wednesday week 2 Flashcards

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1
Q

first step of DNA organization

A

DNA double helix

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2
Q

second step of DNA organization`

A

beads on a string form of cromatin.

  • nucleosome = histone octomer (a heterooctamer) 2x(H2A, H2B, H3, H4)
  • DNA wraps 1.7 times around histone octomer (DNA = negative, octomer = positive
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3
Q

third step of DNA organization

A

30nm chromatin (nucleosome beads on a string wraps into zigzag shape)

  • NOT regular (ex. linker DNA can be very long to allow easy access to DNA for proteins, other sections will be very short)
  • process dependent on histone H1 and histone tails.
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4
Q

linker DNA

A

DNA inbetween the DNA wrapped around nucleosomes essentially the string connecting the nucleosomes in DNA organization

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5
Q

histone H1

A

binds to nucleosomes + changes how tightly wrapped around the DNA is in beads on a string step of DNA organization

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6
Q

fourth step of DNA organization

A

chromatin fibers folded into loops

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7
Q

histone tails

A

scaffolds that link adjacent nucleosomes together

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8
Q

explain how DNA packaging is dynamic

A

local changes in gene expression and global changes during cell cycle

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9
Q

euchromatin

A

less condensed, contains expressed genes

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10
Q

heterochromatin

A

condensed, contains genes/DNA that are not expressed

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11
Q

explain the conservative model of DNA replication

A

replication in which the strand is seperated, copied, and then seperated again and put back (original dna is back together and new copies of each strand come together to form an entirly new strand)

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12
Q

explain the semi-conservative model of DNA replication

A

after strands are split, dna replicated on each strand and attached to that strand. end up with two strands each half with ‘old’ dna and half with ‘new’ dna

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13
Q

explain the dispersive model of DNA replication

A

strands are split virticallyand then split again horizontaly (stay bonded somehow?) into small sections and then randomly recombine to form two double helix strands of dna each with varied ‘old’ and ‘new’ dna sections

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14
Q

explain the methods of meselson stahl’s replication experiment

A

original DNA labeled with heavy nitrogen (15N) and newly generated DNA with light nitrogen (14N)

add generated (15N) radioactive e coli. to 14N medium. centrofuse solution to have gradient by mass - this can be viewed

gradient from centrofuse can be seen on an ultraviolet absorpotions photograph. shows up as line(s)

results can also be viewed from the absorption photograph. shows up as line graph bell curve(s) sort of thing

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15
Q

results of meselson stahl replication experiement

A

main finding: dna replication is semiconservative and semiconservative only.

could tell this becasue as the dna replicated over generations (they tested after each generation), the ratio of DNA containing 15N to 14N DNA was exactly in line with the predictions based on the semiconservative model

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16
Q

topoisomerase

A

enzyme that breaks DNA at entaglement site (in bacteria) to seperate 2 double helixed rings of DNA

17
Q

replicon

A

origen of replication

18
Q

dna replication always goes from BLANK to BLANK

A

5’ to 3’

19
Q

leading strand

A

strand synthesized continously 5’ to 3’

20
Q

direction of overall replication

A

direction the leading strand is going

21
Q

lagging strand

A

strand sythesized discontinuously in 5’ to 3’ fragments called okazaki fragments

22
Q

DNA helicase

A

required for the seperation of strands of DNA (denaturing).

a homohexamer (6 of the same protiens combined into one functioning protien)

uses ATP hydrolysis to propell itself along the DNA strand

23
Q

single stranded binding proteins (SSBs)

A

attach to single stranded DNA after seperation by helicase and stabalizes the ssDNA so it doesnt bind to itself and makes the template available for copying.

24
Q

DNA ligase

A

seals the 5’ to 3’ phosphodieser bonds between the okasaki fragments. requires ATP

25
Q

steps of DNA replication

A
  1. helicase binds to origin and seperates strands. binding proteins (ssbs) keep strands apart. primase makes a short RNA strand (primer) on DNA template
  2. DNA prolymerase adds nucleotides to the RNA primer. DNA prolimerase checks and replaces incorrect bases through proofreading activity
  3. continous strand synthesis continues 5’ to 3’. discontinous synthesis produces okasaki fragements on the 5’ to 3’ template
  4. enzymes remove RNA primers. ligase seals sugar-phosphate background
26
Q

large complex formed by proteins for DNA replication

A

replisome

see handout for specifics

27
Q

why does DNA go 5’ to 3’

A

because otherwise there is no energy to brind in a new nucleotide and make phosphodieser bond between them

28
Q

proofreading activity

A

DNA polymerase activity that reduces the error rate of DNA replication to 1 in 10 million

29
Q

polymerase chain reaction (PCR)

A
  1. denature: heat DNA to seperate strands
  2. annealing: cool the DNA to allow the primers to anneal to target DNA
  3. extention: DNA polymerase replicates the DNA