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Biochemistry > DNA Replication And Repair > Flashcards

DNA Replication And Repair Flashcards

1
Q

Covalent structure of DNA

A

. Double stranded polymer of deoxyribonucleotides joined by 3’-5 phosphodiester bonds

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2
Q

Hydrogen bonding between base pairs in DNA

A

. 3 hydrogen bonds with ____
. 2 H bonds w/ ______
. Stabilizes double helix in non-polar interior

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3
Q

Is phsophodiester connection btw deoxynucleotides directional or not?

A

. Directional

. Connects 5’ phosphate of 1 nucleotide w/ 3’ hydroxyl group of next nucleotide

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4
Q

DNA replication occurs in what phase of cell cycle?

A

S phase

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5
Q

Substrates for DNA replication

A

??

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6
Q

Product of DNA replication

A

2 identical strands???

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7
Q

DNA polymerase

A

. Select nucleotide that is added to 3-OH end of chain
. Catalyzes formation of phosphodiester bond
. Substrates are dATP, dCTP, dGTP, and dTTP and single stranded template DNA

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8
Q

T/F there is one place for replication to begin

A

F, there are multiple sites that start at different times

. When it nears completion the bubbles of newly replicated DNA meet and fuse forming 2 new molecules

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9
Q

DNA chain elongation

A

. DNA polymerase adds deoxyribonucleotides to 3’ end of growing chain
. Dictated by base sequence of template (coding) strand

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10
Q

New DNA strand is synthesized in what direction?

A

5’ to 3’ because it is antiparallel

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11
Q

Leading strand DNA replication

A

. 5’-3’
. In same direction as replication fork movement
.

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12
Q

Landing strand DNA replication

A

. 5’ to 3’
. Synthesis in direction opposite of fork movement
. Short (100-200 nucleotides) fragments (Okazaki fragments) made
. Lipase joins fragments together

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13
Q

DNA helicase

A

. Unwinds short segment of parental duplex DNA by catalyzing ATP dependent strand separation
. Forms replication fork

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14
Q

DNA primase

A

. Initiates synthesis of RNA molecule that primes DNA synthesis on leading and lagging strand
. First few nucleotides are ribonucleotides and then subsequent ones are ribo or deoxyribonucleotides

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15
Q

Singles stranded DNA binding proteins during replication

A

. Bind to single stranded DNA

. Prevent premature annealing of single stranded DNA to double stranded

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16
Q

Proof reading in DNA replication

A

. DNA polymerase w/ 3’-5’ exonuclease activity
. Remove nucleotides that aren’t part of double helix and are mismatched
. Do not has 5’-3’ exonuclease activity

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17
Q

DNA ligase

A

. Seals nick in DNA after DNA polymerase fills gaps left by RNA primers

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18
Q

Topoisomerases

A

. Facilitates unwinding of double helix super twisting to achieve negative supercoils for transcription
. As replication fork moves, daughter molecules rotate around each other and become overcoiled
. Relieve torsional stress by inducing reversible single stranded breaks in DNA at phosphodiester bond

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19
Q

Topoisomerase I

A

. Catalyzes break in only 1 strand of DNA
. Allows unwinding of broken strand
. Rejoin broken ends by catalyzing formation of new phosphodiester bonds

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20
Q

Topoisomerase II

A

. Catalyzes break in both strands of DNA
. Both strands unwind
. Catalyzes formation of new phosphodiester bonds

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21
Q

Classes of DNA synthesis inhibitors

A

. Prevent/reduce purine/pyrimidine synthesis (_____)
. Drugs affect template/priming ability of growing strand (intercalating agent doxorubicin for cancer)
. Topoisomerase inhibitors

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22
Q

DNA gyrase

A

. Bacterial type II topoisomerase

. Introduces neg. supercoils into DNA molecules via ATP dependent reaction ahead of replication fork

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23
Q

quinolone antibacterials

A

. 1st and 2nd generation: Norfloxacin and ciprofloxacin
. 3rd generation: levoflaxacin and moxifloxacin
. DNA gyrase inhibitor via inhibiting strand cutting reaction

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24
Q

Camptothecins

A

. Anti cancer agents

. Inhibit topoisomerase I

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25
Q

Doxorubicin, etoposide, and teniposide

A

. Inhibit human topoisomerase II
. Anti-cancer drugs
. Enhances rate at which topoisomerase II cleaves or reduces rate at which the breaks are resealed

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26
Q

Telomere

A

. Tandem array of simple sequence (TTAGGG)
. DNA replication leaves short gap where RNA primers were removed
. Linear chromosome shortened w/ each cell division, telomeres prevent actual genes form being lost in that

27
Q

Telomere maintenance

A

. RNA dependent DNA polymerase
. Adds TTAGGG repeats to end of chromosomes
. Telomerase ribonucleoprotein complex contains RNA template
. DNA repeats added to leading strand
. Lagging strand completed by DNA polymerase as normal

28
Q

Basal mutations ate

A

. Errors during DNA replication in absence of environmental mutagens
. Spontaneous tautomeric shifts contribute to this (rare)

29
Q

Exogenous agents that damage DNA

A

. Radiation: energy rich enough to react w/ DNA, penetrates whole body causing somatic and germ line mutations
. UV radiation: can’t penetrate beyond outer layer of skin
. Chemical in environment: hydrocarbons
. Chemo chemical: carcinogenic

