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MBG 2040 > Replication > Flashcards

Replication Flashcards

1
Q

Complementary DNA pairs

A

A+T and C+G

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2
Q

Pyrimadine

A

C+T

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3
Q

Purine

A

G+A

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4
Q

How many bp in a turn of the DNA double helix?

A

10 bp/turn

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5
Q

Length of a helical turn?

A

3.4 nm/turn

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6
Q

Distance between bases?

A

0.34 nm

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7
Q

DNA replication is?

A

Semi-conservative:

After one round of DNA replication, each DNA contains one parental and one newly-synthesized strand.

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8
Q

What is DNA synthesis not?

A

Conservative: Formation of a completely new molecule; after one round one parental molecule and one new molecule.

Dispersive: Parental molecule is completely disrupted and reassembled to make a new strand; half of the ds-DNA is the parental and the other half of the helix is new.

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9
Q

Why is DNA replication important?

A

Ensures an exact copy.

If DNA failed to copy, meiosis and mitosis would not occur, and life would not exist.

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10
Q

What are the three modes of DNA replication?

A

Theta replication, Rolling circle replication, Linear chromosome replication.

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11
Q

What is theta replication?

A

(Unwind, replication bubble, replication fork, replication)

  • Occurs in most circular DNA
  • Replication is bidirectional
  • Two circular DNA molecules are produced
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12
Q

What is rolling circle replication?

A

(Break in nucleotide strand, replication of inner strand, cleavage releases a ss-linear DNA and ds-DNA)

  • Occurs in the F factor of some viruses
  • Replication is unidirectional
  • Produces multiple circular DNA molecules
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13
Q

What is linear chromosome replication?

A

(Unwinding, replication bubble, DNA synthesis on both strands at each end of the bubble as replication forks form, forks meet and segments fuse)

  • In eukaryotes
  • Replication is bidirectional
  • Produces two linear DNA molecules
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14
Q

What is required for DNA replication?

A
  • Requires magnesium
  • DNA polymerase
  • dNTPs
  • A template strand
  • RNA primer
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15
Q

What are the features of DNA replication?

A
  • Synthesized 5’ to 3’
  • New strand is complementary and antiparallel to template
  • Held together by hydrogen bonds
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16
Q

DNA chains are susceptible to nuclease cleavage…

A

… can cleave a phosphate group attached to 5’ or 3’ carbon
(gamma, beta, alpha phosphate attached to nitrogenous base)

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17
Q

What is a nucleotide?

A

Phosphate group + a sugar + a nitrogenous base

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18
Q

Where is DNA synthesis continuous?

A

On the leading strand

- By polymerase III

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19
Q

Where is DNA synthesis discontinuous?

A

On the lagging strand creating Okazaki fragments (short fragments of DNA produced by discontinuous synthesis).
- By polymerase III and polymerase I fills in the gaps

20
Q

Where does DNA replication begin?

A

From an “origin”

21
Q

What does prokaryotic DNA replication consist of?

A
  • oriC orgin site
  • four dnaA binding sites
  • an AT rich region that undergoes strand seperatio n
22
Q

What is helicase?

A

Unwinds DNA in the 5’ to 3’ direction

  • Breaks hydrogen bonds and moves the replication fork
  • Binds to the lagging-strand template at each replication fork
23
Q

What are single-strand-binding proteins?

A

Immediately binds to the single-stranded DNA after helicase unwinds it.

  • Keeps DNA linear so it does not fold back on itself
  • Allows DNA to be easily replicable
24
Q

What is DNA gyrase?

A

Topoisomerase II:

  • Encircles DNA and removes torsional stress caused by the helicase unwinding which causes positive supercoils that can stop replicaiton (no more unwinding)
  • Nicks DNA to release supercoils
  • Relieves strain ahead of the replication fork
25
Q

What is an initiator protein?

A

DnaA, binds to oriC and causes a short stretch of DNA to unwind so helicase and ssb proteins can attach.

26
Q

What is topoisomerase II?

A

DNA gyrase

27
Q

What is DNA primase?

A

Synthesizes a short RNA primer that provides the 3’ OH end for the DNA polymerase to begin DNA synthesis

  • Essential to start replication
  • Only one primer is needed on the leading strand
  • A primer is needed for every Okazaki fragment
28
Q

How many DNA polymerases are in E. coli?

A

Five: Polymerase I, II, II, IV, and V.

29
Q

Which polymerases in prokaryotes are used for replication?

A

Polymerases I and III

30
Q

Which polymerases in E. coli are used for DNA repair?

A

Polymerase II, IV, and V

31
Q

What is the function of DNA polymerase I?

A
  • Aids in the removal of primers
  • Has 5’ to 3’ polymerase and 5’ to 3’ exonuclease activity Can remove RNA primer and re-synthesize a short tract of DNA
  • Proofreading: has 3’ to 5’ exonuclease activity
  • Short tract synthesis
  • Mostly lagging strand
32
Q

What is the function of DNA polymerase III?

A
  • Main polymerase
  • 5’ to 3’ polymerase activity
  • Proofreading: has 3’ to 5’ exonuclease
  • DOES NOT HAVE: 5’ to 3’ exonuclease activity; in this case polymerase I takes over
33
Q

What is 5’ to 3’ exonuclease?

A

Can chew away at 5’ RNA primers and fill gaps with DNA.

34
Q

What is 3’ to 5’ exonuclease?

A

Corrects mistakes polymerase may make

35
Q

What is the beta-sliding clamp?

A

A ring-shaped polypeptide that encircles the DNA

  • Interacts with polymerase III
  • Helps to keep ssb proteins on
36
Q

What is DNA ligase?

A

Seals the nick in fragments of DNA with a phosphodiester bond

37
Q

How are both strands able to replicate simultaneously?

A

DNA must form a loop so that 5’ to 3’ synthesis can take place on both anti-parallel strands

38
Q

In what phase of the eukaryotic cell cycle does replication begin?

A

Prepared for replication in G1 phase, actual replicating begins in the S phase.

39
Q

What are short telomeres associated with?

A

Low telomerase activity:

Cellular senescence and cell death, diseases causing premature aging: Progeria, werner’s syndrom.

40
Q

What are long telomeres associated with?

A

High telomerase activity: cancer (promotes growth)

41
Q

What are unique aspects of eukaryotic chromosome replication?

A
  • Shorter RNA primers and Okazaki fragments
  • DNA replication only during S phase
  • Multiple polymerases (15)
  • Bidirectional replication from multiple origins and on each chromosome
  • Nucleosomes
  • Telomeres: shorten at each round of eukaryotic replication
42
Q

What is the problem with telomeres?

A

Chromosome end will be degraded causing chromosome shortening during every round of replication.
Telomerase activity extends eukaryotic chromosome ends in replicating cells to prevent this.

43
Q

What is the first step in the reaction sequence?

A

Proofread and correct mismatch pairs.

44
Q

Which group of enzymes is responsible for making breaks in DNA?

A

Nucleases

45
Q

What is the role of RNA primer?

A

To provide a free 3’OH substrate for polymerase III

MBG 2040 (1 decks)

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