front 1 FUCCI | back 1 Uses Cdt1 (G1 phase = red) and Geminin → (S/G2/M phases = green) yellow = transition |
front 2 Brdu Labeling | back 2 Uses synthetic nucleoside analog of thymidine, then use antibodies against BrdU sees where replicating DNA is flourencent |
front 3 19S cap | back 3 recognize polyubiquitin recycle ubiquitin unfolding |
front 4 20s cap | back 4 chymotrypsin --> cut after hydrophobic Trypsin --> cut after basic Caspase --> cutes after acidic |
front 5 Mono vs Multi vs Poly ubiquitination | back 5 Mono - attach 1 ub (trafficking) Multi - multiple sites (endocytosis) Poly - long chain of ub (degradation) |
front 6 Impact of dwell time | back 6 The longer a protein can be associated with the regulatory subunit of
the |
front 7 How does rRNA contribute to translational efficiency | back 7 rRNA is most of the ribosome catalyzes bind formation for speedy translation anticodon bonds to only specific mRNA+tRNA |
front 8 Ligand | back 8 signal sends info from one cell to another |
front 9 Receptor | back 9 protein on target cell to receive signal |
front 10 Transduction | back 10 Relayer Chain reaction to pass message along |
front 11 Response | back 11 cell changing |
front 12 Molecular switches (example) | back 12 switching between on + off GTP binding (bound to GTP = ON) |
front 13 Cell signal specificity | back 13 receptors unique to certain signals different downstream proteins |
front 14 Collins et al | back 14 26S Proteasome --> degradation of proteins ubiquitination doesn't equal immediate degradation (dwell time) |
front 15 Ribosome Profiling Density | back 15 More reads/higher density = more ribosome |
front 16 Ribosome Profiling Positions | back 16 clustered in codon reading = active translation peaks at start codon = initiation |
front 17 Ribosome Profiling high build ups | back 17 ribosome slowing or stalling to read |
front 18 Ribosome Profiling Translation efficiency | back 18 High mRNA + low ribosome = inefficient |
front 19 Positive feedback | back 19 outputs make the process faster cell division On diagram: loops, plus signs, promoting production |
front 20 Negative feedback | back 20 outputs shut down process inhibition blunt ends, minus signs, product shuts down production |
front 21 Methylation | back 21 creates distinct regions in chromatin regulation keeps charge changes protein - protein interactions |
front 22 Acetylation | back 22 neutralizes charge (+ histones hugging - DNA) opens chromatin to activate genes |
front 23 Glycosylation | back 23 adding sugars for folding, stability, and recognition ID in ER |
front 24 Phosphorylation | back 24 adds large - charged group on/off switch assembles large proteins into complexes |
front 25 Cell cycle check points | back 25 G1/s - transition/start (size? environment? density? attachment?) G2/M - mitosis (replicated? environment?) Meta to Ana - cytokinesis (chromosomes attached? ready to split?) |
front 26 Cyclin classes | back 26 G1 - high levels = expression of G1/S cyclins G1/S - activate cdk to push cell into S phase for cell cycle entry S - stimulate chromosome duplication M - enter mitosis at G2/M and degrade at meta to ana |
front 27 EF-Tu | back 27 EF1 escorts tRNA to A site |
front 28 EF-G | back 28 EF2 uses GTP hydrolysis to provide mechanical push of ribosome forward |
front 29 RF | back 29 Stop codons |
front 30 Transportation into ER + sorting | back 30 entry for secretory pathway use vesicles to go to golgi apparatus sends to final destination |
front 31 Major roles of ER | back 31 Manufacture - lipids + export proteins Quality control - check proteins before fold Storage - store Ca2+ for signal |
front 32 ER resident chaperones | back 32 BiP - helpers - grab floppy proteins and folds correctly Disulfide bonds - staples - keep together |
front 33 ER bound protein translation | back 33 water freezing aa comes out > SRP grabs ribosomes to stop > SRP receptot docks ribosome > translocator in membrane for protein |
front 34 ER sequence signals | back 34 Start transfer - opens door for threading Stop transfer - closes door for threading |
front 35 How would a protein on membrane orient based on ER signaling sequence? | back 35 Standard signal usually cut off N term in ER with C term in cytosol (BC C is +) |
front 36 Class of cell surface receptors | back 36 Ion channels g protein using (GPCR) enzyme coupled |
