Biomolecules Overview

Structure: Alpha-carbon attached to carboxylate (-COO⁻), protonated amino group (-NH₃⁺), hydrogen, and side chain (R group).
Zwitterions: Exist at physiologic pH; neutral molecule with equal positive and negative charges.
Classification: By R group polarity: Hydrophobic (nonpolar), Polar (neutral), Negatively charged (acidic), Positively charged (basic).
- Nonpolar, aliphatic: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline.
- Aromatic: Phenylalanine, Tyrosine, Tryptophan.
- Polar, uncharged: Serine, Threonine, Cysteine, Asparagine, Glutamine.
- Positively charged: Lysine, Arginine, Histidine.
- Negatively charged: Aspartate (Asp), Glutamate (Glu).
Hydrophobic R groups: Sequestered inside protein cores.
Hydrophilic R groups: Interact with water on protein surfaces.
α-Amino Acids: Amino group adjacent to the carboxylate group; 19 of 20 are stereoisomers (glycine is achiral).

Primary: Sequence of amino acids linked by covalent peptide (amide) bonds (-CO-NH-).
Secondary: Local folding into regular 3D structures (α-helix, β-pleated sheet) stabilized by hydrogen bonds between backbone –NH– and –C=O– groups.
Tertiary: Overall 3D shape of a single polypeptide chain, maintained by side-chain interactions (salt bridges, H-bonds, hydrophobic interactions, disulfide bridges).
Quaternary: Arrangement of multiple polypeptide subunits, maintained by same forces as tertiary structure.
Collagen: Most abundant protein; three chains (tropocollagen) held by H-bonds; rich in glycine.

Loss of organized conformation (higher-order structures) due to temperature, pH extremes, solvents, etc.; primary structure remains intact.

Functions: Energy source (\sim 9 kcal/g), membrane structure, hormones, lipid-soluble vitamins, shock absorption, insulation.
Classes: Fatty Acids, Glycerides, Nonglyceride lipids (sphingolipids, sterols, waxes), Complex lipids (lipoproteins).

Long, straight-chain carboxylic acids (10–20 carbons), can be saturated or unsaturated.
Unsaturated fatty acids: Have double bonds (cis) that decrease melting temperature by preventing tight packing.

Glycerol esterified with fatty acids.
Triacylglycerols (TAGs): Three fatty acids to glycerol; energy storage in adipose tissue.
- Oils = unsaturated TAGs (liquid); Fats = saturated TAGs (solid).
- Hydrogenation: Adding H_2 to convert unsaturated to saturated facts.
- Saponification: Base-catalyzed hydrolysis of TAGs to glycerol + fatty acid salts (soap). Soaps form micelles.

Lipids: Phospholipids, glycolipids, sterols.
Cholesterol: Common sterol; modulates membrane fluidity/rigidity; precursor to steroid hormones.
Membrane proteins: Integral (span membrane) and Peripheral (surface).

Synthesized from cholesterol in the liver; amphipathic; form micelles to emulsify fats in the intestine.

Classes: Mineralocorticoids (e.g., aldosterone), Glucocorticoids (e.g., hydrocortisone), Sex hormones (e.g., testosterone, estradiol).

Derived from arachidonic acid (essential fatty acid).
Families: Prostaglandins, Leukotrienes, Thromboxanes.
Functions: Regulate inflammation, vasoconstriction, platelet aggregation.
Aspirin: Inhibits prostaglandin synthesis by acetylating cyclooxygenase (COX).

Transport lipids in blood; neutral lipid core (cholesterol esters/TAGs) surrounded by phospholipids, cholesterol, and protein.
Classes: Chylomicrons (gut to adipose), VLDL (liver to tissues), LDL (cholesterol to tissues), HDL (scavenges cholesterol).
LDL receptor: Defects linked to familial hypercholesterolemia.

Structure: Biomolecules with multiple –OH groups and aldehyde/ketone.
Types: Monosaccharides (e.g., glucose, fructose), Disaccharides (e.g., sucrose, lactose) linked by glycosidic bonds, Oligosaccharides (3-10 monosaccharides), Polysaccharides (long chains like starch, glycogen, cellulose).
Monosaccharide Naming: Aldose (aldehyde) vs. Ketose (ketone), Triose (3C) to Hexose (6C).
Chirality: Many chiral carbons create stereoisomers; 2^n possible for n chiral centers.
Disaccharides: Sucrose (glucose + fructose), Lactose (galactose + glucose, \beta(1\to 4)), Maltose (glucose + glucose, \alpha(1\to 4)).
Polysaccharides:
- Homopolysaccharides (single monomer): Chitin (N-acetylglucosamine, \beta(1\to 4)), Cellulose (glucose, \beta(1\to 4), strong structural), Starch (amylose-linear, amylopectin-branched, \alpha(1\to 4), \alpha(1\to 6) storage in plants), Glycogen (highly branched \alpha(1\to 4), \alpha(1\to 6) storage in animals).
Glycoconjugates: Proteoglycans (protein + sulfated glycosaminoglycans), Glycoproteins (protein + branched carbohydrate chains), Glycolipids (lipid + carbohydrate).
Blood Groups: Determined by oligosaccharide antigens on erythrocyte surface glycoproteins.

Types: DNA (store/transmit genetic info) and RNA (protein synthesis).
Nucleotide Structure: Nitrogenous base (Purines: A, G; Pyrimidines: C, T, U), pentose sugar (deoxyribose/ribose), phosphate group.
DNA Structure: Double helix; sugar–phosphate backbone outside, bases stacked inside. Antiparallel strands (5′→3′, 3′→5′). Base pairing: A-T (2 H-bonds), G-C (3 H-bonds).
Transcription (DNA to RNA): RNA complement to DNA template; U replaces T.
Translation (RNA to protein): mRNA codons read by ribosome; tRNA brings amino acids.
Central Dogma: DNA \to RNA \to Protein (with DNA replication), describing the flow of genetic information.