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BMB 402 > Ch. 20 DNA Replication, Repair, and Recombination > Flashcards

Ch. 20 DNA Replication, Repair, and Recombination Flashcards

1
Q

DNA Replication

A

-occurs at a high rate to copy entire genome
- semiconservative
-duplex DNA template is separated into 2 strands
each daughter molecule contains 1 strand from the original template

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2
Q

DNA replication discovered by?

A

Meselson and Stahl

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3
Q

Conservative replication?

A

one daughter DNA molecule is all new and one is all old DNA

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4
Q

Dispersive replication?

A

each daughter DNA contains a mixture of old and new DNA

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5
Q

What is bidirectional replication?

A

DNA replication occurs through the formation of a replication fork
replication occurs from each end of the replication fork

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6
Q

What happens after the replication fork is formed?

A
  1. Double stranded DNA is converted into single stranded DNA
  2. RNA primer is added
  3. RNA primer is extended
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7
Q

What is the replisome?

A

complex of proteins and enzymes required to replicate DNA

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8
Q

What are Okazaki fragments?

A

Fragments that are synthesized on the discontinuous (lagging) strand

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9
Q

Who visualized replicating DNA?

A

John Cairn in 1963

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10
Q

What did Reiji Okazaki do?

A

described Okazaki fragments, had pulse- chase experiments 3H-thymidine

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11
Q

What are DNA polymerases?

A

-enzymes responsible for the bulk of DNA synthesis
- catalyzes the addition of deoxynucleotide to the 3’ end of the growing DNA strand
-MG2+ is a cofactor
- primers are necessary for function
-synthesizes in the 5’-3’ direction

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12
Q

How does DNA polymerase add deoxynucleotide to 3’ end of DNA?

A
  • nucleophilic attack of the alpha phosphoryl group of incoming dNTP
  • hydrolysis of phosphate (irreversible)
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13
Q

Functions of Prokaryotic DNA Polymerases

A

Pol 1
- proofreading, repair, primer removal
Pol 2
- repair
Pol 3
- main polymerizing enzyme

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14
Q

Functions of Eukaryotic DNA Polymerases

A

Pol delta
- lagging strand synthesis
Pol epsilon
- leading strand synthesis
Pol alpha
- initial synthesis from primer, primase

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15
Q

What is a Klenow Fragment?

A

a large protein subunit produced when DNA pol 1 is cleaved

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16
Q

What is reverse transcriptase?

A

-enzyme used to convert RNA to DNA
- used in HIV replication
- highly prone to error
- NO proofreading function
- similar structure to DNA Pol 1

17
Q

What are DNA helicases?

A

-separates double stranded DNA
-specific to the reaction they catalyze
- involved in DNA repair and replication
- ATP-dependent

18
Q

What is the trombone model of DNA synthesis in prokaryotes?

A
  • coordinated DNA synthesis on leading and lagging strand templates is mediated by the clamp ladder complex
  • A Pol 3 core on the lagging strand template alternates between bound and unbound as each Okazaki fragment is made
19
Q

What are the steps of trombone model of DNA synthesis?

A
  • Pol 3 on lagging strand template extends P2 primer
  • primase synthesizes P3 RNA primer on lagging strand template
  • lagging strand template released by Pol 3 when it reaches 5’ end of P1 RNA primer
  • Pol 3 binds to the lagging strand template at the P3 RNA primer, synthesizes DNA in 5’–3’ direction
20
Q

What is oriC?

A

the site at which DNA must be separated to initiate replication

21
Q

What are termination proteins?

A

sites halfway around the prokaryotic genome that stop bidirectional DNA replication

22
Q

What does telomerase do?

A
  • adds telomeric DNA sequences to the ends of chromosomal DNA
  • shortening is a major factor in aging
  • only in undiffrentiated embryonic stem cells, male germ cells, and activated lymphoctes
23
Q

What is the mechanism of telomerase?

A
  1. telomerase binds to DNA using base pairing between telomerase RNA and template DNA
  2. Telomerase RNA template synthesizes a complimentary strand of DNA in 5’ to 3’ direction
  3. primase adds new RNA primer to facilitate DNA synthesis by the DNA polymerase complex
  4. gap is repaired by DNA ligase
  5. RNA primer is removed by an exonuclease
24
Q

Who discovered telomerase?

A

Elizabeth Blackburn and Carol Greider in 1984

25
Q

What is a mutation?

A
  • permanent change in DNA sequence
  • can affect gene function and alter protein-coding sequence
26
Q

What are somatic mutations?

A

not inherited genetically, result in decreased cell viability, can alter genes that regulate cell division

27
Q

What is the Ames test?

A

biochemical test to determine if a substance is mutagenic

28
Q

Types of DNA damage

A

spontaneous deamination of C to U
- generates an abasic site
- improper base pairing
environmental
- uv radiation
DNA alkylation

29
Q

What is a missense mutation?

A

mutation that causes DNA that encodes one AA to turn into a different AA

30
Q

What is a nonsense mutation?

A

takes DNA that codes for a functional AA and changes it to a stop codon

31
Q

What is a silent mutation?

A

change in the DNA sequence that does not affect the AA produced

32
Q
A

BMB 402 (14 decks)

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