BIO 203 Exam 1 Study Guide: Microbial World, Cell Anatomy, and Metabolism

Chapter 1: The Microbial World and You

Overview of Microorganisms

Microorganisms, or microbes, are living entities too small to be seen with the naked eye. They play essential roles in ecosystems, human health, and industry. Understanding their diversity and characteristics is foundational to microbiology.

• Microorganism/Microbe: A microscopic organism, including bacteria, archaea, fungi, protozoa, algae, viruses, and helminths.

• Microbiome: The collection of microbes living in a particular environment, such as the human body.

• Normal microbiota: Microbes that permanently inhabit the body and usually do not cause disease.

• Transient microbiota: Microbes that are temporarily present in the body.

• Prokaryotes: Organisms without a nucleus (bacteria and archaea).

• Eukaryotes: Organisms with a nucleus (fungi, protozoa, algae, helminths).

• Bacteria: Single-celled prokaryotes with peptidoglycan cell walls; reproduce by binary fission.

• Archaea: Prokaryotes with pseudomurein cell walls; often live in extreme environments.

• Fungi: Eukaryotes with chitin cell walls; include yeasts and molds.

• Protozoa: Unicellular eukaryotes; often motile.

• Microscopic algae: Eukaryotes with cellulose cell walls; photosynthetic.

• Viruses: Acellular entities; require host cells to reproduce.

• Helminths: Parasitic worms; multicellular eukaryotes.

• Pathogenic: Microbes that cause disease.

• Acellular: Not composed of cells (e.g., viruses).

Example: Bacillus thuringiensis is used in pest control due to its production of toxins harmful to insects.

Additional info: The Human Microbiome Project and National Microbiome Initiative are large-scale efforts to study microbial communities and their impact on health and the environment.

Roles of Microbes in the World

Microbes are integral to nutrient cycling, food production, biotechnology, and disease. Their beneficial and harmful roles are diverse.

• Beneficial roles: Decomposition, bioremediation, sewage treatment, food production, oxygen generation via photosynthesis, and biotechnology (e.g., recombinant DNA technology).

• Harmful roles: Pathogenesis, food spoilage, and antibiotic resistance.

Example: Photosynthetic microorganisms (algae, cyanobacteria) produce oxygen and form the base of aquatic food chains.

The Microbiome and Health

The human microbiome influences digestion, immunity, and disease susceptibility. Disruptions can lead to health issues.

• Normal microbiota: Protect against pathogens, aid digestion, and synthesize vitamins.

• Microbiome imbalance: Linked to conditions such as allergies, obesity, and autoimmune diseases.

Classification: Three Domains of Life

All living organisms are classified into three domains based on cellular characteristics.

• Bacteria: Prokaryotic, peptidoglycan cell walls.

• Archaea: Prokaryotic, pseudomurein cell walls, often extremophiles.

• Eukarya: Eukaryotic, includes fungi, protozoa, algae, and helminths.

Microbes in Pest Control and Oxygen Production

Bacteria such as Bacillus thuringiensis are used in agriculture to control pests. Photosynthetic microbes contribute to oxygen production and carbon cycling.

Chapter 1: The Microbial World - Historical Perspective

Scientific Nomenclature and Key Figures

Scientific nomenclature provides a standardized way to name organisms. Historical figures contributed to the development of microbiology.

• Genus and Specific epithet: Scientific names are written as Genus species (e.g., Escherichia coli).

• Carolus Linnaeus: Developed binomial nomenclature.

• Robert Hooke: First observed cells.

• Anton van Leeuwenhoek: First observed living microbes.

• Rudolf Virchow: Proposed biogenesis (life arises from pre-existing life).

• Louis Pasteur: Disproved spontaneous generation; developed pasteurization.

• Alexander Fleming: Discovered penicillin.

Key Concepts in Microbiology

• Spontaneous generation: The (disproven) idea that life arises from non-living matter.

• Biogenesis: Life arises from pre-existing life.

• Pasteurization: Heating to kill microbes in food and beverages.

• Chemotherapy: Treatment of disease with chemicals.

