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Microbiology Lecture Notes Review

Chapter 1: Introduction to Microbiology

Microorganisms (Microbes)

  • Definition: Organisms too small to be seen with the unaided eye, requiring a microscope for observation.

4 Major Microbe Groups:

  1. Bacteria

    • "Study of": Bacteriology

    • Examples: E.coli, Salmonella

  2. Viruses

    • "Study of": Virology

    • Examples: Coronavirus, Herpes, HIV

  3. Fungi

    • "Study of": Mycology

    • Examples: Mold (grows in cold conditions), Yeast (grows in warm/heat conditions)

  4. Parasites

    • "Study of": Parasitology

    • Examples: Protozoan parasites, Worms (organisms that take advantage of a host)

Important Roles of Microbes (Beneficial to Humans)

1. Key Ecological Roles (Natural/Beneficial Processes)

  • Decomposers of organic wastes:

    • Performed by bacteria and fungi.

    • Benefit: Break down wastes and recycle elements back into nature (e.g., breakdown of dead organisms).

  • Photosynthesis:

    • Performed by bacteria (Cyanobacteria) and protozoa (Algae), similar to plants.

    • Benefit: Produce oxygen for the atmosphere and glucose (via reaction: CO2 + H2O \rightarrow glucose + O_2).

  • Nitrogen Fixation:

    • Performed by bacteria that capture free atmospheric Nitrogen (N_2), which is not directly useful to humans.

    • Process & Benefit: Free atmospheric N2 (useless to humans) enters bacteria in the soil at plant roots. Bacteria convert N2 into useful nitrogen compounds (e.g., nitrates) required for plant development. Humans then consume these nitrogen-rich plants.

2. Bioremediation (Artificial/Non-Natural Uses; Human-Developed)

  • Certain bacteria can utilize pollutants as an energy source or produce enzymes to break down toxic waste.

  • Examples:

    • Oil Spills: Bacteria are introduced into the ocean to remove toxic substances.

    • Drain Clogs: Bacterial enzymes are incorporated into drain cleaners to remove clogs without harmful chemicals.

3. Commercial Uses (Food and Beverage Industry)

  • Bacteria:

    • Dairy products (cheese, yogurt).

    • Cosmetic procedures (Botox, derived from bacterial toxins).

  • Fungi (Yeast):

    • Ferment grape sugar to alcohol in alcoholic beverages (wine, beer).

    • Leavening in breads.

4. Application in Medicine

  • Some microbes produce substances used as antibiotics (medications that destroy harmful bacteria).

    • Examples: Penicillin and Neomycin.

    • Production Process (Penicillin): Fungal mold (found in mushroom gills) produces penicillin. Scientists grow this mold in large batch fermenters with sugar and other ingredients, then separate and purify penicillin for medicinal use.

Pathogenic Microbes (Pathogens)

  • Definition: Harmful microbes; living agents capable of causing disease in a host.

  • Not all microbes are harmful; less than 1% of bacteria are pathogenic.

  • Examples of Pathogen-Disease Pairs:

    • Bacteria: Neisseria gonorrhoeae
      ightarrow Gonorrhea.

    • Fungal Yeast: Tinea pedis
      ightarrow Athlete's foot.

    • Virus: SARS-CoV-2
      ightarrow COVID-19.

Normal Microbiota (Normal Flora)

  • Definition: Resident microbes found both inside and outside the human body that typically cause no harm; considered 'friendly' or 'good' microbes.

  • Play important roles in human health and disease prevention.

  • Characteristics:

    • Normal or always found in specific body areas.

    • May be beneficial to the host.

      • Produce useful substances humans cannot make (e.g., Vitamin K for blood clotting, produced by E.coli).

      • Prevent overgrowth of harmful microbes by rapidly dividing and occupying space, leaving no room for invading pathogens.

  • Examples:

    • Streptococci: Found in the mouth.

    • Staphylococci: Found on the skin.

    • E.coli: Found in the colon.

Milestones and Major Contributions to Microbiology

  1. Van Leeuwenhoek

    • "Father of Microbiology"; a lens maker.

    • First scientist to observe live microorganisms through magnifying lenses.

    • Made detailed drawings of microorganisms.

  2. Jenner

    • "Father of Vaccines".

    • Contribution: Immunization and eventual elimination of Smallpox.

    • Observation: Noticed milkmaids infected with Cowpox virus were protected from Smallpox.

    • Experiment: Took material from a cowpox pustule (lesion) and injected it into a healthy human. The recipient never developed Smallpox.

    • Outcome: Developed the first "vaccine" (against Smallpox).

  3. Pasteur

    • Disproved: "Spontaneous Generation" (the idea that non-living things give rise to living things).

    • Established: "Theory of Biogenesis" (living things arise only from pre-existing living cells), later supported by Koch's "Germ Theory of Disease".

    • Germ Theory of Disease: Microorganisms (pathogens) cause disease; diseases do not happen spontaneously.

    • Swan-Neck Flask Experiment: Poured beef broth into a long-necked flask, heated and bent the neck into an S-shape, then boiled the broth. Microorganisms did not appear in the cooled solution, even after long periods. This demonstrated that: (1) Microorganisms were present in open flasks, contaminating broth (cloudy growth); (2) Boiling sterilized the broth; (3) The S-bend prevented external microorganisms from entering, while allowing air.

  4. Lister

    • A surgeon who pioneered the idea of sterile surgical procedures.

    • Began using chemical solutions (antiseptics) to treat surgical wounds and kill microbes.

    • Impact: Reduced surgical infections and deaths significantly.

    • Applied the "Germ Theory of Disease" to medical practices.

  5. Koch

    • Established: The "Germ Theory" – infectious diseases are caused by live pathogens; a specific pathogen causes a specific disease with specific symptoms.

    • Discovery: Identified Bacillus anthracis as the cause of Anthrax in cattle and sheep.

    • Developed: "Koch's Postulates" – a sequence of experimental steps to relate a specific microbe to a specific disease and its symptoms.

  6. Ehrlich

    • Contribution: Treatment of disease with drugs and drug therapy.

    • Developed: The concept of chemotherapy, discovering the first chemical substance (Salvarsan) against syphilis by destroying the pathogen.

    • Coined: The term "magic bullet" to describe a chemical substance that could selectively target and destroy a pathogen without harming the infected host.

  7. Fleming

    • Discovered: The first antibiotic, penicillin, derived from fungal mold.

    • Observation: Noticed that mold colonies contaminating culture plates inhibited the growth of surrounding bacteria (due to penicillin production).

  8. Marshall

    • Proved: Most peptic ulcers were caused by the bacterium H.; pylori (not stress or diet as previously believed).

    • Impact: Led to understanding the causative link between H. pylori
      and gastric (stomach) cancer (chain of events: H. pylori
      ightarrow peptic ulcers
      ightarrow gastric cancer).

