Fundamental Chemistry Concepts for General Biology

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Basic Chemistry for Biology

Introduction

Understanding the chemical basis of life is essential for studying biology. This section covers foundational chemistry concepts relevant to biological systems, including atomic structure, chemical bonds, and properties of water.

Genomics

Study of whole genomes of different species: Genomics involves analyzing the complete DNA sequences of organisms to understand genetic structure, function, and evolution.

Basic Chemical Concepts

Matter: Anything that has mass and takes up space.
Element: A substance that cannot be broken down to other substances by chemical means.
Compound: A substance consisting of two or more elements in a fixed ratio.
Emergent Properties: Characteristics specific to a compound or element that arise from the arrangement and interactions of its parts.

Elements in Biology

Essential Elements: Elements required for life, making up about 96% of living matter. These include carbon, oxygen, hydrogen, and nitrogen. Others like calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium make up most of the remaining 4%.
Trace Elements: Elements required in only minute quantities for life, such as iron and iodine.

Atomic Structure

Atom: The smallest unit of matter that retains the properties of an element.
Subatomic Particles: Components of an atom, including protons, neutrons, and electrons.
Neutrons: Subatomic particles with no charge, located in the atomic nucleus.
Protons: Subatomic particles with a positive charge, located in the atomic nucleus. The number of protons determines the identity of an atom.
Electrons: Subatomic particles with a negative charge, located in electron shells (electron cloud) around the nucleus.

Atomic Mass and Number

Dalton: The unit of measure for atomic mass. Calculated by the sum of proton and neutron masses. Electrons have negligible mass.
Atomic Number: The number of protons in the nucleus of an atom.
Mass Number: The sum of protons and neutrons in an atom.
Atomic Mass: The atom's total mass, which can be approximated by the mass number.
Isotopes: Atoms of the same element that differ in the number of neutrons.

Radioactive Isotopes and Dating

Radioactive Isotopes: Isotopes that decay spontaneously, emitting particles and energy.
Half-life: The time it takes for half of a sample of an isotope to decay.
Radiometric Dating: A method for dating materials by using the decay of radioactive isotopes.

Energy in Atoms

Energy: The capacity to cause change.
Potential Energy: The energy matter possesses due to its location or structure.

Electron Arrangement

Valence Shell: The outermost shell that houses the valence electrons.
Orbital: The three-dimensional space where an electron is found 90% of the time.

Chemical Bonds and Interactions

Types of Chemical Bonds

Chemical Bonds: Attractions that hold atoms together, often by sharing or transferring electrons.
Covalent Bonds: Formed when atoms share pairs of valence electrons.
Single Bond: The sharing of one pair of valence electrons.
Double Bond: The sharing of two pairs of valence electrons.
Molecule: Two or more atoms held together by covalent bonds.
Valence: The bonding capacity of an atom (number of electrons available for bonding).
Electronegativity: An atom's attraction for the electrons in a covalent bond.
Non-polar Covalent Bond: Atoms share electrons equally.
Polar Covalent Bond: One atom is more electronegative, so electrons are not shared equally.
Ions: Atoms or molecules that have gained or lost electrons, acquiring a charge.
Cations: Positively charged ions.
Anions: Negatively charged ions.
Ionic Bond: The attraction between a cation and an anion.
Ionic Compounds/Salts: Compounds formed by ionic bonds.
Hydrogen Bonds: Weak bonds formed when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom (often oxygen, nitrogen, fluorine, or sulfur).
Van der Waals Interactions: Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Chemical Reactions

Chemical Reactions: Processes in which chemical bonds are made or broken. Reactions can be reversible.
Reactants: Starting molecules in a chemical reaction.
Chemical Equilibrium: The point at which forward and reverse reactions occur at the same rate.

Properties of Water

Water's Unique Properties

Cohesion: Water molecules stick together due to hydrogen bonding.
Surface Tension: The measure of how difficult it is to stretch or break the surface of a liquid.
Adhesion: Attraction between different substances, such as water and plant cell walls.

Thermal Properties

Kinetic Energy: Energy of motion.
Thermal Energy: Kinetic energy associated with the random movement of atoms or molecules; also called heat.
Temperature: Average kinetic energy of molecules in a substance.
Calorie (cal): The amount of heat required to raise the temperature of 1 g of water by 1°C.
Joule (J): SI unit of energy; 1 J = 0.239 cal or 1 cal = 4.184 J.
Specific Heat: The amount of heat absorbed or lost for 1 g of a substance to change its temperature by 1°C.
Heat of Evaporation: The heat a liquid must absorb for 1 g to be converted to gas.
Evaporative Cooling: As a liquid evaporates, its remaining surface cools.

Solutions and Solubility

Solution: A homogeneous mixture of two or more substances.
Solvent: The dissolving agent in a solution.
Solute: The substance being dissolved.
Aqueous Solution: A solution in which water is the solvent.
Hydration Shell: The sphere of water molecules surrounding a dissolved ion.
Hydrophilic: Water-loving substances that dissolve easily in water.
Hydrophobic: Water-fearing substances that do not dissolve easily in water.

Molecular Quantities and Structure

Molecular Mass: The sum of all atomic masses in a molecule.
Mole: The number of molecules; 1 mole = molecules (Avogadro's number).
Molarity: The number of moles of solute per liter of solution.

Biologically Important Molecules

Adenosine Triphosphate (ATP): The major energy molecule used in biological processes. ATP consists of adenosine attached to three phosphate groups. The removal of a phosphate group releases energy.
Cis-Trans Isomers (Geometric Isomers): Molecules with the same covalent bonds but different spatial arrangements.
Enantiomers: Isomers that are mirror images of each other.
Functional Groups: Components of organic molecules most commonly involved in chemical reactions.

Table: Types of Chemical Bonds and Interactions

Type	Description	Relative Strength	Example
Covalent Bond	Atoms share pairs of electrons	Strong	H2O, O2
Ionic Bond	Attraction between oppositely charged ions	Strong (in dry conditions)	NaCl
Hydrogen Bond	Attraction between a hydrogen atom and an electronegative atom	Weak (individually)	Between water molecules
Van der Waals Interaction	Weak attractions due to transient local charges	Very weak	Gecko feet on walls

Additional info:

Some definitions and examples have been expanded for clarity and completeness.
Table entries are inferred from standard biology/chemistry knowledge.