General Chemistry: Elements, Bonds, Water, Organic Molecules, and Cell Structure

Elements and Atoms

Elements

Elements are pure substances that cannot be broken down into other substances by chemical reactions. There are 94 naturally occurring elements, but life requires only about 25 of them.

• Major elements in living matter: Carbon, Oxygen, Hydrogen, Nitrogen (often remembered as CHON), and sometimes Phosphorus and Sulfur (CHNOPS).

• Trace elements: Required in minute amounts but essential for health (e.g., iodine, iron).

• Elemental deficiency: Can lead to health issues, such as stunted plant growth due to nitrogen deficiency.

Atoms

An atom is the smallest unit retaining the properties of an element. Atoms are composed of subatomic particles:

• Protons: Positive charge

• Neutrons: No charge

• Electrons: Negative charge

Atoms are neutral when they have equal numbers of protons and electrons. The atomic number is the number of protons, and the mass number is the sum of protons and neutrons.

Atomic Structure

• Protons: Determine chemical identity

• Neutrons: Affect mass and isotopic properties

• Electrons: Involved in chemical bonding and ion formation

Electron Shells

• Electrons occupy shells around the nucleus:

  • 1st shell: 2 electrons

  • 2nd shell: 8 electrons

  • 3rd shell: 8 electrons

• Valence electrons in the outermost shell determine chemical reactivity.

Chemical Bonds

Types of Bonds

Atoms form chemical bonds to achieve stable electron configurations. The main types of bonds are:

Type of Bond	Strength	Notes	Structure	Energy to Break (kJ/mol)
Covalent	Strong	Electrons shared in orbitals	Single, double, or triple bonds	200-500 (single), 500-700 (double)
Ionic	Strong	Electrons transferred, resulting in attraction between ions	Crystal lattice	1,000-7,000 (in ionic crystal)
Hydrogen	Weak	Attraction between slightly charged regions	Between polar molecules	4-50

• Covalent bonds: Electrons are shared between atoms (e.g., H2, O2, H2O).

• Ionic bonds: Electrons are transferred from one atom to another, forming ions (e.g., NaCl).

• Hydrogen bonds: Weak attractions between slightly positive hydrogen and electronegative atoms (e.g., O or N).

• Van der Waals interactions: Weak, transient attractions between molecules.

Electronegativity

• Electronegativity is an atom's tendency to attract electrons in a bond.

• Increases across a period (left to right) and decreases down a group (top to bottom).

• Nonpolar covalent bond: Electrons shared equally.

• Polar covalent bond: Electrons shared unequally, leading to partial charges.

Ionic Bonds

• Formed when the electronegativity difference between atoms is large.

• One atom donates an electron (becomes a cation), the other accepts (becomes an anion).

• Ionic compounds are often soluble in water and form crystalline solids.

Water and Its Properties

Water as a Solvent

• Water is the primary solvent in cells (aqueous solution).

• Many substances dissolve in water due to its polarity.

• Nonpolar compounds do not dissolve well in water.

• Hydrophilic substances interact with water; hydrophobic substances do not.

Properties of Water

• Cohesion: Water molecules stick to each other via hydrogen bonds.

• Adhesion: Water molecules stick to other substances.

• High specific heat: Water resists temperature changes.

• High heat of vaporization: Large amounts of energy required to evaporate water.

• Expansion upon freezing: Ice is less dense than liquid water, so it floats.

pH and Acidity

• Water can dissociate into H+ and OH- ions.

• pH measures the concentration of H+ ions in solution.

• pH = -log[H+]

Organic Molecules

Carbon Chemistry

• Carbon forms the backbone of most organic molecules.

• Can form single, double, or triple bonds; can be arranged in chains or rings.

• Isomers have the same chemical formula but different structures.

Functional Groups

Functional groups are specific groups of atoms within molecules that have characteristic properties.

Name	Formula	Structure	Properties	Common Presence
Hydroxyl	-OH	R-OH	Polar, hydrophilic	Alcohols, sugars
Carbonyl	-CO	R-CO-R'	Polar, hydrophilic	Sugars, ketones, aldehydes
Carboxyl	-COOH	R-COOH	Acidic, hydrophilic	Amino acids, fatty acids
Amino	-NH2	R-NH2	Basic, hydrophilic	Amino acids
Phosphate	-PO4	R-PO4	Acidic, hydrophilic	Nucleic acids, ATP
Sulfhydryl	-SH	R-SH	Polar, forms disulfide bonds	Proteins

Macromolecules

Proteins

• Polymers of amino acids (20 standard types).

• Functions: Enzymatic, defensive, storage, transport, hormonal, receptor, structural.

• Amino acids have a central carbon, amino group (-NH2), carboxyl group (-COOH), hydrogen, and a variable side chain (R group).

Nucleic Acids

• DNA and RNA store and transmit genetic information.

• Nucleotides consist of a sugar, phosphate group, and nitrogenous base.

• Bases: Purines (adenine, guanine), Pyrimidines (cytosine, thymine, uracil).

• DNA is double-stranded; RNA is usually single-stranded.

Carbohydrates

• Monosaccharides (simple sugars), disaccharides, and polysaccharides (complex carbohydrates).

• General formula: (CH2O)n

• Functions: Energy storage (e.g., starch, glycogen), structural (e.g., cellulose).

Lipids

• Hydrophobic molecules, not true polymers.

• Types: Fats (triglycerides), phospholipids, steroids.

• Functions: Energy storage, membrane structure, signaling.

Cell Structure and Classification

Prokaryotes vs. Eukaryotes

	Prokaryotes	Eukaryotes
Nucleus	No (nucleoid region)	Yes
Transcription Location	Cytoplasm	Nucleus
Translation Location	Cytoplasm	Cytoplasm
Cell Membrane Additions	Hopanoids	Sterols (cholesterol)
Size (average)	Small (<1-2 μm)	Larger (10-100 μm)
Ratio to Surface Area to Volume	High	Low
Internal Organization	No organelles (some have plasmids)	Contains organelles

• Prokaryotes: Bacteria and Archaea; generally smaller, lack membrane-bound organelles, DNA in nucleoid region.

• Eukaryotes: Animals, plants, fungi, protists; larger, have nucleus and membrane-bound organelles.

Cell Theory

• All living things are made of cells.

• The cell is the fundamental unit of life.

• All cells arise from pre-existing cells.

• Cells maintain homeostasis.

Classification Based on Cell Type

• Prokaryotic cells: Simpler, no nucleus, no membrane-bound organelles.

• Eukaryotic cells: Complex, nucleus, membrane-bound organelles.

Example: Bacteria are prokaryotes; plants and animals are eukaryotes.