Ch.10 - Protein Synthesis, Processing, and Regulation Flashcards
Where does mRNA translation occur?
in the cytoplasm
what is mRNA translation directed by?
mRNA templates
How are proteins synthesized?
from mRNA templates
Polypeptide chains are synthesized from what to what terminus?
amino (N) to the carboxy (C)
codon definition
3 nucleotides long translated region
What makes mRNA?
RNA polymerase II
What is the tRNA sequence?
3’ CCA
What is the small eukaryotic ribosomal subunit?
40S
What is the large eukaryotic ribosomal subunit?
60S
The editing site of Aminoacyl tRNA synthetases only bind to what amino acid?
the wrong one
What do aminoacyl tRNA synthetases do?
attach tRNA to appropriate amino acid
How is the tRNA attached to the appropriate amino acid (2 steps)?
1) amino acid is joined to AMP –> forms aminoacyl AMP
2) amino acid is transferred to the 3’ CCA end of the tRNA and AMP is released
When is AMP released?
when the amino acid is transferred to the 3’ CCA end of the tRNA
What eukaryotic rRNAs are part of the large ribosomal subunit?
28S, 5.8S, and 5S
What eukaryotic rRNAs are part of the small ribosomal subunit?
18S
What is the large PROKARYOTIC ribosomal subunit?
50S
What is the small PROKARYOTIC ribosomal subunit?
30S
What rRNAs are part of the prokaryotic small ribosomal subunit?
16S
What rRNAs are part of the prokaryotic large ribosomal subunit?
23S and 5S
What are the 3 tRNA binding sites in ribosomes?
EPA
What are the 3 stages of translation?
initiation, elongation, and termination
What is the initiator of translation?
methionyl tRNA
What do methionyl tRNA and mRNA bind to?
the small ribosomal subunit (40S)
What joins last to form a functional ribosome?
large ribosomal subunit (60S)
What eukaryotic transcription factors are required for initiation (that we will be focusing on)?
eIF1A, eIF2, eIF4E, eIF4G
What eukaryotic transcription factors are required for elongation?
eEF1a (alpha), eEF1By (beta, gamma), eEF2
What eukaryotic transcription factors are required for termination?
eRF1, eRF3
What 3 components are part of the initiation ternary complex?
eIF2, met-tRNA, and GTP
eIF2 is what?
a small GTPase (that breaks down GTP to GDP)
What does GAP stand for? (in the CAP-dependent translation initiation)
G - GTPase
A - Activating
P - Proteins
What does GAP do?
tells GTP to be “done”
What does GEF stand for? (in the CAP-dependent translation initiation)
G - Guanine nucleotide
E - Exchange
F - Factor
eIF4E only binds to the 5’ cap if also bound to what?
eIF4G
What binds to the 5’ cap in the CAP-dependent translation initiation?
eIF4E
What happens when all 12 proteins are bound to the mRNA?
ATP —> ADP + P
Once you hit the start site in the CAP-dependent translation initiation, what is broken down + then released?
GTP
When are the 12 proteins in the CAP-dependent released?
when it hits the start site
Why can some viral and cellular eukaryotic mRNAs be CAP-Independent?
they have internal ribosome entry sites (IRESs)
What first happens in CAP-Independent Translation Initiation?
eIF4G binds to IRES
When do the 12 proteins and the met-tRNA bind to the mRNA (in cap-independent)?
after eIF4G binds to IRES
In initiation, tRNA brings methionine to what site?
P
In elongation, tRNA brings amino acids to what site?
A
What 3 things are part of the elongation ternary complex?
tRNA, amino acid, and eEF1a (alpha)
In what step does the large subunit shift?
elongation
Why is there a translocation in elongation?
eEF2 breaks down GTP —> GDP
Which ribosomal subunit works as a decoding center for mismatches?
small ribosomal subunit
what codons does elongation stop at?
UAA, UAG, or UGA
what do release (eRFs) do?
recognize stop codons
How do release factors work?
recognize stop codons in the P site and then bind to the A site to terminate translation
what are polysomes?
when multiple ribosomes translate mRNAs simulatneously
What type of CAP dependency is global translational activity?
