William S. Klug Michael R. Cummings Charlotte A William S. Klug Michael R. Cummings Charlotte A. Spencer Concepts of Genetics Eighth Edition Chapter 13 The Genetic Code and Transcription Copyright © 2005 Pearson Prentice Hall, Inc.

Figure 13-1 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-1 Flow of genetic information encoded in DNA to messenger RNA to protein. Figure 13-1 Copyright © 2006 Pearson Prentice Hall, Inc.

The Genetic Code Exhibits a Number of Characteristics • linear, from mRNA • triplet • unambiguous • degenerate • start and stop signals • commaless • nonoverlapping •nearly universal

Early Studies Established the Basic Operational Patterns of the Code The Triplet Nature of the Code 43 = 64

Figure 13-2 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-2 The effect of frameshift mutations on a DNA sequence repeating the triplet sequence GAG. (a) The insertion of a single nucleotide shifts all subsequent triplet reading frames. (b) The insertion of three nucleotides changes only two codons, but the frame of reading is then reestablished to the original sequence. Figure 13-2 Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-2a Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-2a The effect of frameshift mutations on a DNA sequence repeating the triplet sequence GAG. (a) The insertion of a single nucleotide shifts all subsequent triplet reading frames. (b) The insertion of three nucleotides changes only two codons, but the frame of reading is then reestablished to the original sequence. Figure 13-2a Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-2b Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-2b The effect of frameshift mutations on a DNA sequence repeating the triplet sequence GAG. (a) The insertion of a single nucleotide shifts all subsequent triplet reading frames. (b) The insertion of three nucleotides changes only two codons, but the frame of reading is then reestablished to the original sequence. Figure 13-2b Copyright © 2006 Pearson Prentice Hall, Inc.

The Nonoverlapping Nature of the Code The Commaless and Degenerate Nature of the Code

Studies by Nirenberg, Matthaei, and Others Led to Deciphering of the Code Synthesizing Polypeptides in a Cell-Free System

Figure 13-3 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-3 The reaction catalyzed by the enzyme polynucleotide phosphorylase. Note that the equilibrium of the reaction favors the degradation of RNA, but can be “forced” in the direction favoring synthesis. Figure 13-3 Copyright © 2006 Pearson Prentice Hall, Inc.

Homopolymer Codes

Table 13-1 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-1 Incorporation of 14C-Phenylalanine into Protein Table 13-1 Copyright © 2006 Pearson Prentice Hall, Inc.

Mixed Copolymers

Figure 13-4 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-4 Results and interpretation of a mixed copolymer experiment in which a ratio of is used Figure 13-4 Copyright © 2006 Pearson Prentice Hall, Inc.

The Triplet Binding Assay

Figure 13-5 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-5 An example of the triplet-binding assay. The UUU triplet acts as a codon, attracting the complementary tRNAphe anticodon AAA. Figure 13-5 Copyright © 2006 Pearson Prentice Hall, Inc.

Table 13-2 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-2 Amino Acid Assignments to Specific Trinucleotides Derived from the Triplet-Binding Assay Table 13-2 Copyright © 2006 Pearson Prentice Hall, Inc.

Repeating Copolymers

Figure 13-6 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-6 The conversion of di-, tri-, and tetranucleotides into repeating copolymers. The triplet codons produced in each case are shown. Figure 13-6 Copyright © 2006 Pearson Prentice Hall, Inc.

Table 13-3 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-3 Amino Acids Incorporated Using Repeated Synthetic Copolymers of RNA Table 13-3 Copyright © 2006 Pearson Prentice Hall, Inc.

The Coding Dictionary Reveals Several Interesting Patterns among the 64 Codons

Figure 13-7 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-7 The coding dictionary. AUG encodes methionine, which initiates most polypeptide chains. All other amino acids except tryptophan, which is encoded only by UGG, are represented by two to six codons. The codons UAA, UAG, and UGA are termination signals and do not encode any amino acids. Figure 13-7 Copyright © 2006 Pearson Prentice Hall, Inc.

Degeneracy and the Wobble Hypothesis

Table 13-4 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-4 Anticodon–Codon Base-Pairing Rules Table 13-4 Copyright © 2006 Pearson Prentice Hall, Inc.

The Ordered Nature of the Code (similar amino acids share middle bases) Initiation, Termination

The Genetic Code Is Nearly Universal

Table 13-5 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-5 Exceptions to the Universal Code Table 13-5 Copyright © 2006 Pearson Prentice Hall, Inc.

Different Initiation Points Create Overlapping Genes

Figure 13-8 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-8 Illustration of the concept of overlapping genes. (a) An mRNA sequence initiated at two different AUG positions out of frame with one another will give rise to two distinct amino acid sequences. (b) The relative positions of the sequences encoding seven polypeptides of the phage Figure 13-8 Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-8a Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-8a Illustration of the concept of overlapping genes. (a) An mRNA sequence initiated at two different AUG positions out of frame with one another will give rise to two distinct amino acid sequences. (b) The relative positions of the sequences encoding seven polypeptides of the phage Figure 13-8a Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-8b Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-8b Illustration of the concept of overlapping genes. (a) An mRNA sequence initiated at two different AUG positions out of frame with one another will give rise to two distinct amino acid sequences. (b) The relative positions of the sequences encoding seven polypeptides of the phage Figure 13-8b Copyright © 2006 Pearson Prentice Hall, Inc.

