lecture 7 Flashcards
your patient seems prematurely old, and suffers from osteoporosis, kyphosis (curve of spine), cachexia(muscle wasting) and infertility
What is the problem
defect in NER (nucleotide excision repair) leading to Trichothiodystrrophy (TTD)
NER fix UV light defects (thymine dimers)
your patient has balance disorder, depressed immune system, cerebellar degeneration, extreme sensitivity to Xrays and has developed cancer.
What is the problem
Ataxia Telangiectasia caused by mutation of the ATM gene
ATM protein can see DCB and causes the cell to fix them
P has colon cancer
What gene is mutated?
genes in mismatch DNA repair pathway
heriditary non-polyposis colon cancer HNPPC
how is DNA bonded
sugar-phosphate backbone of DNA
5’ to 3’
helix
GC (stronger 3 hydrogen bones) and AT (weaker 2 hydrogen bonds)
purines attaches to pyrimidines
DNA replication
- topological constraints
- unmasking of chromosomal proteins
- large genome size (needs to be fast) (1000 nucleotides per second), can occur at a bunch of spots on DNA at same time
- accuracy
Semiconservative and bidirectional
explain semiconservative DNA replication
new copy has one strand old one strand new
explain bidirectional DNA replication
starts and then goes in both directions
DNA polymerase can only go ___ to ___. DNA polymerase can only elongate an ____ of DNA or RNA
5’ to 3’
existing primer, only double stranded, with free 3’hydroxyl group available to bind
lagging strand fragments
okazaki
can only go 5’ to 3 ‘
DNA polymerase needs a primer to start
RNA polymerase can start. will attach and will put down RNA which DNA can see and copy. RNA primer will eventually get eaten and replaced by DNA polymerase
at the end of the strand will have RNA primer at end of chromosome
- cant be eaten
-RNA easily degraded
leaving single strand which also gets degraded- BAD cell death
Enzyme telomerase adds repeated sequence at ends to protect DNA from being broken down
ways to damage DNA
radiation
DNA polymerase
heat
ect.
how does DNA know something went wrong
protein sensors
-usually phosphorylation cascade
= stop cell cycle, cell death, turn on genes that fix the problem, and then fix the problem
ATM is one of these proteins
ATM sees double stranded breaks and is a transducer that initiates signaling pathways to inform the cell the DNA is damaged
Defects in ATM leads to
Ataxia telangiectasia
explain BER
base excision repair
PARP is needed to recruit proteins to DNA damage
- recognize problem
glycosylases recognize 1 base error and cut the base out - cut out the damage
endonuclease (ape1) cuts the sugar out of the DNA backbone - fill in proper sequence
DNA polmerase beta fills in the correct nucleotide - close the DNA backbone with ligase
explain NER
nucleotide excision repair
- recognize problem
UV light damage (thymine dimers)
XPA, XPE find problem
TFIIH(XPB and XPD) unwind the helix - cut out the damage
XPF/ERRC1 and XPG cut out section - fill in proper sequence
DNA polymerase put in right section - close the DNA backbone with ligase
explain MMR
mismatch repair
usually seen in colon cancer
in BACTERIA
- recognize problem
will recognize problem and nick DNA
MutS, MutL, MutH, ATP - cut out the damage
Will eat bases and error
Exonuclease, Helicase II ATP - fill in proper sequence
DNA polymerase - close the DNA backbone with ligase
explain HR
homologous recombination
Double stranded breaks (DSB)
bring broken ends together and join them with ligase.
explain NHEJ
what might it help with
nonhomologous end joining
Double stranded breaks (DSB)
bring broken ends together and join them with ligase. Somatic recombination of immunoglobulin genes
explain TS
translesion DNA synthesis
error prone DNA polymerase copy over mutated DNA (ehh it will probably be okay)
Somatic Hypermutation of immunoglobulin genes
how does PARP inhibitors help kill cancer cells
PARP is used to fix 1 strand errors (BER base excision repair)
stop PARP and 1 strand error becomes two stranded error
BRCA tries to come and fix the problem
in cancer BRCA fucks up and causes more breaks
if we stop PARP we stop BRCA and more breaks causes cell to die
NER defects leads to
NER (nucleotide excision repair)
xeroderma pigmentosa
cockayne’s syndrome
trichothiodystrophy
explain xeroderma pigmentosa
NER defect (nucleotide excision repair)
- 7-8 genes cause defect on XPA (finds problem) and XPG (cuts problem)
- unable to repair UV damage (thymine dimers)
- 1000-2000 fold increase in sun-induced skin cancer
- neurological defects in most severe cases
explain cockayne’s syndrome
NER defect (nucleotide excision repair)
caused by mutation of a subset of XP genes (TFIIH XPB, XPD)
no increase risk of cancer
impaired neurological development
dwarfism
premature aging
explain trichothiodystrophy
defect in NER (nucleotide excision repair)
share many of the same conditions as C.S(cockayne’s syndrome)
brittle hair and nails, scaly skin
reduced stature, curved spine (kyphosis)
reproductive problems
how does mismatch repair know which strand is right
old strand has Ch3 (methyl group)
old strand must be right, will attack and fix new strand
HNPCC
heriditary non-polyposis colon cancer
mutations in Mismatch repair
bacteria to human
MutS is similar to MSH1-6
MutL is similar to MLH1, MLH2, PMS1 and PMS2
MLH1 30%
MSH2 60%
PMS1 and PMS2 are sometimes mutated as well
*** a defect in the enzyme, ApeI will affect which DNA repair pathway
base excision repair
Step 2
ApeI is used to cut out the sugar out of the DNA backbone
*** choose one of the DNA repair pathways we discussed in class. Describe it
NER
nucleotide excision repair
- repairs larger lesions in DNA (UV damage thymine dimers)
- XPA and XPE detect the damge
- TFIIH (XPB and XPD) act as helicase and unwind DNA
- XPF and XPG cut out the error
- DNA polymerase then relace the correct base
- ligase then seals the DNA
3 ways DNA sequence are stored
- single copy DNA
- moderately repetive DNA
- Highly repetitive DNA
explain single copy DNA
occur only once, or a few times
70% of genome
encode proteins and spacer DNA
explain moderately repetitive DNA
100- 1000 copies
20%
ribosomal and tRNA, retrotransposons which replicated themselves and reinsert into the genome
highly repetitive DNA
100,000 copies
families of repetitive sequences that can be species specific
10%
SINES- short interspersed DNA sequences 150-300 bp
LINES- long interspersed DNA sequences 5000-6000 bp
type of protein that finds single stranded breaks in DNA
ATR (ATM and Rad3-related protein)
___ is needed in somatic hypermutation of immunoglobulin genes
translesion DNA synthesis.
Error prone polymerases
what happens at the end of the lagging strand
at the end of the strand will have RNA primer at end of chromosome
- cant be eaten
-RNA easily degraded
leaving single strand which also gets degraded- BAD cell death
Enzyme telomerase adds repeated sequence at ends to protect DNA from being broken down
___ is a protein sensor that can see double stranded breaks in DNA
ATM
symptoms of Ataxia telangiectasia
ataxia
extreme sensitivity to Xrays
depressed immune system
6 type of DNA repair
base excision repair (BER) nucleotide excision repair (NER) mismatch repair (MMR) homologous recombination (HR) nonhomologous end joining (NHEJ) translesion DNA synthesis (TS)
PARP is in what type of DNA repair
BER
examples of glycosylases that are used in BER
TDG, MBD4,UNG
