Microbiology Exam I Study Guide: Chapters 1-4

Classification and Naming of Microorganisms

Scientific Naming and Classification

Microorganisms are named and classified using a standardized system to ensure clarity and consistency in scientific communication.

• Scientific names are italicized or underlined; the genus is capitalized, and the species is lower case.

• Names may be descriptive or honor scientists (e.g., Escherichia coli honors Theodor Escherich).

• Classification system developed by Carl Woese (1978): three domains based on cellular organization: Bacteria, Archaea, Eukarya (includes protists, fungi, plants, animals).

Types of Microbes: Shapes and Arrangements

Major Groups of Microorganisms

Microbes are classified into several major groups based on cellular structure, metabolism, and genetic material.

• Bacteria:

  • Prokaryotic cells (no nucleus)

  • Single-celled

  • Cell walls contain peptidoglycan

  • Divide by binary fission

  • Nutrition from organic/inorganic chemicals or photosynthesis

  • May move using appendages called flagella

• Archaea:

  • Prokaryotic cells

  • Lack peptidoglycan in cell walls; may lack cell wall entirely

  • Often live in extreme environments (e.g., methanogens, extreme halophiles, thermophiles)

  • Generally not known to cause disease in humans

• Fungi:

  • Eukaryotic cells (distinct nucleus)

  • Cell walls contain chitin

  • Absorb organic chemicals for energy

  • Yeasts are unicellular; molds and mushrooms are multicellular (molds consist of masses of mycelia, composed of filaments called hyphae)

• Protozoa:

  • Eukaryotic cells

  • Absorb or ingest organic chemicals

  • May be motile via pseudopods, cilia, or flagella

  • Free-living or parasitic (derive nutrients from living host); some are photosynthetic

  • Reproduce sexually or asexually

• Algae:

  • Eukaryotic cells

  • Cellulose cell walls

  • Found in freshwater, saltwater, and soil

  • Photosynthetic: produce oxygen and carbohydrates

  • Sexual and asexual reproduction possible

• Viruses:

  • Acellular (not composed of cells)

  • Consist of DNA or RNA core surrounded by protein coat; may be enclosed in lipid envelope

  • Replicate only when in a living host cell; inert outside living hosts

• Multicellular Animal Parasites:

  • Eukaryotic cells

  • Include helminths (parasitic flatworms and roundworms); some microscopic stages in their life cycles

Spontaneous Generation and Biogenesis

Concepts and Experiments

Spontaneous generation was the belief that life could arise from non-living matter. This was disproved by experiments showing that living cells arise only from preexisting living cells.

• Experiments by Redi and Pasteur proved that living cells arise only from preexisting living cells.

History of Microbiology

Key Scientists and Discoveries

Many scientists contributed to the development of microbiology through discoveries about cells, microbes, and disease.

• Hooke (1665): Reported that living things are composed of cells; marked the beginning of cell theory.

• Leeuwenhoek (1673): First microbes observed; "animalcules" viewed through magnifying lenses.

• Redi: Filled jars with decaying meat and contributed to disproving spontaneous generation.

• Pasteur (1861): Demonstrated that microorganisms are present in the air; used S-shaped flasks to show microbes originate in air or fluids, not mystical forces.

• Lister (1860s): Used Pasteur's work to show microbes cause surgical wound infections; used phenol to prevent surgical wound infections.

• Koch: Showed that a bacterium causes anthrax and provided experimental steps (Koch's postulates) to demonstrate that a specific microbe causes a specific disease.

• Ehrlich: Speculated about a "magic bullet" to destroy pathogens without harming the host; developed a synthetic arsenic drug to treat syphilis.

• Fleming (1928): Discovered the first antibiotic (penicillin) by accident.

• Lancefield (1933): Classified streptococci based on cell wall components.

• Semmelweis: Advocated handwashing to prevent transmission of puerperal fever.

• Avery, McLeod & McCarty (1944): Showed that DNA is the hereditary material.

• Watson & Crick (1953): Proposed a model of DNA structure.

• Jacob & Monod (1961): Discovered the role of mRNA in protein synthesis.

Golden Age of Microbiology

Definition and Significance

The "golden age" of microbiology refers to the period from 1857-1914, beginning with Pasteur's work. Discoveries included the relationship between microbes and disease, immunity, and antimicrobial drugs.

Chemotherapy and Antibiotics

Definitions and Examples

Chemotherapy is the treatment of disease with chemicals. Chemotherapy agents used to treat infectious diseases can be synthetic drugs or antibiotics.

• Antibiotics: Chemicals produced by bacteria and fungi that inhibit or kill microbes.

Basic Chemistry for Microbiology

Atoms, Elements, and Molecules

Understanding the structure of atoms and molecules is essential for studying microbial life.

• Atoms: Smallest unit of matter; cannot be subdivided into smaller substances.

• Composed of electrons (negatively charged), protons (positively charged), and neutrons (uncharged).

