L2 Flashcards

1
Q

dna polymerase

A

● Holds a loose nucleotide (with 3 PO4)
● The 3’ strand of the DNA reacts with the PO4
● DNA polymerase needs to be attached to a DNA or RNA first

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2
Q

rna polymerase

A

does not need a primer

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3
Q

replication process

A

initiation, elongation, termination
● Proteins attach to the DNA, and put it under torsion and de methylate it
● Helicase gets added, which separates the DNA strands
● DNA polymerase is added, and it works from 5’ to 3’, where 3’ gets longer,
in the normal strand
● In the lagging strand, which goes 3’ to 5’, which means it needs to be
synthesized in the opposite direction, for this, primers are put down, which
allow short replication in segments, which are called Okazaki fragments, at
the end of each, the dna polymerase has to move back and do it again.
● DNA polymerase 3 stops at the primer of the next Okazaki fragment
● DNA polymerase 1 degrades the primer, which leaves the two fragments
barely disconnected; they are then fused into a single line by DNA ligase

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4
Q

dna ligase reaction

A
  1. DNA ligase grabs a phosphate bound to ribose and Adenine (also called
    AMP)
  2. In the zone where the DNA is nicked, there is a loose phosphate on one
    side, and a loose OH on the other. The AMP connects to the loose
    phosphate.
  3. The enzyme connects the previously loose phosphate to the loose OH,
    sealing the nick in the DNA and spending. The Ligase and the AMP
    dissociate from each other and the DNA afterwards
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5
Q

dna polymerase 1

A

● Slowest and shortest (20 nucleotides per second)
● Can add between 3 and 200 nucleotides
● Can remove primers
- in e coli also removes okazaki fragments

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6
Q

dna polymerase type 2

A

● Fast-ish, 40 nucleotides per second
● Can add 150 nucleotides before dying

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7
Q

dna polymerase tup 3

A

● Between 250 and 1000 nucleotides per second
● Can add up to 500k nucleotides

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8
Q

dna polymerase

A

needs a primer with 3’OH end to add nucleotide to growing chain

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9
Q

rna primer removal and okazaki fragment ligation

A
  • DNA polymerase III stops at the primer of
    the next Okazaki fragment.
  • DNA polymerase I uses its 5’ → 3’
    exonuclease domain to degrade the RNA
    primer and its 5’ → 3’ DNA synthesis
    activity to replace the RNA primer with
    dNTPs.
  • This leaves one 3’OH – 5’PO4 break.
  • E.coli DNA ligase catalyses the covalent
    closure of this gap at the cost of one NAD+
    molecule.
  • Phage T4 DNA ligase uses one ATP for the
    same ligation reaction.
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10
Q

beta clamp

A

polymerase strongly bound to template via ring, prevents dissociation of the polymerase from the template dna enabling synthesis of dna strand that are long

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11
Q

dna plolymerase choises

A
  1. keep elongating
  2. reverse and use 3’to 5’ exonuclease activity to break down nascent rna (when faulty base pair in binding site which proof reads)
  3. fall of template (inhibited by beta clamps)
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12
Q
A
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