional repression

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21
Q

Tat

A

The first protein synthesized in the human genome of HIV that leads to further expression of the viral genome. There is a tat mimic that fits nicely into the groove of HIV-TAR (tat activated region) to prevent replication of HIV

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22
Q

BER vs NER

A

BER targets damage that does not distort DNA NER targets damage that does distort DNA

BER: recognized by specific glycosylase

NER: recognized by multiprotein complex

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23
Q

Holliday Junction Resolution

A

can make two cuts Vertically: recombinants (DSBR) Horizontally: no recombinatns (synthesis dependent strand anneals)

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24
Q

Intercalation drugs

A

Actinomycin D

Doxorubicin

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25
Q

MGMT

A

is a direct reversal type of DNA repair that reverses base alkylation

removes added methyl group and adds it on itself Glioblatomas have MGMT silenced

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26
Q

How can RNAi be made in body?

A

make small RNA in vivo, purify the enzyme and let is up the RNA introduce it to cells to cleave mRNA in cell. Introduce gene that will express RNA that will naturally fold back on itself to generate siRNA or miRNA that will specifically target domain for degradation.

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27
Q

Cisplatin

A

alkylating agent drug that reacts with nitrogen in the bases to cause crosslinking. This causes too much damage in the cellular DNA when cells are dividing very rapidly and signals them to be sent into apoptosis. Chemotherapy drug.

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28
Q

Xeroderma Pigmentosum (XP)

A

sun hypersensitivity, pigmentation disorders mutation in Global Genome NER

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29
Q

Base Alkylation

A

Addition of hydrocarbon groups on nitrogenous base to form large covalent adducts to DNA that block DNA replication and transcription machinerly Benzenes and derivatives of coal and cigarette smoke

30
Q

De-Purination

A

low pH promotes b-glycosyl bond between base and sugar makes phosphate backbone sensitive to breakage

31
Q

siRNA

A

22 nt generated from longer doubled stranded RNA precursors by ribonuclease dicer Immunity to virus mRNA degradation influences; Chromatin formation, transcriptional silencing, mobile element repression binds in perfect match

32
Q

Actinomycin D

A

naturally occurring antibiotic used in chemotherapy

Cyclic peptides that interact with DNA in a non-covalent manner. Stacks with DNA bases to alter double helical structure in intercalation.

Interferes with DNA replication and transcription.

33
Q

DNA Polymerase I

A

a distributive enzyme Replaces RNA polymerase three functions: 1) DNA polymerase 5’ to 3’ 2) exonuclease 3’ to 5’ (proofreading) 3) exonulcease 5’ to 3’ (primer removal)

34
Q

DNA Pol III

A

Processive responsible for replicating DNA lagging and leading strands Holoenzyme made for 17 proteins DNA pol 5’ to 3’ Exonuclease activity 3’ to 5’

35
Q

what happens with perfect match of miRNA?

A

cleavage and destruction of mRNA

36
Q

Methylation of cytosine

A

5’ position methylated. does not affect base pairing majorly, but represses transcription of DNA sequence. Only occurs at C’s with an adjacent 3’ G.Thus it is thought to be symmetrical

37
Q

DNA damage checkpoint

A

Stalled replication fork, DNA damage, ds break is detected by ATR and ATM, which recruit active signaling Chk1 an Chk2 leads to production of DNA repair proteins reversible cell cycle arrest permanent cell cycle arrest

38
Q

What determines HR vs NHEJ?

A

1) tumor supressor presence a) BRCA1 (HR) or 53BP1 (NHEJ) 2) Point in pathway a) HR is dependent on being in G2 of S 3) protection of ends a) nonprotected (HR) b) protected (NHJE)

39
Q

Exon Skipping

A

target intra-exon junctions or splicing regulatory elements binding to the site inhibits splicing and forces the choice of alternative splice sites.

40
Q

How does extreme pH influence Tm?

A

alter ionization of groups on bases that participate in H bonding

41
Q

Micro RNA

A

21 NT translation repression and degradation

Drosha leaves miRNA to be exported to cyto

Dicer binds to miRNA in cyto and then binds to Argo complex to form Argo-Risk complex

42
Q

what disease have mutations in tRNA?

A

myloclonic epilepsy ragged red riber disease

43
Q

What makes DNA Pol III processive?

A

Proliferating Cell Nuclear Antigen (PCNA) wiht the beta-clamp ring

44
Q

Artemis

A

works in NHEJ attracted by Ku and DNA-PKcs both endonuclease and exonuclease to be able to remove damaged DNA caused by ds break

45
Q

how does miRNA target mRNA?

