Introduction to Biochemistry

• In the atom (protons, neutrons, and electrons):

• Electrons are the most important particles for reactions to take place.
  • • When electrons gain energy, they move from the ground state to the excited state; then back to the ground state losing their energy, this energy will be used in reactions. (E.g. for hydrogen pump in photosynthesis and respiration).

• Isotopes: elements with similar proton numbers but different neutron numbers.

• • Radioactive elements benefits:
    • • Carbon dating.
      • Tracking a molecule.

• Chemical Bonds can be:

• Compounds: can either be: Ionic or Covalent; but in bio we need:

• Isomers: compounds with similar atoms numbers and types with different atomic arrangements for having different functions.
  • C₆H₁₂O₆: Chemical formula for glucose, fructose, or galactose.
    • Each has the same:
      • Number of atoms (24 atoms) = Same numerical proportions of atoms.
      • Types of atoms (C, H, and O).
      • The same molecular weight (Atomic mass can be found in the periodic table).
    • But having different atomic structures means that each has a different function.

Characteristics of Water:

• There are strong forces of attraction between the water molecules which determine their distinctive property.

• Cohesion vs. Adhesion: caused by hydrogen bonds among water molecules. (Helps in the water moving up the plant)

• High specific heat: water resist the change in temperatures (benefits for the aquatic organisms).
• Universal Solvent: Liquid water can dissolve a variety of compounds.
• Expansion on freezing: When water freezes its molecules arrange in a way that make them have more spaces between them, this is why its volume increases when it freezes.
• Surface tension: The attraction forces between water molecules are not equal.
  • Water molecules in the middle have cohesive forces to all neighboring molecules from all sides, upward, and downwards.
  • Water molecules on the surface have cohesive forces only to the neighboring molecules from both sides and downwards.

•  The relationship between H⁺ and pH:
  • When the H⁺ concentration is 0.0001 or 1×10^-4 we say that the pH is 4.

• • pH 7 is neutral (H⁺ & OH^– are equal)
  • pH more than 7: alkaline & H⁺ concentration is less than OH^– concentration.
  • pH less than 7: acid & H⁺ concentration is more than OH^– concentration.
    • pH 4.3 = Acid rain
    • pH 7.4 = Blood
    • pH 1.5 – 2.5 = Gastric fluid
  • When the pH changes from:
    • 2 to 5 ⇒ H⁺ ion concentration decreases by 1000 times.
      • 5 -2 = 3 ⇒ (3 zeros)
    • 7 to 3 ⇒ H⁺ ion concentration increases by 10000 times.
      • 7 – 3 = 4 (4 zeros)

• BUFFERS: are solutions which can resist changes in pH.
  • E.g. Bicarbonate buffer.
  • If the Carbon dioxide increased in the blood ⇒ Carbonic acid ⇒ blood pH decrease.
  • When the blood pH increases “becomes alkaline” the buffer increases the H⁺ concentration to prevent the change.