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Replication Flashcards

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1
Q

What is replication ?

A

Copying and transformation of genetic information found in DNA to daughter cells

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2
Q

When does replication occur ?

A

S phase of the cell cycle

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3
Q

The process of replication is :

A

Semiconservative process

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4
Q

What does semiconservative mean ?

A

The Newley formed two daughters DNA contain one original old strand and Newley formed complementary strand.

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5
Q

Why is the process of semiconservative important ?

A

To transfer genetic information in the correct sequence.

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6
Q

DNA replication is also ……………………. Process

A

Bidirectional

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7
Q

What does bidirectional mean?

A

The replication forks move in both directions, away from the origin.

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8
Q

Steps of DNA replication :

A
  1. Separation of the two DNA strands
  2. Synthesis of the two DNA strands
  3. End of replication
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9
Q

Separation of the two DNA strands is considered to be the …….

A

Initiation process of replication either in prokaryotes or eukaryotes

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10
Q

Separation of the two DNA strands steps :

A

1)DNA a protein regcognizes the origin of replication , binds to the DNA and separates the two DNA strands at a very small region .
2) recruitment and loading a complex of two proteins : DNA b ( helicase )& DNA c ( helicase loader )
3) Recruitment of DNA primase
4) separation of the double helix by helicase
5) the two separated strands are kept apart by single strand DNA binding protein
6) Removing supercoils in the helix by DNA topoisomerase
7) NOW, each relaxed single strand acts as a template to the direct synthesis of a new daughter DNA strand.

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11
Q

What is the origin of replication ?

A

Specific DNA sequence in which DNA replication starts

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12
Q

Origin of replication in prokaryotes :

A

-it is single
- Named as OriC

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13
Q

Origin of replication in eukaryotes

A

-they are multiple
- termed as autonomous replication sequences
- rich in AT base pairs

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14
Q

DNA a protein function requires

A

ATP hydrolysis

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15
Q

What recruits the helicase-helicase loader complex is :

A

Combination of Single Stranded DNA and DNAa protein

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16
Q

Helicase inactivation is due to :

A

Binging of helicase (DNAb protein ) with the helicase loader ( DNAc protein)

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17
Q

Why is helicase inactivation is such important ?

A

To prevent helicase from functioning at inappropriate sites (Non-origin regions )

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18
Q

The process of helicase- helicase loader loading process requires :

A

Opening of the DNA helicase hexameric ring to encircle the targeted ssDNA .

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19
Q

The enzyme that recruits DNA primase is :

A

Helicase ( DNAb protein )

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20
Q

DNA primase functions

A

1) Synthesis of an RNA primer on each strand of the origin
2) Generating the primers for the legging DNA strands
3) Release of helicase loader

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21
Q

Helicase activation

A

The process of releasing helicase loader by DNA primase

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22
Q

Separation of the double helix by DNA helicase occurs by ( mechanism ) :

A

Breaking down hydrogen bonds btwn the two DNA strands by ATP hydrolysis

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23
Q

The importance of single strand DNA binding protein in replication :

A

1) prevent the double helix from rejoining
2) protect the single stranded DNA from nucleuses ( cleave it )

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24
Q

What is preprimiring complex ?

A

DNAa protein, DNAb protein , DNAc protein , SSB proteins

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25
Q

Why is preprimiring complex significant ?

A

1) Replication initiation
2) Maintaining the separation of the two DNA strands

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26
Q

Supercoils formation :

A

While separating the double helix , this creates coils in front of the separated parts preventing further separation of the helix

27
Q

Topoisomerases Mechanism:

A

By its nuclease activity ( Strand cutting ) : they make transient cut in the phosphodiester bonds in one strand or in two strands
By its ligase activity ( strand resealing )

28
Q

Topoisomerases 1 :

A

Cuts in one strand

29
Q

Topoisomerases 2

A

Cut in both strands

30
Q

What is DNA gyrase ?

A

Topoisomerases 2 , found in plants and bacteria

31
Q

DNA gyrase Function :

A

Introduce negative supercoils into relaxed circular DNA by ATP hydrolysis.

32
Q

DNA gyrase in facilitating the future replication:

A

1)Negative supercoils neutralise positive supercoils introduced during opening of the double helix.
2) aids in the transient strand separation during transcription

33
Q

Clinical significance in Anti-biotics and anti-cancers

A

Antibiotics : quinolone as negram ( Nalidixic acid )
- inhibiting bacterial gyrase preventing bacterial replication and transcription

Anticancer drugs : as etoposide
-target human topoisomerase 2

34
Q

Steps of Synthesis of the DNA strands :

A

1) Synthesis of RNA primers.
2) Synthesis of the DNA strands
3) excision of RNA primers and their replacement by DNA
4) connecting the DNA fragments
5) Proofreading of Newley synthesised DNA

35
Q

Synthesis of RNA primers

A

1) occurs in the direction of ( 5’ - 3’ ) direction
2) By Primase ( RNA polymerase )
3) using ribonucleotide triphosphate ( GTP, CTP , ATP , UTP )

36
Q

Synthesis of the DNA strand

A

1) occurs in (5’ - 3’) direction
2) by DNA polymerase 3
3) Using deoxyribonucleotide triphosphate (d GTP , d CTP , d ATP , d TTP )
4) following the base pairing rule ( DNA sequence that is complementary to the template strand )
5) the first added deoxyribonucleotide triphosphate will form phosphodiester bond with OH at the 3’ end of RNA primer with the removal of pyrophosphate , the next added deoxyribonucleotide triphosphate will form phosphodiester bond with the previous added one with hydrolysis of Pyrophosphate

