BIO NOTES FOR FINAL 4 23 13 Translation From RNA to Protein The Big Picture RNA is translated into protein via the genetic code each amino acid is encoded by a 3 Transfer RNA tRNA is the translator for the genetic code matching the correct amino nucleotide combination called a codon acid with each codon The ribosome is a molecular machine that catalyzes peptide bond formation to synthesize proteins in the N terminal to C terminal direction amino group to carboxyl group Initiation complex assembly of mRNA met RNA and ribosome The Genetic Code Genetic code Each word in the code is a 3 letter combination coding for a single amino 20 amino acid but only 4 nucleotides in each DNA and RNA acid the codon Since a 3 nucleotide code produces 64 different combinations sooo most amino acids are specified by multiple codons more than one way to code for 1 amino acid in RNA 3 codons UAA UAG UGA do not specify amino acids but instead designate the end of the protein sequence stop codons The 4th special codon is AUG codes for methionine and also indicates the translational The reading frame has 3 possible positions of where the codon begins and that s why we initiation point start codon need the start codon AUG tRNA the RNA Protein Translator Each tRNA brings one amino acid to the growing polypeptide chain and then the ribosome Job of translating mRNA codons into amino acids is done by transfer RNA tRNA will add the new amino acid to the chain by a peptide bond Ribosome does not add free amino acids in the cell it must come in in tRNA tRNA is a short 80 nucleotides RNA molecule that can fold up bc it can base pair up with itself into a specific structure with 3 stem loop regions cloverleaf structure One loop contains a 3 nucleotide sequence that is complementary to the codon the anticodon The amino acid is attached to the 3 hydroxyl When folded into 3 D it has a L shape with anticodon at one end and amino acid at the other Each tRNA can carry a single amino acid but a given amino adic may use several different tRNAs Anticodon loop at the bottom hydrogen bonds that make 3D L structure amino acid attachment site still antiparallel Matching Amino Acid to Codon Requires 2 molecular recognition events 1 correct amino acid must be attached to specific tRNA 2 correct tRNA must be matched to codon in mRNA o there is some flexibility here the 3rd position can be flexible and can tolerate a o this is called wobble pairing and permits U to pair with either A or G but only at the mismatch 3rd position o ex codon AAU anticodon UUG Charging the tRNA Amino acid is matched and attached to tRNA by the enzyme aminoacyl tRNA synthetase requires ATP to work Each amino acid has its own aminoacyl tRNA synthetase so a given enzyme must recognize every one of the tRNAs associated with an amino acid Recognition and attachment of amino acid to tRNA requires hydrolysis of ATP to AMP requires 2 ATP aka 2 phosphate groups high energy bond Amino acid is first attached to AMP then transferred to tRNA tRNA with amino acid attached is called charged tRNA The Ribosome Molecular Machine Where the process of matching charged tRNA to codon and catalyzing protein synthesis takes place Ribosome consists of 2 subunits large and small each made up of a large number of proteins plus several ribosomal RNAs rRNAs Bacterial and eukaryotic ribosomes are similar in overall structure but there are significant differences Some important antibiotics exploit these differences to affect only bacteria Once assembled the ribosome binds to mRNA growing peptide chain and tRNAs Ribosome contains 3 binding sites for tRNAs o A site holds incoming tRNA with new amino acid o P site holds the tRNA attached to growing polypeptide o Discharged tRNA exits thru E site As protein synthesis occurs ribosome moves along mRNA and tRNA is shifted from A to P to E site released Growing polypeptide passes thru exit tunnel on large subunit where it will eventually be Look at pictures in textbook especially the schematic model with mRNA and tRNA Building a Polypeptide Just like mRNA transcription protein translation consists of 3 stages initiation elongation and termination During initiation ribosome assembles with mRNA with the tRNA carrying first amino acid methionine and several initiation factors First small ribosomal subunit binds mRNA plus initiator tRNA a special tRNA that binds methionine and is only used for initiation In bacteria the small ribosomal subunit can bind mRNA and initaitior tRNA in either order Small ribosomal subunit binds mRNA at a specia sequence just upstream of the AUG start codon In eukaryotes the small ribosomal subunit binds to initiator tRNA first and tehn to 5 cap of mRNA For both the small subunit scans moves from 5 3 direction mRNA until it reaches the first AUG which binds anticodon CAU of tRNA Once AUG is reached the large subunit binds forming the translation initiation complex This is facilitated by several initation factors that use energy from GTP not ATP hydrolysis to ensure proper assembly At this point the initiator tRNA plus attachment methionine sit in the P site Elongation Elongation is the 1by1 addition of amino acids to the growing chain Codons in mRNA are read in the 5 3 direction and the polypeptide elongation occurs in N terminal to C terminal direction Bond formation is believed to be catalyzed by rRNA the ribosome is a ribozyme Elongation is facilitated by additional proteins called elongation factors Elongation cycle is a repeated process o New charged tRNA enters the A site and the codon pairs with the anticodon in that position o Ribosome proofreads match using GTP hydrolysis o Peptide bond is formed between the C terminus of the growing chain and amine group of new amino acid entire peptide chain is transferred from P site to new tRNA at A site o Ribosome translocates exactly one codon in the 3 direction moving new tRNA to P site and old tRNA to E site another GTP is hydrolized here o Old tRNA is released thru E site and the ribosome is ready for the next aminoacyl E P and A sites are located on the first 3 codons and during elongation they move one codon tRNA charged tRNA from the 5 end to the 3 end 4 25 THE BIG PICTURE During elongation tRNAs bring new amino acids to the ribosome to be added rtothe C terminus end of the growing polypeptide chain Termination occurs when the ribosome reaches a stop codon releasing the polypeptide chain In order to synthesize proteins more rapidly one mRNA can be translated by
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