Emerging Infectious Diseases (EIDs)

  • Definition: Diseases that are new or changing, and are increasing (in frequency) or have the potential to increase in the near future.

  • Current Prevalent EIDs:

    • SARS-CoV-2
      ightarrow COVID-19

    • Zika Virus
      ightarrow Zika Virus Disease

    • West Nile Virus
      ightarrow West Nile Virus Encephalitis

    • Influenza Virus
      ightarrow Influenza

Key Factors Contributing to the Emergence of EIDs

  • Global Travel: Facilitates easy and fast spread of pathogens (e.g., air travel).

  • Rapid Urbanization: Can disturb contaminated soil, leading to airborne pathogens.

  • Natural Disasters: Disrupt clean water facilities and electricity, leading to contaminated water and diarrheal diseases.

  • Frequent Gene Mutations: Harmless microbes can undergo DNA changes, becoming harmful.

  • Climate Change:

    • Wet areas: Increase mosquito-transmitted diseases.

    • Dry areas: Increase airborne transmitted diseases.

  • Developing Drug Resistance: Pathogens no longer respond to drugs, making infections harder to treat.

Chapter 2: Organic Compounds

Inorganic Compounds

  • Small, simple molecules that usually lack carbon.

  • Examples: H2O, O2, salts, acids, and bases.

Organic Compounds

  • Large, structurally complex molecules.

  • Always contain carbon (minimum requirement) and are held together by covalent bonds.

Four Most Common Elements in Organic Compounds

  1. Carbon (C)

  2. Hydrogen (H)

  3. Oxygen (O)

  4. Nitrogen (N)

  • Organic compounds usually contain a chain of carbon atoms, forming a "carbon skeleton."

  • Functional Groups: Groups of atoms that can bind to the carbon skeleton.

    • Adding different functional groups results in different types of organic compounds.

    • Examples: Hydroxyl (alcohol, -OH), Amino (-NH2), Carboxyl (-COOH), Phosphate (-PO4).

Building Up vs. Breaking Down of Molecules

Building Up (Synthesis)

  • Process: Dehydration Synthesis (to lose H_2O).

  • Several small monomers combine to form one large polymer.

  • Forms covalent bonds (e.g., -O-O-O-O) by removing -OH from one monomer and -H from another.

Breaking Down

  • Process: Hydrolysis (input of H_2O).

  • One large polymer breaks down into several small monomers.

  • Breaks covalent bonds by adding -OH and -H from water across the bond.

The Major Organic Compounds

1. Carbohydrates (Carbs or Sugars)

  • Composition: Carbon, Hydrogen, Oxygen.

  • Usually end in "-ose."

  • Classified into 3 major groups based on size:

    • i. Monosaccharides ("Simple Sugars")

      • Contain 3-7 carbon atoms.

      • Sweet-tasting, water-soluble.

      • Provide a quick source of energy for living cells (e.g., glucose for humans).

      • Examples: Glucose, Deoxyribose (sugar in DNA), Fructose.

    • ii. Disaccharides

      • Formed when 2 monosaccharides link via a covalent glycosidic bond through dehydration synthesis.

      • Provide structural components for bacterial cell walls.

      • Examples: Sucrose, Lactose.

    • iii. Polysaccharides

      • Consist of tens or hundreds of monosaccharides joined through dehydration synthesis.

      • Function: Provide long-term energy storage and structural components for plant cell walls (cellulose).

      • Examples: Starch (plant cells; long-term energy), Glycogen (animal cells; long-term energy source), Cellulose (plant cell walls; fiber) – all are polymers of glucose.

2. Proteins

  • Composition: Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur.

  • Essential in cell structure and function (structure dictates function).

  • Most diverse among organic compounds in terms of structure and function (many protein shapes = many protein functions).

  • Protein Examples and Key Functions:

    • Structural Proteins: Keratin reinforces skin, providing a physical barrier to infection.

    • Transporter Proteins: In cell membranes (e.g., protein channels, protein carriers) regulate substance movement.

    • Enzymes: Proteins that speed up chemical reactions.

    • Antibodies: Proteins involved in the immune response.

    • Bacterial Toxins: Poisonous proteins produced by some bacteria.

  • Amino Acids: The building blocks (subunits) of proteins.

    • A total of 20 different amino acids exist.

    • Each contains a central carbon atom bonded to 4 things: an amino group ( -NH_2 ), a carboxyl group ( -COOH ), a hydrogen atom ( -H ), and a variable side group (R group), which determines the amino acid's specific properties.

    • Only 2 amino acids contain sulfur, which can cause bends in protein structure.

  • Peptide Bonds: Covalent bonds linking two amino acids together via dehydration synthesis, formed between the amino group of one and the carboxyl group of another (removing -OH from carboxyl and -H from amino).

Protein Structure

  • Protein shape (structure) determines its function.

  • Denaturation: If a protein loses or changes its shape, it loses or changes its function.

    • Occurs when proteins encounter harsh environments (e.g., high temperature, low pH/acidic conditions).

    • May be permanent.

  • Levels of Protein Structure (from simplest to most complex):

    1. Primary Structure: A linear sequence of amino acids, forming a polypeptide chain/strand (no folds or bends).

    2. Secondary Structure: Occurs when the amino acid chain folds and coils into a helix (e.g., hair protein) or a pleated sheet (e.g., skin protein), often stabilized by hydrogen bonds between different parts of the backbone.

    3. Tertiary Structure: Occurs when the helix or pleated sheet folds irregularly into a 3D shape, forming disulfide bridges (between two far-apart sulfur-containing amino acids), hydrogen bonds, and ionic bonds within the single polypeptide chain.

    4. Quaternary Structure: Consists of 2 or more polypeptide chains (tertiary subunits) bound to each other, forming a bulky and complex functional protein.

      • Examples: Hemoglobin (4 subunits), Antibodies (4 tertiary subunits), Enzymes (several subunits).

3. Lipids

  • Composition: Carbon, Hydrogen, and Oxygen.

  • Subunits (Building Blocks): Triglycerides (for simple lipids).

  • Primary components of cell membranes (phospholipid bilayer).

  • Classes of Lipids:

    • i. Simple Lipids (Fats or Triglycerides):

      • Contain 1 glycerol molecule and 3 fatty acid chains, linked by covalent ester bonds via dehydration synthesis.

      • Saturated Fatty Acids: Have no double bonds in their carbon chains (only single bonds), making them solid at room temperature.

      • Unsaturated Fatty Acids: Have one or more double bonds in their carbon chains, making them liquid at room temperature.

      • Key Function: Alternative energy source when carbohydrates are unavailable.

    • ii. Complex Lipids (e.g., Phospholipids):

      • Cell membranes are made of phospholipids, which contain 1 glycerol, 2 fatty acids, and a phosphate group.

