How is the order of nucleotides in mRNA used to generate the linear sequences of amino acids in protein?
process known as translation
process know as transcription
process know as post translational modifications
What process is the most highly conserved across all organism and the most energetically costly?
Transcription is a more formidable challenge than translation.
The hydrophobic side chains of phenylalanine, tyrosine, and tryptophan forms interactions with the mRNA template.
Crick proposed a molecule that directly interacts with the coding units of mRNA. He proposed to also be a molecule.
amino acids that are attached to a class of RNA molecules that represent 15% of all celluar RNA and transfer amino acids to a growing polypeptide chain.
The translation machinery is comprised of ?
aminoacyl-tRNA synthetases (aaRS)
The competent of the translation machinery are always discarded after use.
Provides the information to be interpreted by translation machinery
This region of the mRNA specifies the order of amino acids by the ordered series of 3-nucleotide-long units called codons?
poly A tail
protein coding region
couple amino acids to specific tRNAs that recognize the appropriate codon?
aminoacyl tRNA synthetase
coordinates correct recognition of mRNA by each tRNA and catalyzes peptide bond formation between growing peptide chain and amino acids attached to tRNA
in mRNA containing 2 or more open reading frames that can encode for multiple polypeptide chains
protein coding regions of each mRNA is composed of contiguous, non-overlapping string of codons called?
origin of replication
Eukaryotes, contain a single ORF that encode for multiple protein which is called polycistronic.
translation starts at the end of ORF and proceeds into the 3' end
Start codons in bacteria
eukaryotic cells always use AUG as a stop codon
fundamental unit of an ORF is a
What are the important functions of a start codon?
specify first amino acid incorporation
contains special interactions with tRNA for protein synthesis
defines the reading frame for all subsequent codons
allows for hydrogen bonding to other bases
Since the codons are a 3-nucleotide long, any stretch of mRNA could be translated in three different reading frames by overlapping.
Stop codons are UAG,UGA and UAA in both eukaryotes and prokaryotes
Eukaryotic mRNA recruit ribosomes by the shine-dalgarno sequence which is ribosome binding site(RBS) that recruit the translation machinery.
the ribosome binding site
binds with the 16s rRNA of the ribosome
has a sequnce of CCUCCU
always has poor spacing
in all prokaryote has strong binding
limited complementarity and poor spacing promotes active translation
some prokaryotes lack a strong RBS but can still be actively translated by having a start and a stop codon right next to each other.
who uses their 5' and 3' modified ends to facilitate translation?
a purine, three bases upstream of the start codon and a guanine downstream
extreme 5' end
interacts with initiator tRNA
5' cap allows the ribosome to be recruited in order to go through a process called scanning.
at the end of mRNA enhances the level of translation of mRNA by promoting efficient recycling of .
molecules are 75 to 95 ribonucleotides in length which there are many types of.
The site at which amino acid is attached by the enzyme aminoacyl tRNA syntheses?
Unusual bases found in tRNAs primary structure created by post-transcriptional modifications?
principle features of the tRNA clover leaf are
L-shape reveals the secondary structure of tRNA, which is stabilized by hydrogen bonds only.
charged tRNAs have an amino acid attached to them by amino alkyl linkage
acyl linkage is a high energy bond that is hydrolysis results in a large change in free energy, which helps drive the formation of peptide bonds
step one of aminoacyl-tRNA charging is which amino acid reacts with ATP, amino acid is attached to adenylic acid via group transfer ester bond.
Whats the driving force that make adenylaltion energetically favorable reaction?
the release of pyrophosphate (PPI)
hydrolysis of pyrophosphate (PPi)
In step two of aminoacyl tRNA-charging- the adenylylated amino acid which is highly bound to the synthetase reacts with?
another amino acid
Class 2 tRNA syntheses enzyme attach the amino acid to the 2'OH of the tRNA and are generally monomeric.
each aminoacyl tRNA synthetase attaches a single amino acid to only one tRNA which is know as isoaccepting tRNAs.
most organism have 20 different tRNA synthetase
tRNA structure that determine recognition by specific aminacyl tRNA synthetases?
acceptor stem and discriminator base
Why does aminoacyl-tRNA synthetase face a challenge in selecting the correct amino acid?
