Basic Chemistry for General Biology: Chapter 2 Study Notes

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Basic Chemistry

Introduction to Chemistry in Biology

Chemistry forms the foundation of biological processes. Understanding the basic chemical principles is essential for studying how living organisms function at the molecular level.

Matter: Makes up all living things; anything that has mass and occupies space.
Compounds: Substances consisting of two or more different elements in a fixed ratio.
Elements: Pure substances that cannot be broken down into simpler chemical substances; consist of only one type of atom.
Atoms: The smallest unit of an element that retains the properties of that element.
Example: Water (H2O) is a compound made of hydrogen and oxygen elements.

Elements of Life

Major and Trace Elements

Living organisms are composed of a limited number of elements, most of which are essential for life. These elements are organized in the periodic table.

There are 92 naturally occurring elements.
Four elements—Carbon (C), Hydrogen (H), Oxygen (O), and Nitrogen (N)—make up about 96% of the mass of the human body.
Trace elements are required in minute amounts but are vital for health (e.g., iron, iodine).

Element	Symbol	Percentage Body Weight (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%

Additional info: Trace elements (less than 0.01% of body weight) include chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicon, tin, vanadium, and zinc.

Atomic Structure

Subatomic Particles

Atoms are composed of subatomic particles that determine their chemical properties and behavior.

Protons: Positively charged (+), found in the nucleus, define the atomic number.
Neutrons: Neutral charge, also in the nucleus; number of neutrons plus protons equals atomic mass.
Electrons: Negatively charged (-), orbit the nucleus in shells; crucial for chemical bonding and biological processes.

Atomic Number, Mass Number, and Atomic Mass

These terms describe the composition and identity of atoms.

Atomic Number: Number of protons in the nucleus.
Mass Number: Sum of protons and neutrons.
Atomic Mass: Approximately equal to the mass number (measured in atomic mass units, amu).
Example: Helium atom has 2 protons, 2 neutrons, and 2 electrons; atomic number = 2, mass number = 4.

Isotopes

Definition and Biological Importance

Isotopes are variants of a particular chemical element that differ in neutron number, and thus in mass number.

Isotopes: Atoms of the same element with different numbers of neutrons.
Some isotopes are unstable (radioactive) and decay, releasing energy.
Example: Carbon has three common isotopes: Carbon-12, Carbon-13, and Carbon-14.

Isotope	Protons	Neutrons	Mass Number	Electrons
Carbon-12	6	6	12	6
Carbon-13	6	7	13	6
Carbon-14	6	8	14	6

Bonding and Electrons

Electron Shells and Stability

Atoms bond to achieve stability, which is often reached by filling their outermost electron shells.

Electron shells hold specific numbers of electrons: first shell (2 e-), second and third shells (8 e- each).
Atoms are most stable with full outer shells (valence shells).
Atoms will bond with others to achieve full valence shells.

Types of Chemical Bonds

Chemical bonds are the forces that hold atoms together in compounds and molecules.

Ionic Bonds: Involve the transfer of electrons from one atom to another, resulting in charged ions (cations and anions) that attract each other.
Covalent Bonds: Involve the sharing of valence electrons between atoms; can be single, double, or triple bonds.
Polar Covalent Bonds: Unequal sharing of electrons due to differences in electronegativity (e.g., water).
Nonpolar Covalent Bonds: Equal sharing of electrons (e.g., hydrocarbons).

Example: Sodium chloride (NaCl) forms via ionic bonding; water (H2O) forms via polar covalent bonding.

Properties of Water

Polarity and Hydrogen Bonding

Water is a polar molecule due to the unequal sharing of electrons between oxygen and hydrogen atoms, resulting in partial charges.

Polarity: Oxygen is more electronegative than hydrogen, causing a partial negative charge on oxygen and partial positive charges on hydrogens.
Hydrogen Bonds: Weak bonds formed between the partial positive hydrogen of one water molecule and the partial negative oxygen of another.

Unique Properties of Water

Hydrogen bonding gives water several unique properties essential for life.

Cohesion: Water molecules stick to each other, aiding transport in plants.
Adhesion: Water molecules stick to other substances.
Surface Tension: Water has a high surface tension, making it difficult to break the surface.
High Specific Heat: Water resists temperature changes due to hydrogen bonding; it acts as a thermal buffer.
Evaporative Cooling: As water evaporates, it removes heat, cooling surfaces.
Density of Ice: Ice is less dense than liquid water because hydrogen bonds stabilize and space out molecules in a crystalline structure.

Acids, Bases, and pH

Definitions and Importance

Acids and bases are substances that affect the concentration of hydrogen ions in aqueous solutions, measured by the pH scale.

Acids: Substances that donate H+ ions; have higher H+ concentration than OH-.
Bases: Substances that accept H+ ions or donate OH-; have higher OH- concentration than H+.
pH Scale: Measures the strength of acidic or basic solutions; logarithmic scale (each unit represents a tenfold change in H+ concentration).

Formula:

Example: A solution with [H+] = 1 x 10-4 M has a pH of 4.

Chemical Reactions

Reactants, Products, and Conservation of Matter

Chemical reactions involve the rearrangement of atoms to form new substances, obeying the law of conservation of matter.

Reactants: Starting substances in a chemical reaction.
Products: Substances formed as a result of the reaction.
Law of Conservation of Matter: Matter cannot be created or destroyed in a chemical reaction.

Example Reaction:

Additional info: This is the balanced equation for the combustion of methane.