Microbiology Lecture Notes - VOCABULARY Flashcards

Taxonomy and Major Microorganisms

• Leeuwenhoek’s microorganisms were reclassified into six categories, and later into broader groups: Taxonomy (science of classification) and Binomial nomenclature

  • 1. Bacteria

  • 2. Archaea

  • 3. Fungi

  • 4. Protozoa

  • 5. Algae

  • 6. Small multicellular animals

  • 7. Viruses

  • 8. Prions

• Prokaryote vs. Eukaryote

  • Prokaryote: before the nucleus; no membrane-bound organelles; nucleoid region contains genetic information

  • Eukaryote: true nucleus; membrane-bound organelles

• Classification of microbes

  • Bacteria and Archaea are prokaryotic

  • Unicellular

  • Much smaller than eukaryotes

  • Ubiquitous; found everywhere

  • Reproduce asexually by binary fission

  • Two domains (taxonomic):

  • Bacteria: cell walls made of peptidoglycan

  • Archaea: cell walls made of unique polymers (not peptidoglycan); often in extreme environments

• Fungi

  • Membrane-bound nucleus and organelles

  • Obtain food from other organisms

  • Possess cell walls

• Molds vs. Yeasts (two main types of fungi)

  • Molds: multicellular; grow as long filaments; reproduce by sexual and asexual spores

  • Yeasts: unicellular; reproduce asexually by budding

• Protozoa

  • Single-celled eukaryotes

  • Similar to animals in nutrient needs and cellular structure

  • Live freely in water

  • Grouped under protists when combined

  • Asexual (mostly) and sexual reproduction

  • Most capable of locomotion via:

  • a. Pseudopods (cell extensions flowing toward movement)

  • b. Cilia (numerous short, hairlike structures)

  • c. Flagella (long, whiplike extensions; 1 or 2 present)

• Algae

  • Unicellular or multicellular eukaryotes

  • Photosynthetic; live in fresh and saltwater

  • Simple reproductive structures

  • Categorized based on pigmentation and cell-wall composition

  • Examples of large algae: seaweed, kelp

• Viruses

  • Viruses of bacteria (bacteriophages) and of eukaryotic cells

  • Acellular; obligate intracellular parasites (require a host)

  • Host-specific

• Antoni van Leeuwenhoek

  • Late 17th century

  • Made simple microscopes

  • Examined water and other substances

  • Viewed bacteria, protozoa, algae, and invertebrates

  • By the end of the 19th century, these organisms were regarded as microorganisms

  • Initially no knowledge of the causes of infectious diseases; spontaneous generation was believed; limited understanding of eggs and reproduction

Prokaryotes vs Eukaryotes: Cellular Details

• Prokaryotes vs Eukaryotes (summary)

  • Prokaryotes lack a true nucleus and membrane-bound organelles

  • Eukaryotes have a true nucleus and membrane-bound organelles

• Bacteria vs Archaea (differences)

  • Bacteria: peptidoglycan in cell walls

  • Archaea: walls lack peptidoglycan; composed of unique polymers; often in extreme environments

• Fungi (eukaryotes) continued

  • Obtain food from other organisms

  • Possess cell walls

Key Figures in Microbiology History

• Antoni van Leeuwenhoek

  • Early microscopy and initial observations of microorganisms

• Robert Koch

  • Koch’s Postulates (4 steps to prove an organism causes disease):

  • 1. The suspected causative agent must be found in every case of the disease and be absent from healthy hosts

  • 2. The agent must be isolated and grown outside the host

  • 3. When an agent is introduced into a healthy, susceptible host, the host must acquire the disease

  • 4. The same agent must be found in the diseased experimental host

Bacteria: Characteristics and Classification

• Characteristics used to classify bacteria

  • Morphological (microscopic) features

  • Cultural (colony morphology)

  • Physiological (enzymes)

  • Serological (antibody/antigen reactions)

  • DNA (genetics)

• General themes in microbiology’s role

  • Genetics, molecular biology, biotechnology

  • Environmental microbiology

  • Biochemistry (metabolism)

  • Fermentation as a key concept in metabolism and industry

Biology of Macromolecules and Biochemistry (Chapter 2 overview)

• Organic macromolecules and chemical reactions in living systems

  • Carbon skeletons provided by organic molecules (C-H-O-N-P-S)

  • Functional groups: common atom arrangements that confer properties

  • R-groups: variable side chains in macromolecules

• Macromolecules (major categories)

