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GENETICS AND EVOLUTION > DNA REPLICATION > Flashcards

DNA REPLICATION Flashcards

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Biology 101 flashcards
1
Q

DNA STRUCTURE

A

Nucleic acids: Biopolymers built from smaller molecules (monomers) connected covalently.

DNA structure: Double helix with a sugar-phosphate backbone and nitrogenous bases (A, G, C, T).

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2
Q

DNA replication overview

A

Goal: To ensure each daughter cell receives one copy of DNA.

Semi-conservative replication: Each new DNA molecule has one old and one new strand.

Other theories: Conservative and dispersive models (disproven).

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3
Q

challenges

A
  1. Replicate all bases of long DNA accurately.
  2. Minimize replication errors.
  3. Overcome mechanical stress during unwinding and encounters with transcribed genes.
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4
Q

DNA polymerase and proofreading

A

DNA polymerase: Efficient at proofreading, with 1 error per 10^7 bases.

Exonuclease activity: Removes mismatches during replication to ensure accuracy.

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5
Q

basic nucleotide structure

A

DNA: A, G, C, T bases with deoxyribose sugar.

RNA: A, G, C, U bases with ribose sugar.

Sugar-phosphate backbone supports 5’ to 3’ polymerization.

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6
Q

bacterial genome replication

A

Circular DNA: Replication begins at a single origin (oriC) and proceeds bidirectionally.

Replication is not synchronized with cell division.

Plasmids: May have variable copy numbers.

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7
Q

initiation of DNA replication

A

oriC: A-T rich region where DNA melts due to weaker bonds.

DnaA protein binds to the origin, causing strand separation and allowing helicase attachment.

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8
Q

supercooling and topoisomerase

A

As DNA unwinds, supercoiling occurs.

Topoisomerases: Remove supercoiling to prevent replication machinery from stalling.

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9
Q

leading and lagging strands

A

Leading strand: Continuous synthesis in the 5’ to 3’ direction.

Lagging strand: Synthesized in short fragments (Okazaki fragments) joined by DNA ligase.

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10
Q

key replication enzymes

A

DNA polymerase delta/ 3 : synthesises lagging strand Extends the DNA strand but cannot start it.

Primase: Synthesizes an RNA primer for DNA pol III to extend.

Helicase: Unwinds the DNA strands.

DNA polymerase alpha/ 1: initiates DNA synthesis by adding DNA to RNA primer and removes primers from lagging strand (using 5’ to 3’ exonuclease activity)

DNA pol epsilon/ 2 - synthesis leading strand

DNA ligase: Joins Okazaki fragments.

topoisomerase - relieves supercoiling tension ahead of replication

singe strand binding proteins - binds to ssDNA after unwound to prevent them from reannealing or degradation

clamp protein - holds DNA pol 3 to DNA template

clamp loader - loads clamp to DNA

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11
Q

sugar structure in nucleotides

A

C1: Binds the base.

C2: No OH in DNA; OH present in RNA.

C3 and C5: Interact with phosphate groups for polymerization.

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12
Q

double stranded DNA rules

A

Anti-parallel strands.

Base-pairing: A with T, G with C.

Nucleotides added to the 3’ end using energy from phosphate bond hydrolysis.

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13
Q

polarity in DNA

A

5’ end: Phosphate group.

3’ end: Hydroxyl group.

Results in directionality from 5’ to 3’ in synthesis.

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14
Q

eukaryotic genome replication

A

Requires multiple origins due to larger, linear chromosomes.

Euchromatin origins fire first (early origins).

Heterochromatin origins fire later (late origins).

Replication occurs during the S-phase of the cell cycle.

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15
Q

replicons

A

DNA region replication from a single origin

Bacteria: Each circular DNA is a single replicon.

Eukaryotes: Have multiple replicons, and not all origins fire in every cycle. Some are dormant.

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16
Q

replication forks

A

Prokaryotes: Helicase moves along the lagging strand template.

