9 3 2015 The Central Dogma Central Dogma Differences between RNA and DNA Gene A and gene B can be transcribed at different rates producing different amounts of RNA within the same cell RNA molecules can fold into specific 3D shapes nucleotide sugar is ribose uses uracil instead of thymine typically single stranded Transcription produces an RNA molecule that is complementary to the template strand of DNA have catalytic and structural functions 1 9 3 2015 Polymerases 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 Specific sequences tell bacterial RNA polymerase where to start promoter and stop terminator transcription the sigma factor subunit of RNA polymerase recognizes the promoter the DNA is unwound and transcription begins 2 9 3 2015 Transcription 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 General transcription factors are required for RNA pol II initiation TFIID TBP 11 TAF subunits The TBP subunit of TFIID distorts the DNA double helix TFIIB recognizes the distorted DNA Eukaryotic RNAs are processed prior to export from the nucleus 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 nucleosomes 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 phase mRNAs are capped and polyadenylated 3 9 3 2015 The 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 sequences Proteins initially bound to RNA pol II mediate RNA processing Alternative splicing increases protein diversity Phosphorylation of the tail of RNA polymerase II allows RNA processing proteins To assemble there Only properly processed mRNAs are exported from the nucleus to the cytoplasm The primary transcript of a gene can sometimes be spliced differently so that different exons can be stitched together to produce distinct proteins proteins that recognize the mRNA modifications bind to the RNA and interact with the nuclear pore complex to allow export 4 9 3 2015 How 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 Transfer RNAs tRNAs link codons to amino acids The rules by which the nucleotide sequences of a gene through an intermediary mRNA molecule is translated into the amino acid sequence of a protein 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 tRNA synthetases connect amino acids to the correct tRNA tRNA linkage is proofed in two steps Does the amino acid fit in the synthesis site Is the amino acid excluded from the editing site 20 different synthetases 5 9 3 2015 Ribosomes are made of proteins and rRNAs Ribosomes have binding sites for mRNA and tRNA Small subunit matches tRNA to codons Large subunit catalyzes peptide bond formation A aminoacyl tRNA P peptidyl tRNA E exit General process of translation rRNAs catalyze the formation of the peptide bond ex of a ribozyme form the mRNA and tRNA binding sites Peptide bonds form between an aminoacy tRNA and a peptidyl tRNA positioned in the A and P sites of the ribosome Initiation of translation eIF eukaryotic initiation factors Elongating the peptide chain EF elongation factors peptidyl transferase 6 9 3 2015 Termination of translation A polyribosome or polysome is a single mRNA with multiple ribosomes attached and translating Stop codons UAA UAG UGA Protein folding begins before the completion of translation Proteins are degraded by proteases during proteolysis in proteasomes 19S cap 20S core 19S cap Abnormally folded and short lifespan proteins are tagged with ubiquitin and are targeted to the proteasome 7