Carbon and the Molecular Diversity of Life

Chapter 3: Carbon and the Molecular Diversity of Life

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

Organic chemistry is the study of carbon compounds, which are the foundation of all living organisms. Carbon's unique ability to form four covalent bonds allows it to create large, complex, and diverse molecules essential for life. The four main classes of biomolecules are carbohydrates, lipids, proteins, and nucleic acids.

• Organic compounds contain carbon and are found in all living things.

• Macromolecules are large molecules composed of thousands of covalently connected atoms.

• Carbon can form four covalent bonds due to its four valence electrons, enabling a variety of molecular structures.

The Formation of Bonds with Carbon

The number of covalent bonds an atom can form is called its valence, determined by the number of unpaired electrons in its outer shell. Carbon's valence of four allows it to bond with many elements, including hydrogen, oxygen, and nitrogen, as well as with other carbon atoms, forming chains and rings.

• Double bonds between carbons create flat molecules, while single bonds allow for tetrahedral geometry.

• Hydrocarbons are organic molecules consisting only of carbon and hydrogen.

Carbon Chain Skeletons

Carbon chains form the skeletons of most organic molecules. These chains can vary in length, branching, double bond position, and the presence of rings, contributing to the diversity of organic molecules.

• Length: Chains can be short or long.

• Branching: Chains may be unbranched or branched.

• Double bond position: Double bonds can occur at different locations.

• Rings: Some carbon skeletons form rings.

Three Types of Isomers

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

• Structural isomers: Differ in the covalent arrangement of atoms.

• Cis-trans (geometric) isomers: Differ in spatial arrangement around double bonds.

• Enantiomers: Mirror images of each other, often with different biological activities.

Functional Groups

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

ATP: Important Energy Source for Cellular Processes

Adenosine triphosphate (ATP) is an organic molecule that stores energy for cellular processes. ATP consists of adenosine attached to three phosphate groups. Hydrolysis of ATP releases energy used by cells.

3.2 Macromolecules Are Polymers, Built from Monomers

Polymers and Monomers

Polymers are long molecules made of repeating units called monomers. The synthesis and breakdown of polymers involve dehydration (condensation) and hydrolysis reactions, respectively. Enzymes catalyze these reactions.

• Dehydration reaction: Joins two monomers by removing a water molecule.

• Hydrolysis reaction: Breaks a bond between monomers by adding water.

Carbohydrates

Monosaccharides

Carbohydrates are sugars and polymers of sugars. The simplest carbohydrates are monosaccharides, which serve as major nutrients and building blocks for other molecules. Glucose (C6H12O6) is the most common monosaccharide.

• Monosaccharides are classified by the number of carbons and the position of the carbonyl group.

• In aqueous solutions, most five- and six-carbon sugars form rings.

Disaccharides and Polysaccharides

Disaccharides are formed by joining two monosaccharides via a dehydration reaction, creating a glycosidic linkage. Polysaccharides are carbohydrate polymers with storage (e.g., starch, glycogen) or structural (e.g., cellulose, chitin) roles.

• Starch: Storage polysaccharide in plants.

• Glycogen: Storage polysaccharide in animals.

• Cellulose: Structural polysaccharide in plant cell walls.

• Chitin: Structural polysaccharide in arthropod exoskeletons and fungal cell walls.

Lipids

Fats

Lipids are hydrophobic molecules that do not form true polymers. The most important lipids are fats, phospholipids, and steroids. Fats are constructed from glycerol and three fatty acids, forming triacylglycerol (triglyceride) via ester linkages. Fats are used for energy storage.

Saturated vs. Unsaturated Fatty Acids

Fatty acids can be saturated (no double bonds, solid at room temperature) or unsaturated (one or more double bonds, liquid at room temperature). Trans fats are unsaturated fats with trans double bonds, often produced industrially.

Phospholipids

Phospholipids consist of two fatty acids, a phosphate group, and glycerol. They are major components of cell membranes, forming bilayers with hydrophilic heads and hydrophobic tails.

Steroids

Steroids are lipids with a carbon skeleton consisting of four fused rings. Cholesterol is an important steroid in animal cell membranes and a precursor for other steroids such as hormones.

Proteins

Structure and Function

Proteins are polymers of amino acids and account for more than 50% of the dry mass of most cells. They perform a wide range of functions, including defense, storage, transport, communication, movement, and structural support. The function of a protein is determined by its unique three-dimensional structure.

Amino Acids and Polypeptides

Amino acids are organic molecules with amino and carboxyl groups, differing in their side chains (R groups). Amino acids are linked by peptide bonds to form polypeptides, which fold into functional proteins.

Levels of Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Coils and folds (α helix, β pleated sheet) due to hydrogen bonding.

• Tertiary structure: Overall 3D shape due to interactions among R groups.

• Quaternary structure: Association of multiple polypeptides.

Protein Structure and Disease

A single amino acid substitution can drastically affect protein function, as seen in sickle-cell disease. Protein structure can also be affected by environmental factors such as temperature, pH, and salt concentration, leading to denaturation (loss of structure and function).

Nucleic Acids

DNA and RNA

Nucleic acids store, transmit, and help express hereditary information. DNA and RNA are polymers of nucleotides. DNA contains deoxyribose sugar, while RNA contains ribose. DNA directs synthesis of messenger RNA (mRNA), which controls protein synthesis (gene expression).

Components of Nucleic Acids

• Nucleotide: Nitrogenous base + pentose sugar + phosphate group.

• Nucleoside: Nitrogenous base + pentose sugar.

• Nitrogenous bases: Pyrimidines (C, T, U) and purines (A, G).

Nucleotide Polymers: DNA and RNA

Nucleotides are joined by phosphodiester linkages, forming a sugar-phosphate backbone. DNA is double-stranded, forming a double helix with complementary base pairing (A-T, G-C). RNA is usually single-stranded, with uracil replacing thymine.

Genomics and Proteomics

Genomics is the study of whole sets of genes and their interactions, while proteomics is the study of large sets of proteins. Advances in bioinformatics have accelerated the analysis of genome and proteome data, deepening our understanding of evolution and biological function.

DNA and Proteins as Tape Measures of Evolution

Comparing DNA and protein sequences among species reveals evolutionary relationships. Closely related species have more similar DNA sequences than distantly related species, allowing molecular biology to assess evolutionary kinship.