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

1.5 - DNA Replication Flashcards

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Biology 101 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
Q

What is the origin in the bacterial genome?

A

the replication start site

26
Q

Describe replication in the bacterial genome

A
  • 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
Q

How does DNA replication initiate in bacteria?

A
  • 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
Q

What is oriC?

A

the origin of replication in E.coli

29
Q

Explain origin of replication in eukaryotes

A

eukaryotes need multiple origins of replication
- mid, early and late origins of replication depending where in S-phase are initiated

30
Q

What is a replicon?

A
  • 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
Q

What are unused origins in eukaryotes called?

A

dormant

32
Q

What is the end replication problem?

A
  • each round of replication leaves 50-200bp DNA unreplicated at the 3’end
  • primers do not lie right to the end
33
Q

What are telomeres and what is their role?

A
  • 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
Q

explain the overhangs in DNA replication
draw it out

A
  • 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
Q

What is the role of telomerase?

A
  • extends telomeres
  • reverse transcriptase - uses an RNA template that is part of the complex
36
Q

What is the definition of a DNA nick?

A

one of the two strands has a break in the sugar-phosphate backbone. but no nucleotides are missing

37
Q

What is the definition of a DNA gap?

A

one of the two strands is broken and missing one or more nucleotides

38
Q

What does an arrow show?

A

the 3’ end

39
Q

What are the 3 types of DNA end in dsDNA?

A
  • blunt end
  • 3’ overhang
  • 5’ overhang
40
Q

name 2 structures of branched DNA

A
  • 3-way junction - replication fork
  • 4-way junction - holiday junction
41
Q

What are the 2 different helices and how are they different?

A
  • hexametric helicase - forms a ring around DNA
  • monomeric helicase - DNA slides through
42
Q

What prevents helices from annealing?

A

ss binding proteins in batteris and RPA (replication protein A) in eukaryotes

43
Q

does helicase require energy?

A

it needs ATP

44
Q

Explain helicase directionality

A
  • different helices move in different directions
  • some can more 3’ to 5’ others can move 5’ to 3’
45
Q

name 6 different types of nuclease

A
  • 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
Q

explain endonucleotides and circular DNA

A

Only they can attack circular DNA as exonuclease need DNA ends

47
Q

what is the joint activity of helices and ssDNA specific nucleases?

A
  • create a 3’ overhang
  • helicase create a substrate for the exonuclease
  • importune for DNA repair by recombination
48
Q

Name 4 different nucleic acid polymerases

A
  • DNA polymerase - DNA dependent
  • DNA polymerase - RNA dependent
  • RNA polymerase - DNA dependent
  • RNA polymerase - RNA dependent
49
Q

What is a replicase?

A
  • DNA polymerase - DNA dependent

prokaryotes
- Pol I
- Pol III

eukaryotes
- pol alpha
- pol delta
- pol epsilon

50
Q

What are reverse transcriptases?

A
  • DNA polymerases - RNA dependent
  • telomerase
  • ones coded by retroviruses (HIV)
51
Q

What are transcriptases?

A
  • RNA polymerase - DNA dependent
  • transcription RNA polymerase
  • primases
52
Q

What are RNA replicases?

A
  • RNA polymerase - RNA dependent
  • RNA virus undergo RNA replication and code for RNA replicases
53
Q

What is nascent DNA?

A

the newly formed DNA

54
Q

What is processivity of DNA polymerases?

A
  • how well the polymerase binds to the DNA
  • polymerases less processive in vitro
55
Q

What is a clump?

A
  • 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
Q

What is the eukaryotic clump?

A

PCNA - proliferative cell nuclear antigen

57
Q

What is a clump loader?

A
  • an enzyme
  • catalyses opening of clump ring using ATP
  • interactions between subunits are disrupted
58
Q

Describe DNA replication in eukaryotes

A
  • 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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