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My Packs: (UWO) (BIOCHEM 2280) > (Dr. Heinemann) (Unit C) Topic 15 > Flashcards

(Dr. Heinemann) (Unit C) Topic 15 Flashcards

1
Q

Where does DNA replication start?

A

Replication origins

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2
Q

How many replication origins do organisms use?

A
  • Prokaryotes usually have one
  • Eukaryotes have multiple
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3
Q

What are characteristics of replication origins?

A

Rich in AT base pairs
* Easier to pull apart than CG base pairs

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4
Q

Initiator proteins

A

Bind to sequences at replication origins and pull them apart

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5
Q

Are initiators present in eukaryotes?

A

Yes, they are present in eukaryotes and prokaryotes

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6
Q

Helicase

(Prokaryotes)

A

Binds after initiator proteins pull chains apart
* Consumes ATP to unwind DNA during the replication process

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7
Q

Helicase

(Eukaryotes)

A

Inactive helicase is part of pre-initiation complex that binds to each replication origin
* Upon activation, starts separating strands at each origin

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8
Q

What is the replication bubble?

A

The region which the DNA has become single-stranded

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9
Q

Single-strand binding proteins (SSBs)

A

Associates with unwound regions and prevents them from re-forming base pairs

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10
Q

Replication forks

A

Area where the double stranded DNA becomes single stranded

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11
Q

True or False:

DNA polymerase synthesizes DNA by directly using the template strand

A

False, it needs something to attach nucleotides to

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12
Q

Primase

A

Synthesizes short RNA primers on the separated DNA strands for DNA polymerase to work on

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13
Q

Primers
* How long are they?
* In what direction are they synthesized?

A
  • ~10 nucleotides
  • 5’ to 3’ direction
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14
Q

After primer synthesis, what protein is loaded onto the primer-template complex?

A

Sliding clamp protein

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15
Q

What is the goal of the sliding clamp protein?

A

It will not spontaneously dissociate from douoble-stranded DNA
* Keeps DNA polymerase on the chain

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16
Q

What does DNA polymerase do?

A

Synthesize most of the new DNA

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17
Q

What direction does DNA polymerase synthesize things in?

A

5’ to 3’
* Extends the primer from its 3’ end

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18
Q

What is replicative DNA polymerase known as in prokaryotes?

A

DNA polymerase III

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19
Q

When complementary bases are added by DNA polymerase, what is the by-product?

A

Pyrophosphate (PPi)
* Hydrolysis of ATP to AMP + PPi

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20
Q

Why is DNA polymerase called a “processive” enzyme?

A

Undergoes several rounds of catalysis before dissociating from the template

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21
Q

Replisome

A

The complex of proteins that carries out replication at a replication fork

22
Q

Leading strand

A

Synthesis on this strand is said to be continuous
* DNA synthesis can continue for long distances (usually about 5 * 10^5 using only one primer)

23
Q

Why does the DNA synthesis on the complementary template strand occur in the direction opposite the which the replication fork is moving?

A

DNA is anti-parallel

24
Q

What does discontinuous synthesis of DNA on the lagging strand form?

A

Okazaki fragments

25
Q

What are Okazaki fragments connected by?

A

DNA ligase

26
Q

Okazaki fragments
* Length in prokaryotes
* Length in eukaryotes

A
  • 500-2000 nucleotides long
  • 1/10th of the length in prokaryotes
27
Q

What is the traditional model for explaining the replication on leading and lagging strands occurring concurrently?

A

“Trombone” model

28
Q

What is the present explanation for efficiency of Okazaki fragment synthesis?

A

3 DNA polymerase complexes can associate with the helicase simultaneously

29
Q

Does DNA polymerase have proofreading ability?

A

Human DNA polymerases have proofreading ability
* They are very accurate without proofreading, but it makes it more accurate

30
Q

What kind of activity does DNA polymerase have to proofread?

A

3’ to 5’ exonuclease activity
* Can remove mononucleotides from the 3’ end of a DNA strand

31
Q

What is the accuracy of DNA replication with proofreading?

A

1 error/10^6 or 10^7 bases

32
Q

In the Okazaki fragment, when does DNA polymerase III dissociate?

(Only in prokaryotes)

A

When it encounters the RNA primer from the previously synthesized fragment

33
Q

DNA polymerase I

(Only in prokaryotes)

A
  • Degrades RNA primer
  • Synthesizes DNA
34
Q

What activity does DNA polymerase I have?

(Only in prokaryotes)

A

5’ to 3’ exonuclease activity
* Degrades the RNA primer while synthesizing DNA

35
Q

What does DNA polymerase I synthesizing DNA result in?

(Only in prokaryotes)

A

“Nick translation”

36
Q

What does DNA ligase require to work?

A
  • In bacteria: NAD+
  • In humans: ATP (hydrolyzes to AMP + PPi)
37
Q

What does DNA ligase require on the DNA strands?

A
  • 3’ hydroxyl
  • 5’ phosphate
38
Q

How does Okazaki fragment maturation in eukaryotes work?

A
  • Replicating DNA polymerase does not dissociate from the template
  • RNA primer is removed by another enzyme
39
Q

What is the RNA primer removed by eukaryotes?

A

Examples include:
* RNase H
* Flap endonuclease (removes ssRNA that have been pushed aside by DNA polymerase)

40
Q

What are telomeres?

A

Protein-DNA structures found at the ends of chromosomes

41
Q

Describe:

Human telomeres

A
  • 2000-10000 base pair double-stranded region containing many repeats of a 6-nucleotide sequence (TTAGGG)
  • Followed by 100-300 nucleotide 3’ overhand that loops back and displaces an earlier section of the same strand
42
Q

What are the two main functions of telomeres?

A
  1. Enable cell to distinguish between the end of the chromosomes vs. double-strand break in the middle of the chromosome
  2. Replicating the lagging strand at the ends of chromosomes (provides extra DNA so that coding DNA is not lost during replication)
43
Q

True or False:

Chromosomes get shorter every single time they are synthesized

A

True

44
Q

Telomerase

A

Synthesize and lengthen telomeres
* A type of DNA polymerase
* Uses associated RNA strand as a template

45
Q

Expression of Telomerase
* Normal
* Abnormal

A
  • Expressed during embryo development and in germ-line cells
  • Expressed in adulthood in cancer cells
46
Q

Azido thymidine (AZT)

A

Also called zidovudine or Retrovir
* Anti-viral agent used to combat HIV

47
Q

How does AZT work?

A
  • Taken orally
  • Converted to triphosphate form
  • Used as a substrate in place of dTTP during DNA synthesis
  • New nucleotide cannot be added because it does not have a 3’ hydroxyl group
  • Prevents formation of new virus particles
48
Q

Why is AZT 100 times more effectively on reverse transcriptase than human DNA polymerase?

A

Viral enzyme (reverse transcriptase) has higher affinity for AZT than for dTTP

49
Q

Acyclovir

A

A seletive inhibitor of the herpes virus DNA polymerase

50
Q

How does Acyclovir work?

A

Causes chain termination when incorporated into a growing DNA strand

My Packs: (UWO) (BIOCHEM 2280) (23 decks)

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