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Cell and Molec > Lecture 4 > Flashcards

Lecture 4 Flashcards

1
Q

Base-pairing enables

A

DNA replication

  • DNA synthesis begins at replication origins
  • 2 replication forks form at each replication origin
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2
Q

Semi-conservative replication

A

When DNA replicates, molecule serves as a template for its own replication

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3
Q

DNA polymerase synthesizes DNA using a

A

Parental strand as a template

  • The replication fork is asymmetrical
  • DNA polymerase is self-correcting
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4
Q

Short lengths of RNA act as primers for

A

DNA synthesis

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5
Q

Proteins at a replication fork cooperate to form a

A

Replication machine

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6
Q

Telomerase replicates the ends of eukaryotic chromosomes

A

telomere length varies by cell type and with age

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7
Q

Recall

A

Conserved sequences that all chromosomes have are CENTROMERES, TELOMERES< and REPLICATION ORIGIN

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8
Q

Glycosidic bond holes

A

Carbohydrates

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9
Q

Phosphoanhydride bonds holds

A

Triphosphates

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10
Q

H-bonds hold

A

DNA b/w chains

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11
Q

Phosphodiester bonds hold

A

DNA backbone

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12
Q

DNA is damaged

A

ALL the time

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13
Q

DNA acts as a template for

A

Its own replication

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14
Q

AT rich becuase it is much easier to

A

break

When this sequence is recognized, the helix will be opened at this stie to create a “bubble”

2 replication forks for each origin

Synthesis goes BIDIRECTIONALLY (away from each other)

S phase is ~8 hrs in humans = we MUST have several replication origins

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15
Q

A DNA double helix is opened at

A

Replication origins

Opened with the aid of initiator proteins => single stranded DNA templates ready for DNA synthesis

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16
Q

DNA synthesis occurs at

A

Y-shaped junctions called replication forks

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17
Q

The 2 replication forks formed at a replication origin move AWAY in

A

Opposite directions

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18
Q

Polymer

A

The chain of subunits (DNA, RNA are polymers)

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19
Q

Polymerase

A

Enzyme that makes a polymer (i.e. DNA polymerase makes DNA)

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20
Q

A new DNA strand is synthesized in the

A

5’ to 3’ direction

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21
Q

DNA polymerase MUST add to 3’ hydroxyl, so DNA synthesis can ONLY occur in one direction (5’ to 3’)

A

MUCH energy contained in phosphoanhydride bond; energy comes from the incoming triphosphate

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22
Q

DNA polymerase adds a deoxynucleotide to the

A

3’ end of a growing DNA strand

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23
Q

At a replication fork, the 2 newly synthesized DNA strands are of

A

Opposite polarities

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24
Q

2 different types of strands

A

Leading strand (5’ to 3’) Synthesized CONTINUOUSLY

Lagging strand (3' to 5')
Synthesized DISCONTINUOUSLY
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25
Q

Mutation rate is LOW because enzyme can fix it

A

Removes damaged base IMMEDIATELY

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26
Q

At each replication fork, the lagging DNA strand is synthesized in

A

Pieces

27
Q

During DNA synthesis, DNA polymerase proofreads its own

A

work

28
Q

DNA polymerase contains SEPARATE sites for DNA synthesis and proofreading

A

Editing site is where damaged bases are fixed

29
Q

RNA primers are synthesized by an RNA polymerase called primase, which uses a

A

DNA strand as a template

30
Q

RNA primers used for DNA synthesis

A

Primase = making a primer

For DNA replication: RNA ptimer

31
Q

RNA does ____ need a primer

A

NOT

32
Q

Multiple enzymes are required to synthesize the

A

Lagging DNA strand

33
Q

DNA ligase

A

“Ligates” or fuses DNA

34
Q

DNA ligase joins together

A

Okazaki fragments on the lagging strand during DNA synthesis

35
Q

DNA polymerase

A

Catalyzes the addition of nucleotides to the 3’ end of a growing strand of DNA using a parental DNA strand as a template

36
Q

DNA helicase

A

Uses the energy of ATP hydrolysis to unwind the DNA double helix ahead of the replication fork

37
Q

Single-strand DNA-binding protein

A

Binds to single-stranded Dna exposed by DNA helicase, preventing base pairs from re-forming before the laging strand can be replicated

38
Q

DNA topoisomerase

A

Produces transient nicks in the DNA bafckbone to relieve the tension built up by the unwinding of DNA ahead of the DNA helicase

