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Biochemistry > L2 > Flashcards

L2 Flashcards

1
Q

Starts the initiation of DNA replication

A

DNAa

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2
Q

Binds to the replication fork and unwinds duplex DNA by breaking hydrogen bond using ATP

A

Helicase

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3
Q

Uses ATP

A

Helicase

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4
Q

Keeps strands to separate

A

SSBP

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5
Q

Protects single strand DNA from nucleases

A

SSBP

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6
Q

Breaks one strand from super coil

A

Topoisomerase 1

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7
Q

Breaks the two strands from super coil

A

Topoisomerase2

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8
Q

Synthesizes RNA primer from polymerases (prokaryotes)

A

Primase

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9
Q

A Holoeenzyme that includes 10 subunits that work together for DNA replication (prokaryotes)

A

DNA polymerase 3

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10
Q

Removes incorrect nucleotides when proofreading

A

3’-5’ exonuclease

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11
Q

A holoenzyme that fills the gap in the DNA due to the removal of primers (prokaryotes)

A

DNA polymerase 1

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12
Q

Removes primer from 5’-3’ creating gaps

A

5’-3’ exonuclease of dna pol1

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13
Q

Links DNA fragments with phosphodiester bonds

A

Ligase

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14
Q

The origins of replication in prokaryotes is about ___ bplong

A

245

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15
Q

Ori is mostly contains A/T-rich sequences. Why?

A

ThedoublehydrogenbondedA/T-rich regions are relatively weaker to break than the triple bonded G/C-rich sequences

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16
Q

Stretches the double stranded DNA

A

DnaA

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17
Q

Creates a bubble or Y-shaped structure

A

Stretching of DNA by the help of DNAa

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18
Q

What is the significance of the Y-shaped replication fork

A

Bi directional replication

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19
Q

SSB function (2)

A

protect the DNA from nucleases that might degrade single stranded DNA.

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

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20
Q

Cytidinetriphosphate —> Cytidine monophosphate what had happened?

A

-2p by DNA polemerases 3 when catalyzing a strand

Explanation: Itcatalyzesaddingdeoxynucleotidetriphosphatess(dATP,dTTP, dGTP & dCTP) to the elongating chain & releasing two phosphate molecules (pyro phosphate) from them thereby incorporating a deoxy nucleotide monophosphates.

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21
Q

The DNA strands synthesized from the origins of replication to the replication fork is called

A

Leading strand

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22
Q

DNA strands synthesized from the replication fork to the origin of replication is known as

A

Lagging strand

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23
Q

DNA polymerases reads the parental strand in ___ Direction
what synthesize is a complementary strand in _ direction

A

3’-5’
5’-3 Antiparallel

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24
Q

Interpret: DNA synthesis is semicontinuous

A

The lagging strand is this continuous, while the leading strand is continuous

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25
Q

The 3’→5’ exonuclease activity of DNA polymerase III will remove the incorrect nucleotide”proof read” , why is it 3’→5’ ?

A

Because DNA polymerases runs antiparallel from 5 to 3, so the last sequence is 3.

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26
Q

DNA polymerase 3 can naturally make an error in every ___nucleotide pairs

A

10^7

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27
Q

Leading strand __#gap__# primer
Lagging strand __#gap__# primer 

A

1,1
Many, many

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28
Q

After synthesizing the lagging strand DNARNA primers should be removed. The removal of RNA primers will create gaps in the newly synthesized complementary DNA how to fix this problem.

A

DNA polymerase one will fill the gap with DNA nucleotides

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29
Q

What are the three major activities of DNA polymerase one

A

5’→3’ Exonuclease
• removes the RNA primer from 5’ to 3’ direction.

3’→5’ Exonuclease
•proof reads and corrects the nucleotide mismatch error during synthesis.

5’→3’Polymerase
• fills the gap with DNA
• However, polymerase needs a primer. Where is the primer ?.
• The 3’ end of Okazaki fragment will be used as primer.

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30
Q

What is the major difference between DNA polymerase 1 and 3 using the following terms:
5’-3’ Polymerase
3’-5’ Exonuclease
5’-3’ Exonuclease 

A

Both have
5’-3’ Polymerase —> synthesis
3’-5’ Exonuclease —> proof reading

1 has
5’-3’ exonuclease to remove rna primer

31
Q

What is the difference between endonuclease and exonuclease

A

Endo—> cunts between dna
Exo —> cuts at the end

32
Q

In eukaryotes, multiple(ori) sites are needed for replication. Why?

A

greater length of the eukaryotic DNA.