      • Function: Regulate transport across cell membranes, controlling what enters and leaves the cell (leading to homeostasis).

      • Have polar regions (charged, hydrophilic heads) and nonpolar regions (uncharged, hydrophobic fatty acid tails).

      • Examples: Waxes, Glycolipids (lipids with a carbohydrate attached), Mycolic acid (a waxy lipid material in the cell wall of Mycobacterium tuberculosis).

    • iii. Steroids and Sterols:

      • Formed when three 6-carbon rings (A, B, C) attach to one 5-carbon ring (D).

      • A Sterol is a steroid with an -OH (hydroxyl) group attached to one of the 6-carbon rings.

      • Steroid Examples: Cholesterol, hormones, some vitamins.

      • Function: Structural component of cell membranes in eukaryotic cells.

        • Cholesterol: A sterol found in animal cell membranes.

        • Phytosterol: A sterol found in plant cell membranes.

        • Ergosterol: A sterol found in fungi cell membranes.

4. Nucleic Acids

  • Composition: Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus.

  • Examples: DNA, RNA, and ATP.

  • Subunits (Building Blocks): Nucleotides, linked by covalent phosphodiester bonds via dehydration synthesis.

  • Each Nucleotide Consists of:

    • i. Sugar: A 5-carbon pentose sugar (deoxyribose in DNA, ribose in RNA).

    • ii. Phosphate Group.

    • iii. Base: A nitrogen-containing base, belonging to either the Purine family or Pyrimidine family.

      • Purines: Adenine (A), Guanine (G).

      • Pyrimidines: Cytosine (C), Uracil (U, in RNA), Thymine (T, in DNA).

  • DNA (Deoxyribonucleic Acid):

    • A double-stranded molecule (double helix, twisted).

    • Has a sugar-phosphate backbone.

    • Base pairing: Adenine always pairs with Thymine (A-T) through hydrogen bonds; Cytosine always pairs with Guanine (C-G) through hydrogen bonds.

    • Thymine is only found in DNA.

    • Function: Stores genetic information.

  • RNA (Ribonucleic Acid):

    • Usually a single-stranded molecule.

    • Has a sugar-phosphate backbone.

    • No base pairing (typically).

    • Uracil is usually only found in RNA (replaces thymine).

    • 3 Kinds of RNA: mRNA (messenger RNA), tRNA (transfer RNA), rRNA (ribosomal RNA).

    • Function: Involved in protein synthesis.

  • ATP (Adenosine Triphosphate):

    • Adenosine (sugar and base) is attached to 3 phosphate groups.

    • A nucleic acid but remains as a "single nucleotide."

    • HIGH ENERGY COMPOUND.

    • Stored chemical energy is released by hydrolysis (breaking of bonds) connecting the phosphate groups.

Chapter 4: Functional Anatomy of Typical Prokaryotic Cells

General Characteristics

  • Average Size: Measured in microns (\mu m), important for identification.

  • Monomorphic: Majority of bacteria have an identical shape.

  • Pleomorphic: Some bacteria exhibit several shapes, indicating more than one type of bacteria may be present.

Cell Shape - Prokaryotic Cells

3 Basic Shapes for Bacteria:

  1. Coccus: Round/spherical shape.

  2. Bacillus: Rod-shaped.

  3. Spiral: All motile, with 3 types:

    • a. Vibrio: Comma-shaped/bent rod.

    • b. Spirillum/Spirilla (plural):

      • Rigid cells.

      • Short/thick.

      • Loosely-coiled cells.

      • Move via External Flagella.

    • c. Spirochetes:

      • Flexible cells.

      • Longer/thin cells.

      • Tightly-coiled cells.

      • Move via Endoflagella (internal axial filaments).

Cell Arrangement - Prokaryotic Cells

  • For some bacteria, the Genus name may combine arrangement and shape (e.g., Streptococcus pneumoniae are round cells in chains).

  • Pairs: "diplo-" prefix (e.g., Diplococci, Diplobacilli).

  • Clusters: "staphylo-" prefix (e.g., Staphylococci).

  • Chains: "strepto-" prefix (e.g., Streptococci, Streptobacilli).

  • Groups of 4: Tetrads (cocci only).

  • Cube-like groups of 8: Sarcinae (cocci only).

Prokaryotic Cell Structure

Glycocalyx

  • Optional: Secreted by SOME bacteria; may or may not be present.

  • Location: Layer external to the cell wall, surrounding the bacteria.

  • Description: Viscous, gelatinous (semi-solid), sticky (like maple syrup).

  • Composition: Made up of polysaccharide or polypeptide (protein).

  • Two Types of Glycocalyces:

    • a. Capsule:

      • Made of polysaccharide.

      • Thick, organized, and tightly attached to the cell wall.

      • Function: Helps bacterium attach to host tissue due to its "stickiness."

      • Function: Makes bacterium appear larger, aiding escape from phagocytosis (engulfment by immune cells).

      • Examples: Streptococcus mutans (in mouth), Streptococcus pneumoniae (causes pneumonia, has huge capsules).

    • b. Slime Layer:

      • Made up of protein.

      • Thin, unorganized, and loosely attached to the cell wall.

Flagellum

  • May be found in some bacilli and all spirilla-type bacteria.

  • 3 Parts:

    1. Filament: Outermost region.

    2. Hook: Attaches the filament to the basal body.

    3. Basal Body: Anchors the flagellum to the cell.

Axial Filament (Endoflagellum)

  • Optional: May or may not be present.

  • Found in: Spirochetes.

  • Location: Internal to the cell (intracellular) and anchored at one end, within the cell wall.

  • Composition: Made of proteins.

  • Function: Rotation of endoflagella allows the cell to move in a corkscrew/spiral motion.

Fimbriae

  • Location: External to the cell.

  • Composition: Made of proteins.

  • Function: Hair-like appendages that allow for attachment to surfaces or other cells.

Pili

  • Location: External to the cell.

  • Composition: Made of proteins.

  • Function: Involved in "twitching" motility and DNA transfer from one cell to another (e.g., conjugation pilus facilitates DNA transfer, permanently altering the recipient cell's DNA).

The Cell Wall

  • Location: Outermost layer if no glycocalyx is present (sequence: +/-\ capsule \rightarrow cell : wall \rightarrow cell : membrane).

  • Most bacteria have them, except for Mycoplasma.

  • Functions: Prevents osmotic lysis (bursting) and protects the cell membrane.

  • Composition: Contains peptidoglycan (rows of carbohydrates connected to proteins), with varied amounts per cell.

    • Bacteria with more peptidoglycan are Gram-positive (stain purple).

    • Bacteria with less (thin layer) peptidoglycan are Gram-negative (stain red/pink).

