3. Ribosome and Protein Synthesis Flashcards
describe the central dogma of biology
a protein is equivalent to a ____
DNA is transcribed to RNA which is translated to protein
protein is equivalent to a phenotype
where does translation occur and what is required?
translation happens in the cytoplasm and uses 3 types of RNA molecules and ribosomes
what is the function of ribosomes?
describe the composition of ribosomes
what is the difference in eukary vs prokary?
they catalyze the formation of polypeptide chain. interact physically with the mRNA chain and the tRNA and accessory proteins
eukaryote ribosomes:
- 4 units of rRNA make the subunits
- have a30S and a 50S subunit which add to a 70S
prokaryote ribosomes:
- are composed of 3 units of rRNA which transcribe components for 2 subunits
- large subunit is 60S and smaller unit is 40S which add to 80S
the genetic code has how many possible codons? how many of these are stop codons
- what are the stop codons?
- what are the aa that only have one codon?
- what is the start codon?
stop codons: UGA, UAG, UAA start: AUG (methionine) -Met and Trp only have one codon while other aa have multiple
64 possible codons but only 61 code for an aa bc 3 are stop codons
is the genetic code universal?
yes and no.
for the most part is is universal, but differs in some species especially mitochondrion
compare and contrast the start codons in bacteria and eukaryotes
which synthetase loads tRNA and where? is energy required?
the start codon is the same and is usually AUG which signifies for a methionine
The start codon methionine is actually special bc in prokaryotes this methionine has a formyl group linked to the aa
- this is also special in eukaryotes bc this methionine is different than the one isnerted into the polypeptide AND it begins at the P site during translation instead of the A site like the other ones
- aminoacl-tRNA synthetase (MetRS) charges both tRNAs with methionine
define the reading frame.
the sequence of codons that runs from a specific start codon to a stop codon
describe the structure of tRNA
- size
- modifications
- loops
- terminus?
- where does the aa attach and where does the anticodon attach?
the tRNA is 73-93 ribonucleotides long.
It has a couple modifications including a
-TyC loop (ribothymine-psuedouracil-cystine)
-DHU loop that contains dihydrouracils
-7-15 modified bases like methylated forms of CUGA
- CCA terminus end is the aa attachment site while the
- side opposite the CCA terminus is the anticodon site
how is the tRNA charged
- a aminoacyl-tRNA synthetase couples a specific aa via a high energy ester bond to the 2’ or 3’ OH of the tRNA
this activates the tRNA
- tRNA base pairs with the codon at the site of the anticodon which complements the RNA
describe quality control of tRNA charging
1) during synthesizing of the tRNA, the aa is put in the tRNA
2) editing process can remove aa from the synthesis site and move it to the editing site
explain the wobble position
this explains how tRNA can be multiple for a specific aa.
the 3rd aa is the ‘wobble’ position and this can form a nonstandard base pair with the base in the first position of a tRNA anticodon
describe the binding sites on the ribosome for translation
E=exit
P= peptidyl site where the peptide bond is made
A= aminoacyl site where the next aa comes in
describe in detail the initiation of translation in eukaryotes
- formation of eiF2 ternary complex when eIF2-GTP binds a tRNA (i) Met
- formation of 43 S pre-initiation complex after bidning btwn the 40S subunit and eiF2 ternary sturcture and eIF5
describe in detail the elongation of the peptidyl chain in eukaryotes
- once the 80s ribosome with Met-tRNA (i) met in the ribosome P site is assembled, a ternary complex bearin EF1a and the second aa coded by the mRNA binds ot the A site
describe in detail the termination of translation in eukaryotes
- when ribosome bearing nascent protein chain reaches a stop codon, release factor eRF 1 enters the A site together with eRF3 GTP
how is the efficieny of protein synthesis increased?
by simultaneous translation of a single mRNA by multiple ribosomes forming a polyribosome or polysome
-this is done by protein-protein interactions
compare and contrast eukaryotic vs prokaryotic translation: ribosomes, initiation, and termination
- ribosomes
- eukary have 40S and 60S to form 80S
- prokary has 30S and 50S to form 70S
- eukary ribosomal unit 60S contains 28S, 5S, and 5.8S rRNA
- prokary ribosomal unit 50S contains 28S, 5S, but no 5.8S rRNA
- eukary ribosomal unit 40S contains 18S and total set of 83 proteins
- prokary ribosomal set small unit 30S has 16S rRNA and total set of 52 proteins
- intiation
- prkary requires 3 protein factors
- eukayr requires 11 protein factors
- prokary initaiton met is formylated
- eukary initation met is not formylated
- prokary alignment done by shine dalgarno sequence to align mRNA
- eukary alignment correctly on the 40S is done by 5’ cap
- termination
- prokary have 3 release factors
- eukary has 1 release factor which can recognize 3 stop codons
how do antibiotics work.
which ones block prokary and which ones block eukary and which ones do both?
antibiotics block specific steps of translation
- prokaryote:
1) streptomycin and other aminoglycosides (inhibit initiation and cause misreading of mRNA)
2) tetracycline (binds to the 30S subunit and inhibits the binding of aminoacyl-tRNAs)
3) chloramphenicol (inhibits the peptidyl transfrase activity of the 50S ribosomal unit)
4) erythromycin (binds 50S subunit and inhibits translocation)
eukaryotes:
1) cycloheximide- inhibits translocation
both:
- puromycin- causes premature chain termination by acting as an analog of aminoacytl-tRNA
what makes an inhibitor of protein synthesis a clinically useful antibiotic?
want something toxi to bacteria at concentrations that are not harmful to humans
*this is also tricky bc mitochondrial translaiton is similar to bacteria
describe the antibiotic mechanism of streptomycin
-interferes with the proofreading process causing increased rate of error in synthesis
-inibits translocation where the peptidyl tRNA moves from the A site to the Psite
also
-binds to the bacterial 30S subunit
describe the antibiotic mechanism of puromycin
it resembles the 3’ end of the aminoacylated tRNA
-it will enter the A site and transfer the growing chain, causing premature chain release
describe the diptheria toxin
A fragment of the toxin specifically ADP ribosylates block translocation activity
describe the ricin toxn
protein from castor beans
-A chain is an N glycosidase that removes the adenine base from nucleotide 4324 in the 28S rRNA. this removal prevents binding of elongation factors, effectively inhibiting protein synthesis
