Chapter 8 Microbial Genetics

Q&A E. coli is found naturally in the human large intestine, and there it is beneficial. However, the strain designated E. coli O157:H7 produces Shiga toxin. How did E. coli acquire this gene from Shigella?

Learning Objectives Upon completing this chapter, you should be able to: Define genetics, genome, chromosome, gene, genetic code, genotype, phenotype, and genomics Describe how DNA serves as genetic information Describe the process of DNA replication Describe protein synthesis, including transcription and translation Compare protein synthesis in prokaryotes and eukaryotes Explain the regulation of gene expression in bacteria by induction, repression, and catabolite repression Describe how the Lac operon works Classify mutations by type Define mutagen and provide examples Describe 2 ways in which mutations can be repaired Outline the methods of direct and indirect selection of mutants Define horizontal and vertical gene transfer Compare the mechanisms of genetic recombination in bacteria Describe the functions and usefulness of plasmids and transposons Define translation, transduction, and conjugation and describe how each can occur Discuss how genetic mutation and recombination provide material for natural selection to act upon

Terminology Genetics: The study of what genes are, how they carry information, how information is expressed, and how genes are replicated Gene: A segment of DNA that encodes a functional product, usually a protein Chromosome: Structure containing DNA that physically carries hereditary information; the chromosomes contain the genes Genome: All the genetic information in a cell

Terminology Genomics: The molecular study of genomes Genotype: The genes of an organism (genetic makeup) Phenotype: Expression of the genes (physical appearance)

E. coli Figure 8.1a

Genetic Map of the Chromosome of E. coli Figure 8.1b

The Flow of Genetic Information Figure 8.2

DNA Polymer of nucleotides: Adenine, thymine, cytosine, and guanine Double helix associated with proteins "Backbone" is deoxyribose-phosphate Strands are held together by hydrogen bonds between AT and CG Strands are antiparallel (complementary) Figure 8.3b

Semiconservative Replication Figure 8.3a

DNA Synthesis Figure 8.4

DNA Synthesis DNA is copied by DNA polymerase In the 5'  3' direction Initiated by a primer Leading strand is synthesized continuously Lagging strand is synthesized discontinuously Forms Okazaki fragments primers are removed and Okazaki fragments joined by a DNA ligase

Table 8.1

Table 8.1

DNA Synthesis Figure 8.5

Replication of Bacterial DNA Figure 8.6

Replication of Bacterial DNA ANIMATION DNA Replication: Overview ANIMATION DNA Replication: Forming the Replication Fork ANIMATION DNA Replication: Replication Proteins

Transcription DNA is transcribed to make RNA (mRNA, tRNA, and rRNA) Transcription begins when RNA polymerase binds to the promoter sequence Transcription proceeds in the 5'  3' direction Transcription stops when it reaches the terminator sequence

Transcription Figure 8.7

The Process of Transcription Figure 8.7

The Process of Transcription ANIMATION Transcription: Overview ANIMATION Transcription: Process Figure 8.7

RNA Processing in Eukaryotes Figure 8.11

Translation mRNA is translated in codons (three nucleotides) Translation of mRNA begins at the start codon: AUG Translation ends at nonsense codons: UAA, UAG, UGA Figure 8.2

The Genetic Code 64 codons (61 are sense and 3 are nonsense) on mRNA encode the 20 amino acids The genetic code is degenerate tRNA carries the complementary anticodon Figure 8.2

The Genetic Code ANIMATION Translation: Overview ANIMATION Translation: Genetic Code ANIMATION Translation: Process

The Genetic Code Figure 8.8

Bacteria Undergo Simultaneous Transcription & Translation Figure 8.10

The Process of Translation Figure 8.9

The Process of Translation Figure 8.9

The Process of Translation Figure 8.9

The Process of Translation Figure 8.9

The Process of Translation Figure 8.9

The Process of Translation Figure 8.9

The Process of Translation Figure 8.9

The Process of Translation Figure 8.9

Regulation Constitutive genes are expressed at a fixed rate Other genes are expressed only as needed Repressible genes Inducible genes Catabolite repression

Operon ANIMATION Operons: Overview Figure 8.12

Induction- the process of turning on a gene - Repressor sits on operator; need an inducer to bind to repressor so the repressor moves, thus allowing gene expression. Figure 8.12

Induction Figure 8.12

Repression- inhibits gene expression and production of enzymes - the operon is on, synthesizing a gene product (tryptophan) Figure 8.13

