1Structure of telomere? typical one found in humans
2-25 bp repeats (usually A/T followed by GC)
-TTAGGG
2Length of overhang maintained by telomerase?
around 300 bp
3What happens to dna strands after telmerase finishes?
-overhang invades double stranded repeats, forms T-loop to stabilze shelterin complexes
4What two structures can overhang form?
-G-quadraplexes
-strand exchange or invasion
5Structure of G quadraplexes? where are they found?
triple stack of guanines (each in different positions, all interact with one another)
-stabilized by cations, like K+
-found in genome and ouside to help with regulatory complexes
6What protein helps form coplex for invasion structure?
shelterin
7walk through the formation of invasion structure:
specialized nuclease exoses a portion of the five prime end of telomere (lagging strand), this along with telomere sequence activates group of proteins to form shelterin complex
8What happens if telomere isn't the minimum length to facilitate telomerase?
-chrmosome ends at risk for attatching to one another, action of multiple centromeres may break/damage chromosomes
9In general, what nucleotides may up telomeric sequences across organisms?
T's and A'ls
10Can cells change the amount of telomerase available?
No, its a fixed amount
11What happens to Telomeres as we age?
-gradually shorten, leads to cell death or senescence (no longer divide)
12High rates of telomere loss leads to...
premature aging syndromes
13Abnormally high levels of telomerase leads to...
cancer
14Types of DNA damage covered?
-oxidation
-depurination
-deamination
15Describe oxidation:
addition of oxygen to nucleic acids, alters hydrogen bonding between complementary bases
-could lead to G and A bonding to one another (two purines!)
16Describe depurination?
-loss of purine
-results in DNA monomer without nucleotide (AP site now)
17Structure of purine?
-two carbon-nitrogen rings (six membered ring fused with five membered ring)
Adenine and Guanine
18Structure of Pyrimidines?
-one six membered carbon ring, 4 carbons with 2 nitrogen
19Effect of depurination?
-replication is stalled
-DNA poly replaces empty space with something or a new sequence
20What is deamination?
-loss of amine (now double bonded oxygen)
-leads to changes in hydrogen bonding properties of each nucleotide base (except thymine)
21Deamination of adenine forms
hypoxanthine
22Deamination of guanine forms
xanthine
23Deamination of cytosine forms
uracil
24Deamination of thymine forms
doesn't happen
25How does prok cells detect deamination of cytosine?"
detects false thymine through comparing base pairing to methylated strand (old/original)
26deaminated cytosine produces?
thymine
27mutated thymine results from?
deaminated cytosine
28hypoxanthine results from
deamination of adenine
29xanthine results from
deamination of guanine
30What two categories of DNA repair have cells developed?
-direct reversal and excision repiar
31What is direct reversal repair? give an ex
-undue chemical rx responsible for DNA damage
-prok: (pyrimidine) Thymine dimer repair through photorestoration
32What is excision repair?
removal of damaged bases, followed by replacement of newly synthesized DNA
33What are thymine (pyrimidine) dimers? how do they happen?
-adjacent thymine nucleotides form a dimer (via cyclobutane ring formation), leads to distoration of DNA structure (less flexible), blocks transcription or replication at damaged site
-results from DNA damage
34How do prokaryotes repair thymin (pyrimidine) dimers?
Direct repair via photoreactivation: harnesses energy from visible light to break cyclobutane ring strucutre (holds the thymine dimer)
35How to Humans and mammals correct pyrimidine dimers? be specific
nucleotide excision repair
36Layout the two main categories of DNA repair in humans:
-base exision
-nucleotide excision: thymine (pyrimidine) dimer repair, transcription-related excision repair, mismatch repair
37Describe nucleotide excision repair process in euk:
-excision nuclease (cuts out olignocucleotide)
-helicase (unwinds)
-DNA poly (fills gap)
-Ligase (seals it all up)
38Describe base excision repair process in euk?
-DNA glycosylase (cuts out base)
-AP endonuclease and phosphodiesterase (removes sugar phosphate)
-DNA poly (adds fresh nucelotide)
-DNA ligase (uses ATP to seal up nicks)
39What repair process requires the use of glycosylase?
base excision process in euk
40Purpose of Global genomic repair process? where does it happen?
-cuts out improper olignonucleotides
-happens in euk cell
41Outline Global genomic repair process:
-cuts out olignucleotides
-dissociation
-XP proteins utilized to recognize lesions, recurit protein complexes and polymerases
42What does TC-NER stand for? where does this happen
transcription coupled-nucleotide excision repair (in eukartotes)
43What mechanism does Prokaryotes use to complete nucleotide excision repair?
-UvrA-UvrB complex scans for disotrtions (thymine dimers) and nicks damaged DNA, DNA poly fills gap, and ligase seals
44What repair process is more prominent in prok, second?
photoreactivation than nucleotide excision repair process
45What type of cells rely on methylation to direct repair?
Prokarytoes
46methylation repair process is called?
methyl-directed mismatch repair
47where is methy lgroup present on dna strand?
on adenine in GATC sequence
48Role of MutS and MutL in methyl directed mismatch repair process in prok?
MutS and MutL bind to mismatched nucleotides
49Role of MutH in methyl directed mismatch repair process in prok?
nicks the unmethylated strand opposite of the methylated GATC
50What does fidelity mean?
-accuracy
51In what direction do exonucleases remove nucleotides?
-3' to 5'
52What are euk's version of MutS, MutH, and MutL?
humans have multiple MutS and Mut L homolouges and version of MSH and MLH
53How are mismatches corrected in euk?
MutS and MutL homologues (and structures similar to MLH)
54What cancer is assoicated with mutations in human homologs of MutS and MutL?
Lynch Syndrome (autosomal dominant inheritance)
Hereditary nonpolyposis colorectal cancer
55Role of XP proteins?
global genomic repair in euk
-recognize lesions, recruite proteins (help) and complexes associated with DNA polymerases (facilitate cutting)
56What is GG-NER? required components?
Global Genomic-Nucleotide excision repair
Need: mutation, assembly complex. helicase, machieery to load and cut sequences, poly and ligase
57Role of CSB and CSA in eukarotic dna repair process?
-enables formation of trasncription coupled repair complex (CSB then CSA, then other proteins)
58If CSB and CSA is successful than what?
-rna poly won't have to detach and restart transcription process
59Mutations in what three genes leads to UV-sensitive syndrome (Xeroderma pigmentosum)?
-CSB
-CSA
-UVSSA