• Protons and neutrons make up the nucleus; electrons move around the nucleus.

• Matter: Anything that has mass and takes up space.

• Elements: Pure substances made of one type of atom.

• Isotopes: Atoms with different numbers of neutrons.

• Ions: Charged atoms that have gained or lost electrons.

• Molecules: Smallest unit of matter composed of two or more atoms held together by chemical bonds (e.g., O2, H2O).

Atomic Structure

• Nucleus: Consists of protons and neutrons.

• Electron shells: Surround nucleus and hold electrons.

Atomic Number, Atomic Weight, and Molecular Weight

• Atomic number: Number of protons.

• Atomic weight: Number of protons and neutrons.

• Molecular weight/mass: Sum of the atomic masses in a molecule.

  • Example: $\text{H}_2\text{O}: 2 \times 1 + 16 = 18$

Covalent, Hydrogen, and Ionic Bonds

• Covalent bonds: Forms when two atoms share one or more pairs of electrons. Stronger and more common in organisms than ionic bonds.

• Hydrogen bonds: Forms when a hydrogen atom covalently bonded to an oxygen or nitrogen atom is attracted to another N or O atom in another molecule.

• Ionic bonds: Attraction between ions of opposite charges; one atom loses electrons and another gains electrons.

Properties of Water

Importance in Biological Systems

Water is essential for life, serving as a universal solvent and playing a key role in biological processes.

• Transports nutrients and removes waste products.

• High heat capacity: requires a lot of heat to change temperature, helping maintain stable body temperature.

• High heat of evaporation: absorbs a lot of heat from the surface (e.g., sweating).

• Maintains cellular turgidity (firmness) and provides structural support, especially in plants and organisms with hydrostatic skeletons.

• Repels non-polar substances, contributing to the formation of cell membranes and other cellular structures.

Acids, Bases, and pH

Definitions and Buffer Systems

Acids and bases are defined by their ability to donate or accept hydrogen ions (H+). pH measures the acidity or alkalinity of a solution.

• Acidic: pH below 7; donates H+ ions; tastes sour.

• Basic: pH above 7; releases OH- ions (hydroxide); tastes bitter.

• pH: Potential of hydrogen; scale from 0-14, 0 is most acidic, 14 is most alkaline.

• Buffer: Solution designed to resist significant changes in pH when small amounts of acid or base are added.

  • If acid is added, buffer's base component reacts and neutralizes added hydrogen ions.

  • If base is added, buffer's weak acid component reacts and neutralizes added hydroxide ions.

Organic and Inorganic Molecules

Definitions and Examples

Organic compounds always contain carbon and hydrogen and are typically structurally complex. Inorganic compounds usually lack carbon and are structurally simple.

• Organic compounds: Typically contain carbon and hydrogen; may also contain oxygen, nitrogen, or other elements.

• Inorganic compounds: Typically lack carbon; usually small and structurally simple.

Macromolecules and ATP

Structure and Function

Macromolecules are large polymers made of repeating monomers. ATP is a key molecule for energy storage and transfer in cells.

• Macromolecules: Polymers consisting of many small repeating molecules called monomers, joined by dehydration synthesis or condensation reactions.

• ATP (adenosine triphosphate): Made of ribose, adenine, and three phosphate groups. Stores chemical energy released by some chemical reactions. Releases phosphate groups by hydrolysis to liberate useful energy for the cell.

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

Enzymes and Proteins

• Enzymes: Specialized protein molecules that act as biological catalysts, speeding up chemical reactions within living organisms without being consumed in the process. Highly specific for their substrates.

• Proteins: Made of C, H, O, N, and sometimes S. Essential in cell structure and function; includes enzymes, transport proteins, flagella, and bacterial toxins.

• Amino acids: Protein subunits; contain alpha-carbon, carboxyl group (-COOH), amino group (NH2), and side group. Exist in D or L forms; L-form is most common in nature. Peptide bonds between amino acids are formed by dehydration synthesis.

Metric Units for Measuring Microbes

Common Units and Conversions

Microbes are measured using the metric system, which allows for precise quantification of microscopic entities.

• 1 micrometer (μm) = $10^{-6}$ m = $10^{-3}$ mm

• 1 nanometer (nm) = $10^{-9}$ m = $10^{-6}$ mm

• 1000 nm = 1 μm

• 0.001 μm = 1 nm

Metric Unit	Abbreviation	Equivalent
Meter	m	$10^0$ m
Millimeter	mm	$10^{-3}$ m
Micrometer	μm	$10^{-6}$ m
Nanometer	nm	$10^{-9}$ m
Angstrom	Å	$10^{-10}$ m

Microscopy

Compound Light Microscope: Parts and Function

The compound light microscope is a key tool in microbiology for observing cells and microbes.

• Fine focusing knob: For precise focusing.

• Coarse focusing knob: For initial focusing.

• Diaphragm: Controls the amount of light entering the condenser.

• Condenser: Directs light through the specimen.

