Biochemistry Foundations for General Biology: Elements, Atoms, and Chemical Bonds

Unit 2: Biochemistry

Core Concepts

Biochemistry is the study of the chemical processes and substances that occur within living organisms. Understanding the nature of matter, elements, atoms, and chemical bonds is essential for grasping how biological molecules are formed and interact.

• Life consists of chemical elements in pure form and in combinations called compounds.

• An element's properties depend on the structure of its atoms.

• Formation and function of molecules depend on chemical bonding between atoms.

• Chemical reactions make and break chemical bonds, leading to changes in molecular composition.

Basic Chemistry: Matter and Elements

What is Matter?

All living things are composed of matter, which is anything that takes up space and has mass. Matter exists in three states: solids, liquids, and gases.

• Matter: Anything that occupies space and has mass.

• States of matter: Solid, liquid, gas.

• Law of Conservation of Matter: Matter cannot be created or destroyed, but it can be rearranged.

Elements

Elements are pure substances that cannot be broken down into simpler substances by chemical means. There are over 90 naturally occurring elements on Earth, and they make up all matter.

• Element: A substance consisting of only one type of atom.

• Elements combine in fixed ratios to form compounds (e.g., water is always H2O).

• Examples:

  • Water (H2O): Two hydrogen atoms and one oxygen atom.

  • Hydrogen peroxide (H2O2): Two hydrogen atoms and two oxygen atoms.

Elements in the Human Body

Major and Trace Elements

The human body is composed primarily of a small number of elements, with others present in trace amounts. These elements are essential for life and biological processes.

Element	Symbol	Percentage of Body Mass (including water)
Oxygen	O	65.0%
Carbon	C	18.5%
Hydrogen	H	9.5%
Nitrogen	N	3.3%
Calcium	Ca	1.5%
Phosphorus	P	1.0%
Potassium	K	0.4%
Sulfur	S	0.3%
Sodium	Na	0.2%
Chlorine	Cl	0.2%
Magnesium	Mg	0.1%
Trace elements (less than 0.01% of mass): boron (B), chromium (Cr), cobalt (Co), copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), silicon (Si), tin (Sn), vanadium (V), zinc (Zn)

Chemistry Vocabulary and Key Concepts

Definitions and Examples

• Compound: A substance consisting of two or more different elements combined in a fixed ratio (e.g., CO2).

• Molecule: Two or more atoms held together by covalent bonds (e.g., O2).

• Emergent Properties: New characteristics that arise when elements combine to form compounds, similar to how letters form words.

Atoms: Structure and Properties

Atomic Structure

An atom is the smallest unit of matter that retains the properties of an element. Atoms are composed of subatomic particles: protons, neutrons, and electrons.

• Proton: Positively charged particle found in the nucleus.

• Neutron: Neutral particle found in the nucleus.

• Electron: Negatively charged particle found in electron shells around the nucleus.

• Atomic Number: Number of protons in an atom; defines the element.

• Atomic Mass: Sum of protons and neutrons in the nucleus.

• Isotope: Atoms of the same element with different numbers of neutrons.

Example: Carbon-12 has 6 protons and 6 neutrons; Carbon-14 has 6 protons and 8 neutrons.

Electron Shells and Chemical Behavior

Electron Arrangement

Electrons are arranged in shells around the nucleus. The chemical behavior of an atom is largely determined by the number of electrons in its outermost shell (valence electrons).

• Valence Electrons: Electrons in the outermost shell; involved in chemical bonding.

• Octet Rule: Atoms tend to have eight electrons in their outer shell for stability (except for the first shell, which holds two).

• Atoms with full valence shells are nonreactive; those without are reactive.

Chemical Bonds

Types of Chemical Bonds

Chemical bonds form when atoms interact to complete their valence shells. The main types of bonds are covalent, ionic, and hydrogen bonds.

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

• Ionic Bond: Electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Hydrogen Bond: Weak attraction between a hydrogen atom covalently bonded to a highly electronegative atom (F, O, or N) and another electronegative atom.

Example: In water (H2O), oxygen is more electronegative than hydrogen, so shared electrons are pulled closer to oxygen, creating partial charges and allowing hydrogen bonds to form between water molecules.

Bond Polarity and Electronegativity

• Electronegativity: The tendency of an atom to attract electrons in a bond.

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

• Nonpolar Covalent Bond: Electrons are shared equally (e.g., O2).

Chemical Reactions

Making and Breaking Bonds

Chemical reactions involve the making and breaking of chemical bonds, resulting in changes in the composition of matter.

• Reactants: Substances that start a chemical reaction.

• Products: Substances formed as a result of a chemical reaction.

Example Equation:

$2H_2 + O_2 \rightarrow 2H_2O$

This equation shows hydrogen and oxygen gases reacting to form water.

Summary Table: Types of Chemical Bonds

Bond Type	Basis of Interaction	Example
Covalent	Sharing of electron pairs	H2O, O2
Ionic	Attraction of opposite charges (ions)	NaCl (sodium chloride)
Hydrogen	Attraction between H and electronegative atom (F, O, N)	Between water molecules

Key Terms to Know

• Atom

• Element

• Compound

• Molecule

• Isotope

• Covalent bond

• Ionic bond

• Hydrogen bond

• Electronegativity

• Valence electron

• Octet rule

Additional info: These notes expand on the original slides and images by providing full definitions, examples, and context for each concept, ensuring a self-contained study guide suitable for exam preparation in General Biology.