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

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: $\text{C}<em>6\text{H}</em>{12}\text{O}_6$

• 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).