Study Guide: Viruses, Microbial Growth, and Metabolism

Chapter 6: Viruses and Prions

Nature of Viruses

Viruses are unique infectious agents that differ fundamentally from living cells. They are considered non-living because they lack the cellular machinery necessary for independent life.

• Viruses are not living: They cannot carry out metabolism, reproduce independently, or respond to stimuli outside a host cell.

• Comparison to cells: Unlike prokaryotic and eukaryotic cells, viruses lack organelles, cytoplasm, and a plasma membrane.

Viral Structure

• Capsid: Protein shell that encases the viral genome.

• Envelope: Some viruses possess a lipid membrane derived from the host cell.

• Spikes: Glycoprotein projections that facilitate attachment to host cells.

Viral Genomes

• Genomic variation: Viral genomes may be DNA or RNA, single- or double-stranded, linear or circular, and segmented or non-segmented.

• Genome usage: DNA viruses often use host machinery for transcription, while RNA viruses may carry their own enzymes to synthesize mRNA.

Viral Evolution and Variation

• Reassortment: Exchange of genome segments between viruses, leading to new viral strains.

• Antigenic drift: Gradual accumulation of mutations in viral genes.

• Antigenic shift: Abrupt, major changes due to reassortment, often resulting in pandemics.

Viral Replication

• Phases: Attachment, penetration, uncoating, replication, assembly, and release.

• Lytic cycle: Virus replicates and lyses the host cell.

• Lysogenic cycle: Viral genome integrates into host DNA and replicates with it.

• Phage conversion: Acquisition of new traits by bacteria due to integrated viral genes; medically important as it can lead to toxin production.

Animal Virus Replication

• Attachment to host cell

• Penetration and uncoating

• Biosynthesis of viral components

• Assembly of new virions

• Release from host cell

Host Range and Tropism

• Host range: The spectrum of hosts a virus can infect.

• Tropism: Specificity for certain cell types or tissues.

Persistent Infections

• Chronic: Continuous low-level production of virus.

• Latent: Virus remains dormant, can reactivate later.

Oncoviruses

• Viruses that can induce cancer by disrupting normal cell cycle regulation.

Laboratory Techniques

• Plaque assay: Quantifies infectious virus particles by counting clear zones (plaques) on a cell layer.

• Agglutination: Detects viral antigens or antibodies by visible clumping.

• Fermentation end-products: Used to identify metabolic activity in infected cells.

Antiviral Strategies

• Drugs may inhibit viral entry, replication, or release.

Prions

• Infectious proteins that cause neurodegenerative diseases by inducing abnormal folding of normal proteins.

Vaccine Effectiveness

• Antigenic variation (e.g., in influenza) can reduce vaccine efficacy.

Chapter 7: Fundamentals of Microbial Growth

Microbial Reproduction

• Binary fission: Most common in bacteria; cell divides into two identical cells.

• Budding: New cell develops from a parent cell.

• Spore formation: Some bacteria and fungi produce spores for survival and dispersal.

Generation Time

• Time required for a population to double.

• Calculated using the formula: $n = \frac{\log N_t - \log N_0}{\log 2}$ where $N_t$ is the final cell number, $N_0$ is the initial cell number, and $n$ is the number of generations.

Bacterial Growth Phases

• Lag phase: Adaptation, no division.

• Log (exponential) phase: Rapid cell division.

• Stationary phase: Nutrient depletion slows growth.

• Death phase: Cells die due to lack of resources.

Environmental Factors Affecting Growth

• Temperature, pH, and osmotic pressure are key constraints.

• Temperature terms:

  • Optimal: Best growth rate.

  • Minimum: Lowest temperature for growth.

  • Maximum: Highest temperature for growth.

• Microbe types by temperature:

  • Psychrophiles: Thrive in cold.

  • Psychrotrophs: Prefer cool, but tolerate cold.

  • Mesophiles: Moderate temperatures (most pathogens).

  • Thermophiles: Prefer hot environments.

