BIOLOGY 305 1st Edition Lecture 19 Outline of Last Lecture I Introduction to Transcription II Mechanism of Transcription A Initiation B Elongation C Termination III RNA Processing A Eukaryotic Feature IV Vocabulary and Sample Questions Outline of Current Lecture I Introduction to Translation II Mechanism of DNA Translation A Initiation B Elongation C Termination III Genetic Code A 3 Features of the Genetic Code 2 Experiments B Code Bias and The Wobble Effect IV Vocabulary and Sample Questions Current Lecture I Introduction to Translation Prokaryotes transcription and translation happens in the same place simultaneously Eukaryotes transcription and translation are in different locations has a nucleus mRNA is transcribed processed in nucleus translated in the cytoplasm Ribosomes Ribosomes are the machinery of translation Composed of a large number of proteins Most important processes are carried out by the RNA 3 sites Large subunit A site P site E site peptidyl transferase A aminoacyl P peptidyl E exit Small subunit initial binding of mRNA is a ribozyme the catalytic function is performed by rRNA tRNA Turns into a complex with a specific amino acid on one end an anticodon on the other catalyzed by aminoacyl tRNA synthetase amino acid is on the 3 end Hairpin loop formation aminoacyl tRNA synthetase Enzyme has two pockets one pocket binds the tRNA other binds specific amino acid There are 20 kinds one for each kind of amino acid Important for encoding a specific code II Mechanism of Translation A Initiation Prokaryote Mechanism Small subunit of the ribosome initiates translation by binding to the Shine dalgarno sequence a short sequence recognized by ribosomal subunit Initiation codon first codon to be translated into a polypeptide Initiation factors assist the small ribosomal subunit Binding of initiator tRNA Quickly followed by binding of the large subunit and dissociation of initiation factors N formyl methionine usually the first polypeptide piece to be formed Eukaryotes No shine dalgarno sequence instead the small subunit binds to the 5 cap Start codon initiation codon initiator tRNA binds and then the large ribosomal subunit binds mRNA in Prokaryotes and Eukaryotes Prokayotes many mRNA are polycistronic a single mRNA has several shine dalgarno sequences encoding multiple polypeptides Eukaryotic monocitronic because 5 cap is the only possible site B Elongation Overall mechanism is similar in prokaryotes versus eukaryotes with protein factors being more numerous and complex in eukaryotes First tRNA is on the P site then the next one is able to bind to the A site The site where the actual decoding of mRNA takes place codon must be complementary to anti codon on the new tRNA specificity Secondly there is peptide bond formation where chemical reaction takes place Amino acid from the first tRNA is transferred to the amino acid on the second tRNA The second tRNA now has two amino acids and is shifted to the P site As a result the first emptied tRNA is shifted to the E site and is ejected Repeated until termination C Termination There are three stop codons which determine site of termination Release Factor bind to the A site and the peptide is released The polypeptide dissociates from tRNA tRNA mRNA separate from ribosome the large subunit and small subunit of the ribosome also dissociates So what are you left with Empty tRNA RF peptide mRNA large subunit small subunit Note All can be recycled except tRNA which have to be recharged by synthetase It is possible to have multiple ribosomes translating a single strand III Genetic Code Genomic sequence genetic code Genetic code is just the language hence translation and has nothing to do with the sequence of an organism You will be given this chart on the exam 1 codon amino acid is variable 1 6 2 Three stop codons 3 Universal prokaryotes and eukaryotes The only codon you should know is the start codon AUG A Three Features of the Genetic Code and The Wobble Effect 1 No overlaps no gaps between codons 2 Triplet nature 3 nucleotides per amino acid 3 Degenerate 1 codon per amino acid Non overlapping Ex Geneticode vs Geneticcode non overlapping as c isn t reused If there is a single nucleotide change it only affects a single amino acid Triplet Nature 3 nucleotides per amino acid Helps tell us the length of the sequence based on the polypeptide and vice versa Crick Benner Experiment Fact Proteins are robust and can remain intact even if there is a single nucleotide mutation Thus Crick obtained mutants for single nucleotides and figured out which mutations make a non functional protein introduced multiple insertions and mutations Found that or wild type discovered they were in triplets Suppressor mutations fixes an original mutation The Nirenberg Matthaei Khorana Experiment Interpreted the genetic code and its function in protein synthesis Wanted to assign codons to certain amino acids created synthetic mRNA Found that AGA and GAG could result in either Arginine or Glutamine AGG GGA and GAG could be either Arginine Glycine or Glutamaine Could decipher all proteins B Codon Bias and The Wobble Effect Codon Bias Found that frequency of synonymous codons were different among species Abundance of tRNA differed Expression level of protein differed The amount of tRNA could be low for certain codon so when you want to take a gene from one organism and produce protein in another you have to add tRNA and factors to adjust The Wobble Effect There are 64 codons but only 30 40 tRNA genes which means that the tRNA can recognize more than one codon Remember Anticodons are antiparallel to codons The third position of a codon can vary the 5 end of the anticodon can pair with multiple different codons When doing wobble problems remember 1 What anticodons can interact with this codon 2 Which codons can interact with this anticodon 3 An anticodon should not interact with codons for more than one amino acid 4 An anticodon should not interact with a STOP codon IV Vocabulary and Sample Questions N terminal beginning of the protein corresponds to the 5 end of RNA C terminal carboxyl group of protein corresponds to the 3 end of RNA Triplet nature the genetic code uses three nucleotides to specify one amino acid Initiation codon the first codon to be translated into a polypeptide Stop codons marks the end of a polypeptide chain tRNA reads the information on the mRNA charged tRNA a tRNA with a specific amino acid attached anti codon the base pair triplet sequence on the