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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:
Ionizing radiation
X-rays
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:
Ionizing radiation
X-rays
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:
UV Lights
Chemicals
What is its DNA Lesions?
Nucleotide Excision Repair
How the various agents can damage the DNA structure:
DNA Lesions:
Bulky Adducts
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:
Oxygen radicals
Hydrolysis
Alkylating agents
What is its DNA Lesions?
Base Excision repair
How the various agents can damage the DNA structure:
DNA Lesions:
Abasic sites
single strand breaks
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:
Replication Errors
What is its DNA Lesion?
Mismatch repair
How the various agents can damage the DNA structure:
DNA Lesions:
Base Mismatch
insertions
deletions
What is its DNA Repair Pathways?
Apurinic site
a damage to the dna that refers to the site with a missing purine
Excision repair system
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 .
