02.01 Biochemistry Principals

1. Basic Chemical Concepts

Atoms and Elements

• Atoms: The fundamental units of matter, consisting of protons, neutrons, and electrons.
• Elements: Pure substances composed of only one type of atom, each defined by its atomic number (number of protons).

Molecules and Compounds

• Molecules: Two or more atoms bonded together, representing the smallest unit of a chemical compound that retains its properties.
• Compounds: Substances formed when two or more different elements combine chemically in fixed proportions (e.g., water, CO₂).

Chemical Bonds

• Ionic Bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.
• Covalent Bonds: Involve the sharing of electron pairs between atoms, creating a strong bond.
• Hydrogen Bonds: Weak bonds between a hydrogen atom and a highly electronegative atom (such as oxygen or nitrogen) in another molecule.
• Van der Waals Forces: Weak, non-specific interactions caused by temporary dipoles in molecules.

2. Organic Chemistry

Role of Carbon

• Carbon’s Versatility: Carbon has four valency electrons, allowing it to form four covalent bonds with other atoms, including other carbon atoms. This property enables the formation of complex and diverse organic molecules.
• Catenation: The ability of carbon to form long chains and rings, providing a backbone for complex structures.

Hydrophobic and Hydrophilic Interactions

• Hydrophobic: Molecules or regions of molecules that repel water, typically nonpolar substances (e.g., lipid tails in phospholipids).
• Hydrophilic: Molecules or regions that attract water, typically polar or charged substances (e.g., hydroxyl groups in sugars).

Monomers and Polymers

• Monomers: Small, simple molecules that can join together to form larger, more complex molecules.
  • Examples: Glucose (monomer of carbohydrates), amino acids (monomers of proteins), nucleotides (monomers of nucleic acids), fatty acids and glycerol (components of lipids).
• Polymers: Large, complex molecules made up of repeating monomer units.
  • Examples:
    • Carbohydrates: Polysaccharides like starch and cellulose.
    • Proteins: Polymers of amino acids.
    • Nucleic Acids: DNA and RNA, polymers of nucleotides.
    • Lipids: While not always true polymers, they are composed of fatty acid chains and glycerol.

Functional Groups

• Hydroxyl (-OH): Found in alcohols and carbohydrates.
• Carbonyl (C=O): Present in ketones and aldehydes.
• Amino (-NH₂): Found in amino acids.
• Phosphate (-PO₄³⁻): Present in nucleotides and ATP.
• Carboxyl (-COOH): Found in fatty acids and amino acids.

Isomerism

• Structural Isomers: Compounds with the same molecular formula but different bonding arrangements.
• Stereoisomers: Compounds with the same molecular formula and bonding but different spatial arrangements.

3. Metabolism

Catabolism and Anabolism

• Catabolism: Metabolic pathways that break down complex molecules into simpler ones, releasing energy.
  • Examples: Glycolysis, the citric acid cycle, and fatty acid oxidation.
  • Products: ATP, NADH, and other energy carriers.
• Anabolism: Metabolic pathways that build complex molecules from simpler ones, requiring energy.
  • Examples: Protein synthesis, DNA replication, and gluconeogenesis.
  • Products: Proteins, nucleic acids, and complex carbohydrates.

Enzymes

• Function: Biological catalysts that speed up chemical reactions by lowering the activation energy.
• Enzyme Kinetics: Study of the rates of enzyme-catalyzed reactions.
• Regulation: Enzyme activity can be controlled by inhibitors, activators, and feedback mechanisms.

4. Energy Transfer and Thermodynamics

ATP (Adenosine Triphosphate)

• Role: The primary energy carrier in cells.
• ATP Hydrolysis: The reaction ATP → ADP + Pi releases energy used for cellular processes.

Redox Reactions

• Oxidation: Loss of electrons.
• Reduction: Gain of electrons.
• Electron Transport Chain: Series of redox reactions in cellular respiration that generate ATP.

Thermodynamics

• Enthalpy (ΔH): Total heat content of a system.
• Entropy (ΔS): Measure of disorder or randomness in a system.
• Gibbs Free Energy (ΔG): Determines the spontaneity of a reaction (ΔG = ΔH – TΔS). Negative ΔG indicates a spontaneous reaction.

5. pH and Buffer Systems

pH Scale

• Range: 0-14, measuring the acidity or basicity of a solution.
  • Acid: pH < 7
  • Base: pH > 7
  • Neutral: pH = 7

Buffers

• Function: Solutions that resist changes in pH by neutralizing added acids or bases.
• Biological Importance: Maintain the optimal pH for enzymatic activities and cellular functions.

6. Properties of Water

Polarity

• Structure: Water molecules have a partial positive charge on hydrogen atoms and a partial negative charge on the oxygen atom.
• Hydrogen Bonding: Polar nature allows water to form hydrogen bonds, contributing to its unique properties.

Cohesion and Adhesion

• Cohesion: Attraction between water molecules, leading to surface tension.
• Adhesion: Attraction between water molecules and other substances, aiding in processes like capillary action.

High Specific Heat

• Definition: Ability of water to absorb or release large amounts of heat with minimal temperature change.
• Biological Significance: Helps regulate temperature in organisms and environments.

Solvent Properties

• Universal Solvent: Dissolves many substances, facilitating biochemical reactions and nutrient transport.
• Hydrophilic and Hydrophobic Interactions: Determines solubility and interactions of molecules in aqueous environments.

7. Additional Key Concepts

Chemical Equilibrium

• Definition: A state where the rate of the forward reaction equals the rate of the reverse reaction.
• Biological Relevance: Many biochemical reactions are reversible and exist in equilibrium.
  • Le Chatelier’s Principle: If a dynamic equilibrium is disturbed by changing the conditions, the position of equilibrium moves to counteract the change.
  • Examples in Biology: Binding of oxygen to hemoglobin, enzyme-substrate interactions.

Acid-Base Chemistry

• Importance: Critical for enzyme function, metabolic pathways, and maintaining cellular pH.
• Buffers: Systems that maintain acid-base balance in biological fluids.
  • Buffer Systems in the Body: Bicarbonate buffer system, phosphate buffer system, protein buffers.
• pKa: The pH at which half of the buffer’s species are deprotonated, important for understanding buffer capacity.

Isotopes and Atomic Mass

• Mass Spectrometry: Technique used to determine the composition of isotopes in molecules, aiding in metabolic studies.
• Isotopes: Atoms of the same element with different numbers of neutrons.
• Stable vs. Radioactive Isotopes: Stability affects their roles in biological systems and tracing mechanisms.
• Atomic Mass: Weighted average mass of an element’s isotopes, important in biochemical calculations and tracing metabolic pathways.