Biochemistry and Molecular Biology: Water, Bonds, Organic Compounds, and Proteins

Oxygen

65% of the human body; found mostly in water molecules; needed for cellular respiration (energy production).

Carbon

18% of the human body; the 'backbone' of all organic molecules (carbs, lipids, proteins, nucleic acids).

Hydrogen

10% of the human body; found in water and almost every organic compound; helps maintain pH balance.

Nitrogen

3% of the human body; important for amino acids (proteins) and nucleotides (DNA, RNA).

Pure Covalent Bond

Equal sharing of electrons, resulting in no charges created. Example: H₂, O₂, CH₄.

Polar Covalent Bond

Unequal sharing of electrons, creating slight charges; one atom is more electronegative. Example: H₂O.

Ionic Bond

Electrons are transferred, creating ions; oppositely charged ions attract. Example: Na⁺ + Cl⁻ = NaCl.

Hydrogen Bonding

Attraction between slightly positive H in one molecule and slightly negative O in another molecule.

Cohesion

Water molecules stick together due to hydrogen bonding.

Adhesion

the attraction between different molecules in water

Surface Tension

Acts like a 'skin' on water's surface, allowing small objects to float.

Surfactant

A lipid-protein mix that reduces surface tension in alveoli, preventing collapse during exhalation.

Water Importance

Essential for blood volume, temperature regulation, chemical reactions, and waste removal.

High Heat Capacity

Water takes a lot of heat to change temperature, stabilizing body temperature.

High Heat of Vaporization

Sweating removes heat as water evaporates.

Solvent Properties

Water dissolves polar/ionic substances, transporting nutrients and waste in blood.

Hydrophilic

Water-loving (polar) substances that dissolve in water (e.g., salt, sugar).

Hydrophobic

Water-fearing (nonpolar) substances that do not dissolve in water (e.g., oils, fats).

Major Electrolytes

Sodium (Na⁺), Potassium (K⁺), Calcium (Ca²⁺), Magnesium (Mg²⁺), Chloride (Cl⁻), Bicarbonate (HCO₃⁻), Phosphate (HPO₄²⁻).

pH Definition

pH = −log [H⁺]; measure of hydrogen ion concentration.

Acid

Releases H⁺ (proton donor); pH < 7.

Base

Removes H⁺ (proton acceptor) or releases OH⁻; pH > 7.

pH Scale

Ranges from 0 (acidic) to 14 (basic); lower pH = higher [H⁺] concentration.

Blood pH

Normal range is 7.35-7.45.

Acidosis

Blood pH too low (< 7.35) → depression of CNS, confusion, coma.

Alkalosis

Blood pH too high (> 7.45) → overexcited CNS, muscle spasms, convulsions.

Hydrogen Ion

Hydrogen atom = 1 proton + 1 electron. If electron is lost, only proton remains → H⁺ is just a proton.

Organic Compounds

Carbon + hydrogen (carbs, proteins, lipids, nucleic acids).

Inorganic Compounds

No C-H bonds (water, salts, acids, bases).

Functional Groups

Clusters of atoms that give organic molecules specific properties. Examples: hydroxyl (−OH), carboxyl (−COOH), amino (−NH₂), phosphate (−PO₄³⁻).

Monosaccharides

Simple sugar (glucose, fructose).

Disaccharides

Two monos linked (sucrose, lactose).

Polysaccharides

Many monos (starch, glycogen, cellulose).

Glycogen

Polysaccharide storing glucose in liver & muscles → quick energy reserve.

Dehydration Synthesis

Water removed → bonds form → bigger molecule.

Hydrolysis

Water added → bonds break → smaller molecules.

Amino Acid

Building block of proteins. Contains: Amino group (−NH₂), Carboxyl group (−COOH), R group (side chain) that changes per amino acid.

Peptide

Chain of amino acids.

Peptide Bond

The covalent bond linking each amino acid.

Denaturation

Protein loses shape → loses function. Caused by heat, pH changes, radiation, chemicals, heavy metals.

Primary Protein Structure

Linear amino acid chain.

Secondary Protein Structure

Alpha helices & beta sheets (H-bonds).

Tertiary Protein Structure

3D folding (globular shape).

Quaternary Protein Structure

Multiple polypeptides forming one protein (e.g., hemoglobin).

Enzyme Characteristics

Biological catalysts, Lower activation energy, Highly specific for substrates, Work best at specific temp/pH, Not consumed in reactions.

Phospholipids

Make up plasma membrane → hydrophilic heads face water, hydrophobic tails face inward → barrier but allows controlled exchange.

DNA

Double helix, stores genetic info.

RNA

Single strand, carries out instructions to make proteins.

Phosphorylation

Adds phosphate → stores energy (ADP → ATP).

Dephosphorylation

Removes phosphate → releases energy.

ATP

3 phosphates → high energy.

ADP

2 phosphates → less energy.

AMP

1 phosphate → very low energy.