Microbiology Core Concepts and Metabolic Pathways Study Guide

Microbes and Microbiota

Overview of Microorganisms

Microorganisms are diverse life forms including bacteria, archaea, fungi, protozoa, algae, viruses, and helminths. They play essential roles in ecosystems and human health.

• Beneficial roles: CO2 production, nitrogen fixation, recycling/decomposition, food industry, antibiotics, vitamins, insulin, solvents (acetone, ethanol).

• Harmful roles: Pathogens, food spoilage.

• Normal microbiota: Live on/in humans, protect against pathogens, produce vitamins.

• Transient microbiota: Temporary, may be pathogenic.

• Germ theory of disease: Microorganisms can cause disease.

Classifying Microorganisms

Bacteria and Archaea

Bacteria and archaea are prokaryotic cells that reproduce by binary fission. They lack membrane-bound organelles and have peptidoglycan cell walls (bacteria only).

• Bacteria: Prokaryotes, peptidoglycan cell walls, binary fission.

• Archaea: Prokaryotes, no peptidoglycan, extreme environments.

Fungi

• Structure: Eukaryotic, absorb/ingest organic chemicals, molds (multicellular), yeasts (unicellular).

Protozoa

• Structure: Eukaryotic, absorb/ingest organic chemicals, motile (flagella, cilia, pseudopodia).

Algae

• Structure: Eukaryotic, cellulose cell walls, photosynthetic.

Viruses

• Structure: Acellular, DNA or RNA core, protein coat, need host to replicate.

Helminths

• Structure: Parasitic worms, multicellular.

Prokaryotic Cells

Characteristics

Prokaryotic cells reproduce by binary fission and lack membrane-bound organelles. They typically have a circular chromosome and a plasma membrane.

• Cell wall: Peptidoglycan (selective barrier, ATP production site).

• Ribosomes: 70S (50S + 30S).

• Gram stain:

  • Gram positive: thick peptidoglycan, teichoic acids, sensitive to lysozyme.

  • Gram negative: thin peptidoglycan, outer membrane with LPS (endotoxin).

• Endospores: Survival structures (e.g., Bacillus, Clostridium).

Eukaryotic Cells

Characteristics

Eukaryotic cells contain membrane-bound organelles and a plasma membrane composed of a phospholipid bilayer with sterols.

• Organelles:

  • Centrosome: microtubule organizing center (not for food storage).

  • Golgi: modifies, packages, secretes proteins.

  • Lysosome: digestive enzymes.

• Cell wall: Cellulose (plants), chitin (fungi), none in animals/protozoa.

• Ribosomes: 80S (40S + 60S), except mitochondria and chloroplasts (70S).

Membrane Transport

Types of Transport

Cells use various mechanisms to move substances across membranes.

• Simple diffusion: Passive movement, high to low concentration.

• Facilitated diffusion: Passive, uses transporter proteins.

• Osmosis: Diffusion of water, sometimes through aquaporins.

• Active transport: Requires energy (ATP), moves against concentration gradient.

• Oxygen: Diffuses easily (small, nonpolar), but glucose requires facilitated diffusion.

Microscopy

Principles and Techniques

Microscopy is essential for visualizing microorganisms. The metric system is used for measurement (1 mm = 1000 μm; 1 μm = 1000 nm).

• Magnification: Ocular × objective.

• Resolution: Ability to distinguish fine detail, improves with shorter wavelengths.

• Refractive index: Immersion oil used at 100× objective to prevent light loss.

• Microscopy types:

  • Brightfield: stained specimens, bright background.

  • Darkfield: bright specimen, dark background, useful for living organisms.

  • Phase-contrast: internal details of living cells without stains.

  • Fluorescence: UV light, fluorochrome dyes, rapid ID techniques.

Staining

Techniques and Gram Stain

Staining helps visualize and differentiate microorganisms.

• Fixation: Kills microbes and adheres them to slide.

• Simple stain: Single dye, shows size and shape.

• Differential stain: Gram stain differentiates bacteria into Gram-positive and Gram-negative based on cell wall structure.

Gram Stain Steps

• Crystal violet (primary stain): Stains all cells purple.

• Iodine (mordant): Binds with crystal violet to form large complexes inside cells.

