GCD 3022 1st Edition Lecture 18 Outline of Last Lecture I Transcription Definition II Gene expression a Structural genes b mRNA c central dogma of genetics III Overview of Transcription a Regulation of RNA synthesis b Role of proteins c Gene expression IV Functions of RNA transcripts a Polypeptides b RNA molecules c Nonstructural genes V Transcription in bacteria a Promoters b Initiation i RNA polymerase ii Holoenzyme These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute iii Closed and open complexes c Elongation i Overview ii Template and coding strands d Termination i Overview ii Termination mechanisms in E coli VI Transcription in Eukaryotes a Major differences b RNA polymerases i RNA polymerase I ii RNA polymerase II iii RNA polymerase III c Sequences of Eukaryotic structural genes i Core promoter ii Regulatory elements iii Transcription factors iv Cis and Trans acting elements VII RNA modification a Colinearity of gene expression b RNA splicing excision i Introns ii Exons iii Spliceosome and subunits iv snRNP s v Intron advantage c Processing d Capping i Overview ii 7 methylgaunosine cap e Polyadenylation tailing i polyA tail ii mechanism VIII Identification of Introns via microscopy a The experiment b The result IX RNA editing a Common types of editing i Addition or deletion of bases ii Conversion of bases Outline of Current Lecture I Protein synthesis review a Structural genes b Translation II Codons a Codon traits b Special codons III Polypeptide chain a Directionality b Amino groups i Two ends of an amino group ii R groups c Peptide bonds IV Structure of proteins a Levels of structure i Primary ii Secondary iii Tertiary iv Quaternary b Function of proteins i Relationship between function and structure ii Enzymes V Structure and function of tRNA a Adaptor hypothesis b RNA has two functions c Common structural features i Folding of tRNAs ii Charging of tRNAs d Wobble rule VI Functional sites of ribosomes a Location of mRNA during translation b Ribosome sites VII Stages of translation a Initiation i Initiation complex ii Start codon iii Binding of mRNA to 30S subunit iv Eukaryote initiation summary b Elongation i Addition of amino acids c Termination i Stop codon ii Release factors VIII Bacterial translation a Bacterial cell structure b Translation patterns in bacteria Current Lecture I Protein synthesis review a Structural genes genes that encode polypeptides Also called protein encoding genes These genes are transcribed into mRNA b Translation mRNA is translated into functional proteins II Codons groups of three nucleotides in mRNA that code for amino acids the building blocks of proteins a Codon traits more than one codon can specify the same amino acid in most instances the third base is the variable base ex GGU GGC GGA and GGG all code for glycine the code is nearly universal b Special codons there are start and stop codons that code for the initiation of translation and the termination of translation the start codon in eukaryotes is AUG and defines the reading frame for all the following codons The stop codon is UAA UAG or UGA III Polypeptide chain a Directionality synthesized in 5 to 3 direction parallel to orientation of mRNA b Amino groups i Two ends of an amino group carboxyl group also called C terminal and amino group also called N terminal ii R groups also known as side chains unique to each amino acid Can be positively charged negatively charged hydrophobic or hydrophilic c Peptide bonds formed between the carboxyl group of the last amino acid and amino group in polypeptide chain of the amino group in the amino acid being added IV Structure of proteins a Levels of structure i Primary amino acid sequence while being translated folding will occur which may be aided by chaperones ii Secondary can be alpha helix or beta sheet or a combination stabilized by hydrogen bonds between atoms located in the polypeptide backbone iii Tertiary 3 dimensional final composition of proteins that are composed of a single polypeptide structure is determined by hydrophobic and ionic interactions as well as hydrogen bonds and van der Waals interactions iv Quaternary protein complexes made up of two or more polypeptides this is usually the final structure of a functional protein b Function of proteins i Relationship between function and structure a protein s structure determines its function ii Enzymes a category of proteins that catalyze reactions including chemical modifications cleavage and synthesis V Structure and function of tRNA a Adaptor hypothesis founded by Francis Crick in 1950 s stated that tRNAs play a direct role in the recognition of codons in the mRNA b tRNA has two functions recognizing a 3 base codon in mRNA and carrying an amino acid that is specific for that codon c Common structural features i Folding of tRNAs tertiary structure involves additional folding of secondary structure In addition to normal A U G and C nucleotides tRNAs commonly contain modified nucleotides secondary structure looks like a cloverleaf it contains 1 Three stem loop structures 2 A few variable sites 3 An acceptor stem with a 3 single strand region CCA added by enzyme at 3 end ii Charging of tRNAs when amino acid attaches to tRNA using aminoacyltRNAsynthetases enzyme and ATP energy d Wobble rule in the codon anticodon recognition process the first two positions pair strictly according to the A U G C rule but the third position can actually wobble or move a bit discovered by Francis Crick in 1966 VI Functional sites of ribosomes a Location of mRNA during translation during bacterial translation the mRNA lies on the surface of a 30S subunit and the polypeptide that is formed exits through a channel with a 50S subunit b Ribosome sites peptidyl site P site aminoacyl site A site and exit site E site VII Stages of translation a Initiation i Initiation complex made up of mRNA initiator tRNA and ribosomal subunits ii Start codon sequence in mRNA that is recognized by initiator tRNA iii Binding of mRNA to 30S subunit facilitated by a ribosomal binding site or Shine Dalgarno sequence iv Eukaryote initiation summary assembly of initiation complex is similar to bacteria but additional factors are required eukaryotic initiation factors eIF also the start codon is AUG in eukaryotes 1 Initiator factor protein complex binds to 5 cap in mRNA which is joined by a complex consisting of the 40S subunit tRNA and