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 Codeo 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 radioactiveo In vivo, polynucleotide phosphorylase degrades RNAo 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 combinationso Observed that ribosomes bind to the codons and form a similar complex as in vivoo RNA has a complementary codon to the ribosome- Gobind Khorana chemically synthesized long RNA molecules- Coding Dictionaryo 61 codons assigned to amino acids, remaining three are termination signalso UAA,UAG, UGA= stopo 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 tRNAo hydrogen bonding at the third position of the codon-anticodon interaction would be less spatiallyconstrained and need not adhere as strictly to the established base pairing rules- Ordered Genetic code o The fact that chemically similar amino acids often share one or two “middle” bases in the different triplets encoding for them- Initiation Codonso In vivo= highly specifico 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)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 removedo In eukaryotes, unformylated methionine is the initial amino acid of polypeptide synthesis, methionine residue may also be cleared from the polypeptide- Termination Codonso Do not code for any amino acido Are not recognized by a tRNA moleculeo 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- MS2o A bacteriophage that infects bacteria o Only has three geneso The amino acid sequence was completed in 1970 and the nucleotide sequence of the gene anda number of nucleotides on each end of it were reported in 1972o 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 Universalo The codon UGA normally codes termination but specifies the insertions of tryptophan during translation in yeast and human mitochondria - Different Initiation points create overlapping geneso A single mutation may affect more than one protein thus increase the chances that the change will be deleterious or lethal- Transcriptiono 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 polymeraseo Directs RNA synthesiso Similar to DNA polymerase except the substrate nucleotides contain the ribose rather than the deoxyriboseo No primer is required to initiate synthesiso Holoenzyme- Subunit of RNA polymeraseo Sigma Factor- Subunit of RNA polymerase- Plays a regulatory function in the initiation of RNA transcription- Transcription in Prokaryoteso Template binding occurs where RNA polymerase sigma subunit recognizes the promoter (5’ region)o The helix is then denaturedo Transcription start site is typically where transcription beginso DNA is then converted from its double-stranded form to its open structure exposing the templte strando 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 RNAo 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 terminationo When termination is achieved, RNA is released from DNAo 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 polymeraseo mRNA must move out of the nucleus into the cytoplasmo Initiation requires compact chromatin fiber; chromatin remodeling- when the helix is opened, when chromosome structure is changedo Relies on transcription factors to scan and bind to DNAo Promotors are requiredo Pre-mRNA, heterogeneous nuclear RNA (25% are converted to mRNA), mRNA, tRNAo Initation:- RNA Polymerase