37
Q

Providing energy for the reaction of connecting DNA nucleotides :

A

Hydrolysis of pyrophosphate from the added triphosphate

38
Q

Each DNA molecule consists of :

A

Leading strand and lagging strands

39
Q

Leading strand is

A

DNA strand that is synthesised continuously, complementary to the parent strand that has the direction of ( 3’ - 5’ ), with the direction of the advancing replication fork

40
Q

Lagging strand

A

DNA strand in which many RNA primers are required to form Okazaki fragments that are eventually rejoined to form DNA strand ( synthesised discontinuously) , complementary to the parent strand that has the direction of ( 5’ - 3’ ) , away from the replication fork opening direction

41
Q

What are Okazaki fragments ?

A

Short stretches of DNA nucleotides

42
Q

Excision of RNA primers and their replacement

A

1) Occurs by DNA polymerase 1 ( 5’ exonuclease activity )
2) excise the RNA primer and the gap filled by DNA nucleotides

43
Q

Connecting the DNA fragments:

A

By DNA ligase

44
Q

What does proofreading means ?

A

Each nucleotides , that is added, is checked to be correctly matched with its complementary base on the template strand . if NOT , the (3’ - 5’) exonuclease activity correct the mistake .

45
Q

Proofreading occurs by …………………… that has both ………………. & ………………….

A

DNA polymerase 3 , ( 5’ - 3’ ) polymerase activity & ( 3’ - 5’ ) exonuclease activity

46
Q

What are telomeres ?

A

1) complexes of Noncoding DNA plus Proteins
2) it is located at the ends of linear chromosomes
3) their DNA consists of thousands of repeats of a six nucleotide sequences ((( 5’ - TTAGGG - 3’ )) at the 3’ end of each DNA strand.

47
Q

Telomeres importance :

A

1) Maintain the structural integrity of the chromosomes preventing attack by nucleases
2) allow repair system to distinguish a true end from a break in dsDNA

48
Q

DNA overhanging and its significance:

A
  • The 3’ end overhangs the 5’ end by a few hundred nucleotides long
  • the overhanging end folds back on itself AND binds proteins that protect it from recombination
49
Q

What is end replication problem ?

A

Following the removal of RNA primer from the 5’ end of the lagging strand , there is no way to fill in the remaining gap with DNA

50
Q

How is the problem of end replication solved ?

A

By an enzyme called telomerase

51
Q

About telomerase :

A
  • Ribonucleoprotein , found in Germ cells , Stem cells and cancer cells .
  • it is a reverse transcriptase .
  • it maintains telomeric length in theses cells by the presence of an RNA molecule in its structure , which is complementary to the TTAGGG repeat.
52
Q

Telomerase Mechanism :

A

1) It recognises the single 3’ terminus
2) uses its RNA molecule As a template to elongate the parental strand
3) this elongated parental strand is used as a template for synthesis of the telomere of the lagging strand

53
Q

Steps of Replication initiation in Eukaryotes during G1 phase :

A
  1. Association of The ATP- bound origin recognition complex with the replicator
  2. Recruitment of ATP-bound Cdc6 and two copies of the Mcm2-7 helicase bound to a second helicase loading protein (Cdt1)
  3. Triggering ATP hydrolysis by Cdc6
    3”. Loading of head-to-head diner of the Mcm2-7 complex encircling double-stranded origin DNA
    3””. The release of Cdc6 and Cdt1 from the origin
54
Q

Steps of replication initiation in eukaryotes during S phase :

A
  1. Activation of helicases ( starts to separate the two DNA strands )
  2. Cdc45 and GINS proteins binding to the Mcm2-7 helicase
  3. Formation of Mcm2-7 - GINS ( CMG ) complex
55
Q

What is Origin Recognition Complex ( ORC ) ?

A

Multi-subunit DNA binding complex that binds to the origin of replication in all eukaryotes in an ATP-dependent manner
* the subunits are encoded by ORC1 , ORC2, ORC3, ORC4, ORC5 and ORC6

56
Q

What is pre-replicative complex :

A

Assembly of many replication factors that are :
1) ORC 2) Cdc6 protein 3) Cdt1 protein
4) Mcm2-7

57
Q

Pre-RCs importance :

A

It’s required for replication licensing from chromosomes
Occurs in G1 phase prior to DNA synthesis during S phase

58
Q

Loading of ( Mcm 2-7 ) complex onto the DNA :

A

Occurs by ORC, Cdc6 , Cdt1

It is thought that Cdc6p- Cdt1 complex uses ATP hydrolysis to thread DNA through the central hole of the MCM

59
Q

Kinases that are responsible for the conversion of pre-RC into the initiation complex ( activation of Pre-RC ) :

A

DDK targets the loaded helicase
CDK targets two other replication proteins

60
Q

What are replicators ?

A

Specific DNA sequence on the origin of replication that initiates the initiation of DNA

61
Q

What triggers ATP hydrolysis by Cdc6 is :

A

The assembly of pre-RC proteins

62
Q

When does the actual unwinding starts ?

A

After cells pass from the G1 to the S phase

63
Q

About CMG complex :

A
  • the active form of the Mcm2-7DNA helicase
    -it is the combination of Mcm2-7 ATPase and helicase activities which is stimulated by Cdc45 and GINS

Genetics (3 decks)

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