IMAT Biology Lecture: Biochemistry - The Chemistry of Living Things

Introduction

• Focus: Section 2 of IMAT, Biology.
• Topic: Chemistry of living things (Biochemistry).
• First concept: Biological importance of weak interactions.

Basic Chemistry and Atomic Structure

• Atoms like Sodium (Na) and Chlorine (Cl) exchange electrons to form bonds.
• Valence Shell: Outer shell of an atom containing valence electrons.
• Octet Rule: Atoms prefer having 8 valence electrons (stability).
  • Sodium has 1 valence electron; Chlorine has 7.
  • Unstable atoms (not fulfilling octet rule) are reactive.

Formation of Bonds

• Unstable atoms interact to form bonds, e.g., sodium gives an electron to chlorine.
• Sodium loses a valence electron, becomes stable (8 electrons in the new valence shell).
• Chlorine gains an electron, fulfills octet rule.

Weak Non-Covalent Interactions

• Atoms and biomolecules are mainly held by strong covalent bonds.
• Non-Covalent Interactions: Weak interactions that can become powerful cumulatively.
• Four types: Ionic interactions, hydrogen bonds, van der Waals interactions, hydrophobic interactions.

Ionic Interactions

• Electrostatic interactions between charged particles.
• Example: Sodium (Na+) and Chlorine (Cl-) form ionic bonds.
• Strongest in vacuum; weaker in aqueous environments due to water's interaction with charges.
• Occurrence: Amino acids (e.g., lysine and glutamate) in proteins.

Hydrogen Bonds

• Form when hydrogen is covalently bonded to an electronegative atom (e.g., O, N, S).
• Involves partial charges creating attraction (dipoles).
• Biological example: DNA base pairing (Adenine-Thymine, Cytosine-Guanine) relies on hydrogen bonds.

Van der Waals Interactions

• Occur between uncharged atoms at specific distances (van der Waals radius).
• Types based on dipoles:
  • Dipole-Dipole: Two molecules with permanent dipoles.
  • Dipole-Induced Dipole: Permanent dipole induces a dipole in another molecule.
  • Induced Dipole-Induced Dipole: Interaction due to temporary dipoles.

Hydrophobic Interactions

• Occur between nonpolar molecules in water.
• Nonpolar molecules group together to minimize contact with water, minimizing surface area.
• Important in 3D protein structure formation by excluding water.

Conclusion

• Next topic: Organic molecules and their functions in organisms.