Atoms, Molecules, and Life: Foundations of Biological Chemistry

Atoms, Molecules, and Life

Introduction

Understanding chemistry is essential in biology because atoms form the basis of all matter, including living organisms. The properties and interactions of atoms and molecules underpin the structure and function of biological systems.

The Atom: Basic Unit of Matter

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

• Atoms cannot be broken down into simpler substances by ordinary chemical means.

• Atoms consist of three main subatomic particles:

  • Protons: Positively charged particles located in the nucleus.

  • Neutrons: Uncharged particles also found in the nucleus.

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

	NEUTRON	PROTON	ELECTRON
Charge	Uncharged	+1	-1
Location	At the core of the atom (nucleus)	At the core of the atom (nucleus)	Orbiting around the nucleus in electron shells

Elements

• Element: A collection of atoms of the same type. An element cannot be broken down into other substances by chemical reactions.

• Each element is defined by its number of protons (atomic number).

• Some elements are present in trace amounts in living organisms but are still essential for life.

The Atomic Nucleus

Atomic Number and Atomic Mass

• Atomic number: The number of protons in an atom of a particular element. This number is unique for each element.

• Atomic mass (weight): The sum of the number of protons and neutrons in an atom.

• Isotopes: Atoms of the same element with different numbers of neutrons, resulting in different atomic masses. Some isotopes are unstable and undergo radioactive decay.

The Electron Shells

Structure and Energy Levels

• Electron shells: Three-dimensional orbital spaces around the nucleus where electrons are likely to be found (about 90% of the time).

• Each shell occupies a specific distance from the nucleus; the farther away, the higher the energy level.

• Shells can change positions if they absorb or release energy.

• The chemical behavior of an atom is determined by the number of electrons in its outermost shell (valence electrons).

• Atoms with incomplete outer shells are reactive and tend to form bonds to achieve a full shell.

Chemical Bonds: Joining Atoms to Make Molecules

Introduction to Chemical Bonds

• Chemical bond: An attraction that holds two or more atoms together.

• Atoms form chemical bonds to fill their valence shells and achieve stability.

Molecules, Compounds, and Mixtures

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

• Compound: A molecule composed of two or more different elements in a fixed ratio (e.g., NaCl).

• Mixture: Two or more elements or compounds combined in a variable ratio (e.g., air).

Formation of Ions and Ionic Bonds

• If an atom has an almost empty or almost full outer electron shell, it is likely to form an ion (a charged atom or molecule).

• Cation: Positively charged ion (loss of electrons).

• Anion: Negatively charged ion (gain of electrons).

• Ionic bond: Formed by the attraction between oppositely charged ions after electron transfer.

• Ionic compounds are called salts and usually form crystals (e.g., sodium chloride).

Sharing Electrons: Covalent Bonds

Covalent Bonds

• Covalent bond: A bond formed when two atoms share electrons to fill their outer shells.

• Types of covalent bonds:

  • Single covalent bond: Shares one pair of electrons.

  • Double covalent bond: Shares two pairs of electrons.

  • Triple covalent bond: Shares three pairs of electrons.

• Nonpolar covalent bond: Electrons are shared equally between atoms.

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges on the molecule.

Comparison of Covalent Bonds

Bond Type	Number of Electron Pairs Shared	Example	Strength
Single	1	H-H	Lowest
Double	2	O=O	Medium
Triple	3	N≡N	Highest

Charge Disparity and Polarity

• Polar molecules have a charge disparity, with one side being more positive and the other more negative (e.g., water molecule).

• Oxygen in water is more electronegative, pulling electrons closer and making it partially negative, while hydrogen becomes partially positive.

Hydrogen Bonds

Hydrogen Bonds in Biology

• Hydrogen bond: A weak attraction between a hydrogen atom covalently bonded to one atom and another electronegative atom.

• Hydrogen bonds are about 20 times easier to break than covalent bonds.

• They are crucial in stabilizing the three-dimensional structure of large biological molecules (e.g., DNA, proteins).

• Hydrogen bonds are reversible and can form between or within molecules.

Water and Life

Importance of Water

• Cells are composed of 70-95% water.

• Water covers about 70% of the Earth's surface.

• Water's unique properties are essential for life, including its ability to form hydrogen bonds, high specific heat, and solvent capabilities.

Additional info: The notes above are expanded and clarified for academic completeness, with definitions, examples, and tables added for clarity and exam preparation.