CAP-dependent
what does global translational activity respond to?
stress, nutrient availability, and growth factor stimulation
Regulation of ferritin translation by _____ proteins.
repressor
If there is no iron in the translational regulation of ferritin process, then what happens?
iron regulatory protein (IRP) binds to the iron response element (IRE) in the 5’ UTR, blocking translation
When there is an adequate amount of iron for the translational regulation of ferritin, what binds to the IRE?
40S ribosomal subunit (which allows more eukaryotic proteins to bind)
What is the repressor that binds to IRE (in translational regulation of ferritin) that blocks 40S ribosomal subunit from binding to IRE?
IRP (iron regulatory protein)
In the translation of mRNA, a translational repressor binds to what 3’ codon to inhibit translation?
UTR
Why is translation inhibited when a translational repressor binds to 3’ UTR?
the initiation factor eIF4E can no longer bind eIF4G
Phosphorylation of eIF2 and eIF2B by regulatory protein kinases blocks what?
the exchange of bound GDP for GTP, inhibiting initiation of translation
What do growth factors activate in the regulation of eIF4E?
protein kinases that phosphorylate regulatory proteins (such as eIF4E binding proteins and 4E-BPs)
mRNA translation cannot occur when what is hypophosphorylated?
mTORC1 or 4E-BP1
What are folded and modified to become functional proteins?
polypeptide chains
3-D conformation (tertiary) is due to what?
side chains and amino sequence
chaperone protein functions
1) facilitate protein folding
2) assist the self-assembly process
3) bind to and stabilize unfolded or partially folded polypeptides
____ binds to polypeptide chains that are still being translated on ribosomes.
chaperones
Why do chaperones bind to polypeptide chains that are still being translated on ribosomes?
to protect the chain from improper folding or aggregation with other proteins until synthesis of an entire domain is complete
What stabilizes unfolded polypeptide chains during transport into organelles?
chaperones
what were the first types of chaperones identified?
heat shock proteins (Hsp)
heat shock proteins (Hsp) are expressed in what cells?
cells subjected to high temperatures
Hsp70 do what?
1) stabilize polypeptide chains during translation
2) transport by binding to short hydrophobic segments
chaperonins are what Hsp?
Hsp60
chaperones are what Hsp?
Hsp70
When a polypeptide is transferred to a chaperonin, what takes place?
folding
chaperonins are what?
subunits in two stacked rings that form a double-chambered structure
Defects in protein folding are responsible for what?
protein misfolding diseases
What neurodegenerative disease has the Amyloid-B aggregating protein?
alzheimer’s disease
What neurodegenerative disease has the alpha-Synuclein aggregating protein?
Parkinson’s disease
What neurodegenerative disease has the Huntingtin aggregating protein?
Huntington’s disease
What neurodegenerative disease has the superoxide dismutase aggregating protein?
amyotrophic lateral sclerosis
What neurodegenerative disease has the prion protein aggregating protein?
spongiform encephalopathies
What non-neurodegenerative disease has the amylin aggregating protein?
type 2 diabetes
What non-neurodegenerative disease has the crystallins aggregating protein?
cataracts
What non-neurodegenerative disease has the insulin aggregating protein?
injection-localized amloidosis
What systemic disease has the immunoglobulin light chain aggregating protein?
amyloid light-chain amyloidosis
What systemic disease has the serum amyloid A protein aggregating protein?
amyloid A amyloidosis
What systemic disease has the transthyretin aggregating protein?
senile systemic amylodisis
When 2 enzymes act as chaperones by catalyzing protein folding…
protein disulfide isomerase (PDI)
protein disulfide isomerase (PDI) is abundant where in the cell?
ER
what does protein disulfide isomerase (PDI) catalyze?
catalyzes disulfide bond formation
Oxidizing environments allow _____ linkages
disulfide
what does peptidyl prolyl isomerase do?
catalyzes isomerization of peptide bonds that involve proline residues
If the isomerization between the cis and trans configurations of prolyl-peptide bonds did not have peptidyl prolyl isomerase, what would happen?
would be a rate-limiting step in protein folding
proteolysis does what?
cleavage of a polypeptide chain
signal sequences do what?
target protein for transport to a specific destination
how does the signal sequence work?
inserted into a membrane channel as it emerges from the ribosome and the polypeptide chain passes through as translation proceeds
What is the signal sequence cleaved by?
signal peptidase (a membrane protease)
what is proteolytic processing?
formation of active enzymes or hormones by cleavage or larger precursors
what is an example of proteolytic processing?
insulin
Insulin is synthesized as what?
a precursor polypeptide (2 cleavages produce the mature insulin)
what happens in glycosylation?
carbohydrate chains are added to proteins (glycoproteins)
What important roles do the carbohydrate moieties play?
