Carbon and the Molecular Diversity of Life: Structure and Function of Biomolecules

Carbon and the Molecular Diversity of Life

Overview of Biomolecules

Biomolecules are the fundamental molecules that constitute living organisms. The four main classes of biomolecules are carbohydrates, lipids, proteins, and nucleic acids. Each class has unique structural features and functions essential for life.

Carbon Atoms and Molecular Diversity

Bonding Properties of Carbon

Carbon atoms are central to organic chemistry due to their ability to form four covalent bonds, allowing for a vast diversity of molecular structures. The number of covalent bonds an atom can form is called its valence, determined by the number of unpaired electrons in its outer shell.

• Valence of Carbon: 4 (can form four bonds)

• Valence of Hydrogen: 1

• Valence of Oxygen: 2

• Valence of Nitrogen: 3

Formation of Bonds with Carbon

Carbon can form single, double, or triple bonds with other atoms, including hydrogen, oxygen, nitrogen, and other carbon atoms. Double bonds between carbon atoms result in planar (flat) molecules, while single bonds allow for rotation and more complex shapes.

Carbon Skeletons

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

• Length: Number of carbon atoms in the chain

• Branching: Chains may be unbranched or branched

• Double Bond Position: Location of double bonds can vary

• Rings: Some carbon skeletons are arranged in rings (e.g., cyclohexane, benzene)

Isomers and Functional Groups

Types of Isomers

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

• Structural Isomers: Differ in covalent arrangement of atoms

• Cis-trans Isomers: Differ in arrangement around double bonds (cis: same side, trans: opposite sides)

• Enantiomers: Mirror images of each other; often only one is biologically active

Functional Groups

Functional groups are chemical groups attached to carbon skeletons that affect molecular function and participate in chemical reactions. Seven functional groups are most important in biological chemistry: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl.

ATP: Cellular Energy Source

Adenosine triphosphate (ATP) is an organic molecule consisting of adenosine attached to three phosphate groups. ATP stores potential energy and releases it upon hydrolysis, fueling cellular processes.

Macromolecules: Polymers and Monomers

Polymer Formation and Breakdown

Macromolecules are polymers built from monomers. Polymer synthesis occurs via dehydration reactions (removal of water), while breakdown occurs via hydrolysis reactions (addition of water).

• Dehydration Reaction: Joins monomers, releases water

• Hydrolysis Reaction: Splits polymers, consumes water

Carbohydrates

Monosaccharides

Carbohydrates are sugars and their polymers. The simplest carbohydrates are monosaccharides (simple sugars), classified by the number of carbons and the placement of the carbonyl group. Glucose (C6H12O6) is the most common monosaccharide.

Ring Formation in Aqueous Solutions

Monosaccharides, such as glucose, often form ring structures in aqueous solutions, which are the most stable forms under physiological conditions.

Disaccharides

Disaccharides are formed when two monosaccharides are joined by a dehydration reaction, creating a glycosidic linkage. Sucrose is a common disaccharide composed of glucose and fructose.

Polysaccharides

Polysaccharides are carbohydrate polymers with storage and structural roles. Their function depends on the identity of monomers and the positions of glycosidic linkages.

• Starch: Storage polysaccharide in plants, composed of glucose monomers

• Glycogen: Storage polysaccharide in animals, stored in liver and muscle cells

Structural Polysaccharides

Cellulose is a major component of plant cell walls and the most abundant organic compound on Earth. Chitin is found in arthropod exoskeletons and fungal cell walls, similar to cellulose but with a nitrogen-containing group.

Lipids

General Properties

Lipids are hydrophobic molecules that do not form true polymers. They consist mostly of hydrocarbons with nonpolar covalent bonds. The most biologically important lipids are fats, phospholipids, and steroids.

Fats

Fats are constructed from glycerol and three fatty acids via dehydration reactions, resulting in an ester linkage and forming triacylglycerol (triglyceride). Fats are efficient energy storage molecules.

Saturated vs. Unsaturated Fatty Acids

Fatty acids vary in length and the number/location of double bonds.

• 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, mostly plant and fish fats

• Trans Fats: Unsaturated fats with trans double bonds, often produced by hydrogenation

Phospholipids

Phospholipids consist of two fatty acids, a phosphate group, and glycerol. They are essential for cell membrane structure, forming a bilayer with hydrophobic tails and hydrophilic heads.

Steroids

Steroids are lipids with a carbon skeleton of four fused rings. Cholesterol is a key steroid in animal cell membranes and a precursor for other steroids such as testosterone and estrogen.

Proteins

Structure and Function

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

Amino Acid Monomers

Amino acids are organic molecules with carboxyl and amino groups, differing in their side chains (R groups). The R group determines the amino acid's identity, structure, and function.

Polypeptides

Polypeptides are polymers of amino acids linked by peptide bonds. Each polypeptide has a unique sequence, with an amino (N-terminus) and carboxyl (C-terminus) end.

Protein Structure Levels

Protein function depends on its structure, which is organized into four levels:

• Primary: Sequence of amino acids

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

• Tertiary: Overall 3D shape from interactions among R groups

• Quaternary: Association of multiple polypeptides

Sickle-Cell Disease: Protein Structure Example

A single amino acid substitution in hemoglobin causes sickle-cell disease, demonstrating how primary structure affects protein function.

Protein Denaturation

Physical and chemical conditions (temperature, pH, salt concentration) can disrupt protein structure, leading to denaturation and loss of function.

Nucleic Acids

DNA and RNA: Structure and Function

Nucleic acids store, transmit, and help express hereditary information. DNA is composed of monomers called nucleotides, which consist of a nitrogenous base, a pentose sugar, and one or more phosphate groups. RNA is similar but uses ribose and uracil instead of thymine.

Nucleotide Polymers

Adjacent nucleotides are joined by phosphodiester linkages, forming a sugar-phosphate backbone. DNA polymers have directionality (5' and 3' ends), and base sequences are unique for each gene.

Structures of DNA and RNA

DNA consists of two polynucleotide strands forming a double helix, with antiparallel backbones and complementary base pairing (A-T, G-C). RNA is single-stranded, with A-U pairing.

Genomics and Proteomics

Bioinformatics and Molecular Evolution

Genomics and proteomics involve the analysis of large sets of genes and proteins, often using bioinformatics tools. DNA and protein sequences can be used to assess evolutionary relationships among species.

DNA and Proteins as Tape Measures of Evolution

Linear sequences of nucleotides in DNA are inherited and can be compared to assess kinship and evolutionary relationships. Closely related species have more similar DNA sequences.