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2B: Genetics and Evolution > 1.5 - DNA Replication > Flashcards

1.5 - DNA Replication Flashcards

1
Q

What is a polymer?

A

molecule built from smaller identical or similar molecules, monomers, connected covalently

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2
Q

What are the monomers in nucleic acids?

A

Nucleotides

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3
Q

Is ATP a deoxyribonucleotide or a ribonucleotidse?

A

ribonucleotide

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4
Q

What are the purines?

A
  • adenine
  • guanine
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5
Q

What are the pyramidines?

A
  • cytosine
  • uracil
  • thymine
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6
Q

How do nucleotides connect together to form the backbone?

A
  • 5’ carbon bound to phosphate
  • 3’ carbon of another nucleotide bound to the same phosphate
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7
Q

What arrangement is a DNA sequence always written in?

A

5’ to 3’

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8
Q

What direction does DNA or RNA extend?

A

3’

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9
Q

What and how adds nucleotides to growing DNA or RNA strands?

A
  • DNA polymerase
  • nucleotide that is to be added is a triphosphate as DNA synthesis requires energy
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10
Q

What direction will an arrow head always go on?

A

3’

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11
Q

What were the 3 different theories of DNA replication?

A
  • conservative
  • semiconservative
  • dispersive
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12
Q

Name 3 challenges of DNA replication

A
  • replicate all bases of very long strands
  • do it accurately with minimal mistakes
  • mechanistic stress is put on the strand during unwinding and when replication comes across genes that are being transcribed, need to avoid breaking strand
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13
Q

Explain bacterial DNA polymerase III

A
  • very accurate
  • one error every 10^7 bases
  • if any errors are missed they are removed by the repair system on the pol called the exonuclease
  • this is an active site on the pol
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14
Q

What is the function of topoisomerase?

A
  • when replication machinery os moving along the strand it generates super coils
  • Topoisomerase unwinds these coils
  • causes breaks then reseals the DNA
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15
Q

What is the process of DNA replication in prokaryotes?

A
  • helicase separates strands
  • RNA primers synthesised by primase (around every 500bp for the lagging strand)
  • DNA Pol III extends new strands
  • on the leading strand it will continue to the end, on lagging strand it will continue to the next primer
  • DNA Pol I removes primer, and fills in this gap
  • DNA ligase seals the nick between fragments by connecting a phosphate on the 5’ end to the ribose on the 3’ end
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16
Q

What is the role of DNA Pol I?

A
  • exonuclease
  • removes RNA primer and replaces with newly synthesised DNA
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17
Q

What is the role of Pol III?

A
  • main enzyme that adds nucleotides in the 5’-3’ direction
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18
Q

What is the role of helicase?

A
  • opens the DNA helicase by breaking hydrogen bonds between nitrogenous bases
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19
Q

What is the role of ligase?

A
  • seals the gaps between Okazaki fragments to create one continuous DNA strand
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20
Q

What is the role of primase?

A
  • synthesises RNA primers needed to start replication
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21
Q

What is the role of the sliding clamp?

A
  • helps hold the DNA polymerase in place while nucleotides are being added
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22
Q

What is the role of single-strand binding proteins (SSB)?

A
  • binds to single-stranded DNA to avoid DNA rewinding back
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23
Q

Name _ differences in the replication fork in eukaryotes and prokaryotes

A
  • different DNA polymerases in eukaryotes
    • Pol alpha
    • Pol delta
    • Pol epsilon
  • replicative helicase move on lagging strand in prokaryotes and the leading strand in eukaryotes
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24
Q

What is the roles of pol alpha, pol delta and pol epsilon?

