Chapter 18: The Genetics of Viruses and Bacteria

Chapter 18: The Genetics of Viruses and Bacteria

Chapter 18: The Genetics of Viruses and Bacteria What is Microbiology? Microbiology is the science that studies microorganisms Microorganisms, roughly, are those living things that are too small to be seen with the naked eye Microorganisms cannot be distinguished phylogenetically from Macroorganisms, e.g.,

includes fungi as well as bacteria, etc. (that is, they are not, as a whole, a closely related group of organisms) Microbiology is more a collection of techniques: Aseptic technique, Pure culture technique, Microscopic observation of whole organisms, etc. A microbiologist usually first isolates a specific microorganism from a population and then cultures it Importance of Microbes Microbes are producersthey provide energy to

ecosystems Microbes are fixersthey make nutrients available from inorganic sources, e.g., nitrogen Microbes are decomposersthey free up nutrients from no longer living sources Microbes form symbioses (such as mycorrhizal fungi associated with plant rootsthough these are somewhat macroscopic; also the bacteria found in legume root nodules, etc.) Microbes serve as endosymbionts (e.g., chloroplasts and mitochondria) Microbes make fermentation products (ethanol!), food (beer! Cheese! Yogurt! Half-sour pickles!), Biotech

products (e.g., recombinant insulin), etc. Germ theory of disease; Normal flora Relative Microbe Sizes Examples of Types of Viruses What is a Virus? Viruses consist of protein capsids and nucleic acid (DNA or RNA) plus some viruses (virions) have a lipid envelope (enveloped viruses) Viruses are ...infectious agents of small size

and simple composition that can multiply only in living cells of animals, plants and bacteria [plus fungi & protozoa]. Viruses are obligate parasites that are metabolically inert when they are outside their hosts. They all rely, to varying extents, on the metabolic processes of their hosts to reproduce themselves. The viral diseases we see are due to the effects of this interaction between the virus and its host cell (and/or the hosts response to this interaction). Encyclopedia Britannica

Virus (Virion Particle) The Virion is what defines a virus as a virus A Virion is the extracellular state of a virus The job of Virions is to find new cells to infect As such, Virions are a durable state that is designed to attach to susceptible cells The Virion is then responsible for translocation of the virus genome into the cell The Virion consists of a DNA (or RNA) genome surrounded by Protein that, in turn, may be surrounded by a Lipid Bilayer The Protein layer is called a Capsid

The Lipid Bilayer is called an Envelope Steps of Virus Replication 1. Adsorption (attachment) 2. Penetration (nucleic-acid release) 3. Synthesis (of RNA and proteins, as well as DNA if DNA genome) 4. Maturation (assembly of virion) 5. Release (lysis or chronic release, e.g., budding, with the latter coinciding with release for various enveloped viruses) Caveat: It is important to realize that variation among

viruses is between virus strains/species; any one kind of virus cannot replicate in multiple ways, have more than one virion morphology, or vary in genome type, etc. DNA Virus Life Cycle Lysis Bacteriophage Lytic Cycle Lysis Lysogenic Cycle (Temperate Phage)

Lysi s Only temperate phage are able to display lysogeny Enveloped RNA Virus An

example of an animal virus Budding Acquisition of plasma membrane as envelope HIV Life Cycle Budding HIV Life Cycle

Bacteria Sex Viruses move genetic material from cell to cell Mostly this material is their own genomes, i.e., genes that collectively code for the production of new viruses Bacteria DNA also can move from cell to cell Once received by a cell, this DNA may be incorporated into the bacterial genome via recombination This idea of DNA sourced from different

parents recombining into a single chromosome is equivalent to eukaryotic sex (i.e., fertilization followed by recombination) Transformation, Transduction, Conjugation Why study bacterial genetics? Its an easy place to start history we know more about it systems better understood simpler genome good model for control of genes

build concepts from there to eukaryotes bacterial genetic systems are exploited in biotechnology Bacteria Bacteria review one-celled organisms prokaryotes reproduce by binary fission rapid growth generation every ~20 minutes 108 (100 million) colony overnight!

dominant form of life on Earth incredibly diverse Bacterial genome Single circular chromosome haploid naked DNA no histone proteins ~4 million base pairs ~4300 genes 1/1000 DNA in eukaryote

