Biomolecules

Biomolecules are the molecular machinery of life—carbohydrates, proteins, nucleic acids, lipids, vitamins, and hormones. They're synthesized, transported, and degraded in orchestrated chemical reactions within living cells. Understanding their structures reveals how organisms store energy (carbohydrates), build tissues (proteins), pass genetic information (nucleic acids), and regulate processes (hormones, enzymes). Chemistry and biology intertwine at the molecular level: proteins are polymers of amino acids connected by peptide bonds; nucleic acids are polymers of nucleotides; carbohydrates are polymers of simple sugars. This chapter explores the architecture and chemistry of life's building blocks.

Carbohydrates: The Energy Source

Carbohydrates are organic compounds with the general formula Cₓ(H₂O)ₓ—though not all compounds fitting this formula are carbohydrates, and not all carbohydrates fit it exactly. They're broadly classified by their complexity.

Monosaccharides: The Basic Unit

Monosaccharides are simple sugars with 3-7 carbons. The most important is glucose (C₆H₁₂O₆), the universal fuel of cells.

Structure: Glucose exists in two forms:

• Linear form (open-chain, aldehyde): CHO (carbonyl at position 1) followed by 5 CHOH groups
• Cyclic form (hemiacetal): The aldehyde reacts with the hydroxyl on carbon 5, forming a six-membered ring (pyranose)

In aqueous solution, glucose overwhelmingly exists as the cyclic form. The ring can close in two ways, creating α-glucose and β-glucose (anomers), differing only in the configuration at the anomeric carbon (C1).

Other monosaccharides:

• Fructose (fruit sugar): A ketohexose; sweeter than glucose
• Galactose: Differs from glucose only at C4; important in lactose
• Ribose and Deoxyribose: Five-carbon sugars (pentoses) in RNA and DNA

Disaccharides: Two Units Joined

Disaccharides form when two monosaccharides join via a glycosidic bond—a C-O-C link between the anomeric carbon of one sugar and a hydroxyl of another.

Common disaccharides:

• Sucrose (table sugar): Glucose + fructose; no free anomeric carbon, so it doesn't reduce Tollens or Fehling reagent (non-reducing sugar)
• Lactose (milk sugar): Glucose + galactose; the β-1,4-glycosidic bond; a reducing sugar
• Maltose (malt sugar): Glucose + glucose; the α-1,4-glycosidic bond; a reducing sugar

Polysaccharides: Polymers of Monosaccharides

Polysaccharides are long chains of monosaccharides. Three are crucial:

Starch: A polymer of glucose with two components:

• Amylose: Unbranched polymer of glucose (α-1,4-glycosidic bonds)
• Amylopectin: Branched polymer (mostly α-1,4 bonds, with α-1,6 branches every 25-30 units)

Starch is the energy storage carbohydrate in plants.

Cellulose: A polymer of glucose with β-1,4-glycosidic bonds. The β-linkage (different from starch's α-linkage) makes cellulose linear and rigid. Humans lack the enzyme cellulase, so we can't digest cellulose, but it's essential dietary fiber. Cows and termites have cellulase-producing bacteria in their guts, allowing them to digest plants.

Glycogen: The animal equivalent of starch; a branched polymer of glucose (like amylopectin but more highly branched). Stored in liver and muscles; rapidly mobilized when energy is needed.

Function of Carbohydrates

Energy: Glucose oxidation releases energy; cells capture it as ATP.

Structural: Cellulose in plant cell walls; chitin (a modified carbohydrate) in arthropod exoskeletons.

Recognition: Carbohydrates on cell surfaces are "ID cards" for cells; immune cells recognize these patterns.

Proteins: The Builders

Proteins are polymers of amino acids—organic compounds with an amino group (NH₂), a carboxylic acid group (COOH), a hydrogen, and a side chain (R) bonded to a central carbon (α-carbon).

Amino Acids: The 20 Standard Varieties

Twenty standard amino acids occur in proteins, differing only in their R groups:

Nonpolar (hydrophobic) R groups: glycine (R = H), alanine (R = CH₃), valine, leucine, isoleucine (branched alkyl chains), phenylalanine (aromatic), proline (cyclic), methionine, tryptophan.

Polar (hydrophilic) R groups: serine, threonine, tyrosine, asparagine, glutamine, cysteine.

Charged (hydrophilic) R groups:

• Acidic: aspartate, glutamate (negatively charged)
• Basic: lysine, arginine, histidine (positively charged)

Peptide Bonds and Protein Structure

Amino acids join through peptide bonds (amide linkages formed between the carboxyl of one amino acid and the amino of the next). This creates a linear chain with a backbone of C-N-C-C-N-C and variable R groups hanging off.

Levels of protein structure:

Primary Structure: The sequence of amino acids. A protein with 100 amino acids has 20¹⁰⁰ possible sequences! The sequence determines all higher structures.

