Term
| Semi-discontinuous process |
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Definition
| leading (one piece) + lagging strands |
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Term
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Definition
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Term
| direction of REPLICATION (DNA Synthesis) |
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Definition
|
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Term
| how is replication processive? |
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Definition
| (done all at once, not in bit and pieces) sliding clamp, loader |
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Term
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Definition
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Term
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Definition
| make DNA by elongating the primer |
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Term
| prokaryotic primosome components |
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Definition
| DnaA binds oriC, DnaB (helicase) melts dsDNA (needs DnaC for binding), Primase makes makes RNA primer |
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Term
| prokaryotic Replisome components |
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Definition
| POL 3 (the primary replicative polymerase) makes DNA; POL 1 removes primer |
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Term
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Definition
| 5' to 3' polymerase activity; 3' to 5' exonuclease proofing activity |
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Term
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Definition
| 5' to 3' exonuclease proofing |
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Term
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Definition
| cut and rejoin DNA to resolve supercoils |
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Term
| prokaryotic Topoisomerase example & drug which targets it |
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Definition
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Term
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Definition
|
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Term
| what are the diff. euk. POLs? |
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Definition
| alpha, beta, delta, epsilon, gamma |
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Term
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Definition
| initiation; primase activity; 5'-3' polymerase |
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Term
|
Definition
| DNA repair; 5'-3' polymerase |
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Term
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Definition
| elongation & repair; 5'-3' polymerase; 3'-5' exonuclease |
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Term
|
Definition
| elongation & repair; 5'-3' polymerase; 3'-5' exonuclease |
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Term
|
Definition
| mitochondrial replication; 5'-3' polymerase; 3'-5' exonuclease |
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Term
| what do Euk. have to replicate along w/DNA? |
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Definition
| Nucleosomes (duplicated during DNA synthesis); histones (synthesized in S phase) |
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Term
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Definition
| chromosome ends; tandem repeats of a hexanucleotide sequence (AGGGTT); get shorter with each cell division |
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Term
| ribonucleoprotein complex |
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Definition
| telomerase (replaces lost telomere DNA); NOT present in most normal somatic cells |
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Term
|
Definition
| RNA template for DNA synthesis; Protein polymerase (reverse transcriptase) |
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Term
| Which end on which strand gets lengthened by telomerase? |
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Definition
| 3' end of the 5' to 3' strand (the already longer strand) |
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Term
| Excision repair: how accomplished? |
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Definition
| Recognition, removal, replacement, resealing |
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Term
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Definition
| eliminates errors missed by proofreading |
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Term
|
Definition
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Term
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Definition
| recognizes mismatched bases |
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Term
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Definition
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Term
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Definition
|
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Term
| how is daugther strand recognized? |
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Definition
| parental strand is DAM (DNA adenine methylation) |
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Term
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Definition
| homologous to prok. (MSH, MLH; no MHH) system except for strand ID (no DAM) |
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Term
|
Definition
| HNPCC (colorectal cancer) |
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Term
| BER (base excision repair) acts on |
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Definition
|
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Term
|
Definition
| glycosylases cleave glycosidic bond (b/t base and the sugar); AP site; Remove sugar; replace dNMP and ligate |
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Term
|
Definition
| bulky lesions, pyrimidine dimers from UV |
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Term
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Definition
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Term
|
Definition
| XP proteins that recognize and remove |
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Term
|
Definition
| deficiency in any of the XP proteins; photosensitivity & skin cancers |
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Term
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Definition
| Deficiencies in additional proteins required for |
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Term
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Definition
| some DNA is lost; repair by NHEJ (non-homologous end joining) or HR (homologous recombination) |
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Term
| NHEJ (non-homologous end joining) |
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Definition
| rejoin the ends without replacing the lost DNA |
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Term
| HR (homologous recombination) |
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Definition
| uses homologous DNA as a template for the replacement of the lost DNA |
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Term
| Defects in homologous recombination leads to |
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Definition
|
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Term
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Definition
| finds template in homologous recombination |
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Term
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Definition
| special group of DNA POLs can bypass DS lesion and synthesize DNA in spite of the damage |
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Term
| what does transcription lack? |
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Definition
| primer; 3'-5' exonuclease (proofreading) activity |
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Term
