Biochem Chap 20

Front 1

What is a holoenzyme?

Back 1

-asymetric dimer which has 2 copies of each polypeptide ( alpha, episilon, and theta)
- these poly. form 2 core complexs.

in addition I believe this thing also contains the y comples and the beta subunit

Front 2

What are two factors that are important for DNA inititation?

Back 2

- happens at specific DNA sequences
- need additional proteins.

Front 3

what is a replisome?

Back 3

a protien machine that aids in the rapid and accurate DNA replication; usually found in at the end of a replication fork

Front 4

what is the y complex?

Back 4

-this helps the replisome assemble the parental strand.

Front 5

what is significant about the direction dna is replicated?

Back 5

bidirectional

Front 6

what is dna poly 3

Back 6

- helps dna elongaion
-is apart of the replisome

Front 7

what does the assembly of the replisome contribute

Back 7

it yields two dna daughter strands/ by synthesizing two strands.

Front 8

what is a terminating site

Back 8

where they two replisomes meet to form releasing two complete daughter DNA

Front 9

what is bidirectional chromosomal dna replication

Back 9

- a dna repliccation that begins at a unique origin and goes both directions

Front 10

what is the core complex

Back 10

this includes the alpha, epsilon, and theta
- this is responsible for polymerization reaction

Front 11

dna polyermerace I has two functions?

Back 11

repairs dna
synthesizes new DNA

Front 12

what do topoisomerases do?

Back 12

unwind the supercoling so the replisome can move down the fork.

Front 13

what are the 3 key differences between prok. and eukary. in dna replication?

Back 13

1. euk have many origins to replication
2. euk have smaller ozaki fragments
3. dna replication in euk is slower due to nucleosome.

Front 14

dna poly 2

Back 14

helps dna repair

Front 15

`what is the sole difference in leadig and lagging strands ?

Back 15

- in leading strands everything is synthesized coninuelsy
- lagging has discontiunes agianst the directions of the replication fork .

Front 16

beta subunit

Back 16

this is a sliding clamp ( head to tail dimer) which is apart of the replication fork and it bind to the two DNA strands.

Front 17

y complex

Back 17

- helps assemble the replisome onto the dna so it will not fall off

Front 18

who discoverd the dna polyermerase

Back 18

aurther kornberg

Front 19

list the 3 points in the sanger method?

Back 19

1. dideonucleotide terminates the elongaiton chain
2. each of the 4 dideaneocloetides is used to terminate the synthesis and seperation reaction
3. the order of nucleotides is the leangth of the terminating fragments

Front 20

what are two factors of dna replicaiton?

Back 20

- specitifc sites
- uses additional proteins

Front 21

what happens during dna elongation?

Back 21

additon: the nucleotides are added with the catalizing the ncleotides from 5' to 3' end
reparing: the exonuclease fix the DNA errors from the 3' to the 5' end

Front 22

what is a processize and distributive enzyme?

Back 22

this is an enzyme which stays bound to the dna chain after polymerization has ended (processive )
distrbutive comes off of the chain

Front 23

define a dna daughter

Back 23

this has one orginal parent and a new synthesized one.

Front 24

what do helicases do

Back 24

unwind the parental strand

Front 25

what is a ssb do

Back 25

binds to single stranded dna and prevents it the from refroming the double between the parental dna templates.

Front 26

how is a leading strand of the ozaki fragments synthesized there are three steps?

Back 26

1. RNA primers initiate this by binding to the lagging strand of the OZaki.
2. the DNA poly 1 extends the Ozaki nucleotides 10-12 while its exonuclease goes 5 to 3 removes primers which causes the nick to move and putting in DNA= nick translation
3. then Dna poly 1 goes away and ligase binds DNA with phosphosdiester bounds.

Front 27

what is the replisome made of ?

Back 27

dna poly
helicase
primase

Front 28

what do direct repair mechanism do

Back 28

these fix errors in dna by mutagen

Front 29

direct excision repair

Back 29

fixes errors in dna caused by mutagens

Front 30

what two things fix errors in dna

Back 30

exicions repair

and direct repair mechanism which repair the defects with out altereing the backbone.

Front 31

what is the limitation of DNA polymerase 1

Back 31

it can only add nucleotides but it can not start replication

Front 32

how can this limitation of the dna polymerase 1 be fixed

Back 32

well by the rna primer

Front 33

dna primase

Back 33

synthesizis the RNA primer which start the dna replication

Front 34

what complex is the dna primase apart of?

Back 34

it is apart of primosome

Front 35

what is a primossome ?

Back 35

this is a larger complex which the primase (maker of RNA primers ) is a apart of. thus is contains several others polpepetides + primase.

Front 36

Where is this initiation site for DNA picked and how?

Back 36

a bunch of portiiens coordinate this but the main one DNNa:
1. unwind the origninal region
2. control the frequency of initiation

Front 37

what is the INITIAL stie for DNA sysnthesis start like what is this place called

Back 37

Origin

Front 38

What did Sanger do exactly ?

Back 38

who: Sanger
what: sequenced DNA
how: enzymatically
using: dideoxyribonucleotide

Front 39

what is photodimerization ?

Back 39

uv light causes the mutations on the forming adjacent thymine dymers.

Front 40

why can not replication occur when we have thymine dimers?

Back 40

due to distorition in the template strand.

Front 41

how can thymine dyimers be removed?

Back 41

photoreactionvation by the enyzme photolase where binds to the dimer and in presence of light the enyzmes cleaves the dimer allowing replication.

Front 42

what is an example of direct repair

Back 42

photoreactivation

Front 43

What are the two type of thing that a general excision repair can be used for?

Back 43

1. loss of heterocylic bases
2. deanimation

Front 44

what are the step to an general excision repair?

Back 44

1. detiection of damaged dna: the endonucleas goes and nicks it out of backbone on both sides of the DNA
2. this leaves a gap filled in by DNA poly
3. sealed by the DNA ligase.

Front 45

main difference between an excision repair and direct repair?

Back 45

direct repair no back bone breaking
and the other excison one you have to.

Front 46

most common dna damage?

Back 46

deanimation of cytosine.

Front 47

how to fix a deanimation of cytosine?

Back 47

1. since the deanimation creates a urcail. the N glycosylase recognizes this and hydrloizes the N glycosidic bond givin AP site
2. AP site reconized by endonuclease and it removes the deoxy ribose phospate
3. yeilds a gap filled by dna poly 1 and sealed by ligase.

Front 48

steps to systhesizing leading and the lagging strand in THE SAME DIRECTION?

Back 48

the systhesis of dna can be done by one enxyme going same direction
1.begins by looping around lagging start around replisome.
2. helicase unwinds and primase makes primers that attached RNA pirmers and hte lagging strand polermase 3 goes until it runs into another Ozaki. so goes to another new synthesisze of ozaki.