Chemical Principles

The Structure of Atoms and Chemical Reactions

Atoms and Their Structure

• Atoms are the smallest units of matter that participate in chemical reactions.

• Each atom has a nucleus containing:

• Protons (+ charge)

• Neutrons (neutral)

• Electrons (- charge) orbit the nucleus in electron shells.

• Atoms are electrically neutral when the number of protons equals electrons.

• Atomic number = Number of protons.

• Atomic mass = Total number of protons + neutrons.

Chemical Elements and Isotopes

• There are 92 naturally occurring elements, but only 26 are commonly found in living organisms.

• Isotopes = Atoms of the same element with different neutron numbers.

• Example: Oxygen has three stable isotopes.

Chemical Bonds

1. Ionic Bonds

• Form between oppositely charged ions when electrons are transferred.

• Cations = Atoms that lose electrons (+ charge).

• Anions = Atoms that gain electrons (- charge).

2. Covalent Bonds

• Form when atoms share electrons.

• Stronger and more common in living organisms than ionic bonds.

3. Hydrogen Bonds

• Weak bonds that occur when a hydrogen atom is attracted to oxygen or nitrogen.

• Do not form molecules but serve as bridges between molecules.

• Important in proteins and nucleic acids (DNA, RNA).

Chemical Reactions

1. Synthesis Reactions (Anabolism)

• Smaller molecules combine to form larger molecules.

• Example: Formation of proteins from amino acids.

2. Decomposition Reactions (Catabolism)

• Larger molecules break down into smaller molecules, ions, or atoms.

• Example: Breakdown of glucose for energy.

3. Exchange Reactions

• Both synthesis and decomposition occur simultaneously.

4. Reversible Reactions

• Reactions that can proceed in both directions under different conditions.

Inorganic vs. Organic Compounds

Inorganic Compounds

• Do not contain carbon-hydrogen (C-H) bonds.

• Examples: Water, oxygen, carbon dioxide, salts, acids, and bases.

Organic Compounds

• Always contain carbon and hydrogen.

• More complex than inorganic compounds.

• Examples: Sugars, amino acids, vitamins, proteins, nucleic acids.

Water and Its Importance

• Most abundant component of living cells (65-75%).

• Polar molecule: Oxygen has a slight negative charge, and hydrogen has a slight positive charge.

• Properties:

• Temperature buffer due to hydrogen bonding.

• Excellent solvent (dissolves salts, acids, and bases).

• Dissociates into hydrogen ions (H⁺) and hydroxide ions (OH⁻).

Acids, Bases, and Salts

• Acids: Release H+ ions in solution (proton donors).

• Bases: Release OH- ions (proton acceptors).

• Salts: Dissociate into ions but do not release H+ or OH-.

pH Scale

• Measures H+ concentration in a solution.

• Scale ranges from 0 to 14:

• pH 7 = Neutral.

• Below 7 = Acidic (higher H+ concentration).

• Above 7 = Basic (Alkaline) (higher OH- concentration).

• Organisms must maintain a stable pH to function properly.

• pH buffers help regulate pH in organisms and lab cultures.

• Most microbes grow best between pH 6.5 - 8.5:

• Fungi tolerate acidic conditions.

• Cyanobacteria prefer alkaline conditions.

Organic Compounds

1. Overview of Organic Compounds

• Organic molecules contain carbon, which bonds with hydrogen and other elements.

• The carbon skeleton is the chain of carbon atoms in an organic molecule.

• Functional groups are specific groups of atoms that determine chemical properties.

• Macromolecules are large organic molecules, often polymers made of repeating monomers.

• Dehydration synthesis: Monomers join by removing water (H + OH → H2O).

2. Carbohydrates

• Contain carbon (C), hydrogen (H), and oxygen (O) in a 2:1 ratio of H to O.

• Functions: Energy storage, structure (cell walls), and cellular recognition.

Types of Carbohydrates

• Monosaccharides (simple sugars): 3-7 carbon atoms (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., sucrose, lactose).

• Polysaccharides: Long chains of monosaccharides.

• Glycogen: Energy storage in animals and some bacteria.

• Cellulose: Structural component of plant and algal cell walls.

• Chitin: Found in fungal cell walls.

3. Lipids

• Non-polar, insoluble in water.

• Functions: Energy storage, membrane structure, and signaling molecules.

Types of Lipids

• Simple lipids (fats & oils):

• Made of glycerol + 3 fatty acids.

• Saturated: No double bonds, solid at room temp.

• Unsaturated: One or more double bonds, liquid at room temp.

• Phospholipids:

• Made of glycerol + 2 fatty acids + phosphate group.

• Main component of cell membranes (hydrophilic head & hydrophobic tail).

• Steroids:

• Carbon ring structures (e.g., cholesterol, hormones).

• Sterols have a hydroxyl (-OH) group.

4. Proteins

• Functions: Structure, enzymes, transport, defense (antibodies, toxins), movement.

• Made of amino acids (contain C, H, O, N, and sometimes S).

• Peptide bonds link amino acids to form polypeptides (via dehydration synthesis).

Levels of Protein Structure

1. Primary: Sequence of amino acids.

2. Secondary: Hydrogen bonds create alpha helices or beta-pleated sheets.

3. Tertiary: 3D folding due to interactions between side chains.

4. Quaternary: Multiple polypeptides form a functional protein.

Types of Proteins

• Simple proteins: Contain only amino acids.

• Conjugated proteins: Combined with other molecules:

• Glycoproteins (contain sugars).

• Lipoproteins (contain lipids).

• Metalloproteins (contain metal ions).

5. Nucleic Acids (DNA & RNA)

• Function: Store and transmit genetic information.

• Made of nucleotides, which contain:

1. Pentose sugar (deoxyribose in DNA, ribose in RNA).

2. Phosphate group.

3. Nitrogen base (A, T/U, G, C).

DNA (Deoxyribonucleic Acid)

• Double-stranded, forms a double helix.

• Bases pair via hydrogen bonds:

• Adenine (A) pairs with Thymine (T).

• Guanine (G) pairs with Cytosine (C).

• Genes are sequences of nucleotides that code for proteins.

RNA (Ribonucleic Acid)

• Single-stranded.

• Uracil (U) replaces Thymine (T).

• Three types of RNA in protein synthesis:

1. mRNA (messenger RNA) - carries genetic info.

2. rRNA (ribosomal RNA) - forms ribosomes.

3. tRNA (transfer RNA) - carries amino acids for protein synthesis.

Summary

Adenosine Triphosphate (ATP)

1. Structure of ATP

• ATP is the primary energy carrier in cells.

• Composed of:

• Adenosine unit = Adenine (nitrogen base) + Ribose (sugar).

• Three phosphate groups (P-P-P).

• ATP is essentially Adenosine Monophosphate (AMP) + two extra phosphate groups.

2. Function of ATP

• Stores and provides energy for cellular activities.

• Energy is released when the terminal (last) phosphate bond is broken via hydrolysis:

• ATP → ADP (Adenosine Diphosphate) + Pi (inorganic phosphate) + Energy.

• The energy released is used for:

• Muscle contraction.

• Active transport (moving molecules across membranes).

• Biosynthesis of macromolecules.

3. ATP Regeneration

• ATP is regenerated from ADP + Pi using energy from oxidation reactions (e.g., cellular respiration).

• This cycle ensures a continuous supply of energy for the cell.

4. Summary