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Biochemistry > DNA Replication And Repair > Flashcards

DNA Replication And Repair Flashcards

(63 cards)

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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
Doxorubicin, etoposide, and teniposide
. Inhibit human topoisomerase II . Anti-cancer drugs . Enhances rate at which topoisomerase II cleaves or reduces rate at which the breaks are resealed
26
Telomere
. 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
Telomere maintenance
. 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
Basal mutations ate
. Errors during DNA replication in absence of environmental mutagens . Spontaneous tautomeric shifts contribute to this (rare)
29
Exogenous agents that damage DNA
. 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
Base analogs
. Can cause mutations . Erroneously incorporated into DNA . Bromouracil incorporated in place of thymine
31
Alkylation agents
. 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
Dominating agents
. Turn adenine to hypoxanthine . Guanine to xanthine . Cytosine to uracil . Lead to errors in replication
33
Categories of DNA mutations
. Point mutations | . Length mutations
34
Point mutations
. Change occurring in single nucleotide | . Transitions of transversions
35
Transition mutation
.pyrimidine changed to another pyrimidine | . Purine changes to another purine
36
Transversions
. Purine to pyrimidine . Pyrimidine to purine . Less common than transitions showing mutations are non random
37
Missense mutation
. Amino acid substitution
38
Nonsense mutation
. Mutation causes stop codon to be introduced to coding sequence
39
Sense/silent mutation
. Mutation but no change in amino acid sequence
40
Cystic fibrosis mutation
. No single mutation is responsible | . Single point, deletion, and insertions found
41
Types of length mutations
. Insertion . Deletion . Affect reading frame depending on nu,bear of nucleotides inserted or deleted
42
Frame shift mutation
. Not a multiple of 3 nucleotides are inserted in sequence | . Resulting amino acid may be radically different from that point onward
43
Inframe mutation
. If 3 nucleotides added or deleted, an AA is added or lost, but it does not effect sequence further down the line
44
Translocation mutation
. 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
Mutation in intron-exon boundary
. Results in abnormal splicing | . Nonfunctional protein product
46
Mutation in promoter or enhancer
. Leaves polypeptide structure intact | . Inc. or dec. rate of synthesis
47
Gene amplification
. Portions of chromosomes amplify resulting in large excess of the protein product
48
Sickle cell gene mutation
. Missense mutation | . GAG to GTG
49
T/F larger genes show mutations more often
T
50
Mutational hot spots
. 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
How age of parent affects gene mutation rate
. Some chromosomal abnormalities inc. w/ age of parent
52
DNA damage response (DDR)
. 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
Types of DNA repair mechanisms
. Mismatch repair . Base excision . Nucleotide excision . Double-stranded break
54
Mismatch repair
. 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
Microsatellite instability
. Happens when mismatch enzymes are dysfunctional | . Can cause cancers
56
Base excision repair
. 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
Nucleotide excision repair
. 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
Transcription-coupled nucleotide excision repair
. DNA damaged recognized when transcription is stalled at DNA-damage site
59
Global genomic nucleotide excision repair
. DNA lesion detected on scanning of genome by enzymes (xeroderma pigmentosum group of proteins)
60
Xeroderma pigmentosum
. 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
Cockayne syndrome
. Loss of transcription-coupled repair . Cachexia, growth retardation . No predisposition to skin cancer
62
Double strand break repair
. 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
BRCA 1 and 2 proteins
. 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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