39
Q

Sliding clamp

A

Keeps DNA polymerase attached to the template, allowing the enzyme to move along without falling off as it synthesizes new DNA

40
Q

Clamp loader

A

Uses the enrgy of ATP hydrolysis to lock the sliding clamp onto DNA

41
Q

Primase

A

Synthesizes RNA primers along the lagging-strand template

42
Q

DNA ligase

A

Uses the energy of ATP hydrolysis to join Okazaki fragments made on the lagging-strand template

43
Q

DNA synthesis is carried out by a group of proteinas that act together as a

A

Replication machine

44
Q

DNA topoisomerases relieve the tension that builds up in front of a

A

Replication fork

Clips DNA, let unwind to relieve pressure repeat

45
Q

Without a special mechanism to replicate the ends of linear chromosomes, DNA

A

Would be lost during each round of replication

Linear DNA has this problem, NOT circular DNA

Okazaki fragments start with RNA primer, remove RNA primer, DNA fills in, left with primer on one end, DNA veiws as damage and eats back until its gone

This is BAD, could eventually reach somehting important

Solution: Add telomeres to ends using complementary base-pairing

Telomeres are hundresds - thousands of sequences long

ONly EUKARYOTES need telomeres, prokaryotes do NOT

46
Q

Telomeres and telomerase prevent

A

Linear eukaryotic chromosomes from shortening with each cell division

if you mutate this RNA, it can’t bind well to DNA, and it will get shroter (could cause cancer or some other damage)

47
Q

3 different types of DNA damage:

A

Mistakes
Mutigens/Chemical
Double-stranded breaks (Most severe)

48
Q

DNA damage occurs

A

Continually in cells

49
Q

Cells possess a variety of mechanisms for repairing DNA

A

A DNA mismatch repair system removes replication errors that escape proofreading

Double-strand DNA breaks require a different strategy for repair

50
Q

Failure to repair DNA damage can have

A

Severe consequences for a cell or organism

51
Q

Depurination and deamination

A

The most frequent chemical reactions known to create DNA damage in cells

52
Q

Depurination

A

Removing a purine (A or G) through spntaneous biochemical reaction, hydrolysis removes base

Without repair, causes a frameshift due to missing purine

53
Q

Deamination

A

Occurs with cytosine: C is hydrolyzed, amine removed, C becomes U (shouldn’t be present in DNA)

Without repair, One strand will have a mutated sequence

54
Q

UV Radiation

A

In sunlight can cause the formation of thymine dimers

Removes bonds between thymines, bringing them closer together and resulting in a kink in the DNA structure

Proteins that need to bind to DNA can’t because form isn’t right

55
Q

The basic mechanism of DNA repair involves 3 steps

A

1) Damaged segment is excised
2) Repair DNA Polymerase fills in missing nucleotide in top strand using bottom strand as template
3) DNA ligase seals nick

56
Q

Direct and Excision Repair

A

Mostly for damaged nucleotides

57
Q

MMR

A

Repairs replication errors (if DNA polymerase doesn’t correct errors)

58
Q

DBS

A

Repairs double-stranded breaks (can be done by nonhomologous end joining or homologous recombination)

59
Q

General overview of DNA repair pathways

A

Look for mistakes, cut them out, DNA polymerase will come in and replace, DNA ligase gets rid of gaps

60
Q

NO need for a ____ in DNA repair

A

Primer

61
Q

Proteins scan DNA, look for change in DNA structure (shape is altered by errors); mistake found =

A

Cut out mistake (might cut just mistake or cut out big segment)

62
Q

Errors made during DNA replication must be corrected to avoid

A

Mutations

63
Q

Cells can repair double-stranded breaks in one of two ways

A

Nonhomologous end joining:

  • Break
  • Processing of DNA end by nuclease
  • Bigger gap
  • End joining by DNA ligase
  • Deletion of DNA sequence as a result
  • Very error prone

Homologous recombination

  • Break
  • Processing of broken ends by recombination-specific nuclease
  • Double strand break ACCURATELY repaired by using undamaged DNA as template
  • ALL organisms use this; may use chromosome 10 from dad to heal chromosome 10 from mom that was broken (don’t need to be identical)
  • Crossing over is homoologous recombination
64
Q

A single nucleotide change causes the disease

A

Sickel cell anemia

Cell and Molec (9 decks)

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