Foundations of Biochemistry

Key Elements and Body Composition

The human body is primarily composed of a few key elements and a mixture of organic and inorganic compounds. Understanding these components is fundamental to biochemistry.

• Four Key Elements: Oxygen (65%), Carbon (18%), Hydrogen (9.5%), Nitrogen (3.2%)—together comprising ~96% of body mass.

• Body Composition: Water (60%), Protein (16%), Triglycerides (13%), Salts (6.2%), Carbohydrates (1.5%), Nucleic acids (0.2%).

• Inorganic Components: Water and salts.

• Organic Components: Carbohydrates, lipids (triglycerides), proteins, and nucleic acids.

Body Fluids and Fluid Balance

Body fluids are essential for physiological processes and are classified by their location.

• Intracellular Fluid (ICF): Fluid within cells (e.g., cytosol).

• Extracellular Fluid (ECF): Fluid outside cells (e.g., interstitial fluid, plasma, lymph, cerebrospinal fluid, synovial fluid, digestive fluids).

• Fluid Balance: Maintained when intake (beverages, food, metabolism) equals output (urine, skin/lungs, sweat, feces).

• Imbalance Consequences: Dehydration (excessive loss) and water intoxication (excessive gain) can be life-threatening.

Properties of Water

Water is the most abundant inorganic compound in the body and is vital for life due to its unique properties.

• Polarity: Water is a polar molecule, making it an excellent solvent.

• Thermal Properties: High heat capacity and high heat of vaporization.

• Cohesion and Adhesion: Water molecules stick to each other and to other surfaces.

• Chemical Reactivity: Participates in chemical reactions, lubricates, and cushions tissues.

Solutions and Electrolytes

Understanding solutions and electrolytes is crucial for grasping biochemical reactions in aqueous environments.

• Solution: Homogeneous mixture of solute(s) dissolved in a solvent.

• Solvent: The dissolving medium (water in biological systems).

• Electrolytes: Substances that dissociate into ions and conduct electricity (e.g., NaCl, KCl).

• Non-electrolytes: Substances that dissolve but do not form ions (e.g., glucose).

• Major Electrolytes: Potassium (K+) is the main intracellular cation; sodium (Na+) is the main extracellular cation; chloride is the main extracellular anion.

pH and Buffer Systems

pH is a measure of hydrogen ion concentration and is tightly regulated in the body.

• pH Scale: Ranges from 0 (acidic) to 14 (alkaline); pH 7 is neutral.

• Physiological pH: Normal plasma pH is 7.35–7.45.

• Buffer Systems: Bicarbonate, phosphate, and protein buffers maintain pH stability.

• Acid-Base Disorders: Four major types: respiratory acidosis, respiratory alkalosis, metabolic acidosis, metabolic alkalosis.

Equation for pH:

Biomolecules: Structure and Properties

Major Biomolecules

The four major classes of biomolecules are essential for structure and function in living organisms.

Common Properties of Biomolecules

• Contain carbon (C), hydrogen (H), and oxygen (O).

• Form polymers via condensation (dehydration synthesis) and are broken down by hydrolysis.

• Exist as isomers: positional, geometric (cis-trans), and optical isomers.

• Biological properties are determined by noncovalent interactions.

Noncovalent Interactions

Noncovalent interactions are weak, reversible forces that are essential for biomolecular structure and function.

• Types: hydrogen bonds, dipole-dipole, electrostatic, ion-dipole, hydrophobic interactions, van der Waals forces.

• Functions: maintain solubility, stabilize 3D structure, enable binding and cellular functions.

Cellular Diversity and Biomolecular Composition

Cell Types and Functions

Different cell types arise from variations in biomolecular composition, affecting structure and function.

• Plasma membrane: lipids (phospholipids, cholesterol), proteins, carbohydrates.

• Cytosol: primarily proteins, water, electrolytes.

• Organelles: proteins, lipids, nucleic acids, carbohydrates.

• Cytoskeleton: proteins.

Amino Acids: Structure, Stereochemistry, and Classification

Basic Structure of Amino Acids

Amino acids are the building blocks of proteins, each with a central α-carbon, amino group, carboxyl group, hydrogen atom, and variable R group.

• R group determines chemical properties and interactions.

Stereochemistry of Amino Acids

• Most amino acids are chiral (except glycine), existing as L- and D-isomers.

• L-amino acids are incorporated into proteins in humans.

Classification of Amino Acids by R Group

• Non-polar aliphatic

• Aromatic

• Sulfur-containing

• Alcohol-containing

• Amide-containing

• Acidic (negatively charged)

• Basic (positively charged)

• Imino (proline)

Essential vs Non-Essential Amino Acids

• Essential: Cannot be synthesized by the body; must be obtained from diet.

• Non-essential: Can be synthesized by the body from metabolic intermediates.

Example: Phenylalanine (essential) is converted to tyrosine (non-essential) by phenylalanine hydroxylase.

Phenylketonuria (PKU)

PKU is a genetic disorder caused by defective phenylalanine hydroxylase, leading to toxic accumulation of phenylalanine and neurological damage if untreated.

• Managed by dietary restriction of phenylalanine.

Zwitterions and Buffering

Amino acids can exist as zwitterions, molecules with both positive and negative charges but overall neutrality.

• At pH = pI: neutral (zwitterion).

• pH < pI: positive charge.

• pH > pI: negative charge.

Buffering: Amino acids can accept or donate H+, making them effective buffers.

Peptides and Protein Structure

Peptide Bond Formation

Peptide bonds form via condensation (dehydration) reactions between amino acids.

Levels of Protein Structure

• Primary (1°): Linear sequence of amino acids.

• Secondary (2°): Local folding (α-helices, β-sheets) stabilized by hydrogen bonds.

• Tertiary (3°): Overall 3D shape of a single polypeptide, stabilized by R group interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, London dispersion forces).

• Quaternary (4°): Association of multiple polypeptide chains (subunits) into a functional protein complex.

Oligopeptides

• Short chains of amino acids (few residues).

• Do not form higher-order structures; often function in cell communication (e.g., peptide hormones).

Protein Denaturation and Hydrolysis

• Denaturation: Loss of 3D structure (secondary, tertiary, quaternary) due to disruption of non-covalent or disulfide bonds; primary structure remains intact.

• Hydrolysis: Breaking peptide bonds by addition of water, yielding free amino acids or smaller peptides.

Effects of Temperature and pH on Proteins

• Extreme temperature or pH disrupts non-covalent interactions, leading to denaturation and loss of function.

• Normal body temperature: ~37°C; normal blood pH: 7.35–7.45.

Protein Function and Structure-Function Relationships

Major Functions of Proteins

• Catalysis (enzymes)

• Defence (immune proteins)

• Structure and motion (cytoskeleton, contractile proteins)

• Regulation (gene expression, cellular activities)

• Transport (hemoglobin, membrane transporters)

• Signalling (hormones, receptors)

Structure-Function Examples

Summary Table: Protein Structure and Function

Additional info: The above notes expand on the original content by providing definitions, examples, and context for key biochemical concepts, as well as summarizing structure-function relationships in proteins.