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Chapter 13

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University of Toronto Scarborough
Biological Sciences

 Chapter 13  Gene Structure and Expression  13.1 The Connection between DNA, RNA, and Protein  13.1a Genes Specify Either Protein or RNA Products  Archibald Garrod – studied alkaptonuria  causes urine to turn black  Studied families with William Bateson  Concluded:  It is an inherited trait  They excrete homogentisic acid, that should be metabolized  It is an inborn error of metabolism  Relationship = Genes & metabolism  George Beadle and Edward Tatum – studied Neurospora crassa orange bread mold growing on minimal medium (MM)  They exposed spores to X-rays that would cause mutations  Concluded:  Some mutants wouldn’t grow unless MM had additional nutrients – auxotroph (nutritional mutants)  Auxotroph’s had a defect in gene coding for an enzyme that would synthesize a nutrient that would be added to MM  Wild-type (control could make nutrients for itself from taw materials in MM. By testing specific nutrients, they found that it needed Arginine, it didn’t have the enzyme to synthesize it.  Arginine auxotroph’s = arg mutants. Synthesis of arg is multistep  found that different arg mutants have defects in different enzymes and block growth at different steps  each step controlled by a gene that encoded the enzyme for the step  One gene-one enzyme hypothesis – relationship b/w genes & enzymes  restated one gene-one polypeptide hypothesis – because some proteins consist of more than one polypeptide and not all proteins are enzymes  Figure 13.2  experiment  Blocks in order Ornithine (argE blocked) , Citrulline (argF blocked) , Argininosuccinate (argG blocked) , Arginine (argH blocked)  13.1b The Pathway from Gene to Polypeptide Involves Transcription and Translation  Transcription – information encoded in DNA is made into a complementary RNA copy  Translation – use information encoded in RNA to assemble amino acids into a polypeptide  Francis Crick – “Central Dogma” – flow of info. From DNA  RNA  protein  Transcription: RNA polymerase creates RNA complementary to DNA  complementary base pairing.  Template strand – read by RNA polymerase  Messenger RNA – transcribed from a gene encoding a polypeptide  Translation: ribosome – particle on which amino acids are linked into polypeptide chains move along mRNA, amino acids specified by mRNA are joined one by one to form polypeptide.  Prokaryotes  transcription and translation occurs at the same time  Eukaryotes  transcription and process mRNA in nucleus, translation in cytoplasm on ribosomes  13.1c The Genetic Code is written in Three-Letter Words Using a Four-Letter Alphabet  DNA Alphabet = A,T,C,G  RNA Alphabet = A,U (uracil),C,G  T replaces U  Breaking the Genetic Code:  Genetic code – nucleotide information that specifies the amino acid sequence of a polypeptide  mRNA uses 3 bases out of 4  20 amino acids with 64 combinations  Codon – three-letter sequence of RNA nucleotides for amino acids  Transcription – RNA polymerase reads 3’-5’ DNA template strand and makes complementary RNA (A = U)  Translation – each codon designates an amino acid in the resulting polypeptide  Marshall Nirenberg and Philip Leder – identified most codons and that codons bind to ribosomes and cause a transfer RNA (tRNA) with its linked amino acid to bind to the ribosome.  H. Ghobind Khorana – made artificial mRNAs with only one nucleotide repeated  added to ribosomes  amino acids  polypeptide chains  Niernberg, Leder, Khorana identified the coding assignments of all codons  Features of Genetic Code:  Start codon – AUG, it is the first codon translated in any mRNA in prokaryotic & eukaryotic cells  Stop codons – three codons that don’t specify amino acids UAA UAG UGA that indicate the end of a polypeptide encoding sequence.  Degeneracy – there are many synonyms in the nucleic code for amino acids  Commaless – words of the nucleic acid code are sequential, with no indicators to mark the end of one codon and the start of another  ONE correct reading frame for mRNA – due to Commaless it can only be read correctly at the start of the codon  Universal – few exceptions, same codons specify the same amino acids in all living organisms and viruses.  