GCD 3022 1st Edition Lecture 18Outline of Last Lecture I. Transcription DefinitionII. Gene expressiona. Structural genesb. mRNAc. central dogma of genetics III. Overview of Transcriptiona. Regulation of RNA synthesisb. Role of proteinsc. Gene expressionIV. Functions of RNA transcriptsa. Polypeptidesb. RNA moleculesc. Nonstructural genesV. Transcription in bacteriaa. Promotersb. Initiationi. RNA polymeraseii. HoloenzymeThese 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 complexesc. Elongationi. Overview ii. Template and coding strandsd. Terminationi. Overviewii. Termination mechanisms in E. coliVI. Transcription in Eukaryotesa. Major differencesb. RNA polymerasesi. RNA polymerase Iii. RNA polymerase IIiii. RNA polymerase IIIc. Sequences of Eukaryotic structural genesi. Core promoterii. Regulatory elementsiii. Transcription factorsiv. Cis and Trans acting elementsVII. RNA modificationa. Colinearity of gene expressionb. RNA splicing/excisioni. Intronsii. Exonsiii. Spliceosome and subunitsiv. snRNP’sv. Intron advantagec. Processingd. Cappingi. Overviewii. 7-methylgaunosine cape. Polyadenylation (tailing)i. polyA tailii. mechanismVIII. Identification of Introns via microscopya. The experimentb. The resultIX. RNA editinga. Common types of editingi. Addition or deletion of basesii. Conversion of basesOutline of Current LectureI. 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 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 bacteriaCurrent LectureI. Protein synthesis reviewa. Structural genes: genes that encode polypeptides. Also called protein-encoding genes. These genes are transcribed into mRNAb. Translation: mRNA is translated into functional proteinsII. Codons: groups of three nucleotides in mRNA that code for amino acids, the buildingblocks of proteinsa. 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 universalb. Special codons: there are “start” and “stop” codons that code for the initiation oftranslation 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 chaina. Directionality: synthesized in 5’ to 3’ direction (parallel to orientation of mRNA)b. Amino groupsi. 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 hydrophilicc. 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 addedIV. Structure of proteinsa. Levels of structurei. Primary: amino acid sequence, while being translated folding will occur, which may be aided by chaperonesii. Secondary: can be alpha helix or beta sheet (or a combination), stabilized by hydrogen bonds between atoms located in the polypeptide backboneiii. 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 interactionsiv. Quaternary: protein complexes made up of two or more polypeptides, this is usually the final structure of a functional proteinb. Function of proteinsi. Relationship between function and structure: a protein’s structure determines its functionii. Enzymes: a category of proteins that catalyze reactions including chemicalmodifications, cleavage, and synthesisV. Structure and function of tRNAa. Adaptor hypothesis: founded by Francis Crick in 1950’s; stated that tRNAs play a direct role in the recognition of codons in the mRNAb. tRNA has two functions: recognizing a 3-base codon in mRNA and carrying an amino acid that is specific for that codonc. Common structural featuresi. 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 lookslike a cloverleaf; it contains:1. Three stem-loop structures2. A few variable sites3. 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 aminoacyl-tRNAsynthetases (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 1966VI. Functional sites of ribosomesa. 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 subunitb. Ribosome sites: peptidyl site (P site), aminoacyl site (A site), and exit site (E site)VII. Stages of translationa. Initiationi. Initiation complex: made up of mRNA, initiator tRNA, and ribosomal subunitsii. Start codon: sequence in mRNA that is recognized by initiator tRNAiii. Binding of mRNA to 30S subunit: facilitated by a ribosomal-binding site, or Shine-Dalgarno sequenceiv. Eukaryote initiation summary: assembly of initiation complex is similar to bacteria but additional factors are required (eukaryotic initiation factors (eIF)); also the