Gram-Negative Cell Wall

  • Less/thin peptidoglycan layer.

  • No teichoic acids.

  • Possesses an Outer Membrane containing Lipo-poly-saccharide (LPS).

    • 3 Components of LPS:

      1. Lipid A: Embedded in the cell wall's outer membrane; functions as a toxin.

      2. Core Polysaccharide: "Middle man"; joins Lipid A and O Polysaccharide.

      3. O Polysaccharide: Sticks out; acts as a surface marker (antigen), helping distinguish between subspecies/strains (e.g., E.coli O157:H7, where O157 refers to the O polysaccharide).

  • Resistance: Resistant to penicillin.

Gram-Positive Cell Wall

  • Thick peptidoglycan layer.

  • Contains Teichoic Acids (Gram-positive only).

    • Function: Attracts ions to make the cell wall stronger and adds rigidity.

  • No outer membrane.

  • Sensitivity: Sensitive to penicillin (PCN destroys Gram-positive bacteria).

Gram Staining: Differential Staining of Gram-Positive vs. Gram-Negative Bacteria

  • Purpose: Differential (classifies and identifies different populations of bacteria) based on cell wall differences. Helps identify bacteria by: (1) Gram reaction, (2) shape, (3) arrangement, (4) size.

  • Staining Principle: Stains the peptidoglycan-containing cell wall (which picks up certain dyes).

  • Steps:

    1. Application of crystal violet (purple dye): All cells turn purple/violet.

    2. Application of iodine (mordant): Forms large crystal violet-iodine complexes within cells.

    3. Alcohol wash (decolorization): Washes away dye from Gram-negative cells, but Gram-positive cells retain it.

    4. Application of safranin (counterstain): Stains Gram-negative cells red/pink.

Atypical Cell Walls

  • Genus Mycobacterium:

    • Have an extra waxy lipid (mycolic acid) "bound" to peptidoglycan in their cell wall's outer membrane.

    • Mycolic acid prevents digestion by phagocytosis; phagocytes engulf the bacteria, but they are not destroyed.

    • Requires acid-fast stain instead of Gram stain.

  • Genus Mycoplasma:

    • Rare; lack cell walls entirely.

  • Domain Archaea:

    • No peptidoglycan present in their cell walls.

The Plasma (Cell) Membrane

  • Location: Deep to the cell wall.

  • Composition: Phospholipid bilayer that encloses the cytoplasm.

  • Proteins: Peripheral proteins on the membrane surface; Integral and transmembrane proteins penetrate the cell membrane.

  • Functions:

    1. Transport: Allows for the passage of some molecules but not others ("selective permeability").

    2. Site of ATP Production: Because bacteria lack mitochondria.

    3. Site of Photosynthesis: In certain bacteria (e.g., Cyanobacteria in Kingdom Monera), because they lack chloroplasts.

Movement of Material Across Cell Membranes

  • Passive Transport:

    • Movement of particles from an area of high concentration to low concentration.

    • No energy required.

    • Types:

      • Simple Diffusion: Movement of small, uncharged particles directly across the cell membrane.

      • Facilitated Diffusion: Movement of large, charged particles that require a protein channel or carrier.

      • Osmosis: Movement of H_2O across a membrane, driven by a concentration difference. Water moves TOWARDS the area of high particle concentration.

        • Isotonic solution: Same particle concentration inside and outside the cell; no net H_2O movement.

        • Hypotonic solution: Low particle concentration outside the cell; cell swells because H_2O enters.

        • Hypertonic solution: High particle concentration outside the cell; cell shrinks because H_2O leaves.

        • Summary: Water moves from a low solute (hypotonic environment) to a high solute (hypertonic environment).

  • Active Transport:

    • Movement of particles from an area of low concentration to high concentration.

    • Requires energy (ATP).

    • Typically for large and charged particles.

Cytoplasm

  • Location: The substance deep to the plasma membrane; the cell membrane surrounds the cytoplasm.

  • Composition: 80\% water plus proteins, carbohydrates, lipids, and ions.

  • No organelles present, except for ribosomes.

Bacterial Ribosomes

  • Are called 70S ribosomes.

  • Not surrounded by a membrane (non-membrane bound).

  • Site of protein synthesis.

  • Composed of 2 subunits fused together: a large subunit and a small subunit.

Genetic Material - The Nucleoid and Plasmid

  • Nucleoid (not a nucleus):

    • "Nucleus-like" region.

    • Contains the bacterial chromosome – a circular thread of DNA, supercoiled/compacted, containing most of the cell's genetic information.

    • NOT surrounded by a nuclear membrane.

  • Plasmid:

    • Small, circular, extrachromosomal genetic material.

    • Carry "non-crucial" genes that play a role in adaptability and survival (e.g., genes for antibiotic resistance and production of toxins).

Inclusion Bodies ("Reserve Deposits")

  • Structures that store reserve material in the cytoplasm.

  • Examples:

    • Metachromatic granules: Phosphate reserve/storage.

    • Polysaccharide granules: Energy reserve of polysaccharide (peptidoglycan + LPS).

    • Lipid inclusions: Energy reserve of fat.

    • Carboxysomes: Enzyme reserves involved in photosynthesis (found in bacteria like cyanobacteria, major producers of oxygen).

Endospores

  • Formed inside the cell (endogenous).

  • Specialized "resting" (dormant) forms of cells, seen in only a few bacteria (e.g., produced by Genus Bacillus and Genus Clostridium).

  • Also called "spore formers."

  • Produced when nutrients are depleted (when the cell is stressed), for survival.

  • Contain the bacterial cell's genetic material.

  • Highly resistant to desiccation (dryness), heat, chemicals, and radiation – making them very tolerant and dangerous because they can become active later.

  • Sporulation: The process of endospore formation (resting cell state).

  • Germination: The process where an endospore returns to an active cell state.

  • Note: Before a bacterium dies, it can separate and safeguard some of its DNA, which becomes part of the spore (with multiple coats). The endospore can be released and, if viable, can germinate to produce a new active cell, ensuring survival even if the original cell dies.

Comparison: Prokaryotes vs. Eukaryotes

Prokaryotes

  • One circular chromosome (supercoiled), not enclosed in a membrane.

  • No membrane-bound organelles.

  • 70S ribosomes.

  • Unicellular.

  • Divide by binary fission.

Eukaryotes

  • Paired chromosomes within a nuclear envelope (nucleus).

  • Membrane-bound organelles.

  • 80S ribosomes.

  • Polysaccharide in cell walls (if cell wall present).

  • Unicellular and multicellular.

  • Divide by mitosis and meiosis.

Eukaryotic Cell Structures (Brief Overview)

  • Cell Wall:

    • Found in plants, algae (Kingdom Protista), and fungi.

    • Made of carbohydrates: Cellulose (fiber) in plants, Chitin in fungi.

