Ch 6 Exam 2

Question 1

What did the meselson-Stahl experiments show

Answer 1

That DNA replication is semiconservative

Question 2

What’s the really important enzyme that DNA replication needs

Answer 2

DNA polymerase. 5’-3’ prime

Question 3

WHat is released when a nucleotide is added by DNA polymerase

Answer 3

a pyrophosphate

Question 4

What are the lagging strands called

Answer 4

oakizaki fragments

Question 5

what are the four steps of lagging strands

Answer 5

primer synth
elogation
primer removal with gap filling
joining of okazaki fragments

Question 6

What is a replisom

Answer 6

a multiprotein machine with a suite of basic enzmatic functions:
Helicase
primase
dna polymerase
3’ to 5’ exonuclease

Question 7

WHat are single strand binding proteins

Answer 7

stabling single strand so it doesn’t fold on it’s self
RPA in humas
SSB in bacteria

Question 8

What does DNA polymerase do

Answer 8

strand elongation
RNA primer removal

Question 9

Which polyimerases are for replication of

Answer 9

1 and 3

Question 10

DNA polymerase 1

Answer 10

Primer removal, gap filling between okazaki frgaments and nucleotide excision repair pathway

Question 11

Two fragments of pol 1

Answer 11

Klenow fragment has 5’ to 3’ polymerase activity and 3 to 5 exonuclease activity(for proof reading)

Question 12

DNA polymerase III

Answer 12

main replicative polymerase. both 3 to 5 and 5 to 3

Question 13

DNA polymerase II, IV, V

Answer 13

DNA repair mechanisms

Question 14

Where does dna rep begin

Answer 14

origin.
some have as many as 3
A-T rich
DnaA can only bind to negatively supercoided origin DNA

Question 15

WHat does helicase do

Answer 15

unwind

Question 16

Steps in rep innitiation

Answer 16

Initiator protein (DnaA) binds to Origin
DNA helicase unwinds helix
two replication forks are formed
replication is bidirectional
Two sliding clamps tether DNA polymerase to DNA polymerase
Single-standed binding proteins (SSBPs) keep dna helix open and protec from nuclease attack
Primase synthesize RNA primer

Question 17

WHat’s a clamp loader

Answer 17

uses ATP to open and close the sliding clamps aroud DNA

Question 18

steps for DNA elongation

Answer 18

two molecules of DNA polymerase III catalyzes DNA synthesis at the time.
DNA template
all four deoxyribonucleoside triphosphates (dNTPs)
primer

Question 19

what’s the main polymerase for elongation

Answer 19

polymerase III

Question 20

What direction does DNA polymerase synthesize and what direction does it read

Answer 20

5’ to 3’
reads 3’ to 5’

Question 21

what removes the RNA primer and syntehsize DNA complementary deoxyribonucleotdies

Answer 21

Poly 1

Question 22

WHat does DNA ligase do

Answer 22

catalyzes phosphodiester linkage between adjacent fragments of. seals it up

Question 23

what’s the end site of replication

Answer 23

Ter site

Question 24

What topoisomers

Answer 24

forms of DNA that have the same sequencing but different linking number and mobility. varying amount of coiling

Question 25

Bacterial type 1 topoisomerase

Answer 25

relax negative supercoils relax negative and positive supercoiling can detangle do not require ATP single strand breaks

Question 26

Type II topoisomerase

Answer 26

relax both negative and positive supercoils unknot or decatenate entangled DNA molecule Needs ATP^^ gyrase introduces negative supercoid double sttrand breaks

Question 27

What can block leading strand synthesis

Answer 27

damaged of template

Question 28

What are the origin on eurkaroites

Answer 28

internal sites on linear chromosomes

Question 29

Autonomous replicating sequence

Answer 29

in saccharomyces cerevisiae

Question 30

origins "fire" how many times per cell division

Answer 30

once

Question 31

are the origins activated at the same or different times

Answer 31

uniformly activated

Question 32

E First step

Answer 32

Histone removal. Histone modification and chromatin remodeling factors are some ideas

Question 33

What stage does origin selection occur in

Answer 33

G1 Phase

Question 34

What phase does DNA replication happen in

Answer 34

S

Question 35

What does the prereplication complex (pre-RC) do

Answer 35

Forms at origin. Assembly of proteins: ORC (origin recognition complex), Cdc6 and Cdt1 (load MCM helicase complex), and MCM helicase (unwinds the DNA) Licensing for replication (only happens once) Transitions from licensed state into S phase to active replication

