Essential Chemistry for Biology

Key Terms and Definitions

This section introduces foundational chemistry concepts essential for understanding biological processes. Mastery of these terms is crucial for further study in biology.

• Matter: Anything that has mass and occupies space.

• Element: A substance that cannot be broken down into other substances by chemical means; each element is defined by its number of protons.

• Trace Element: An element required by an organism in only minute quantities (e.g., iron, iodine).

• Atom: The smallest unit of an element that retains the properties of that element.

• Proton: A positively charged subatomic particle found in the nucleus of an atom.

• Neutron: A subatomic particle with no charge, located in the nucleus.

• Electron: A negatively charged subatomic particle found in electron shells surrounding the nucleus.

• Atomic Number: The number of protons in an atom's nucleus; unique to each element.

• Mass Number: The sum of the number of protons and neutrons in an atom's nucleus.

• Average Atomic Mass/Atomic Weight: The weighted average mass of the atoms in a naturally occurring sample of the element.

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

• Radioactive Isotope: An isotope whose nucleus decays spontaneously, giving off particles and energy.

• Electron Shell: The energy levels where electrons are found around the nucleus.

• Valence Shell: The outermost electron shell of an atom.

• Valence Electron(s): Electrons in the outermost shell, involved in chemical bonding.

• Chemical Bond: The force that holds atoms together in compounds.

• Ion: An atom or molecule with a net electric charge due to the loss or gain of electrons.

• Ionic Bond: A chemical bond formed between oppositely charged ions.

• Ionic Compound: A compound composed of ions held together by ionic bonds.

• Molecule: Two or more atoms held together by covalent bonds.

• Polar: A molecule with an uneven distribution of charge, resulting in positive and negative ends.

• Hydrogen Bond: A weak bond between a hydrogen atom in one molecule and an electronegative atom in another.

• Chemical Reaction: The process by which substances change into different substances through the breaking and forming of bonds.

• Reactant(s): The starting substances in a chemical reaction.

• Product(s): The substances formed as a result of a chemical reaction.

• Cohesion: The attraction between molecules of the same substance (e.g., water molecules).

• Surface Tension: The measure of how difficult it is to stretch or break the surface of a liquid.

• Adhesion: The attraction between different kinds of molecules.

• Heat: The total amount of kinetic energy due to molecular motion in a body of matter.

• Temperature: The measure of the average kinetic energy of the particles in a substance.

• Solution: A homogeneous mixture of two or more substances.

• Solvent: The dissolving agent in a solution (e.g., water in saltwater).

• Solute: The substance that is dissolved in a solution.

• Aqueous Solution: A solution in which water is the solvent.

• Acid: A substance that increases the hydrogen ion (H+) concentration in a solution.

• Base: A substance that reduces the hydrogen ion concentration in a solution, often by increasing OH- ions.

• pH: A measure of hydrogen ion concentration; ranges from 0 (most acidic) to 14 (most basic).

• pH Scale: The scale used to specify the acidity or basicity of an aqueous solution.

• Neutral Solution: A solution with a pH of 7, where [H+] = [OH-].

• Neutral pH: pH value of 7, indicating neither acidic nor basic.

• Buffer: A substance that minimizes changes in pH by accepting or donating H+ ions.

States of Matter

Matter exists in three primary physical states, each with distinct properties.

• Solid: Definite shape and volume; particles are closely packed and vibrate in place.

• Liquid: Definite volume but no definite shape; particles are less tightly packed and can move past one another.

• Gas: No definite shape or volume; particles are far apart and move freely.

Atomic Structure

Atoms are composed of subatomic particles with specific properties and locations.

• Protons: Positive charge (+1), mass ≈ 1 atomic mass unit (amu), located in the nucleus.

• Neutrons: No charge (0), mass ≈ 1 amu, located in the nucleus.

• Electrons: Negative charge (-1), negligible mass, located in electron shells around the nucleus.

The nucleus contains protons and neutrons, while electrons occupy shells at varying distances from the nucleus.

Determining Subatomic Particles from Atomic Symbols

Given an atomic symbol, you can determine the number of protons, neutrons, and electrons:

• Protons: Equal to the atomic number.

• Electrons: Equal to the atomic number in a neutral atom.

• Neutrons: Mass number minus atomic number.

Example: For 23Na (sodium): Atomic number = 11, Mass number = 23. Protons = 11, Neutrons = 12, Electrons = 11.

Using the Periodic Table

The periodic table provides atomic numbers and atomic weights for each element.

• Atomic Number: Number of protons (and electrons in a neutral atom).

• Atomic Weight: Average mass of all isotopes, weighted by abundance.

• Neutrons: Atomic weight (rounded to nearest whole number) minus atomic number.

Electron Shells and Valence Electrons

Electrons are arranged in shells around the nucleus. The first shell holds up to 2 electrons, the second up to 8.

• First shell: Maximum 2 electrons.

• Second shell: Maximum 8 electrons.

Valence electrons are those in the outermost shell and determine chemical reactivity and bonding.

Valence Electrons and Covalent Bonds

The number of valence electrons can be determined from the periodic table. Atoms tend to form covalent bonds to fill their valence shell (octet rule).

• Example: Carbon has 4 valence electrons and can form 4 covalent bonds.

Formation of Ions

Neutral atoms become ions by gaining or losing electrons:

• Cation: Loses electron(s), becomes positively charged.

• Anion: Gains electron(s), becomes negatively charged.

Ionic vs. Covalent Bonding

Atoms bond to achieve stable electron configurations.

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

• Covalent Bond: Sharing of electron pairs between atoms.

Example: NaCl is an ionic compound; H2O is a covalent molecule.

Hydrogen Bonding

Hydrogen bonds form between polar molecules, where a hydrogen atom is covalently bonded to a highly electronegative atom (e.g., O, N, F).

• Example: Water molecules form hydrogen bonds with each other.

Hydrogen bonds are weaker than ionic or covalent bonds but are crucial for the properties of water and biological molecules.

Properties of Water

Water's unique properties are due to its polarity and hydrogen bonding.

• Cohesion: Water molecules stick together, leading to surface tension.

• Adhesion: Water molecules stick to other substances.

• Surface Tension: Allows small objects to "float" on water's surface.

• Ice Floats: Ice is less dense than liquid water because hydrogen bonds hold water molecules apart in a crystalline structure.

Solutions and Solubility

Water is a universal solvent due to its polarity.

• Polar and ionic compounds dissolve easily in water (hydrophilic).

• Nonpolar compounds do not dissolve well in water (hydrophobic).

Acids, Bases, and pH

The pH scale measures the concentration of hydrogen ions in a solution.

• Acid: Increases [H+], pH < 7.

• Base: Decreases [H+], pH > 7.

• Neutral: [H+] = [OH-], pH = 7.

pH Calculation:

• The pH scale is logarithmic: a difference of 1 pH unit represents a tenfold difference in [H+].

Example: A solution with pH 4 is 10 times more acidic than one with pH 5.

Buffers and pH Regulation

Buffers help maintain a stable pH in biological systems by accepting or donating H+ ions as needed.

• Example: Blood contains bicarbonate buffer to maintain pH near 7.4.

When acid or base is added, the buffer minimizes changes in pH.

Summary Table: Types of Chemical Bonds

Additional info:

• Understanding these chemistry concepts is foundational for topics such as metabolism, enzyme function, and cellular structure in biology.