Term
| What are the primary (genetic) causes of ageing? |
|
Definition
| Genomic instability, telomere attrition, epigenetic alterations and loss of proteo stasis |
|
|
Term
| What are the initial responses to ageing damage? |
|
Definition
| Deregulated nutrient sensing, mitochondrial dysfunction, senescence |
|
|
Term
| Symptoms of ageing (cellular)? |
|
Definition
| Stem cell exhaustion, altered intercellular communication |
|
|
Term
| What are the three best reasons for increased lige expectancy? |
|
Definition
Eradication of childhood diseases
Reduced maternal death following childbirth
Improved healthcare |
|
|
Term
| What are the adaptive and non-adaptive theories of ageing? |
|
Definition
Adaptive - genetically programmed to age
Non-adaptive - not genetically programmed to age |
|
|
Term
| Is ageing genetically programmed? |
|
Definition
| No. Obviously not. It would make literally zero sense. |
|
|
Term
| Why is ageing not genetically programmed? |
|
Definition
Natural selection operates at level of individual, not species - no benefit to reducing fitness for good of others
Strong evidence for accumulation of macromolecular damage
No genes known to cause ageing damage, and many preventing or repairing it |
|
|
Term
| Why does ageing occur if it is deleterious? |
|
Definition
Acts late- after reproduction
Trade-off - energy goes to reproduction rather than repair |
|
|
Term
| Whyis Caneorhabditis elegans useful for studying ageing? |
|
Definition
| Can convert to a non-reproductive larval form with reduced metabolic activity (dauer form). |
|
|
Term
|
Definition
| C elegans reproductive signal triggered under good nutrition conditions, it inactivates transcription factor DAF-16, allowing reproductive development |
|
|
Term
| What do mutations that reduce Daf2 signalling in C elegans promote? |
|
Definition
| Dauer-form characteristics such as longer development, reduced reproduction, increased lifespan - example of trade-off |
|
|
Term
| What does restricting calorie intake do? |
|
Definition
|
|
Term
| What is a way of measuring ROS damage? |
|
Definition
| One ROS is thymine glycol, which is excreted in urine and can be measured |
|
|
Term
| How does the genome protect itself from ageing? |
|
Definition
Damage avoidance, eg melatonin
DNA repair enzyme systems that remove lesions or ROS
Recombination
Cell cycle checkpoints |
|
|
Term
| What do telomeres have to do with the Hayflick limit and who first made the connection? |
|
Definition
| Every time lagging strand replicates, end cut of as cant replicate end, so telomere shortened. Takes about 50 divisions to be cut down long enough that would start to be an issue - then sensence occurs. This is Hayflick limit. Olovnikov discovered - was behind Iron Curtain at time so relatively little known. Little bit of extra knowledge there. |
|
|
Term
| What happens when telomerase is knocked out in mice? |
|
Definition
Mice naturally have long chromosomes
First generation fine
Later generations have shortened lifespan, frailty, tissue atrophy |
|
|
Term
| What is normally the medical term for death from old age? |
|
Definition
|
|
Term
| What are the two types of DNA lesions and what do they cause? |
|
Definition
Mutagens - repair and mutation -cancer
Cytotoxic - senescence and apoptosis - ageing |
|
|
Term
| What are the parts of DNA? |
|
Definition
Pruine/Pyrimidine base
Deozyribose sugar
Phosphate |
|
|
Term
| What are the three types of lesions classified by their effect on replication? |
|
Definition
Coding -allow replication to procede
Miscoding - allow replication with mutation
Noncoding- block replication |
|
|
Term
|
Definition
| Loss of purine bases by hyrolysis |
|
|
Term
|
Definition
| Oxidation of amine groups on the bases to aldehydes |
|
|
Term
| What are tautomeric shifts? |
|
Definition
|
|
Term
| What occurs during depurination? |
|
Definition
| Loss of purine sit e leaves an apurinic or AP site |
|
|
Term
| What does deamination of 5-methyl cytosine cause? |