A

pol alpha - synthesises first stretch of DNA after primer

pol delta - primary lagging strand polymerase

pol epsilon - primary leading strand polymerase

25
What is the origin in the bacterial genome?
the replication start site
26
Describe replication in the bacterial genome
- replications starts at the origin and goes in both directions around the circle and stops opposite the origin - replication is not tied to cell division, they can accumulate 4-8 copies then dive without replication
27
How does DNA replication initiate in bacteria?
- Genome has an A-T rich region and DNA binding sites - DnaA protein binding to DNA makes the A-T rich region melt - ssDNA formed becomes a substrate for loading replicative helicase to unwind the strands further - primase makes RNA primers on both strands and starts leading strand replication by Pol III in both directions - after replication DnaA wint bind for a bit so replication does happen too often
28
What is oriC?
the origin of replication in E.coli
29
Explain origin of replication in eukaryotes
eukaryotes need multiple origins of replication - mid, early and late origins of replication depending where in S-phase are initiated
30
What is a replicon?
- a DNA region replicated from a single origin - in prokaryotes every piece of circular DNA is a replicon - in eukaryotes the number of replicons is normally lower than number of origins as not all will be used
31
What are unused origins in eukaryotes called?
dormant
32
What is the end replication problem?
- each round of replication leaves 50-200bp DNA unreplicated at the 3'end - primers do not lie right to the end
33
What are telomeres and what is their role?
- at the end of linear chromosomes - non-coding DNA which is repetitive and G-C rich - all vertebrates have the same sequence of TTAGGG - proteins recognise this and bind - complex formed in humans is called sheltering - creates a gap that prevents DNA degradation - in many species the 3' end is longer than the 5' end
34
explain the overhangs in DNA replication draw it out
- 3' parental strand is longest - 5' replicated strand is shorter to create a 3' overhang - 3' replicated strand is same length as 5' replicated overhang - 5' parental is shorter then 3' replicated to create 3' overhang
35
What is the role of telomerase?
- extends telomeres - reverse transcriptase - uses an RNA template that is part of the complex
36
What is the definition of a DNA nick?
one of the two strands has a break in the sugar-phosphate backbone. but no nucleotides are missing
37
What is the definition of a DNA gap?
one of the two strands is broken and missing one or more nucleotides
38
What does an arrow show?
the 3' end
39
What are the 3 types of DNA end in dsDNA?
- blunt end - 3' overhang - 5' overhang
40
name 2 structures of branched DNA
- 3-way junction - replication fork - 4-way junction - holiday junction
41
What are the 2 different helices and how are they different?
- hexametric helicase - forms a ring around DNA - monomeric helicase - DNA slides through
42
What prevents helices from annealing?
ss binding proteins in batteris and RPA (replication protein A) in eukaryotes
43
does helicase require energy?
it needs ATP
44
Explain helicase directionality
- different helices move in different directions - some can more 3' to 5' others can move 5' to 3'
45
name 6 different types of nuclease
- ss specific 5' - 3' exonuclease - ss specific endonuclease - will cleave both strands - ss specific 3' - 5' exonuclease - ds specific 5' - 3' exonuclease - ds specific endonuclease - will cleave both strands - ds specific 3' - 5' exonuclease
46
explain endonucleotides and circular DNA
Only they can attack circular DNA as exonuclease need DNA ends
47
what is the joint activity of helices and ssDNA specific nucleases?
- create a 3' overhang - helicase create a substrate for the exonuclease - importune for DNA repair by recombination
48
Name 4 different nucleic acid polymerases
- DNA polymerase - DNA dependent - DNA polymerase - RNA dependent - RNA polymerase - DNA dependent - RNA polymerase - RNA dependent
49
What is a replicase?
- DNA polymerase - DNA dependent prokaryotes - Pol I - Pol III eukaryotes - pol alpha - pol delta - pol epsilon
50
What are reverse transcriptases?
- DNA polymerases - RNA dependent - telomerase - ones coded by retroviruses (HIV)
51
What are transcriptases?
- RNA polymerase - DNA dependent - transcription RNA polymerase - primases
52
What are RNA replicases?
- RNA polymerase - RNA dependent - RNA virus undergo RNA replication and code for RNA replicases
53
What is nascent DNA?
the newly formed DNA
54
What is processivity of DNA polymerases?
- how well the polymerase binds to the DNA - polymerases less processive in vitro
55
What is a clump?
- closed ring which slides along DNA with polymerase which cannot fall off - it is not an enzyme but a structural protein - stabilises replication and repair enzymes
56
What is the eukaryotic clump?
PCNA - proliferative cell nuclear antigen
57
What is a clump loader?
- an enzyme - catalyses opening of clump ring using ATP - interactions between subunits are disrupted
58
Describe DNA replication in eukaryotes
- primase creates RNA primer - Pol alpha extends just after primer - Pol delta is primary lagging strand polymerase - Pol epsilon is primary leading strand polymerase - RNAse removes primer - Pol alpha fills gap left by primer - ligase seals the nick

2B: Genetics and Evolution (25 decks)

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