Chapter 1: Introduction to Microbiology

Types of Microorganisms

Microorganisms are classified based on cellular structure and function. Understanding their differences is fundamental to microbiology.

• Eukaryotes: Organisms with a distinct nucleus enclosed by a membrane.

• Prokaryotes: Organisms lacking a true nucleus; DNA is not membrane-bound.

• Bacteria: Prokaryotic cells with cell walls containing peptidoglycan.

• Pathogens: Microbes that cause disease in hosts.

Notable Scientists and Their Discoveries

• Louis Pasteur: Disproved spontaneous generation; developed pasteurization.

• Robert Hooke: First to observe cells in cork; coined the term "cell."

• Joseph Lister: Introduced antiseptic techniques in surgery.

• Antonie van Leeuwenhoek: First to observe living microorganisms using a microscope.

• Robert Koch: Established Koch's postulates; linked specific microbes to specific diseases.

• Ignaz Semmelweis: Advocated handwashing to prevent puerperal fever.

Theories of Life

• Spontaneous Generation (Abiogenesis): Life arises from nonliving matter.

• Biogenesis: Life arises only from preexisting living cells.

Binomial Nomenclature System

• Two-name system: Genus species

• Genus: Capitalized; Species: lowercase; Both italicized (e.g., Escherichia coli).

Classification Hierarchy

• Order from largest to smallest: Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species

• Three Domains: Archaea, Bacteria, Eukarya

Symbiotic Relationships

• Parasitism: One organism benefits, the host is harmed.

• Mutualism: Both organisms benefit.

• Commensalism: One benefits, the other is unaffected.

Glycocalyx and Biofilms

• Glycocalyx: Sticky, protective layer surrounding a cell.

• Biofilm: Community of microorganisms encased in a self-produced matrix, adhering to surfaces.

Staining Techniques

• Basic Dyes: Positively charged; stain negatively charged cell components.

• Acidic Dyes: Negatively charged; stain background (negative staining).

• Gram Stain Steps:

  1. Crystal violet (primary stain)

  2. Iodine (mordant; complexes with crystal violet)

  3. Alcohol (decolorizer)

  4. Safranin (counterstain)

Chapter 2: Biochemistry Basics

Ions and pH

• Cations: Atoms that have lost electrons; positive charge.

• Anions: Atoms that have gained electrons; negative charge.

• Acids: Donate hydrogen ions (H+).

• Bases: Donate hydroxide ions (OH−).

• pH Scale: Measures hydrogen ion concentration.

  • Neutral: pH = 7

  • Acidic: pH < 7

  • Basic: pH > 7

• pH formula:

• Phenol red: pH indicator; turns yellow in acidic conditions.

Energy in Reactions

• Exergonic Reactions: Release more energy than they consume.

• Endergonic Reactions: Consume more energy than they release.

Macromolecules

• Amino Acids: Building blocks of proteins; linked by peptide bonds.

• Carbohydrates: Composed of sugars; provide energy and structure.

• Peptidoglycan: Structural component of bacterial cell walls.

• Capsules: Smooth glycocalyx; aids in adherence and evasion of phagocytosis.

• Mycolic Acid: Waxy coat in acid-fast bacteria (e.g., Mycobacterium tuberculosis).

Nucleic Acids

• DNA: Deoxyribonucleic acid; bases: A, T, G, C; sugar: deoxyribose.

• RNA: Ribonucleic acid; bases: A, U, C, G; sugar: ribose.

• Genes: Segments of nucleic acids encoding functional products.

Chapter 3: Prokaryotic Structure

General Features

• No nucleus; DNA in nucleoid region.

• 70S ribosomes (smaller than eukaryotic 80S).

• Divide by binary fission.

• Pleomorphism: Ability of some bacteria to alter shape or size in response to environmental conditions.

• Mycoplasma species: Lack a cell wall.

Binary Fission

• Process by which prokaryotes reproduce asexually.

• Steps:

  1. DNA replication

  2. Cell elongation

  3. Septum formation

  4. Cell separation

Transport Mechanisms

• Diffusion: Passive movement from high to low concentration.

• Simple Diffusion: Direct movement across membrane.

• Facilitated Diffusion: Requires transporter proteins.

• Active Transport: Moves substances from low to high concentration; requires energy and transporter.

