CHPATER 12 Protein Synthesis Translation is the process by which mRNA transcripts are All protein synthesis involves three phases converted into peptides proteins o Initiation involves binding of mRNA and initiator aminoacyl tRNA ro small subunit followed by binding of large subunit o Elongation synthesis of all peptide bonds with tRNAs bound to acceptor a and peptidyl P sites o Termination occurs when stop codon reached Genetic Code Bases A G C U Code codon 3 bases A triplet code means that a sequence of three bases codon is needed to specify one amino acid Theoretically possible genetic codes o The term nonoverlaping indicates that no bases are shared between consecutive codons the ribosome moves along the mRNA three bases at a time rather than one or two at a time o If the ribosome moved along the mRNA more than 3 bases at a time this situation would be referred to as a punctuated code Each amino acid may have more than one codon so the genetic code is a little redundant but no codon can encode more than one amino acid All 64 codons have been assigned meanings with 61 of them coding for amino acids and the remaining 3 serving as the termination signals Tryptonphan methionine have only ONE codon each Leucine and arginine have SIX codons The bases that are common to several codons are usually the first and second bases with more room for variation in the third base which is called the wobble base Wobble base is pretty much the last base in the codon that doesn t really matter if there was a mutation in that third base the amino acid wouldn t change This type of mutation is called a silent mutation Only 8 of the amino acids L V S P T A G and R have a irrelevant third base Codon Anticodon Pairing and Wobble A codon forms base pairs with a complementary anticodon of a tRNA when an amino acid is incorporated during protein synthesis The wobble rules state that a first base anticodon U can recognize either an A or a G codon in the third base position First base anticodon G can recognize either U or C in the 3rd base codon position And anticodon I can recognize U C or A in the 3rd base codon position Thus codons with A or G which are degenerate for a particular amino acid look at codon table codons with third base pyrimidines are always degenerate except Met and Trp in third base position could be served with a single tRNA with first base anticodon U are always degenerate and could be served by single tRNA species with a first base anticodon G Wobble involving first base anticodon I further reduces the number of distinct tRNAs needed to translate the 61 sense codon http www youtube com watch v iIIa631nDug More importantly codons with third base pyrimidines C or U 30 25 in video for better explanation Prokaryotic Translation Chain initiation Figure 12 10 39 00 in video codon o Small ribosomal subunit initiates binding to mRNA o Locates 5 end of mRNA o Small subunit ribosome finds first AUG codon start Prokaryotic cells rely on N formyl Met tRNA to This particular tRNA has a number of distinctive initiate protein synthesis features that are not found in the noninitiator tRNAs Although AUG sometimes GUG also codes for internal Met the AUG start codon is situated 10 residues down from the Shine Dalgarno sequence at the 5 end of mRNAs This sequence determines the start site o Large ribosome binds o tRNA carries the amino acid methionine to first position How does the ribosome know where to start translating o Video 21 29 o Prokaryotes have multiple genes on a single mRNA this means we have to have a specific place where the first genes begins translating and then where it ends where does the next one start o We know AUG is the start codon there are several AUGs throughout the mRNA of a prok how does the cell know which AUG to start at This is solved by assitance of the 16S rRNA o The Shine Dalgarno sequence binds to a pyrimidine rich sequence on the 16S ribosomal RNA part of the 30S subunit and aligns it for proper translation beginning with the AUG start codon is where the start codon is o This sequence is pretty much telling the ribosome here o There is no Shine Dalgarno sequence in eukaryotic cells In eukaryotes have two tRNAs for Met The ribosome simply scans the mRNA until it finds the first AUG and that starts translation Chain Elongation Figure 12 12 o There are 3 tRNA binding sites that are called the P peptidyl site the A aminoacyl site and the E exit site o The P binds to a tRNA that carries a peptide chain and the A site binds an incoming aminoacyl tRNA The E site carries an uncharged tRNA that is about to be released o Chain elongation begins when the binding of a tRNA which recognizes the next codon in the mRNA to the A site of the ribosome this is catalyzed by the EF Tu transcription factor and requires the hydrolysis of a GTP o Once the tRNA binds in the A site of the ribosome the polypeptide chain is moved from the tRNA in the P site to the amino acid attached to the tRNA in the A site o Peptidyl transferase a protein RNA complex present in the 50S ribosomal subunit catalyzes the formation of this new peptide bond between the amino acids o The ribosome then translocates to the next codon This process is promoted by elongation factor G and requires another GTP Chain termination o This places the empty tRNA molecule in the E site of the ribosome and moves the tRNA containing the growing polypeptide chain in the P site The next codon in the mRNA chain is positioned in the A site o The uncharged or empty tRN in the E site then leaves the ribosome and a cycle of chain elongation is completed o http www youtube com watch v v6h5sXfJ72Q o reach a stop codon UAG UAA or UGA Instead of a t o the whole complex dissociates setting free the release RNA they are recognized by proteins called release factors One of the 2 release factors is required as is GTP which is bound to a third release factor RF 3 factors tRNA mRNA and the 30S and 50S ribosomal subunit o net cost of translation 4 phosphate bonds amino acid added CHAPTER 4 3D Protein Structure Protein Structure and Function The confirmation of a protein which is biologically active is For any given protein there are 4 levels of structure called the Native Conformation o Primary amino acid order o Secondary the arrangement of the amino acid o Tertiary the 3D structure of the entire protein o Quaternary the arrangement of multiple subunits backbone including prosthetic group 4 2 Primary Structure All polypeptide molecules share a