    • Provides structure and protection.

  • Cell Membrane:

    • Has sterols (a type of steroid with an -OH group) bound to the cell membrane.

    • Has carbohydrates for attachment and cell-to-cell recognition.

    • Capable of endocytosis:

      • Phagocytosis: Engulfing particles.

      • Pinocytosis: Engulfing fluids and dissolved substances.

  • Ribosomes: 80S ribosomes; site of protein synthesis.

  • Nucleus: Double-membrane structure (nuclear envelope) containing the cell's DNA.

  • Endoplasmic Reticulum (ER):

    • A folded transport network.

    • Rough ER: Studded with ribosomes; sites of protein synthesis.

    • Smooth ER: No ribosomes; site of cell membrane, fat, and hormone synthesis.

  • Golgi Complex (Apparatus): Modifies, sorts, and packages proteins from the ER.

  • Lysosomes: Vesicles formed by the Golgi complex; contain digestive enzymes.

  • Vacuoles: Cavities in the cell formed by the Golgi complex; bring food into cells and provide storage.

  • Mitochondria: Double membrane with inner folds (cristae) and fluid (matrix); involved in cellular respiration (ATP production).

  • Chloroplasts: Locations for photosynthesis; contain flattened membranes with chlorophyll pigment.

  • Centrosomes: Located at polar regions of the cell; form the mitotic spindle and play a critical role in cell division (not the same as centromeres).

Chapter 10: Classification of Living Things

Why Classify Living Things?

  • Helps in the quick identification of microbes.

  • Identification is useful for diagnosis, treatment, and prevention (education, vaccines).

  • Taxonomy: The science of classification.

  • Taxon/Taxa: A class, group, or category of something being classified.

  • Phylogeny: Shows evolutionary relationships between organisms in a group (e.g., humans vs. apes).

The Taxonomic Hierarchy

  • Used for naming and identifying living things.

  • 8 taxa ranked in order.

  • Highest Taxa: Domain and Kingdom (broad, large groups/categories).

  • Lowest Taxa: Genus and species (very specific, small groups).

    • Example: Panthera pardus

Binomial Nomenclature

  • A two-part naming system for living organisms.

  • Consists of the Genus name (capitalized), followed by the species name (lowercase, spelled out fully).

  • Examples:

    • Escherichia coli, Helicobacter pylori (bacteria)

    • Penicillium chrysogenum (fungus/mold)

    • Homo sapiens (humans)

The 3 Domains System (Developed in 1990)

  • Based on cell type: Prokaryote vs. Eukaryote. All cellular life exists as either prokaryotic or eukaryotic cells.

  • 1. Domain Archaea (Prokaryotic Cell)

    • Kingdom: Monera (historically).

    • No peptidoglycan in cell walls.

    • Inhabit extreme habitats (e.g., hot springs, foot of volcanoes, high Na^+ environments/halo-, methanogens).

  • 2. Domain Bacteria (Prokaryotic Cell)

    • Kingdom: Monera (historically).

    • Yes, peptidoglycan in cell walls (gives structure).

    • Inhabit normal habitats.

  • 3. Domain Eukarya (Eukaryotic Cell)

    • Contains Kingdoms: Protista, Fungi, Plantae, Animalia.

The 5 Kingdoms (LUCA - Last Universal Common Ancestor)

(Note: Kingdom Monera is split into Domains Bacteria and Archaea in the 3-Domain system, but is included here from the older 5-Kingdom perspective.)

  1. Kingdom Monera (Domain Bacteria and Archaea)

    • Prokaryotic.

    • Unicellular.

    • Ex: Bacterium, E.coli

  2. Kingdom Protista

    • Simplest eukaryotes.

    • Mostly unicellular.

    • Ex: Amoeba, Algae.

  3. Kingdom Fungi

    • Eukaryotic.

    • Some unicellular (Yeast, thrives in warm/heat), others multicellular (Mold, thrives in cold temps).

  4. Kingdom Plantae

    • Eukaryotic.

    • Multicellular, autotrophs (self-feeders by photosynthesis), has cell wall.

    • Ex: Plants.

  5. Kingdom Animalia (Part of Domain Eukarya)

    • Eukaryotic.

    • Multicellular, complex, heterotrophs (rely on other organisms for food).

    • Ex: Animals (large roundworms, houseflies).

Autotrophs vs. Heterotrophs

  • Autotrophs: Organisms that can produce their own food ("self-feeders").

    • Types: Photoautotrophs (use light energy), Chemoautotrophs (use chemical energy).

    • Examples: Plants (Kingdom Plantae), Algae (Kingdom Protista).

  • Heterotrophs: Organisms that rely on consuming other organisms for food.

    • Types: Photoheterotrophs, Chemoheterotrophs.

    • Examples: Herbivores, carnivores, omnivores (Kingdom Animalia).

Species and Subspecies (Not a Taxon)

  • Species: The lowest taxon; spelled with a lowercase letter.

1. Prokaryotic Species (Bacterial Species)

  • A population of bacterial cells with similar characteristics.

    • Example: Streptococcus species include Streptococcus pneumoniae and Streptococcus pyogenes .

  • Clones: A population of bacterial cells derived from a single parent cell; all are generally identical.

  • Subspecies/Strain/Serovar: Members of a clone (species) that are no longer genetically identical due to genetic mutations (changes in DNA) over time. These are ALWAYS PATHOGENIC.

    • Subspecies/strains are identified by numbers or letters that follow the species name (e.g., E.coli O157:H7).

2. Eukaryotic Species (Non-Bacterial)

  • A group of organisms that differ from each other but are closely related genetically.

  • Several related species can form a Genus (e.g., Homo neanderthalensis, Homo erectus, Homo sapiens).

Classification of Viruses

  • Viruses are not cells; they are "acellular" (no cell membrane or cytoplasm). They are not prokaryotic or eukaryotic, and thus have no domain or kingdom.

  • Obligate Intracellular Parasites: Must invade a host cell to multiply.

  • Classification Hierarchy: Usually by FAMILY ightarrow GENUS and SPECIES.

    • Family: Highest taxon for viruses; family names end in "-viridae" (e.g., Retroviridae).

    • Genus: Genus names end in "-virus" (e.g., Enterovirus, Influenzavirus).

    • Species: A group of viruses sharing similar genetic information and an ecological niche (host) (e.g., HIV, SIV).

  • Can have viral subspecies/strains (e.g., strains of influenza A virus: H1N1 (swine flu), H5N1 (avian flu)).

Methods of Classifying and Identifying Microbes

  1. Morphological (Structural) Characteristics: Look at the shape, arrangement (single, pairs, groups), and size of bacteria.

  2. Differential Staining: Using dyes (e.g., Gram staining of bacterial cell walls) to differentiate bacteria based on the chemical composition of their cell wall (amount of peptidoglycan).

