Microbiology Study Guide: Viruses, Microbial Metabolism, and Microbial Growth

Viruses and Virus-Like Agents

Basic Characteristics of Viruses

Viruses are acellular infectious agents that require a living host cell to replicate. They are much smaller than bacteria and cannot be seen with a light microscope.

• Obligate intracellular parasites: Viruses cannot reproduce or carry out metabolism outside a host cell.

• Structure: All viruses contain genetic material (DNA or RNA) and a protein coat (capsid). Some have an additional lipid envelope.

• Minimum components: The bare minimum for a virus is nucleic acid (genome) and a protein capsid.

Structure and Classification of Viruses

• Capsid: Protein shell that encloses the viral genome.

• Envelope: Some viruses have a lipid membrane derived from the host cell; these are called enveloped viruses. Those without are non-enveloped (naked) viruses.

• Shapes: Viruses can be helical, icosahedral, complex, or spherical in shape.

• Genetic material: Viral genomes may be DNA or RNA, single-stranded or double-stranded, linear or circular.

Bacteriophages and Plaques

• Bacteriophage: A virus that infects bacteria.

• Plaque: Clear zones on a bacterial lawn caused by lysis of bacteria due to viral infection.

Host Range and Susceptibility

• Domains susceptible to viruses: Viruses can infect all domains of life: Bacteria, Archaea, and Eukarya.

• Host range: Some viruses have a broad host range, while others are specific (narrow host range).

Viral Life Cycles

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

• Lysogenic cycle: Viral genome integrates into host DNA and replicates with it without causing immediate lysis.

• Steps of lytic cycle:

  1. Attachment

  2. Penetration

  3. Biosynthesis

  4. Maturation

  5. Release

• Animal virus replication: Involves attachment, entry (often by endocytosis or fusion), uncoating, biosynthesis, assembly, and release.

Viroids and Prions

• Viroid: Infectious RNA molecules without a protein coat, mostly affecting plants.

• Prion: Infectious proteins that cause neurodegenerative diseases (e.g., Creutzfeldt-Jakob disease).

• Difference from viruses: Viroids lack protein; prions lack nucleic acid.

Virus Cultivation

• Viruses must be grown in living cells (bacterial cultures, animal cells, or embryonated eggs) because they require host machinery for replication.

Microbial Metabolism

Basic Concepts and Definitions

• Metabolism: All chemical reactions in a cell.

• Anabolism: Biosynthetic reactions that build complex molecules (require energy).

• Catabolism: Breakdown of complex molecules (release energy).

• Exergonic: Reactions that release energy.

• Endergonic: Reactions that require energy input.

ATP: Structure and Function

• ATP (Adenosine Triphosphate): Main energy currency of the cell.

• Structure: Adenine base, ribose sugar, and three phosphate groups.

• Function: Stores and transfers energy for cellular processes.

Energy Carriers and Redox Reactions

• NAD+, FAD, NADP+: Electron carriers that shuttle electrons during metabolic reactions.

• Energy is carried via oxidation-reduction (redox) reactions:

$\text{Oxidation: loss of electrons}$ $\text{Reduction: gain of electrons}$

Enzymes and Their Regulation

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

• Properties: Specificity, efficiency, affected by temperature, pH, and substrate concentration.

• Inhibitors:

  • Competitive: Compete with substrate for active site.

  • Non-competitive: Bind elsewhere, changing enzyme shape.

  • Feedback inhibition: End product inhibits an earlier step.

Energy Sources and Pathways

• Good energy sources: Molecules with many electrons (e.g., glucose, lipids).

• Respiration vs Fermentation: Respiration uses an electron transport chain and produces more ATP; fermentation does not use an ETC and yields less ATP.

Glycolysis and Alternatives

• Glycolysis: Converts glucose to pyruvate, generating ATP and NADH.

• ATP is generated by substrate-level phosphorylation in glycolysis.

• End products: 2 pyruvate, 2 ATP, 2 NADH per glucose.

• Alternative pathways: Pentose phosphate pathway, Entner-Doudoroff pathway.

Aerobic vs Anaerobic Respiration

• Aerobic: Uses oxygen as final electron acceptor; produces more ATP.

• Anaerobic: Uses other inorganic molecules as final electron acceptor; less ATP produced.

Citric Acid Cycle (Krebs Cycle)

• Starting molecule: Acetyl-CoA (derived from pyruvate).

• Products: CO2, NADH, FADH2, ATP (or GTP).

• Called a cycle because oxaloacetate is regenerated.

