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Genetics Fall 2015 > 10/15 > Flashcards

10/15 Flashcards

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1
Q

Primer:
1)
2)

A

Primer: for the initiation of synthesis

1) a short oglionucleotide chain that is complementary to template strand
2) functions to provide a free 3’OH group for the incoming nucleotide to be added to by a phosphodiester bond
* no known DNA polymerase (DNAP) can initiate synthesis on a bare template. DNAPs always have to have something to add on to

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2
Q

dNTPs:

A

dNTPs: dATP, dCTP, dGTP, dTTP. Monomeric units of DNA molecules. Substrates of synthesis reaction.

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3
Q

DNAPs (DNA Polymerases):

A

DNAPs: enzymes that carry out synthesis

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4
Q

DNA synthesis is simply….

A

DNA synthesis is simply the linkage together of nucleotides (complimentary to template) by a covalent phosphodiester bond

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5
Q

Direction of DNA synthesis is always…

A

Direction of DNA synthesis is always 5’—3’.

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6
Q

DNA replication in E. Coli (bacterial system) initiates at the origin called ______.

A

DNA replication in E. Coli (bacterial system) initiates at the origin called OriC —> chromosomal origin of replication.

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7
Q

OriC is a ____ base pair region on the xsomal DNA.

A

OriC is a 245 base pair region of the xsomal DNA.

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8
Q

OriC contains ___________________ that are important in the initiation of DNA synthesis.

A

OriC contains two sets of repeat sequences that are important in the initiation of DNA synthesis: series of three 13-mer repeats and a series of four 9-mer repeats.
(13-mer is an oglionucleotide 13 bases long)

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9
Q

Why are the two sets of repeat sequences in the OriC important?

A

The repeats are important in binding proteins needed for initiation of synthesis.

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10
Q

The OriC repeats are A/T rich…

A

The repeats are A/T rich, which is important to the function bc A/T pairing represents weak H-bonds and the OriC facilitates the unwinding of the dbl helix.

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11
Q

Steps to bacteria DNA replication-initiation:

A

Initiation: binding of the HU protein and initiation protein to the series 9-mer repeats

  • requires ATP for energy to drive bonding rxn
  • results in DNA coiling around the proteins. Coiling puts torsional strain on dbl helix.
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12
Q

What does initiation result in in bacteria DNA replication?

A

Initiation results in the DNA coiling around the HU and initiation proteins, and the coiling puts a torsional strain on the dbl helix.

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13
Q

-

A

Unwinding: in order to release the torsional strain caused by the DNA coiling around the HU and I proteins, there is unwinding at the A/T rich regions (weak spot).

  • this generates localized region of ssDNA to form a replication bubble
  • unwound state is stabilized by binding of a single stranded DNA binding proteins (ssb)
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14
Q

What does unwinding generate in bacteria DNA replication?

A

Unwinding generates a localized region of the ssDNA to form a replication bubble.

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15
Q

The unwound state of bacterial DNA is stabilized by:

A

The unwound state of bacterial DNA is stabilized by: single stranded DNA binding proteins (ssb)

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16
Q

Purpose of ssb’s:

A

Purpose of ssb’s: to keep the helix “open” long enough for DNA to be copied p, by preventing base pairing from reforming the dbl helix

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17
Q

The initial unwinding is a physical reaction in response to the _______________.

A

The initial unwinding is a physical reaction in response to the torsional strain.

18
Q

Further unwinding of the dbl helix is carried out by enzymes called:

A

Further unwinding of the dbl helix is carried out by enzymes called: helicases. Helicases enzymatically break H-bonds of the dbl helix as replication proceeds from origin.

19
Q

___________ enzymatically break H-bonds of dbl helix as replication proceeds from the origin.

A

Helicases enzymatically break H-bonds of dbl helix as replication proceeds from the origin.

20
Q

Helicases bind to ssDNA at the _______________ and break H-bonds btwn bases as replication moves forward.

A

Helicases bind to ssDNA at the replication fork and break H-bonds as replication moves forward.

21
Q

What results from Helicase unwinding?

A

As a result of helicase unwinding, a superficial knot builds up in front of the replication fork.

22
Q

What works to remove the knot caused by Helicase unwinding the dbl helix?

A

DNA gyrase is a topoisomerase type 2 that works to remove knots two supercoils at a time.