33
Q

contrast between prokaryotes first and eukaryotes next:

Ori

34
Q

contrast between prokaryotes first and eukaryotes next:
RNA primer synthesis

A

Primase
Polymerase alpha

35
Q

contrast between prokaryotes first and eukaryotes next:

Leading strand synthesis

A

DNA polymerase 3
Polymerase E

36
Q

contrast between prokaryotes first and eukaryotes next:
Lagging strand synthesis

A

DNA polymerase 3
Polymerase s

37
Q

contrast between prokaryotes first and eukaryotes next:
Proof reading

A

3’-5’ exonuclease for both

38
Q

contrast between prokaryotes first and eukaryotes next:
RNA primer removal

A

5’-3’ exonuclease of DNA POL1
RNase + REN1

39
Q

contrast between prokaryotes first and eukaryotes next:

RNA primer gap is filled with DNA by

A

DNA POL1
Polymerase E

40
Q

During eukaryotic somatic cell division replication at thechromosome end (telomere) is always a problem in the___ strand.

41
Q

the gap created at the 5’ end of the lagging strand upon the removal of the primer can’t be filled with DNA by polymerase because

A

There is no primer for DNA POL

42
Q

Eukaryotic normal somatic cells,
telomeres will therefore be shortened with each successive cell division why?

A

After FEN1 and RNase remove the primers, polymerase E cannot add nucleotides therefore it will permanently be shortened.

43
Q

No end replication problem in cancer cells, germs cells or stem cells why?

A

Dna telomerases

44
Q

Telomerase is an enzyme and composed of

A

Reverse transcriptase
RNA nucleotides template

45
Q

Reverse transcriptase is also known as

A

RNA-dependent DNA polymerase—> synthesize complementary DNA from RNA template.

46
Q

In germ, stem and cancer cells, telomerase helps synthesizing ____DNA at the end of the____ strand using its RNA template

A

telomeric repeat

lagging

47
Q

In Normal somatic cells synthesizing telomeres at the telomeric end is it not possible why

A

Because telomerase activity in naturally inhibited

48
Q

Telomerase synthesizes telomere DNA repeat at the 3’ end of the leading strand, instead of filling the gap in lagging strand, Why…?

A

Because,polymerase can add nts ONLY in the5’-3’direction using the 3’-OH of last nucleotide

49
Q

T/F?

polymerase can add nts ONLY in the 5’-3’direction using the 3’-OH of last nucleotide

50
Q

Telomerase synthesizes telomere DNA repeat steps

A

1- Polymerase a (primase) synthesizes a RNA primer on the LAGGING strand complementary to the leading strand

2-DNA Polymerase s(pol s) fills the gap till it hits the 5’ end of the lagging strand.

3-Ligase seals the DNA fragments

4-RNA primer will be removed by RNase H & FEN1

51
Q

T/F? its better that telomerase synthesizes telomeric repeats and looses few bases

A

T
Because telomeres sacrifice themselves


52
Q

Telomerase synthesizes telomere DNA repeat on the __ strand

53
Q

Explain how Didanosine or 2’,3’-dideoxyinosine (DDI) works

A
  • is an analog of ATP (Adenosine).
    the 3’-OH group on the deoxyribose sugar moiety has been replaced by hydrogen —> prevents formation of phosphodiester bonds between the 3’-OH and 5’-phosphate
54
Q

Azidothymidine (AZT) also known as

A

Zidovudine

55
Q

Azidothymidine is an analog of

56
Q

In AZT, the 3’-OH group on the deoxyribose sugar moiety has been replaced by

A

azido group (N3)

57
Q

What are the 2 nucleoside analogs

A

AZT=thymidine
DDI=adenosine

58
Q

Inhibition of DNA replication in cancer cells by Anti-cancerous drugs include

A

Camptothecin, T1 inhibitor

Etoposide, T2 inhibitor

59
Q

How does Anti-cancerous drugs work

A

binds to the DNA at the topoisomerase I
cleavage site and prevents the uncoiling of DNA and thus inhibiting the replication of cancer cells

60
Q

Results in replication fork

61
Q

Releases torsional strains

A

Topoisomerase

62
Q

How are the okazaki fragments bound together

63
Q

Although somatic cells have telomerase, they cannot synthesize telomeres why

A

It is naturally inhibited

64
Q

Stretches DNA

65
Q

Aids in genetic motility

A

Reverse transcriptase

66
Q

Antiviral drugs DNA termination Depends on failing ___
While Anti-can serious drugs depends on failing ___

A

Phosphodiester bonds
Topoisomerase 1 and 2

67
Q

What is the last step of DNA replication

A

Ligation of okazaki fragments

68
Q

MAIN function of DNA polymerase

A

Adding nucleotides

69
Q

Synthesis complementary DNA using DNA template

A

DNA polymerase

70
Q

Synthesize complementary RNA using DNA template

A

RNA polymerase, primase

71
Q

Synthesize complementary DNA using RNA template

A

Reverse transcriptase, telomerases

72
Q

What type of a polymerase is Telomerase

A

RNA dependent DNA polemerase, reverse transcriptase

73
Q

Why primer is needed to synthesize RNA primer for the initiation of DNA replication why not use the DNA polymerase to synthesize the RNA primer

A

Because DNA polymerase is DNA dependent DNA not RNA dependent DNA.

74
Q

T/F: primase is an
DNA dependent RNA polymerase
Or
RNA dependents DNA polymerase

Biochemistry (9 decks)

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