PL2 Flashcards
what is DNA subjected to
constant damage
name the types of damage DNA is subjected to
Hydrolytic depurination
cytosine deamination
guanidine oxidation
methylation
what can damage DNA
many chemical processes in cell and effects from environmental factors (chemicals and radiation)
what is a mutation
permanent and transmissible changes to genetic material of a cell or organism
why/when can mutations occur
can occur spontaneously
by transposable elements (segments of DNA that can move around in genome)
by errors during replication
what are mutagens
chemical compounds or UV radiation or ionizing radiation that increase frequency of mutations
like r rays and atomic particles
what happens if mutation in germline
can be passed to progeny
what happens if mutation in somatic cells
wont go to progeny but cause functional changes in soma
what are carcinogens
agents that cause cancer
many are mutagens
damaged somatic cells and divide uncontrollably
why do mechanism exist to repair damage to DNA
since DNA stores all info of cell
stability of DNA is very important
name a few diseases that are caused by defects in DNA repair systems - 5
hereditary nonpolyposis colorectal cancer
xeroderma pigmentosum
blooms syndrome
fanconi anemia
hereditery breast cancer - BRCA1 and BRCA2 deficiency
are DNA polymerases perfect
uhmmmno
they introduce 1 error every 10,000 incorporated nucleotides
what is measured rate of incorrect incorporation in cells and why
1 in 1,000,000,000
largely due to proofreading
what do DNA polymerases have
proofreading activity
which polymerases have proofreading activity
polymerases epsilon and delta have a 3’ to 5’ associated exonuclease (proofreading activity)
which DNA polymerase does not have proofreading activity
alpha
describe proofreading activity
Incorporation of incorrect base casues polymerase to pause
3’ end of new strand is free to move (flops around) to the 3’ to 5’ exonucleuase site and mispaired base is removed - chomps and digests it
what is a point mutation
single base change
what is most common point mutation
C to T
explain point mutation from C to T
chemical reaction - deamination that can affect either cytosine or methylated cytosine
if methyl cytosine undergoes deamination the amino group is replaced with keto group = thymine
how can a T-G mismatch be fixed
base excision repairs
in a mismatched base pair which base is correct and which base is wrong
T-G mismatches almost always result from deamination of C to U or 5mC to T
so T is wrong and should be replaced by C
*always assume T is wrong
what is first step in BER (base excision repair)
DNA glycosylase breaks bond between T and sugar phosphate backbone
what is second step in BER (base excision repair)
APEI endonucleases cuts DNA strand where it missing a base (on one side - a basic site)
what is third step in BER (base excision repair)
AP lyase (part of DNA pol beta) removes deoxyribose phosphate
want to get rid of one unit of sugar phosphate backbone so it can place a base there
what is a mismatch excision repair
fixes errors introduced during replication
including base pair mismatches and insertions or deletions of one/few nucleotides
in a mismatch excision repair which strand is correct and which is wrong
newly synthesized strand is wrong one
mechanisms can recognize which strand it is
when do mismatch excision repairs happen
after DNA replication
what point mutation can occur from deamination of cytosine
produce uracil from cytosine
when must repair occur if a point mutation occurs
before replication - once it replicates there is no mismatch anymore
must recognize before
what is fourth step in BER (base excision repair)
special DNA polymerase (beta) inserts C using G as template
ligase repairs sugar phosphate backbone
how to tell which strand is correct for mismatch excision repair in e coli
extensive methylation of the strands is common but newly synthesized strands are not very methylated (since methylation happens after replication)
how to tell which strand is correct for mismatch excision repair in mammalian cells
recognition of 3’ free end of DNA being synthesized - interacts with this - template does not have this 3’ free end
describe step 1 of mismatch excision repair
MSH2 and MSH6 recognize the mismatch and distinguish the newly synthesized daughter strand
describe step 2 of mismatch excision repair
MSH2 and MSH6 recognition (step 1) triggers binding and activity of MLH1 endonucleases (dimerized with PMS2)
MLH1 cuts the newly synthesized strand
DNA helicases unwind DNA
exonucleases digests seveal nucleotides of the daughter strand (always cuts a few)
describe step 3 of mismatch excision repair
DNA polymerase (delta) fills in gaps (missing nts) using the other strand as template
ligase repairs the sugar phosphate backbone
what do nucleotide excision repairs do
operates to fix DNA regions where chemically modified bases locally distort double helix
give an example of a region that would be fixed by nucleotide excision repair
thymine-thymine dimer
caused by uv radiation
two adjacent thymine bases become chemically bonded together (covalent bond distorts shape of duplex)
what other outside factors can locally distort double helix
chemicals that can bind to DNA bases including many carcinogens can also distort double helix
what is step 1 of nucleotide excision repair
XP-C and 23B proteins recognize distorted double helix
what is step 2 of nucleotide excision repair
TFIIH XP-G and RPA unwind the helix
makes a bubble of ~25 nucleotides.