early in evolution  13.2 Transcription: DNA Direction RNA Synthesis  In transcription (NOT DNA replication):  Only 1 strand is the template – NOT both strands  Only the sequence encoding part of a gene is the template – NOT full strand  RNA polymerases catalyze nucleotide into RNA strand – NOT DNA poly.  RNA  single polypeptide chains – NOT double  13.2a Transcription Proceeds in Three Steps  Gene = promoter – control sequence for transcription + transcription unit – section of genes that is copied into RNA molecule  Initiation – molecular machinery that carries out transcription assembles at the promoter and begins synthesizing an RNA copy of the gene  Elongation – RNA polymerase moves along the gene extending the RNA chain  Termination – transcription ends and the RNA molecule – the transcript – and the RNA polymerase are released from the DNA template  When RNA polymerase started transcription, another one starts when there is room at promoter  continues till it is closely on a gene, making RNA transcript.  Roger Kornberg – described the molecular structure of the eukaryotic transcription apparatus and how it acts in transcription  Figure 13.6 gene RNA polymerase II - 2 types of specific DNA sequences organizatio enzymes that called terminators - signal the end n transcribed protein of transciption of the gene after elongation coding genes, cannot they are transcibed. Similarites Eukabind to DNA; it goes to Prokar1. terminator sequence on mRNA promoter once uses complementary base-pairing transcription factors with itself to form a hairpin have bound. bacteria - RNA 2. a protein binds to a particular polymerase binds to terminator sequence on the DMA --> it is directed to mRNA. promoter by a protein Both trigger the terminaton of factor that is released transciption and the release of the once transciption begins RNA and RNA polymerase from the template.   13.2b Transcription of Non-Protein-Coding Genes Occurs in a Similar Way  Eurkaryotes: RNA polymerase II - transcribes protein-coding genes, RNA polymerase III - transcribes tRNA genes and the gene for 1 rRNAs, RNA polymerase I - transcribes genes for the 3 other rRNAs. Promoters are specialized for the assembly of coding transcription machinery (correct RNA polymerase type)  Bacteria: single type of RNA polymerase transcribes all genes. Promoters same. ^  13.3 Processing of mRNAs in Eukaryotes  13.3a Eukaryotic Protein-Coding Genes Are Transcribed into Precursor mRNAs That Are Modified in the Nucleus  Eukaryotic protein-coding gene is transcribed into a precursor mRNA (pre- mRNA) that is processed in the nucleus to produce translatable mRNA  cytoplasm  Modifications of Pre-mRNA and mRNA ends:  At 5’ end of Pre-mRNA is 5’ guanine cap  Capping enzyme adds this after RNA polymerase II begins transcription  Cap connected to the chain by 3 P groups remains when pre-mRNA is processed to mRNA  Cap protects mRNA from degradation & its where ribosomes attach at the start of translation  Transcription of eukaryotic gene:  NO terminator sequence  instead near 3’ end of gene is a DNA sequence that is transcribed into pre-mRNA. Proteins bind to the polyadenylation signal in the RNA and cleave it downstream  signals RNA polymerase to stop transcribing. Enzyme poly(A) polymerase adds chain 50-250 adenine nucleotides (one at a time) to the new 3’ end of pre-nRNA NO complementary BP (poly T)  Poly (A) Tail – string of adenine nucleotide enables the mRNA produced from the pre-mRNA to be translated efficiently and protects it from attack by RNA- digesting enzymes in the cytoplasm  Figure 13.7  Sequences Interrupting the Protein-Coding Sequence:  Introns – transcribed into pre-mRNAs but are removed from pre-mRNAs during processing in the nucleus.  Exons – amino acid-coding sequences retained in finished mRNAs from ^  13.3b Introns Are Removed During Pre-mRNA Processing to Produce Translatable mRNA  mRNA splicing – in the nucleus, it’s the removal of introns from pre-
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