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Biochem Block 3 > DNA REPLICATION > Flashcards

DNA REPLICATION Flashcards

1
Q

Bidirectional

A

Replication begins in the interior of a DAN molecule, and proceeds in both directions

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2
Q

Semiconservative

A

Each copy of the DNA molecule, after replication, contains one strand from the original template and one newly synthesized strand
-the end product is heterogeneous

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3
Q

Differences between prokaryotic and eukaryotic DNA

A

Pro: ONE origin of replication, circular DNA (highly enriched with A and T)
Euk: multiple origins of replication, in order to replicate Ina reasonable amount of time, linear

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4
Q

Separate two complementary DNA strands

A
  • origin of replication needs to be melted
  • origin of replication sequences are usually almost exclusively composed of A and T
  • accomplished by 20-50 monomers of DnaA protein
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5
Q

Single stranded binding proteins

A

Bind to single strands to prevent reanneling and protect DNA from nuclease degradation

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6
Q

DNA helicase

A

Move toward the double stranded region (toward the replication fork) and force the strands apart

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7
Q

Supercoiling

A

-DNA is a helix, so when helicase said separate the strands of DNA, supercoiling ahead of the replication form will occur

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8
Q

Topoisomerases

A

Alleviate supercoiling ahead of the replication fork

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9
Q

Type 1 topoisomerase

A

Creates a nick inONE strand which allows the DNA to swivel around the intact strand, then seals the nicked strand

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10
Q

Type II topoisomerase

A

Cut BOTH strands to relieve the supercoiling, the re-legates the two strands

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11
Q

DNA gyrase

A
  • a special type II topoisomerase
  • induces negative supercoiling
  • cuts both strands, sends loops into each other, then puts them back
  • protects DNA
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12
Q

What inhibits DNA gyrase?

A

Quinolones

-toxic in high doses on eukaryotes, but in low doses just stops prokaryotes from cell division and protecting DNA

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13
Q

What direction do polymerases that synthesize nucleus acids move in?

A

5’ to 3’

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14
Q

How is the DNA template mead in?

A

3’ to 5’ (because DNA is anti parallel)

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15
Q

Leading strand

A

-strand of the DNA fragment that can be replicated continuously as the replication fork advances

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16
Q

Lagging strand

A
  • strand of the DNA fragment that is synthesized DISCONTINUOUSLY
  • as the replication fork advances, small fragments of DNA Are synthesized 5’ to 3’ away from the replication fork
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17
Q

Okazaki fragments

A
  • the discountinuously synthesized fragments

- later joined to become a continuous segment of DNA

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18
Q

RNA primer

A
  • promise (an RNA polymerase) does not require a free 3’ OH group to begin synthesis
  • copies the first 10 nucleotides to prime a synthesis
  • each new DNA fragment on the lagging strand begins with the action of laying down an RNA primer
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19
Q

Why do you need an RNA primer?

A

-DNA polymerase needs a free 3’ OH group to begin synthesis

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20
Q

DNA polymerase reaction

A
  • they catalyze a reaction between the 3’ OH group of the strand being synthesized, and the 5’ triphosphate of an incoming nucleotide specified by the template being copied
  • addition of a nucleotide to a growing DNA strand and the release of a pyrophosphate
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21
Q

What happened to the pyrophosphate that is released in the growing of a DNA strand?

A

It is cleaved to inorganic phosphate to make the reaction irreversible and drive the reaction Ina forward direction

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22
Q

Coupled irreversible reaction

A

-two high energy bonds are cleaved for each added nucleotide in a growing DNA chain

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23
Q

DNA polymerase III

A

The enzyme in PROKARYOTES that elongates both the leading and lagging strands

  • has proofreading activity
  • checks each added nucleotide to make sure it it correctly base-paired with the template strand
24
Q

3’ to 5’ exonuclease activity

A

When there is a mistake, it shifts backward one nucleotide and excises the misincorporated nucleotide
-DNA pol III does this

25
Q

How do you complete the replication in prokaryotes and join the Okazaki fragments?

