Chapter 3: Carbon and the Molecular Diversity of Life – Study Notes

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Carbon and the Molecular Diversity of Life

Introduction to Biomolecules

Living organisms are composed of a vast array of organic compounds, primarily built on the element carbon. These compounds are large, complex, and varied, forming the foundation of biological macromolecules. The four main classes of biomolecules are carbohydrates, lipids, proteins, and nucleic acids. Each class plays a unique and essential role in cellular structure and function.

The four classes of biomolecules and their monomers

3.1 Carbon Atoms Can Form Diverse Molecules by Bonding to Four Other Atoms

The Chemical Versatility of Carbon

Carbon's ability to form four covalent bonds with a variety of atoms makes it uniquely suited to form the backbone of organic molecules. This property allows for the construction of large, complex, and diverse molecules essential for life.

Valence: The number of covalent bonds an atom can form, determined by the number of unpaired electrons in its outer shell. Carbon has a valence of 4.
Common bonding partners: Hydrogen, oxygen, nitrogen, and other carbons.
Macromolecules: Large molecules composed of thousands of covalently connected atoms.

Valence and electron distribution of H, O, N, and C

Formation of Bonds with Carbon

Carbon atoms can form single, double, or triple bonds, resulting in molecules with different shapes and properties. The geometry of these bonds influences the three-dimensional structure of organic molecules.

Tetrahedral geometry: When carbon forms four single bonds, the molecule adopts a tetrahedral shape.
Double bonds: When two carbons are joined by a double bond, the molecule is planar (flat) around the double bond.

Molecular shapes: methane, ethane, ethene

Carbon Skeletons and Hydrocarbons

Carbon atoms can bond to each other to form chains of varying length, branching, and ring structures. These skeletons form the framework for most organic molecules.

Hydrocarbons: Molecules consisting only of carbon and hydrogen. They are hydrophobic and serve as energy storage molecules.
Variation in skeletons: Carbon chains can vary in length, branching, double bond position, and ring formation.

Branching in carbon skeletons Length variation in carbon skeletons Double bond position in carbon skeletons Presence of rings in carbon skeletons

Isomers: Structural Diversity

Isomers are compounds with the same molecular formula but different structures and properties. There are three main types:

Structural isomers: Differ in the covalent arrangement of atoms.
Cis-trans (geometric) isomers: Differ in spatial arrangement around a double bond.
Enantiomers: Mirror images of each other, often with different biological activities.

Structural isomers Cis-trans isomers Enantiomers

Functional Groups

Functional groups are specific chemical groups attached to carbon skeletons that participate in chemical reactions and confer unique properties to molecules. Seven functional groups are most important in the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl.

ATP (Adenosine Triphosphate): An important energy-carrying molecule in cells, consisting of adenosine attached to three phosphate groups. Hydrolysis of ATP releases energy for cellular processes.

ATP structure ATP hydrolysis releases energy Phosphate group functional group

3.2 Macromolecules Are Polymers, Built from Monomers

Polymers and Monomers

Most macromolecules are polymers, long molecules built from repeating units called monomers. The diversity of polymers results from the arrangement of a small set of monomers into unique sequences.

Dehydration (condensation) reaction: Joins two monomers by removing a water molecule, forming a covalent bond.
Hydrolysis reaction: Breaks a covalent bond by adding a water molecule, splitting a polymer into monomers.
Enzymes: Biological catalysts that speed up both dehydration and hydrolysis reactions.

Dehydration and hydrolysis reactions Dehydration and hydrolysis schematic

Carbohydrates

Monosaccharides: Simple Sugars

Carbohydrates are sugars and their polymers. The simplest carbohydrates are monosaccharides, which serve as major nutrients and building blocks for other molecules. They have the general formula (CH2O)n.

Classification: By number of carbons (triose, pentose, hexose) and position of the carbonyl group (aldose or ketose).
Glucose (C6H12O6): The most common monosaccharide.
Ring formation: In aqueous solutions, most five- and six-carbon sugars form rings.

