The Chemical Context of Life: Biological Molecules and Their Properties

Chapter 2: The Chemical Context of Life

Introduction

This chapter introduces the chemical principles essential for understanding biological molecules and their roles in living organisms. It covers the structure and properties of water, the nature of chemical bonds, and the major classes of biological macromolecules.

Vocabulary

• Adhesion

• Buffer

• Capillary action

• Cohesion

• Covalent bond

• Electronegativity

• Ionic bond

• Heat of vaporization

• Hydration shell

• Hydrogen bond

• Hydrophilic

• Hydrophobic

• Polarity

• Specific heat

• Surface tension

Learning Objectives

Chemistry Review

• Define and describe ionic, covalent, and hydrogen bonds. Understand how these bonds form and their relative strengths.

• Distinguish among nonpolar covalent, polar covalent, and ionic bonds. Recognize how differences in electronegativity affect bond type.

• Describe hydrogen bonds. Explain their role in the structure and properties of water and biological molecules.

• Explain why weak bonds are important to living organisms. Discuss their role in molecular interactions and biological processes.

Properties of Water

• Relate the polarity of water molecules and their tendency to form hydrogen bonds to the special properties of water that make it the basis for life on earth.

• Define hydrogen bond and give its characteristics.

• Describe biological significance of cohesion, adhesion, capillary action, and heat of vaporization. Explain the relationship of each to the concepts of polarity and/or hydrogen bonding.

• Describe the biological significance of the cohesiveness of water.

• Explain how water’s high specific heat, high heat of vaporization, and low density as a solid affect both aquatic and terrestrial ecosystems.

• Distinguish between hydrophilic and hydrophobic interactions.

• Write the equation for the dissociation and re-formation of water.

• Describe the pH scale. Explain what it measures and how it is used in biology.

• Define acid, base, buffer, and explain why living organisms require pH that remain within a narrow range.

• Using the bicarbonate buffer system as an example, explain how buffers work.

• Explain the water cycle.

Macromolecules: Structure and Function

Vocabulary

• Alpha (α) helix

• Amino acid

• Beta (β) pleated sheet

• Carbohydrate

• Carboxyl group

• Chaperone

• Cholesterol

• Dehydration synthesis

• Deoxyribonucleic acid (DNA)

• Disaccharide

• Disulfide bridge

• Double helix

• Fatty acid

• Functional group

• Glycogen

• Glycosidic linkage

• Hydrocarbon

• Hydrolysis

• Hydrophobic interaction

• Lipid

• Macromolecule

• Methyl group

• Monomer

• Monosaccharide

• Nucleic acid

• Nucleotide

• Peptide bond

• Phospholipid

• Polymer

• Polynucleotide

• Polypeptide

• Polysaccharide

• Primary structure

• Purine

• Pyrimidine

• Quaternary structure

• Ribose

• Saturated fatty acid

• Steroid

• Steroid

• Tertiary structure

• Triglyceride

• Unsaturated fatty acid

Learning Objectives

Functional Groups

• Explain how carbon’s electron configuration determines the kinds and numbers of bonds that carbon will form.

• Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules.

• Name the major functional groups and, given a structure, identify the functional groups in a molecule.

Polymer Principles

• Explain how monomers are used to build polymers. Describe the process of dehydration synthesis and hydrolysis.

• List the four major classes of biomolecules and the building block units of which they are composed. (Carbohydrates, lipids, proteins, nucleic acids)

• Compare the differences in the functions of each of these classes of compounds.

Carbohydrates: Fuel and Building Material

• Describe the distinguishing characteristics of carbohydrates and explain how they are classified.

• Distinguish between monosaccharides and disaccharides.

• Identify a glycosidic linkage and describe how it is formed.

Lipids: Diverse and Nonpolar Macromolecules

• Explain what distinguishes lipids from other major classes of macromolecules.

• Describe the unique properties, building-block molecules, and biological importance of the three important groups of lipids: fats, phospholipids, and steroids.

• Distinguish between a saturated and an unsaturated fat and list unique emergent properties that are a consequence of these structural differences.

Proteins: Many Structures, Many Functions

• Describe the characteristics that distinguish proteins from the other major classes of macromolecules and explain the biologically important functions of this group.

• List and describe the four components of an amino acid. Explain how amino acids may be grouped according to the physical and chemical properties of the side chains.

• Identify a peptide bond and explain how it is formed.

• Distinguish between a polypeptide and a protein.

• Explain what determines protein conformation and why it is important.

• Define primary structure.

• Describe the two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining the structure.

• Explain how weak interactions and disulfide bridges contribute to tertiary protein structure.

• Describe quaternary protein structure.

• Define denaturation and explain how proteins become denatured.

• Explain how protein folding occurs in cells.

Nucleic Acids: Informational Polymers

• Describe the characteristics that distinguish nucleic acids from the other major groups of macromolecules.

• Summarize the functions of nucleic acids.

• List the major components of a nucleotide, and describe how these monomers are linked to form a nucleic acid.

• Distinguish between a pyrimidine and a purine; know which nucleotides are purines and which are pyrimidines.

• Briefly describe the three-dimensional structure of DNA.

• Explain how the structure of DNA and proteins can be used to document the hereditary background of an organism.

Key Table: Major Classes of Biological Macromolecules

Class	Monomer	Polymer	Function
Carbohydrates	Monosaccharide	Polysaccharide	Energy storage, structural support
Lipids	Glycerol, fatty acids	Triglyceride, phospholipid, steroid	Energy storage, membrane structure, signaling
Proteins	Amino acid	Polypeptide	Catalysis, structure, transport, signaling
Nucleic Acids	Nucleotide	DNA, RNA	Information storage, transmission

Important Equations and Concepts

• Dissociation of Water: $H_2O \rightleftharpoons H^+ + OH^-$

• pH Calculation: $pH = -\log[H^+]$

• Formation of a Peptide Bond: $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

• Dehydration Synthesis (General): $\text{Monomer}_1 + \text{Monomer}_2 \rightarrow \text{Polymer} + H_2O$

Summary

• Understanding the chemical context of life is essential for studying biological molecules and their functions.

• Water’s unique properties arise from its polarity and hydrogen bonding, making it vital for life.

• Biological macromolecules—carbohydrates, lipids, proteins, and nucleic acids—are built from specific monomers and have diverse functions in living organisms.

• Functional groups and the structure of carbon-based molecules contribute to the diversity of organic chemistry in biology.