|
Definition
| Produces thymine, which pairs with adenine - if fixed permanent mutation |
|
|
Term
| What is deamination more rapid in? |
|
Definition
|
|
Term
| What are the three most common ROS and how are they produced? |
|
Definition
superoxide radical (O2 + e- -> O2-)
Hyrdrogen peroxide (O2- + e- + 2H+ -> H2O2)
Hydroxyl radical (H202 + e- + h+ -> H2O + oOH) |
|
|
Term
| How can radiation have indirect effects on DNA? |
|
Definition
| Affected other molecules that interact with DNA - e.g. radiolysis of water creates ROS |
|
|
Term
| How does radiation have direct effects on DNA? |
|
Definition
| Bonds holding the sugar phosphate chain absorb energy until they break, mostly ss but 10% ds |
|
|
Term
|
Definition
| Miscoding lesion that pairs with A, product of ROS or radiation |
|
|
Term
| What do crosslinking agents do? |
|
Definition
| Covalently join two bases in complementary strands - block transcription and replication |
|
|
Term
| How many times has Thorsten told us nitrogen mustard is a crosslinking agent? |
|
Definition
|
|
Term
| What do intercalating agents do? |
|
Definition
| Messes with stacking forces between layers? |
|
|
Term
| What does psoralen (an intercalating agent) do? |
|
Definition
| Forms thymine-psoralen adducts that are activated by UV light to form crosslinks, preventing repair and inducing cell death - enhances pigmentation |
|
|
Term
| Which mutagens are activated by liver metabolism? |
|
Definition
Acetyl aminofluorene - converted to alkylating agent by esterification
Benzoapyrene - metabolized to an apoxide
aflatoxins - metabolized to oxide derivative that acts on N7 of guanine |
|
|
Term
|
Definition
| Electron leakage from REDOX chain |
|
|
Term
| What does superoxide dismutase and catalase do? |
|
Definition
Superoxide dismutase:
2O2- + 2H+ -> H2O2 + O2
Catalase
2H2O2 -> 2H2O2 + O2 |
|
|
Term
| What does glutathione peroxidase (GSH) do? |
|
Definition
| H2O2 + 2(GSH) -> 2H2O + GSSG (reduced glutatione) |
|
|
Term
| Name three natural antioxidants? |
|
Definition
| Glutathione, Beta-carotene and vitamins C/E |
|
|
Term
| What are ssDNA breaks normally caused by? |
|
Definition
| Ionising radiation, failure to join Okazaki fragments or abortive topoisomerase activity during replication |
|
|
Term
| Why is repair of ss breaks essential? |
|
Definition
| to avoid replication fork collapse |
|
|
Term
| What fixes ss breaks in eukaryotes? |
|
Definition
|
|
Term
| What fixes ss breaks in prokaryotes? |
|
Definition
| AMP and nicotinamide mononucleotide |
|
|
Term
| What do DNA ligases need and do? |
|
Definition
| Join 3-OH and 5-P groups in DNA, need an energy co-factor (ATP/NAD) and Mg2+ |
|
|
Term
| When is DNA ligation aborted and what unblocks this? |
|
Definition
| If 3' sugar is damaged, aprataxin |
|
|
Term
| Steps in ligation reaction? |
|
Definition
Adenyl group transferred from ATP or NAD to lysine at enzyme active site, Adenylyl group transferred from enzyme to 5'-P at ssDNA break
Ligase catalyses 3-OH attack on activated 5-P, adenyl group displacement
ss break sealed |
|
|
Term
| What does loss of aprataxin cause? |
|
Definition
| Ataxia with oculomotor apraxia, due to loss of repair in the brain, which isnt very proliferative, but very metabolic heavy |
|
|
Term
|
Definition
| Removes 5'-adenylate from DNA, allowing ligation of DNA 'dirty' breaks |
|
|
Term
| What repairs pyrimidine dimers |
|
Definition
| DNA photolyases (not in mammals), contain two chromophores which activate repair |
|
|
Term
| How are pyrimidine dimers repaired? |
|
Definition
| Complex od DNA and photolyase formed, folate absorbs visible light, transfers to flavin, which breaks apart dimer by donating an electron, enzyme releases undamaged DNA |
|
|
Term
| How does CPD photolyase lock onto DNA? |
|
Definition
| Bends it and flips a thymine dimer out |
|
|
Term
| How is O6-methylG repaired? |
|
Definition