23
Q

DNA gyrase

A

DNA gyrase: is a type two topoisomerase that works to remove the knot caused by Helicase two supercoils at a time.

24
Q

DNA gyrase is necessary in order for synthesis to replicate to completion.

A

DNA gyrase is necessary in order for synthesis to replicate to completion.

25
Q

Steps to bact DNA replication-priming:
1)
2)

A

Priming: carried out by enzyme primase, a special type of RNA polymerase that functions in DNA replication.

1) primase binds to Helicase and sets down a short oligonucleotide of RNA bases that are complementary to exposed ssDNA template.
2) primer, made by primase, serves to provide a free 3’OH group to which DNAP can add new bases

26
Q

What do all DNAPs require?

A

All DNAPs require a preexsisting 3’OH group to initiate synthesis. RNAPs do not have this requirement.

27
Q

_______, made by primase, serves to provide a free 3’OH group to which DNAPs can add new bases.

A

Primer, made by primase, serves to provide a free 3’OH group to which DNAPs can add new bases.

28
Q

All biological DNA synthesis begins w a short ______ primer that needs to be removed before replication is complete.

A

All biological DNA synthesis begins w a short RNA primer that needs to be removed before replication is complete.

29
Q

-

A

Elongation: addition of nucleotides that are complementary to template strand

  • once DNA is primed, it proceeds in a 5’-3’ direction until a terminator signal is encountered or two replication forks meet
  • elongation is carried out by DNAPs
30
Q

Elongation is carried out by ______.

A

Elongation is carried out by DNAPs.

31
Q

DNAPs carry out ___________.

A

DNAPs carry out elongation.

32
Q 
Characteristics of all DNAPs:
1)
2)
3)
4)
5)
A

1) DNAPs synthesize new strands of DNA that are complimentary and anti parallel to the template
2) DNAPs have, by definition, 5’-3’ polymerase activity
3) DNAPs use dNTPs as substrates
4) DNAPs require a primer for initiation
5) DNAPs catalyze the formation of phosphodiester bonds btwn 3’OH of one nucleotide and 5’PO4 of another

33
Q

DNAPs use ______ as substrates.

A

DNAPs use DNTPs as substrates.

34
Q

DNAPs require a ________ for initiation.

A

DNAPs require a primer for initiation.

35
Q

3’-5’ exonuclease activity:

A

3’-5’ exonuclease activity: used to proofread errors/misincorporated bases

36
Q

5’-3’ exonuclease activity:

A

5’-3’ exonuclease activity: used in removal and replacement of RNA primers

37
Q

An exonuclease:

A

An exonuclease: enzyme activity that works by binding to the end of a DNA molecule and removing/chewing away bases. This removal refers to nuclease: degrades DNA

38
Q

DNAPIII

A

DNAPIII: main workhorse of replication. It is the one at replication copying all of the DNA.

  • 5’-3’ polymerase activity
  • 3’-5’ exonuclease activity (proofreading)
39
Q

DNAPI

A

DNAPI: removes the RNA primer with its 5’-3’ exonuclease activity and replaces w DNA using its 5’-3’ polymerase activity

  • 5’-3’ polymerase activity
  • 5’-3’ exonuclease activity (RNA primer removal)
40
Q

DNAPII

A

DNAPII: mostly functions in post replication repair

  • 5’-3’ polymerase activity
  • 3’-5’ exonuclease activity (proofreading)
41
Q 
DNA synthesis is described as being semi discontinuous bc:
1)
2)
3)
4)
A

1) strands of the dbl helix are anti parallel BUT
2) DNA synthesis only,occurs in the 5’-3’ direction.
3) therefore, DNA synthesis proceeds in opposite physical directions along the parental template
4) one strand is made continuously (leading strand) and the other is made dis continuously (lagging strand)

42
Q 
Basic cellular components of replication:
1)
2)
3)
4)
5)
A

1) ssDNA template: what you want to copy
2) dNTPs: monomer of units of DNA molecules. Substrates of synthesis reaction.
3) primer: for initiation of synthesis
4) DNAPs: enzymes that carry out synthesis
5) Mg ions: essential metal cofactor required for the function of DNAPs. Cannot function of lacking Mg ions bc it has no stability

Genetics Fall 2015 (6 decks)

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