BIO210 Microbiology: Study Guide for Chapters 3, 5, and 6 (Cell Structure, Metabolism, and Growth)

Introduction to Microbiology

What are Microbes?

Microbes are microscopic organisms that include bacteria, archaea, fungi, protozoa, algae, viruses, and some multicellular parasites. They are found in virtually every environment on Earth and play essential roles in health, disease, and ecological balance.

• Prokaryotes: Unicellular organisms lacking a nucleus (bacteria and archaea).

• Eukaryotes: Organisms with a nucleus and membrane-bound organelles (algae, protozoa, fungi, animals, plants).

• Viruses: Acellular entities composed of genetic material and a protein/lipid coat; obligate intracellular parasites.

Global Impact of Microbes

Infectious Diseases and Mortality

Microbial diseases remain leading causes of death worldwide, especially in low-income countries. Lower respiratory infections, diarrheal diseases, tuberculosis, malaria, and HIV/AIDS are among the top causes of death due to infectious agents.

Case Study: Cyclospora Outbreak

Cyclospora cayetanensis

Cyclospora cayetanensis is a protozoan parasite that causes cyclosporiasis, a diarrheal disease transmitted via ingestion of contaminated food or water. Outbreaks are often linked to fresh produce.

• Oocysts are excreted in feces and contaminate the environment.

• Humans ingest sporulated oocysts from contaminated food/water.

• Diagnosis is by identification of oocysts in stool samples.

Good Microbes: The Human Microbiome

Role of the Gut Microbiome

The gut microbiome consists of beneficial microbes that aid in digestion, synthesize vitamins, and protect against pathogens. Disruption (dysbiosis) can lead to disease.

Organizing the Microbial World

Classification of Microbes

Microbes are classified into three domains: Bacteria, Archaea, and Eukarya. Infectious agents also include viruses, viroids, and prions.

Prokaryotes: Bacteria and Archaea

• Bacteria: Ubiquitous, some pathogenic, reproduce asexually.

• Archaea: Similar to bacteria but with distinct cell wall and membrane chemistry; rarely pathogenic.

Eukaryotic Microbes

• Algae: Unicellular or multicellular, photosynthetic, classified by pigments and cell wall composition.

• Protozoa: Single-celled, animal-like, classified by locomotion (pseudopodia, cilia, flagella).

• Fungi: Eukaryotic, non-photosynthetic, cell walls, includes molds (multicellular) and yeasts (unicellular).

Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes: No nucleus, small size (~1 µm), simple structure, no membrane-bound organelles.

• Eukaryotes: Nucleus, larger size (10–100 µm), complex structure, membrane-bound organelles.

Microbial Metabolism

Overview of Metabolism

Metabolism is the sum of all biochemical reactions in a cell, divided into catabolism (breakdown, energy-releasing) and anabolism (biosynthesis, energy-consuming).

• Catabolic pathways: Break down molecules, exergonic.

• Anabolic pathways: Build complex molecules, endergonic.

ATP Production and Pathways

• Glycolysis: Glucose → 2 pyruvate, net 2 ATP, 2 NADH.

• Krebs Cycle: Acetyl-CoA → CO2, NADH, FADH2, 2 ATP per glucose.

• Electron Transport Chain (ETC): NADH/FADH2 donate electrons, proton gradient drives ATP synthesis (oxidative phosphorylation).

Net ATP yield (prokaryotes): 38 ATP per glucose.

Alternative Pathways

• Pentose Phosphate Pathway: Generates NADPH and ribose-5-phosphate for biosynthesis.

• Fermentation: Incomplete oxidation of glucose, regenerates NAD+, produces organic acids/alcohols.

Microbial Nutrition and Growth

Requirements for Growth

• Chemical: Carbon, nitrogen, sulfur, phosphorus, trace elements, growth factors.

• Physical: Temperature, pH, osmotic and hydrostatic pressure.

Oxygen Requirements

• Obligate aerobes: Require O2.

• Obligate anaerobes: Killed by O2.

• Facultative anaerobes: Can use O2 or grow without it.

• Aerotolerant anaerobes: Tolerate O2, do not use it.

• Microaerophiles: Require low O2 levels.

Biofilms and Quorum Sensing

Biofilms are complex communities of microbes attached to surfaces, coordinated by quorum sensing (chemical signaling).

Microbial Reproduction

• Binary fission: Main method of bacterial reproduction; leads to exponential (logarithmic) growth.

• Generation time: Time required for a population to double.

Laboratory Techniques in Microbiology

Aseptic Technique

Procedures to prevent contamination by unwanted microbes, including sterilization of media and instruments (autoclave, incinerator).

Staining Techniques

• Simple stain: Reveals cell shape, size, arrangement.

• Gram stain: Differentiates bacteria by cell wall structure (Gram-positive: thick peptidoglycan, purple; Gram-negative: thin peptidoglycan, pink).

• Negative stain: Stains background, not cells; useful for capsules.

• Acid-fast stain: Identifies Mycobacterium and Nocardia (waxy cell wall, mycolic acid).

Measuring Microbial Growth

• Direct methods: Plate counts, microscopic counts, membrane filtration, most probable number (MPN).

• Indirect methods: Turbidity (spectrophotometry), metabolic activity, dry weight.

Biosafety in the Microbiology Laboratory

Biosafety Levels (BSL)

• BSL-1: Non-pathogenic microbes, open bench work.

• BSL-2: Moderate risk, agents associated with human disease, use of biosafety cabinets.

• BSL-3/4: High/Extreme risk, not used in undergraduate labs.

Basic Lab Safety

• Wear gloves, lab coats, and eye protection as needed.

• Practice proper hand hygiene and decontamination procedures.

• Dispose of biomedical waste and sharps appropriately.

Summary Table: Classification of Microbes

Domain	Cell Type	Cell Wall	Examples
Bacteria	Prokaryotic	Peptidoglycan	Escherichia coli, Staphylococcus aureus
Archaea	Prokaryotic	Polysaccharide/protein (no peptidoglycan)	Halophiles, thermophiles
Eukarya	Eukaryotic	Varies (cellulose, chitin, none)	Algae, fungi, protozoa
Viruses	Acellular	Protein/lipid coat	Influenza virus, HIV

Key Equations

• Generation time: $G = \frac{t}{n}$

• Population size: $B = b \times 2^n$

• ATP from fatty acid oxidation: $([N/2]-1) \times 5 + ([N/2] \times 12)$

Practice Questions

• What is the difference between Gram-positive and Gram-negative bacteria?

• How does the electron transport chain generate ATP?

• What are the main biosafety practices in a BSL-2 laboratory?