Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Medical Biochemistry > Ch. 22: DNA Replication, Repair, & Mutagenesis > Flashcards

Ch. 22: DNA Replication, Repair, & Mutagenesis Flashcards

1
Q

What are the 3 general features of DNA replication?

A

1) DNA replication is semiconservative
2) Replication is bi-directional
3) Replication is semi-discontinuous

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What were the 3 proposed models of DNA replication? Describe each.

A

1) Conservative Replication: parent molecule directs synthesis of new double-stranded molecule; after 1 round of rep ➡️ one molecule conserved as 2 old strands
2) Semi-conservative Replication: 2 parent strands separate, each makes copy of itself; after 1 round of rep ➡️ 2 daughter molecules both have 1 new & 1 old strand
3) Dispersive Replication: Random distribution of parent material between 2 daughter molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are the 3 active sites on E. coli DNA polymerase I? What is the function of each site?

Which one is the smaller fragment? Which two are part of the larger fragment?

A

1) 3’ to 5’ exonuclease activity: proofreading & editing
2) 5’ to 3’ exonuclease activity: DNA repair
3) 5’ to 3’ polymerase activity: nick translation (nick & replace old strand)

Smaller fragment: 5' exonuclease
Larger fragment (Klenow fragment): polymerase & 3' exonuclease
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the chief DNA replicating enzyme of E. coli?

Which subunits have polymerase function? Which subunits have proofreading ability (3’ to 5’ exonuclease)?

A

E. coli DNA polymerase III

Alpha subunits: polymerase function
Epsilon subunits: proofreading ability

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

E. coli DNA polymerase I & III: Molecular weight of each?

A

Polymerase I: 105,000

Polymerase III: 130,000

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

E. coli DNA polymerase I & III: How many molecules/cell for each?

A

Polymerase I: ~400

Polymerase III: ~10

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

E. coli DNA polymerase I & III: How many nucleotides/second for each?

A

Polymerase I: ~20

Polymerase III: ~1000

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

E. coli DNA polymerase I & III: which has 3’ Exonuclease activity?

A

Polymerase I: yes

Polymerase III: no

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

E. coli DNA polymerase I & III: which has 5’ Exonuclease activity?

A

Polymerase I: yes

Polymerase III: no

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

E. coli DNA polymerase I & III: what is the biological function of each?

A

Polymerase I: RNA primer excision, DNA repair

Polymerase III: Replicase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What experiment showed DNA replication is semiconservative?

A

Meselson and Stahl experiment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Where in the cell is eukaryotic DNA polymerase alpha located?

What is its biological activity?

A

Nucleus

Replication (primase, replication initiator)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Where in the cell is eukaryotic DNA polymerase beta located?

What is its biological activity?

A

Nucleus

DNA repair (base excision repair)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Where in the cell is eukaryotic DNA polymerase gamma located?

What is its biological activity?

A

Mitochondria

Mitochondrial DNA replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Where in the cell is eukaryotic DNA polymerase delta located?

What is its biological activity?

A

Nucleus

Replication (main polymerase at leading & lagging strand)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Where in the cell is eukaryotic DNA polymerase epsilon located?

What is its biological activity?

A

Nucleus

Replication (leading & lagging strand)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are the main eukaryotic DNA polymerases?

A

DNA polymerases alpha and delta

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are the 3 enzymatic activities of reverse transcriptase?

A

1) RNA-directed DNA polymerase activity
2) RNase H activity: exonuclease that specifically degrades RNA chains in DNA:RNA hybrids
3) DNA-directed DNA polymerase activity: replicates ssDNA, forms dsDNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is an example of a reverse transcriptase?

What drug inhibits this enzyme?

A

HIV reverse transcriptase

AZT (3’-azido-2’,3’-dideoxythymidine): ➖ DNA synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What enzymes are used to unwind the DNA helix?

A

DNA gyrase: ATP dependent negative supercoiling

Helicase: ATP dependent unwinding of DNA double helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What enzyme, as an RNA polymerase, synthesizes DNA primers?

A

Primase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What enzyme seals nicks in dsDNA?

A

DNA ligase: ATP dependent, joins Okazaki fragments together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Where does initiation of DNA replication occur in E. coli?