  • Lipids

  • Carbohydrates

  • Proteins

  • Nucleic acids

• Monomers and polymers

  • Monomers: basic building blocks

  • Polymers: macromolecules formed by linking monomers

• Dehydration synthesis (condensation) vs decomposition

  • Dehydration synthesis: building macromolecules by removing water

  • Decomposition: breakdown into smaller units

• Lipids

  • Not composed of regular subunits; largely hydrophobic

  • Four groups: fats (triglycerides), phospholipids, waxes, steroids

  • Triglycerides common in blood; energy storage

• Carbohydrates

  • General formula: (CH2O)n

  • Functions: long-term energy storage, energy source, backbone of nucleic acids, nutrient reservoir for cell walls, intracellular interactions

  • Types: monosaccharides, disaccharides, polysaccharides

• Lipids (expanded)

  • Hydrophobic; hydrophilic interactions vary by group

• Proteins

  • Composed of C, H, O, N, S

  • Functions: structure, enzymatic catalysis, regulation, transport, defense

• Nucleotides and nucleic acids

  • DNA and RNA are essential genetic materials

  • RNA can act as enzyme and help form polypeptides

• Nucleotides and nucleosides

  • Nucleotides: phosphate, pentose sugar (deoxyribose or ribose), one of five nitrogenous bases

  • Nucleosides: nucleotides lacking one or more phosphate groups

• Nucleic acids structure

  • Polymers of nucleotides linked by phosphodiester bonds

  • Base-pairing: 3 H-bonds between C-G; 2 H-bonds between A-T (or A-U in RNA)

• ATP (adenosine triphosphate)

  • Main short-term energy carrier

  • Energy released from phosphate bond hydrolysis

  • Capture of energy via phosphorylation processes

• Processes of life (overview)

  • Growth, reproduction, responsiveness, metabolism

Central Metabolism: Energy and Substrate Conversion

• Metabolism concept

  • Metabolism = controlled biochemical reactions in cells

  • Catabolism: breaking down larger molecules to smaller units; exergonic (releases energy)

  • Anabolism: building larger molecules from smaller units; endergonic (consumes energy)

• Nutrients and macromolecules

  • Macromolecules (carbs, proteins, lipids) are catabolized to smaller units for energy and building blocks

• Phosphorylation and ATP production

  • Phosphorylation: adding a phosphate group to ADP to form ATP

  • ADP + P_i
    ightarrow ATP

  • Three types of phosphorylation in catabolic pathways:

  • Substrate-level phosphorylation: direct transfer of phosphate between two substrates

  • Oxidative phosphorylation: energy from electron transport chain creates a proton motive force to power ATP synthase

  • Photophosphorylation: energy from light drives phosphorylation (not detailed here, but listed)

Redox Chemistry and Electron Carriers

• Oxidation-reduction (redox) reactions

  • Oxidation: loss of electrons (or gain of oxygen)

  • Reduction: gain of electrons (or loss of oxygen)

  • Redox reactions involve transfer of electrons from donors to acceptors

• Electron carriers

  • NAD^+/NADH

  • NADP^+/NADPH

  • FAD/FADH_2

• Cofactors and proteins

  • Cofactors: inorganic ions or small organic molecules required by some enzymes

  • Enzymes: biological catalysts; some require cofactors

  • Enzymes have active sites; inhibitors can be competitive or noncompetitive; allosteric regulation

Enzymology in Metabolism

• Enzymes

  • Usually proteins; a few ribozymes (RNA enzymes)

  • Active site binds substrates and facilitates chemical reactions

  • Enzymes are sensitive to pH, ionic strength, temperature

  • Enzyme activity can be influenced by temperature, pH, ionic concentration, substrate concentration, and inhibitors

• Enzyme inhibition

  • Competitive inhibitors compete with substrate for the active site

  • Noncompetitive inhibitors bind to an allosteric site, changing the enzyme’s shape

  • Allosteric regulation affects enzyme activity

• Amino acids and proteins

  • 21 standard amino acids; linked by peptide bonds

  • Side chains determine protein folding and interactions

Carbohydrate Catabolism and Energy Pathways

• Carbohydrate catabolism overview

  • Carbohydrates (CH_2O)n are common energy sources

  • Glucose is the most commonly used substrate

• Glycolysis

  • Location: cytoplasm

  • Glucose (6 carbons) converts to 2 pyruvate (3 carbons each)

  • Net yield per glucose: 2 ext{ ATP}, 2 ext{ NADH}, 2 ext{ pyruvate}

  • Phosphorylation of substrates yields ATP via substrate-level phosphorylation

  • Some electrons are carried to the electron transport chain for oxidative phosphorylation

