9/3/20151Central Dogma The Central DogmaGene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell.Differences between RNA and DNA• nucleotide sugar is ribose• uses uracil instead of thymine• typically single strandedRNA molecules can fold into specific 3D shapes.-have catalytic and structural functionsTranscription produces an RNA molecule that is complementary to the template strand of DNA.9/3/20152Polymerases catalyze the formation of phosphodiester bonds.RNA polymerases mediate transcription.Genes are transcribed by many RNA polymerases at the same time.A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecule’s synthesis is completed.Bacterial transcription• the sigma factor subunit of RNA polymeraserecognizes the promoter• the DNA is unwound and transcription beginsSpecific sequences tell bacterial RNA polymerase where to start (promoter) and stop (terminator) transcription.9/3/20153Transcription in bacteria • The sigma subunit of bacterial RNA polymerase recognizes promoter sites in the DNA.• RNA polymerase (along with its sigma subunit) can initiate transcription on its own.• Bacterial cells contain a single RNA polymerase. • Bacterial cells lack nucleosomes.Eukaryotic transcription differs from prokaryotic transcription.• Three types of RNA polymerases transcribe different types of genes• Transcription factors are needed to initiate transcription• Initiation requires dealing with nucleosomesEukaryotic transcriptionGeneral transcription factors are required for RNA pol II initiation• TFIID = TBP + 11 TAF subunits• TFIIB recognizes the distorted DNAThe TBP subunit of TFIID distortsthe DNA double helix.Eukaryotic transcription• TFIIF – stabilizes interaction between RNA pol II & TFIID/B• TFIIE – recruits TFIIH• TFIIH– unwinds DNA at start site– phosphorylates RNA pol II CTD• After phosphorylation, RNA pol II disassociates from the TFs and enters elongation phaseEukaryotic RNAs are processed prior to export from the nucleus.mRNAs are cappedand polyadenylated.9/3/20154The coding regions (exons) of eukaryotic genes are interrupted by introns.Splicing removes the introns and is mediated splicesomes.Splicesomes• consist of multiple small nuclear ribonucleoproteins(snRNPs) which contain small nuclear RNAs (snRNAs) and proteins• recognize specific RNA sequencesProteins initially bound to RNA pol II mediate RNA processing.Phosphorylation of the tail of RNA polymerase II allows RNA processing proteinsTo assemble there Alternative splicing increases protein diversity.The primary transcript of a gene can sometimes be spliced differently so that different exons can be stitched together to produce distinct proteins Only properly processed mRNAs are exported from the nucleus to the cytoplasm.-proteins that recognize the mRNA modifications bind to the RNA and interact with the nuclear pore complex to allow export9/3/20155How is RNA read?• groups of 3 nucleotides (codons) encode individual amino acids• the genetic code is redundant: Several different codons can specify a single amino acid.• three possible reading frames• The rules by which the nucleotide sequences of a gene, through an intermediary mRNA molecule, is translated into the amino acid sequence of a proteinTransfer RNAs (tRNAs) link codons to amino acids.61 amino acid encoding codons, ?? tRNAs, 20 amino acids• some amino acids are attached to multiple tRNAs• some transfer RNAs can bind multiple codons– wobble in the third base pair(The number of tRNAs encoded by a genome varies from organism to organism.)In tRNA charging, aminoacyl-tRNAsynthetases connect amino acids to the correct tRNA.20 different synthetasestRNA linkage is proofed in two steps• Does the amino acid fit in the synthesis site?• Is the amino acid excluded from the editing site?9/3/20156Ribosomes are made of proteins and rRNAs.• Small subunit– matches tRNA to codons• Large subunit– catalyzes peptide bond formationRibosomes have binding sites for mRNA and tRNA.A = aminoacyl-tRNAP = peptidyl-tRNAE = exitrRNAs– catalyze the formation of the peptide bond (ex. of a ribozyme)– form the mRNA and tRNA binding sitesGeneral process of translationPeptide bonds form between an aminoacy-tRNA and a peptidyl-tRNApositioned in the A and P sites of the ribosomeInitiation of translationeIF = eukaryotic initiationfactorsElongating the peptide chainEF = elongationfactorspeptidyl transferase9/3/20157Termination of translationStop codons: UAA, UAG, UGAA polyribosome or polysome is a single mRNA with multiple ribosomes attached and translating.Protein folding begins before the completion of translation.Proteins are degraded by proteases during proteolysis in proteasomes.20S core19S cap19S capAbnormally folded and short lifespan proteins are tagged with ubiquitin and are targeted to the