Microbiology Study Guide: Chapters 1–6 (Exam 1)

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Chapter 1: Foundations of Microbiology

Scientific Contributions and Historical Figures

This section covers the foundational scientists and their contributions to microbiology, as well as the development of the scientific method and key discoveries.

Key Contributors: Antonie van Leeuwenhoek (first observations of microorganisms), Louis Pasteur (disproved spontaneous generation, developed pasteurization), Robert Koch (Koch's postulates, germ theory), Ignaz Semmelweis (hand hygiene), Joseph Lister (antiseptic surgery), Edward Jenner (smallpox vaccine), Florence Nightingale (nursing and infection control).
Prokaryotes vs. Eukaryotes: Prokaryotes lack a nucleus and membrane-bound organelles; eukaryotes possess both.
Scientific Method: A systematic approach to research involving observation, hypothesis, experimentation, and conclusion.
Spontaneous Generation: The disproven idea that life arises from non-living matter. Pasteur's experiment with swan-neck flasks provided evidence against this theory.
Louis Pasteur: Demonstrated the role of microbes in fermentation and disease; developed vaccines for rabies and anthrax.
Robert Koch: Developed Koch's postulates to link specific microbes to specific diseases.

Koch's Postulates:

The microorganism must be found in all organisms suffering from the disease, but not in healthy organisms.
The microorganism must be isolated from a diseased organism and grown in pure culture.
The cultured microorganism should cause disease when introduced into a healthy organism.
The microorganism must be re-isolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Chapter 2: Chemical and Genetic Foundations

pH Scale and Nucleic Acids

This chapter introduces the chemical basis of life, focusing on pH and the structure and function of nucleic acids.

pH Scale: Measures the concentration of hydrogen ions () in a solution. Ranges from 0 (acidic) to 14 (basic), with 7 being neutral. Humans 7.35-7.45
Nucleotides and Nucleic Acids: Nucleotides are the building blocks of nucleic acids (DNA and RNA).
Nitrogenous Bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G), and Uracil (U) in RNA.
Classes of Nucleic Acids:
- DNA (Deoxyribonucleic acid): Stores genetic information.
- RNA (Ribonucleic acid): Involved in protein synthesis and gene regulation.

Chapter 3: Cell Structure and Function

Prokaryotic and Eukaryotic Cells

This section explores the structure, function, and classification of microbial cells.

Major Processes of Living Cells: Metabolism, growth, reproduction, response to stimuli, and homeostasis.
Prokaryotes vs. Eukaryotes: Prokaryotes (Bacteria, Archaea) lack a nucleus; eukaryotes (Protists, Fungi, Plants, Animals) have a nucleus.
Glycocalyx: A protective, sticky layer outside the cell wall; important for adherence and protection.
Capsules vs. Slime Layers: Capsules are organized and firmly attached; slime layers are loose and unorganized.
Flagella: Long, whip-like structures for motility; arrangement can be monotrichous, lophotrichous, amphitrichous, or peritrichous.
Pili and Fimbriae: Short, hair-like structures for attachment and conjugation.
Cell Walls:
- Gram-positive: Thick peptidoglycan layer, stains purple.
- Gram-negative: Thin peptidoglycan layer, outer membrane, stains pink.
- Acid-fast: Waxy cell wall, resists decolorization (e.g., Mycobacterium).
Gram Stain: A differential staining technique to classify bacteria.
Ribosomes: Sites of protein synthesis; prokaryotic (70S) and eukaryotic (80S) ribosomes differ in size and structure.
Endosymbiotic Theory: Eukaryotic organelles (mitochondria, chloroplasts) originated from prokaryotic cells engulfed by ancestors of eukaryotes.

Chapter 4: Microbial Taxonomy and Staining

Classification and Identification

This chapter discusses the classification of microorganisms and laboratory techniques for their identification.

