Microbial Biochemistry & Metabolism: Core Concepts and Exam Guide

Microbial Biochemistry

Big Picture: Why Biochemistry Matters in Microbiology

All cells (including bacteria, fungi, protozoa, algae, and even viruses to a degree) are constructed from four major biomolecule families: proteins, carbohydrates, lipids, and nucleic acids. These molecules are primarily made of carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur, and are linked by covalent bonds. Their structure and function are determined by their chemical properties and the way they interact in aqueous environments.

1. Carbon & Functional Groups: "Molecular Personality"

Carbon atoms form the backbone of biological molecules, with functional groups attached that determine chemical behavior, reactivity, and interactions. Functional groups are key to understanding how molecules behave in cells.

Group	Looks Like	Charge (pH 7)	Polar?	Where Found / Functions
Hydroxyl	-OH	0	Yes	Bonding, solubility. In sugars, alcohols, Ser/Thr/Tyr side chains. Phosphorylation target.
Carbonyl	C=O (aldehyde/ketone)	0	Moderately	Reactive hotspot (electrophile). In sugars, peptide bonds (amides), amino acids (arginine C=O).
Carboxyl	-COOH or -COO-	Negative	Yes	Acids. Gives negative charge. Forms salt bridges, amino acids, fatty acids.
Amino	-NH2, -NH3+	Positive	Yes	Bases. Gives positive charge. ATP energy, DNA/RNA backbone, protein side chains.
Phosphate	-PO4-	Super negative	Yes	ATP energy, DNA/RNA backbone, metabolic intermediates.
Sulfhydryl (thiol)	-SH	0	No	Disulfide bonds (cysteines) stabilize protein shape, coenzymes.

Hydrolysis is the process of splitting polymers into monomers using water. Dehydration synthesis joins monomers by removing water.

2. Carbohydrates (Energy & Structure: "Lego Block")

Carbohydrates are essential for energy storage and structural integrity in cells. They exist as monosaccharides, disaccharides, and polysaccharides.

• Monosaccharides: Simple sugars (e.g., glucose, fructose, ribose). Ribose is found in RNA; deoxyribose in DNA.

• Disaccharides: Two sugars joined (e.g., lactose, sucrose, maltose).

• Polysaccharides: Many sugars linked. Functions include energy storage (glycogen, starch) and structure (cellulose in plants, chitin in fungi/exoskeletons, peptidoglycan in bacteria).

Sticky EPS (biofilm glue): Dextran (α-1,6 in dental plaque), capsule polysaccharides in pathogens.

3. Lipids (Membranes, Energy Storage, Waterproofing)

Lipids are hydrophobic molecules that form membranes, store energy, and provide waterproofing.

• Triglycerides (fats/oils): Glycerol + 3 fatty acids (ester bonds). Saturated = solid, unsaturated = liquid.

• Phospholipids: Amphipathic molecules with hydrophilic heads and hydrophobic tails. Form bilayers in membranes, providing fluidity and selective permeability.

• Steroids: Rigid rings (cholesterol, ergosterol).

• Waxes: High-melting lipids (e.g., mycolic acids in Mycobacterium).

4. Proteins (Workhorses & Scaffolds)

Proteins are polymers of amino acids, performing structural, enzymatic, and regulatory functions.

• Amino acids: Contain amino (-NH2), carboxyl (-COOH), and unique R group.

• Peptide bond: Formed by dehydration between -COOH and -NH2.

Levels of Protein Structure:

1. Primary: Sequence of amino acids (peptide bonds).

2. Secondary: Local shapes (α-helix, β-sheet) via H-bonds.

3. Tertiary: 3D folding via hydrophobic packing, ionic bonds, disulfide bridges.

4. Quaternary: Multiple polypeptides (e.g., hemoglobin).

Denaturation disrupts higher-order structure, affecting function.

5. Nucleic Acids & ATP (Information & Energy)

Nucleic acids store genetic information and energy. Nucleotides are the monomers, consisting of a base, sugar, and phosphate.

• DNA: Double helix, bases A-T, G-C.

• RNA: Single-stranded, bases A-U, G-C.

• ATP: Adenosine + 3 phosphates. Breaking phosphoanhydride bonds releases energy.

6. Cell Structures Built from These Molecules

• Membranes: Composed of phospholipids, proteins, and carbohydrates. Functions include selective transport, signaling, and energy conversion.

• Cell Walls: Provide rigidity and protection. Bacterial cell walls contain peptidoglycan; Gram-positive have thick PG, Gram-negative have thin PG plus outer membrane. Fungi have chitin; algae have cellulose.

• Cytoskeleton: Microtubules (eukaryotes), actin, flagella (bacteria).

• Storage Molecules: Glycogen (short-term), fat (long-term).

7. Viruses: Key Structural Features

• Genome: DNA or RNA.

• Capsid: Protein shell, sometimes with envelope (lipid from host).