• Osmosis: Movement of water across a membrane from high to low water concentration.

• Hypertonic Solution: Water exits cell; cell shrinks.

• Hypotonic Solution: Water enters cell; cell may burst.

• Isotonic Environment: No net water movement.

Flagella Arrangements

• Monotrichous: Single flagellum at one end.

• Lophotrichous: Cluster of flagella at one or both ends.

• Amphitrichous: Single flagellum at both ends.

• Peritrichous: Flagella distributed over entire cell surface.

Chemotaxis

• Movement of bacteria in response to chemical gradients (toward attractants, away from repellents).

Cell Wall Differences

• Gram-positive: Thick peptidoglycan layer; retains crystal violet stain (purple).

• Gram-negative: Thin peptidoglycan layer; outer membrane present; loses crystal violet, stains pink with safranin.

Fimbriae and Pili

• Fimbriae: Short, numerous; aid in attachment to surfaces.

• Pili: Longer, less numerous; involved in attachment and genetic exchange.

Archaea Cell Walls

• Contain pseudomurein instead of peptidoglycan.

Endospores

• Dormant, resistant structures formed by some bacteria under stress (e.g., Bacillus, Clostridium).

• Enable survival in harsh conditions.

Chapter 4: Eukaryotic Structure

General Features

• Defined nucleus with nuclear membrane.

• 80S ribosomes.

• Usually divide by mitosis.

Endosymbiotic Theory

• Explains origin of mitochondria and chloroplasts as formerly free-living prokaryotes engulfed by ancestral eukaryotic cells.

Mycology and Fungi

• Mycology: Study of fungi.

• Mycoses: Fungal infections.

• Dermatophytes: True pathogenic fungi infecting skin, hair, and nails.

• Dimorphic: Fungi that can exist as both yeast and mold forms.

Phagocytosis and Endocytosis

• Phagocytosis: Cell engulfs large particles or microbes.

• Endocytosis: General process of importing substances into the cell.

• Exocytosis: Exporting substances out of the cell.

Other Eukaryotic Pathogens

• Plasmodium: Causes malaria.

• Helminths: Parasitic worms.

Chapter 5: Genetics

Genomes and DNA Structure

• Genome: Entire genetic material of a cell or virus.

• Double-stranded DNA is antiparallel: one strand 5' to 3', the other 3' to 5'.

• Nucleotide components:

  • Phosphate group

  • Sugar (deoxyribose in DNA)

  • Nitrogen base (A, T, G, C)

• Base pairing: A-T, G-C.

• In RNA, uracil (U) replaces thymine (T).

• Types of RNA: Messenger RNA (mRNA), Transfer RNA (tRNA), Ribosomal RNA (rRNA).

DNA Replication

• Semiconservative process: Each new DNA molecule has one old and one new strand.

Gene Structure

• Exons: Coding regions.

• Introns: Non-coding regions.

Protein Synthesis

• Start codon: AUG (codes for methionine, MET).

Mutations

• Substitution: Incorrect nucleotide added.

• Insertion: Addition of one or more nucleotides.

• Deletion: Removal of one or more nucleotides.

Gene Regulation

• Operons: Groups of genes regulated together by a shared regulatory element.

• Transposons: "Jumping genes" that can move within the genome.

Chapter 6: Viruses and Prions

General Features of Viruses

• Acellular; require host cells to reproduce.

• Structure:

  • Capsid: Protein coat.

  • Genetic material: DNA or RNA.

  • Some have an envelope (lipid membrane).

  • Spikes (peplomers): Glycoprotein extensions for host cell attachment.

• Host specificity (tropism) determined by viral surface factors.

Viral Evolution

• Antigenic drift: Minor changes in viral proteins (e.g., influenza HA and NA spikes) due to mutations.

• Antigenic shift: Major genetic reassortment, leading to new viral strains.

Bacteriophages

• Viruses that infect bacteria.

Antiviral Drugs

• Acyclovir: Used to treat herpes virus infections.

Animal Virus Replication Cycle

• Six steps:

  1. Attachment

  2. Penetration

  3. Uncoating

  4. Replication

  5. Assembly

  6. Release

Prions

• Infectious proteins; lack nucleic acids.

• Cause spongiform encephalopathies (e.g., Creutzfeldt-Jakob disease).