Transcription Synthesizes RNA on a DNA Template

Studies with Bacteria and Phages Provided Evidence for the Existence of mRNA

Table 13-6 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-6 Base Compositions (in mole percents) of RNA Produced Immediately Following Infection of E. Coli by the Bacteriophages T2 and T7 in Contrast to the Composition of RNA of Uninfected E. Coli Table 13-6 Copyright © 2006 Pearson Prentice Hall, Inc.

RNA Polymerase Directs RNA Synthesis

Figure 13-9 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-9 The early stages of transcription in prokaryotes, showing (a) the components of the process; (b) template binding at the site involving the sigma subunit of RNA polymerase and subsequent initiation of RNA synthesis; and (c) chain elongation, after the sigma subunit has dissociated from the transcription complex and the enzyme moves along the DNA template. Figure 13-9 Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-9a Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-9a The early stages of transcription in prokaryotes, showing (a) the components of the process; (b) template binding at the site involving the sigma subunit of RNA polymerase and subsequent initiation of RNA synthesis; and (c) chain elongation, after the sigma subunit has dissociated from the transcription complex and the enzyme moves along the DNA template. Figure 13-9a Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-9b Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-9b The early stages of transcription in prokaryotes, showing (a) the components of the process; (b) template binding at the site involving the sigma subunit of RNA polymerase and subsequent initiation of RNA synthesis; and (c) chain elongation, after the sigma subunit has dissociated from the transcription complex and the enzyme moves along the DNA template. Figure 13-9b Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-9c Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-9c The early stages of transcription in prokaryotes, showing (a) the components of the process; (b) template binding at the site involving the sigma subunit of RNA polymerase and subsequent initiation of RNA synthesis; and (c) chain elongation, after the sigma subunit has dissociated from the transcription complex and the enzyme moves along the DNA template. Figure 13-9c Copyright © 2006 Pearson Prentice Hall, Inc.

Promoters, Template Binding, and the Sigma Subunit Initiation, Elongation, and Termination of RNA Synthesis

Transcription in Eukaryotes Differs from Prokaryotic Transcription in Several Ways Heterogeneous Nuclear RNA and Its Processing: Caps and Tails

Figure 13-10 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-10 Posttranscriptional RNA processing in eukaryotes. Heterogeneous nuclear RNA (hnRNA) is converted to messenger (mRNA), which contains a cap and a -poly-A tail, which then has introns spliced out. Figure 13-10 Copyright © 2006 Pearson Prentice Hall, Inc.

Table 13-7 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-7 RNA Polymerases in Eukaryotes Table 13-7 Copyright © 2006 Pearson Prentice Hall, Inc.

The Coding Regions of Eukaryotic Genes Are Interrupted by Intervening Sequences

Figure 13-11 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-11 An electron micrograph and an interpretive drawing of the hybrid molecule (heteroduplex) formed between the template DNA strand of the chicken ovalbumin gene and the mature ovalbumin mRNA. Seven DNA introns, A–G, produce unpaired loops. Figure 13-11 Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-12 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-12 Intervening sequences in various eukaryotic genes. The numbers indicate the number of nucleotides present in various intron and exon regions. Figure 13-12 Copyright © 2006 Pearson Prentice Hall, Inc.

Table 13-8 Copyright © 2006 Pearson Prentice Hall, Inc. Table 13-8 Contrasting Human Gene Size, mRNA Size, and the Number of Introns Table 13-8 Copyright © 2006 Pearson Prentice Hall, Inc.

RNA Editing Substitution editing Insertion/deletion editing (guide RNA)

Transcription Has Been Visualized by Electron Microscopy

Figure 13-15 Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-15 Electron micrographs and interpretive drawings of simultaneous transcription of genes in E. coli (a) and Notophthalmus (Triturus) viridescens (b). (a) O.L. Miller, Jr. Barbara A. Hamkalo, C.A. Thomas, Jr. Science 169:392–395, 1970 by the American Association for the Advancement of Science. F:2. Figure 13-15 Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-15a Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-15a Electron micrographs and interpretive drawings of simultaneous transcription of genes in E. coli (a) and Notophthalmus (Triturus) viridescens (b). (a) O.L. Miller, Jr. Barbara A. Hamkalo, C.A. Thomas, Jr. Science 169:392–395, 1970 by the American Association for the Advancement of Science. F:2. Figure 13-15a Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 13-15b Copyright © 2006 Pearson Prentice Hall, Inc. Figure 13-15b Electron micrographs and interpretive drawings of simultaneous transcription of genes in E. coli (a) and Notophthalmus (Triturus) viridescens (b). (a) O.L. Miller, Jr. Barbara A. Hamkalo, C.A. Thomas, Jr. Science 169:392–395, 1970 by the American Association for the Advancement of Science. F:2. Figure 13-15b Copyright © 2006 Pearson Prentice Hall, Inc.