Introduction to Biochemistry

Biomolecules

  • All contain carbon.
  • Include proteins (amino acids), sugars (monosaccharides), nucleic acids (nucleotides), and lipids (fatty acids & glycerol).
  • Assembling these requires energy.

Energy and Thermodynamics

  • Thermodynamics describes energy.
  • First Law: Energy cannot be created or destroyed, only transformed.
  • Second Law: Entropy (disorder) of the universe increases.

Gibbs Free Energy (G)

  • Components: Enthalpy (H) and Entropy (S)
  • Enthalpy (H): Heat content of a system.
  • Entropy (S): How energy is dispersed in a system.
  • Formula: ΔG=ΔH−TΔS\Delta G = \Delta H - T\Delta S
  • Exothermic reactions release heat (\\Delta H < 0\$).
  • Endothermic reactions absorb heat (\ΔH>0\Delta H > 0\$).

Spontaneous Reactions

  • Spontaneous (exergonic): \\Delta G < 0\$
  • Nonspontaneous (endergonic): \ΔG>0\Delta G > 0\$
  • At equilibrium: \\Delta G = 0\$
  • Reactions with decreased enthalpy and increased entropy are spontaneous at all temperatures.
  • Nonspontaneous reactions can proceed in vivo by coupling with spontaneous reactions.

Cell Types

  • Prokaryotes: Small, unicellular, lack a discrete nucleus and internal membranes.
  • Eukaryotes: Larger, uni/multicellular, have a discrete nucleus and internal membranes.

Eukaryotic Organelles

  • Lysosomes: Degrade macromolecules.
  • Peroxisomes: For oxidative reactions.
  • Vacuoles: For storage.
  • Nucleus: Has a double membrane.

Human Body

  • Contains ~10 trillion cells and 4-100 trillion microorganisms (microbiome), mostly in the intestine.

Water

  • Fundamental for life; ~60% of human body weight.
  • Molecular geometry: bent; Electron geometry: tetrahedral.

Molecular Forces

  • Intramolecular (e.g., covalent bonds) and intermolecular forces (e.g., hydrogen bonds).
  • Complementarity of bases in DNA/RNA: A-T (2 H-bonds), G-C (3 H-bonds).

Water as a Solvent

  • High dielectric constant (DC) diminishes electrostatic interactions between ions.
  • \↑\uparrow\$DC = $\$\downarrow\$ ability of ions to associate with each other.

Amphiphilic Molecules

  • Have polar and nonpolar components; may form spherical micelles or sheets.
  • Examples: Palmitate.

Sweating and Sports Drinks

  • Sweating causes evaporation, which has a cooling effect (2.5 kJ heat released per gram/mL of water lost).
  • Exercise leads to water and electrolyte (Na+, Cl-, K+) losses.
  • Short workouts (<90min): water is enough; Long/intense: sports drinks needed.

Cell Membrane Permeability

  • Carbon dioxide, oxygen gas, and steroids can freely cross the cell membrane.

Acid-Base Chemistry

  • H+ combines with water to form hydronium ion (H3O+).
  • Proton jumping: Protons move and are shared among nearby water molecules.
  • K_w = [H^+][OH^-] = 10^{-14}
  • Neutral: [H+] = [OH-] = 10^{-7}\$ M
  • Acidic: [H+] > [OH-]
  • Basic: [H+] < [OH-]
  • pH = -log [H+]
  • Neutral: pH = 7; Acidic: pH < 7; Basic: pH > 7; Physiologic: pH = 7.4
  • BAAD: Bases Accept H+, Acids Donate H+

Weak Acids/Bases

  • Higher Ka = Lower pKa = Acid more likely to ionize (higher tendency to donate a proton).

Henderson-Hasselbalch Equation

  • pH = pK_a + log \frac{[A^-]}{[HA]}
  • When pH = pKa, the acid is half dissociated ([A-] = [HA]).

Buffers

  • Resist changes in pH by:
  • Combining added protons with the conjugate base.
  • Donating protons from the acid to neutralize added hydroxide ions.
  • Effective buffering capacity: generally within one pH unit of its pKa.

Bicarbonate Buffer System

  • Principal buffer in interstitial fluid and blood plasma.
  • CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons H^+ + HCO_3^-$$

Le Chatelier's Principle

  • Normal, excess, or insufficient acid conditions shift the equilibrium accordingly.

Clinical Correlation: Acid-Base Homeostasis

  • Hyperventilation: ↓ CO2 in blood → ↓ carbonic acid → ↓ H+ ions, pH rises (respiratory alkalosis).
  • Paper bag helps rebreathe CO2.
  • Increased CO2 in blood: Shifts to right to produce more H+ (e.g., diabetic ketoacidosis and metabolic acidosis).