Repression – once tryptophan is synthesized, it binds to the inactive repressor protein, making it active. It binds to the operator, so synthesis is turned off. ANIMATION Operons: Induction ANIMATION Operons: Repression Figure 8.13

Catabolite Repression (a) Growth on glucose or lactose alone (b) Growth on glucose and lactose combined Figure 8.14

Lactose present, no glucose = lac operon on Lactose + glucose present = lac operon off Figure 8.15

Mutation A change in the genetic material Mutations may be neutral, beneficial, or harmful Mutagen: Agent that causes mutations Spontaneous mutations: Occur in the absence of a mutagen

Mutation Base substitution (point mutation) Change in one base Missense mutation Change in one base Result in change in amino acid Figure 8.17a, b

Mutation Nonsense mutation Results in a nonsense codon Figure 8.17a, c

Mutation Frameshift mutation Insertion or deletion of one or more nucleotide pairs Figure 8.17a, d

The Frequency of Mutation Spontaneous mutation rate = 1 in 109 replicated base pairs or 1 in 106 replicated genes Mutagens increase to 10–5 or 10–3 per replicated gene ANIMATION Mutations: Types

Chemical Mutagens - Analogs Figure 8.19a

Chemical Mutagens - Analogs ANIMATION Mutagens Figure 8.19b

Radiation Ionizing radiation (X rays and gamma rays) causes the formation of ions that can react with nucleotides and the deoxyribose-phosphate backbone

Radiation UV radiation causes thymine dimers Figure 8.20

Repair Photolyases separate thymine dimers Nucleotide excision repair ANIMATION Mutations: Repair Figure 8.20

Selection Positive (direct) selection detects mutant cells because they grow or appear different Example: finding those microbes that are resistant to an antibiotic by growing cells on a plate containing the antibiotic biotic. Negative (indirect) selection detects mutant cells because they do not grow (looking for auxotrophs) Replica plating

Replica Plating Figure 8.21

Checking for possible mutagens or carcinogens: use the Ames Test Figure 8.22

Checking for possible mutagens or carcinogens: use the Ames Test Figure 8.22

Genetic Transfer and Recombination 1. Differentiate horizontal and vertical gene transfer. 2. Compare the mechanisms of genetic recombination in bacteria. 3. Describe the functions of plasmids and transposons.

Genetic Recombination Vertical gene transfer: Occurs during reproduction between generations of cells (parent to offspring). Horizontal gene transfer: The transfer of genes between cells of the same generation (cell to cell). ANIMATION Horizontal Gene Transfer: Overview

Genetic Recombination Exchange of genes between two DNA molecules Crossing over occurs when two chromosomes break and rejoin Figure 8.23

Genetic Recombination Figure 8.25

Genetic Transformation- naked DNA is picked up an incorporated into another cell ANIMATION Transformation Figure 8.24

Bacterial Conjugation Figure 8.26

Conjugation in E. coli Figure 8.27a

Conjugation in E. coli Figure 8.27b

Conjugation in E. coli ANIMATION F Factor ANIMATION Chromosome Mapping ANIMATION Conjugation: Overview ANIMATION Hfr Conjugation Figure 8.27c

Transduction by a Bacteriophage ANIMATION Generalized Transduction ANIMATION Specialized Transduction Figure 8.28

Q&A E. coli is found naturally in the human large intestine, and there it is beneficial. However, the strain designated E. coli O157:H7 produces Shiga toxin. How did E. coli acquire this gene from Shigella?

Plasmids Conjugative plasmid: Carries genes for sex pili and transfer of the plasmid Dissimilation plasmids: Encode enzymes for catabolism of unusual compounds R factors: Encode antibiotic resistance

R Factor, a Type of Plasmid mer = mercury resistance sul = sulfonamide resistance str = streptomycin resistance cml = chloramphenicol resistance tet = tetracycline resistance Figure 8.29

Transposons Segments of DNA that can move from one region of DNA to another Contain insertion sequences for cutting and resealing DNA (transposase) Complex transposons carry other genes, such as antibiotic resistance Figure 8.30a, b

Transposons Figure 8.30c

Transposons ANIMATION Transposons: Overview ANIMATION Transposons: Insertion Sequences ANIMATION Transposons: Complex Transposons

Genes and Evolution Genetic mutation and recombination provide material for natural selection to act upon!!!!

Genes and Evolution Mutations and recombination provide diversity Fittest organisms for an environment are selected by natural selection

Evolution - The evolution of WNV Clinical Focus, p. 223

Evolution Which strain is more closely related to the Uganda strain? How did the virus change? Strain % Similar to Uganda Kenya 71% U.S. 51%