| Ada protein also known as O6-methylguanine methyl transferase, removes methyl groups in a suicide reaction, when Cys38 on Ada is methylated it becomes a transcription factor for itself |
|
|
Term
| What can excision repair fix? |
|
Definition
| Damaged bases, mismatches, crosslinks |
|
|
Term
|
Definition
Removal of damaged base and replacement
Removal of short nucleotide patch and replacement
Removal of mispaired base shortly after replication |
|
|
Term
|
Definition
Deamination
Loss of bases (depurination)
ROS damage
Methylated bases |
|
|
Term
| What are the basic steps of BER? |
|
Definition
Removal of damaged base by a DNA glycosylase leaves an AP site
AP endonuclease cleaves backbone
Removal of deoxyribose phosphate
DNAP fills in base
Ligase seals gaps |
|
|
Term
| What do DNA glycosylases do? |
|
Definition
| Hydrolyse the N-glycosidic bond, releasing the base and leaving the DNA with an AP site |
|
|
Term
| What normally causes uracil in DNA? |
|
Definition
| Deamination of cytosine, or failure of Dut to convert dUTP to dUMP |
|
|
Term
|
Definition
| It is a dUTPase that converts dUTP to dUMP, reducing the pool of dUTP in the cell so that Uracil is not incorporated into DNA |
|
|
Term
| What fixes uracil in DNA? |
|
Definition
| Uracil DNA glycosylase cleaves N glycosidic bond and removes uracil fromm ss or ds DNA |
|
|
Term
| How does uracil DNA glycosylase recognise uracil and lock onto DNA? |
|
Definition
| Flips out uracil into a special pocket outher bases dont fit in |
|
|
Term
| How do archaeal polymerases deal with uracil? |
|
Definition
| Read-ahaead recognition stalls at uracil or hypoxanthine, before uracil is bound in a special pocket |
|
|
Term
| What is somatic hypermutation and where does it occur? |
|
Definition
| Delberate deamination of cytosine in order for error prone repair proccesses to create many muatations - immunoglobin genes |
|
|
Term
| What does thymine DNA glycosylase do? |
|
Definition
| Removes thymine from G T mispair, acts in demethylation of CpG islands and interacts with AID (Activation induced cytidine deaminease |
|
|
Term
| What do Class I (beta-lyase) AP endonucleases do? |
|
Definition
| Cleave 3' of AP site by beta-elimination, product removed by a 3' phosphodiesterase. Many are also DNA glycosylases |
|
|
Term
| What do class II AP endonucleases do? |
|
Definition
| More abundant, cleave by hydrolysis 5' of AP site, remove groups at 3' termini that block ligation, AP product processed by a 5' phosphodiesterase |
|
|
Term
| Which enzyme not mentioned elsewhere is involved in BER of pyrimidine dimers? |
|
Definition
| T4 enodnuclease V - glycosylase and AP lyase |
|
|
Term
| Which class of endonuclease normally leads to long patch BER? |
|
Definition
|
|
Term
| What repairs 8-oxoG lesions and how? |
|
Definition
| hOGGI, or 8-oxoguanine glycosylase, scans DNA for 8-oxoG, when comes into contact with cytosine extrudes guanine into G specific pocket, only 8-oxoG will fit into both pockets, then glycosylase goes to work |
|
|
Term
| How many nucleotides are removed in bacterial and eukaryote NER? |
|
Definition
|
|
Term
| What is the basic process of NER in bacteria? |
|
Definition
Damage recognised through backbone distortion
DNA incision at the 8'th bond 5' of the lesion and 4/5th bond 3' of the lesion
Nucleotides excised
DNAP and ligase resynthesize and seal |
|
|
Term
|
Definition
| Binds UV-damaged dsDNA, dimerises to forms complex with UvrB. Two ATP binding sites and two zinc fingers. |
|
|
Term
|
Definition
Binds UvrA2 to stimulate 5’ - 3’ helicase-like acivity, which is used to
generate preincision complex. |
|
|
Term
|
Definition
Interacts with UvrB:DNA complex, two endonuclease sites
make incisions 5’ and 3’ of lesion. |
|
|
Term
|
Definition
| 3’ - 5’ helicase, unwinds and releases oligonucleotide with DNA damage. |
|
|
Term
|
Definition
| DNA photolyase (photoreactivating enzyme). Stimulates repair by UvrABC |
|
|
Term
|
Definition
Ensures specificity for repair of transcribed DNA strand by UvrABC.