• Antibiotics: Substances produced by microbes that inhibit other microbes.

• Biofilms: Communities of microbes attached to surfaces; can be beneficial or problematic.

• Emerging infectious diseases: New or increasing diseases.

• Antibiotic resistance: The ability of microbes to resist the effects of drugs.

Example: Biofilms are found on medical devices, teeth (plaque), and water pipes.

Additional info: The "Golden Age of Microbiology" refers to periods of rapid discovery linking microbes to disease and later to molecular biology.

Chapter 4: Functional Anatomy of Prokaryotic Cells

Prokaryotic Cell Structure and Function

Prokaryotic cells (bacteria and archaea) have unique structures that distinguish them from eukaryotic cells. Understanding these features is crucial for identifying microbes and targeting them with antibiotics.

• DNA/Chromosome: Single, circular DNA molecule; no nucleus.

• Histone: Proteins associated with DNA in eukaryotes (absent in most prokaryotes).

• Binary fission: Asexual reproduction method in prokaryotes.

• Ribosomes: 70S in prokaryotes, 80S in eukaryotes.

• Cell walls: Peptidoglycan in bacteria; pseudomurein in archaea.

• Shapes: Coccus (spherical), Bacillus (rod-shaped), Spiral (vibrio, spirillum, spirochete), Coccobacillus.

• Arrangements: Diplo- (pairs), Strepto- (chains), Tetrad (groups of four), Sarcinae (cubical groups), Staphylo- (clusters).

• Glycocalyx: External polysaccharide layer; includes capsule (organized) and slime layer (unorganized).

• Flagella: Motility structures; H antigen is a flagellar protein.

• Fimbriae/Pili: Attachment and conjugation structures.

• Plasma membrane: Selective barrier; site of metabolic processes.

• Inclusions: Storage granules (e.g., magnetosomes).

• Endospores: Resistant structures for survival.

Example: Antibiotics like penicillin target peptidoglycan, harming bacterial cells but not eukaryotic cells.

Additional info: Structures such as flagella, capsule, and cell wall components can be antigenic, triggering immune responses.

Comparison of Prokaryotic and Eukaryotic Cells

• Similarities: Both have plasma membranes, ribosomes, and genetic material.

• Differences: Prokaryotes lack a nucleus and membrane-bound organelles; have 70S ribosomes and peptidoglycan cell walls.

Bacterial Cell Size, Shape, and Arrangement

• Size: Typically 0.2–2.0 µm in diameter.

• Shape: Coccus, bacillus, spiral, vibrio, spirochete, coccobacillus.

• Arrangement: Diplo-, strepto-, tetrad, sarcinae, staphylo-.

Chapter 4: The Cell Wall

Structure and Function of Bacterial Cell Walls

The cell wall provides structural support and protection. Its composition is key to bacterial classification and antibiotic targeting.

• Peptidoglycan: Polymer of disaccharides (NAG and NAM) and peptide cross-bridges.

• Gram-positive cell walls: Thick peptidoglycan, teichoic acids.

• Gram-negative cell walls: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS), lipoproteins, phospholipids.

• LPS components: O polysaccharide, Lipid A (endotoxin).

• Porin: Protein channels in gram-negative outer membrane.

• Acid-fast cell wall: Contains mycolic acid; found in Mycobacterium.

• Mycoplasma: Lack cell walls.

Gram Stain and Antibiotic Action

• Gram stain: Differentiates bacteria based on cell wall structure.

• Penicillin: Inhibits peptidoglycan synthesis, more effective against gram-positive bacteria.

• Lysozyme: Enzyme that breaks down peptidoglycan.

• Exotoxin: Secreted toxins.

• Endotoxin: LPS component (Lipid A) in gram-negative bacteria.

Comparison Table: Gram-Positive vs. Gram-Negative Cell Walls

Feature	Gram-Positive	Gram-Negative
Peptidoglycan	Thick	Thin
Teichoic acids	Present	Absent
Outer membrane	Absent	Present
LPS	Absent	Present
Penicillin sensitivity	High	Low
Lysozyme sensitivity	High	Low
Exotoxin	Often produced	Often produced
Endotoxin	Absent	Present (Lipid A)

Chapter 5: Microbial Metabolism

Concepts in Metabolism

Metabolism encompasses all chemical reactions in a cell, divided into catabolic (energy-releasing) and anabolic (energy-consuming) pathways. Enzymes catalyze these reactions, and energy is transferred via ATP.

