Atoms, Elements, and Chemical Bonds: Foundations of General Biology

Atoms and Matter

Basic Structure of Atoms

All matter is composed of atoms, which are the fundamental units of chemical elements. Atoms consist of a central nucleus containing protons and neutrons, surrounded by electrons in orbitals.

• Proton: Positively charged particle found in the nucleus.

• Neutron: Neutrally charged particle found in the nucleus.

• Electron: Negatively charged particle that orbits the nucleus in electron shells.

Example: The hydrogen atom consists of one proton and one electron, with no neutrons in its most common form.

Atomic Number and Atomic Mass

• Atomic Number (Z): The number of protons in the nucleus; defines the element.

• Atomic Mass (A): The sum of protons and neutrons in the nucleus.

Formula:

$\text{Atomic Mass} = \text{Number of Protons} + \text{Number of Neutrons}$

Isotopes

Isotopes are atoms of the same element that have the same number of protons but different numbers of neutrons.

• Protium (\( ^1_1\text{H} \)): 1 proton, 0 neutrons

• Deuterium (\( ^2_1\text{H} \)): 1 proton, 1 neutron

• Tritium (\( ^3_1\text{H} \)): 1 proton, 2 neutrons

Elements and the Periodic Table

The Periodic Table of Elements

The periodic table organizes all known elements by increasing atomic number and groups them based on similar chemical properties.

• Groups: Vertical columns with elements sharing similar valence electron configurations.

• Periods: Horizontal rows indicating the number of electron shells.

Major Elements in the Human Body

Six elements make up the majority of the human body by mass:

• Oxygen (O)

• Carbon (C)

• Hydrogen (H)

• Nitrogen (N)

• Calcium (Ca)

• Phosphorus (P)

Electron Shells and Energy Levels

Electron Configuration

Electrons occupy energy levels or shells around the nucleus. The arrangement of electrons determines the chemical properties of an atom.

• First shell: Up to 2 electrons

• Second shell: Up to 8 electrons

• Third shell: Up to 18 electrons

• Fourth shell: Up to 32 electrons

The valence shell is the outermost shell and determines an atom's reactivity.

Energy and Electron Transitions

• Electrons in higher shells have more energy.

• Electrons can absorb energy and move to higher shells (excited state).

• Electrons can release energy and fall back to lower shells, emitting light (e.g., in fluorescent lights).

Chemical Bonds and Molecules

Types of Chemical Bonds

Atoms combine to form molecules through chemical bonds. The main types of bonds are:

• Covalent Bonds: Sharing of electron pairs between atoms. Can be single, double, or triple bonds depending on the number of shared pairs.

• Ionic Bonds: Complete transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Hydrogen Bonds: Weak bonds between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.

• Van der Waals Interactions: Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Bond Strengths and Energies

The strength of chemical bonds varies, influencing the stability and energy content of molecules.

Bond Type	Typical Length (nm)	Strength (kcal/mol)
Covalent	0.15	90 (377)
Ionic	0.25	80 (335)
Hydrogen	0.30	4 (16.7)
Van der Waals	0.35	0.1 (0.4)

Additional info: Values in parentheses are in kJ/mol. 1 calorie = 4.184 joules.

Electronegativity and Polarity

Electronegativity is the tendency of an atom to attract electrons in a chemical bond. Differences in electronegativity between atoms lead to bond polarity.

• Nonpolar Covalent Bond: Electrons are shared equally (e.g., in methane, CH4).

• Polar Covalent Bond: Electrons are shared unequally, resulting in partial charges (e.g., in water, H2O).

Acids, Bases, and the pH Scale

Acids and Bases

Acids and bases are substances that alter the concentration of hydrogen ions (H+) in a solution.

• Acid: Increases the H+ concentration in a solution.

• Base: Decreases the H+ concentration, often by accepting H+ or releasing OH-.

The pH Scale

The pH scale measures how acidic or basic a solution is, ranging from 0 (most acidic) to 14 (most basic), with 7 being neutral.

• pH < 7: Acidic solution (e.g., gastric acid, vinegar, tomato juice)

• pH = 7: Neutral solution (e.g., pure water)

• pH > 7: Basic solution (e.g., household ammonia, bleach)

Formula:

$\text{pH} = -\log_{10}[\text{H}^+]$

Summary Table: Key Atomic and Chemical Properties

Element	Atomic Number	Electrons in Valence Shell	Reactivity
Hydrogen	1	1	Reactive
Carbon	6	4	Reactive
Nitrogen	7	5	Reactive
Oxygen	8	6	Reactive
Phosphorus	15	5	Reactive
Sulfur	16	6	Reactive
Chlorine	17	7	Reactive
Potassium	19	1	Reactive
Calcium	20	2	Reactive