Displaces RNA polymerase and interacts with UvrA. |
|
|
Term
| How does UvrB hold onto DNA? |
|
Definition
| Bends the DNA 130 degrees and inserts a beta hairpin between two strands of DNA, flipping out a nucleotide behind it into a small pocket |
|
|
Term
| What does UvrC require for activation? |
|
Definition
|
|
Term
| How does UvrD move along the DNA? |
|
Definition
| Has two motor domains that need ATP hydrolysis |
|
|
Term
| What is the more detailed NER in bacteria? |
|
Definition
Damage recognition by UvrA2B-ATP interaction
Bind to damage
DNA unwound and bent 130 degrees by UvrB
UvrA released, UvrC binds
UvrC locates 3' incision site, makes it, then relocates to 5' and makes second incision
UvrD binds and displaces UvrC, the unwinds damaged strand
UvrD releases 12-13bp strand
DNAP and ligase do their shit and also release UvrB |
|
|
Term
| What can Cho do and what is it? |
|
Definition
| Homologue of UvrC that can cut lesions cut poorly by UvrC or extend the NER so a longer patch is excised |
|
|
Term
| What can NER repair in bacteria? |
|
Definition
| Mostly intrastrand crosslinks but can also recognise and repair interstrand crosslinks |
|
|
Term
| How are intER strand crosslinks repaired in bacteria? |
|
Definition
NER on one strand
Gap expanded by helicases and exonucleases
Homologous recombination to fill in excised material
NER of other strand
DNAP and ligase do their shit |
|
|
Term
| What recognizes RNAP stalled (in bacteria) and what does it do? |
|
Definition
Transcription Repair Coupling Factor (TRCF), attracts UvrABC to repair lesion
Also known as Mfd |
|
|
Term
| What are the steps to bacterial transcription coupled excision repair? |
|
Definition
| TRCF recognises and removes RNAP and mRNA, attracts UvrA2B, TRCF and UvrA released, NER occurs |
|
|
Term
| What is ppGpp and what does it do? |
|
Definition
| Alarmone, promotes UvrD action, required for efficient NER, destabilizes RNAP and renders it prone to backtracking by UvrD |
|
|
Term
| What three groups of genes are involved in eukaryotic NER? |
|
Definition
RAD3 - NER
RAD6 - Mutagenesis
RAD52 -Recombination |
|
|
Term
| How can you tell if two genes function in the same pathway? |
|
Definition
| Knock one out, then the other, then both. If knocking out both has a similar effect to knocking out one, probably same pathway |
|
|
Term
| How many genes are in the RAD3 group? |
|
Definition
|
|
Term
| Which three human genetic diseases are associated with defects in NER? |
|
Definition
Xeroderma pigmentosum
Cockayne syndrome
Trichothiodystrophy |
|
|
Term
|
Definition
| Mutations in XPA, XPD, XPC, XPE, XPF or XPG |
|
|
Term
| What causes cockayne syndrome? |
|
Definition
| Mutations in CS-A or CS-B - involved in TCR |
|
|
Term
|
Definition
| Mutation in TTD-A, XPB or XPD |
|
|
Term
|
Definition
| Recognises DNA lesion in complex with HR23B and Centrin 2, or recruited by DDB1/2 |
|
|
Term
| What recognises damage in eukaryotes for NEr? |
|
Definition
| XPC/HR23b, DDb1/2, stalled RNAPII or ATL (BER) |
|
|
Term
| How does XPC lock onto DNA? |
|
Definition
| Inserts beta hairpin between two strands of DNA and flips out two damaged base pairs |
|
|
Term
| How does NER work in eukrayotes? |
|
Definition
Damage recognition by DDb1/2 or X{C/HR23B, and formation of pre-incision complex
Recruitment of XPA, XPG nuclease and stabilisation of PIC
Recruitment of XPF/ERCCI nuclease - PIC finished
Dual incision by XPF/ERCCI and XPG nucleases
Dissociation of PIC and recruitment of DNAP
DNAP and ligase do their shit |
|
|
Term
| How does TCR work in eukaryotes? |
|
Definition
Transcription initiated by promoter opening by TFIIH
RNAPII stalls at lesion and recruits CSB chromatin remodelling factor
CSB recruits TFIIH, CSA, RPA and XPA
TFIIH unwinds DNA to expose lesion and recrutis ERCC1/XPF and XPG
NER occurs
RNAP resumes transcription |
|
|
Term
|
Definition
| Recruits NER to repair O6 methyl guanine |
|
|
Term
| What is the IGF signalling pathway regulated by, and why does it matter? |
|
Definition
| Pituitary growth hormone (GH), and it modulates the speed of ageing and the resources allocated to maintenance compared to growth |
|
|
Term
| What happens in DNA repair defective cells that leads to ageing? |
|
Definition
| Attempt somatic growth attenuation, but ongoing DNA damage will exhaust stem cells |
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