  • Extreme thermophiles: Survive in very high heat.

• Microbe types by pH:

  • Acidophiles: Grow in acidic conditions.

  • Neutralophiles: Prefer neutral pH.

  • Alkaliphiles: Thrive in basic environments.

• Halophiles: Require high salt concentrations.

Oxygen Requirements

• Obligate aerobes: Require oxygen.

• Obligate anaerobes: Killed by oxygen.

• Facultative anaerobes: Can grow with or without oxygen.

• Microaerophiles: Require low oxygen.

• Aerotolerant anaerobes: Tolerate oxygen but do not use it.

Energy Sources

• Phototrophs: Use light as energy source.

• Chemotrophs: Obtain energy from chemical compounds.

Culture Media

• Complex media: Contains unknown chemical composition.

• Defined media: Exact chemical composition is known.

• Selective media: Inhibits some microbes, allows others.

• Differential media: Distinguishes microbes based on biochemical reactions.

Measuring Microbial Growth

• Direct methods: Cell counts using microscopy or plate counts.

• Indirect methods: Turbidity, metabolic activity, or dry weight measurements.

Control of Microbial Growth

• Decontamination: Removal of microbes to safe levels.

• Sterilization: Destruction of all microbes.

• Disinfection: Elimination of most pathogens (not spores).

• Microbiostatic: Inhibits growth.

• Microbiocidal: Kills microbes.

• Disinfectant: Used on inanimate objects.

• Antiseptic: Safe for use on living tissue.

Physical and Chemical Controls

• Heat treatments: Autoclaving, pasteurization, dry heat.

• Filtration: Removes microbes from liquids or air; used for heat-sensitive materials.

• Chemical controls: Alcohols, phenolics, halogens, and more.

Chapter 8: Microbial Metabolism

Metabolism Overview

Metabolism encompasses all chemical reactions within a cell, divided into two main categories: anabolism and catabolism.

• Anabolism: Biosynthetic reactions that build complex molecules from simpler ones; require energy.

• Catabolism: Breakdown of complex molecules into simpler ones; releases energy.

• Catabolic and anabolic reactions are interdependent; energy from catabolism fuels anabolism.

ATP and Energy Transfer

• ATP (adenosine triphosphate): Composed of adenine, ribose, and three phosphate groups.

• ADP is recharged to ATP by addition of a phosphate group.

• ATP is the main energy currency of the cell.

Enzymes

• Biological catalysts that speed up reactions by lowering activation energy.

• Active site: Region on enzyme where substrate binds.

• Factors affecting activity: temperature, pH, substrate concentration, inhibitors.

• Competitive inhibition: Inhibitor binds active site.

• Noncompetitive inhibition: Inhibitor binds elsewhere, changing enzyme shape.

Redox Reactions

• Involve transfer of electrons; always occur in pairs (oxidation and reduction).

• Electron carriers: NAD+ and FAD.

ATP Production Mechanisms

• Substrate-level phosphorylation

• Oxidative phosphorylation

• Photophosphorylation

Cellular Respiration

• Process by which cells harvest energy from organic molecules.

• General equation: $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{ATP}$

• Major steps:

  • Glycolysis: Glucose to pyruvate; produces ATP and NADH.

  • Preparatory reaction: Pyruvate to acetyl-CoA; produces NADH and CO2.

  • Citric acid cycle: Acetyl-CoA oxidized; produces NADH, FADH2, ATP, CO2.

  • Electron transport chain: Electrons transferred to oxygen; generates most ATP.

• Chemiosmosis: Proton gradient drives ATP synthesis via ATP synthase.

• ATP synthase: Enzyme that produces ATP from ADP and inorganic phosphate.

• Final electron acceptors: Oxygen (aerobic), other molecules (anaerobic).

• Most ATP is produced during the electron transport chain step.

Fermentation

• Main goal: Regenerate NAD+ for glycolysis in the absence of oxygen.

• Produces various end-products (e.g., lactic acid, ethanol).