Chemistry of Life – Inorganic & Organic Compounds (Class Notes)

Course Logistics & Upcoming Lab

  • Class duration: 4 hours ⇒ instructor offers 2 breaks of 20 minutes each (instead of two 10-minute breaks).

  • Next meeting held in the DLC lab:

    • Access to computers, smart screens, anatomical models.

    • Activity: photograph assigned structures while using your ID badge as a pointer so you can later identify each part yourself.

    • A lab manual (pp. 8–90 mentioned) accompanies the exercise.

Fundamental Chemistry Review

  • Atoms = basic unit of matter.

  • Molecule = \ge 2 atoms bonded together.

  • Element = molecule whose atoms are all the same type (pure substance).

  • Compound = molecule containing \ge 2 different atoms.

  • Chemists’ vs. biochemists’ “organic” definition:

    • Chemistry: requires \text{C–C} or \text{C–H} bonds.

    • Biology shortcut: “contains carbon.”

Inorganic vs. Organic Compounds

Characteristic

Inorganic

Organic

Contains carbon?

Usually no

Yes (carbon based)

Size/complexity

Smaller, simpler

Larger, more complex

Key body examples

\text{H}_2\text{O}, \text{NaCl}, acids, bases

Carbohydrates, lipids, proteins, nucleic acids

Inorganic Compound #1 – Water

  • Most abundant inorganic molecule in the body.

    • Adults ≈ \tfrac{2}{3} (\approx 66\%) of body mass.

    • Newborns ≈ 80\%.

  • Physiologic roles

    • Transport medium (e.g.

    • Blood plasma ≈ 90\% water.)

    • Reactant/product in chemical reactions (e.g. hydrolysis).

    • Universal solvent for salts, sugars, etc.

    • Cushioning & shock absorption (e.g. cerebrospinal fluid ≈ plasma).

    • High heat capacity ⇒ buffers body-temperature swings; warmed irrigation fluids (kept at 37^{\circ}\text{C}) prevent intra-operative hypothermia.

  • Clinical pearls

    • Dehydration can be life-threatening.

    • Brain-freeze: very cold liquid → rapid heat transfer → meningeal vasoconstriction → headache.

Inorganic Compound #2 – Salts & Electrolytes

  • Salt = ionic compound that dissociates in water → ions (electrolytes).

    • Example: \text{NaCl} \rightarrow \text{Na}^+ + \text{Cl}^-.

  • Physiologic importance

    • \text{Na}^+ & \text{K}^+ essential for nerve impulses; \text{K}^+ affects cardiac contraction.

    • Pre-operative serum-electrolyte panel; significant imbalances corrected before elective surgery ("optimizing" the patient).

Inorganic Compound #3 – Acids, Bases, & the pH Scale

  • pH scale: 0 \rightarrow 14 (logarithmic; each integer step = \times 10 change in [\text{H}^+]).

    • Neutral: \text{pH}=7 (pure water: \text{H}^+ = \text{OH}^-).

    • Acid: \text{pH} < 7 (greater [\text{H}^+]).

    • Base/Alkali: \text{pH} > 7 (greater [\text{OH}^-]).

  • Common body acid: \text{HCl} in stomach, \text{pH}\approx1–2.

    • Protected by thick mucus barrier; imbalance → hyperacidity, GERD.

    • Therapy ladder: antacids (bases) → H2 blockers → proton-pump inhibitors → surgical vagotomy ± pyloroplasty.

    • Helicobacter pylori infection weakens mucus, linked to ulcers ⇒ add antibiotics.

  • Base examples: \text{NaOH}, \text{NaHCO}_3 (baking soda).

  • Neutralization: Acid + Base → Salt + Water.

    • Eg: \text{NaOH} + \text{HCl} \rightarrow \text{NaCl} + \text{H}_2\text{O}.

  • Representative household pH values

    • Blood 7.4 (slightly basic)

    • Milk \sim 6.4

    • Coffee 5

    • Soft drink 3

    • Lemon juice 2

    • Bleach 9.5

    • Ammonia 11

    • Lye 13.5

Organic Compounds Overview

  1. Carbohydrates

  2. Lipids

  3. Proteins

  4. Nucleic acids (brief mention only)

1 Carbohydrates

  • Composition: \text{C}, \text{H}, \text{O}; \text{H} : \text{O} = 2 : 1 ⇒ "hydrates of carbon."

  • Nomenclature: “-ose” (sugars).

  • Classification & examples

    • Monosaccharides (1 sugar)

    • Glucose (blood sugar)

    • Fructose (fruit sugar)

    • Galactose

    • Disaccharides (2 sugars)

    • Lactose = glucose + galactose

    • Sucrose = glucose + fructose

    • Maltose = glucose + glucose

    • Polysaccharides (≥3 sugars)

    • Starch (plant storage)

    • Cellulose (plant fiber)

    • Glycogen (human storage; liver & skeletal muscle)

  • Hormonal regulation

    • Glucagon stimulates glycogenolysis (breakdown of glycogen).

