Organic Compounds – Lecture Vocabulary

Expected Learning Outcomes

• Explain why carbon is uniquely suited as the structural foundation of biological molecules.
• Describe the biological relevance of polymers and outline how dehydration synthesis and hydrolysis build-up or break-down macromolecules.
• Identify the main classes, structures, and functions of carbohydrates, lipids, and proteins.
• Elucidate the mechanisms of enzyme action.

Carbon Compounds & Functional Groups

• Organic chemistry = study of carbon-containing compounds.
• Four biological macromolecule categories:
  • Carbohydrates
  • Lipids
  • Proteins
  • Nucleotides (monomers) ⇨ Nucleic acids (polymers)
• Carbon properties
  • 4 valence electrons ⇒ forms up to four covalent bonds; obeys the octet rule by sharing electrons.
  • Can bond with C, H, O, N, S, P ⇒ immense molecular diversity.
  • Forms backbones: long chains, branches, rings; permits functional-group substitution.
• Functional groups (small clusters of atoms that impart characteristic chemical properties)
  • Hydroxyl (—OH) · sugars, alcohols
  • Methyl (—CH₃) · fats, oils, steroids, amino acids
  • Carboxyl (—COOH)· amino acids, proteins
  • Amino (—NH₂) · amino acids, proteins
  • Phosphate (—H₂PO₄)· nucleic acids, ATP

Monomers & Polymers

• Macromolecule = very large organic molecule (e.g.
  proteins, DNA); very high molecular mass.
• Monomer = single subunit; Polymer = chain of repeating monomers.
  • Example: starch ≈ 3{,}000 glucose units.

Polymerization Processes

• Dehydration synthesis (condensation)
  • Joins monomers ⇒ covalent bond.
  • Removes \text{–OH} from one monomer + \text{–H} from another ⇒ produces \text{H}_2\text{O}.
• Hydrolysis (reverse)
  • Adds \text{H}_2\text{O} ⇒ cleaves bond.
  • \text{H}^+ added to one fragment, \text{OH}^- to the other.
• Biological relevance
  • Central to digestion, metabolism, DNA replication, protein elongation.

Carbohydrates

• Hydrophilic organic molecules; general formula \text{(CH}2\text{O)}n (≃ “hydrated carbon”).
  • Hydrogen:oxygen ≈ 2:1 — reminiscent of water.
• Nomenclature
  • Root “sacchar-” or suffix “-ose” ⇒ “sugar.”

Monosaccharides (C₆H₁₂O₆)

• Glucose (blood sugar)
• Galactose (converted to glucose in liver)
• Fructose (fruit sugar → glucose)
• Isomers: identical formula, different arrangement ⇒ different properties.

Disaccharides

Oligo- & Polysaccharides

• Oligosaccharide = 3–10(+) monosaccharides; often attached to proteins/lipids (glycoproteins).
• Polysaccharide ≥ 50 units.
  1. Glycogen
  • Animal glucose storage; synthesized in liver, muscles, brain, uterus, vagina.
  • Liver: post-meal glucose ↗ ⇒ glycogen build; between meals ⇒ glycogenolysis shares glucose with blood.
  • Muscles store for their own “greedy” use.
  • Uterine glycogen nourishes embryo.
  1. Starch
  • Plant glucose storage; only significant digestible plant polysaccharide.
  1. Cellulose
  • Plant cell wall structural fiber; indigestible → dietary fiber (↑ gut motility, ↓ cholesterol).

Functions & Conjugated Forms

• Rapid energy: all dietary CHO → glucose → oxidized → \text{ATP}.
• Conjugated carbohydrates
  • Glycolipids – outer cell membrane.
  • Glycoproteins – membrane + mucus (respiratory, GI tracts).
  • Proteoglycans – gels ↗ tissue adhesion, lubrication (joints, umbilical cord, vitreous humor), cartilage resilience.

Lipids

• Hydrophobic organic molecules; high H:O ratio ⇒ ↓ oxidation ⇒ ↑ calories/gram.
• Principal classes: Fatty acids, Triglycerides, Phospholipids, Eicosanoids, Steroids.

