Chapter 13 The Genetic Code and Transcription Summary page 1 The Genetic Code Uses Ribonucleotide Bases as Letters o General Features that Characterize the Genetic Code Written in linear form using letters ribonucleotide bases that compose mRNA molecules ribonucleotide sequence is derived from the complementary nucleotide bases in DNA Consists of triplet codes called codons Unambiguous each codon specifies only a single amino acid Degenerate a given amino acid can be specified by more than one codon this is the case for 18 or 20 amino acids Contains one start and three stop signals that initiate and terminate translation Commaless no punctuation Nonoverlapping Codons in a gene are collinear with the sequence of amino acids making up the encode protein Universal with minor exceptions coding dictionary used by viruses prokaryotes archaea and eukayotes Francois Jacob and Jacques Monod discovered messenger RNA Nirenber Matthaei and Others Lead to Deciphering of the Code o Used enzyme Polynucleotide Phosphorylase which allowed the production of synthetic mRNAs doesn t require a DNA template o To trace the progress of protein synthesis one or more of the amino acids must be radioactive o In vivo polynucleotide phosphorylase degrades RNA o In vitro in high concentrations can force the reaction in the opposite direction synthesizing RNA RNA Homopolymers are RNA molescules containing only one type of ribonucleotide UUUU AAAA CCCC or GGGGGG o UUU phenylalaine AAA lysine CCC proline RNA Heteropolymers are two or more different ribonucleoside diphospgate were used in combination Triplet binding assay by Nirenburg and Leder lead to specific assignments of triplet combinations o Observed that ribosomes bind to the codons and form a similar complex as in vivo o RNA has a complementary codon to the ribosome Gobind Khorana chemically synthesized long RNA molecules Coding Dictionary o 61 codons assigned to amino acids remaining three are termination signals o UAA UAG UGA stop o AUG start methionine o UGG tryptophan is only represented by one codon The Wobble Hypothesis Crick o Predicted that the initial two ribonucleotides of triplet codes are often more critical than the third member in attracting the correct tRNA o hydrogen bonding at the third position of the codon anticodon interaction would be less spatially constrained and need not adhere as strictly to the established base pairing rules o The fact that chemically similar amino acids often share one or two middle bases in the Ordered Genetic code different triplets encoding for them Initiation Codons o In vivo highly specific o In bacteria the initial amino acid inserted into all polypeptide chains is modified form of methionine N formylmethionine Chapter 13 The Genetic Code and Transcription Summary page 2 Termination Codons o In bacteria either the formyl group is removed from the initial methionine upon completion of synthesis of a protein or the entire formylmethionine residue is removed o In eukaryotes unformylated methionine is the initial amino acid of polypeptide synthesis methionine residue may also be cleared from the polypeptide o Do not code for any amino acid o Are not recognized by a tRNA molecule o Mutations that produce any of the three codons internally in a gene also result in termination Only a partial polypeptide is synthesized since it is prematurely released from the ribosome Called a nonsense mutation MS2 o A bacteriophage that infects bacteria o Only has three genes o The amino acid sequence was completed in 1970 and the nucleotide sequence of the gene and a number of nucleotides on each end of it were reported in 1972 o Comparing genes and its encoded proteins collinear The linear sequence of triplet codons formed by the nucleotides corresponds precisely with the linear sequence of amino acids in the protein Genetic Code is NEARLY Universal o The codon UGA normally codes termination but specifies the insertions of tryptophan during translation in yeast and human mitochondria Different Initiation points create overlapping genes will be deleterious or lethal Transcription o A single mutation may affect more than one protein thus increase the chances that the change o The process by which RNA molecules are synthesized on a DNA template DNA is in the nucleus but protein synthesis occurs in the cytoplasm in eukaryotes RNA is synthesized in the nucleus then migrates to the cytoplasm RNA is generally proportional to the amount of protein in a cell RNA polymerase o Directs RNA synthesis o Similar to DNA polymerase except the substrate nucleotides contain the ribose rather than the deoxyribose Subunit of RNA polymerase o No primer is required to initiate synthesis o Holoenzyme o Sigma Factor Transcription in Prokaryotes Subunit of RNA polymerase Plays a regulatory function in the initiation of RNA transcription o Template binding occurs where RNA polymerase sigma subunit recognizes the promoter 5 region strand o The helix is then denatured o Transcription start site is typically where transcription begins o DNA is then converted from its double stranded form to its open structure exposing the templte o RNA polymerase then initiates RNA synthesis no primer required o Ribonucleotie complements are inserted and linked together by phosphodiester bonds 5 3 Chapter 13 The Genetic Code and Transcription Summary page 3 o Creates an antiparallel temporary duplex of DNA and RNA o Reaches a stop codon which is folded back onto itself called a hairpin secondary structure held together by hydrogen bonds o It can also be a termination factor rho a large hexameric protein that physicallt interacts with the growing RNA transcript facilitating termination o When termination is achieved RNA is released from DNA o Polycistronic mRNA is where genes with similar proteins are often clustered together along the chromosome in eukaryotes Monocistronic mRNA Transcription in Eukaryotes if different than Prokaryotes o Occurs in the nucleus under the direction of three separate forms of RNA polymerase o mRNA must move out of the nucleus into the cytoplasm o Initiation requires compact chromatin fiber chromatin remodeling when the helix is opened when chromosome structure is changed o Relies on transcription factors to scan and bind to DNA o Promotors are required o Pre mRNA heterogeneous nuclear RNA 25 are converted to mRNA mRNA tRNA o Initation RNA Polymerase II depends on cis acting elements and trans acting elements Four cis acting elements o Core