Eukaryotes: Helicase moves along the leading strand template.

Pol ε: Synthesizes the leading strand in eukaryotes.
Pol δ: Synthesizes the lagging strand in eukaryotes.

17
Q

protein phosphorylation in replication

A

Protein phosphorylation regulates origin firing during the S-phase.

Ensures each origin fires only once per cell cycle.

18
Q

end replication problem

A

telomeres shortener with each round of replication

Each replication cycle leaves unreplicated 50-200 bp at the 3’ end.

Telomeres: Non-coding, repetitive DNA sequences (e.g., TTAGGG) protect chromosome ends.

19
Q

Telomeres and Aging

A

Telomeres shorten with each replication cycle, limiting cell proliferation.

Short telomeres protect against cancer, but in cancer cells, telomere length is stabilized.

20
Q

Telomerase

A

Telomerase: An enzyme that extends telomeres, compensating for DNA loss during replication.

Functions as a reverse transcriptase.

21
Q

types of circular DNA

A

ssDNA or dsDNA: No DNA ends.

Circular nicked: Backbone broken, but all bases paired.

Circular gapped: Contains unpaired bases.

22
Q

types of linear DNA

A

Linear dsDNA or ssDNA: No gaps in structure.

Linear nicked: Backbone is broken.

Linear gapped: Contains unpaired bases.

23
Q

types of ends in liner DNA

A

Blunt ends: No overhangs.

3’ overhang: Extra nucleotides on the 3’ end.

5’ overhang: Extra nucleotides on the 5’ end.

24
Q

branched DNA structures

A

3-way junctions: Seen in replication forks.

4-way junctions: Recombination or repair intermediates.

25
Q

DNA end representation

A

3’ end: Always marked with an arrowhead.

5’ end: No arrowhead.

26
Q

key enzymes in DNA PROCESS

A

Helicase: Unwinds DNA strands.

Nuclease: Cleaves the sugar-phosphate backbone.

Polymerase: Synthesizes nucleic acids.

Clumps: Assist enzymes, not enzymes themselves.

Ligase: Joins nucleotides together.

27
Q

helices types

A

Hexameric helicases: DNAb (prokaryotes), MCM (eukaryotes).

Monomeric helicases: Involved in DNA repair and replication assistance.

28
Q

helicase energy source and directionality

A

Energy source: ATP hydrolysis for movement and unwinding.

DNAb direction: 5’ to 3’ (prokaryotes).

MCM direction: 3’ to 5’ (eukaryotes).

29
Q

nuclease overview

A

Break the sugar-phosphate backbone at C3 or C5.

Can be specific to ssDNA or dsDNA.

30
Q

types of nuclease

A

5’ to 3’ exonucleases: Cleaves one nucleotide at a time, cannot cleave circular DNA.

Endonucleases: Cleaves within DNA without needing ends, can cleave circular DNA.

3’ to 5’ exonucleases: Cannot cleave circular DNA.

31
Q

helices nuclease team

A

Helicase unwinds dsDNA, creating a substrate for ssDNA nucleases.

Commonly seen in DNA repair and generation of 3’ overhangs.

32
Q

DNA polymerase directionality

A

All polymerases synthesize DNA in the 5’ to 3’ direction by adding nucleotides to the 3’ end.

Cannot extend the 5’ end in the cell.

33
Q

DNA polymerase proofreading

A

Uses 3’ to 5’ exonuclease activity to remove incorrect, non-complementary nucleotides.

34
Q

DNA polymerase processivity

A

Processivity: The ability to extend a DNA strand without dissociating.

Higher processivity in vivo compared to in vitro.

35
Q

eukaryotic clump - PCNA

A

PCNA: A structural protein that forms a closed ring, stabilizing replication and repair enzymes on DNA.

Clump loader: An enzyme that opens the PCNA ring using ATP.

clumped loader binds to DNA and clump, open clump and loads onto DNA

clump loader releases clump and dissociates from DNA

GENETICS AND EVOLUTION (26 decks)

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