A

The RNA primer must be removed and replaced with dNTPs

26
Q

Excision of RNA primers and their replacement by DNA

A

DNA polymerase I: 5’ to 3’ polymerase activity. Removes RNA and adds DNA
exonuclease activity: 3’ to 5’ and 5’ to 3’

27
Q

DNA polymerase I

A
  • removes RNA primer (5’ to 3’ exonuclease)
  • replaces rNTP with dNTP (5’ to 3’ polymerase)
  • proof reads and corrects( 3’ to 5’ exonuclease)
28
Q

DNA ligament

A

Seals the nick that remains after the RNA primer is removed and replaced with dNTPs

29
Q

G1 phase

A

-in this phase, eukaryotic cells will go through division

30
Q

G0 phase

A
  • can go into G1 phase of leave G1 phase in this phase

- takes the cell out of the cycle

31
Q

S phase

A

(Eukaryotes)

  • replication of DNA
  • s stands for synthesis
32
Q

G2 phase

A

(Eukaryotes)

-cell prepares to divide

33
Q

M phase

A

(Eukaryotes)

  • the stage of cell division
  • M stands for mitosis
34
Q

Pol alpha

A

(Eukaryotic DNA polymerase)

-contains primase and DNA polymerase( lays down primer and can start synthesis)

35
Q

Pol delta

A
  • eukaryotic DNA polymerase

- DNA polymerase and proofreading

36
Q

Pol beta and epsilon

A
  • eukaryotic DNA polymerase

- DNA repair enzyme

37
Q

Pol gamma

A
  • eukaryotic DNA polymerase

- mitochondrial DNA polymerase

38
Q

Hang off

A

-eukaryotic chromosomes are linear, so the end of the DNA molecule, lagging strand, will have a gap once the RNA primer is removed

39
Q

Telomerase

A
  • extends the ends of linear chromosomes
  • contains a segment of RNA that is complementary to the telomere that can repeat and extend to act as a template
  • also contains reverse transcriptase to turn the new RNA template into DNA
40
Q

Telomere

A

6- nucleotide repeats added onto the ends of eukaryotic chromosomes

41
Q

Why is telomerase good?

A

Because it can transcribe RNA into DNA AND THE RNA was already added onto the end (so not part of the original) it protects the DNA so that if it is clipped, it will clip that and not the regions important for coding

42
Q

When is there an overhang?

A

There will always be a section of DNA left single stranded

-the 3’ over hang has special proteins to help protect the end of the DNA

43
Q

Do all cells have telomerase?

A

Nose

-it is expressed in cells that continually divide and are not terminally differentiated

44
Q

What about cells that don’t have telomerase?

A
  • they have their chromosome shortened at the end of each cell division
  • eventually they will run out and die
  • some cells can activate telomerase and that causes cancer
45
Q

Reverse transcriptase

A
  • goes against the normal flow and goes from RNA to DNA
  • RNA dependent DNA polymerase
  • telomerase does this
  • common strategy in viruses(most enter as RNA)
  • lack proof reading ability(viruses can change things and no one notices)
46
Q

Strand directed mismatch repair

A

Corrects errors made during replication

47
Q

Damage repair

A

Caused by toxins or UV light, not just mis matched nucleotides

48
Q

Endonuclease

A

Remove the damaged region in the forward direction

49
Q

Exonuclease

A

Remove the damaged region in the reverse dir cation

50
Q

DNA repair

A

Pol I fills in previously damaged region and DNA ligase seals the final nick

51
Q

Hereditary nonpolyposis colorectal cancer

A
  • defect in mismatch repair

- one of the most common inherited cancers

52
Q

What causes DNA mutations?

A
  • replication errors
  • spontaneous mutations from exposure to chemical radiation
  • cigarette smoke
53
Q

UV light

A

-causes pyramiding dimers-usually thymine dimers

54
Q

Repair UV light problems

A
  • UV specific endo uncle
  • cuts DNA on both sides of damage and removes it
  • gap filled in by repair DNA polymerase (pol I in prokaryotes)
55
Q

Xeroderma pigments sum

A

Rare genetic disorder

  • results from a deficiency in exclusion endonuclease
  • you can’t repair damaged DNA!

Biochem Block 3 (10 decks)

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