• Stage: Holds the microscope slide in position.

• Objective lens: Primary lens that magnifies the specimen.

• Body tube: Transmits the image from the objective lens to the ocular lens.

• Ocular lens (eyepiece): Magnifies the image formed by the objective lens.

Microscope Concepts

• Total magnification: Objective lens magnification × ocular lens magnification.

• Field of view: Area visible through the microscope.

• Resolution: Ability to distinguish two points as separate.

• Parfocal: When switching objectives, the specimen remains in focus.

Types of Microscopy

• Brightfield microscopy: Dark objects visible against a bright background; light reflected off specimen does not enter objective lens.

• Darkfield microscopy: Light objects visible against a dark background; opaque disk in condenser, only light reflected off specimen enters objective lens.

• Phase-contrast microscopy: Enhances contrast of transparent specimens without staining.

• Differential interference contrast (DIC) microscopy: Uses differences in refractive indices to produce high-contrast images.

• Fluorescence microscopy: Uses UV light; fluorescent substances absorb UV and emit visible light.

• Confocal microscopy: Uses laser light to scan specimens and produce three-dimensional images.

• Two-photon microscopy: Uses two photons of red light to excite dyes; can image living cells up to 1 mm deep.

• Super-resolution light microscopy: Uses two laser beams to improve resolution.

• Electron microscopy: Uses electrons instead of light; higher resolution and magnification.

  • Transmission electron microscopy (TEM): Electrons pass through thin sections; high resolution.

  • Scanning electron microscopy (SEM): Electrons scan the surface; produces three-dimensional images.

  • Scanning tunneling microscopy: Uses a probe to scan the surface; atomic detail.

  • Atomic force microscopy: Uses a diamond probe; produces three-dimensional images.

Staining Techniques

Types of Stains

• Acidic dye: Chromophore is an anion.

• Basic dye: Chromophore is a cation.

• Simple stain: Uses a single basic dye; highlights the entire cell.

• Differential stain: Uses two or more dyes to distinguish between groups of cells or cell components (e.g., Gram stain, acid-fast stain).

Gram Stain

The Gram stain is a differential staining technique used to classify bacteria based on cell wall composition.

• Primary stain: Crystal violet

• Mordant: Iodine (forms complex with crystal violet)

• Decolorization: Alcohol wash (removes stain from Gram-negative cells)

• Counterstain: Safranin (stains Gram-negative cells pink/red)

Acid-Fast Stain

• Binds only to bacteria with waxy material in cell walls (e.g., Mycobacterium).

• Primary stain: Carbolfuchsin

• Decolorizing agent: Acid-alcohol

• Counterstain: Methylene blue

Prokaryotic vs. Eukaryotic Cells

Comparison of Cell Types

Feature	Prokaryotes	Eukaryotes
Nucleus	No	Yes
Chromosomes	One circular	Multiple linear
Organelles	Absent	Present
Cell wall	Peptidoglycan	Polysaccharide (when present)
Division	Binary fission	Mitosis

Shapes of Bacteria

Major Morphologies

• Coccus: Spherical

• Bacillus: Rod-shaped

• Spiral: Includes vibrio, spirillum, spirochete

Prokaryotic Cell Structure

Key Components

• Nucleoid: Region in cytoplasm containing single circular DNA

• Cytoplasm: Site of many cellular processes

• Ribosomes: Synthesize proteins

• Plasmids: Small circular DNA pieces; may carry genes for antibiotic resistance

• Capsule: Outer layer that helps protect cell and aids in attachment

• Cell wall: Provides structural support and shape; protects from osmotic pressure

• Cell membrane: Controls passage of substances in and out of cell

• Flagella: Whip-like appendages for motility

Gram-Positive vs. Gram-Negative Cell Walls

• Gram-positive: Thick peptidoglycan layer

• Gram-negative: Thin peptidoglycan layer sandwiched between two membranes; contains polysaccharides in outer membrane

Eukaryotic Cell Structure

Key Organelles

• Nucleus: Contains DNA; controls cell activity

• Cytoplasm: Site of many biological processes

• Endoplasmic reticulum (ER): Rough ER (with ribosomes) synthesizes proteins; smooth ER synthesizes lipids

• Mitochondria: Site of energy production

• Lysosomes: Contain digestive enzymes

• Ribosomes: Synthesize proteins

• Chloroplasts: Site of photosynthesis (in plant cells)

• Cytoskeleton: Provides structural support and aids in movement

Flagellar Arrangements in Bacteria

Types of Flagella

• Monotrichous: Single flagellum at one end

• Lophotrichous: Tuft of flagella at one end

• Amphitrichous: Flagella at both ends

• Peritrichous: Flagella all over cell surface

• Atrichous: No flagella

Endosymbiotic Theory

Origin of Eukaryotic Organelles

The endosymbiotic theory proposes that larger host cells engulfed smaller prokaryotic cells, which then became symbiotic organelles such as mitochondria and chloroplasts.