Atoms, Molecules, and Properties of Water: General Biology Study Notes

Atoms and Elements

Element

An element is a chemical substance made of only one type of atom. Elements are the fundamental building blocks of matter and cannot be broken down by chemical means.

• Examples: Hydrogen (H), Carbon (C), Oxygen (O)

Atom

An atom is the smallest unit of an element that retains the properties of that element. Atoms are electrically neutral and consist of a nucleus surrounded by orbiting electrons.

• Nucleus: Contains protons (positive charge, +1) and neutrons (neutral charge)

• Electrons: Negatively charged (-1), orbit the nucleus

Atomic Number

The atomic number is the number of protons in the nucleus of an atom. It defines the identity of the element.

• Example: Carbon has an atomic number of 6 (6 protons)

Mass Number

The mass number is the sum of protons and neutrons in an atom.

• Protons and neutrons both have a weight of approximately 1 dalton

• Electrons are much lighter and do not contribute significantly to mass number

• If the number of protons changes, the element changes

Isotopes

Isotopes are atoms of the same element that have different numbers of neutrons, resulting in different mass numbers.

• All carbon atoms have 6 protons

• Carbon-12: 6 protons, 6 neutrons

• Carbon-14: 6 protons, 8 neutrons

• Some isotopes are radioactive and decay over time

Major Elements in Biology

CHNOPS Elements

The elements Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur (CHNOPS) make up over 99% of atoms in the body.

• The number of unpaired electrons determines the number of bonds an atom can form

Element	Valence Electrons	Typical Bonds Formed
Hydrogen	1	1
Carbon	4	4
Nitrogen	5	3
Oxygen	6	2
Phosphorus	5	3 or 5
Sulfur	6	2 or 6

Molecules and Compounds

Molecule vs. Compound

• Molecule: Two or more atoms held together by covalent bonds (e.g., H2, H2O)

• Compound: Substance made of atoms of different elements (e.g., H2O, NaCl)

Electron Sharing and Bond Polarity

Electrons in covalent bonds are not always shared equally. The tendency of an atom to attract electrons is called electronegativity.

• Electronegativity order: O > N > C ≈ H

• Nonpolar covalent bond: Electrons shared equally (e.g., H2)

• Polar covalent bond: Electrons shared unequally (e.g., H2O)

Ion Formation and Ionic Bonding

• Cation: Atom loses electron, becomes positively charged

• Anion: Atom gains electron, becomes negatively charged

• Ionic bond: Electron is transferred from one atom to another, resulting in attraction between oppositely charged ions

Transfer gives each atom a full valence shell

Simple Molecules Formed from C, H, N, and O

Covalent Bonding and Molecular Structure

Each unpaired electron in the valence shell can make up half of a covalent bond. The number of unpaired electrons determines the number of bonds an atom can form.

• Atoms with more than one unpaired electron can form double or triple bonds

Molecule	Formula	Bond Type
Methane	CH4	Single bonds
Ammonia	NH3	Single bonds
Water	H2O	Single bonds
Carbon dioxide	CO2	Double bonds

Properties of Water

Water Structure and Polarity

Water is a polar molecule. Oxygen atoms have a partial negative charge, and hydrogen atoms have a partial positive charge. Water molecules have a bent geometry.

• Partial positive charge on hydrogen attracts partial negative charge on oxygen of another molecule

• These weak electrical interactions are called hydrogen bonds

Examples: H---O---N

Solubility of Molecules

• Polar molecules and ionic compounds dissolve readily in water due to hydrogen bonding and electrostatic interactions

• Nonpolar molecules do not dissolve in water (hydrophobic effect)

Unique Properties of Water

• Cohesion: Water molecules hydrogen-bond to each other, resulting in surface tension

• Adhesion: Water molecules adhere to other surfaces, often to negative charges

• Water is denser as a liquid than a solid; ice floats

• Water has a high capacity for absorbing energy

• Specific heat: Amount of energy needed to raise temperature of 1 g of substance by 1°C

• Heat of vaporization: Energy required to change 1 g of substance from liquid to gas

The Role of Water in Acid-Base Chemical Reactions

Water Dissociation

Water molecules can dissociate into hydrogen ions (H+) and hydroxide ions (OH-):

$H_2O \rightleftharpoons H^+ + OH^-$

• The reaction is reversible

• When the rates of forward and reverse reactions are the same, the reaction reaches chemical equilibrium

Summary Table: Key Properties of Water

Property	Description
Cohesion	Water molecules stick to each other via hydrogen bonds
Adhesion	Water molecules stick to other surfaces
Surface Tension	Result of cohesion at the surface of water
High Specific Heat	Water resists changes in temperature
High Heat of Vaporization	Requires much energy to convert water from liquid to gas
Density	Ice is less dense than liquid water

Additional info: These notes expand on the original content by providing definitions, examples, and tables for clarity and completeness, suitable for General Biology students.