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BZ 310 Exam 3
| Question | Answer |
|---|---|
| 3 types of filaments | microfilaments (actin), intermediate, microtubules |
| microfilament characteristics | dynamic and flexible |
| intermediate filament characteristics | relatively stable, very strong, rope-like |
| microtubule characteristics | dynamic, hollow/rigid tubules |
| functions of microfilaments (4) | support, shaping, movement of cell, muscle contraction |
| microfilament growth | fast at + end, slow at - end (or degrading) |
| microfilament 'treadmilling' | fast growth at +, slow at - (moves in direction of + end) |
| myosin I/V | cargo (+ end directed) |
| myosin II | muscle (+ end directed) |
| how does listeria monocytogenes move? | microfilaments |
| ATP dependent myosin walking | ATP binding= release, hydrolysis= binding, Pi release= power stroke |
| what is a bunch of fused cells called? | syncytium (muscle cells) |
| transverse tubule | on the muscle, depolarizes with the membrane |
| how is calcium moved back into the sarcoplasmic reticulum? | P-type pump (ATP dependent) |
| 3 troponin subunits | ITC (C= calcium binds here) |
| function of intermediate filaments | mechanical stability |
| example of intermediate filaments | keratin |
| which filament is involved in desmosomes and hemi-desmosomes? | intermediate filament |
| functions of microtubules (4) | support, internal organelle movement, chromosome separation, motion |
| difference between alpha and beta tubulin | both bind GTP, but only beta hydrolyzes it |
| centrosome aka (2) | centrioles, basal body |
| centrosome | the place from which microtubules grow, microtubule organizing center |
| regulation of microtubules | done by MAPs (microtubule associated proteins) prevention of GTP hydrolysis (stabilizes MT) |
| FRAP | fluorescence recovery after photo-bleaching |
| FRAP experiment | GFP-labeled MT, destroy GFP, watch MTs grow |
| two MT motor proteins | dyenin (- end directed), kinesin (+ end directed) |
| two domains of dyenin and kinesin | motor domain, cargo-binding domain |
| possible cargo of dyenin and kinesin (4) | vesicles, organelles, chromosomes, other microtubules |
| cilia filaments | use dyenin motors, filament sliding |
| look up figure 12-24 | |
| most important type of regulation | transcriptional |
| post transcriptional control (4) | alternative splicing, mRNA stability, translation, protein stability |
| most abundant RNA | rRNA |
| rRNA transcribed by | Pol I |
| tRNA transcribed by | Pol III |
| mRNA transcribed by | Pol II |
| relative abundances of RNAs | rRNA, tRNA, mRNA, small RNA |
| which RNA polymerase is regulated? | Pol II (transcribes mRNA) |
| where is rRNA formed? | nucleolus |
| physical DNA state and RNA pol | histone modifications; euchromatin=open, heterochromatin= closed |
| Barr Bodies | calico cats, irises; one X chromosome turned off |
| cis elements | regulatory DNA sequences close to or in gene (promoter) |
| trans factors | regulatory proteins (transcription factors) |
| enhancer sequences | can be 1000 BP away; often palindromic sequence; recognized by specific TF |
| what first binds to TATA box? | TFIID (TATA binding protein + TATA binding association factors) |
| what activates RNA polymerase? | TFIIH |
| most TFs are ___ | positive regulation |
| housekeeping genes are | constitutively expressed |
| promoters compete for TFs... | regulation occurs by promoter strength |
| three signals that affect transcription initiation | cell type, nutrition, hormones |
| three things that affect PEPCK regulation | blood sugar, growth factor, hunger |
| response element mechanism | affects histone structure |
| 5' cap | G-nucleotide in reverse orientation to 5' end |
| RNA processing (3) | get 5' cap, introns removed, 3' poly A tail |
| what performes splicing? | RNA and protein complex |
| where rRNA assembled | still in nucleus |
| three mechanisms of splicing | spliceosome, self-splicing introns, tRNA splicing |
| where does self-splicing occur? | mitochondria and chloroplasts |
| spliceosome intron removal | lariat structure from 5'-2' phosphodiester linkage, 2 trans-esterifications |
| gene silencing | double-stranded RNA cleaved, turned into siRNA, mRNA degraded |
| mi-RNA | nuclear genes, transcribed by RNA pol II |
| miRNA multiple genes example | 3 copper-binding proteins, binds and degrades mRNA for all 3 |
| siRNA is derived from | two overlapping complementary RNA regions |
| siRNA processed by | dicer dependent machinery |
| 2 proofreading steps in translation | amino acid tRNA coupling, tRNA-mRNA base pairing |
| RBS prokaryotes | AGGA |
