Lecture 2b

Question 1

(DNA Rep Initiation) How many subunits are there in the protein complex of ORC

Answer 1

6 subunits

Question 2

(DNA Rep Initiation) Which subunit contains a BAH domain?

Answer 2

ORC1

Question 3

(DNA Rep Initiation) The ORC1 BAH domain containing subunit mediates binding to what?

Answer 3

Mediates binding to H4K20me2, which are heavily enriched in Rep Origins

Question 4

(DNA Rep Initiation) What associates with the ORC complex

Answer 4

Cdc6 and Cdt1

Question 5

(DNA Rep Initiation) The association of Cdc6 and Cdt1 with the ORC is required for the recruitment of what?

Answer 5

Recruiting the Mcm helicase and formation of the pre-RC

Question 6

(DNA Rep Initiation) In what phase does the formation of the pre-RC take place?

Answer 6

G1

Question 7

(DNA Rep Initiation) Once S phase begins, what happens to Cdc6

Answer 7

Gets phosphorylated

Question 8

(DNA Rep Initiation) The phosphorylation of Cdc6 is by what?

Answer 8

By the cyclin dependent kinase complex, Cdk

Question 9

(DNA Rep Initiation) What happens to Cdc6 after phosphorylation?

Answer 9

Becomes inactivated and degraded

Question 10

(DNA Rep Initiation) What happens to the ORC while Cdc6 is degraded?

Answer 10

The ORC becomes phosphorylated

Question 11

(DNA Rep Initiation) After phosphorylation of ORC, what happens?

Answer 11

Leads to recruitment of other protein factors
Activation of the Mcm Helicase
Start of DNA replication

Question 12

What is the main problem with DNA replication?

Answer 12

Okazaki fragments near the end of the chromosome can not be primed

Question 13

What is a telomere?

Answer 13

Repeating DNA sequences at both ends of a linear chromosome

Question 14

What is the issue with chromosomes lacking telomeres?

Answer 14

They become unstable and may be involved in chromosomal rearrangements

Question 15

The subtelomeric region is often rich in what?

Answer 15

Pseudo-genes and transposable elements

Question 16

The telomere repeat is complementary to what?

Answer 16

A section of the RNA portion

Question 17

How does telomerase extend the telomeric DNA?

Answer 17

Extends it at the 3’-end using the RNA in its structure

Question 18

DNA synthesis occurs using what protein component of telomerase?

Answer 18

Reverse transcriptase (TERT)

Question 19

What are the functions for telomeres?

Answer 19

Prevent chromosomes from losing base pair sequences at their ends (Degradation)
prevent chromsomes from fusing to each other

Question 20

describe the mechanism of telomerase briefly

Answer 20

telomerase binds to 3’ flanking end of telomere that is complementary to telomerase RNA. So it binds to the 3’ end of the leading strand. Bases are added to the leading strand using Telomerase RNA as a template. Telomerase then relocates and this step is repeate. DNA polymerase then complements the lagging strand.

Question 21

Telomerase activity is high where and low where?

Answer 21

High in stem cells , germ cells and cancer cells

Low activity or absent in somatic cells, decreases with age and cells senesce (Stop dividing)

Question 22

How does depurinatoin and depyrimidination and deamination happen?

Answer 22

Via hydrolysis

Question 23

What is depurination? What can it cause?

Answer 23

Loss of G or A
Causes 1bp deletions, so after replication the old strand is mutated as that base pair is deleted and the other stand remains unchanged

Question 24

Deamination of C

a) is what?
b) leads to what
c) describe what happens after replication

Answer 24

a) the removal of NH3 on cytosine, so a h20 and NH3 is produced as a byproduct and a Uracil is produced in place of the cytosine
b) Lead to a G–> A mutation
c) The mutated strand has an U+A pairing. The U base from the original strand is paired with an A.
The other strand remains unchhanged and has a C + G pairing

Question 25

UV light can cause what?

Answer 25

Pyrimidine dimers

thymine dimers

Question 26

What are the repair systems for the following damages

1) Missing or altered base
2) Distortion of DNA with damage on one strand
3) Incorrect base pairing
4) Both strands are damaged

Answer 26

1) Base excision repair
2) Nucleotide excision repair
3) Mismatch repair
4) Double stranded break repair

Question 27

Base excision repair

a) usually occurs with what damage?
b) the dna is missing what?
c) what enzymes are used
d) what do the enzymes do?
e) what is left after the first 3 enzymes are used?
f) what enzymes are then used after step e)

Answer 27

a) Deamination of C
b) DNA helix is missing a base
c) DNA Glycolase, removes the damaged base. AP Endonuclease creates a nick in the phosphodiester backbone of the AP site. Phosphodiesterase remove sugar phosphate (so it removed the backbone), these are used first. Then DNA polymerase adds new nucleotides. DNA ligase seals the nick
e) DNA helix with single nucleotide gap
f) DNA polymerase and DNA ligase

Question 28

Nucleotide excision repair

a) used for what damage?
b) what 4 enzymes are used?
c) when are these enzymes used?
d) what happens to the DNA helix?

Answer 28

a) thymine dimer
b) Excision nuclease, DNA helicase, DNA polymerase and DNA ligase
c) Exicision nuclease used to excise the dna backbone and DNA helicase unwinds the helix to overall remove the excised fragment.
d) The DNA helix has a 12-nucleotide gap which is then filled used dna polymerase and dna ligase

Question 29

Mismatch repair and double stranded break rpeair

a) look at griffith notes

Answer 29

okay