Electron Transport Chain (ETC)

• Electrons from NADH and FADH2 are transferred through a series of carriers, releasing energy to produce ATP.

• Most ATP is generated here by oxidative phosphorylation.

• ATP synthase is powered by the proton gradient (proton motive force).

$\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

Fermentation

• Occurs when no final electron acceptor is available for respiration.

• Produces less ATP; organisms grow more slowly.

• End products depend on the organism and enzymes present (e.g., lactic acid, ethanol).

• Energy is derived from glycolysis only.

Other Energy Sources

• Cells can use lipids, proteins, and other carbohydrates for energy, often feeding into central metabolic pathways.

Photosynthesis

• Light-dependent reactions: Capture light energy to produce ATP and NADPH.

• Light-independent reactions (Calvin cycle): Use ATP and NADPH to fix CO2 into organic molecules.

• In prokaryotes, these occur in the cytoplasmic membrane; in eukaryotes, in chloroplasts.

• Photosystems: Protein complexes that absorb light and initiate electron transport.

• ETS in respiration vs photosynthesis: Both use electron carriers and generate a proton gradient, but the electron source and final acceptor differ.

• Oxygenic vs anoxygenic photosynthesis: Oxygenic produces O2 (e.g., plants, cyanobacteria); anoxygenic does not (e.g., purple sulfur bacteria).

Calvin Cycle

• Three stages: Carbon fixation, reduction, regeneration.

• CO2 enters the cycle; ribulose-1,5-bisphosphate (RuBP) is regenerated.

• ATP and NADPH from light reactions power the cycle.

• Enzyme catalyzing first step: Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase).

Microbial Growth

Binary Fission and Generation Time

• Binary fission: Main method of reproduction in prokaryotes; one cell divides into two identical cells.

• Generation time: Time required for a cell to divide (or for a population to double).

Phases of Growth in a Closed System

• Lag phase: Cells adapt to environment; no division.

• Log (exponential) phase: Rapid cell division; highest metabolic activity.

• Stationary phase: Growth rate slows; nutrients deplete; waste accumulates.

• Death phase: Cells die faster than they divide.

Biofilms

• Biofilm: Community of microorganisms attached to a surface and embedded in a self-produced matrix.

• Stages of formation: Attachment, microcolony formation, maturation, dispersion.

• Biofilms are more resistant to antibiotics and disinfectants due to the protective matrix and altered metabolic states.

• Biofilms differ from planktonic (free-living) growth in broth or on agar plates.

Environmental Factors Affecting Growth

• Each microorganism has optimal conditions for growth (temperature, pH, salt concentration, oxygen).

• Growth slows or stops if conditions are outside optimal ranges.

Oxygen Requirements and Tolerance

• Not all organisms require O2 for growth.

• Reactive oxygen species (ROS): Toxic byproducts of oxygen metabolism (e.g., superoxide, hydrogen peroxide).

• Enzymes that neutralize ROS: Superoxide dismutase (SOD) and catalase.

Group	Oxygen Requirement
Obligate aerobe	Requires O2
Obligate anaerobe	Cannot tolerate O2
Facultative anaerobe	Grows with or without O2 (better with O2)
Aerotolerant anaerobe	Does not use O2, but tolerates it
Microaerophile	Requires low O2 levels
Capnophile	Requires elevated CO2 levels

pH and Temperature Classification

• Organisms are classified by pH preference: acidophiles (low pH), neutrophiles (neutral pH), alkaliphiles (high pH).

• Most human pathogens are neutrophiles.

• Cardinal temperatures: Minimum, optimum, and maximum temperatures for growth.

• Temperature groups:

  • Psychrophile: Cold-loving

  • Psychrotroph: Grow at low temperatures, but optimum is higher

  • Mesophile: Moderate temperatures (most human pathogens)

  • Thermophile: Heat-loving

  • Hyperthermophile: Very high temperatures

Osmotic Pressure and Salt Tolerance

• High salt environments cause water to leave cells (plasmolysis).

• Halotolerant: Can survive in high salt, but do not require it.

• Halophilic: Require high salt concentrations for growth.

Classification by Energy and Carbon Source

• Organisms are categorized by energy and carbon source:

Type	Energy Source	Carbon Source
Photoautotroph	Light	CO2
Chemoautotroph	Chemicals	CO2
Photoheterotroph	Light	Organic compounds
Chemoheterotroph	Chemicals	Organic compounds

Additional info: Some explanations and tables were expanded for clarity and completeness based on standard microbiology textbooks.