Notes on Biochemistry I: Inorganic and Organic Compounds

Inorganic Compounds

A. Water (H₂O)

• Comprises 60-80% of cells, acting as a fundamental solvent for biochemical reactions and cellular processes.

  1. Heat Capacity:

  • Water has a high heat capacity, allowing it to absorb and store significant amounts of heat. This property helps organisms maintain stable internal temperatures through thermoregulation, vital for enzymatic functions and cellular activities.

  1. Heat of Vaporization:

  • Water requires a large amount of energy to evaporate, which serves as an effective means of cooling in organisms (e.g., sweating). This property protects organisms from overheating, particularly in active environments.

  1. Polarity/Solvency:

  • Water's polarity enables it to dissolve a wide range of substances, making it ideal for cellular transport of ions, nutrients, and waste products. Its solvents nature specifically enhances the visibility of salts and macromolecules like proteins in biological systems.

    1. Salts and macromolecules:

       • Typically found dissolved in solution, facilitating biochemical reactions.

  1. Reactivity:

  • Water participates in numerous chemical reactions:
    i. Hydrolysis - Water is added to break larger molecules into their components:
    $ext{glycogen} + H₂O \ <br>ightarrow ext{glucose} + ext{glucose} + ext{glucose} + \text{…}$
    ii. Dehydration - Water is removed to synthesize larger molecules from smaller ones:
    $ext{glucose} + ext{glucose} + ext{glucose} + \text{…} \rightarrow ext{glycogen} + H₂O$

B. Salts

• Composed of cations (e.g., Na⁺) and anions (e.g., Cl⁻), excluding H⁺/OH⁻, salts play critical roles in maintaining physiological functions.

  1. Salts dissociate into their ions in water, forming solutions that conduct electricity; this property is essential for nerve impulses and muscle contractions.

  2. Known as electrolytes because their ions carry electrical charges necessary for physiological processes.

  3. Examples:

     • Na⁺ (sodium ions), Cl⁻ (chloride ions), K⁺ (potassium ions), Ca²⁺ (calcium ions) are crucial for maintaining membrane potential and excitability.

     • Ca²⁺ and PO₄³⁻ contribute to bone mineralization, forming calcium phosphates essential for skeletal structure.

     • Fe²⁺, Mg²⁺, Zn²⁺, and Cu⁺ are vital for enzymatic functions and play roles in metabolism.

  4. Kidneys: These organs regulate the balance of water and salts in the body, ensuring homeostasis and influencing blood pressure.

C. Acids and Bases

1. Acids:

   • Defined as H⁺ donors; they increase H⁺ concentration in a solution, leading to increased acidity.

     • Example: Hydrochloric Acid (HCl)
       $ext{HCl} \rightarrow ext{H}^+ + ext{Cl}^-$

     • Acetic Acid (HC₂H₃O₂) also serves as a weak acid commonly found in vinegar.

2. Bases:

   • Defined as H⁺ acceptors; they produce OH⁻ ions in solution, which increases alkalinity.

     • Example: Sodium Hydroxide (NaOH)
       $ext{NaOH} \rightarrow ext{Na}^+ + ext{OH}^-$

     • Ammonia (NH₃) functions as a weak base, crucial in biological systems for pH regulation.

3. pH:

   • The pH scale measures the concentration of H⁺ ions, with lower values indicating greater acidity.

     • $ext{H₂O} \rightleftarrows ext{H}^+ + ext{OH}^-$

     • In pure water, 1 in 10^7 molecules dissociate, leading to $ext{[H⁺]} = 1/10,000,000 = 10^{-7}$ and a neutral pH of 7.0.

4. Neutralization:

   • This is the reaction of an acid with a base, typically resulting in the formation of water and a salt as products.

     • Example: $ext{HCl} + ext{NaOH} \rightarrow ext{H₂O} + ext{NaCl}$

5. Buffers:

   • Biological buffers resist changes in pH by neutralizing excess acids or bases. Blood serum pH is maintained between 7.35-7.45, slightly basic.

     • Strong acids and bases dissociate completely, while weak acids and bases only partially dissociate, providing a buffering capacity.

6. Carbonic Acid - Bicarbonate Buffer System:

   • This crucial buffer system operates in both acidic and basic environments,

     • $ext{H₂CO₃} \rightleftarrows ext{HCO₃}^- + ext{H}^+$

Organic Compounds

A. Characteristics of Organic Compounds

1. Exclusions: Carbon-containing compounds such as carbon monoxide (CO), carbon dioxide (CO₂), and elemental carbon (C in graphite and diamond) are not classified as organic.

2. Carbon's tetravalence allows it to form four covalent bonds, making it a versatile element in organic chemistry.

3. Its relative electroneutrality enables carbon to stabilize various functional groups through covalent bonding.

4. Carbon readily forms bonds with hydrogen (H), oxygen (O), and nitrogen (N), allowing for a diversity of organic structures.

5. Carbon can form single (C-C), double (C=C), and triple bonds (C≡C), leading to structural variety in organic molecules.

B. Carbohydrates (C, H, O)

1. Monosaccharides:

   • The simplest forms of carbohydrates, such as glucose, can be linear or cyclic.