| mRNA can be ___ in prokaryotes | polycistronic |
| wobble | some tRNA molecules pair with more than one codon |
| where does the AA bind on tRNA? | 3’ end |
| eukaryote ribosomes Sv | 40S+60S= 80S |
| prokaryote ribosomes Sv | 30S + 50S= 70S |
| what mediates small ribosomal subunit binding in eukaryotes? | 5’ cap |
| what mediates small ribosomal subunit binding in prokaryotes? | RBS |
| poly A tail is needed for | initiation by Ifs |
| EF-Tu hydrolyzes GTP if | the tRNA is correctly base paired |
| Termination | release factor binds (because of stop codon) |
| ATP cost of protein synthesis | about 4 ATP per amino acid |
| eIF-2 | GDP-GTP; inhibited by phosphorylation |
| eIF-4 and small ribosomal subunit regulation | controlled via TOR in response to nutrition, ATP/ADP ratio, and growth factors |
| translation slows | when rare codons are used |
| abundant proteins use | codons for abundant tRNAs |
| codon bias | when abundant proteins use abundant tRNAs |
| 2 stages in protein folding | fast hydrophobic collapse, slow shuffling to native shape |
| why do proteins need help folding? | they would collapse on each other and fold slowly |
| HSP 70 aka | chaperone |
| HSP 60 aka | chaperonin |
| HSP 70 works with | HSP 40 |
| HSP 60 works with | HSP 20 & 10 |
| HSP 40 stimulates | ATPase in HSP 70 |
| HSP proteins work ___ | sequentially (70, then 60) |
| 5 changes that can stabilize polypeptides | disulfide, cofactors, sugars, proteolytic cleavage, covalent modifications |
| ubiquitin | transferred to target proteins, if poly-ubiquitinated, proteins destroyed by proteasome |
| protein sorting requires energy from | ATP, GTP, or PMF (or a combination) |
| protein translocation | passage through one or more membranes |
| vesicular transport | vesicle budding and fusion w/ endomembrane system (does not pass thru a membrane) |
| what is imported into nucleus/how | needs NLS; polymerase, histones, TFs, etc. |
| what is exported from nucleus/how | needs NES; mRNA, tRNA, assembled ribosomal subunits |
| four main protein translocation pathways | into ER, into peroxisomes, into mitochondria, into plastids |
| ER translocation | uses N-terminal or internal signal sequence(s) |
| Peroxisome translocation | C or N terminals peroxisomal terminating sequence (3 AA) |
| Mitochondria translocation | N-terminal pre-sequence with sub-organellar sorting |
| Plastid translocation | N-terminal transit sequence with sub-organellar sorting (related to ER and bacterial systems) |
| Signal hypothesis | when made in cytosol, larger than when in organelle b/c of signal sequence (cleaved in organelle and becomes native protein) |
| Pulse-chase | put radioactive amino acids (35S methionine), kill cells, collect protein w/ antibody, analyze with EM or SDS-page |
| Example pulse-chase experiment | add AA that does beta decay and reduces silver, find where silver is |
| What is needed for pulse chase in vitro | mRNA, ribosomes, IFs, EFs, TFs, tRNA, ATP/GTP, amino acids, labeled amino acid |
| Advantages of in-vitro reconstitution of transport | conditions are controlled, find mechanisms, can modify coding sequence |
| 4 main findings from pulse chase/ in vitro reconstitution experiments | 4 pathways, signals often cleaved after transport, can be co-translational (ER only) or post-translational, requires energy |
| conditional lethal mutants | recessive, temperature sensitive (will de-nature at moderately high temperature) |
| problem in finding mutant | machinery will have housekeeping & always needed (mutants will die) |
| pulse chase SDS PAGE results WT vs mutant | mutant has a longer chase time (will take longer for signal sequence to be cleaved) |
| PMF stimulates translocation in | bacterial IM, mitochondrial IM, thylakoids |
| What has a lot of co-translational translocation? (3) | hydrophobic proteins, membrane proteins, cells w/ a lot of secretion |
| Three SRP functions | signal sequence recognition, translational pause, targeting ER translocon |
| E site is called | exit site |
| P site is called | peptidyl tRNA |
| A site is called | aminoacyl tRNA |
| 3 energy consuming steps of elongation | add AA to tRNA (ATP-AMP), EF-tu hydrolyzes GTP if correctly base paired, EF-G translocates (GTP) |
| 3 proteins in energy consuming steps of elongation | amino-acyl tRNA synthetase (proofread), EF-tu (proofread), EF-G (direction) |
| why do mutants have extra bands on SDS PAGE? | glycosylation in ER |
| Which component mediates regulated protein degradation of ubiquitinated proteins? | proteasome (26S) |
Created by:
melaniebeale
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