What occurs? (What binds to start initiation?)

A

Occurs at origin (special site, rich in A-T ➡️ easily separated)

dnaA protein binds at origin ➡️ local denaturation of DNA ➡️ 2 replisomes assemble at this site ➡️ bidirectional replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Where does termination of DNA replication occur in E. coli?

What occurs to cause termination?

A

Special site opposite origin

Terminator utilization substance (tus) binds to DNA ➡️ ➖ helicase & prevents replisome from passing through

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Elongation of DNA replication: What is the leading strand synthesis?
1st RNA primer synthesized by primase ➡️ DNA polymerase III synthesized DNA progressively until reaches terminus
27
Elongation of DNA replication: What is the lagging strand synthesis?
Each Okazaki fragment made & joined to those made previously: RNA primers w/each Okazaki fragment removed by 5' to 3' exonuclease activity of DNA polymerase I (replaces RNA w/DNA) ➡️ nick between Okazaki fragments sealed by DNA ligase
28
What is the function of single stranded DNA binding proteins in DNA replication?
(After DNA helicase unwinds dsDNA): Keeps DNA strands from coming back together
29
Fidelity of DNA replication: How many errors are made per # of bases?
1 error/10^8 bases
30
What is rolling circle replication used for?
Phage DNA replication Bacterial mating process
31
What are 4 important characteristics of rolling circle replication?
1) primer synthesis not necessary 2) leading strand covalently linked to template 3) Replication can continue for many rounds ➡️ generates concatameric branches 4) leading strand template never separates from circular part of molecule
32
How is DNA replication in eukaryotes initiated?
via extracellular signal (from other cells, usually paracrine)
33
In eukaryotes, what is required for progression of the cell cycle?
Timed activation of cell cycle via cyclin/cdk complexes (via signal transduction)
34
What 3 "special considerations" occur in eukaryote DNA replication (not in prokaryotes)?
1) multiple initiation sites (due to huge chromosome) 2) Histone complexes 3) telomere structures
35
What are the phases of the cell cycle?
G0: senescence ➡️ metabolism done, cell eventually dies (can't return to cell cycle) G1 (gap): external signal to replicate is sent to nucleus & protein synthesis enables passage to S phase S: DNA synthesis G2 (gap): ⬆️ cell size M: mitosis (chromosomes & cells divide)
36
What molecules drive the cell cycle? What molecules inhibit the cell cycle?
➕: oncoproteins ➖: tumor suppressor proteins
37
Purpose of G1➡️S checkpoint of cell cycle?
Check for DNA damage ➡️ if damage detected, cell arrested in G1 and DNA repaired
38
What protein is important at G1➡️S checkpoint ("guardian of the genome")? What are the functions of this protein?
p53 (tumor suppressor) ``` cell cycle arrest DNA repair Apoptosis (if DNA damage extensive) Senescence (if DNA damage extensive) Autophagy Metabolic reprogramming ```
39
What is metabolic reprogramming? (In relation to p53 & tumor suppression)
p53 inhibits glycolysis (needed by cancer cells) ➡️ alpha-ketoglutarate important in hydroxylation reactions
40
Purpose of G2➡️M checkpoint in cell cycle?
Check for complete DNA replication ➡️ if not, cell arrested in G2 & DNA replication completed
41
How many replication forks are there in average human chromosome? In Drosophila embryogenesis?
Humans: 100-200 Drosophila: 6000
42
Compare histones for the leading versus lagging strand during DNA replication.
Histones retained by leading strand barely dissociate After replication, lagging strand bare (as new histones made & assembled)
43
What type of DNA do histones have ⬆️ affinity for?
dsDNA
44
Which is bigger: DNA or histone proteins?
DNA much bigger than histones proteins
45
Describe steps of what occurs with nucleosomes during DNA replication.
1) nucleosome (histone octamer) unwinds & 2 halves divide 2) Replication fork passes & new DNA strands synthesized 3) both halves of nucleosome attached to same daughter strand (leading) ➡️ recombine 4) new histone octamer will be quickly made and added to other daughter strand (lagging)
