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Biochemistry: The Chemistry of Life

Rates of Chemical Reactions

  • Heat increases molecular motion; more collisions with enough energy lead to more reactions.
  • Higher concentrations of reactants increase encounter rate and reaction likelihood.
  • Smaller particle size makes it easier for molecules to move and collide.
  • Catalysts speed up reactions by participating in the process but are not consumed or changed overall; enzymes in cells are biological catalysts.
  • Practical exam note: you’ll be asked to draw the planetary model based on information given (atom/atomic structure).

Biochemistry: The Chemistry of Life

  • Body contains inorganic vs organic compounds.
  • Organic compounds always contain carbon; major examples include glucose (C6H12O6).
  • Carbon is uniquely versatile because:
    • It can form four bonds, enabling 3D molecular structures.
    • It can form simple and complex chains and rings (e.g., glucose can form ring structures).
  • Two exceptions to the rule that all carbon-containing compounds are organic: carbon monoxide (CO) and carbon dioxide (CO2) are not considered organic.
  • Inorganic compounds include water, salts, and many minerals.

Water and Inorganic Compounds

  • Body water content: about 60% of body weight in adults; newborns ~75%; elderly can be <50%.
  • Water’s properties largely come from hydrogen bonding, giving:
    • High heat capacity (temperature changes are buffered by water).
    • High heat of vaporization (requires a lot of energy to vaporize).
    • Polar solvent properties (facilitates chemical reactions in solution).
    • Cushioning effects (physical protection).
  • Polar compounds have positive and negative charges; water interacts via hydrogen bonds.
  • Salts (ionic compounds) dissociate in water; surrounded by hydration shells:
    • Example: NaCl(s) in water → Na+(aq) + Cl−(aq)
    • Hydration involves water’s oxygen facing cations and hydrogen facing anions.
  • Important electrolytes: Na⁺, K⁺, Cl⁻, Ca²⁺, phosphate (PO₄³⁻) – essential for physiology.
  • Acids and bases:
    • Acids donate hydrogen ions (H⁺) in water; bases accept H⁺ or release OH⁻.
    • Example acids/bases: HCl → H⁺ + Cl⁻; NaOH → Na⁺ + OH⁻.
    • When strong acid and strong base mix, neutralization yields salt and water.
    • Neutralization reaction: ext{H}^+ + ext{OH}^-
      ightarrow ext{H}_2 ext{O}
  • pH scale:
    • Range 0–14; 7 is neutral; below 7 is acidic; above 7 is basic (alkaline).
    • Physiological pH (blood) = approximately pH ext{(blood)} \approx 7.4
    • Scale is a negative logarithmic scale: pH = -\log_{10}[\text{H}^+] and [\text{H}^+] = 10^{-pH}
    • Consequences:
    • A pH of 5 has 10× more H⁺ than pH 6; a pH of 4 has 10× more H⁺ than pH 5, etc. (general rule: each unit change is a tenfold change in hydrogen ion concentration).
  • Buffers in blood:
    • Carbonic acid–bicarbonate system: \text{H}2\text{CO}3 \rightleftharpoons \text{H}^+ + \text{HCO}_3^-
    • Buffer pairs resist pH changes by binding or releasing H⁺ as needed.
    • Example: If strong acid enters blood, bicarbonate can accept H⁺; if strong base enters, carbonic acid can donate H⁺ to neutralize.
  • Key takeaways:
    • Water’s properties enable life-supporting chemistry and stable body pH.
    • pH control through buffers is critical for homeostasis.

Organic Compounds: Carbohydrates

  • Carbohydrates = hydrated carbon (empirical formula roughly (CH2O)n ).
  • Monosaccharides (simple sugars): glucose, fructose, galactose (all commonly hexoses; C6H12O6).
    • Glucose: C6H{12}O_6
    • Fructose: C6H{12}O_6 (isomer of glucose)
    • Galactose: C6H{12}O_6 (isomer of glucose)
  • Carbon in five-carbon sugars (pentoses) used as building blocks for DNA and RNA (e.g., deoxyribose: C5H{10}O_4).
  • Disaccharides (two monosaccharides linked by dehydration synthesis):
    • Sucrose (glucose + fructose): C{12}H{22}O_{11}
    • Maltose (glucose + glucose): C{12}H{22}O_{11}
    • Lactose (galactose + glucose): C{12}H{22}O_{11}
    • Note from lecture: lactose was described as two glucose; correction: lactose is galactose + glucose.
  • Lactose intolerance explained: the enzyme that cleaves lactose (lactase) declines with age, leading to undigested lactose in the gut, osmotic effects, bloating/diarrhea.
  • Blood glucose storage:
    • When blood glucose is high, liver and skeletal muscles convert excess glucose to glycogen via dehydration synthesis for storage.
    • Brain neurons require a constant glucose supply; glycogen mainly stored in liver and skeletal muscle; neurons rely on circulating glucose.
  • Polysaccharides: starch (plants), glycogen (animals).
  • Polymerization and depolymerization:
    • Dehydration synthesis (condensation): monomers join; water is released: Monomer + Monomer → Polymer + H₂O.
    • Hydrolysis: polymer is broken into monomers with water input: Polymer + H₂O → Monomer + Monomer.
  • Example of linkage and hydrolysis: glucose + fructose → sucrose via dehydration synthesis; hydrolysis breaks sucrose back into glucose and fructose.
  • Key equation for polymers in digestion and metabolism is the water-in, water-out concept via dehydration and hydrolysis.

