Section 2: Carbon Atoms and Large Biological Molecules

This section explores the structure, properties, and functions of major classes of biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids. Understanding these molecules is fundamental to the study of biology, as they form the basis of cellular structure and function.

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically with a hydrogen:oxygen atom ratio of 2:1. They serve as energy sources and structural components in cells.

• Monosaccharides: The simplest carbohydrates, also known as simple sugars. General formula: .

• Example: A monosaccharide with three carbons is triose, with the formula .

• Disaccharides: Formed by joining two monosaccharides via a dehydration reaction (removal of water). Example: Two glucose molecules () join to form maltose () and water.

• Isomers: Molecules with the same molecular formula but different structures. Glucose and fructose are structural isomers (differ in the arrangement of atoms).

Application: High-fructose corn syrup is made by converting glucose to its isomer, fructose, which is sweeter. Both are used in processed foods.

Lipids

Lipids are a diverse group of hydrophobic molecules, including fats, phospholipids, and steroids. They are not polymers but are grouped together due to their insolubility in water.

• Fats (Triglycerides): Composed of glycerol and three fatty acids. Formed by dehydration reactions between the hydroxyl group of glycerol and the carboxyl group of fatty acids.

• Saturated Fats: Fatty acids with only single C–C bonds. Solid at room temperature. Found in animal fats.

• Unsaturated Fats: Fatty acids with one or more double C=C bonds (usually cis). Liquid at room temperature. Found in plant oils and fish.

• Phospholipids: Similar to fats but have two fatty acids and a phosphate group attached to glycerol. The phosphate head is hydrophilic, while the fatty acid tails are hydrophobic. They form bilayers in aqueous environments, making up cell membranes.

• Steroids: Lipids with a carbon skeleton of four fused rings. Example: Cholesterol, which is a component of animal cell membranes and a precursor for steroid hormones.

Proteins

Proteins are polymers of amino acids and perform a vast array of functions in living organisms, including catalysis, defense, transport, signaling, movement, and structural support.

• Amino Acids: The monomers of proteins. Each has a central (alpha) carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group (side chain).

• Peptide Bonds: Covalent bonds formed by dehydration between the carboxyl group of one amino acid and the amino group of another.

• Polypeptide: A polymer of amino acids linked by peptide bonds.

• Protein Structure:

  • Primary Structure: The unique sequence of amino acids in a polypeptide.

  • Secondary Structure: Local folding into alpha helices and beta pleated sheets, stabilized by hydrogen bonds.

  • Tertiary Structure: The overall 3D shape of a polypeptide, determined by interactions among side chains (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions).

  • Quaternary Structure: The association of two or more polypeptide subunits to form a functional protein (not present in all proteins).

• Denaturation: Loss of protein structure (and function) due to changes in temperature, pH, or other environmental factors. Some proteins can renature if conditions return to normal.

• Example: Sickle-cell disease is caused by a single amino acid substitution in the hemoglobin protein, demonstrating the importance of primary structure.

Nucleic Acids

Nucleic acids store, transmit, and help express hereditary information. The two main types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• Nucleotides: The monomers of nucleic acids, each consisting of a nitrogenous base, a pentose sugar (ribose or deoxyribose), and a phosphate group.

• Nitrogenous Bases: Purines (adenine, guanine) and pyrimidines (cytosine, thymine in DNA, uracil in RNA).

• Polynucleotides: Nucleotides are joined by phosphodiester bonds between the 5' phosphate and 3' hydroxyl groups, forming a sugar-phosphate backbone.

• DNA Structure: Double helix with two antiparallel strands held together by hydrogen bonds between complementary bases (A pairs with T, G pairs with C).

• RNA Structure: Usually single-stranded, but can form complex 3D shapes through internal base pairing.

• Central Dogma: DNA directs its own replication and the synthesis of RNA (transcription), which is then used to synthesize proteins (translation).

Key Equations and Concepts

• General formula for monosaccharides:

• Dehydration reaction (formation of maltose):

• Peptide bond formation:

• Phosphodiester bond (nucleic acids):

Additional info:

• Prokaryotes in the gut are essential for digestion and health; antibiotics can disrupt this balance, so 'gut culture' restores beneficial microbes.

• Protein folding is critical for function; misfolding can lead to diseases such as Alzheimer's, Parkinson's, and mad cow disease.