DNA Replication and Repair

Question 1

What is Semiconservative DNA synethesis?

Answer 1

Each strand is copied in it’s entirety and you end up with two new alpha helices each one with one copy of each of the original template strands

Question 2

Which direction does DNA replication proceed in?

Answer 2

5’ to 3’ always

Question 3

Where are phosphodiester bonds formed in DNA growing chains? - also known as polymerization

Answer 3

between the 3’ hydroxyl of 1 sugar and the 5’ hydroxyl of the next sugar

Question 4

What is the substrate for polymerization of DNA?

Answer 4

deoxyguanine triphosphate

Question 5

What is released as you are performing polymerization of DNA and forming phosphodiester bonds?

Answer 5

releasing pyrophosphate

Question 6

What is the clinical significance of Polymerization?

Answer 6

If you can mess with the polymerization of the invading gemome without hurting a host genome you have the potential to control infection

Question 7

How do AZT and Acyclovir work?

Answer 7

They affect 5’ to 3’ phosphodiester bond formation - in other words they both mess with DNA polymerization

Question 8

How does AZT work?

Answer 8

it messes with DNA polymerization - insead of 3’ OH that analogue has N3 - so the DNA chain can’t grow

Question 9

How does acyclovir work?

Answer 9

it’s a modified nucleotide that is converted into acyclo-GTP which is then used by viral polymerases resulting in cain termination and thus controlling of the invading organism

Question 10

Which enzymes are utillized in DNA replication?

Answer 10

Helicase

Gyrase

Topoisomerases

Single Strand binding Proteins

Question 11

What does Helicase do in DNA replication?

Answer 11

it breaks apart the base pairs

Question 12

What do Topoisomerases I and II do?

Answer 12

they stop the supercoiling of DNA molecules to allow the replication fork to form

Question 13

What do the Single Strand Binding Proteins do?

Answer 13

They stop the base pairs from reforming and the strands from rehybridizing (coming back together)

Question 14

What are the steps of DNA replication?

Answer 14

The strands are separated by Helicase enzyme

SSBP keep the strands from coming back together

The leading strand has a priming event

One DNA strand encodes the leading strand using DNA Polymerase III

RNA primase lays down an RNA primer on the lagging strand

DNA polymerase 3 lays down new DNA

Process repeats with new DNA and primers

DNA polymerase I replaces RNA primers with DNA

DNA ligase links fragments together

Question 15

Which enzymes or molecules are utilized in DNA replication?

Answer 15

DNA polymerase I

Topoisomerase

SSBP

Helicase

3’ hydroxyl of deoxy in base

Primase

Deoxynucleotide triphosphates

KEY:

NO ATP USED

Question 16

Which enzyme is involved in Proofreading Activity?

Answer 16

DNA polymerase - removes and replaces erroneously introduced nucleotides

Question 17

When does the Mismatch Repair Mechanism come into play?

Answer 17

When a mistake is missed by the Proofreading mechanism

Question 18

What is the enzyme responsible for DNA replication?

Answer 18

DNA polymerase

Question 19

What are the primary Prokaryotic DNA polymerases?

Answer 19

Pol I, II and III

DNA polymerase I replaces the RNA primers with DNA in replication

DNA polymerase II is involved in DNA repair

DNA polymerase III is the major DNA maker!

Question 20

How many polymerase genes do Eukaryotes have?

Answer 20

15

Question 21

What diseases are caused by defective DNA replication?

Answer 21

Neurological diseases:

Myotonic dystrophy

Friedrichs’s ataxia - it’s the fault of the underlying DNA structure - lots of repeats confuse the enzymes and they can’t properly unwind the DNA to add in new bases - the polymerases get lost

Question 22

What are the 4 types of DNA damage?

Answer 22

1) Oxidative Deamination
2) Depurination
3) UV light crosslinking
4) Oxidative Methylation

Question 23

What happens in Oxidative deamination DNA damage?

Answer 23

conversion of cytosine to uracil in nucleus during replication

Question 24

What happens during Depurination DNA damage?

Answer 24

glycosyl bond removes guanine base

Question 25

What happens with UV light in regard to DNA damage?

Answer 25

Crosslinking of thymines make a cyclobutane

Question 26

What are the 2 types of repair mechanisms

Answer 26

Base Excision repair

&

Nucleotide repair

Question 27

What happens during Base Excision repair?

Answer 27

A scanning mechanism recognizes a problem or mismatched base

This mechanism brings in an enzyme glycosylase to remove the bad base from the backbone

Adds a new base via polymerase

DNA ligase Seals it up by making a new phosphodiester bond

Question 28

What happens during a nucleotide repair?

Answer 28

The scanning mechanism recognizes a base that is mismatched

The enzyme takes out a chunk of problem area

Endonuclease comes in and breaks phophodiester bonds

Bad piece floats away leaving gap of single stranded DNA template

DNA polymerase comes in and adds complementary bases

DNA ligase replaces phosphodiester bond to seal the gap

Question 29

What is an example of a disease caused by defective DNA repair?

Answer 29

Herediatary nonpolyposis colon cancer - mutation in the mismatch repair gene

Question 30

What happens with epithelial cells when you don’t have properly functioning mismatch repair mechanisms?

Answer 30

Epithelial cells undergo DNA replication at a far greater rate - so when mistakes get missed they start piling up faster and faster until you form polyps and eventually the possibility of cancer