GCD 3022 1st Edition Lecture 19Outline of Last Lecture I. Protein synthesis reviewa. Structural genesb. TranslationII. Codonsa. Codon traitsb. Special codonsIII. Polypeptide chaina. Directionality b. Amino groupsi. Two ends of an amino groupii. R-groupsc. Peptide bondsIV. Structure of proteinsa. Levels of structurei. Primaryii. Secondaryiii. Tertiaryiv. Quaternary 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.b. Function of proteinsi. Relationship between function and structureii. EnzymesV. Structure and function of tRNAa. Adaptor hypothesisb. RNA has two functionsc. Common structural featuresi. Folding of tRNAsii. Charging of tRNAsd. Wobble ruleVI. Functional sites of ribosomesa. Location of mRNA during translationb. Ribosome sitesVII. Stages of translationa. Initiationi. Initiation complexii. Start codoniii. Binding of mRNA to 30S subunitiv. Eukaryote initiation summaryb. Elongationi. Addition of amino acidsc. Terminationi. Stop codonii. Release factorsVIII. Bacterial translationa. Bacterial cell structureb. Translation patterns in bacteriaOutline of Current LectureI. Transcriptiona. Rho independent and rho dependentb. Sigma factori. Mutationii. Transcription initiation and role of sigma factorc. Transcription regiond. Coding and template strandsII. Translationa. Gene mappingb. Splicingi. Mutationii. Introns and exonsiii. Coding information in eukaryotesc. Translated RNAsi. Type of translated RNAii. tRNA anticodond. Mistakes in translationi. Anti-codon mutationii. Start and stop codonse. Termination of translationi. Site of terminationii. Number of codons translatedf. Prokaryotic vs. Eukaryotic initiationg. A, P, and E sites III. Consensus sequenceIV. Degenerate genetic codeCurrent LectureI. Transcriptiona. Rho independent and rho dependent: both types of transcription termination require the formation of the stem loop secondary structure in RNA. b. Sigma factori. Mutation: if there is a strain of bacteria that produces a non-functional sigma factor then that bacteria will be unable to identify and tightly bind promoter elements. ii. Transcription initiation and role of sigma factor: sigma factor associates with the RNA polymerase core enzyme to create the holoenzyme. Sigma factor is responsible for identifying “good” -35 to -10 sequences to which it binds tightly to form a closed complex. A short RNA is made and an open complex is formed. Then the sigma factor is released from the initiation complex and elongation begins. c. Transcription region: the promoter and terminator define the region of transcription in a protein-encoding gene.d. Coding and template strands: if given two sample sequences of DNA and one sequence of RNA and asked to identify which strand is coding and which is the template, remember that RNA polymerase moves along the template strand in the 3’ to 5’ direction, and that the coding strand’s sequence matches that of the RNA strand in the 5’ to 3’ direction.II. Translationa. Gene mapping: a specific disease-causing mutation is mapped and found to follow the Mendelian inheritance pattern (mutation is recessive). But there is no evidence of the mutation when the exons are sequenced. The two possible reasons for not being able to see the mutation are:i. The mutation is a wobble baseii. The mutation is a transcriptional control sequenceb. Splicingi. Mutation: if there is a mutation such that the 5’ splice site is eliminated from intron 2 of a string of pre-mRNA with 4 exons, then both intron 2 will remain in the final mRNA product (exon 1-exon 2-intron 2-exon 3-exon 4)ii. Introns and exons: splicing removes introns and joins exons to form mRNA. iii. Coding information in eukaryotes: the regions of DNA that contains the coding information for a protein in eukaryotes are called exonsc. Translated RNAsi. Type of translated RNA: the type of RNA that is translated is mRNAii. tRNA anticodon: a tRNA anticodon is both antiparallel and complimentaryto the mRNA codon. Therefore, a tRNA with the sequence 5’-GAA- 3’ will match with its complementary and antiparallel codon 5’-UUC-3’ which codes for the amino acid phenylalanine d. Mistakes in translationi. Anti-codon mutation: the least likely event that would lead to the wrong amino acid in a protein would be the change in the wobble base of the codon. ii. Start and stop codons: if a mutation changes a start codon to a stop codon, then the cell will be unable to translate the mRNA into a functional protein.e. Termination of translationi. Site of termination: translation is terminated when a stop codon is presented at the A site of the ribosomeii. Number of codons translated: an mRNA with the sequence 5’-CCAGAUGGUUACAAAAUAACAUCAA-3’ will begin translation with the AUG start codon and end with UAA, UAG, or UAC stop codon. That meansthat there will be 4 amino acids in this polypeptide and the last amino acid in this chain would be lysine (AAA).f. Prokaryotic vs. Eukaryotic initiation: : In eukaryotes, the ribosome binds at the 5ʹ end of the mRNA and then scans in the 3ʹ direction in search of an AUG start codon. If it findsone that reasonably obeys Kozak’s rules, it will begin translation at that site. In prokaryotes, sequences in the 16S ribosomal RNA bind to a Shine-Dalgarno sequences which positions the ribosome to initiate translation at an AUG codon a few nucleotides downstream from the SD sequenceg. A, P, and E sitesi. Initiation: once the ribosome is positioned on a “good” AUG codon, an initiator tRNA is brought into the P site to begin translation.ii. Elongation: another tRNA binds to the A site (next to the P site). A peptide bond is formed between the first amino acid and the second. Theinitiator tRNA then leaves (through the E site) when the ribosome translocates to the next codon. This process continues with new tRNAs binding to the A site. iii. Termination: a stop codon is reached on the mRNA strand. The presence of the stop codon in the A site causes the ribosome to dissociate from themRNA and the polypeptide to break off from the tRNAIII. Consensus sequence: a consensus sequence is the collective sequence of multiple strands of DNA based on the most common bases. IV. Degenerate genetic code: this means that more than one codon can code for a singleamino