• Alcohol or acetone (decolorizer, critical step):

  • Gram-positive: retains purple.

  • Gram-negative: thin peptidoglycan + outer membrane disrupted → complex washed out = colorless.

• Safranin (counterstain): Stains Gram-negative cells red/pink; Gram-positive remain purple.

Results

• Gram-positive: thick peptidoglycan, teichoic acids, purple.

• Gram-negative: thin peptidoglycan, outer membrane with LPS, pink/red.

• Diagnostic importance: Guides treatment (Gram-negative more resistant).

Enzymes

Structure and Function

Enzymes are proteins produced by living cells that lower activation energy and catalyze biochemical reactions.

• Apoenzyme: Protein part.

• Cofactor: Nonprotein helper (metal ion).

• Coenzyme: Organic helper (NAD+, FAD, CoA).

• Holoenzyme: Apoenzyme + cofactor (active enzyme).

• Specificity: One enzyme per substrate.

• Influenced by: Temperature, pH, substrate concentration.

• Inhibitors:

  • Competitive: Compete for active site.

  • Noncompetitive: Bind allosteric site → shape change.

• Compartmentalization: In eukaryotes, enzymes often localized in organelles.

• True/false check: Enzymes catalyze reactions without being consumed = True.

Metabolism and Energy Pathways

Overview

Metabolism includes all chemical reactions in cells, divided into catabolism (breakdown, exergonic, releases energy) and anabolism (building, endergonic, requires energy). ATP is the main energy currency.

• Catabolism: Breakdown, releases energy.

• Anabolism: Building, consumes energy.

• ATP: Adenosine triphosphate.

• Produced by: Substrate-level phosphorylation, oxidative phosphorylation, photophosphorylation.

• To generate energy from glucose, microbes use fermentation and respiration.

Glycolysis (Embden-Meyerhof Pathway)

Glycolysis is the central pathway for glucose catabolism, occurring in the cytoplasm.

• Inputs: 1 glucose, 2 ATP.

• Outputs: 2 pyruvate, 2 ATP (net), 2 NADH.

• Pyruvate goes to Krebs cycle (respiration) or fermentation.

Alternate Pathways

• Pentose Phosphate Pathway: NADPH, 5-carbon sugars for biosynthesis.

• Entner-Doudoroff Pathway: 1 ATP, 1 NADH, 1 NADPH; diagnostic for some bacteria.

Krebs Cycle (Citric Acid Cycle)

The Krebs cycle completes oxidation of glucose carbons, producing energy carriers.

• Per glucose: 6 NADH, 2 FADH2, 2 ATP, 4 CO2.

Electron Transport Chain (ETC)

ETC uses NADH/FADH2 to create a proton gradient for ATP synthesis.

• Location: Plasma membrane (prokaryotes), mitochondrial inner membrane (eukaryotes).

• Outputs: ~34 ATP per glucose.

• Final electron acceptor: Aerobic: O2; Anaerobic: nitrate, sulfate, etc.

Fermentation

Fermentation is an anaerobic process that regenerates NAD+ and produces organic end products.

• Products: Lactic acid or ethanol + CO2.

Metabolic Pathways Summary Chart

Pathway	Location	Inputs	Outputs (per glucose)	Notes
Glycolysis (Embden-Meyerhof)	Cytoplasm	1 glucose, 2 ATP	2 pyruvate, 2 ATP (net), 2 NADH	Occurs with or without O2
Pentose Phosphate (PPP)	Cytoplasm	Glucose-6-phosphate	NADPH, 5-carbon sugars	Precursors for nucleotides, amino acids
Entner-Doudoroff (ED)	Cytoplasm (some bacteria)	1 glucose	1 ATP, 1 NADH, 1 NADPH	Used by Pseudomonas, Bacillus
Krebs Cycle (TCA)	Eukaryotes: mitochondria Prokaryotes: cytoplasm	2 acetyl-CoA	6 NADH, 2 FADH2, 2 ATP, 4 CO2	Completes oxidation of glucose carbons
Electron Transport Chain (ETC)	Membrane (eukaryotes: mitochondria; prokaryotes: plasma membrane)	NADH, FADH2, O2	~34 ATP, H2O	Proton gradient drives ATP synthase
Fermentation	Cytoplasm	2 pyruvate, 2 NADH (from glycolysis)	Organic end products, NAD+	No O2, no ETC; only 2 ATP (from glycolysis)
Photosynthesis (Light Reactions)	Thylakoid membranes/plasma membrane	Light, H2O, ADP, NADP+	ATP, NADPH, O2	ATP only; Noncyclic: ATP + NADPH + O2
Photosynthesis (Calvin Cycle)	Stroma/cytoplasm	CO2, ATP, NADPH	Sugars (glucose), ADP, NADP+	Light-independent

