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Biochem > Basic Concepts of DNA Replication > Flashcards

Basic Concepts of DNA Replication Flashcards

1
Q

DNA replication is

A

Semiconservative

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2
Q

one strand of the parent double helix is

A

conserved in each new

DNA molecule.

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3
Q

Initiation process

A

1- unwinded of DNA

2- breaking the hydrogen bonds

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4
Q

Proteins/enzymes involved in DNA replication

A
  • DnaA
  • Helicase
  • Single strand binding proteins
  • Topoisomerase l
  • Topoisomerase lol
  • Primase
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5
Q

Elongation (Proteins / Enzymes involved in DNA replication)

A

DNA polymerase lll

3’-5’ exonuclease

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6
Q

RNA primers removal & the gap filling with DNA

A
  • DNA polymerase l
  • 5’-3’ exonuclease
  • 3’-5’ exonuclease
  • Ligase
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7
Q

Chromosome end replication problem & process in Eukaryotes

A
  • telomerase
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8
Q

In prokaryotes, DNA replication begins at a site called

A

The origin of replication (ori)

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9
Q

The ori contains specific

A

A/T rich sequences

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10
Q

Why ones the ori contain specific A/T rich sequences?

A

The double bonded A/T-rich regions are relatively weaker to break than the triple bonded G/C-rich region.

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11
Q

1st DnaA rote in binds onto the Ori site

WHYY??

A

stretches the double strand DNA each other.

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12
Q

When the two strands unwindthey create a a Y-shaped structure in both sides called

A

Replication fork

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13
Q

Replication fork allows to start the replication

A

Bi-directionally

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14
Q

Helicase binds to the replication fork and unwinds the duplex DNA by

A

breaking the hydrogen bonds and using ATP as energy source.

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15
Q

Single stranded binding proteins

A

SSB helps to keep the two strands of DNA separated so that the DNA polymerase can bind and start replication.

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16
Q

SSB

A

Protect the DNA from uncleared the might degrade single stranded DNA

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17
Q

Supercoiled DNA will be unwound by

A

DNA Topoisomerase

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18
Q

DNA Topoisomerase

A

Cuts the DNA strand,
Unwinds the super coil,
And reseals the cut.

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19
Q

To initiate replication

A

DNA polymerase requires a RNA primer

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20
Q

RNA primer is synthesized by

A

primase

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21
Q

Primase, a RNA polymerase enzyme

A

synthesizesa short stretch of RNA (~10 nts long) that are complementary and antiparallel to the DNA template.

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22
Q

What starts synthesizing the complementary DNA strand after putting small RNA primer?

A

DNA polymerase III

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23
Q

DNA polymerase III is a

A

Holoenzyme

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24
Q

DNA polymerase enzyme activities are

A

5’-3’ DNA polymerase

3’-5’ exonuclease

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25
Q

DNApolymeraseIIIholoenzymeencirclesthe DNA strand forming like a

A

sliding clamp and moves along the template strand.

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26
Q

The strand synthesized in the 5’→3’ direction towards the replication fork

A

leading strand

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27
Q

The strand synthesized in the 5’→3‘ direction opposite to the replication fork

A

is known as lagging strand

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28
Q

In leading strand

A

Use not one RNA primer

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29
Q

On the lagging strand template, primase continuously synthesizes many RNA primers…Why ?

A

Because, in lagging strand, primase waits for the helicase breaking the replication fork

30
Q

DNA polymerase III extends each RNA primer as a short DNA fragment of ~ 1000 nts.

A

These fragments are called Okazaki fragments

31
Q

DNA replication is

A

Semi-discontinuous

32
Q

DNA polymerase III can naturally make an error every

A

10^7 nucleotide pairs

33
Q

The 3’→5’ exonuclease activity of DNA polymerase III

A

will remove the incorrect nucleotide.

34
Q

Then the 5’-3’ polymerase subunit of DNA polymerase III

A

Replaces is with the correct nucleotide

35
Q

all the RNA primers synthesized by primase should be removed from the DNA.

A

This creates many gaps in the newly synthesized DNA including in between Okazaki fragments

36
Q

The gap will be filled by the

A

DNA polymerase I

37
Q

Major three activities of DNA polymerase I

A

5’-3’ polymerase
5’-3’ exonuclease
3’-5’ exonuclease

38
Q

5’-3’ exonuclease

A

Removes RNA primer from 5’ to 3’ direction

39
Q

5’-3’ polymerase of DNA polymerase I

A

Fills the gap

40
Q

3’-5’ exonuclease

A

Proofreads if an roar occurs during synthesis

41
Q

The 3’-5’ exonuclease

A

remove only one nucleotide at the 3’ end

42
Q

The 5’-3’ exonuclease

A

remove many nucleotides from the 5’ to 3’ direction

43
Q

the newly synthesized all DNA fragments will be linked with phosphodiester bonds by

A

The enzyme DNA ligase

44
Q

Ori of replication for prokaryotes

45
Q

Ori of replication for eukaryotes

A

Multiple sites

46
Q

RNA primer synthesis for prokaryotes

A

By primase

47
Q

RNA primer synthesis for eukaryotes

A

Polymerase α (alpha)

This also initiates DNA synthesis

48
Q

Leading strand synthesis & proof reading for prokaryotes

A

DNA polymerase III

3’-5’ exonuclease

49
Q

Leading strand synthesis & proof reading for eukaryotes

A

Polymerase ε (pol ε)

3’-5’ exonuclease

50
Q

RNA primer removal for prokaryotes

A

5’-3’ exonuclease activity of DNA polymerase I

51
Q

RNA primer removal for eukaryotes

A

RNase H & flap endonuclease

52
Q

RNA primer gap is filled by DNA for prokaryotes

A

DNA polymerase I

53
Q

RNA primer gap is filled by DNA for eukaryotes

A

Polymerase ε

54
Q

Lagging strand synthesis & proof reading in eukaryotes

A

Polymerase γ

55
Q

tandem repetitive nucleotides

A

Is a telomere

56
Q

Telomere is located at

A

At end of each eukaryotic chromosome

57
Q

In humans, average telomere length decrease from

A

11 kb ——> 4 kb

58
Q

Telomere will not be shortened in

A

Germ cells
Stem cells
Cancer cells

Because of the telomerase enzyme

59
Q

Telomerase activity

A 
RNA nucleotides (UCCCAA) template 
Reverse transcriptase activity
60
Q

Telomerase activity is naturally inhibited in

A

Normal somatic cells

61
Q

telomerase synthesizes complementary telomere repeat (AGGGTT) at the 3’ end of the full length leading strand (5’-3’ direction) by using its

A

reverse transcriptase activity & RNA template (UCCCAA)

62
Q

Inhibition of Viral DNA replication in the host cells by

A

nucleoside analogs

63
Q

Didanosine

A

Used to treat HIV patients

Anti-retro viral medacation

64
Q

Didanosine

A

2’,3’ dideoxyinosine

ANALOG OF ADENOSINE

65
Q

In didanosine

A

3’-OH group on the deoxyribose sugar moiety has been replaced by hydrogen.

66
Q

Azidothymidine = zidovudine = (AZT)

A

Analog of thymidine

Antiretroviral medication

67
Q

In AZT the 3’OH group

A

replaced by an azido group

68
Q

Camptothecin (CPT)

A

Is Topoisomerase I inhibitor

69
Q

CPT binds to the DNA at the topoisomerase I

cleavage site

A

And it prevents DNA uncoiling and thus inhibiting the replication of cancer cells.

70
Q

Etoposide

A

topoisomerase II inhibitor.

Biochem (8 decks)

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