• Cellular respiration (aerobic) overview

  • Complete oxidation of pyruvate to CO2 and H2O

  • ATP production via oxidative phosphorylation (ETC and chemiosmosis)

  • Three main stages:

  • Pyruvate to Acetyl-CoA (preparatory step)

  • Krebs (Citric Acid) Cycle

  • Electron Transport Chain (ETC) with oxidative phosphorylation

• Pyruvate fate and acetyl-CoA formation

  • Pyruvate is converted to acetyl-CoA, releasing CO_2 and generating NADH

• Krebs cycle (Citric Acid Cycle)

  • Occurs in the cytosol of prokaryotes; mitochondria matrix in eukaryotes

  • Acetyl-CoA combines with oxaloacetate to form citrate, cycling back to oxaloacetate

  • Outputs per glucose molecule (two turns of the cycle per glucose):

  • 2 ext{ ATP}, 2 ext{ FADH}2, 6 ext{ NADH}, 4 ext{ CO}2

• Electron transport chain (ETC) and oxidative phosphorylation

  • NADH and FADH_2 donate electrons to the chain

  • Electrons are passed through a series of carriers, creating a proton gradient across a membrane

  • Proton motive force drives ATP synthase to convert ADP + P_i to ATP (oxidative phosphorylation)

  • Location differences:

  • In eukaryotes: mitochondrial inner membrane

  • In prokaryotes: cytoplasmic (inner) membrane

  • Final electron acceptor in aerobic respiration: O_2

  • Final electron acceptors in anaerobic respiration: SO4^{2-}, NO3^-, CO_3^{2-}, etc.

• Oxidative phosphorylation specifics

  • Proton gradient drives ATP synthase to convert ADP + P_i to ATP

  • Typical yield: roughly 36 ATP (eukaryotes) to 38 ATP (prokaryotes) per glucose, depending on shuttle mechanisms

Fermentation (Alternate Energy Pathway)

• Fermentation as an alternative to respiration when O_2 is limited

  • Glycolysis provides ATP via substrate-level phosphorylation

  • Pyruvate is converted to other organic compounds (e.g., lactate, ethanol) to regenerate NAD^+ for glycolysis

  • Fermentation yields less ATP overall than respiration

  • Does not use ETC; NADH is oxidized to NAD^+ by transferring electrons to organic molecules

• General definition

  • Partial oxidation of sugars (or other molecules) using an organic molecule as the electron acceptor

  • NADH is oxidized to NAD^+; organic molecule is reduced

Cellular Architecture and Organelles (Prokaryotes vs Eukaryotes)

• Cytoplasm and cytosol

  • Cytosol: mostly water; site of many metabolic reactions

• Ribosomes

  • Prokaryotic ribosomes: 70S (composed of 30S and 50S subunits)

  • Eukaryotic ribosomes: 80S (composed of 40S and 60S subunits)

  • Ribosomes are sites of protein synthesis

• Endospores

  • Unique, highly resistant structures formed by some bacteria (e.g., Bacillus, Clostridium)

  • Formed during nutrient limitation as a defensive strategy; vegetative cells transform into endospores

• Inclusions

  • Reserve deposits or storage bodies within the cytoplasm

• Cytoplasmic membranes (cell membranes)

  • Phospholipid bilayer with embedded proteins

  • Fluid mosaic model

  • Functions: selectively permeable barrier; harvests light energy in photosynthetic bacteria (where applicable)

• External structures of bacterial cells

  • Glycocalyces: gelatinous, sticky outer layer

  • Composed of polysaccharides, polypeptides, or both

  • Capsule: organized, firmly attached; can prevent host recognition

  • Slime layer: loosely attached; water-soluble; helps attachment

  • Flagella: motility organelles; structure: filament, hook, basal body

  • Flagellar function: rotation propels cell; direction changes (CCW vs CW) alter movement; taxis responses

  • Fimbriae: sticky, bristlelike projections used for adhesion

  • Pili (conjugation pili): longer than fimbriae; used for DNA transfer between cells

  • Relationship: pilus is considered distinct from fimbriae; conjugation involves pili

Bacterial Cell Walls and Membranes

• Purpose of the cell wall

  • Provides structure, shape, and osmotic protection

  • Helps attach to surfaces or other cells; affects antimicrobial susceptibility

  • Targeted by many antibiotics

• Composition and classification

  • Primarily composed of peptidoglycan

  • Two basic wall types:

  • Gram-positive: thick peptidoglycan layer; teichoic and lipoteichoic acids; stains purple