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Definition
| coding strand of DNA (except for U/T) |
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Term
| prok. RNA polymerase composition |
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Definition
| hexameric holoenzyme (includes sigma factor) |
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Term
| sigma subunit in prok. RNA POL |
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Definition
| recognizes and binds the promoter |
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Term
| euk. RNA polymerase composition |
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Definition
| 3 different multisubunit RNA POLs |
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Term
|
Definition
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Term
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Definition
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Term
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Definition
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Term
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Definition
| Region on the gene where RNA POL binds (sigma in prok and TFs in euk) to initiate transcription |
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Term
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Definition
| -35 and -10 (TATAAT or Pribnow box) consensus sequences |
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Term
|
Definition
| none universally found; examples are TATAAA (Hogness box) centered at ~ -25 and Inr |
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Term
|
Definition
| holoenzyme via sigma binds promoter, DNA melts, several abortive attempts---once past ~ 10 nt sigma leaves |
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Term
|
Definition
| inhibits prok. initiation |
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Term
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Definition
| RNA made 5'-3' with 3'-5' phosphodiester links |
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Term
|
Definition
| inhibits prok. & euk. elongation |
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Term
| prok. intrinsic or rho-independent termination |
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Definition
| sequence in DNA causes stem-loop structure in the RNA that terminates transcription |
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Term
| prok. rho-dependent termination |
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Definition
| POL pauses at terminatino site, rho crawls up RNA using ATPase activity & when it encounters RNA/DNA hybrid it pushes DNA out of the way (helicase activity) |
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Term
| main POL in euk. transcription (mRNA) |
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Definition
|
|
Term
|
Definition
|
|
Term
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Definition
| TBP (TATA binding protein) binds TATA sequence; TAFs (TATA associated factors) join in; analogous to sigma in prok. |
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Term
|
Definition
| ferries POL II to TFIID/DNA |
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Term
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Definition
| unwinds helix using ATP hydrolysis; performs several abortive attempts; phosphorylates C-terminus of POL II; elongation begins |
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Term
|
Definition
| regulate when/where/how much RNA is made; 2 functional domains: DNA-binding & transcription activation |
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Term
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Definition
| part of STF; binds to DNA sequence on response elements (RE), UAS |
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Term
| transcription activation domain |
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Definition
| part of STF; recruits and binds other proteins such as the GTFs, other STFs, co-activators |
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Term
|
Definition
| some help solve the chromatin problem (chromatin to tightly bound to transcribe) |
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Term
|
Definition
| histone acetyl transferase; acetylate histones to loosen chromatin & enhance transcription |
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Term
|
Definition
| histone deacetlases; repress transcription by de-acetylating chormatin (tightens it) |
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Term
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Definition
| position/orientation independent |
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Term
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Definition
| (prok. & euk.) cleaved at 5' end, CCA added to 3' end, many bases modified (e.g. U to T) |
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Term
| euk. post-transcription processing |
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Definition
| 5' cap; 3' poly-A; intron splicing |
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Term
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Definition
| 7-methyl-guanine in 5'-5' linkage |
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Term
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Definition
| 3' end using ATP; mRNA first cleaved after AAUAAA signal then polyadenylated; not directed by DNA |
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Term
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Definition
| removes introns; composed of snRNP (small nuclear ribonucleoproteins) (eg. U1-U6); assembly requires ATP hydrolysis |
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Term
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Definition
| binds 5' splice donor site in splicing |
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Term
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Definition
| binds branch site A (in intron) in splicing |
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Term
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Definition
| bind and the spliceosome is complete |
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Term
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Definition
| exon 1 cut from intron & forms 2'-5' linkage w/intron (forming lariat); free exon OH attacks exon 2 & lariat is released |
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Term
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Definition
| linkage of tRNA w/amino acid; occurs in cytocol; requires aminoacyl tRNA synthetases & ATP (2 equivalents) |
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Term
| aminoacyl tRNA synthetases |
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Definition
| links tRNA to appropriate a.a.; requires ATP; can proofread |
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Term
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Definition
| small subunit of ribosome binds mRNA & aminoacyl tRNA; large ribosome subunit joins; energy (GTP) required |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| Aminoacylated tRNA binds here |
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Term
|
Definition
| Peptide bond formed as tRNA held here |
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Term
|
Definition
| Empty tRNA held here until it Exits |
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Term
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Definition
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Term
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Definition
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Term
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Definition
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Term
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Definition
| binds small ribosomal subunit to eIF2-GTP-met-tRNA (at P site); aided by eIF1 |
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Term
|
Definition
