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BZ 310 Exam 3

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