Staining Techniques:
- Simple Stain: Uses a single dye to color cells.
- Gram Stain: Differentiates bacteria by cell wall structure.
- Acid-fast Stain: Identifies acid-fast bacteria (e.g., Mycobacterium).
- Endospore Stain: Detects bacterial endospores.
Binomial Nomenclature: The two-part scientific naming system (Genus species).
Three Domains (Carl Woese): Bacteria, Archaea, Eukarya.
Taxonomic Procedures: Use of morphological, biochemical, and genetic tests to identify microorganisms.

Chapter 5: Microbial Metabolism

Metabolic Pathways and Energy Production

This section covers the biochemical processes that provide energy and building blocks for microbial life.

Metabolism: The sum of all chemical reactions in a cell.
Anabolism: Biosynthetic reactions that build complex molecules.
Catabolism: Degradative reactions that break down molecules for energy.
ATP (Adenosine Triphosphate): The main energy currency of the cell.
Enzymes: Biological catalysts that speed up reactions; affected by temperature, pH, substrate concentration, and inhibitors.
Enzyme Inhibition:
- Competitive: Inhibitor competes with substrate for active site.
- Noncompetitive: Inhibitor binds elsewhere, altering enzyme function.
Glycolysis, Krebs Cycle, Electron Transport Chain: Central metabolic pathways for energy production.
- Glycolysis: Glucose is converted to pyruvate, producing ATP and NADH.
- Krebs Cycle: Pyruvate is further oxidized, generating more ATP, NADH, and FADH2.
- Electron Transport Chain: Electrons are transferred to oxygen, producing ATP.
Fermentation: Anaerobic process that regenerates NAD+ and produces useful end products (e.g., lactic acid, ethanol).
Photosynthesis: Conversion of light energy to chemical energy; involves chlorophyll and other pigments.

Chapter 6: Microbial Growth and Nutrition

Growth, Nutrition, and Environmental Factors

This chapter examines how microbes obtain nutrients, grow, and respond to environmental conditions.

Categories of Organisms by Carbon and Energy Source:
- Autotrophs: Use CO2 as a carbon source.
- Heterotrophs: Use organic compounds as a carbon source.
- Phototrophs: Use light as an energy source.
- Chemotrophs: Use chemical compounds as an energy source.
Oxygen Requirements:
- Aerobes: Require oxygen.
- Anaerobes: Do not require oxygen.
- Facultative Anaerobes: Can grow with or without oxygen.
- Microaerophiles: Require low levels of oxygen.
Reactive Oxygen Species (ROS): Toxic byproducts of oxygen metabolism; microbes have enzymes (e.g., catalase, superoxide dismutase) to detoxify ROS.
Nitrogen Fixation: Conversion of atmospheric nitrogen (N2) to ammonia (NH3); essential for biosynthesis.
Quorum Sensing and Biofilms: Cell-to-cell communication that regulates gene expression and biofilm formation.
Streak Plate Method: Technique to isolate pure bacterial colonies.
Cultural Media:
- General Purpose Media: Supports growth of many microbes (e.g., nutrient agar).
- Selectives and Differentials: Select for or differentiate between microbial types.
Binary Fission: Asexual reproduction in bacteria; one cell divides into two identical cells.
Bacterial Growth Curve: Four phases: lag, log (exponential), stationary, and death.
Measuring Bacterial Reproduction: Direct methods include plate counts, filtration, and microscopy.

Example Table: Comparison of Prokaryotic and Eukaryotic Cells

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	Absent	Present
Membrane-bound Organelles	Absent	Present
Ribosome Size	70S	80S
Cell Wall Composition	Peptidoglycan (Bacteria)	Cellulose (Plants), Chitin (Fungi), None (Animals)
Examples	Bacteria, Archaea	Protists, Fungi, Plants, Animals

Key Equations

pH Calculation:
ATP Yield from Glucose (Aerobic Respiration):

Additional info:

Some details, such as the specific names of the five nitrogenous bases and the phases of the bacterial growth curve, were inferred for completeness.
Descriptions of the Gram stain, endosymbiotic theory, and metabolic pathways were expanded for academic clarity.