Foundations of Chemistry in Biology: Atoms, Bonds, and Water

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Key Concepts in Biology

Introduction to Biology

Biology is the scientific study of life, encompassing a wide range of topics from the molecular basis of life to the diversity of organisms. Understanding unifying themes and the role of evolution is essential for grasping the unity and diversity of life.

Biology: The study of living organisms and their interactions with each other and their environments.
Unifying themes: Concepts such as organization, information, energy and matter, interactions, and evolution that connect all areas of biology.
Evolution: The process by which different kinds of living organisms have developed and diversified from earlier forms; explains both the unity and diversity of life.
Domains of life: Bacteria, Archaea, and Eukarya are the three major domains.
Eukaryotic vs. Prokaryotic cells: Eukaryotic cells have a nucleus and membrane-bound organelles; prokaryotic cells do not.
Matter: Consists of chemical elements in pure form and in combinations called compounds.
Element properties: Determined by the structure of their atoms.

The Importance of Chemistry to Life

Role of Chemistry in Biological Systems

Chemistry is fundamental to understanding biological processes, as all living things are composed of chemical elements and compounds. Everyday substances such as vitamins, hormones, and synthetic drugs are all products of chemical interactions.

Applications: Chemistry is involved in the production and function of vitamins, hormones, drugs, cleaners, synthetic fabrics, and more.
Biological molecules: Include carbohydrates, lipids, proteins, and nucleic acids, all of which are essential for life.

Atoms and Elements

Structure of Atoms

Atoms are the basic units of matter, consisting of a nucleus (protons and neutrons) and electrons that orbit the nucleus in shells. The arrangement of electrons determines the chemical properties of an element.

Element: A substance that cannot be broken down into other substances by chemical means.
Atom: The smallest unit of an element, retaining its properties.
Electron shells: Electrons are arranged in shells around the nucleus, each with a characteristic energy level.

The Energy Levels of Electrons

Electron Shells and Energy

Energy is the capacity to cause change. In atoms, an electron’s energy level is correlated with its average distance from the nucleus. Electrons can move between shells by absorbing or releasing energy.

Energy: The ability to do work or cause change.
Electron shells: Each shell represents a different energy level; electrons further from the nucleus have higher energy.
Electron transitions: Electrons absorb energy to move to higher shells and release energy to move to lower shells.

Electron Distribution and Chemical Properties

Valence Electrons and Reactivity

The chemical behavior of an atom is largely determined by the number of electrons in its outermost shell, known as the valence shell. Atoms with incomplete valence shells are reactive and tend to form chemical bonds.

Valence electrons: Electrons in the outermost shell; determine an atom’s chemical reactivity.
Reactivity: Atoms with incomplete valence shells seek to fill them by gaining, losing, or sharing electrons.
Stable atoms: Atoms with full valence shells are chemically inert (unreactive).

Chemical Bonds

Types of Chemical Bonds

Atoms with incomplete valence shells can share or transfer electrons, resulting in chemical bonds. The main types of bonds are covalent, ionic, hydrogen, and van der Waals interactions.

Covalent bonds: Strong bonds formed by the sharing of electron pairs between atoms.
Ionic bonds: Strong bonds formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions.
Hydrogen bonds: Weak bonds formed when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom.
Van der Waals interactions: Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Covalent Bonds

Electronegativity: The tendency of an atom to attract shared electrons. Higher electronegativity means stronger attraction.
Nonpolar covalent bond: Electrons are shared equally (e.g., O2).
Polar covalent bond: Electrons are shared unequally, leading to partial charges (e.g., H2O).

Ionic Bonds

Ions: Atoms that have gained or lost electrons, becoming charged (cations are positive, anions are negative).
Ionic compounds: Formed from the attraction between cations and anions (e.g., NaCl).

Weak Chemical Interactions

Hydrogen bonds: Important in stabilizing the structures of proteins and DNA.
Van der Waals forces: Allow geckos to climb walls due to the cumulative effect of many weak interactions.

Molecular Shape and Function

Shape Determines Function

The shape of a molecule is crucial for its function in the cell. Molecules with complementary shapes can interact specifically, such as enzymes and substrates or hormones and receptors.

Molecular recognition: Based on shape complementarity.
Example: Morphine mimics endorphins by binding to the same receptors due to similar shapes.

Chemical Reactions

Making and Breaking Bonds

Chemical reactions involve the making and breaking of chemical bonds, transforming reactants into products. Photosynthesis is a key example in biology.

Reactants: Starting materials in a chemical reaction.
Products: Substances formed from a chemical reaction.
Example equation:

Water and Its Properties

Structure of Water

Water is essential for life due to its unique properties, which arise from its polar covalent bonds and ability to form hydrogen bonds.

Polarity: Water has a partial negative charge near the oxygen atom and partial positive charges near the hydrogen atoms.
Hydrogen bonding: Each water molecule can form up to four hydrogen bonds with neighboring molecules.

Properties of Water

Cohesion: Water molecules stick to each other, contributing to surface tension.
Adhesion: Water molecules stick to other substances, aiding in capillary action.
Surface tension: The surface of water behaves like a stretched membrane due to cohesive forces.
Expansion upon freezing: Ice is less dense than liquid water, so it floats, insulating aquatic life in winter.
Temperature moderation: Water has a high specific heat, stabilizing temperatures in organisms and environments.
Evaporative cooling: As water evaporates, it removes heat, cooling surfaces (e.g., sweating).
Versatility as a solvent: Water dissolves many substances due to its polarity, making it the universal solvent.

Hydrophilic vs. Hydrophobic Substances

Property	Hydrophilic	Hydrophobic
Definition	Attracted to water; dissolves in water	Repelled by water; does not dissolve
Examples	Table salt (ionic compounds)	Oil (nonpolar covalent compounds)

Summary

The formation and function of molecules depend on chemical bonding between atoms.
Strong bonds include covalent and ionic bonds; weak interactions include hydrogen bonds and van der Waals forces.
Chemical reactions make and break chemical bonds (e.g., photosynthesis).
Hydrogen bonding gives water its unique properties, making life possible on Earth.
Key properties of water: cohesion, adhesion, surface tension, expansion upon freezing, evaporative cooling, temperature moderation, and solvent versatility.