    • Glycolysis ≠ Glycogenolysis (glucose catabolism vs. glycogen breakdown).

  • Nutrition/athletics

    • Primary, preferred energy source.

    • Carb-loading for endurance; digestion begins in duodenum, glucose available ≈ 30 min post-ingestion.

    • Glycogen storage capacity limited; excess glucose converted to fat.

2 Lipids (Fats)

  • Major forms: Triglycerides, Phospholipids, Steroids (incl. cholesterol).

  • Properties

    • Insoluble in water (hydrophobic) but soluble in other lipids.

    • Energy density ≈ 2× carbohydrate/protein ("calorically dense").

  • Triglycerides

    • Stored subcutaneously as adipose tissue ⇒ energy reserve & insulation.

  • Phospholipids

    • Form bilayer of cell membranes.

    • Structure: polar (hydrophilic) "head" + non-polar (hydrophobic) "tails".

  • Steroids & cholesterol

    • Cholesterol maintains membrane fluidity; transports lipids as lipoproteins:

    • HDL (“good”): removes excess cholesterol.

    • LDL (“bad”): deposits cholesterol → atherosclerosis.

    • Vitamin D, steroid hormones, prostaglandins = lipid-derived.

  • Dietary health

    • Saturated fats (animal, solid): raise \text{LDL}; risk of atherosclerosis.

    • Unsaturated fats (plant oils, liquid): “heart-healthy.”

    • Trans fats = overheated/hydrogenated oils (cloudy); hazardous.

    • Omega-3 fatty acids (fish, flax, chia, walnuts) reduce cardiovascular risk.

3 Proteins

  • Constitute >50\% of body’s organic matter.

  • Monomer = amino acid (≈20 types).

    • Each contains \text{NH}_2 (amine) + \text{COOH} (acid) + variable R-group.

    • Essential amino acids must come from diet; non-essential synthesized endogenously.

  • Structural hierarchy

    1. Primary: linear polypeptide chain (peptide bonds).

    2. Secondary: \alpha-helix (coil) & \beta-pleated sheet (folds).

    3. Tertiary: secondary structures fold into 3-D glob.

    4. Quaternary: \ge 2 polypeptides assemble (e.g. hemoglobin = 4 subunits).

  • Categories & examples

    • Fibrous (structural)

    • Collagen (most abundant; skin, CT)

    • Keratin (epidermis, hair shaft)

    • Elastin (stretchy CT)

    • Globular (functional)

    • Enzymes (biological catalysts)

    • Protein hormones (insulin, thyroid hormone)

    • Antibodies/Immunoglobulins (immune defense)

    • Myoglobin & hemoglobin (O$_2$‐binding)

4 Nucleic Acids (preview)

  • DNA & RNA also carbon-based ⇒ formally organic, but detailed treatment reserved for later lectures.

Clinical, Surgical, & Everyday Connections

  • OR irrigation: sterile water warmed to 37^{\circ}\text{C} when used inside major cavities to prevent hypothermia; room-temp adequate for superficial procedures.

  • Electrolyte correction crucial pre-op; emergent surgeries manage abnormalities intra-op.

  • GERD management ladder: lifestyle → antacid (basic) → H2-blocker → PPI → vagotomy ± pyloroplasty.

  • Brain freeze & vasoconstriction illustrate water’s thermal conductivity.

  • Atherosclerosis pathophysiology links saturated/trans fats & \text{LDL} to vascular disease.

  • Hydration: water as “most important nutrient;” dehydration is potentially fatal.

Key Chemical Formulas & Equations (quick reference)

  • Water: \text{H}_2\text{O}

  • Glucose: \text{C}6\text{H}{12}\text{O}_6

  • Hydrochloric acid: \text{HCl}

  • Sodium hydroxide: \text{NaOH}

  • Baking soda: \text{NaHCO}_3

  • Salt dissociation: \text{NaCl} \rightarrow \text{Na}^+ + \text{Cl}^-

  • Neutralization: \text{Acid} + \text{Base} \rightarrow \text{Salt} + \text{H}_2\text{O}

  • Energy hierarchy: Carbs → Fats → (Proteins last resort)

Study Tips

  • Memorize pH cutoffs and logarithmic nature ("1-unit change = 10-fold").

  • Know monosaccharide → di/polysaccharide relationships.

  • Be able to diagram phospholipid bilayer orientation (polar vs. non-polar).

  • Associate lipid classes with health impact (LDL vs. HDL, saturated vs. unsaturated vs. trans).

  • Distinguish glycogenolysis from glycolysis; glucagon vs. insulin roles.

  • Recall protein structural levels and representative examples (collagen, hemoglobin, enzymes).

  • Constantly link structure ↔ function ↔ clinical relevance (e.g., mucus barrier & ulcers, CSF cushioning).