1) protein folding in the ER
2) targeting proteins for transport
3) recognition sites in cell-cell interactions
N-linked glycoproteins
the carbohydrate is attached to the nitrogen atom in the side chain of asparagine
O-linked glycoproteins
the carbohydrate is attached to the oxygen atom in the side chain or serine or threonine
glycosylation starts where during translation?
ER
O-linked oligosaccharides are added in the ____.
golgi
How are O-linked oligosaccharides formed?
by addition of one sugar at a time in the golgi
Many cytoplasmic, nuclear proteins, and transcription factors are modified by addition of one what?
O-linked N-acetylglucosamine residue
What are 2 fatty acids that are lipid anchors that modify some eukaryotic proteins?
1) myristic acid
2) palmitic acid
What are 2 prenyl groups that are lipid anchors that modify some eukaryotic proteins?
1) farnesyl
2) geranylgeranyl
N-myristoylation is a type of what?
lipid anchor
In N-myristoylation, what is attached to what?
myristic acid is attached to an N-terminal glycine
Prenyl groups attach to sulfur in the _______
side chains of cysteine near the C terminus in prenylation.
Many of the prenylation proteins are involved in what?
1) control of the cell growth
2) differentiation including the Ras oncogene proteins
In palmitoylation, palmitic acid is added to sulfur in the ___________.
side chains of internal cysteine residues
Palmitoylation is important in what?
association of some proteins with the cytosolic face of the plasma membrane
glycolipids are lipids that are linked to what?
oligosaccharides
Glycolipids are added to ___-terminus ____ groups
1) C
2) carboxyl
what anchors some proteins to the external plasma membrane?
glycolipids
what are the anchors in glycolipids?
glycophosphatidylinositol (GPI) anchors
What are the 3 mechanisms that regulate the amounts/activities of their proteins?
1) regulation by small molecules
2) phosphorylation
3) protein-protein interactions
What is allosteric inhibition?
the end product inhibits the production of more products by binding to the other site on the site where it was first produced
what is a common regulation?
GTP or GDP binding
What happens when there are subtle conformational differences in the inactive GDP-bound formation?
cannot work
What interacts with its target molecule signaling cell division?
Ras-GTP
25% of human cancers are from mutations in ____ genes.
ras
Ras protein is locked in the ______________, which always allows signaling of cell division.
GTP-bound conformation
What is the reversibility of phosphorylation?
reversible
what does phosphorylation do in terms of regulation of protein function?
activates or inhibits proteins due to environmental signals
protein kinases do what?
transfer phosphate groups from ATP to amino acids
What are the 2 most common amino acids that protein kinases transfer phosphate groups to?
1) Serine
2) Threonine
The protein-tyrosine kinase was discovered when?
1980
How was protein-tyrosine kinase discovered?
studies of Rous sarcoma virus
What are 4 other covalent modifications?
1) acetylation of lysine
2) methylation of lysine and arginine
3) nitrosylation (addition of NO groups) to cysteine
4) glycosylation of serine and threonine
What is an example of protein-protein interactions?
cAMP-dependent protein kinase (PKA)
How are protein levels determined?
by rates of synthesis and rates of degradation
Half-lives (t1/2) of proteins are what?
differential rates of degradation that are important in cell regulation
What is short t1/2?
many regulatory proteins; allows levels to change quickly in response to external stimuli
What is the Ubiquitin-proteasome pathway?
a major pathway of protein degradation in eukaryotes
Ubiquitin is what?
1) highly conserved in all eukaryotes
2) added to the amino group of the side chain of a lysine residue (more are added to form chain)
What does a proteasome do?
recognizes and degrades polyubiquinated proteins
Ubiquitination is a multistep process involving what enzymes?
E1, E2, E3
Which enzyme, in Ubiquitination, selectively targets proteins for degradation?
E3
What are targets for regulated ubiquitylation and proteolysis?
many proteins that control fundamental cellular processes