Organic Compounds: Lipids

  • Lipids are nonpolar and hydrophobic; do not mix with water.
  • Major lipid types: triglycerides (fats and oils), phospholipids, steroids.
  • Triglycerides:
    • Structure: glycerol backbone + three fatty acids → triglyceride; commonly written as a glycerol molecule connected to three fatty acid chains.
    • State at room temperature determines naming: fats (solid) vs oils (liquid).
    • Fatty acids can be saturated (no C=C bonds) or unsaturated (one or more C=C bonds).
    • Saturated triglycerides pack tightly and are usually solid at room temperature; unsaturated fats have kinks due to double bonds, leading to liquids at room temperature and generally healthier profiles.
    • Hydrogenation: chemical process that adds hydrogen to unsaturated fats, can produce trans fats, which have been linked to negative cardiovascular effects by raising LDL and lowering HDL cholesterol.
    • Trans fats example: Crisco historically used to mimic solid fats; hydrogenation can create trans double bonds; many jurisdictions have restricted trans fats due to health concerns.
  • Phospholipids:
    • Modified triglycerides with two fatty acid tails and a phosphate-containing head group.
    • Amphipathic: hydrophobic tails and polar hydrophilic head (phosphate group).
    • In water, tails aggregate away from water while heads face the aqueous environment, forming lipid bilayers that are fundamental to cell membranes.
    • Visuals: membranes often drawn as a two-layer “popsicle” structure with hydrophobic tails inside and hydrophilic heads outside.
  • Steroids:
    • Lipid-derived molecules with a characteristic four-ring carbon skeleton (nonpolar) and various side chains.
    • Cholesterol is a key steroid that modulates membrane fluidity and serves as a precursor for other steroids.
    • Vitamin D is derived from cholesterol via UV exposure in the skin; kidneys convert it to active vitamin D.
    • Steroid hormones (examples): testosterone, estrogen, aldosterone – regulate metabolism, reproduction, and electrolyte balance.
  • Bile salts:
    • Steroid-derived molecules stored in the gallbladder and released into the small intestine to emulsify fats, aiding digestion.
  • Role of lipids in membranes:
    • Cholesterol sits among phospholipid tails, helping stabilize membranes and modulate fluidity.
  • Practical health context:
    • Distinguish saturated vs unsaturated fats for dietary choices; trans fats are particularly detrimental to health.
    • Phospholipids and cholesterol are essential for cell membrane structure and function; steroids serve as signaling molecules and in digestion.

Membranes and Detergents: Amphipathic Molecules

  • Amphipathic molecules have both hydrophilic (water-loving) and hydrophobic (water-fearing) parts.
  • Detergents act like amphipathic molecules: the hydrophobic tail interacts with oils/grease; the hydrophilic head interacts with water, enabling mixing of oil and water.
  • In membranes, phospholipids arrange into bilayers: tails inward, heads outward, creating a selective barrier that regulates passage of substances.

Proteins (Outline for Next Section)

  • The course will continue with proteins; they are made of amino acids and form polymers (polypeptides) that fold into functional structures.
  • This section will build on the lipid-containing membrane context and introduce how proteins contribute to enzymes, transport, signaling, and structural roles.

Course Logistics and Exam Overview

  • This course includes a practical exam and a lecture exam:
    • First practical exam: next Thursday.
    • First lecture exam: the Tuesday after that.
  • Mastering assignments are posted two days before each exam; this pattern repeats throughout the semester.
  • Current lecture emphasized chapters 1 and 2 for the upcoming exams; more on proteins to be covered in the next sessions.
  • There are 104 slides in the current module.

Key Formulas and Quick References

  • pH relationship with hydrogen ion concentration:
    • pH = -\log_{10}[\text{H}^+]
    • [\text{H}^+] = 10^{-pH}
  • Neutralization (strong acid + strong base):
    • \text{H}^+ + \text{OH}^- \rightarrow \text{H}_2\text{O}
    • Example acid/base dissociations:
    • \text{HCl} \rightarrow \text{H}^+ + \text{Cl}^-
    • \text{NaOH} \rightarrow \text{Na}^+ + \text{OH}^-
  • Carbohydrate formula basics:
    • Monosaccharides: simple sugars (e.g., glucose: C6H{12}O_6)
    • General carbohydrate unit: (CH2O)n
    • Disaccharides (examples): sucrose, maltose, lactose (all broadly formula C{12}H{22}O_{11})
  • Dehydration synthesis vs hydrolysis:
    • Dehydration synthesis: Monomer + Monomer → Polymer + H₂O
    • Hydrolysis: Polymer + H₂O → Monomer + Monomer
  • Lipid structural notes:
    • Triglyceride: glycerol + 3 fatty acids → triglyceride
    • Saturated fats: no C=C bonds; straight chains; usually solid at room temperature.
    • Unsaturated fats: contain C=C bonds; kinked chains; usually liquid at room temperature; healthier in general.
    • Hydrogenation can create trans fats (unfavorable health effects).
  • Membrane structure:
    • Phospholipids form a bilayer with hydrophilic heads facing water and hydrophobic tails inward.
    • Cholesterol stabilizes membranes; steroid hormones and vitamin D derive from cholesterol.
  • Polymers and monomers in biology:
    • Proteins: amino acids (monomers) → polypeptides (polymer).
    • Carbohydrates: monosaccharides → disaccharides → polysaccharides (glycogen, starch).
    • Lipids: glycerol backbone + fatty acids; phospholipids; steroids.
  • Core biological connections:
    • Carbon’s tetravalence enables diverse, complex biomolecules essential for life.
    • Water’s properties enable biochemical reactions and homeostasis.
    • pH balance and buffer systems maintain physiological conditions essential for enzyme activity and metabolism.