• Spikes: Proteins for attachment.

• Enzymes: For replication (e.g., reverse transcriptase).

8. Inorganic Molecules in Cells

• Water: Polar, forms hydrogen bonds, drives hydrolysis/dehydration.

• Ions: Na+, K+, Ca2+, H+ for membrane potential, pH control, enzyme function.

9. Key Bond Names

• Glycosidic: Sugar-sugar (carbs).

• Ester: Fatty acids to glycerol (lipids), also in phospholipids.

• Phosphodiester: Sugar-phosphate in DNA/RNA backbone.

• Peptide: Amino acid-amino acid (proteins).

• Disulfide: Cys-Cys (protein stabilization).

10. Fast Cues for Exams

• Polysaccharide bonds: Glycosidic.

• Peptide bonds: -COOH + -NH2.

• Gram-negative bacteria: LPS (lipopolysaccharide).

• Amphipathic phospholipids: Hydrophilic heads, hydrophobic tails.

Microbial Metabolism

Big Picture: What is Metabolism?

Metabolism encompasses all chemical reactions in a cell. It includes catabolism (breaking down molecules to release energy) and anabolism (building molecules using energy). Energy is stored and transferred via ATP and electron carriers (NADH, FADH2, NADPH).

Key Vocabulary

• Redox: Oxidation = loss of electrons (LEO), Reduction = gain of electrons (GER).

• ATP: Adenosine + 3 phosphates. Breaking the terminal phosphate releases energy.

• Electron carriers: NAD+/NADH, FAD/FADH2, NADP+/NADPH.

• Chemiosmosis: Flow of protons through ATP synthase generates ATP.

Energy Carrier Table

Carrier	Oxidized Form	Reduced Form	Main Role
ATP	ADP	ATP	Direct energy for work (motility, biosynthesis)
NAD+	NAD+	NADH	Catabolic e- carrier to ETC (ATP power, electrons)
FAD	FAD	FADH2	Catabolic e- carrier to ETC (ATP power)
NADP+	NADP+	NADPH	Anabolic e- carrier (biosynthesis, nucleotides)

Enzymes

• Protein catalysts with specific active sites; lower activation energy.

• Regulation: Competitive inhibitors (active site), noncompetitive inhibitors (allosteric site).

• Environmental effects: Temperature extremes can denature enzymes.

Metabolic Classifications

Microbes are classified by their energy and carbon sources:

Type	Energy Source	Carbon Source	Example
Photoautotroph	Light	CO2	Cyanobacteria, algae, plants
Photoheterotroph	Light	Organic C	Some purple non-sulfur bacteria
Chemolithotroph	Chemical e- donors (H2, NH3, Fe2+)	CO2	Nitrifying bacteria
Chemoheterotroph	Chemicals (organic)	Organic C	Most pathogens, fungi, animals

Pathways That Turn Food into ATP

1. Glycolysis (cytoplasm, all cells):

   • Glucose (6C) → 2 pyruvate (3C)

   • Net: 2 ATP, 2 NADH

2. Transition Step (pyruvate → acetyl-CoA):

   • Per pyruvate: 1 CO2, 1 NADH, 1 acetyl-CoA

3. Krebs / Citric Acid Cycle:

   • Per acetyl-CoA: 3 NADH, 1 FADH2, 1 ATP/GTP, 2 CO2

4. ETC & Chemiosmosis (membranes):

   • Electron carriers donate e- to ETC, creating proton motive force (PMF)

   • ATP synthase uses PMF to make ATP

Classic yield: ~36 ATP per glucose (aerobic respiration).

Fermentation

When cells lack an ETC, they use fermentation to regenerate NAD+ and keep glycolysis running. Yields less ATP (2 per glucose). Common products: lactic acid (Lactobacillus), ethanol (yeast), mixed acids (E. coli).

Alternate Bacterial Pathways

• Pentose Phosphate Pathway (PPP): Makes NADPH + ribose-5-P for biosynthesis.

• Entner-Doudoroff (ED) Pathway: Alternative glycolysis in some Gram-negatives.

Lipid & Protein Catabolism

• Lipases hydrolyze triglycerides → glycerol + fatty acids.

• Proteases hydrolyze proteins → amino acids (deamination removes NH2).

Lab Plate Tie-Ins

• MacConkey agar (MAC): Selects Gram-negatives; lactose fermenters = pink.

• EMB agar: Selects Gram-negatives; strong lactose fermenters = metallic green sheen.

Exam Traps & Practice

• Dehydration synthesis joins monomers; hydrolysis splits them.

• Peptide bond: -COOH + -NH2.

• Cellulose and chitin are structural and hard to digest.

• Peptidoglycan is unique to bacteria.

Additional info: These notes expand on the original bullet points with definitions, examples, and context for key microbiology concepts, including tables for functional groups, energy carriers, and metabolic classifications. All major topics from the provided materials are covered and organized for exam preparation.