Photosynthesis (Pathways of Light)

• Light-dependent: ATP + NADPH produced, O2 released.

• Light-independent (Calvin cycle): CO2 fixed → sugars.

• Cyclic photophosphorylation: ATP only.

• Noncyclic photophosphorylation: ATP, NADPH, O2.

Common Trick Questions (Quick Drill)

• Prokaryotes lack a plasma membrane = False. They do have a plasma membrane.

• Prokaryotes lack membrane-bound organelles = True.

• Prokaryotes typically have a circular chromosome = True.

• Gram-positive cell wall statements:

  • Retains shape = True.

  • Sensitive to acids = True.

  • Sensitive to lysozyme = True.

  • Protects the cell in a hypertonic environment = False (that's the trick).

• Membrane transport:

  • Active transport = requires ATP, moves low → high concentration.

  • Simple diffusion = passive, high → low.

  • Facilitated diffusion = passive but uses proteins.

  • Aquaporins = water channels (osmosis).

• Organelle functions:

  • Centrosome = microtubule organizing center (NOT food storage).

  • Golgi = modifies, packages, secretes.

  • Mitochondria = ATP production.

  • Lysosome = digestive enzymes.

• Organelle inside a prokaryotic cell = mitochondrion (double membrane, DNA, 70S ribosomes).

• Phospholipids found in plasma membrane + organelle membranes (not ribosomes or inclusions).

• Oxygen crosses plasma membrane by simple diffusion = True (small, nonpolar).

• Glucose crosses by facilitated diffusion = True (large, polar).

• Enzyme facts:

  • Enzymes catalyze reactions by lowering activation energy = True.

  • Enzymes are proteins = True.

Metabolic Pathways: Key Concepts

• Catabolism = releases energy, breakdown.

• Anabolism = consumes energy, building.

• ATP = adenosine triphosphate.

• Energy from glucose produced by fermentation and respiration.

• Oxidation = loss of electrons (often loss of H).

• Reduction = gain of electrons (often gain of H).

• Glycolysis main product = pyruvic acid.

• Carbohydrate oxidation produces ATP = True.

What Will Not Be on Test (Instructor Notes)

• No discoveries from Paul.

• Third golden age.

• Pay attention to Pasteur, Koch, Jenner, Lister.

• Specific types of microscopy will not be on the test.

• Light field, darkfield, fluorescence will be on the test.

• Atypical cell walls do not need to be tested.

• Role of mesosomes will not be tested.

• Translocation will not be tested.

• Main points: glycolysis, electron transport, the cycles. What is going in and how many ATPs come out and what comes out.

• Fermentations.

• Locations where cycles occur in eukaryotic vs prokaryotic.

Key Equations

• ATP production (glycolysis): $1\ \text{glucose} + 2\ \text{ATP} \rightarrow 2\ \text{pyruvate} + 2\ \text{ATP (net)} + 2\ \text{NADH}$

• Krebs cycle (per glucose): $2\ \text{acetyl-CoA} \rightarrow 6\ \text{NADH} + 2\ \text{FADH}_2 + 2\ \text{ATP} + 4\ \text{CO}_2$

• Electron transport chain (aerobic): $NADH + FADH_2 + O_2 \rightarrow \sim 34\ \text{ATP} + H_2O$

• Fermentation (lactic acid): $2\ \text{pyruvate} + 2\ \text{NADH} \rightarrow 2\ \text{lactic acid} + 2\ \text{NAD}^+$

• Fermentation (alcohol): $2\ \text{pyruvate} + 2\ \text{NADH} \rightarrow 2\ \text{ethanol} + 2\ \text{CO}_2 + 2\ \text{NAD}^+$