1-26 Protein Synthesis Flashcards
Start codon for translation
AUG
what does “the code is degenerate” mean?
there are more codons than amino acids, several codons can code for the same amino acids
translation of mRNA goes from
5’ to 3’
Codon table trends
right - hydrophobic
charged - left/lower left
middle - polar
what does the start codon do
AUG - indicates where synthesis will start and establishes the reading frame
silent mutations
does not change the actual amino acid, generally a change in the third letter
however, this mutation can effect the rate of translation, which alters polypeptide folding, leading to proteins with different 3d structure.
this can change the properties of the protein
transcription
segment of DNA is transcribed into an mRNA by RNA polymerase
Translation
mRNA is decoded at/by ribosome to create polypeptides to form protein
describe tRNA structure
cloverleaf stabalized by watson crick pairing
base pairing between 5’3 forms the acceptor
anticodon loop in middle interacts with codon of mRNA
aminoacyl tRNA synthetase
enzyme that charges tRNA to amino acid with high energy bond.
uses ATP which gets hydrolyzed to AMP
ribosomes are comprised of
a large and small subunit
how many binding sites does the ribosome have for tRNA
where?
3
Exit, Peptidyl, Aminoacyl
at the interface of the small and large subunit
how do bacteria know which AUG to use?
the shine-delagno sequence just upstream (g-rich) of the correct AUG.
how do eukaryotes know which AUG to usee?
eukaryotic mRNA has a 5’ cap in the 5’ UTR, this tells ribosome that downstream is the correct AUG
how is mRNA read in bacteria and eukaryotes?
bacteria - linearly
eukaryotes - read in circle. Poly A- tail binds to 5’ cap during reading. can be read by several at the same time, increasing efficiency.
what additional factors help transcription?
Initiation factors (IF), elongation factors (Ef-), and Termination/release factors (RF-)
eurkaryotes have an “e” before.
eIF, eEF, eRF ad more of them
initiation (Genera)
- mRNA binds to small ribosomal subunit and is aligned with correct reading frame
- initiator amino-acyl tRNA binds
- ribosome assembles from small and large subunits
the 30s initiation complex
eIF-2-GTP initiator tRNA binds to small subunit
circular mRNA binds, ribosome searches for start codon
GTP hydrolyzed, releases the initiation factors
large subunit binds, leaving the initator tRNA in P site
elongation
- aminoacyl tRNA binds and checks codon-anticodon match
- new peptide bond Is formed.
- Growing chain is translocated from A site to P side, mRNA pulled so next codon is exposed to A site. 4.
Catalytic rRNA of the ribosome creates the peptide bond, no additonal energy needed.
tRNA comes in, peptide bond formed (transpeptidation), mRNA gets pulled so next codon exposed to A site, shifted by one.
describe transpeptidation
does not require additional energy, uses the energy from the high energy amino acyl tRNA.
Reaction is catalyzed by the ribosome itself (ribozyme activity).
the growing chain is translocated from
the A site to the P site
where is the peptide bond formed?
to the c-terminus of the growing chain
Termination
- stop codon in A site
- release factor binds A site
- release factor brings in water to hydrolyze peptide chain and released. (the water mimics an incoming amino acid)
- the complex dissociates
rate of translation in eurkayotes vs bacteria?
rate faster in bacteria
rate limiting step?
hydrolysis of GTP bound to Elongation factor (Ef-Tu)
as well as proofreading
describe the high energy cost of protein syntehsis
Charging tRNA takes ATP
Initiation takes one GTP and unknown ATP
Elongation takes two GTP per amino acid incorporated
Termination takes one GTP to release
Unknown amount for proofreading/proper folding
describe a major way that protein syntehsis is regulated
minor way?
the lifetime of mRNA
at the level of translation
what can inhibit protein synthesis?
toxins
two cases where protein synthesis is regulated at the level of translation
- at translation initiation controlling the phosphorylation of elongation factor 2 (heme and HCI inhibitor)
- sequence elements within the mRNA structure - enzymes will chew on poly-a tail. once the tail is degraded, in eukaryotes it will come apart from the 5’cap and the mrna will quickly be degraded
since protein synthesis is so expensive, its generally controlled at the
initiation step, ussually by regulating the availabilty of eIF-2. when phosphorylated by specific kinases, decreases the rate of synthesis.
Ferritin/transferrin is an example of
regulatory elements within the structure of the eukaryotic mRNA
interferons
viruses produce dsRNA, which is not normally present in cells. this signals the cell that it is infected and induces secretion of IFN’s.
IFN’s bind to surfaces of other cells and induce expression of two new enzymes that when in the precense of dsRNA, inhibit protein synthesis.
What happens when eIF-2 is phosphorylated?
Inhibition of translation
The _______ of an mRNA usually contains elements that influence translational efficiency, whereas the _____ usually affects mRNA stability.
5’ UTR = translational efficiency (shine delgano, etc..)
3’UTR - mRNA stability (poly a tail)
All mature tRNA molecules have a CCA sequence at their 3’-ends. t/f?
t
During protein synthesis, the newly synthesized peptide is covalently bound to
tRNA
If you were developing a new antibiotic that specifically targeted bacterial protein synthesis and did not affect eukaryotic protein synthesis, which of the following enzymes, structures, or molecules would be good targets?
an enzyme that formylates the initiator methionine
Activation of an amino acid prior to its incorporation into a polypeptide chain
C. involves transient formation of an aminoacyl-AMP intermediate before the amino acid is transferred to tRNA.
GTP, which is used during the translation process,
D. is hydrolyzed to GDP, which causes a conformational change of translation factors¸ usually allowing them to dissociate from the ribosome.
Interferons cause decreased synthesis of viral proteins by which of the following mechanisms?
D. inhibition of translation of both host and viral proteins by phosphorylation of eIF-2
codons are read
5-3
anticodons are read
3-5