• Catabolic: Breakdown of molecules; exergonic.

• Anabolic: Synthesis of molecules; endergonic.

• ATP: Adenosine triphosphate; main energy currency.

• Enzymes: Biological catalysts; lower activation energy.

• Activation energy: Energy required to start a reaction.

• Substrate: Molecule acted upon by an enzyme.

• Coenzyme/Cofactor: Non-protein helpers for enzyme function (e.g., NAD+, NADP+, FAD).

• Competitive inhibitor: Binds active site, blocking substrate.

• Noncompetitive inhibitor: Binds elsewhere, altering enzyme function.

• Feedback inhibition: End product inhibits pathway.

Example: NAD+, NADP+, and FAD act as electron carriers in redox reactions.

Additional info: Microbes in extreme environments may have unique enzymes and metabolic pathways.

ATP Coupling and Electron Carriers

• ATP couples reactions: Energy from catabolic reactions is used to drive anabolic reactions.

• Electron carriers: NAD+, NADP+, FAD shuttle electrons during metabolism.

Key Equations:

• $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

• $\text{NAD}^+ + 2e^- + 2H^+ \rightarrow \text{NADH} + H^+$

Factors Affecting Enzyme Activity

• Temperature

• pH

• Substrate concentration

• Presence of inhibitors

Chapter 5: Carbohydrate Catabolism

Phases of Cellular Respiration

Cellular respiration is the process by which cells extract energy from glucose. It consists of four main phases:

• Glycolysis

• Pyruvate oxidation

• Citric acid cycle (Krebs cycle)

• Electron transport chain (ETC) and chemiosmosis

Glycolysis, Pyruvate Oxidation, and Citric Acid Cycle

• Glycolysis: Glucose (6C) is split into two pyruvate (3C); net gain of 2 ATP and 2 NADH.

• Pyruvate oxidation: Pyruvate converted to acetyl-CoA; produces NADH and CO2.

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

Energy investment/payoff: Glycolysis uses 2 ATP, produces 4 ATP (net 2), 2 NADH.

Chemiosmotic Model for ATP Generation

• Electron transport chain creates proton gradient across plasma membrane.

• ATP synthase uses gradient to produce ATP.

Key Equation:

• $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$ (via ATP synthase)

Aerobic Respiration

• Electron donor: Glucose

• Electron acceptor: Oxygen

• Majority of ATP: Produced during electron transport chain/chemiosmosis

Oxidative vs. Substrate-Level Phosphorylation

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP.

• Oxidative phosphorylation: ATP generated by ETC and chemiosmosis; produces more ATP.

Chapter 5: Anaerobic Respiration & Fermentation

Aerobic vs. Anaerobic Respiration

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

• Anaerobic: Uses other acceptors (e.g., nitrate, sulfate); less ATP produced.

Example: Escherichia coli can use nitrate in anaerobic respiration.

Fermentation

• Purpose: Regenerate NAD+ for glycolysis.

• Products: Lactic acid, ethanol, CO2, etc.

• ATP yield: Low (2 ATP per glucose).

• Significance: Allows energy production without oxygen.

Key Equation:

• $\text{Glucose} \rightarrow 2 \text{Lactic acid} + 2 \text{ATP}$

• $\text{Glucose} \rightarrow 2 \text{Ethanol} + 2 \text{CO}_2 + 2 \text{ATP}$

ATP Yield Comparison Table

Process	ATP per Glucose
Cellular Respiration (Aerobic)	~36-38
Oxidative Phosphorylation	Majority of ATP (approx. 34)
Substrate-Level Phosphorylation	Small amount (approx. 4)
Fermentation	2

Additional info: Growth rate is highest in aerobic respiration due to greater ATP yield; lowest in fermentation.