There is more proofreading after the aminoacyl-tRNA synthetase has used its editing pocket to charge tRNAs with low accuracy.
when cysteinyl-tRNA ^cys converted to alanine-tRNA^ cys ( by reduction) and added to a cell free protein synthesizing system, alanine-tRNA^cys introduces alanines at the codons that are suppose to be cysteine. why?
ribosomes recognize tRNA not amino acid that its carrying
wrong tRNA has been incorporated
the tRNA is isoaccepting therefore can carry more than one amino acid
Eukaryotes can commence translation of the mRNA as it emerges from the RNA polymerase because the transcription machinery and the translation machinery are in the same compartment.
The ribosome is made up of large subunit which contains the and the small subunit that contains the .
mRNA with multiple ribosomes
spaced 80 nt apart
happen in eukaryotes
happen in prokaryotes
When small and large subunits undergo of the ribosome associate with each other and the mRNA, translate the target mRNA, then dissociate after each round of sythesis.
sedimentation by centrifugation
from 5' to 3'
from N terminal to C-terminal
by attaching new amino acid to the C-terminus of a growing polypeptide chain
substrate(s) for a round of amino acid addition are
2 charged species of tRNA
1 charged species of tRNA
The bond between the aminoacyl-tRNA and the amino acid is not broken during the formation of the next peptide bond.
What drives the peptide bond formation?
simultaneous hydrolysis of nucleoside triphosphate
breaking the high energy acyl bond that joins the growing polypeptide chain to the tRNA
ribosomal RNAs are represent the main component of the ribosome because
are located in the interior of the ribosome
essential for the peptidyl transferase reaction and binding the anticodon loop of tRNAs
are larger then proteins
protein stable rRNA by shielding negative charges of their sugar phosphate backbones
what are the three binding sites for tRNA on a ribosome
peptidyl transferase center
formed by 20 nucleotides of 23s RNA
the 3'OH group of the tRNA in the P site is critical for activity and assist a concerted proton transfer
orients tRNAs in optimal proximity for peptidyltransferase rxn to occur
what allows only unpaired RNA to pass through the small and large subunit of the ribosome?
entry and amino channel
exit and adjacent channel
entry and exit channel
channel is through the small subunit which is only wide enough to let unpaired mRNA through and too narrow for a structure. Ensures that codons in mRNA will be exposed and available for pairing with the anticodon loops of tRNA.
the kink in the mRNA between two codons are included after ribosome translocation to not allow any entry of the mRNA
channel lets nascent polypeptide through. Some secondary structures can form inside but some can't. But and quaternary structure will not be formed until after its exit the ribosome.
Successful initiation in translation occurs when?
ribosome is recruited to the mRNA
ribosome placed over the start codon
charged tRNA placed into P site
tRNA goes through hydrolysis
translation initiation in prokaryotes is mostly done in the absence of the full ribosome
Specialized charged tRNA that binds directly to the P site and not the A site during initiation.
One of the three initiation factors, that binds to the small subunit and block its from reassociating with the large subunit or from binding charged tRNAs.
purple-one of the three initiation factors in prokaryotes, it is a GTAPase which interacts with IF 1, charged initiator tRNA, and the small subunit.
yellow-prevents tRNAs from binding to the portion of the small subunit that will become part of the A site.
the last step in initiation is the 70s initiation complex, where fmet-tRNA, start codon, base pair which allows the small subunit to undergo a conformational change.
In eukaryotic initiation, the 43s pre-initiation complex
1A attaches at the exit site
Met-tRNA^met is bound to e1F3
EIF1,3,5 are bound to the exit site
the initiation factors attach to the 40s ribosome
recognition of eukaryotic mRNAs after 43S pre initiation complex,
recognition of 5' cap mediated by 3 subunits
recognition is mediated by a 3 subunit protein that specifically binds to RNA
unstructured mRNA recruits the 43S pre initiation complex to mRNA by eIF4F and eIF5
once the complex is assembled at the 5' end of the mRNA, they move along the 5'-3' direction by a process that ATP-dependent
eIF4F-associated RNA helices
finding the start codon
base pairing of the anticodon
The reason why the initiator tRNA must bind to the small subunit before it binds to the mRNA is because it is used in scanning by recognizing the start codon through base pairing between anticodon of tRNA and start codon.
