Carbohydrates, Lipids & Intro to Proteins – Comprehensive Study Notes

Metabolism: The Big Picture

• Living cells constantly cycle between two complementary processes:
  • Catabolism (break-down): hydrolysis of food polymers → monomeric sub-units + release of usable energy.
  • Anabolism (build-up): condensation (a.k.a. dehydration synthesis) of monomers → new cellular polymers + storage of energy.
• Instructor’s metaphor: “script” (specific reaction) vs “schema” (overall metabolic story) – always keep both levels in mind.

Condensation & Hydrolysis Reactions

• Condensation (Dehydration) Reaction
  • Removes one \text{H}_2\text{O} to join two monomers.
  • Creates a covalent bond specific to the macromolecule type (glycosidic, ester, peptide, etc.).
  • Requires energy input (“little push” to add the next bead on a string).
• Hydrolysis Reaction
  • Adds \text{H}_2\text{O} to cleave a polymer → releases individual monomers + energy.
  • Reversible counterpart to condensation; essential for digestion.

Carbohydrates

1. Energy-Storage Polysaccharides

• Starch (plants)
  • Helical \alpha-glucose polymer; modest branching.
  • Example: potato, rice.
• Glycogen (animals; esp. muscle & liver)
  • Similar helix but highly branched → more non-reducing ends → faster mobilization.
  • Instructor Q&A: Extra branching accommodates muscle physiology.
• Branching principle: more branch points ⇒ more accessible glucose units ⇒ larger energy reserve.

2. Structural Polysaccharides

• Cellulose (plants)
  • \beta-glucose; straight, parallel chains.
  • Extensive inter-strand hydrogen bonding (yellow dotted lines in slide) ⇒ rigid cell wall scaffolding.
  • Function: maintains plant shape against osmotic stress (cannot “walk away” from flood/drought).
• Chitin (fungi cell wall & arthropod exoskeleton)
  • \beta-glucose + \text{N}-\text{acetylglucosamine} (NAG) side group; still H-bonded.
  • Analogy: chemically akin to human fingernails.
• Peptidoglycan (bacterial cell wall)
  • Alternating carbohydrate chains cross-linked by peptide bridges (stronger than H-bonds).
  • Drug relevance: \beta-lactam antibiotics (e.g., penicillin) inhibit trans-peptidation → weaken wall → lysis; emergence of resistance emphasised.

3. Alpha vs Beta Glucose Recap

• Spatial orientation of the glycosidic bond (outward vs inward) defines \alpha (readily metabolised) vs \beta (storage/structural) forms.

Lipids

1. Shared Chemical Traits

• Rich in \text{C–C} and \text{C–H} bonds ⇒ non-polar, hydrophobic.
• When a molecule has both hydrophobic tail & hydrophilic head it is amphipathic.

2. Hydrocarbon Tail Types

• Isoprenoid chain
  • Repeating isoprene units; found in pigments, vitamins, cholesterol, steroid precursors.
• Fatty-acid chain
  • Hydrocarbon tail + terminal carboxyl (\ce{COOH}).
  • Variations:
  • Saturated – only single bonds; straight; solid at room T (butter).
  • Unsaturated – ≥1 \text{C=C}; kinks; liquid at room T (vegetable oil).
  • Long saturated tails → waxy, highly viscous (beeswax).
  • Dietary debate noted (industrial trans-fats vs natural saturated fats).

3. Major Cellular Lipid Classes

• Fats (Triglycerides)
  • Glycerol + 3 fatty acids linked by ester bonds.
  • Superb energy density: higher \text{C–H} ratio than carbohydrates ⇒ >2× energy per gram.
  • Soap/detergent action = hydrolysis of ester linkages.
• Phospholipids
  • Glycerol + 2 fatty acids + phosphate head (often + small charged alcohol).
  • Amphipathic ⇒ spontaneous bilayer/vesicle formation; head = hydrophilic, tails = hydrophobic.
  • Domain nuance: Bacteria & Eukarya use fatty-acid tails; Archaea often use isoprenoid tails (membrane stability in extremes).
• Steroids
  • Four fused carbon rings + variable functional groups.
  • Cholesterol: membrane fluidity buffer & precursor for all steroid hormones.
  • Anabolic steroids: exogenous testosterone analogues → rapid muscle anabolism, health/ethical issues (feedback shutdown, acne, unsustainable gains).

4. Membrane Function & Selective Permeability

• First cells likely formed when amphipathic lipids self-assembled into vesicles enclosing cytosol.
• Membrane allows regulated exchange; basis for internal metabolism.

Proteins (Intro)

1. Amino Acid Basics

• General formula: Central (alpha) C attached to
  • \ce{H}
  • Amino group \ce{NH2} → \ce{NH3^+} in water.
  • Carboxyl group \ce{COOH} → \ce{COO^-} in water.
  • Variable side chain R.
• Twenty common amino acids differ only in R-group chemistry.
  • Acidic (negative R) vs Basic (positive R) vs Polar uncharged vs Non-polar (hydrophobic).
  • Side-chain properties dictate solubility, hydrogen bonding, & intra-protein interactions.

2. Polymerisation → Polypeptides

• Peptide bond formation = condensation between carboxyl of one AA & amino of next.
  \ce{AA1{-}COOH + H2N{-}AA2 ->[{-H2O}] AA1{-}CO{-}NH{-}AA2}
• Strong, planar; adjacent single bonds permit rotation → chain flexibility.
• Directionality: written N-terminus → C-terminus (like reading left→right).
• Proteins are not rigid like cellulose; flexibility enables folding & dynamic function.

3. Functional Diversity Preview

• Collagen: rope-like extracellular support (skin firmness).
• Aquaporin: barrel-shaped membrane pore for water regulation (kidney osmolarity).
• DNA-binding proteins: shape complements double helix for replication/repair.
• Enzymes: active sites precisely oriented side chains for catalysis.

4. Practical & Ethical Connections

• Protein folding errors → disease (e.g., prions; not yet covered but hinted relevance).
• Antibiotic targeting of peptide cross-links in peptidoglycan underpins modern medicine; resistance an escalating concern.
• Dietary amino acid sourcing: humans are heterotrophs; essential AAs must come from food.

Cross-Topic Connections & Take-Home Patterns

• Bond Type ↔ Macromolecule
  • Carbohydrate: glycosidic.
  • Lipid (fats): ester.
  • Protein: peptide.
• Structure ⇒ Function
  • Helical, branched carbs → rapid energy.
  • Parallel, H-bonded carbs → rigid support.
  • Amphipathic lipids → membranes.
  • Flexible peptide backbone + variable R → immense functional repertoire.
• Energy Logic
  • More \text{C–H} bonds (fat) = higher caloric yield than hydroxyl-rich carbs.
  • Storage hierarchy: fat > glycogen/starch > free glucose.
• Real-World Relevance
  • Keto diet forces lipid catabolism (ketosis) but mimics starvation phenotype.
  • Soap & detergents exploit ester hydrolysis chemistry.
  • Performance-enhancing steroids illustrate endocrine feedback and ethical issues in sport.
  • Cell-wall-targeting antibiotics rely on understanding of carbohydrate-protein cross-links.

Looking Ahead

• Next lecture will dissect the four hierarchical protein structures (primary → quaternary) and introduce nucleic acids to complete the biomolecule suite.