what is step 3 of nucleotide excision repair
XP-F and XP-G cut the damaged strand
what is step 4 of nucleotide excision repair
DNA polymerase fills in missing nts using other strand as template
ligase repairs sugar phosphate backbone
what do XP-n names derive from + explain
xeroderma pignmentosum
genetic disease that causes a high disposition to uv induced cancer
mutations that affect XP proteins can disease
what happens if a thymine-thymine dimer is not repaired and it enters a replication fork - step 1
normal replicative DNA polymerases (delta and epsilon) stall when they reach a thymine-thymine dimer
what happens if a thymine-thymine dimer is not repaired and it enters a replication fork - step 2
special translesion polymerase (n -eta) reads through dimer
but lacks proofreading ability
what happens if a thymine-thymine dimer is not repaired and it enters a replication fork - step 3
region in vicinity of dimer will be likely to have mutations caused by replication errors
eventually pol eta will be replaced by one of the normal replicative polmerases
what is NHEJ
double strand break repair end joining
what can cause double strand breaks in DNA
radiation - x rays and gamma rays
anticancer drugs (ex bleomycin)
what happens if double strand break is not repaired
the part of the chromosome distal to the break would be lost at next cell division
probably lethal to cells
very bad
what does NHEJ do
rejoins broken chromosome ends
base pairs are usually lost at the joining point - produces a small deletion
describe step 1 of NHEJ
Ku and DNA-PK bind the end of a double-strand break (DSB)
describe step 2 of NHEJ
the 2 DSBs bound by the proteins (step 1 ) come together and recruit nucleases - they remove several bases (clean ups ends - single stranded loose ends)
describe step 3 of NHEJ
the 2 double stranded molecules are ligated together
why can the NHEJ mechanism produce chromosomal rearrangements
since mechanism does not ensure that what is ligated together comes from the adjacent parts of the same chromosome
can fuse DSBs coming from different chromosomes or far apart on the same chromosome
usually fine since cytoplasm is viscous and the breaks stay together
describe double strand break repair by homologous recombination
damaged DNA sequence is replaced by copy of undamaged copy of the same sequence on the homologous chromosome in diploid organisms
involves exchange of strands between separate DNA molecules (process of recombination)
describe BRCA1 & BRCA2 genes (double strand break repair by homologous recombination)
these mutations (associated with increases chances to breast cancer) encode proteins involved in homologous recombination repair
what mechanism can repair a collapsed replication fork
double strand break repair by homologous recombination
what can point mutations be repaired by
base excision repair
mismatch repair
nucleotide excision repair
what can double strand breaks be repaired by
non homologous end joining
homologous recombination
are DNA repair systems of all organisms the same
No
some organisms have highly efficient DNA repair systems and are highly resistant to radiation (tardigrades, deinococcus)
describe step 1 of double strand break repair by homologous recombination
parental strands - light and dark blue
replication of light blue strand (synthesis of dark green) stops when break (in backbone) is reached
generally lethal to one daughter cell since partial chromosome loss
describe step 2 of double strand break repair by homologous recombination
light green daughter strand gets ligated to segment of parental strand distal to the break to make unbroken chromosome
5’ exonuclease acts on broken end
describe step 3 of double strand break repair by homologous recombination
strand invasion is key part of recombination process
newly ligated strand anneals to the dark green daughter strand whose synthesis was interrupted by break
describe step 4 of double strand break repair by homologous recombination
branch migration
an increased stretch of the dark green strand denatures from light blue parental strand and anneals to light green daughter strand
allows light blue parental strand to cross over and anneal to dark blue parental strand
describe step 5 of double strand break repair by homologous recombination
cut strands at crossover
no more double strand break
describe step 6 of double strand break repair by homologous recombination
ligate ends
produces a similar structure to a replication fork
describe step 7 of double strand break repair by homologous recombination
rebuild replication fork and continue replication
recruitment of replication fork proteins enables further extension of the leading strand, re initiation of lagging strand synthesis and continuation of replication
a similar mechanism can…
repair a double-strand break in a chromosome and can also produce an exchange of segments between two double-stranded DNA molecules
what is holliday structure
involves all 4 strands can be resolved in 2 alternative ways
describe the 2 alternative ways of holliday structure
regenerates original chromosomes
produces 2 uniparental strands and 2 recombinant strands containing DNA from both parents
what do diagonals represent (in drawing of homologous recombination double strand break repair)
only a single phosphodiester bond between single adjacent nucelotides