46
Describe structure & function of telomeres.
Repeated terminal sequences (T & G), w/# of telomere repeats ranging from 20-100 (single celled eukaryotes) to >1500 in mammals Help stabilize chromosome
47
Why would chromosomes become shorter with each round of replication without telomerase?
RNA primers at 5' removed by polymerase alpha ➡️ cannot fill gap because no 3' OH group present
48
What is the short RNA sequence which telomerase carries?
AUC-CCA-AUC
49
Compare telomerase activity of normal somatic cells versus germ-line (stem) cells.
Somatic: lack telomerase activity ➡️ chromosome shortening to senescence/cell death Germ-line: telomerase extends 5' end of lagging strand ➡️ cells have long life span/immortal
50
What disease does telomerase contribute to? How may this potentially impact treatment of this disease?
Contributes to immortality of cancer cells Anti-telomerase drugs being investigated to treat cancer
51
What is responsible for this action in (1) prokaryotes versus (2) eukaryotes during DNA replication? Inducing (➖) supercoils ahead of replication fork
1) pro: gyrase | 2) euk: nucleosome unwinding
52
What is responsible for this action in (1) prokaryotes versus (2) eukaryotes during DNA replication? Unwinds dsDNA ➕supercoils
Both pro & euk: helicase
53
What is responsible for this action in (1) prokaryotes versus (2) eukaryotes during DNA replication? Adds RNA primers at start of Okazaki fragments at 5' end
1) pro: primase | 2) euk: primase subunit of DNA polymerase alpha
54
What is responsible for this action in (1) prokaryotes versus (2) eukaryotes during DNA replication? Polymerizes leading & lagging strands 5' ➡️ 3'
1) pro: DNA polymerase III | 2) euk: DNA polymerase delta, DNA polymerase alpha
55
What is responsible for this action in (1) prokaryotes versus (2) eukaryotes during DNA replication? Exonuclease removes primers & fills in DNA gaps
1) pro: DNA polymerase I | 2) euk: DNA polymerase beta, assisted by DNA polymerase alpha
56
What is responsible for this action in (1) prokaryotes versus (2) eukaryotes during DNA replication? Links Okazaki fragments
Both pro & euk: Ligase
57
What is responsible for this action in (1) prokaryotes versus (2) eukaryotes during DNA replication? Extends 3' ends of DNA strands Fills in complementary strand of telomere
1) pro: not necessary (circular DNA) | 2) euk: telomerase, DNA polymerase alpha
58
What are the 3 main classes of inhibitors of DNA replication?
1) prevent/reduce synthesis of precursors (bases, nucleotides) 2) affect either template or priming ability of growing strand 3) act directly on polymerases or other enzymes needed for replication
59
What do intercalating agents do to DNA?
1) Induce unwinding, lengthening, & stiffening of DNA double helix 2) Inhibits binding of enzymes (DNA/RNA polymerases, topoisomerase) 3) induce mutations during DNA replication ➡️ ➖ cell division
60
Examples of intercalating agents?
Acridines Ethidium bromide Actinomycin D Anthracyclines (daunomycin, doxorubicin, epirubicin, idarubicin)
61
What agents covalently bind to DNA ➡️ cause chain breakage?
Bleomycin | Zinostatin
62
What agents cause cross-linking of DNA strands?
Alkyl sulphonates Anthramycin Mitomycin Nitrogen mustards
63
What compounds bind to guanine ➡️ ➖ DNA expression?
Platinum & gold coordination compounds
64
What agents prevent extension of growing DNA chain?
2',3'-dideoxyribonucleosides | cordycepin
65
agents which act on & inhibit DNA polymerases: Acyclovir: specific inhibition?
inhibits DNA polymerase of HSV
66
agents which act on & inhibit DNA polymerases: Aphidicolin: specific inhibition?
Inhibits DNA polymerase alpha & delta
67
agents which act on & inhibit DNA polymerases: 2'-dideoxyazidocytidine: specific inhibition?
Inhibits bacterial primase
68
agents which act on & inhibit DNA polymerases: Which agents inhibit DNA gyrase in bacteria?
Coumermycin Novobiocin Oxolinic acid Nalidixic acid
69
What is the function of topoisomerase I?