  • Gram-negative: thin peptidoglycan layer; outer membrane with lipopolysaccharide (LPS); stains pink

• Gram-positive specifics

  • Teichoic acids and lipoteichoic acids present

  • Can contain up to ~60% mycolic acid in acid-fast bacteria, aiding survival in harsh conditions

• Gram-negative specifics

  • Outer membrane contains LPS; Lipid A component can trigger fever, vasodilation, inflammation, shock, and coagulation (important clinically)

  • May impede antibiotic treatment

• Bacteria with no cell walls

  • Mycoplasma and some others lack cell walls; often mistaken for viruses due to small size and absence of peptidoglycan

• Bacterial cytoplasmic membrane details

  • Phospholipid bilayer with integral and peripheral proteins

  • Fluid mosaic model describes current understanding of membrane structure

Archaea: Distinctive Features

• External structures and cell walls

  • Some archaea have fimbriae; some possess hami (tubular, grappling-hook like fimbriae) for attachment

• Cell walls

  • Archaea lack peptidoglycan; walls built from various polysaccharides and proteins

• Cytoplasmic membranes

  • Present across Archaea; membranes can contain unique lipids

Eukaryotic Cells: Structure and Transport

• Eukaryotic cell walls (where present) and cytoplasmic membranes

  • Fungi, algae, plants, and some protozoa have cell walls

  • Cell walls composed of different materials depending on lineage:

  • Plants: cellulose

  • Fungi: cellulose, chitin, and/or glucomannan

  • Algae: varied polysaccharides

• Cytoplasmic membranes (plasma membranes) in eukaryotes

  • Fluid mosaic of phospholipids and proteins

  • Steroid lipids present to maintain membrane fluidity

  • Regions with lipids and proteins; selective transport across the membrane

• Endocytosis and exocytosis (in eukaryotes)

  • Endocytosis includes phagocytosis (solid particles) and pinocytosis (liquids)

  • Pseudopods surround substances; vesicles form and internalize material

  • Exocytosis: vesicles fuse with the plasma membrane to secrete contents

• Organelles and energy production

  • Mitochondria: two membranes; produce most ATP; contain 70S ribosomes and circular DNA

  • Chloroplasts (in photosynthetic organisms): similar endosymbiotic origin; can contain 70S ribosomes

  • Both mitochondria and chloroplasts support the endosymbiotic theory

• Endosymbiotic theory (Ch. 3, general concept)

  • Eukaryotes formed from symbiotic unions of smaller prokaryotes

  • Aerobic prokaryotes became mitochondria; photosynthetic prokaryotes (cyanobacteria) became chloroplasts

• Evolutionary note on metabolism in eukaryotes vs prokaryotes

  • Mitochondria and chloroplasts retain remnants of bacterial features (70S ribosomes, circular DNA)

Chapter 3 and Chapter 11: Microbial Diversity and Pathogens (Highlights)

• Cyanobacteria and chloroplasts

  • Cyanobacteria are photosynthetic prokaryotes; chloroplasts in plants and algae likely originated from cyanobacterial ancestors

• Pleomorphism and arrangements

  • Bacteria can be pleomorphic; arrangements result from planes of division and separation of daughter cells

• Modern prokaryotic classification (ongoing debate)

  • Based on rRNA sequence relatedness and cultural, morphological, and pathological data

• Survey of bacteria (highlights)

  • Low G+C Gram-positives (<50% G+C in genome)

  • Notable genera and pathogens:

  • Clostridium: obligately anaerobic gram-positive bacilli; form endospores; includes:

    • C. botulinum (botulism toxin) – exotoxin causing muscle paralysis

    • C. tetani (tetanus) – exotoxin affecting muscle relaxation

    • C. perfringens (gas gangrene)

    • C. difficile – severe colitis (diarrhea)

  • Bacillus: common in soil; some species form endospores

  • Staphylococcus: normal skin/nasal flora; can cause pneumonia, wound infections, toxic shock syndrome, prosthetic infections; toxin production; biofilms; antibiotic resistance concerns (MRSA)

    • S. aureus, S. agalactiae, S. saprophyticus; S. epidermidis notable for hospital-associated infections

    • MRSA: methicillin-resistant S. aureus; significant healthcare burden

  • Corynebacterium: pleomorphic; includes C. diphtheriae (diphtheria) – upper respiratory tract infection; vaccine: DTaP for children, TDaP for adults

• End of CH.11 notes

Chapter 5: Metabolism (Deep Dive)

• Metabolism and microbial diversity

  • Bacteria share many metabolic pathways with humans but some have unique pathways useful for environmental and industrial applications

