Lecture 2 Flashcards

1
Q

What is involved in DNA metabolism ?

A

Replication
Repair + recombination

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2
Q

What does it mean for dna to be semi conservative

A

One strand is parent
One strand is daughter strand

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3
Q

What did cairn prove

A

DNA strands are replicated simultaneously bidirectionally from origin
-not only is each strand replicated at once
-each direction of each strand replicated at once

2 forks per replication

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4
Q

Ozaki fragment sizes

A

Bacteria = 1000-2000bps

Eukaryotes = 150-250 bps

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5
Q

Nuclease Enzyme Definition

A

Degrade dna
NOT RNA
2 classes
-exonucleases = end
-endonucleases = specific middle sites = fragments

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6
Q

DNA Polymerases

A

DNA synthesizers
Strand that is growing is 5’->3’

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7
Q

What about the dna polymerase mechanism requires 5-3 directionality ?

A

The nucleotide is the 3’ hydroxyl at the end of the growing strand
-If the 3’ is always at the end of the strand post addition and
-the 5’ carbon of the incoming dNTP is connected to the phosphorus group that is receiving the attacking nucleophile
5-3 directionality required

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8
Q

DNA polymerase basic reaction

A

(dNMP)n + dNTP —> (dNMP)n+1 + PPi

PPi is inorganic pyrophosphate
Hydrolyzed by pyrophosphatase —> true source of energy favorability

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9
Q

Can DNA polymerases spontaneously add to dna?

A

NO
Require primer
Primers = fee hydroxyl group at primer terminus

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10
Q

Processivity definition

A

Number of nucleotides added to strand before polymerase dissociates

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11
Q

E Coli mistake rate

A

1/ 10^9 - 10^10

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12
Q

What do correct base pairs depend on?

A

-hydrogen bonds between bases
-common geometry for complements (will not fit if wrong pair in polymerase active site)

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13
Q

Topoisomerases ability to work on certain dna

A

Topoisomerase I : relaxes negatively supercoiled dna (+1)

Topoisomerase ii: relaxes both pos and neg supercoiled dna (-2)

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14
Q

Type of structural change induced by nucleosome

A

?
No Lk change

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15
Q

2 structural components for dna molecule to maintain negative supercoiling

A

-covalently closed
-circular dna ( or bound on either end )

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16
Q

Cruciform dna

A

Form at palindromic sequences

17
Q

Can supercoiled dna be found closer to top or bottom of agarose gel

A

Bottom
More compact so travels faster even if same number of base pairs

18
Q

What happens when negatively super coiled dna is treated with Topoisomerase 1 for a medium amount of time?
Long time?
Think about agarose gel

A

Positively supercoils DNA until relaxed
Only adds +1 Lk each time so needs to relax the dna step wise
Each step = new Lk = new topoisomer

Long time = 100% DNA in relaxed form

Cannot positively supercoiled relaxed dna

19
Q

E coli have 4 Topoisomerases

A

I and iii
Relax by removing negative super coils

ii = dna gyrase - needs atp

20
Q

Eukaryotes type I and ii topoisomerases

A

Type I : I and III

Type II: Alpha and beta
Cannot underwind dna but can relax towards zero both pls and neg supercoils

21
Q

Catenanes

A

DNA circles topologically linked

Chromosomes tangled = relaxed via Topoisomerase IV

22
Q

Plectonemic coiling

A

Twisted thread
Main axis but branches coming off
40% of original length
Right handed turns

23
Q

Solenoidal supercoiling

A

Garden hose
Works on underwound dna
Tight left handed turns
Better compaction than plectonemic
Twist around histone

24
Q

describe the consistency of the chromosome structure

A

Changes throughout cell cycle
Uncondensed throughout interphase
More condensed during prophase
Less condensed after telophase

25
Phases of cell cycle
G1 (gap) S (synthesis) G2 (cohere) Mitosis
26
Mitosis phases
Pro Meta Ana Telo
27
Chromatin
Strands of protein to dna 1:1
28
Nucleosome
Basic structural unit for packaged dna DNA wrapped around histone cores Linking strands Beads on a string
29
Why is compaction vital for cells?
Cell diameter : 5-10 mm DNA length: 10^5 mm long Requires 10,000 fold compaction
30
How many base pairs bound tightly to histone core? How many in linking strands?
146 34 Histone core dna remains safe during digestion treatments
31
Nucleosome made up of
Octamer of histones Diameter : 10-11 nm
32
Nucleosome attaches to what kind of dna?
Relaxed dna Introduces negative supercoiling But pos supercoiling induced on unlinked dna Overall Lk is the same!! Topoisomerases can then relax pos unlinked dna so overall is negative
33
Epigenetics
Information passed down that is not encoded in DNA
34
Euchromatin
Chromatin region being actively transcribed
35
Chromatin immunoprecipitation
Antibodies bind to nucleosome With or without dna attached
36
Nucleosome core compaction
7 fold Need 10,000 fold Requires use of Topoisomerase II to compact without tangling If topo II inhibited = antibiotics = kills rapidly dividing cells
37
Heterochromatin
Highly condensed dna that is transcriptionally inactive Active and inactive compartments are separated = TAD + binding site for base of loop
38
How can E. coli have a 20 minute cell cycle?
New round of replication begins before previous is completed