Relieves torsional stress in DNA by inducing reversible single strand break (no energy required) ➡️ essential in DNA replication & cell growth
70
What do topoisomerase inhibitors do? Example?
Produce double strand breaks in DNA that are irreversible ➡️ leads to cell death Camptothecins
71
What two things contribute to genetic stability?
1) highly accurate DNA replication system | 2) DNA repair system when DNA damaged
72
What is a mutation?
Any change in genetic material or base sequence of DNA
73
Compare somatic mutations to germ-line mutations.
Somatic: cell changes = mostly deleterious for affected individual Germ-line: heritable or stable changes ➡️ lead to evolution, new species
74
At what rate (rate/cell cycle) do mutations continuously occur?
1 mutation / 10^9 base pairs
75
Small scale mutations: single/a few base changes Types?
1) Base substitution: transition, transversion (based on base change); silent, missense, nonsense (based on consequence) 2) Base deletion 3) Base insertion
76
Large scale mutations: chromosomal mutations Translocations?
Interchange of large segments of DNA
77
Large scale mutations: chromosomal mutations Inversions?
Region of DNA flips its orientation w/respect to rest of chromosome
78
Large scale mutations: chromosomal mutations Deletion?
Loss of important genes
79
Large scale mutations: chromosomal mutations Nondisjunction?
Lost track of where they are supposed to go in cell division
80
What base changes = transition? What base changes = transversion?
Transition = purine ➡️ purine (A ↔️ G) or pyrimidine ➡️ pyrimidine (C ↔️ T) Transversion = purine ↔️ pyrimidine (A ↔️ C , A ↔️ T, G ↔️C, G ↔️ T)
81
What occurs in silent mutations? Missense? Nonsense?
1) Silent: no amino acid change 2) Missense: amino acid change 3) Nonsense: introduces new stop codon ➡️ termination of protein synthesis
82
Insertions & deletions may cause what?
Codon frame shifts: changes reading frame of base sequence of gene ➡️ synthesis of completely different protein 3 base insertions or deletions do not change reading frame but may cause diseases: fragile X syndrome (CGG repeat ➡️ mental retardation), Huntington's disease (CAG repeat ➡️ chorea, dementia, death)
83
What is a mutagen?
Physical/chemical agent that causes mutations
84
What is mutagenesis?
Process of producing a mutation (induced or spontaneous)
85
What mutations do chemical mutagens cause?
Modification of bases (alkylation) Insertion between bases
86
What mutations does UV & ionizing radiation cause?
Cross-linking of base pairs Ring opening DNA strand breaks
87
What is the Ames test?
Determines if a chemical is a mutagen Assumption: any substance that is mutagenic may also be a carcinogen (cause cancer)
88
Types of DNA damage: Base loss?
Base lost but sugar-P backbone intact ➡️ strand can't replicate if not repaired
89
Types of DNA damage: Base modification?
1) Deamination of cytosine ➡️ uracil 2) chemical modification: ROS and environmental chemicals can modify bases via alkylation 3) photodamage (UV) ➡️ thymine dimers
90
Types of DNA damage: Replication errors?
During DNA replication: mismatch, insertion, deletion
91
Types of DNA damage: Inter-strand cross links?
Crosslinks formed via bifunctional alkylating agents, UV, ionizing radiation
92
Types of DNA damage: DNA-protein crosslinks?
Crosslinks between DNA strands & protein molecules formed via bifunctional alkylating agents, UV, ionizing radiation
93
Types of DNA damage: Strand breaks?
ss nicks and ds breaks via ionizing radiation
94
Types of DNA repair: Direct reversal of damage: 3 examples?
1) Light induced (300-600 nm) enzymatic cleavage of T, C, and CT dimers via photolyase (does not occur in placental mammals) 2) O6-methyl-guanine-DNA-methyltransferase: O6-methyl group transferred from DNA ➡️ Cys of enzyme 3) DNA ligase seals nicks
95
Types of DNA repair: Excision repair + replacement with new DNA: 3 types? (In both pro & euk)
1) mismatch repair 2) base excision repair 3) nucleotide excision repair

Medical Biochemistry (23 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions