Notes on Cytoplasmic Matrix and Biological Chemistry

All of life is conditioned by the chemistry of water.
Cells, tissues, and organs are composed of chemicals identical to those found in non-living systems.
Biochemistry is the study of chemical compounds in living systems and the reactions they undergo.
Molecular biology focuses on the structure and behavior of individual molecules.
Protoplasm is comprised of non-living constituents, including:
- Proteins
- Nucleic acids
- Lipids (fats)
- Carbohydrates
- Vitamins
- Minerals
- Waste metabolites
- Crystalline aggregates
- Pigments
The organization and interactions of these molecules constitute the essence of life.
Understanding protoplasm's functioning through chemical principles helps illuminate the phenomenon of life.

The cytosol is the fluid and soluble portion of the cytoplasm outside organelles.
Characteristics of cytosol:
- Colorless or greyish, translucent, and gelatinous substance.
- Heavier than water and capable of flowing.

Reticular Theory: Suggests a matrix composed of a reticulum of fibers or particles within a ground substance.
Alveolar Theory: Proposes that the matrix consists of many suspended droplets, resembling bubbles (Butschill, 1892).
Granular Theory: Posits that the matrix contains granules of various sizes, known as bioplasts (Altmann, 1893).
Fibrillar Theory: Indicates that the matrix exhibits a fibrillar nature (Fleming).
Colloidal Theory: Recently proposed based on electron microscope observations, stating that the matrix contains both true solution and colloidal systems.

Solutions
- Mixture of solvent (usually water) and solutes (e.g., glucose, amino acids).
- Particle size in solution: < 1/10,000 mm.
Colloidal System
- Contains a liquid medium with particles ranging 1/1,000,000 to 1/10,000 mm.
- Comprises two phases:
- Dispersed phase (discontinuous phase)
- Continuous phase (dispersion phase)
Protoplasm is essentially a colloidal solution, primarily protein-based, stabilizing colloids through charges and hydration layers.

Cytosol exhibits phase reversal:
- Example: Gelatin in water forms a sol in thin consistency but becomes a gel with cooling.
- Stability depends on chemical bonds (H-H, C-H, C-N).
- Phase reversals influenced by physiological, mechanical, and biochemical activities within cells.

Approximately 46 of the 92 naturally occurring elements found in cytosol.
Essential Elements (24 total): Major roles include:
- Carbon (C): 20%
- Hydrogen (H): 10%
- Nitrogen (N): 3%
- Oxygen (O): 62%
- Phosphorus (P): 0.14%
- Sulfur (S): 0.14%
Trace Elements: Present in minute amounts, important for life:
- Iron (Fe): 0.10%
- Iodine (I): 0.014%
- Includes several others like Mo, Mn, Co, Zn, etc.

Ions maintain osmotic pressure and acid-base balance.
Concentration gradients of ions differ between intracellular fluid (e.g., high K+ and Mg++) and extracellular fluid (e.g., high Na+ and Cl-).
Phosphates (H2PO4- and HPO4--) act as buffers for pH stabilization.

Inorganic Compounds:
- Make up about 70% of the cell's content, primarily water (65-80% of matrix).
- Non-living components such as salts, minerals, etc.
Organic Compounds:
- Constitute about 30% of the cell.
- Include carbohydrates, proteins, lipids, nucleic acids, vitamins, etc.

Exists as free water (95% of total cellular water) and bound water (5% linked to proteins).
Mostly used as a solvent for various compounds necessary for cellular functions.

Solvent Properties: Excellent solvent due to its polarity, impacting biological reactions and solubility.
Thermal Properties: High specific heat and heat of vaporization, helping regulate temperature.
Surface Tension: Cohesiveness influences cellular form and movement within tissues.
Transparency: Enables photosynthesis in plant cells.

Carbohydrates: Main energy source, categorized into monosaccharides, oligosaccharides, and polysaccharides.
Proteins: Formed from amino acids, crucial for structural and functional roles.
Lipids: Hydrophobic organic compounds important for energy storage and cellular structure.
Nucleic Acids: DNA and RNA, essential for heredity and protein synthesis.

Proteins classified by structure:
1. Primary structure: Sequence of amino acids.
2. Secondary structure: Regular arrangements (alpha-helix, beta-pleated sheets).
3. Tertiary structure: Three-dimensional folding, stabilized by various bonds.
4. Quaternary structure: Assembly of multiple polypeptides.

Enzymes act as biological catalysts, categorized into six classes (e.g., oxidoreductases, transferases).
Factors affecting enzyme action include pH, temperature, and substrate concentration.

Vitamins essential for metabolic functions; deficiencies lead to disorders.
Hormones regulate various biological activities in cells, synthesized by endocrine glands.

Two main types: DNA (double helix, genetic material) and RNA (single strand, involved in protein synthesis).

Tyndall's Effect: Light scattering through colloidal particles.
Brownian Movement: Random movement of particles due to collision with water molecules.
Cyclosis: Intracellular streaming due to cytosol's properties.
Surface Tension: Force maintaining stability and structure in cytoplasm.
Adsorption: Increase in concentration at liquid interface.
Stability in pH due to buffering systems.

Irritability: Sensitivity to stimuli, leading to cell response.
Conductivity: Transmission of excitatory signals in nerve cells.
Metabolism: All chemical processes (anabolic and catabolic) occurring in the matrix.
Growth and Reproduction: Continuous increase in volume leading to cell division.