Monosaccharide structures Carbonyl group in sugars Ring formation in glucose

Disaccharides and Glycosidic Linkages

Disaccharides are formed when two monosaccharides are joined by a dehydration reaction, creating a covalent bond called a glycosidic linkage. Sucrose (table sugar) is a common disaccharide composed of glucose and fructose.

Formation of sucrose from glucose and fructose

Polysaccharides: Storage and Structural Roles

Polysaccharides are large carbohydrate polymers with storage or structural functions, depending on their monomer composition and glycosidic linkages.

Starch: Storage polysaccharide in plants, composed of glucose monomers. Includes amylose (unbranched) and amylopectin (branched).
Glycogen: Storage polysaccharide in animals, highly branched, stored in liver and muscle cells.
Cellulose: Structural polysaccharide in plant cell walls, composed of unbranched glucose polymers with different glycosidic linkages than starch.
Chitin: Structural polysaccharide in arthropod exoskeletons and fungal cell walls, similar to cellulose but with nitrogen-containing groups.

Glycogen and starch branching Cellulose vs. chitin structure Starch, glycogen, and cellulose in cells Alpha and beta glucose linkages in starch and cellulose

Lipids

Structure and Function of Lipids

Lipids are a diverse group of hydrophobic molecules that do not form true polymers. They are primarily composed of hydrocarbons and serve as energy storage, structural components of membranes, and signaling molecules.

Fats (triacylglycerols): Constructed from glycerol and three fatty acids via dehydration reactions, forming ester linkages. Store energy efficiently.
Saturated fatty acids: No double bonds, solid at room temperature, mostly animal fats.
Unsaturated fatty acids: One or more double bonds, liquid at room temperature, found in plants and fish.
Trans fats: Unsaturated fats with trans double bonds, often produced industrially.

Phospholipid structure and bilayer Synthesis of a fat (triacylglycerol)

Phospholipids and Steroids

Phospholipids are major components of cell membranes, consisting of two fatty acids, a phosphate group, and glycerol. Steroids are lipids with a carbon skeleton of four fused rings, including cholesterol and hormones like testosterone and estrogen.

Phospholipid bilayer: Forms the structural basis of cell membranes, with hydrophilic heads and hydrophobic tails.
Cholesterol: Maintains membrane fluidity and serves as a precursor for steroid hormones.

Phospholipid bilayer structure Steroid structure Estradiol and testosterone structures

Proteins

Structure and Function of Proteins

Proteins are polymers of amino acids and account for more than 50% of the dry mass of most cells. They perform a wide variety of functions, including catalysis, defense, storage, transport, communication, movement, and structural support.

Amino acids: Organic molecules with amino and carboxyl groups, differing in their side chains (R groups).
Polypeptides: Polymers of amino acids linked by peptide bonds.
Protein structure: Determined by the sequence of amino acids and organized into four levels: primary, secondary, tertiary, and quaternary.

Amino acid structure Polypeptide formation Protein structure levels Primary and secondary structure Tertiary and quaternary structure

Protein Structure and Function

The function of a protein is determined by its three-dimensional structure, which is specified by its amino acid sequence. Even a single amino acid substitution can drastically affect protein function, as seen in sickle-cell disease.

Denaturation: Loss of native structure due to changes in temperature, pH, or salt concentration, rendering the protein inactive.

Sickle-cell disease: effect of amino acid substitution

Nucleic Acids

DNA and RNA: Information Molecules

Nucleic acids store, transmit, and help express hereditary information. DNA and RNA are polymers of nucleotides, each consisting of a nitrogenous base, a pentose sugar, and one or more phosphate groups.

DNA: Double-stranded helix, stores genetic information, bases are A, T, G, C.
RNA: Single-stranded, involved in protein synthesis, bases are A, U, G, C.
Central Dogma: DNA → RNA → Protein.

DNA structure Nucleotide structure DNA and RNA structure

Genomics and Proteomics

Modern biology uses genomics and proteomics to analyze large sets of genes and proteins, respectively. Bioinformatics employs computational tools to manage and interpret biological data, revolutionizing our understanding of genetics and evolution.

Human Genome Project: Sequenced the entire human genome, enabling rapid advances in medicine and biology.
Evolutionary relationships: DNA and protein sequences are used to assess evolutionary kinship among species.