    • Gram-positive bacteria vs. Gram-negative bacteria.

  3. Biochemical Tests (Physiological Tests): Using a series of "yes or no" questions to determine metabolic characteristics of bacteria.

    • Example: "Can unknown bacterium break down glucose?" Yes: E.coli; No: H.; pylori or S.; pneumoniae

  4. Serology (Study of Blood Serum): Serological testing helps differentiate among strains within species by analyzing DNA sequences or detecting antibodies against specific microorganisms.

    • Example: Distinguishing pathogenic E.coli from non-pathogenic (normal) E.coli .

  5. PCR (Polymerase Chain Reaction): "DNA amplification" (like a photocopier).

    • Method used to make many copies (amplify) a specific DNA segment from a single DNA sequence, useful for identification.

  6. Textbooks/Manuals: Bergey's Manual of Determinative Bacteriology provides systematic schemes for identifying unknown bacteria (often considered the "Bible of bacterial identification").

Chapter 13: Viruses

General Characteristics of Viruses (Not Cells)

  • Size: Extremely small, measured in nanometers (vs. bacteria measured in micrometers).

  • Mission: To multiply themselves by taking over host cells.

  • Acellular: Not a cell; lacks cell membrane and cytoplasm. Not prokaryotic or eukaryotic, therefore no domain or kingdom.

  • Nucleic Acid: Contains a single type of nucleic acid – either DNA or RNA (some can start life as RNA).

  • Obligate Intracellular Parasite: Must invade a living host cell to multiply; harms the host cell.

  • No Reproduction: Viruses do NOT reproduce (only living things reproduce); they cannot perform binary fission, mitosis, or meiosis.

Structural Components

  • Core: Contains DNA or RNA (the genetic material).

  • Capsid: Surrounds the core; made of protein subunits called capsomeres. Protects the DNA (like a brick wall, where individual bricks are capsomeres).

  • Envelope: Optional outer part (non-enveloped/naked vs. enveloped viruses).

  • Spikes: Optional part, only present if an envelope is present. Spikes anchor to the envelope and help the virus attach to host cells.

Host and Tissue Range

  • Host Range: Viruses have a specific host range (host specificity).

    • Plant viruses attack plant cells.

    • Animal viruses attack animal cells.

    • Bacterial viruses (Bacteriophages) attack bacteria.

  • Tissue Range: Viruses infect specific tissues (tissue specificity).

    • Animal viruses causing viral hepatitis infect the liver.

    • Animal viruses causing viral encephalitis infect the brain.

Virus Transmission

  • Various modes: air, food/water, direct contact, insects (if the insect is infected, it can transmit the disease).

Virus Terminology

  • "Phage": Represents the word "virus."

  • Bacteriophage: A bacterial virus; its host is a bacterium.

  • Phage DNA: Viral DNA.

General Morphology of Viruses (Based on Capsid Architecture)

  1. Helical Viruses: Twisted, staircase-like, cylindrical, hollow in the middle.

  2. Polyhedral Viruses: Have several triangular bases.

  3. Complex Viruses: Only exist as bacterial viruses.

    • Have a capsid (head) surrounding the core, usually with a tail fiber, baseplate, pin, and sheath that can elongate or shorten.

Viral Taxonomy (No Domain, No Kingdom - Not Cells)

  • Family Names: End in "-viridae" (e.g., Herpesviridae, Retroviridae).

  • Genus Names: End in "-virus" (e.g., Enterovirus, Influenzavirus).

  • Viral Species (Lowest Taxon): A group of viruses sharing similar genetic information and an ecological niche (host) (e.g., HIV, SIV (in primates-monkeys)).

  • Viral Subspecies/Strains: (e.g., HSV-1, HSV-2 (herpes simplex virus), Influenza H1N1, Influenza H5N1).

Growing Viruses in the Laboratory

  • Bacteriophages: Grown in bacteria (as their host cells).

    • Form plaques (clear spaces) on bacterial lawns, indicating viral growth and cell damage by a single virus.

    • Plaques correspond to plaque-forming units (PFU).

    • Viruses invade and kill bacterial hosts, leaving clear areas of dead bacteria.

  • Animal Viruses: Grown in living animals, embryonated eggs, or animal tissue cultures ("growing chick").

    • Virally infected animal cells are detected by their deterioration, called cytopathic effect (CPE).

    • CPE indicates damage done ONLY to animal host cells.

Viral Identification

  • Cytopathic Effects (CPE): The type of damage done to animal host cells.

  • Serological Tests: The most common method; involves looking for antibodies against a virus in blood samples.

  • Polymerase Chain Reaction (PCR): Isolating and making many copies of viral DNA to identify the virus.

Virus Multiplication

  • Viruses must invade a living host cell to multiply because they are obligate intracellular parasites.

  • Viruses must take over the host's metabolic machinery (host's DNA). They "hijack" the host cell, forcing it to make viral parts and assemble them.

Multiplication of Bacteriophages

  • Bacteriophages can multiply by two cycles:

    1. Lytic Cycle (Required): Phases cause lysis and death of the bacterial host cell.

      • Virus enters, completes the lytic cycle, leading to host cell death.

    2. Lysogenic Cycle (Optional): Phage does NOT cause the death of the bacterial host cell immediately.

      • Phage DNA is incorporated into the bacterial host cell's DNA.

      • Virus can enter the lytic cycle, pause, enter and complete the lysogenic cycle (making many copies of the infected bacteria host cell), then re-enter and complete the lytic cycle, leading to host cell death.

  • Virion: A newly-formed, mature virus; capable of infecting a new cell; leaves the bacterial host cell once made.

Bacteriophage Lytic Cycle (Stages: AP-BMR)

  1. Attachment (Adsorption): Phage attaches to the host cell.

    • Bacterial virus tail fibers attach to specific cell wall receptors.

    • A hole is needed for viral DNA to enter; the entire bacterial virus does NOT enter.

  2. Penetration: Phage penetrates the host cell and injects its DNA.

    • The viral sheath contracts, pushing viral DNA into the bacterial host cell.

  3. Biosynthesis: Phage DNA directs the synthesis of viral components by the host cell ("to make viral parts").

    • Viral DNA incorporates into bacterial host DNA, forming "hybrid DNA".

    • The bacterial host cell is forced to make viral components (e.g., capsomeres, tail fibers) through transcription and translation (Hybrid DNA
      ightarrow RNA
      ightarrow protein).

  4. Maturation: Viral components are assembled into virions.

    • Newly made viral components are assembled into mature virions, capable of infecting other cells.

  5. Release: Host cell lyses, and new virions are released.

    • Leads to the death of the bacterial host cell.

Bacteriophage Lysogenic Cycle

  • Interrupts the lytic cycle between penetration and biosynthesis.