30
Q

Base analogs

A

. Can cause mutations
. Erroneously incorporated into DNA
. Bromouracil incorporated in place of thymine

31
Q

Alkylation agents

A

. Alkylate N Or O atoms in bases
. Found in food, Tobacco smoke, endogenous metabolic products
. O-methyl guanine is major carcinogenic lesion on DNA
. Methylguanine DNA methyl transferase important for genomic stability to repair these lesions

32
Q

Dominating agents

A

. Turn adenine to hypoxanthine
. Guanine to xanthine
. Cytosine to uracil
. Lead to errors in replication

33
Q

Categories of DNA mutations

A

. Point mutations

. Length mutations

34
Q

Point mutations

A

. Change occurring in single nucleotide

. Transitions of transversions

35
Q

Transition mutation

A

.pyrimidine changed to another pyrimidine

. Purine changes to another purine

36
Q

Transversions

A

. Purine to pyrimidine
. Pyrimidine to purine
. Less common than transitions showing mutations are non random

37
Q

Missense mutation

A

. Amino acid substitution

38
Q

Nonsense mutation

A

. Mutation causes stop codon to be introduced to coding sequence

39
Q

Sense/silent mutation

A

. Mutation but no change in amino acid sequence

40
Q

Cystic fibrosis mutation

A

. No single mutation is responsible

. Single point, deletion, and insertions found

41
Q

Types of length mutations

A

. Insertion
. Deletion
. Affect reading frame depending on nu,bear of nucleotides inserted or deleted

42
Q

Frame shift mutation

A

. Not a multiple of 3 nucleotides are inserted in sequence

. Resulting amino acid may be radically different from that point onward

43
Q

Inframe mutation

A

. If 3 nucleotides added or deleted, an AA is added or lost, but it does not effect sequence further down the line

44
Q

Translocation mutation

A

. Transfer of genetic material from one chromosomal location to another
. Large chunk or whole arm of chromosome
. Expressed normally as long as regulatory site is not severed

45
Q

Mutation in intron-exon boundary

A

. Results in abnormal splicing

. Nonfunctional protein product

46
Q

Mutation in promoter or enhancer

A

. Leaves polypeptide structure intact

. Inc. or dec. rate of synthesis

47
Q

Gene amplification

A

. Portions of chromosomes amplify resulting in large excess of the protein product

48
Q

Sickle cell gene mutation

A

. Missense mutation

. GAG to GTG

49
Q

T/F larger genes show mutations more often

A

T

50
Q

Mutational hot spots

A

. CG region accounts for over 30% of all single nucleotide substitutions
. More common due to issues with converting cytosine to methylcytosine because spontaneous hydrolysis of methylcytosine makes thymine

51
Q

How age of parent affects gene mutation rate

A

. Some chromosomal abnormalities inc. w/ age of parent

52
Q

DNA damage response (DDR)

A

. DNA damage sensors that detect damage and launch activation of stress response pathways
. Temporary arrest in cell cycle for DNA damage to be repaired
. Enzymes can recognize, remove, repair, and relegate strand

53
Q

Types of DNA repair mechanisms

A

. Mismatch repair
. Base excision
. Nucleotide excision
. Double-stranded break

54
Q

Mismatch repair

A

. Occurs w/ error in DNA polymerase
. Corrects mismatches of normal bases
. Repair proteins coded by MSH2, MLH1, MSH6, PMS-1, and PMS2 genes
. Mutations in these repair genes cause person more likely to get colon cancer and other cancers

55
Q

Microsatellite instability

A

. Happens when mismatch enzymes are dysfunctional

. Can cause cancers

56
Q

Base excision repair

A

. Fixes issues w/ spontaneous depurination of cytosine to uracil and deamination
. Removes nucleotides that have lost a base as result of either of these
. Endonuclease recognizes space from lost base, DNA polymerase and ligase fill in space and seal nick in strand

57
Q

Nucleotide excision repair

A

. Fixes issues from environmental damage
. Forms pyrimidine-pyrimidine dimers from adjacent pyrimidine bases in DNA
. Smoking causes formation of benzopyrene that interacts w/ DNA
. Transcription-coupled repair or global genomic repair

58
Q

Transcription-coupled nucleotide excision repair

A

. DNA damaged recognized when transcription is stalled at DNA-damage site

59
Q

Global genomic nucleotide excision repair

A

. DNA lesion detected on scanning of genome by enzymes (xeroderma pigmentosum group of proteins)

60
Q

Xeroderma pigmentosum

A

. Disease that suggests 10 proteins required for excision of damaged bases in DNA by single repair system
. Autosomal recessive
. Defective repair of thymine dimers
. Prone to developing skin cancers

61
Q

Cockayne syndrome

A

. Loss of transcription-coupled repair
. Cachexia, growth retardation
. No predisposition to skin cancer

62
Q

Double strand break repair

A

. Fixes environmental damage
. Homologous recombination: gets info from homologous chromosome for break repairs, sister chromatid is template to repair
. Non-homologous end joining: permits joining of ends if there is no sequence similarity btw them
. May proteins involved in this

63
Q

BRCA 1 and 2 proteins

A

. Play role in homologous recombination repair
. Inc. breast and ovarian cancer risk if dysfunctional
. Homozygous mutations in BRCA 2 cause Fanconi’s anemia

Biochemistry (64 decks)

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