Atoms, Molecules, and Life

Introduction

This chapter explores the fundamental chemical principles that underlie all biological processes. Understanding atoms, molecules, and their interactions is essential for comprehending the structure and function of living organisms.

What Are Atoms?

Definition and Structure

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

• Element: A pure substance made of only one kind of atom; cannot be broken down by ordinary chemical reactions.

• Atoms are composed of subatomic particles:

  • Protons: Positively charged particles located in the nucleus.

  • Neutrons: Uncharged particles also in the nucleus.

  • Electrons: Negatively charged particles orbiting the nucleus in electron shells.

• Atomic number: The number of protons in an atom's nucleus; defines the element.

• Mass number: The sum of protons and neutrons in the nucleus.

Common Elements in Living Organisms

Living organisms are primarily composed of a few key elements, with the most abundant being oxygen, carbon, hydrogen, and nitrogen.

Subatomic Particles: Mass and Charge

Isotopes and Radioactivity

• Isotopes: Atoms of the same element with the same number of protons but different numbers of neutrons.

• Example: Carbon has three isotopes—C-12, C-13, and C-14. All have 6 protons, but 6, 7, and 8 neutrons, respectively.

• Radioactive isotopes: Unstable isotopes that spontaneously break apart, releasing energy or particles (radioactive decay).

• Applications: Used in medical imaging and treatment, such as detecting brain tumors.

The Periodic Table

• Elements are organized by atomic number and chemical properties.

• Horizontal rows are called periods; vertical columns are groups.

• Noble gases (e.g., helium, argon) have full outer electron shells and are chemically inert.

Electron Shells and Energy Levels

• Electrons occupy shells (energy levels) around the nucleus.

• First shell: up to 2 electrons; second: up to 8; third: up to 16 (in practice, 8 for main group elements).

• Electrons in the outermost shell (valence electrons) determine chemical reactivity.

• Atoms are most stable when their outermost shell is full.

Energy Capture and Release by Electrons

• Electrons can absorb energy and move to higher shells (excited state).

• When they return to lower shells, they release energy as heat or light.

How Do Atoms Interact to Form Molecules?

Formation of Molecules

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

• Atoms with incomplete outer shells tend to react to achieve stability.

• Noble gases are stable and unreactive due to full outer shells.

Free Radicals

• Free radicals: Atoms or molecules with unpaired electrons in their outer shell; highly reactive.

• Formed during normal metabolic processes (e.g., respiration).

• Can damage cells by "stealing" electrons from other molecules.

• Antioxidants (e.g., vitamin E) neutralize free radicals.

Chemical Bonds

• Chemical bond: Attractive force that holds atoms together in molecules.

• Formed when atoms gain, lose, or share electrons.

• Three major types:

  1. Ionic bonds

  2. Covalent bonds (polar and nonpolar)

  3. Hydrogen bonds

Ionic Bonds

• Formed when one atom transfers electrons to another, creating ions.

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

• Oppositely charged ions attract each other (e.g., Na+ and Cl- form NaCl).

Covalent Bonds

• Formed when two atoms share one or more pairs of electrons.

• Most biological molecules are held together by covalent bonds.

• Nonpolar covalent bond: Electrons are shared equally (e.g., O2, N2, H2).

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

Hydrogen Bonds

• Weak attractions between the slightly positive hydrogen atom of one polar molecule and the slightly negative atom (often oxygen or nitrogen) of another.

• Responsible for many unique properties of water.

Summary Table: Types of Bonds in Biological Molecules

Why Is Water So Important to Life?

Cohesion and Adhesion

• Cohesion: Tendency of water molecules to stick together due to hydrogen bonding; responsible for surface tension.

• Adhesion: Tendency of water molecules to stick to other polar substances; enables capillary action.

• Both properties are essential for water transport in plants.

Water as a Solvent

• Solvent: A substance that dissolves other substances (solutes).

• Water is an excellent solvent for ionic and polar substances (hydrophilic).

• Nonpolar substances (hydrophobic), such as oils and fats, do not dissolve in water.

Thermal Properties of Water

• High specific heat: Water absorbs a lot of energy before its temperature rises; helps stabilize temperatures in organisms and environments.

• High heat of vaporization: Requires significant energy to evaporate; sweating cools the body as water evaporates.

• Ice is less dense than liquid water: Ice floats, insulating aquatic life in cold climates.

Acids, Bases, and pH

• Water can dissociate into hydrogen ions (H+) and hydroxide ions (OH-):

• Acid: Substance that increases H+ concentration in solution (e.g., HCl).

• Base: Substance that increases OH- concentration or accepts H+ (e.g., NaOH, NH3).

• pH scale: Measures acidity or basicity (0-6 acidic, 7 neutral, 8-14 basic).

Buffers

• Buffer: A molecule that helps maintain a stable pH by accepting or releasing H+ as needed.

• Example: Bicarbonate (HCO3-) in human blood.

• Buffer action: In excess H+: In excess OH-:

Key Takeaways

• Atoms and molecules are the foundation of all biological structures and processes.

• Water's unique properties are essential for life.

• Chemical bonds determine the structure and function of biological molecules.

• Acids, bases, and buffers are crucial for maintaining homeostasis in living organisms.