Fatty Acids

• 4–24 C chain; terminal carboxyl (acid) + methyl.
• Saturation status
  • Saturated: no \text{C}=\text{C} (e.g.
    palmitic acid).
  • Unsaturated: ≥ one \text{C}=\text{C} (cis or trans).
  • Polyunsaturated: many double bonds.
  • Essential fatty acids: must come from diet (ω-3, ω-6).

Triglycerides (Neutral Fats)

• 3 fatty acids esterified to glycerol.
  • Oils = liquid (mostly plant, polyunsat.)
  • Fats = solid (animal, saturated).
• Stored in adipocytes ⇒ energy reserve, insulation, shock absorption.
• Hydrolyzed by lipases to glycerol + FA.

Phospholipids

• Triglyceride-like but one FA replaced by phosphate group + N-containing base (e.g.
  choline).
• Amphiphilic: hydrophilic head + hydrophobic tails.
• Structural basis of cellular membranes, micelles, lipoproteins.

Trans vs.

Cis Fatty Acids & Cardiovascular Ethics

• Trans-FA: hydrogens on opposite sides of \text{C}=\text{C}.
  • Produced by partial hydrogenation of vegetable oils.
  • Resist enzymatic degradation ⇒ linger in blood, deposit in arteries ⇒ ↑ heart-disease risk.
  • Regulatory and public-health concern; mandatory labeling.
• Cis-FA: hydrogens on same side ⇒ natural, enzyme-friendly.

Eicosanoids

• 20-C derivatives of arachidonic acid.
• Prostaglandins, leukotrienes, thromboxanes.
  • Local hormone-like signalling: inflammation modulation, blood clotting, vasomotor tone, labor induction.
  • Pharmacological target (NSAIDs inhibit COX-mediated prostaglandin synthesis).

Steroids & Cholesterol

• Steroid nucleus = four fused rings (17 C atoms).
• Cholesterol = “parent” steroid; synthesized mainly in liver (≈ 85 %), remainder dietary (≈ 15 %).
  • Integral to membrane fluidity, precursor to vitamin D, bile acids, cortisol, aldosterone, sex hormones.
• Lipoproteins (“good/bad” label)
  • HDL (high-density): ↑ protein/↓lipid; scavenges excess cholesterol ⇒ protective.
  • LDL (low-density): ↓protein/↑lipid; delivers cholesterol to tissues ⇒ arterial plaque formation.
  • Lifestyle & genetics influence profiles; ethical implications for food industry & public health.

Proteins

• Polymers of 20 amino acids (AAs); name from Greek “protos” = first/primary.
• Each AA has amino group \text{–NH}_2, carboxyl \text{–COOH}, hydrogen, and variable R-group.
  • R-group dictates polarity, acidity, etc.
  • 8 (9) essential AAs = must be dietary.

Peptides → Proteins

• Peptide bond = \text{C–N} linkage via dehydration ((\text{–COOH} + \text{–NH}_2)).
• Terminology
  • Dipeptide (2 AA), Tripeptide (3), Oligopeptide (

Structural Hierarchy

1. Primary – linear AA sequence (gene-encoded).
2. Secondary – alpha helix or beta sheet via \text{H}-bonds between \text{C}=\text{O} & \text{N–H}.
3. Tertiary – further folding (hydrophobic interactions, disulfide bridges) ⇒ globular or fibrous shapes.
4. Quaternary – association of ≥2 polypeptides (e.g.
   hemoglobin: 2α + 2β + heme prosthetic groups).

• Conformation determines function; can reversibly change (e.g.
  membrane channels, muscle contraction).
• Denaturation: irreversible conformational loss via extreme \text{pH} or heat (egg-white cooking metaphor).
• Conjugated proteins contain non-AA moieties (prosthetic groups), e.g.
  heme in hemoglobin.