Intro to Bacteria video No nucleus! No nuclear membrane chromosome in cytoplasm transcription & translation are coupled together no processing of mRNA no introns but Central Dogma still applies

use same genetic code Binary fission Replication of bacterial chromosome Asexual reproduction offspring genetically identical to parent where does variation come from? Variation in bacteria

Sources of variation spontaneous mutation transformation plasmids DNA fragments transduction conjugation transposons bacteria shedding DNA Transformation

Transformation: DNA picked up directly from the medium and recombined into the genome Competent cell: capable of picking up DNA Generalized Transduction Plasmids Conjugation

Moves plasmid more so than chromosomal DNA Bacterial Genetics Regulation of Gene Expression Bacterial metabolism Bacteria need to respond quickly to changes in their environment if have enough of a product, need to stop production

why? waste of energy to produce more how? stop production of synthesis enzymes if find new food/energy source, need to utilize it quickly why? metabolism, growth, reproduction how? start production of digestive enzymes Regulation of Metabolism e.g., transcription

Reminder: Regulation of metabolism Feedback inhibition product acts as an allosteric inhibitor of 1st enzyme in tryptophan pathway - = inhibition

Another way to Regulate metabolism Gene regulation block transcription of genes for all enzymes in tryptophan pathway saves energy by not wasting it on unnecessary protein synthesis -

= inhibition Gene regulation in bacteria Control of gene expression enables individual bacteria to adjust their metabolism to environmental change Cells vary amount of specific enzymes by regulating gene transcription turn genes on or turn genes off ex. if you have enough tryptophan in your cell then you dont need to make enzymes used to build tryptophan

waste of energy turn off genes which codes for enzymes Control of Gene Expression Operons- sequence of DNA that directs particular biosynthetic pathways 4 Major Components of an operon Regulatory gene- produces a repressor protein that prevents gene expression by blocking DNA polymerase Promotor region- sequence of DNA where RNA

Polymerase attaches for transcription Operator region- can block action of RNA Polymerase if region is occupied by repressor protein Structural gene- contain DNA sequence that code for several related enzymes that direct production of an end product. Control of Gene Expression It makes energetic sense to make or use proteins responsible for certain metabolic processes only when those processes are needed.

Trp Operon- enzymes make needed tryptophan Repressor inactivated in response to presence of tryptophan Tryptophan acts as Corepressor Repressable enzymes- Usually turned on and has to be turned off. Lac Operon Controls breakdown of lactose Lactose presence needed to turn on Operon inducible enzymes- Usually turned off and needs to be turned on. So how can genes be turned

off? First step in protein production? transcription stop RNA polymerase! Repressor protein binds to DNA near promoter region blocking RNA polymerase binds to operator site on DNA blocks transcription Genes grouped together

Operon genes grouped together with related functions ex. enzymes in a synthesis pathway promoter = RNA polymerase binding site single promoter controls transcription of all genes in operon transcribed as 1 unit & a single mRNA is made operator = DNA binding site of regulator protein Trp Operon (low trp densities) Recall that the promoter is the site of RNA

polymerase binding Dont worry about the names of these genes and products Trp Operon (higher trp densities) Corepressio n Negative regulation

Equilibrium: Likelihood of being in bound state depends on trp density Repressor protein model Operon: operator, promoter & genes they control serve as a model for gene regulation RNA polymerase RNA

repressor TATA polymerase promoter operator gene1 gene2 gene3

gene4 DNA Repressor protein turns off gene by blocking RNA polymerase binding site. repressor repressor protein Repressible operon: tryptophan

Synthesis pathway model RNA polymerase When excess tryptophan is present, binds to tryp repressor protein & triggers repressor to bind to DNA RNA repressor TATA polymerase

gene1 blocks (represses) transcription gene2 gene3 gene4 repressor promoter operator

DNA repressor protein tryptophan repressor tryptophan repressor protein complex conformational change in repressor protein!

Tryptophan operon What happens when tryptophan is present? Dont need to make tryptophan-building enzymes Tryptophan binds allosterically to regulatory protein Inducible operon: lactose Digestive pathway model RNA polymerase

When lactose is present, binds to lac repressor protein & triggers repressor to release DNA RNA repressor TATA polymerase gene1 induces transcription gene2

gene3 repressor promoter operator gene4 DNA repressor protein

lactose repressor lactose repressor protein complex conformational change in repressor protein! Lactose operon What happens when lactose is present? Need to make lactose-digesting enzymes

Lactose binds allosterically to regulatory protein

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