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Biochem > Lecture 2 > Flashcards

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
Q

Phases of cell cycle

A

G1 (gap)
S (synthesis)
G2 (cohere)
Mitosis

26
Q

Mitosis phases

A

Pro
Meta
Ana
Telo

27
Q

Chromatin

A

Strands of protein to dna
1:1

28
Q

Nucleosome

A

Basic structural unit for packaged dna
DNA wrapped around histone cores
Linking strands
Beads on a string

29
Q

Why is compaction vital for cells?

A

Cell diameter : 5-10 mm
DNA length: 10^5 mm long

Requires 10,000 fold compaction

30
Q

How many base pairs bound tightly to histone core? How many in linking strands?

A

146
34

Histone core dna remains safe during digestion treatments

31
Q

Nucleosome made up of

A

Octamer of histones
Diameter : 10-11 nm

32
Q

Nucleosome attaches to what kind of dna?

A

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
Q

Epigenetics

A

Information passed down that is not encoded in DNA

34
Q

Euchromatin

A

Chromatin region being actively transcribed

35
Q

Chromatin immunoprecipitation

A

Antibodies bind to nucleosome
With or without dna attached

36
Q

Nucleosome core compaction

A

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
Q

Heterochromatin

A

Highly condensed dna that is transcriptionally inactive
Active and inactive compartments are separated
= TAD + binding site for base of loop

38
Q

How can E. coli have a 20 minute cell cycle?

A

New round of replication begins before previous is completed

Biochem (23 decks)

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