     • 5-carbon sugars:

       • Ribose (part of RNA) and Deoxyribose (part of DNA).

     • 6-carbon sugars:

       • Glucose (the primary energy source in blood), Galactose (an isomer of glucose), and Fructose (found in fruits and honey).

2. Disaccharides:

   • Formed by the condensation reaction of two monosaccharides.

     • Examples:

       • Sucrose (glucose + fructose), commonly known as table sugar.

       • Maltose (glucose + glucose), found in malted foods and beverages.

       • Lactose (glucose + galactose), the sugar in milk, important for energy in infants.

3. Polysaccharides:

   • Complex carbohydrates composed of many monosaccharide units; vital for energy storage and structural functions.

     • Starch: A storage polysaccharide in plants; can be digested by humans.

     • Glycogen: The storage form in animals, especially in the liver and muscle tissues, providing quick energy release when needed.

4. Functions:

   • Serve as quick energy sources (e.g., glucose).

   • Function as energy storage molecules (e.g., glycogen and starch).

   • Play structural roles in cells (e.g., forming part of glycolipids in membranes).

C. Lipids

1. Neutral Fats (Triglycerides):

   • Formed from glycerol and three fatty acid chains; mostly non-polar and insoluble in water.

     • Saturated Fats: Contain only single carbon-to-carbon bonds, typically solid at room temperature (e.g., butter).

     • Unsaturated Fats: Possess one or more double bonds, resulting in kinks that keep them liquid at room temperature (e.g., oils).

     • Functions include insulation (keeping organisms warm), protection (cushioning organs), and energy storage (providing significant caloric reserve).

2. Phospholipids:

   • Composed of glycerol, two fatty acids, and a phosphate group (which contains a hydrophilic head that interacts with water and a hydrophobic tail that repels water).

     • A major component of plasma membranes, aiding in creating a barrier that separates the cell from its environment.

3. Steroids:

   • Characterized by a ring structure; cholesterol serves as a precursor for steroid hormones.

     • Examples:

       • Vitamin D (important for calcium metabolism), sex hormones (estrogen and testosterone), cortisol (involved in stress response), and aldosterone (regulating sodium and potassium levels).

D. Proteins

1. Molecular Structure:

   • Proteins are composed of 20 different amino acids linked together by peptide bonds through dehydration synthesis; the sequence of amino acids determines the protein's specific function.

2. Levels of Structure:

   • Primary: The linear sequence of amino acids.

   • Secondary: Coiling (alpha-helix) and folding (beta-pleated sheet) due to hydrogen bonding.

   • Tertiary: The three-dimensional shape formed by interactions among various side chains.

   • Quaternary: Complexes formed by multiple polypeptides (e.g., hemoglobin contains four polypeptide chains).

3. Functions:

   • Fibrous Proteins: Structural roles (collagen, keratin, and elastin) that provide strength and support; also contribute to movement (actin and myosin in muscles).

   • Globular Proteins: Enzymes (e.g., peroxidase, amylase) that catalyze biochemical reactions; transport proteins (hemoglobin) carrying oxygen; hormones (insulin, growth hormone) regulating physiological processes.

4. Enzyme Function:

   • Enzymes catalyze specific reactions, typically being proteins that require cofactors (e.g., metal ions such as Fe and Cu) or coenzymes (organic molecules like vitamins) for maximal effectiveness.

   • They operate under the induced fit model, meaning substrates bind to the active site of an enzyme, inducing a change that stabilizes the transition state.

5. Denaturation:

   • Denaturation is the process of losing the three-dimensional shape of a protein due to factors like heat or pH changes, resulting in loss of function. This process can sometimes be reversible or irreversible, depending on the nature and severity of the cause.

E. Nucleic Acids (DNA & RNA)

1. Nucleotide:

   • The fundamental building block of nucleic acids, comprised of a nitrogenous base (adenine, thymine, cytosine, guanine in DNA; uracil in RNA), a pentose sugar (ribose or deoxyribose), and a phosphate group.

2. Base Pairing:

   • Nucleotides pair in specific patterns: A with T (or U in RNA), and C with G. This specificity maintains the integrity of genetic information during replication and protein synthesis.

3. DNA Structure:

   • DNA structures in a double helix formation with two strands running in opposite directions, which provides stability and redundancy essential for genetic fidelity.

4. Genetic Code:

   • The sequence of nucleotides determines the coding for an amino acid sequence in proteins, with the genetic code being nearly universal among organisms.

5. Gene:

   • A gene is a specific nucleotide sequence that encodes for one gene product, primarily proteins, which influence organisms' traits and functions.

F. ATP as "Energy Currency"

1. Glycogen and lipids act like energy savings bonds, stored for later use when energy is needed.

2. Glucose is akin to a larger, usable check that can be tapped into when immediate energy is required for cellular functions.

3. Adenosine triphosphate (ATP) serves as directly spendable energy for various cellular processes:

   • High-energy phosphate bonds can be broken to release energy. $ext{ATP} \rightleftarrows ext{ADP} + P_i + ext{Energy}$

     • The breaking of these bonds is crucial for powering cellular activities, such as muscle contractions, nerve impulses, and biosynthetic reactions.