front 37 Second messengers | back 37 molecules that spread signals deep into a cell after receptor activation cAMP |
front 38 Fast vs Slow signaling | back 38 Fast - exocytosis Slow - cell cycle entry |
front 39 GCPR activation (Gs vs Gi) | back 39 Gs - activates adenylyl cyclase Gi - inhibits adenylyl cyclase |
front 40 GCPR activation steps | back 40 ligand binds to GCPR > GDP kicked out > GTP let in > split into a and B > signal stops once a subunit times out > GTP turned back to GDP |
front 41 How is the 26S proteasome processive? | back 41 26S proteasome is processive because it binds, unfolds, translocates, and fully degrades proteins in one continuous operation without releasing them halfway |
front 42 Ubiquitination process | back 42 E1 picks up + activates Ub with ATP > E2 carries live Ub from E1 to E3 > E3 acts as a matchmaker for Ub and specific target protein |
front 43 Yip et al | back 43 UBE20 binds best with Ub and NAP1L1 |
front 44 Formicheva et al | back 44 NF-kB family of transcription factors noncanonical path implicated in regulating cell signaling high density = stop cell division |
front 45 Ignolia et al | back 45 Measure translation genome wide at single codon resolution |
front 46 Kinase structure + activity | back 46 Small N term, large C term, active site in middle T loop regulation (phosphorylated = moving loop and active site to be available) |
front 47 Non proteolytic signaling | back 47 changing location/activity |
front 48 tRNA | back 48 bridge between mRNA codon + aa anticodon binds w tRNA |
front 49 RPN 1, 10, 13 | back 49 initial Ub binding |
front 50 USP 6, 14 + UCH37 | back 50 ub removal + 19S activation |
front 51 RPN11 | back 51 removing final Ub |
front 52 RPT1-6 | back 52 substrate binding + unfolding |
front 53 RPT 2, 3, 5 | back 53 20s gate open |
front 54 A vs P vs E site | back 54 A - aminoacyl - charged tRNA entry P - peptidyl - holding tRNA attached to growing polypeptide E - exit - uncharged DNA |
front 55 Lipidation | back 55 anchors protein to cell membrane since fats like to be near each other |
front 56 M cdk | back 56 assembles miotic spindles ensure sister chromatids apart chromosome condensation break down of nuclear envelope |
front 57 Ribosome profiling procedure | back 57 freeze ribosome > lyse cells > digest unprotected RNA > isolate ribosome > convert to cRNA > sequence > align |
front 58 Cyclins | back 58 cell division regulating proteins activated when needed |
front 59 PTM regulation of cdks | back 59 phosphorylates T loop wee1 adds P but not active til cell is ready cdc25 removes inhibiting P --> burst of energy |
front 60 Proteasome check + balance | back 60 DUBs > removing Ub to recycle Narrow 20S gate |
front 61 Cell cycle phases | back 61 Interphase (G1, S, G2) - growing, synthesizing, growing M phase - mitosis Cytokinesis - splitting |
front 62 Prophase | back 62 Chromosome condense |
front 63 Prometaphase | back 63 nuclear envelope breaks |
front 64 Metaphase | back 64 chromosomes line up in middle |
front 65 Anaphase | back 65 sister chromatins pulled apart |
front 66 Telophase | back 66 2 nucli formed |
front 67 cdks | back 67 phosphorylates target T loop can expose active site |
front 68 Anaphase Promoting Complex (ACP/C) | back 68 catalyzes ub in exit of mitosis cleans up ends cell division and destroys proteins w cyclins |
front 69 P21 and P27 | back 69 P21 - safety brake - stops if DNA damaged P27 - stop and stay - signal to stop growth in G1 |
front 70 cdc20 and cdh1 | back 70 cdc20 - triggers ACP/C activity cdh1 - maintains ACP/C activity after anaphase clean up |
front 71 SCF | back 71 destroys P27 so cell can move from G1 to S target must be phosphorylated |
front 72 CDK1 to active M cdk | back 72 cdk1 + M cyclin = inactive M cdk CAK + wee1 + inactive M cdk = inactive M cdk with active P and inhibiting P cdc25 takes inhibiting P and creates active M cdk |
front 73 ACP/C... +cdh1 +cdh20 | back 73 cdh1 - keeps cyclin levels low so cell can grow and not reenter S phase cdh20 - destroys securin + M cyclins |
front 74 Sequential activation of cdks | back 74 G1 - cdk4/6 - cyclin D - kicks off mitosis G1/S - cdk2 - cyclin E - push cell past start S - cdk2 - cyclin A - triggers DNA replication M - cdk1 - cyclin B - cell division |
front 75 K11 vs K63 vs K48 vs K29/33 | back 75 K11 -marks cyclins for rapid degradation in mitosis K63 - DNA repair K48 - degrade proteasome, unfolds so protein can be shredded K29/33 - protein trafficking |