Term
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Definition
the sexual spore-bearing cell produced in ascomycete fungi (e.g. the cluster of 4 haploid spores in S.cervaceae)
On average, asci normally contain *eight ASCOSPORES*, produced by a meiotic cell division followed, in most species, by a mitotic cell division |
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Term
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Definition
Protein that binds telomere end and promotes loop structure to form.
The studies that demonstrated this loop structure by EM used psoralen to UV-cross link it |
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Term
| which part of DNA pol binds incoming nucleotides? Is the catalytic site? |
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Definition
| fingers bind incoming nucleotides; Palm is catalytic site |
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Term
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Definition
| fragment of polymerase that has (5'->3') synthesis & proofreading capability, but lacks 5'->3' exonuclease activity |
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Term
| What does DnaA do to initiate replication at the origin of e.coli? |
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Definition
| Binds DNA and stabilizes positive supercoils in front of origin. this causes origin to form negative supercoils and become unwound. The DnaA filament will propagate into the ssDNA region and stabilize it |
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Term
| describe 2d gel electrophoresis |
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Definition
1st dimension: low voltage -> separate by size
2nd dimension: high voltage -> separate by morphology (more branching/bubbling/circling moves slower. |
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Term
| what is methylated in prokaryotes after replication and how does this prevent replication from re-initiating? |
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Definition
GATC loci are methylated on template strand (hemimethylated);
hemimethylated GATC loci bind SeqA -> prevent DnaA from binding
- Also, DnaA actually is titrated! -> will bind other sites of genome after initiation has begun
- Also, DnaA hydrolyses ATP->ADP (less active form) in the presence of the beta-clams and Hda (a paralog of DnaA) |
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Term
what does each subunit do in Pol-III?:
Beta
Gamma |
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Definition
Beta = sliding clamp (dimer of trimers in PKs, trimer of dimers in EKs)
Gamma = helps "load" (and unload) Pol-III from DNA via Beta (using delta); It interacts with Beta and delta & probably hydrolyses ATP to allow delta to misshape beta to open up and load DNA |
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Term
| which genes are aligned with replication direction in e.coli? |
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Definition
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Term
| what are Ter sites? What binds them? |
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Definition
Ter sites are bound by Tus protein. These arrest the convering replication forks and begin the process of separation of daughter strands.
ASIDE: catenated DNA strands need topoisomerase IV to get uncatenated |
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Term
| what is benzo-a-pyrene and what does it do? |
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Definition
| carcinogen of nicotene. Metabolized to a nucleophilic form and attacks a guanine to intercalate into DNA |
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Term
| how does O6-methylguaning methyltransferase regulate its expression? |
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Definition
| its methylated form serves as its own transcription factor (remember, it's a suicide enzyme that removes methyl groups from O6 guanine) |
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Term
| name the 3 enzymes in BER |
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Definition
DNA glycosylases (many different isoforms -> different ones recognize different bases, uracil one is very important)
AP endonuclease (cleaves phosphate backbone @ 5' end)
DNA phosphodiesterase (removes deoxyribose phosphate that originally was connected to the damaged base) |
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Term
| how are CpG islands DEmethylated? |
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Definition
base-excision-repair (methyl group is oxidized a few times and then the BER machinery takes over)
NOTE: mice homozygous for loss of this glycosylase are embryonically lethal (not the case for other glycosylases!) |
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Term
why are ribonucleotides (RNA) in DNA so toxic to DNA?
How are they removed? |
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Definition
because the 2' OH group can cleave the phosphodiester backbone! This causes DNA-strand breakage that is 100k -fold higher than DNA
Removed via RNAses (e.g. H2 in yeast); a mouse knockout of RNAseH causes embryonic lethality via p53-mediated cell death (10^6 RNAs per cell = p53-mediated death)
NOTE: RNAs are much more abundant that DNAs in cell (10-100x higher per base!) |
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Term
| explain role of UvrA,B,&C in NER |
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Definition
UvrAB = translocates along DNA to find lesion (uses ATP); Distorts helix @ this point and then releases UvrA
UvrC = nicks DNA 12-13 nt apart (recruited by UvrB) |
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Term
| T4 endonuclease V function? |
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Definition
| nicks DNA after cyclobutane pyrimidine dimer |
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Term
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Definition
specific defect in NER during transcription (TCR)
presents as extreme sensitivity to UV radiation with dwarfism, neurological disordrs, and death in early life |
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Term
| Function of XPB & D? XPA & C? XPF & G? |
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Definition
B&D = helicases for TFIIH
A&C = detect DNA damage (C is first to bind)
F & G = endonucleases |
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Term
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Definition
proliferating cell nuclear antigen. It is the clamp on pol delta & epsilon (the 2 replicative polymerases replicated lagging & leading strand, respectively)
it is modified to recruit DNA repair machinery |
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Term
| What is the defect in fanconi anemia? |
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Definition
| messed up protein complex that is involved in trans-lesion synthesis of DNA cross-linked regions during replication |
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Term
| which pol removes RNA primers? |
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Definition
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Term
| What is methylated in the GATC sequence? |
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Definition
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Term
| recBCD participates in what type of DNA repair? |
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Definition
recBCD = homologous recombination (via single nick -> D-loop formation -> holiday junction); recBCD is a helicase that unwinds to a specific sequence ("chi structure"); Also will resect DNA 5' end to allow for HR
RecA binds single-stranded DNA; SSB accellerates this process by melthing hairpins
The mammalian homologs are Mre11/Rad50/Nbs1 (for RecBCD); Rad51 (for RecA); NOTE: RPA binds resected ssDNA before Rad51 does
in eukaryotes: DSB signal ATM->Chk2; resected DNA bound to RPA & SSB signal ATR->Chk1 |
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Term
| briefly describe bacterial SOS response |
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Definition
| RecA is activated by UV light to its co-protease form -> cleaves LexA (repressor on umuDC operon) -> error-prone polymerase is produced |
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Term
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Definition
| CDK phosphorylates things throughout cell cycle (at least 2 factors: Sae2/CtIP and Dna2) |
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