The binding of the large subunit to the small subunit in eukaryotes
releases initiation factors by GTP hydrolysis
FMet-tRNA is placed in the P site of the 80s initiation complex
start codon and initiator tRNA in the P site is now ready to accept charged tRNAs
Poly-A-binding protein and eIF4G interact by the 5' and 3' end of the mRNA to
make mRNA linear
stabilize mRNA (exonucleases)
decrease efficiency of translation
helps recycling ribosomes
Exceptions to eukaryotic polypeptide being encoded by an open reading frame that starts with AUG?
internal ribosome entry sites
eIF4G adaptor role when an mRNA is capped?
eIF4G directly binds to IRES
eIF4G binds to poly A tail
eIF4G serves as an adaptor between the pre initiation complex and the EIF4E bound to it
Elongation is very different in prokaryotes and eukaryotes.
Whats this step in this mechanism?
When EF-Tu is bound to GDP and lacking any bound nucleotide it shows high affinity for aminoacyl-tRNAs.
What are one of the three mechanisms that contributes to the fidelity of codon recognition?
two adjacent adenine residues in 16S
Third mechanism in correct codon-anticodon incorporation is accommodation
GTP hydrolysis( accommodation, GTP hydrolysis ), which is rotation of tRNA into the peptidyl transferase center.
Reason why ribosome is a ribozyme?
23S rRNA catalyzes peptide bond formation by base pairing with the CCA variable loop of the tRNAs in the A and the P sites with help position alpha amino go of aminoacyl tRNA to attack carbonyl of growing peptide attached to peptidyl-tRNA.
EF-Tu( EF-G, EF-Tu ) is an elongation factor that completes translocation by binding to the ribosome's factor binding center with GTP.
all elongation factor( molecular mimicry, all elongation factor ) in which a protein takes on the appearance of a tRNA to facilitate association with the same binding site.
Exchange of GDP for GTP for both EF-TU-GDP and EF-G-GDP are? ( in order)
GDP release and binds to new GTP, exchanging GDP for GTP by complex
exchanging GDP for GTP by complex, GDP release and binds to new GTP,
Eukaryotic factors analogous to EF-Tu (eEF1
EIF1A( eEF1, EIF1A )) and EF-G(eEF2
EF-Tu( eEF2, EF-Tu )) are name differently but have similar function.
how many molecules of ATP and GTP are used for peptide bond formation?
2 ATP and 1 GTP
2GTP and 1 ATP
3 ATP and 0 GTP
Termination of translation is done by
RF1: recognizes UGA
RF2: recognizes UGA
the name of the codon on the release factor the recognizes a stop codon?
Class II release factor RF3,
has higher affinity for GDP than GTP
conformational change in ribosome, the class 1 RF stimulates GDP to GTP exchange
No class 1 RF, RF-3-GDP has high affinity for ribosome
ribosome recycling factor
works with EF-G and IF3
Puromycin is an aminoglycoside antibiotic which binds to the 16rRNA causing misreading of the genetic code
tetracycline is a polyketide, which block the p site.
used for cleaning purposes
What is this mechanism?
what machanism is this?
protein mediated regulation in bacteria
inhibition of 30s initiation complex binding
secondary structure of mRNA can inhibit translation initiation
RNA sensors for regulation of translation
binding to its own mRNA
regulation of translation by small RNA (sRNA) in bacteria
initiation in eukaryotic translation is globally regulated by
gene specific regulation of translation through cap sequestration in eukaryotes
Iron regulation is mediated by amino acids acting as sensor via steric hinderance
upregulation( Translation, upregulation ) of GCN4 is controlled by short upstream ORFs.