Question 36

What is ORC

Answer 36

DNA binding complex that binds Cdc6 to origins

Question 37

What happens after the Mcm 2-7/Cdt1 binds to Cdc6

Answer 37

Cdc45/GINScomes in and Cdc 6 and Cdt1 leave. After the pre-replication complex is formed (G1) and the cell enter S phase, Cdc45 binds to MCM helicase

Question 38

What happens after Cdc6 is bound to DNA

Answer 38

Recruits Mcm 2-7 with Cdt1

Question 39

E What is licensing

Answer 39

It's a process that ensures that replication only occurs once per cell cycle Prepares origin to be used during the S phase

Question 40

What is licensing controlled by

Answer 40

cyclin-dependent kinases (CDKs)

Question 41

What are CDKs activated by

Answer 41

cyclin

Question 42

What phase is CDK low and what does that allow

Answer 42

G1, allows Mcm 2-7 can be loaded

Question 43

CDK is high

Answer 43

S and G2 CDK plumets during M phase causing licensed origins fire, but can't be reloaded, phosphorylates Mcm2-7. Mcm2-7 can not be loaded

Question 44

In Eurkaryotes, which strand is the Helicase loaded onto

Answer 44

Leading

Question 45

in bacteria where does the helicase load

Answer 45

lagging

Question 46

what are the singlge strand binding proteins for eurkaryotes

Answer 46

RPAs

Question 47

What's the RNA primer for eurkaryotes

Answer 47

it is synthesized by DNA polalpha and it's associated primase

Question 48

What does pol alpha/primase enzyme synthesize first

Answer 48

7-10m bases of RNA, then 25-35 bases of initiator DNA (iDNA

Question 49

WHat polymerases are after pol alpha

Answer 49

Leading strand: polymerase e lagging strand: polymerase delta handoff between dna pol alpha to the appropriate one

Question 50

What are the DNA polymerases in mammals used for chromosomal DNA replication?

Answer 50

DNA pol alpha, pol delta, pol epsilon Mitochon: Pol y ALl the rest of them: repair

Question 51

What's the name of the E clamp

Answer 51

PCNA loader is RFC. opens and closes clamp, subunits

Question 52

Steps in proofreading

Answer 52

pause melting translocation of incorrect to the exonuclease removal of the 3' terminal base It's identified by abnormal geometry of mismatcehd base pairs and base-base hydrogen bonding

Question 53

After repair what needs to happen to

Answer 53

RNA primer removal gap fill-iin joining of okazaki fragments on the lagging strand

Question 54

what fills in and joins okazaki fragments

Answer 54

FEN1 and DNA ligase 1

Question 55

Histone reassembly

Answer 55

quick.

Question 56

Rolling circle replication

Answer 56

a common mode of viral and factor replication

Question 57

Steps in rolling circle replication

Answer 57

donor cell attackes to recipient with pilus cells contact one another one strand of plasmid DNA transfers to recipient recipient synthesizes a complementary strand

Question 58

What are telomers

Answer 58

end of chromosome and DNA

Question 59

How to telomerases solve the lagging strand problem?

Answer 59

has a RNP complex that reverse transcriptase activity. . Essentially has a primer to it. contains an RNA component that provideas a template for telomere repeat synthesis

Question 60

Two parts of telomer

Answer 60

RNA: Telomerase RNA component (TERC) Protein: Telomerase reverse transcriptase (TERT)

Question 61

What happens after telomerase elongates the DNA

Answer 61

it forms a T-loop

Question 62

WHat helps make the DNA legnth after the telomermase just right

Answer 62

TZAP

Question 63

Is telomerase always on and being used

Answer 63

yes

Question 64

Does progressive shortening of telomeres in human somatic cells happen?

Answer 64

yes

Question 65

What happens when cells have little telomerase activity

Answer 65

Hayflick limit. The cells become senescent. Don't grow and divide.

Question 66

shelterin

Answer 66

The telomeres are essential for maintaining chromosomal stability, and shelterin plays a key role in ensuring that they are protected from unwanted DNA damage responses and inappropriate DNA repair processes.

Question 67

Which strand does telomeres elongate

Answer 67

The 3' strand ends up longer, no problem, shelterin makes it all safe and good