General Biology Study Guide: The Chemical Context and Molecular Diversity of Life

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Chapter 2: The Chemical Context of Life

Chemical Elements and Compounds

Understanding the basic chemical principles is essential for studying biological systems. Living organisms are composed of chemical elements, which combine to form compounds.

Element: A substance that cannot be broken down into other substances by chemical means.
Compound: A substance consisting of two or more different elements combined in a fixed ratio. Compounds can be broken down into their constituent elements.

Exploring Life on Its Many Levels

Life is composed primarily of a few key elements. These elements make up the majority of living matter.

Major elements in living organisms: Carbon, Nitrogen, Oxygen, Phosphorus, Sulfur, Hydrogen.
These six elements account for approximately 96% of living matter.

Atoms and Molecules

Atoms are the basic units of matter, and their structure determines the properties of elements and compounds.

Atomic number: Number of protons in an atom.
Mass number: Sum of protons and neutrons in an atom.
Isotopes: Atoms of the same element with different numbers of neutrons.
Valence electrons: Electrons in the outermost shell, important for chemical bonding.
Radioactive isotopes: Unstable isotopes that decay, emitting radiation. Used in biological research and medicine (e.g., dating fossils, tracing atoms in metabolism).
Covalent bond: A chemical bond formed when two atoms share one or more pairs of electrons.
Ionic bond: A bond formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions.
Hydrogen bond: A weak bond between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.
Van der Waals interactions: Weak attractions between molecules or parts of molecules that result from transient local partial charges.
Electronegativity: The tendency of an atom to attract electrons toward itself in a chemical bond.

Example: Water molecules are held together by hydrogen bonds, which are responsible for many of water's unique properties.

Effects of Water's Polarity

Water's molecular structure and polarity give rise to its unique properties, which are essential for life.

Polarity: Water is a polar molecule, with a partial negative charge near the oxygen atom and a partial positive charge near the hydrogen atoms.
Hydrogen bonding: The polarity of water molecules allows them to form hydrogen bonds with each other and with other polar molecules.

Properties of Water

Cohesion: Water molecules stick together due to hydrogen bonding, contributing to phenomena like surface tension.
Adhesion: Water molecules can also stick to other substances, aiding processes like capillary action in plants.
Ability to moderate temperature: Water has a high specific heat, meaning it can absorb or release large amounts of heat with only a slight change in its own temperature.
Expansion upon freezing: Water expands as it freezes, making ice less dense than liquid water. This property allows ice to float, insulating aquatic environments.
Versatility as a solvent: Water's polarity allows it to dissolve many substances, making it the "universal solvent" for biological systems.

Table: Properties of Water and Their Biological Importance

Property	Description	Biological Importance
Cohesion	Attraction between water molecules	Enables transport of water in plants
Adhesion	Attraction between water and other substances	Helps water move against gravity in plant vessels
High specific heat	Resists temperature change	Stabilizes climate and body temperature
Expansion upon freezing	Ice is less dense than liquid water	Prevents bodies of water from freezing solid
Versatile solvent	Dissolves many substances	Facilitates chemical reactions in cells

Dissociation of Water Molecules

Water can dissociate into ions, which is important for acid-base chemistry in biological systems.

Dissociation reaction: Water can act as both an acid and a base, forming hydronium () and hydroxide () ions.

Equation:

Acids: Substances that increase the hydrogen ion concentration in a solution (pH < 7).
Bases: Substances that decrease the hydrogen ion concentration in a solution (pH > 7).
pH scale: Measures the concentration of hydrogen ions; lower pH is more acidic, higher pH is more basic.

Chapter 3: Carbon and the Molecular Diversity of Life

The Importance of Carbon

Carbon is the backbone of biological molecules due to its ability to form four covalent bonds, allowing for a diversity of stable structures.

Carbon skeletons can vary in length, branching, and double bond position, contributing to molecular diversity.

Functional Groups

Functional groups are specific groups of atoms within molecules that have characteristic properties and reactivity.

Phosphate group
Carboxyl group
Hydroxyl group
Sulfhydryl group
Methyl group

These groups determine the chemical behavior of organic molecules.

Polymer Principles

Many biological molecules are polymers, made by joining smaller units called monomers.

Polymer: A long molecule consisting of many similar or identical building blocks linked by covalent bonds.
Monomer: The subunit that serves as the building block of a polymer.
Dehydration synthesis: Reaction that joins monomers by removing a water molecule.
Hydrolysis: Reaction that breaks bonds between monomers by adding water.

Carbohydrates: Fuel and Building Material

Carbohydrates include sugars and polymers of sugars. They serve as energy sources and structural materials.

Monosaccharide: Simple sugar (e.g., glucose).
Disaccharide: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose).
Polysaccharide: Polymers of many monosaccharides (e.g., starch, cellulose, glycogen).

Example: Starch is a storage polysaccharide in plants; glycogen is a storage polysaccharide in animals.

Lipids: Diverse Hydrophobic Molecules

Lipids are a diverse group of hydrophobic molecules, including fats, phospholipids, and steroids.

Fats: Constructed from glycerol and fatty acids. Used for energy storage.
Phospholipids: Major component of cell membranes, with hydrophilic heads and hydrophobic tails.
Steroids: Lipids with a carbon skeleton consisting of four fused rings (e.g., cholesterol).
Saturated fatty acids: No double bonds between carbon atoms; solid at room temperature.
Unsaturated fatty acids: One or more double bonds; liquid at room temperature.

Proteins: Many Structures, Many Functions

Proteins are polymers of amino acids and perform a wide variety of functions in cells.

Amino acid: Organic molecule with an amino group, carboxyl group, hydrogen atom, and R group (side chain).
Polypeptide: Polymer of amino acids linked by peptide bonds.
Primary structure: Sequence of amino acids in a protein.
Secondary structure: Coiling or folding of the polypeptide chain (e.g., alpha helix, beta sheet) due to hydrogen bonding.
Tertiary structure: Overall 3D shape of a polypeptide, determined by interactions among side chains.
Quaternary structure: Association of multiple polypeptide chains.

Example: Hemoglobin is a protein with quaternary structure, consisting of four polypeptide subunits.

Table: Levels of Protein Structure

Level	Description	Stabilizing Bonds
Primary	Sequence of amino acids	Peptide bonds
Secondary	Alpha helix, beta sheet	Hydrogen bonds
Tertiary	3D folding of polypeptide	Hydrogen, ionic, disulfide, hydrophobic interactions
Quaternary	Association of multiple polypeptides	Same as tertiary

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