| 5'cap- binding complex; joins to mRNA-PAB-protein, which joins to small ribosomal subunit & other eIFs; scans mRNA for AUG, using ATP |
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Term
|
Definition
| helps large subunit join small subunit complew w/help of GTP; Forces eIF3 & eIF1 to leave |
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Term
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Definition
| prep. for translation elongation in euk.; mediated by eIF4 family members & PAB protein |
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Term
| eIF4 role in circularization |
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Definition
| eIF4A uses ATP to find 1st AUG; eIF4E interacts w/5' End; eIF4G grabs onto E& PAB to hold RNA in circular form |
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Term
|
Definition
| brings all other aa~tRNAs to A site; GTP-->GDP |
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Term
|
Definition
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Term
|
Definition
| a ribozyme of the large subunit; forms the peptide bond between met_i and aa #2 |
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Term
|
Definition
| causes translocation as GTP-->GDP (what was in A [dipeptide] is now in P, so A is now empty) |
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Term
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Definition
| ADP-ribosylation; inhibits EF2 |
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Term
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Definition
| (euk. release factor) recognizes stop codon at A; binds eRF3-GTP |
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Term
|
Definition
| hydrolyzes peptide; GTP hydrolyzed |
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Term
| ATP needed for translation? |
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Definition
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|
Term
| GTP needed for translation? |
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Definition
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|
Term
| anti-bacterial translation inhibitors |
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Definition
| streptomycin, tetracycline, erythromycin |
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Term
| anti-euk. translation inhibitors |
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Definition
| cyclohexamide, phosphorylation of eIF2, ADP-ribosylation of EF2 by diptheria toxin |
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Term
| anti-euk. & - prok. translation inhibitors |
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Definition
| puromycin, chloramphenicol |
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Term
|
Definition
| (Sec): Ser modified to Sec & inserted into signals that allow for Sec placement into stop codon |
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Term
|
Definition
| help insert Sec into peptide chain |
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Term
| ATP needed for initiation of translation? |
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Definition
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|
Term
| targeting pathway of Secreted proteins |
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Definition
| co-translational; N-terminal signal sequence recognized/bound by SRP; translation stops; goes to RER; SRP attaches to R (docking protein); moves to translocon (GTP-->GDP); translation resumes; peptide threaded into ER lumen; signal sequence removed; vesicles containing the nascent protein bud off from ER, go to Golgi then to cell membrane, and contents are secreted |
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Term
| targeting for ER-retrieval/resident proteins |
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Definition
| 2nd signal KDEL (lys, asp, glu, leu) si retrieval signal (prevents secretion); co-translational |
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Term
| targeting for membrane proteins |
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Definition
| threading into ER lumen stops due to hydrophobic stop transfer; cell (plasma) membrane is default location |
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Term
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Definition
| protein gets N-glycosylated; TERMINAL MANNOSE GETS PHOSPHORYLATED AT C6 (Mannose-6-Phosphate) |
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Term
| how is C6 on mannose phosphorylated for lysosome targeting? |
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Definition
| Phosphotransferase adds GlcNac-P to C6 of the mannose; phosphoglycosidase removes GlcNAc so just the P is left |
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Term
|
Definition
| deficiency in phosphotransferase; leads to lysosomal acid hyrdolases in the blood |
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Term
|
Definition
| NLS recognized by importins; protein-importin complex enters through NPC (nucleus pore complex), binds Ran-GTP, protein released, importin-Ran-GTP leave nucleus, GTP-->GDP |
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Term
| nuclear localization sequence |
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Definition
| (NLS); short, basic, internal (not on terminal ends), not removed after targeted |
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Term
|
Definition
| due to defect in NLS of SRY; leads to female phenotype in XY |
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Term
|
Definition
| Mitochondrial N-terminal matrix-targeting signal |
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|
Term
| targeting to mitochondria |
|
Definition
| unfolded-protein/amphipathic alpha-helix complex moves laterally to TOM-TIM interface, entry requires proton-motive force, ATP; signal removed |
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Term
|
Definition
| PTS1 (C-terminal) or PTS2 (N-terminal); peroxins function as chaperones |
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Term
|
Definition
| defects in peroxins; neurological impairment |
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Term
|
Definition
| Ndoplasmic reticulum (ER) to amide N of asn; pre-formed oligosaccharide built on dolichol-P (lipid of ER membrane) is transferred en bloc to asn; trimmed in ER + Golgi; additional sugars added in Golgi |
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Term
| CDG (congenital disorders of glycosylation) |
|
Definition
| result of defects in N-glycosylation |
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Term
|
Definition
| in GOlgi to OH of ser/thr + hyl; sugars added 1 by 1 |
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|
Term
| Proteasomal degradation characteristics |
|
Definition
| highly selective; ATP-requiring; proteasome and Ub (ubiquitin) |
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|
Term
| Proteasomal degradation pathway |
|
Definition
| Ub tags proteins w/E1, E2, E3 (ligase); proteasome removes/recycles Ub; protein degraded |
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Term
| N-end rule and internal PEST |
|
Definition
| sequences which mark protein for Ub-mediated degradation |
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Term
|
Definition
| Three alpha chains of Gly-X-Y |
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|
Term
| Intracellular collagen reactions |
|
Definition
| Cleavage of signal sequence; hydroxylation of propeptides by vitamin C-dependent hydroxylases; Triple helix formation; O-glycosylation of selected Hyp |
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Term
|
Definition
| triple helix made of 3 alpha chains |
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|
Term
| Extracellular collagen reactions |
|
Definition
| Cleavage of N-and C-terminal propeptides (forming tropocollagen); Lateral association of tropocollagen (forming fibrils); Cross-linking of fibrils (forming mature collagen fibers) |
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|
Term
|
Definition
| stretchy skin from deficiency in lysyl oxidase |
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