Secondary Structure: Local folding patterns:

• α-helix: A right-handed spiral where the backbone coils and hydrogen bonds form between C=O of one residue and N-H four residues down
• β-sheet: Extended strands aligned side-by-side with hydrogen bonds between adjacent strands
• Loops and turns: Unstructured regions connecting secondary structure elements

Tertiary Structure: The overall 3D shape. Determined by:

• Hydrophobic interactions (nonpolar R groups cluster inside, away from water)
• Hydrogen bonds (between R groups and backbone)
• Disulfide bonds (between two cysteine residues: -S-S- cross-links)
• Ionic interactions (between charged R groups)

Quaternary Structure: Multiple protein chains associating. Hemoglobin is four subunits (two α, two β chains) cooperating to bind oxygen.

Functions of Proteins

Enzymes: Catalyze biochemical reactions with extraordinary specificity.

Transport: Hemoglobin transports O₂; albumin carries fatty acids.

Structure: Collagen (in connective tissue), keratin (in hair), elastin (in ligaments).

Defense: Antibodies recognize and neutralize pathogens.

Regulation: Hormones (insulin, growth hormone) regulate physiological processes.

Nucleic Acids: Information Storage

Nucleic acids (DNA and RNA) store genetic information and direct protein synthesis. They're polymers of nucleotides.

Nucleotide Structure

Each nucleotide consists of three parts:

1. Nitrogenous base: Purines (adenine, guanine) or pyrimidines (cytosine, thymine in DNA; cytosine, uracil in RNA)
2. Five-carbon sugar: Ribose (RNA) or deoxyribose (DNA; lacks one oxygen at C2)
3. Phosphate group: Links nucleotides together

DNA vs. RNA

DNA (Deoxyribonucleic Acid):

• Contains deoxyribose and thymine
• Double-stranded helix (Watson-Crick base pairing: A-T, G-C)
• Stable; stores genetic information
• Mostly in nucleus

RNA (Ribonucleic Acid):

• Contains ribose and uracil (instead of thymine)
• Usually single-stranded
• Less stable; diverse roles (mRNA carries genetic information from DNA; tRNA brings amino acids; rRNA part of ribosomes)

DNA Structure: The Double Helix

DNA's elegance lies in its structure. Two sugar-phosphate backbones wind around each other in a helix, with base pairs (A-T, G-C) hydrogen-bonded inside. The structure immediately suggests replication: each strand serves as a template for synthesizing a new complementary strand.

Genetic Code and Protein Synthesis

DNA encodes proteins through the genetic code: each three nucleotides (codon) specify an amino acid (or stop signal). mRNA copies DNA; ribosomes read mRNA and use tRNA to assemble amino acids into proteins. This central dogma (DNA → RNA → Protein) governs how genetic information flows.

Lipids: Varied Roles

Lipids are diverse molecules largely hydrophobic (fatty). Key types:

Triglycerides (Fats and Oils): Esters of glycerol and three fatty acids. Packed with energy (more than twice that of carbohydrates by mass). Saturated fats (no C=C double bonds) are solid; unsaturated fats (with C=C) are liquid.

Phospholipids: Like triglycerides but with a phosphate group instead of one fatty acid. Amphipathic (hydrophilic head, hydrophobic tail); form the lipid bilayer of cell membranes.

Cholesterol: A sterol; regulates membrane fluidity; precursor for steroid hormones.

Waxes: Very long-chain fatty acids esterified with long-chain alcohols. Protective coatings on skin, feathers, plant leaves.

Vitamins: Essential Micronutrients

Vitamins are organic compounds required in small amounts for normal metabolism. Many are coenzymes (helpers for enzymes).

Water-soluble vitamins (B-complex, vitamin C): Not stored; must be regularly consumed.

Fat-soluble vitamins (A, D, E, K): Stored in fatty tissues; can accumulate to toxic levels if over-consumed.

Hormones: Chemical Messengers

Hormones are signaling molecules regulating physiological processes:

Steroid hormones (e.g., testosterone, estrogen): Lipid-derived; cross cell membranes.

Protein hormones (e.g., insulin, growth hormone): Water-soluble; act on cell surface receptors.

Amino acid-derived hormones (e.g., epinephrine, thyroid hormone): Modified amino acids or small peptides.

Socratic Questions

1. Why can humans digest starch (α-1,4-glycosidic bonds) but not cellulose (β-1,4-glycosidic bonds), even though both are polymers of glucose?

1. Proteins fold such that nonpolar amino acids hide inside and polar/charged ones face water. Why is this arrangement thermodynamically favorable?

1. In DNA, each base pair has a specific pairing rule (A-T, G-C). How does this enable accurate replication and why is hydrogen bonding (not covalent bonding) used for base pairing?

1. Unsaturated fats have C=C double bonds while saturated fats don't. How does this structural difference affect physical state (liquid vs. solid) at room temperature?

1. The genetic code uses 64 codons to specify 20 amino acids. Why is the code "degenerate" (multiple codons for one amino acid), and how might this reduce the impact of mutations?

Related Topics

Organic Chemistry Fundamentals - Polymers and functional groups Amines - Amino acids and their chemistry Aldehydes, Ketones and Carboxylic Acids - Carbonyl groups in sugars and proteins Biochemistry - Metabolic pathways and enzyme kinetics