D. Eukaryotic DNA polymerases and their functions: Error Correction in DNA Replication

exonucleases

are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain.

endonuclease

a close relative of exonucleases, which cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain.

5’ to 3’ exonuclease

3’ to 5’ exonuclease

poly(A)-specific 3’ to 5’ exonuclease

Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA. What are these?

5’ to 3’

type of exonuclease that is a dependent decapping protein

5’ to 3’

type of exonuclease that is an independent protein

proofreading

those with exonuclease activity are the ones which are involved in?

Example:

DNA polymerase gamma, delta, epsilon in Eukaryotes

DNA polymerase I and II in Prokaryotes

3’ free -OH

The primer provides a _____ end to which DNA polymerase can attach the appropriate nucleotide.

no DNA synthesis

What happens when there is no primer?

primosome

Primase, together with DNA helicase, comprise what is called a...

DNA polymerase α

In eukaryotic cells, DNA primase is associated with another polymerase, _________, which initiates the leading strand and all Okazaki fragments.

Replication error

DNA Damage

Errors in DNA replication can be due to?

a. addition of nucleotide with an incorrect base (mispairing)

b. insertion or deletion

c. strand slipage

Replication error can be? (3)

Strand slipage

an error wherein a DNA strand can slip during replication and can cause addition or deletion of a nucleotide.

extra nucleotide

If newly synthesized strand loops out, it will result in a new strand that has?

missing nucleotide

If template strand loops out, it will result in new strand that has?

Chemical Damage

Radiation

Attack by water

DNA Damage can be caused by?

Double/single strand breaks

intra/interstrand crosslinks

How the various agents can damage the DNA structure:

DNA DAMAGING AGENTS:

1. Ionizing radiation

2. X-rays

3. Anti-tumor drugs

What is its DNA Lesions?

Non Homologous End Joining (NHEJ)

Homologous Recombination (HR)

How the various agents can damage the DNA structure:

DNA DAMAGING AGENTS:

1. Ionizing radiation

2. X-rays

3. Anti-tumor drugs

What is its DNA Repair Pathways of Double/single strand breaks & intra/interstrand crosslinks?

Bulky Adducts

Pyrimidine Dimers

How the various agents can damage the DNA structure:

DNA Lesions:

1. UV Lights

2. Chemicals

What is its DNA Lesions?

Nucleotide Excision Repair

How the various agents can damage the DNA structure:

DNA Lesions:

1. Bulky Adducts

2. Pyrimidine Dimers

What is its DNA Repair Pathways?

Abasic sites

single strand breaks

8-oxoguanine lesions

How the various agents can damage the DNA structure:

DNA Damaging agents:

1. Oxygen radicals

2. Hydrolysis

3. Alkylating agents

What is its DNA Lesions?

Base Excision repair

How the various agents can damage the DNA structure:

DNA Lesions:

1. Abasic sites

2. single strand breaks

3. 8-oxoguanine lesions

What is its DNA Repair Pathways?

Base Mismatch

insertions

deletions

How the various agents can damage the DNA structure:

DNA Damaging Agents:

1. Replication Errors

What is its DNA Lesion?

Mismatch repair

How the various agents can damage the DNA structure:

DNA Lesions:

1. Base Mismatch

2. insertions

3. deletions

What is its DNA Repair Pathways?

Apurinic site

a damage to the dna that refers to the site with a missing purine

1. Excision repair system

2. mismatch repair system

2 Repair systems

Base-pair er

Nucleotide er

short patch and long patch er

Excision repair system has 4 types. What are these?

BER

for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication.

DNA glycosylase

The process of BER is initiated by __________, which recognize and remove specific damaged or inappropriate bases, forming AP sites.

short patch

a single nucleotide is replaced

long patch

2-10 new nucleotides are synthesized

pyrimidine dimer

formation of bonds between adjacent pyrimidines is called

excision nuclease

In nucleotide excision repair, __________ makes a cut a few nucleotides upstream (to 5’ end), thus making the removal of a longer segment possible.

short patch er

varies from base-pair excision in that the enzymes will recognize and remove "short patches" of DNA that are damaged.

radiation

Short patch er is ______-induced and leads to the bond formation between adjacent thymine bases on the same strand of DNA.

Long patch er

follows the same mechanism as the short-patch type but involves a longer segment of DNA.

mismatch repair system

a repair system that is able to identify mismatch errors because such damage leads to a

small distortion in the DNA backbone.

exonuclease

In MMR, once it has identified a mismatched base pair, it marks the spot with a cut and then uses an ________ to digest or "eat up" the DNA at the marker .