• Metabolism as a two-phase process

  • Catabolism: breaking down molecules to release energy

  • Anabolism: building larger molecules from smaller units

• Major energy carriers and reactions

  • ATP production and energy storage via phosphorylation

  • Nutrients: macromolecules as energy sources

  • Major pathways: aerobic respiration and fermentation

• Aerobic vs anaerobic respiration

  • Aerobic respiration uses oxygen as the final electron acceptor; yields more ATP

  • Anaerobic respiration uses alternate final electron acceptors (e.g., NO3^-, SO4^{2-}, CO_3^{2-})

• Phosphorylation types in metabolism

  • Substrate-level phosphorylation: direct phosphate transfer between substrates to form ATP

  • Oxidative phosphorylation: electron transport chain generates a proton gradient; ATP synthase converts ADP to ATP

  • Photophosphorylation: light-driven phosphorylation (occurs in photosynthetic organisms)

Detailed Components of Metabolic Pathways

• Oxidation-reduction (Redox) chemistry in metabolism

  • Electron carriers: NADH, NADPH, FADH_2

  • Redox reactions linked to energy capture and ATP production

• Cyclic pathways and energy flow

• Glycolysis (revisited)

  • Location: cytoplasm

  • Substrates: glucose → 2 pyruvate

  • Net ATP yield: 2 ext{ ATP} (substrate-level) per glucose

  • Net NADH yield: 2 ext{ NADH} per glucose

  • Pyruvate is available for entry into Krebs cycle or fermentation

• Krebs cycle (Citric Acid Cycle) (revisited)

  • Occurs in mitochondria (eukaryotes) or cytosol (prokaryotes)

  • Per glucose: 2 ext{ ATP}, 6 ext{ NADH}, 2 ext{ FADH}2, 4 ext{ CO}2

• Electron Transport Chain (ETC) overview (revisited)

  • Location of carriers differs by organism (mitochondrial inner membrane vs cytoplasmic membrane in prokaryotes)

  • Energy capture in the form of a proton gradient across the membrane

  • Final electron acceptor depends on respiration type (O_2 for aerobic)

• Fermentation (revisited)

  • Provides regenerating NAD^+ for glycolysis under anaerobic conditions

  • End products vary (e.g., lactate, ethanol)

Summary of Key Concepts and Notation

• Definitions and abbreviations

  • DNA, RNA: nucleic acids carrying genetic information

  • ATP: main energy currency of the cell

  • NAD^+/NADH, NADP^+/NADPH, FAD/FADH_2: key electron carriers

• Important structures and terms

  • Glycocalyx: capsule or slime layer aiding in attachment and immune evasion

  • Flagella: motility organelles

  • Fimbriae and pili: adhesion and DNA transfer (conjugation)

  • Endospore: resistant dormant cell type

  • Cytoplasmic membrane: selective barrier for transport and energy processes

  • Cell wall: Gram-positive vs Gram-negative; teichoic acids; LPS; mycolic acids; peptidoglycan

  • Mitochondria and chloroplasts: energy production and photosynthesis components; 70S ribosomes in these organelles; endosymbiotic origin

• Process flow: from macromolecules to energy

  • Carbohydrates → glycolysis → pyruvate → acetyl-CoA → Krebs cycle → ETC → ATP (oxidative phosphorylation)

  • If oxygen is absent or limited: glycolysis → fermentation to regenerate NAD^+; ATP produced by substrate-level phosphorylation

• Ethical, philosophical, and practical implications

  • Understanding microbial metabolism informs biotechnology, fermentation industries, and environmental remediation

  • Antibiotic targets include cell wall synthesis and metabolic enzymes; antibiotic resistance (e.g., MRSA) presents significant clinical challenges

• Mathematical and chemical notation used in notes

  • Reaction energy and stoichiometry examples include:

  • ADP + P_i
    ightarrow ATP (phosphorylation)

  • Classic yields in metabolism (per glucose):

  • Glycolysis: 2 ext{ ATP}, 2 ext{ NADH}

  • Krebs cycle: 2 ext{ ATP}, 2 ext{ FADH}2, 6 ext{ NADH}, 4 ext{ CO}2

  • Overall aerobic yield: ~36-38 ext{ ATP} per glucose (depending on shuttle systems)

• Connections to broader topics

  • Fermentation theory links to industrial microbiology and food biotechnology

  • Endosymbiotic theory connects cell biology to evolutionary biology

  • Biofilms (via glycocalyces) relate to infection control and dental/oral microbiology