Chapter 2: The Chemical Context of Life

I. Matter Consists of Chemical Elements in Pure Form and Compounds

All living organisms are composed of matter, which consists of elements and compounds. Understanding the basic chemical principles is essential for studying biological processes.

• Matter: Anything that has mass and occupies space.

• Element: A substance that cannot be broken down into other substances by chemical means.

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

• Compound: A substance formed when two or more elements are chemically bonded together. Example: Water (H2O)

• There are about 25 elements essential for life; the most common are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

• 96% of living matter is composed of C, H, O, and N. Additional info: Table 2.1 in textbooks often lists these elements and their biological roles.

• Trace elements: Elements required by organisms in minute quantities (e.g., iron, iodine).

II. Properties of Elements: Atomic Structure

The structure of atoms determines the properties of elements and how they interact in biological systems.

A. Subatomic Particles

• Atoms are composed of three main subatomic particles:

  • Proton: Positively charged (+)

  • Neutron: No charge (neutral)

  • Electron: Negatively charged (-)

• Atomic number: Number of protons in the nucleus.

• Mass number: Sum of protons and neutrons.

• Atomic mass: The total mass of an atom, approximately equal to the mass number.

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

• Radioactive isotopes: Unstable isotopes that decay over time, useful in biological research and medicine. Example: Carbon-14 in radiometric dating.

B. Energy

• Energy: The ability to do work.

• Potential energy: Stored energy due to position or structure.

• Energy levels/shells: Electrons occupy energy levels around the nucleus; differences in energy levels affect electron potential energy.

• Valence shell: The outermost electron shell, important for chemical bonding.

C. Electron Orbitals

• Electron orbitals: Regions around the nucleus where electrons are likely to be found. Example: s, p, d, and f orbitals (see Fig. 2.8).

III. Chemical Bonds and Interactions

Chemical bonds are forces that hold atoms together in molecules and compounds. The type of bond affects the properties and functions of molecules in biological systems.

A. Chemical Bonds

• Ionic bonds: Atoms transfer electrons, resulting in charged ions that attract each other.

• Covalent bonds: Atoms share electrons to achieve stability. Can be single, double, or triple bonds.

• Hydrogen bonds: Weak bonds between a hydrogen atom and an electronegative atom (e.g., oxygen or nitrogen).

• Van der Waals interactions: Weak attractions between molecules due to temporary charge differences.

B. Electronegativity (EN)

• Electronegativity: The ability of an atom to attract electrons in a covalent bond.

• Atoms like sodium (Na) and magnesium (Mg) have low EN; atoms like chlorine (Cl) and fluorine (F) have high EN.

C. Covalent Bonds: Sharing Electrons

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

• Single bond: Sharing one pair of electrons.

• Double bond: Sharing two pairs of electrons.

• Structural formula: Shows arrangement of atoms in a molecule.

• Molecular formula: Shows the types and numbers of atoms (e.g., H2O).

• Valence: The bonding capacity of an atom, usually equal to the number of unpaired electrons in the valence shell.

D. Nonpolar and Polar Covalent Bonds

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

• Polar covalent bond: Electrons are shared unequally, creating partial charges (see Fig. 2.11).

• Outer shell is full when it has 8 electrons (except for the first shell, which is full at 2).

E. Ionic Bonds

• Ionic bond: Occurs when one atom donates an electron to another, forming ions.

• Ion: A charged atom or molecule.

  • Cation: Positively charged ion.

  • Anion: Negatively charged ion.

• Ionic compounds/salts: Compounds formed by ionic bonds (e.g., NaCl).

F. Hydrogen Bonds

• Hydrogen bond: A weak bond between a hydrogen atom and an electronegative atom (such as oxygen or nitrogen). Example: Bonds between water molecules (see Fig. 2.14).

G. Van der Waals Interactions

• Van der Waals interactions: Weak attractions between molecules due to transient local partial charges.

H. Bond Strength Comparison

I. Molecules with Biological Functions

• The function of a molecule is related to its shape or structure.

• Shape determines how molecules interact with each other in biological systems.

IV. Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, transforming substances into new products.

• Reactants: Starting materials in a chemical reaction.

• Products: Ending molecules formed from a reaction.

• Chemical equilibrium: The point at which the concentrations of reactants and products remain constant over time.

Key Equation Example

• General chemical reaction:

• Example:

Additional info: These concepts form the foundation for understanding biochemistry, molecular biology, and physiology in living organisms.