DNA Replication in Eukaryotes

Question 1

What is the eukaryotic version of helicase?

Answer 1

MCM

Question 2

What is one difference about the replication fork/complex in eukaryotes?

Answer 2

A pre-replication complex (pre-RC) must form on ARS (origin of rep) before helicase can act

Question 3

More Pre-RC are ______ (assembled) than _______ (used).

Answer 3

Licensed

Fired

Question 4

What causes Meier-Gorlin Syndrome?

Answer 4

Mutations in genes that encode the proteins required for the the Pre-RC complex.

Question 5

What are symptoms of Meier-Gorlin syndrome?

Answer 5

Failture to thrive
Patella hypoplasia
Small upper and lower jaw

Question 6

What causes DK?

Answer 6

Defective telomerase/telomere shortening

Question 7

What is unique about telomerase?

Answer 7

It contains a reverse transcriptase component

Question 8

Why are telomeres needed?

Answer 8

The lagging strand gets left with a left over primer that when removed, would shorten the DNA. Telomerase replaces the gap.

Question 9

How does telomerase work?

Answer 9

It positions itself at the end, add a telomere repeat, reposition, etc.

Question 10

Do telomerases use DNA or RNA?

Answer 10

RNA

Question 11

In order to protect itself telomeres…

Answer 11

Loop back on themselves and create a t-loop and a d-loop

Question 12

What are symptoms of DK?

Answer 12

Premature aging
Oral leukoplakia
Skin hyperpigmentation
Nail dystrophy/ridging
Bone marrow failure/aplastic anemia

Question 13

What is Hoyeraal-Hreiderasson (H-H) syndrome?

Answer 13

Rare variant of DK

Diagnosed in first months

Question 14

What are the symptoms of H-H syndrome?

Answer 14

Aplastic anemia
Severe immunodeficiency
Cerebellar hypoplasia
Mutation in hTERT, hTR

Question 15

Disease of telomere shortening show anticipation due to loss of telomerase function in _____ cells.

Answer 15

Germ

Question 16

What are the two major methylated bases in prokaryotes?

Answer 16

Adenine and Cytosine:

N6-methyladenine
N4-methylcytosine

Question 17

What is the role of methylation in bacteria?

Answer 17

Protects bacteria’s DNA from cleavage by restriction endonucleases

Question 18

In E. coli methylation of adenine residues in the sequence ____ is involved in mismatch error correction.

Answer 18

GATC

Question 19

What bases are methylated in eukaryotes?

Answer 19

Cytosine only!

5-methylcytosine

Question 20

What is the sequence of methylation in eukaryotes?

Answer 20

CG and complementary CG will be also methylated in the corresponding position

Question 21

Is methylation heritable or inheritable?

Answer 21

Heritable

Question 22

A ______ promoter tends to be expressed and a _______ promoter tends not to be expressed.

Answer 22

unmethylated = expressed

methylated = not expressed

Question 23

How can you reverse the methylation of genes?

Answer 23

Treatment with 5-azacytidine, a cytidine analog that cannot be methylated

Question 24

What are common causes of DNA mutation?

Answer 24

Mistakes during replication
Deamination of cytosine
UV damage
Chemical damage

Question 25

What happens due to deamination of 5-methylcytosine?

Answer 25

CG to AT transition mutation

Question 26

What is a transition point mutation?

Answer 26

Exchange of one pyrimidine-purine base pair for another pyrimidine-purine pair.

Question 27

What is a transversion point mutation?

Answer 27

Pu-Py exchanged for Py-Pu This is worse!

Question 28

What are common causes of deletion or insertion mutations?

Answer 28

Intercalating agents that fit in between adjacent base pairs Transposable elements Triplet repeats

Question 29

What is the worst result of a deletion/insertion mutation?

Answer 29

Changing the reading frame

Question 30

What are inter or intra strand break and crosslinks?

Answer 30

Photodimerization for example causes intra stand dimerization of adjacent (pyrimidine) dimers.

Question 31

Is O6-alkylguanine an especially deleterious form of DNA damage?

Answer 31

Yes

Question 32

What does O6-alkylguanine have a high probability of being base paired with during replication?

Answer 32

Thymine

Question 33

How are O6-alkylguanine repaired in prokaryotes and eukaryotes?

Answer 33

O6-alkylguanine DNA methyltransferase (MGMT) transfers the methyl group to itself i.e. self alkylates and restores the guanine.

Question 34

How does excision repair work?

Answer 34

Damaged DNA is recognized, removed, and then replaced by DNA polymerase

Question 35

What does nucleotide excision repair (NER) fix?

Answer 35

Intra strand thymine dimers caused by UV radiation

Question 36

What are the steps of NER?

Answer 36

1. Recognition of damage 2. Repair proteins stall at damage 3. Bend DNA 4. UVrA displaced, UVrC joins complex 5. Endonuclease cuts 3' to 5' and a helicase removes damaged piece 6. DNA Pol I replaces excised DNA 7. DNA ligase seals nick.

Question 37

What is base excision repair?

Answer 37

DNA-N-glycosylases removed incorrect BASES in DNA

Question 38

What enzyme removed mismatched uracil in prokaryotes?

Answer 38

Uracil DNA-N-glycosylase

Question 39

What enzyme repairs DNA in eukaryotes?

Answer 39

DNA Pol Beta

Question 40

What two types of mechanisms exist for repairing eukaryotic DNA by excision repair?

Answer 40

Short patch BER | Long patch BER

Question 41

What is mismatch repair?

Answer 41

Nascent DNA scanned for errors - mismatched bases and single base insertions or deletion Errors are corrected

Question 42

How does mismatch repair occur?

Answer 42

MutHLS system: 1. Recognition of damage 2. MutHLS complex searches for *methylated* GATC sequence closest to damage 3. MutH (endonuclease) cuts the backbone 5' to the G in GATC 4. Helicase unwinds DNA past damage 5. Exonuclease removes DNA past damage 6. DNA Pol III fills the gap 7. Nick in backbone sealed by DNA ligase It looks for methylated strand because it knows that is the correct parent strand. Daughter strand not yet methylated

Question 43

What genes are affected in patients with CMMRD?

Answer 43

MSH (mismatch repair) genes

Question 44

What are common symptoms of CMMRD?

Answer 44

``` Childhood onset of brain tumors Colorectal cancers Neurofibromatosis-1 Cafe au lait spots Hematological malignancies ```

Question 45

What are symtpoms of xeroderma pigmentosum?

Answer 45

Superficial reddening of the skin Freckling Rapid development of skin cancer despite little sun exposure

Question 46

What causes xeroderma pigmentosum?

Answer 46

Failure to conduct nucleotide excision repair

Question 47

What are the two types of eukaryotic NER?

Answer 47

Global genome NER: probes the genome for lesions Transcription-coupled NER: removes transcription-blocking lesions to permit unperturbed genome expression