A

base pairing of miRNA to target mRNA to 3’ UTR serves to guide effector complex Seed region is critical a single miRNA will have multiple binding sites in one 3’ UTR or a single 3’ URT will be attached by different miRNA

46
Q

Purine

A

two cyclic nitrogenous base Adenine Guanine

47
Q

Spo11

A

programs DS breaks in HR leaves DS breaks with overhang mutation in ATM leads to more initiation of Spo11

48
Q

Seed Region

A

nucleotides 2-8 form the seed region and determine whether miRNA will target the region

49
Q

Doxorubicin

A

intercalator

50
Q

miRNA biogenesis

A

miRNA folds on itself to generate ds RNA structure

51
Q

Spontaneous Deamination

A

Changes a cytosine to a Uracil in DNA Repaired by Base exision repair 100-500 per cell per day

52
Q

Puromycin

A

necleotide analog that mimics tRNA to terminate translocation covalently links to amino acid

53
Q

Glycosylase in BER

A

flips out damaged base and removes by hydrolyzing bond specific to particular base damage, inappropriate base or mispairing

54
Q

NHEJ

A

imperfect, loss of few NTs, occurring throughout cell cycle most associated with Immune function and antibody diveristy of VDJ either through Rag pathway or Ku with DNA-PKcs wuick repair, not sequence dependent

55
Q

RNA-Induced Silencing Complex

A

catalytic effector complex of RNAi mediated gene silencing. multiprotein complex that works with arg to incorporate one strand of siRNA and miRNA.

56
Q

Myloclonic Epilepsy and Ragged Red fiber disease

A

mutation in tRNA gene

57
Q

Arognaut

A

bind to small RNAs and are conserved in all domains. mediate target recognition. multiple argonauts in cell, depending on what arg binds to small RNA, function will dependentant

58
Q

Action of 53BP1

A

positively regulates NHEJ by promoting synapsis of distal broken ends blocks resection of 3’ OH end

59
Q

How is mismatch repair different in P vs E?

A

MutS and MutL in bacteria recognize damage

MSH and MLH in mammals

Bacteria - old strand is methylated

Euk: new strand has more nicks due to the okazaki fragments and RNase H2.

60
Q

Mismatch NT repair

A

during replication and before methylation

MutS and MutL (B) and MSH and MLH (E) recognizes DNA errors and Pol III cleaves bond, exonuclease chew away strand with mismatch while helicase unwinds, Pol Adds dNTPs to gap and ligase seals

61
Q

Lynch Syndrome

A

Due to Mismatched Base Repair mutation in humans Hereditary Non-Polyposis Colorectal Cancer increased risk of colon cancer

62
Q

drugs that target topoisomerase

A

Etoposide and camptothecin

63
Q

RNase H-dependent ASO

A

binds to complimentary mRNA and cleaves site to reduce gene expression or block ribosome.

64
Q

Homologous Recombination (basic)

A

Perfect repair, requires sister chromatids, limited to S and G2 no gain of loss of NTs assures genetic diversity of gamets Can act with BRCA1 to form holliday junction

65
Q

how does NER recognize damage?

A

Global Genome NER: recognizes distortions in whole genome Transcription coupled NER: recognizes damage in actively transcribed regions

66
Q

De-Amination

A

cleavage of amine group, leading cytosine to be transformed into thymine. damage is hard to detect sometimes naturally, but caused by nitrous acid in smoke and preservatives

67
Q

piRNA

A

24-27 NT deviation can vary in different organisms and loci, flies and mammals form long precursors and worms form short. RNA protein complex that interact with piwi proteins. Function: immunogenesis maintenance of germ line controls of mobile elements (transposons)

68
Q

Stability of components of nucleotides

A

Pyrimidine is more soluble than purine. Nucleotide > nucleoside > base

69
Q

VDJ Recomination

A

each heavy and light chain contains variable repeats Constant, variable, Diversity (H) and Joining VDJ is recombination so that there is one copy of each segment in a given lymphocyte leads to enormous antibody repertoire.

70
Q

Drosha

A

RNAse III that is implicated in processing newly transcribed primary miRNA in nuclease.

71
Q

Base Alkylation

A

Addition of methyl group to cause point mutation ex. BP: CG becomes GT and eventually mutates to AT

M2M unit 1 (6 decks)

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