Functional Diversity

• Structural: Keratin (hair, nails), Collagen (skin, bone, cartilage).
• Communication: peptide hormones; receptors; ligand binding.
• Membrane transport: channels & carriers; nerve/muscle excitability.
• Catalysis: enzymes (see below).
• Recognition & protection: antibodies, clotting factors.
• Movement: motor proteins (actin/myosin).
• Cell adhesion: integrins, cadherins; tissue integrity, immune surveillance.

Enzymes & Metabolism

• Enzyme = biological catalyst (usually protein) that lowers activation energy E_a, enabling rapid reactions at 37^\circ\text{C}.
• Naming: substrate + “-ase” (e.g.
  sucrase, amylase).

Mechanism

1. Substrate binds active site ⇒ enzyme–substrate complex (lock-and-key specificity).
2. Enzyme catalyzes bond formation/breakage (often via induced fit).
3. Products released; enzyme unchanged ⇒ reusable (~ millions cycles/min).

• Example: Sucrase + sucrose → \text{glucose} + \text{fructose} (hydrolysis).

Environmental Factors

• Optimum \text{pH} varies (salivary amylase ≈ 7; pepsin ≈ 2).
• Optimum temperature ≈ 37^\circ\text{C}; high fever or refrigeration can inhibit activity.
• Extreme conditions ⇒ denaturation.

Metabolic Pathways

• Sequential enzyme-catalyzed reactions: A \xrightarrow{\alpha} B \xrightarrow{\beta} C \xrightarrow{\gamma} D.
• Regulation via enzyme activation/inhibition allows cells to control end-product levels; foundational principle in pharmacology & endocrinology.

Nucleotides, ATP & Nucleic Acids

Nucleotide Components

• Nitrogenous base (purine/pyrimidine)
• Pentose sugar (ribose or deoxyribose)
• ≥1 phosphate groups

Adenosine Triphosphate (ATP)

• Structure: adenine + ribose + 3 \text{PO}_4^{3-}.
• High-energy bonds (~) between P-groups; especially between 2nd–3rd.
• Central energy currency
  • Stores energy from exergonic reactions (e.g.
    glucose oxidation) and releases it for work within seconds.
  • \text{ATP} \leftrightarrow \text{ADP} + \text{P}_i + \text{energy}
• Continuous turnover: full body ATP supply would sustain life <1 min without regeneration; cyanide lethally blocks ATP synthase.
• Major uses: muscle contraction, ciliary beating, active transport, anabolism, phosphorylation cascades.

ATP Production (Cellular Respiration)

1. Glycolysis → 2 ATP + pyruvic acid (cytosol).
2. • If no \text{O}2: Anaerobic fermentation → lactic acid (regenerates \text{NAD}^+, no extra ATP). • With \text{O}2: Aerobic respiration (mitochondria) → ~36 ATP, 6\text{CO}2 + 6\text{H}2\text{O}.

Other Nucleotides

• cAMP (cyclic AMP): second messenger in hormone signalling.
• GTP, NAD⁺, FAD: energy transfer & redox cofactors.

Nucleic Acids

• DNA (10⁸–10⁹ nucleotides): genetic blueprint; replicates for cell division; encodes proteins.
• RNA (70–10,000 nt): mRNA, rRNA, tRNA; interprets DNA & assembles proteins in correct AA order.

Connections, Implications & Real-World Relevance

• Carbon versatility underlies biochemical complexity; understanding functional groups benefits drug design.
• Dietary choices (complex carbs vs.
  simple sugars; trans-fats; fatty-acid profiles) affect metabolism, cardiovascular health.
• Fiber (cellulose) impacts gut microbiota and cholesterol.
• Enzyme specificity & regulation form the basis of clinical diagnostics (e.g.
  serum amylase in pancreatitis) and pharmacotherapy (enzyme inhibitors).
• Protein denaturation principles explain food science (cooking), sterilization, and toxin action.
• ATP dynamics highlight the continuous energy demand; informs critical care (cyanide poisoning, mitochondrial diseases).
• Nucleic acid knowledge drives genetics, forensic science, and biotechnology (PCR, CRISPR).