wednesday week 2

Question 1

first step of DNA organization

Answer 1

DNA double helix

Question 2

second step of DNA organization`

Answer 2

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

Question 3

third step of DNA organization

Answer 3

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.

Question 4

linker DNA

Answer 4

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

Question 5

histone H1

Answer 5

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

Question 6

fourth step of DNA organization

Answer 6

chromatin fibers folded into loops

Question 7

histone tails

Answer 7

scaffolds that link adjacent nucleosomes together

Question 8

explain how DNA packaging is dynamic

Answer 8

local changes in gene expression and global changes during cell cycle

Question 9

euchromatin

Answer 9

less condensed, contains expressed genes

Question 10

heterochromatin

Answer 10

condensed, contains genes/DNA that are not expressed

Question 11

explain the conservative model of DNA replication

Answer 11

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)

Question 12

explain the semi-conservative model of DNA replication

Answer 12

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

Question 13

explain the dispersive model of DNA replication

Answer 13

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

Question 14

explain the methods of meselson stahl’s replication experiment

Answer 14

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

Question 15

results of meselson stahl replication experiement

Answer 15

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

Question 16

topoisomerase

Answer 16

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

Question 17

replicon

Answer 17

origen of replication

Question 18

dna replication always goes from BLANK to BLANK

Answer 18

5’ to 3’

Question 19

leading strand

Answer 19

strand synthesized continously 5’ to 3’

Question 20

direction of overall replication

Answer 20

direction the leading strand is going

Question 21

lagging strand

Answer 21

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

Question 22

DNA helicase

Answer 22

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

Question 23

single stranded binding proteins (SSBs)

Answer 23

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.

Question 24

DNA ligase

Answer 24

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

Question 25

steps of DNA replication

Answer 25

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

Question 26

large complex formed by proteins for DNA replication

Answer 26

replisome

see handout for specifics

Question 27

why does DNA go 5’ to 3’

Answer 27

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

Question 28

proofreading activity

Answer 28

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

Question 29

polymerase chain reaction (PCR)

Answer 29

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