  • Bacterial host cell does NOT die; it divides instead, copying the viral DNA along with its own.

  • Lysogeny: Phage DNA integrates with the bacterial host DNA and remains "dormant" in the bacterial host cell.

    • Phage DNA production is delayed; biosynthesis is delayed.

  • Mechanism: Phage DNA is incorporated into host cell DNA, forming a "hybrid DNA" called a prophage.

  • When the bacterial host cell replicates (by binary fission), it also replicates the prophage. This does NOT immediately lead to the production of phage particles because biosynthesis has not started yet.

  • Lysogeny alters host cell's characteristics and results in:

    1. Phage Conversion: Non-pathogenic (harmless) bacteria become pathogenic (harmful).

    2. Latent Viral Infections: Virus "hides-out" inside the host cell (e.g., Herpes, Shingles).

    3. Transformation: Virus induces cancer-causing genes (oncogenes) to be expressed, turning normal cells into cancerous cells (e.g., cervical cancer).

      • This happens when the oncovirus' DNA integrates into the host cell's DNA, inducing tumors (by turning on oncogenes).

  • Multiplication Option #2 (with lysogeny): Attachment
    ightarrow Penetration
    ightarrow Lysogenic Cycle (reproduces by binary fission, making many prophage copies)
    ightarrow Re-enter Lytic Cycle at Biosynthesis stage
    ightarrow Biosynthesis
    ightarrow Maturation
    ightarrow Release
    ightarrow Host Cell Death.

Multiplication of Animal Viruses (Lytic Cycle)

  1. Attachment: Virus attaches to host cell receptors.

  2. Entry (analogous to penetration): The entire animal virus enters the animal host cell.

    • Fusion: Enveloped viruses fuse their envelope with the host cell membrane, allowing the capsid to enter.

    • Receptor-Mediated Endocytosis (RME) "Engulfment": Non-enveloped viruses (and some enveloped) are taken into the cell within an internal vesicle.

  3. Uncoating: By viral or host enzymes, the capsid is removed to expose the genetic core (viral DNA/RNA).

    • Occurs after entry, distinct to animal viruses.

  4. Biosynthesis: Viral genetic material directs synthesis of viral components by the host cell.

    • Viral DNA integrates into animal host DNA, forming a "hybrid DNA" called a provirus.

    • Provirus
      ightarrow transcription
      ightarrow mRNA (for biosynthesis)
      ightarrow translation
      ightarrow protein (viral parts).

    • All viral parts come from different proteins made through translation.

  5. Maturation: Viral components are assembled into new virions.

  6. Release: Leads to animal host cell death.

    • Budding: Enveloped animal viruses are released by budding; the cell membrane of the animal host cell becomes the virus's envelope.

    • Rupture: Non-enveloped viruses are released by host cell lysis (rupture).

  • Unique Phases for Animal Viruses: Entry and Uncoating.

DNA vs. RNA Animal Viruses

  • DNA Animal Viruses:

    • Animal virus DNA incorporates into the animal host cell's DNA to form a provirus.

  • RNA Animal Viruses (Bacterial viruses do NOT have RNA):

    • Animal virus RNA cannot directly incorporate into animal host cell's DNA.

    • Animal virus RNA must first be converted to DNA by the enzyme Reverse Transcriptase.

      • Process: RNA
        ightarrow DNA (Reverse Transcription).

      • This newly synthesized viral DNA can then incorporate into the animal host cell's DNA to form a provirus.

      • Example: Retroviridae family (e.g., HIV) possesses reverse transcriptase.

    • Summary: Attachment of RNA (enveloped)
      ightarrow Fusion of envelope
      ightarrow Uncoating
      ightarrow Reverse Transcription
      ightarrow Viral DNA insert into host
      ightarrow Integration as a Provirus.

Virus Families (DNA vs. RNA)

  • RNA Virus Families:

    • Retroviridae: HIV/AIDS, COVID-19 (though SARS-CoV-2 is typically Coronaviridae, it's an RNA virus).

  • DNA Virus Families:

    • Poxviridae: Smallpox, Cowpox.

    • Herpesviridae: Cold sores, Chickenpox, Shingles, Genital herpes (no cure, never leave the body).

Viruses and Cancer

  • Some cancers are caused by viruses called oncoviruses.

  • Cancer may develop long after viral infection.

  • Some oncoviruses can "turn on" oncogenes found in normal cells, leading to uncontrolled cell division and transforming normal cells into cancerous cells.

  • Mechanism: The oncovirus's DNA becomes integrated into the host cell's DNA and induces tumors by activating oncogenes.

Infectious Viruses (Cause Disease)

  1. Acute Viral Infections: Rapid onset of symptoms, short duration of infection (e.g., influenza).

  2. Latent Viral Infections: Hidden (usually in the nervous system), inactive, dormant infection (e.g., genital herpes, shingles).

  3. Persistent/Chronic Viral Infections: Late onset of symptoms, long duration, subclinical (mild, long-lasting) symptoms (e.g., HIV/AIDS (untreated)).

Viroids and Prions

  • Viroids:

    • Smallest infectious pathogens in the world.

    • Infectious RNA molecules (lacking a capsid).

    • Cause plant diseases (e.g., potato spindle tuber disease).

  • Prions:

    • Infectious proteins (misfolded protein particles).

    • Highly resistant (hard to destroy); only incineration (burning) is fully effective.

    • Cause transmissible neurological diseases (spongiform encephalopathies – inflammation of the brain, causing spongy appearance).

      • Examples: Mad cow disease (Bovine Spongiform Encephalopathy), Creutzfeldt-Jakob disease (CJD) in humans, Scrapie in sheep.

Chapter 6: Microbial (Bacterial) Growth

How Microbial Growth is Determined in the Lab

  • Observation of a Culture Medium:

    • Agar (plate): Looking for visually distinct colonies (large populations) of bacterial growth.

    • Broth (test tube): Looking for color change or cloudiness (turbidity).

  • Bacteria primarily grow by binary fission (asexual reproduction).

Requirements for Microbial Growth of Bacteria

Physical Requirements

  • Temperature:

    • As temperature increases, bacterial growth generally increases until an optimum temperature is reached, after which it rapidly declines.

    • Minimum, Optimum, and Maximum growth temperatures.

    • Preferences:

      • Psychrophiles: "Cold-loving" bacteria (e.g., refrigerators, snow, arctic regions, deep ocean).

      • Thermophiles: "Hot-loving" bacteria (e.g., hot springs, foot of volcanoes).

      • Mesophiles: "Middle-loving" bacteria; grow best at moderate temperatures (e.g., human body temperature is ideal for many pathogens).

  • pH of Environments (pH = measure of H^+ concentration):

    • Scale: 1 (acidic) - 14 (alkaline/base); 7 is neutral.

