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Block One > HRR: DNA synthesis > Flashcards

HRR: DNA synthesis Flashcards

1
Q

what is semiconservative replication

A

each DNA molecule has a parent strand and a daughter strand

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2
Q

bonds formed with DNA polymerase are formed ___’ to ___’

A

3 to 5

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3
Q

DNA synthesis occurs ___’ to ___’

A

5 to 3

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4
Q

complementary base pairing is required ___ forming 3’ to 5’ bonds

A

before

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5
Q

what does DNA need in order for the polymerase to work?

A

a free 3’ hydroxyl end

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6
Q

prokaryotic DNA polymerase I: function

A

removes the primer and helps fill in the gaps on the lagging strand. Single protein folded into a tertiary structure with three functional domains: 5 to 3 exonuclease, 3 to 5 exonuclease, and 5 to 3 polymerases

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7
Q

prokaryotic DNA polymerase II

A

involved in repair; not required for replication. has 5 to 3 elongation and 3 to 5 exonuclease

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8
Q

prokaryotic DNA polymerase III

A

main one; synthesizes leading and lagging strands. has 5 to 3 elongation and 3 to 5 exonuclease

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9
Q

describe the functions of 5 to 3 exonuclease, 3 to 5 exonuclease, and 5 to 3 polymerase

A
  • 5’ to 3’ exonuclease: removes primer
  • 3’ to 5’ exonuclease proofreads
  • 5’ to 3’ polymerase forms phosphodiester bonds at 10 per second
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10
Q

Define the functions of the a, b and e subunits of DNA polymerase III in DNA replication of prokaryotes.

A

A: 5 to 3 polymerase activity of 1000 nucleotides per second

B: form dimers around the strand called a sliding clamp. This helps the enzyme go quickly.

E: 3 to 5 exonuclease activity for proofreading. If the polymerase messes up, this will stall it and correct the mistake

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11
Q

what is in the central component of DNA Pol III

A

the clamp loader and helicase

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12
Q

Specify the 3 main mechanisms that contribute to the high fidelity of DNA replication.

A

-Complementary base pairing by DNA polymerase

  • Proofreading: performed by 3 to 5 exonucleases. The polymerase will be stalled, the 3 to 5 bond will be hydrolyzed and the base will be removed, and DNA polymerase will place the correct base in its spot.
  • DNA repair
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13
Q

Describe initiation of DNA synthesis in prokaryotes

A
  • Initiator protein binds to the origin of replication. This recruits the polymerase
  • The helicase in the polymerase starts to unwind the DNA. Single stranded binding proteins help protect the DNA
  • The RNA primers are synthesized
  • The DNA replication bubble is formed. The bubble has two replication forks.
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14
Q

briefly describe a replication fork

A

The replication fork has a leading strand and a lagging strand. The leading is 5 to 3, and lagging is 3 to 5

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15
Q

differentiate between a replication bubble, a replication fork, and an origin of replication

A

The replication bubble has two forks moving in opposite directions. the leading/lagging strands will be on opposite sides of the two forks. The origin of replication is where the initiator binds to recruit the polymerase and form the replication bubble

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16
Q

describe the difference between the leading and lagging strands

A
  • the leading strand is primed once, while the lagging strand is primed multiple times
  • the leading strand is synthesized continuously, while the lagging strand is synthesized in smaller pieces called okazaki fragments.
  • the leading strands runs 5’ to 3’, while the lagging runs 3’ to 5’
17
Q

describe the function of primase

A

Primase: enters with helicase/polymerase. It is complementary to the template and allows the DNA polymerase to begin synthesis via a free 3’ hydroxyl group

18
Q

describe the function of helicase

A

Helicase helps unwind the DNA

19
Q

describe the function of topoisomerase

A

Topoisomerase in prokaryotes can either relax positive/negative supercoils or crease negative supercoils to prevent issues with the DNA winding

20
Q

Which strand “loops” during synthesis? What is the function of this?

A

The lagging strand: it allows the pol III to synthesize both stands at the same time. The clamp on the loop with dissociate and reassociate to release the slack on the loop while forming Okazaki fragments

21
Q

Explain the role of DNA ligase in the synthesis of the lagging strand.

A

It catalyzes the formation of the phosphodiester bond between Okazaki fragments

22
Q

What are the main DNA polymerases in eukaryotes

A

Alpha, delta, epsilon

23
Q

describe the alpha subunit of DNA polymerase in eukaryotes

A

generates RNA-DNA primers to initiate lagging strand synthesis

24
Q

describe the delta subunit of DNA polymerase in eukaryotes

A

main enzyme for synthesizing the lagging strand and helps fill the gaps between Okazaki fragments

25
Q

describe the epsilon subunit in DNA polymerase in eukaryotes

A

main enzyme for synthesizing the leading strand

26
Q

What is PCNA in eukaryotic DNA synthesis

A

A sliding clap protein that allows for processivity of polymerases epsilon and gamma

27
Q

In eukaryotes, which topoisomerase addresses tangles behind the replication fork?

A

Topoisomerase II

28
Q

Describe initiation of DNA synthesis in eukaryotes

A

As opposed to having one replication bubble, we have multiple per DNA strand. The bubbles ultimately come together and fuse

29
Q

what are telomeres?

A

Repeating DNA sequences at the ends of chromosomes that allow the lagging strand to loop. This allows for the entire strand to replicate without losing DNA, thus protecting the strand

30
Q

specify the functions of telomeres

A
  • Protects the chromosomes from degradation
  • Prevents the ends of DNA joining by ligase
  • Prevents homologous recombination of chromosome ends by recombination enzymes.
31
Q

Do tumor cells have higher or lower telomere activity than normal somatic tissue cell

A

higher

32
Q

what is a telomerase

A

an enzyme that makes telomeres

33
Q

what are the two components of telomerase

A

RNA template: encodes the telomere repeat sequence

reverse transcriptase: synthesizes DNA from RNA template

34
Q

Describe the mechanism by which telomerases “cap” the ends of DNA with telomeres.

A
  • A telomerase brings its RNA template to the parent strand with 3’ overhang
  • The telomerase preforms reverse transcription, synthesizing in the 3’ to 5’ direction
  • The telomerase translocate along the new strand and repeats the process, lengthening the strand
  • The other strand synthesizes via complementary base pairing to the telomere
35
Q

what is the function of RNAase H

A

removing the primer in eukaryotes

Block One (60 decks)

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