Microbiology Study Notes: Introduction, Biochemistry, and Cell Structure

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Chapter 1: Introduction to Microbiology

Microorganisms and Microbiology

Microbiology is the study of microorganisms, which are organisms too small to be seen with the naked eye. This field includes bacteria, archaea, fungi, protists, and viruses.

Microorganisms: Include bacteria, archaea, fungi, protists, and viruses. Some are beneficial, while others can cause disease.
Microbiota: The community of microorganisms living in a particular environment, such as the human body.
Pathogens: Microbes that cause disease. About 1,400 pathogens are known to infect humans.
Opportunistic Pathogens: Cause disease only in a weakened host.

Spontaneous Generation vs. Biogenesis

Historically, scientists debated whether life could arise spontaneously or only from existing life.

Spontaneous Generation: The idea that life comes from nonliving matter.
Biogenesis: The principle that life emerges from existing life. Louis Pasteur disproved spontaneous generation by showing that microbes do not grow in sterilized broth unless exposed to air containing microorganisms.

Germ Theory of Disease and Robert Koch

The germ theory states that microbes cause infectious diseases. Robert Koch developed techniques to determine the specific etiological agent of disease.

Koch's Postulates:
1. The organism must be present in every case of the disease.
2. The organism must be isolated from the diseased host and grown as a pure culture.
3. The isolated organism should cause the same disease when inoculated into a susceptible host.
4. The organism must be re-isolated from the inoculated, diseased animal.

Scientific Method and Hypotheses

The scientific method is a systematic process for answering questions and testing ideas.

Steps: Ask a question, form a hypothesis, test the hypothesis, analyze data, and draw a conclusion.
Scientific Law: A principle that is always true under specific conditions.
Scientific Theory: A powerful explanation of a natural phenomenon, supported by evidence.

Binomial Nomenclature and Taxonomy

Binomial nomenclature is a two-name system for classifying organisms. Taxonomy organizes living things into hierarchical categories.

Taxonomic Hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.
Strain: A genetic variant of the same species.
Genus and Species: The genus is the first part and species is the second part of a microbe's scientific name.

Microbiome and Symbiosis

The microbiome is the collection of microbes that live on and in our bodies. Symbiosis describes relationships between microbes and hosts.

Mutualism: Both organisms benefit.
Parasitism: One organism benefits, the other is harmed.
Biofilm: A sticky, structured community of microbes.

Roles of Microbes in Ecosystems and Bioremediation

Microbes play crucial roles in ecosystems, such as decomposition and nutrient cycling. Bioremediation uses microbes to clean up spills.

Phototrophic Microbes: Produce oxygen and contribute to the nitrogen cycle.
Bioremediation: Uses microbes to degrade pollutants.

History and Contributions in Microbiology

Understanding the history of microbiology helps appreciate its development and impact.

Antonie van Leeuwenhoek: Refined microscopes and made first descriptions of cells.
Semmelweis, Lister, Nightingale: Advanced aseptic techniques and infection control.

Chapter 2: Biochemistry Basics

Atoms, Ions, and Molecules

Atoms are the smallest units of elements. Molecules are formed by two or more atoms bonded together.

Atom: Consists of a nucleus (protons and neutrons) and electrons.
Atomic Number: Number of protons in an atom.
Atomic Mass: Sum of protons and neutrons.
Chemical Symbol: One- or two-letter abbreviation for an element.
Ion: An atom with an unequal number of protons and electrons.
Anion: Gains electrons, negative charge.
Cation: Loses electrons, positive charge.
Isotope: Atoms of the same element with different numbers of neutrons.
Molecule: Two or more atoms bonded together.
Compound: Molecule made of more than one type of element.
Isomer: Molecules with the same molecular formula but different structures.

Chemical Bonds and Functional Groups

Chemical bonds hold atoms together in molecules. Functional groups are specific groups of atoms that confer particular properties to molecules.

Covalent Bond: Atoms share electrons.
Ionic Bond: Atoms transfer electrons.
Hydrogen Bond: Weak bond between hydrogen and electronegative atoms.
Functional Groups: Common groups include hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), and phosphate (-PO4).

pH and Buffers

pH measures the acidity or basicity of a solution. Buffers help maintain pH stability in biological systems.

pH Scale: Ranges from 0 (acidic) to 14 (basic); 7 is neutral.
Buffer: Combination of a weak acid and base that stabilizes pH.

Macromolecules: Proteins, Carbohydrates, Nucleic Acids, Lipids

Macromolecules are large, complex molecules essential for life.

Proteins: Made of amino acids; perform diverse functions including catalysis, structure, and transport.
Carbohydrates: Provide energy and structural support; include sugars and polysaccharides.
Nucleic Acids: DNA and RNA; store and transmit genetic information.
Lipids: Nonpolar molecules; include fats, oils, and phospholipids; important for cell membranes.

Polymerization and Hydrolysis

Macromolecules are formed by polymerization and broken down by hydrolysis.

Dehydration Synthesis: Builds polymers by removing water.
Hydrolysis: Breaks polymers by adding water.

Protein Structure and Function

Proteins have four levels of structure: primary, secondary, tertiary, and quaternary. Structure determines function.

Primary Structure: Amino acid sequence.
Secondary Structure: Alpha helices and beta-pleated sheets.
Tertiary Structure: 3D folding.
Quaternary Structure: Multiple polypeptides.

Carbohydrates and Lipids

Carbohydrates are classified by size and function. Lipids include fats and phospholipids, which are key components of cell membranes.

Monosaccharides: Simple sugars.
Polysaccharides: Complex carbohydrates.
Phospholipids: Major component of cell membranes.

Table: Comparison of Macromolecules

Macromolecule	Monomer	Function
Proteins	Amino acids	Catalysis, structure, transport
Carbohydrates	Monosaccharides	Energy, structure
Nucleic Acids	Nucleotides	Genetic information
Lipids	Fatty acids, glycerol	Membranes, energy storage

Key Equations

pH Calculation:
Atomic Mass:

Example:

Biofilm Formation: Mycobacterium tuberculosis forms biofilms that contribute to its pathogenicity.
Buffer Example: Blood contains buffers to maintain pH around 7.4.

Additional info: Some context and definitions were expanded for clarity and completeness.