Protein synthesize Flashcards
How much energy does protein synthesis take from overall energy of the cell
90%
What are the outcomes that protein synthesize is very energy demanding process
The number of protein copies made = number of proteins needed
What is the method of regulation of proteins
Degradation
After the synthesize of the protein is finished, ___
Post translational modifications take place, for example 3d structure of the protein
Where do tRNA has AA and where is the part that recognizes mRNA
Adaptor site and 3’ end of tRNA, to which amino acid is bound to
How many codons we have and are they nonoverlapping or overlapping?
we have 64 combinations
Nonoverlapping code, that is taken by one AA only
The code ( codon) is written in ___ ( direction)
5’ to 3’
Are all bases in codon important for binding
No, the first two are most important for tRNA
First codon establishes ____ and why it is important
The reading frame
Important , because if it is thrown off by a base or two, all subsequent codons are out of order
There are __ stop codons and they are
3 codons
UAA
UGA
UAG
What is particular about AUG
It codes for both Methyanine and it is an initiation codone
What AA have only one codon
Methionine
tryptophan
Why mitochondria is so unique
It has its own ribosomes and 13-14 proteins it can synthesize by itself
UGA encodes tryptophan ( instead if stop)
AGA/AGG encode stop ( instead of Arg)
How do we number codon and anticodon
In antiparallel fashion
Codon 123
Anticodon 321
What base determines how many codones will be read by tRNA
3 base on codon
describe five stages of protein synthesis
1 The tRNAs are aminoacylated. 2
Translation is initiated when an mRNA and an aminoacylated tRNA are bound to the
small ribosome. 3 When the first AA is brought ( Met)->large ribosome is brought .3.1In elongation, the
ribosome moves along the mRNA, matching tRNAs to each codon and catalyzing peptide bond formation. 4 Translation
is terminated at a stop codon, and the ribosomal subunits are released and recycled for another round of protein synthesis.
5 Following synthesis, the protein must fold into its active conformation and ribosome components are recycled.
tRNa has __ arms
4 arms D arm Anticodon arm TwC arm Amino acid arm
All tRNa has what sequence
CCA that is added in postranslational modification process at amino acid arm
What is done to attach AA to tRNA
aminoacylation
Describe aminoacylation
Carboxyl group of AA attacks Alpha phosphate group on ATP, forming 5' aminoacyl adenylate( aminoacyl-AMP) Then the process divides into two parts -> class 1 aminoacyl-tRNA synthetases and class II aminoacyl-tRNA synthetases
The difference in class I and class II aminoacyl tRNA transferases
For class I enzymes, 2a the aminoacyl group is transferred first to the 2′-hydroxyl group of the 3′-terminal A residue, AMP gives off AA and leaves
then from carbon 2’ to 3′-hydroxyl group by a transesterification reaction.
For class II enzymes, the aminoacyl group is transferred directly to the 3′-hydroxyl group of the terminal adenylate.
The first AA in protein synthesize is
Met, because AUG codes for the start codone as well
What happens in mitochondria and prokaryotes with the first methionine
initiation tRNA inserts n-Formylmethionine (fMet) and the rest of AUGs will be normal Met
Initiation of translation in eukaryotes
Initiation factors eIF1A and eIF3 ,eIF1 bind to the 40S subunit , blocking tRNA binding to the A site (eIF1A) and premature
joining of the large and small ribosomal subunits, respectively
The factor eIF1 binds to the E site.
The charged initiator( the first with Met) tRNA is bound by the initiation factor eIF2, which also has bound GTP.
2)eIF5B bonded to GTP also comes and everything together they bond. first tRNA come to P site, The only tRNA that comes there. Now it is called 43 S preinitiation complex
3)The mRNA binds to the eIF4F complex, which, in step , mediates its association with the 43S
preinitiation complex and brings to 43 S complex with the usage of ATP. Now it is called 48S complex
4)This complex scans the
bound mRNA, starting at the 5′ cap, until an AUG codon is encountered.
5) the next tRNA comes to A site
6) As soon as the first codon is bonded, the complex disassembles and the large subunit comes.
How is the first peptide bond is created?
This occurs by transfer
of the initiating N-formylmethionyl group from its tRNA to the amino group of the second amino acid,
now in the A site . The α-amino group of the amino acid in the A site acts as a
nucleophile, displacing the tRNA in the P site to form a peptide bond. This reaction produces a
dipeptidyl-tRNA in the A site, and the now “uncharged” (deacylated) tRNAfMet remains bound to the
P site. The tRNAs then shift to a hybrid binding state, with elements of each spanning two different
sites on the ribosome.
The enzymatic activity that catalyzes peptide bond formation has historically been referred to as
peptidyl transferase and was widely assumed to be intrinsic to one or more of the proteins in the
large ribosomal subunit. We now know that this reaction is catalyzed by the 23S rRNA
What factors bring in aminoacyl tRNA to A site
EF-Tu-GTP
What happens if the right tRNA has been brought
EF-Tu-GTP is hydrolized to EF-Tu-GDP and exits
How does the tRNAs change places
the
ribosome moves one codon toward the 3′ end of the mRNA . This movement shifts the
anticodon of the dipeptidyl-tRNA, which is still attached to the second codon of the mRNA, from the
A site to the P site, and shifts the deacylated tRNA from the P site to the E site, from where the tRNA
is released into the cytosol.
Who pushes dipeptidyl -tRNA to Psite
EF-G-GTP
When it pushes, it will exit as EF-G-GDP and then A site is empty to receive another aa-tRNA
How is ther protein synthesis is terminated?
Synthesis is terminated in response to a termination
codon in the A site. First, a release factor, RF (RF1 or RF2, depending on which termination codon is present), binds to the
A site. This leads to hydrolysis of the ester linkage between the last added polypeptide and the tRNA in the P site and release
of the completed polypeptide. Finally, the mRNA, deacylated tRNA, and release factor leave the ribosome, which
dissociates into its 30S and 50S subunits, aided by ribosome recycling factor (RRF), IF3, and energy provided by EF-G–
mediated GTP hydrolysis. The 30S subunit complex with IF3 is ready to begin another cycle of translation
Some proteins require ___ before the fully active conformation is achieved
Modification
Examples of post-translational modification
Enzymatic removal of formyl group from first residue, or removal of Met and sometimes additional residues
- Acetylation of N-terminal residue
- Remocal of some regions
- Forming disulfide links
- Attaching carbohydrates
Half-life range of proteins is
from seconds to month
Hmoglobin is ___
long-lived protein, 120 days
Proteins for rapidly changing needs are ___, as well as defective proteins
Short-lived
What is done recognize what proteins should be degraded
Adding polyUbiquitin to lysine
How ubiquitin is added on proteins
First, the free carboxyl group of ubiquitin’s carboxyl-terminal Gly residue becomes linked to
an E1-class activating enzyme wuth the hydrolyses of ATP to ADP. The ubiquitin is then transferred to an E2 conjugating enzyme. An E3
ligase ultimately catalyzes transfer of the ubiquitin from E2 to the target, linking ubiquitin ε-amino group of a Lys residue in the target protein
