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Flashcards in Protein Synthesis Deck (28)
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common structure of all peptides

-R group
-amino group
-carboxyl group


human subunits

sites of polypeptide assembly
-60s and 40s make a 80s subunit
found either free in cytoplasm or bound to ER


when is RNA to be made into a protein exported into the cytoplasm?

after it has been processed
poly a tail


composition of mRNA from 5' to 3'

cap, 5'UTR, coding region, 3'UTR, poly A tail


-degenrative nature of mRNA

-a group of 3 bases
-there are more than one codon per amino acid
-code is universal


tRNA structure
-secondary structure
-acceptor and anticodon location and relation
-acceptor sequence

-76-80 bases
-have a high content of unusual bases
-can be written in a clover leaf secondary struct
-acceptor end and anticodon are opposite each other
-3' end holds CCA-OH which binds the aa
-highly processed


post transcriptional modifications of tRNA

-addition of 3' CCA
-modification of bases at specific locations to create unusual bases


purpose of attaching an aa to the 3' end of a tRNA prior to forming the peptide bond

-covalently links an aa to a tRNA with the appropriate anticodon
-attachment to the tRNA activates the AA, generating a high energy linkage at its carboxyl end


aminoacyl-tRNA synthetase

-responsible to binding the correct aa to the correct tRNA by recognizing the correct anticodon
-there is a unique synthetase for every AA


activation of an aa

-AMP is first added to the aa creating aminoacyl-adenylate
-this molecule it then bound to tRNA which kicks off the AMP and forms aminoacyl-tRNA
-facilitated by aminoacyl tRNA synthetase


wobble hypothesis

-more relaxed bonding takes place between the 3' base of the codon and the 5' base of the anticodon
-this allows a single tRNA to recognize several codons


-mechanism and factors involved

-mRNA is recognized by the 5'cap
-eIF2-GTP-Met-tRNA complex interact with the 40S ribosomal subunit before mRNA is even introduced
-this comlex goes forth and finds the 5'cap (with the help of eIF4)
-once recognized, the complex moves 5' to 3' to the AUG site
-eIF2-GDP and other initiation factors are then booted off the mRNA as the 60S subunit is recruited to form the full ribosome and begin translation


-3 sites
-broad overview of what it is

-there are three sites on ribosome P, A, and E
-P: containts the peptidyl tRNA complex
-A: accomodates the incoming aminoacyl-tRNA
-E: exit site for lonely tRNA's
-elongation factors are required to position subsequent aminoacyl tRNAs on the ribosome this is called translocation


-what does it regulate

elongation factor 1
-catalyzyes the GTP-dependent binding of aminoacyl tRNA to ribosomes in the A site
-this regulates the fidelity and the rate of polypeptideelongation during translation
-one of the more abundant proteins in euks



elongation factor 2
-this protein is necessary for translocation
-translocation is the process by which the ribosome moves in the 5'to3' direction, opening up the A site for new aminoacyl-tRNA's


peptide bond formation

this is the linkage between peptides during elongation
-happens between the amino and carboxyl group of the aa
-catalyzed by peptidyl-transferase


stop codons

once one these is reached during elongation, temination begins
-a termination factor binds to the stop codon causing termination
-stop codons are UAA, UAG =, and UGA



-the peptidyl-tRNA is bound to the ribosome in the P site with the stop codon exposed in the A site
-RF1 or RF2 recognizes the stop codon, catalyzed by RF3, and promotes hydrolysis of the ester bond between the polypeptide and the tRNA, releasing the polypeptide



this is observed in euk mRNA, we only have one stop and one start codon within a given mRNA



multiple sequential initiation events will take place on a single strand of mRNA allowing many proteins to be synthesized from one strand of mRNA


missense mutation
-cryptic splice site

-this is when one nucleotide is switched for another causing a single aa change in the polypeptide
-they may also cause cryptic splice sites: this is when a the splicing of a pre-mRNA sequence is altered


nonsense mutation

-a point mutation which causes a premature stop codon
-this can make the protein much shorter than origiinally intended


frame shift mutation

-this is when a mutation -causes the reading frame of an mRNA strand to be altered and usually causes significant changes in the polypeptide composition
-this is generally due to a deletion that has occured in the DNA sequence


regulation of translation
-primary mechnism

during periods of stress (starvation, dsRNA), a key control mechanism is the phosphorylation of eIF2, inactivating eIF2


micro RNA

play an important role in the regulation of translation
-21nt long, noncoding
-usually target the 3'UTR and they recruit the RISC complex and either cause stalling of translation or degradation of the mRNA


internal ribosome entry sites

sequences used by viruses to recruit the pre-initiation complex in a manner that does not involve the initial scanning process


learning and memory

protein synthesis is very important for learning and memory


clinical context, glioblastoma
-what protein are they looking for specifically

physicians are now sequencing patients total mRNA to find every mutation in that persons genome.
-this allows them to make specialized therapy decisions
-specifically they look for the methylation of the MGMT protein which is responsible for reapir
-if this gene is silenced, then they will give Temozolamide