    • Most bacteria prefer a near-neutral pH (around pH 7).

    • Molds and yeasts prefer slightly acidic conditions (pH 5-6).

    • Acidophiles: Grow best in highly acidic environments (pH 1-2) (e.g., H.; pylori in stomach contents).

  • Osmotic Pressure (water movement from low to high concentration of particles):

    • If osmotic pressure is unequal inside and outside the cell, the cell will either shrink or swell, leading to cell death.

    • An isotonic solution is ideal for cell survival.

    • Halophiles: "Salt-loving" bacteria found in oceans.

      • High osmotic pressure outside the cell (due to high salt) would normally cause cells to shrink.

      • Halophiles are capable of producing positively charged solutes inside, balancing the osmotic pressure and allowing the cell to survive.

Chemical Requirements

  • Macronutrients: Chemicals required by microbes in large quantities.

    • Microbes use and metabolize different chemical elements.

    • Carbon: Microbes need carbon to produce energy.

      • Autotrophs: Use CO_2 to generate energy.

      • Heterotrophs: Obtain carbon from organic compounds to generate energy.

    • Nitrogen: Essential for proteins (amino groups in amino acids) and nucleic acids (nitrogenous bases in nucleotides).

    • Sulfur: Needed for proteins (specifically, in two sulfur-containing amino acids).

    • Phosphorus: Needed for nucleic acids (phosphate group in nucleotides) and for cell membrane formation (phospholipid bilayer).

  • Micronutrients (Trace Elements): Chemicals required by microbes in small quantities.

    • Usually function as inorganic enzyme cofactors (ions).

    • Also include organic growth factors (e.g., vitamins and animal extracts) that enhance growth.

  • Oxygen Requirements (Bacteria) (in a test tube, O_2 is high at the top, low at the bottom):

    • O_2 requirements vary greatly:

      1. Obligate Aerobe: Requires an O2-rich environment; will grow at the top; dies without O2 .

      2. Obligate Anaerobe: Requires low or no O2; will grow at the bottom; dies if exposed to O2 .

      3. Facultative Anaerobe: Grows throughout the test tube but prefers O_2 (mainly grows at the top).

      4. Microaerophile: Loves a little O2; grows in the middle with low O2 concentration.

Culture Media (Growth in Lab)

  • A solid or liquid preparation for microbial growth.

  • 1. Solid (Agar) Media: In the form of a plate (mostly) or slants.

    • Allows for visualization of discrete colonies.

  • 2. Liquid (Broth) Media: Allows for visualization of color changes/cloudiness (turbidity).

  • Inoculum: Introduction of microbes into a medium.

  • Culture: Microbes growing in or on a culture medium.

  • Pure Culture: Contains only one species, ideally seen on a solid agar plate, where all colonies look similar with no contamination.

  • Colony: A large population of cells originating from a single cell or a group of attached cells. Often called a colony-forming unit (CFU).

Culture Media for Bacterial Growth

  • Streak Plate Method: Used to isolate pure bacterial cultures by spreading, separating, and isolating individual colonies (CFUs).

Culture Media for Viral Growth (Viruses use host cells then kill them)

  • Viruses require a host cell (e.g., a bacterial cell for bacteriophages).

  • Form a viral plaque (clear areas) where no bacteria are present, indicating viral growth and host cell death.

  • Measured in plaque-forming units (PFU).

Types of Culture Media

  1. Chemically Defined Media: The exact chemical composition is known.

  2. Complex Media: Chemical composition varies from batch to batch (e.g., "partially digested media" with unknown protein amounts).

  3. Reducing Media: All available O_2 is removed; designed for the growth of obligate anaerobes.

    • Contain chemicals that combine with O_2 to deplete it (e.g., anaerobic jar).

  4. Selective Media: Suppress (inhibit) unwanted microbes and encourage the growth of desired microbes (only one type of bacteria will grow).

    • Example: EMB agar selects for gram-negative bacteria (e.g., E.coli forms shiny green metallic streaks) and selects against gram-positive bacteria.

  5. Differential Media: Allow differentiation between bacteria within the same group (e.g., between different gram-negative or gram-positive bacteria).

    • Example: Blood agar can differentiate hemolytic capabilities.

    • Some media have both selective and differential characteristics (e.g., EMB is selective for gram-negatives and differential between two gram-negatives based on colony appearance).

  6. Enrichment Media: Rich in growth factors, considered non-selective (everything will grow).

    • Stimulates the growth of many different types of bacterial species, including fastidious bacteria ("picky/difficult eaters" that require many growth factors and are hard to grow in the lab).

    • Usually exists as liquid (nutrient broth).

The Growth of Bacterial Cultures

  • Bacterial Division: An increase in the number of cells (not cell size).

    • Process called binary fission (each cell splits into 2); a type of asexual reproduction.

  • Generation Time: Time required for a cell to divide (to double).

    • Ranges from minutes to hours.

  • Bacterial growth is represented by growth curves.

4 Phases of the Growth Curve

  1. Lag Phase: Intense activity preparing for population growth, but no increase in population size. Cells are metabolically active (e.g., DNA replication), but not dividing rapidly.

  2. Log Phase (Exponential Growth): Logarithmic or exponential increase in population. Optimal conditions lead to rapid doubling of cells.

  3. Stationary Phase: Period of equilibrium where microbial deaths balance the production of new cells. Population stops increasing because bacteria run out of nutrients or accumulate waste products.

  4. Death Phase: Population is decreasing at a logarithmic rate due to accumulation of toxic metabolic waste and depletion of resources.

Measurement of Microbial Growth

Direct Measurements (Directly Counting)

  • Plate Count: Counting colonies after serial dilutions.

    1. Perform serial dilutions of a sample (transferring from test tube to test tube).

    2. Plate out serial dilutions onto agar.

    3. Count colonies (CFUs) after incubation (30-300 colonies for statistical significance).

  • Filtration Method: For samples with low bacterial numbers.

    • A solution is passed through a filter that collects bacteria.

    • The filter is then transferred to a Petri dish and grown to form colonies on the surface.

  • Direct Microscopic Count: A volume of bacterial suspension is placed on a special cell counter slide (with a grid).

    • The average number of bacteria per viewing field is calculated.

Indirect Measurements (Not Directly Counting; Assuming)

  • Turbidity: Measuring the cloudiness of broth in a test tube (light passing through).

    • Observed visually or with a spectrophotometer.

    • No growth
      ightarrow light passes through; Growth (turbidity)
      ightarrow less light passes through.

    • Assumes bacterial population size based on how much light passes through.

  • Metabolic Activity: The amount of metabolic waste is proportional to the number of bacteria (more waste
    ightarrow more bacteria).

  • Dry Weight: Weighing the bacteria. A larger dry weight value indicates a larger population of bacteria.