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Chapter 2: The Chemical Context of Life – General Biology Study Notes

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Chapter 2: The Chemical Context of Life

Matter: Elements, Compounds, and Emergent Properties

Matter is anything that takes up space and has mass. In biology, understanding the chemical basis of life begins with atoms, elements, and compounds, and how their properties combine to form the substances essential for living organisms.

  • Element: A substance that cannot be broken down into other substances by chemical reactions. Examples include sodium (Na) and chlorine (Cl).

  • Compound: A substance consisting of two or more elements in a fixed ratio, joined by chemical bonds. Example: Formic acid (CH2O2) contains carbon, hydrogen, and oxygen.

  • Emergent Properties: Compounds often have properties different from those of their constituent elements. For example, sodium (a reactive metal) and chlorine (a toxic gas) combine to form sodium chloride (NaCl), which is table salt.

  • Atoms: The smallest unit of an element, retaining its properties.

Example: Sodium (Na) and chlorine (Cl) are both highly reactive elements, but when combined, they form sodium chloride (NaCl), a stable compound used as table salt.

Elements in the Human Body

Living organisms are composed of a limited number of elements, with a few making up the majority of body mass. The following table summarizes the major elements found in the human body:

Element

Symbol

Percentage of Body Mass (including water)

Oxygen

O

65.0%

Carbon

C

18.5%

Hydrogen

H

9.5%

Nitrogen

N

3.3%

Calcium

Ca

1.5%

Phosphorus

P

1.0%

Potassium

K

0.4%

Sulfur

S

0.3%

Sodium

Na

0.2%

Chlorine

Cl

0.2%

Magnesium

Mg

0.1%

Additional info: Trace elements (less than 0.01% of mass) include boron (B), chromium (Cr), cobalt (Co), copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), silicon (Si), tin (Sn), vanadium (V), and zinc (Zn).

Atomic Structure and Subatomic Particles

Atoms are composed of subatomic particles that determine their chemical properties and behavior.

  • Proton: Positively charged particle found in the nucleus; mass = 1 dalton.

  • Neutron: Neutral particle found in the nucleus; mass = 1 dalton.

  • Electron: Negatively charged particle orbiting the nucleus in electron shells; mass ≈ 1/1836 dalton.

  • Atomic Number: Number of protons in an atom; defines the element.

  • Mass Number: Number of protons plus neutrons in an atom.

  • Isotopes: Atoms of the same element with different numbers of neutrons; some are radioactive.

Example: Oxygen has 8 protons (atomic number 8). Its most common isotope has 8 neutrons, giving it a mass number of 16.

Electron Shells and Energy Levels

Electrons are arranged in shells around the nucleus, each with a specific energy level. The distribution of electrons determines an atom's chemical reactivity and bonding capacity.

  • First shell: Holds up to 2 electrons (lowest energy).

  • Second shell: Holds up to 8 electrons (higher energy).

  • Third shell: Holds up to 18 electrons (highest energy in this model).

  • Electrons fill the lowest available energy levels first.

Example: Oxygen has 8 electrons: 2 in the first shell, 6 in the second shell. It needs 2 more electrons to fill its outer shell, so it tends to form 2 bonds.

Chemical Bonds: Types and Properties

Chemical bonds are the forces that hold atoms together in molecules and compounds. The main types relevant to biology are:

  • Covalent Bonds: Electrons are shared between atoms.

    • Nonpolar Covalent: Electrons are shared equally (e.g., H2).

    • Polar Covalent: Electrons are shared unequally, creating partial charges (e.g., H2O).

  • Ionic Bonds: Electrons are transferred from one atom to another, forming ions (charged atoms).

  • Hydrogen Bonds: Weak attractions between a hydrogen atom (attached to an electronegative atom like O, N, or S) and another electronegative atom.

Example: In water (H2O), oxygen forms polar covalent bonds with hydrogen, resulting in a molecule with partial positive and negative charges, which allows hydrogen bonding between water molecules.

Molecular Formulas and Structural Representations

Molecules can be represented in several ways to show their composition and structure:

  • Molecular Formula: Shows the number and type of atoms (e.g., CH4 for methane).

  • Lewis Dot Structure: Shows valence electrons and bonding.

  • Structural Formula: Shows how atoms are connected (e.g., H–O–H for water).

Example: Methane (CH4) has a central carbon atom bonded to four hydrogen atoms.

Biological Molecules and Function

The structure of molecules determines their function in biological systems. For example, the shape of morphine and endorphin molecules allows them to bind to the same brain cell receptors, affecting pain perception.

  • Structure-Function Relationship: The specific shape and chemical properties of a molecule enable it to interact with biological targets.

Example: Endorphins and morphine have similar structures, allowing both to bind to endorphin receptors in the brain.

Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, transforming reactants into products. These reactions are fundamental to all biological processes.

  • Reactants: Starting materials in a chemical reaction.

  • Products: Substances formed as a result of the reaction.

  • General Equation:

Example: The reaction of hydrogen and oxygen to form water:

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