The Structure and Function of Large Biological Molecules

Chapter 5: The Structure & Function of Large Biological Molecules

Overview: The Molecules of Life

All living organisms are composed of four major classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids. These molecules are essential for structure, function, and regulation of the body's tissues and organs. Within cells, small organic molecules are joined together to form larger molecules, known as macromolecules, which are composed of thousands of covalently connected atoms. The structure of these molecules is closely related to their function.

• Macromolecules: Large molecules made up of smaller subunits (monomers) joined by covalent bonds.

• Molecular structure and function are inseparable: The shape and arrangement of atoms in a molecule determine its role in the cell.

Monomers, Polymers, and Macromolecules

Definitions and Relationships

Most macromolecules are polymers, built from repeating units called monomers. The exception is lipids, which do not form true polymers.

• Monomer: A small organic molecule that serves as a building block for polymers.

• Polymer: A long molecule consisting of many similar or identical monomers linked by covalent bonds.

• Macromolecule: A giant molecule formed by the joining of smaller molecules, usually by a condensation reaction.

Examples:

• Amino acid → peptide → polypeptide → protein (increasing size and complexity)

• Lipids do not have true monomers or polymers.

Polymer Formation and Breakdown

Polymers are synthesized and broken down by two main types of reactions:

• Dehydration Synthesis (Condensation Reaction): Monomers are joined together by covalent bonds, with the removal of a water molecule. This process builds polymers.

• Hydrolysis: Polymers are broken down into monomers by the addition of a water molecule, breaking the covalent bond.

Enzymes are macromolecules that speed up both dehydration and hydrolysis reactions.

Summary Table: Polymerization and Depolymerization

Process	Purpose	Reaction	Example
Dehydration Synthesis	Build polymers	Monomer + Monomer → Polymer + H2O	Formation of maltose from two glucose molecules
Hydrolysis	Break down polymers	Polymer + H2O → Monomer + Monomer	Digestion of starch into glucose

Carbohydrates

Functions and Types

Carbohydrates serve as fuel (short-term energy) and as building material (structural support) in living organisms. They include simple sugars and their polymers.

• General formula: $C_{n}H_{2n}O_{n}$ (e.g., glucose: $C_6H_{12}O_6$)

• Monosaccharides: Simple sugars (e.g., glucose, ribose)

• Disaccharides: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose, maltose)

• Polysaccharides: Polymers of many monosaccharides (e.g., starch, glycogen, cellulose, chitin)

Classification of Monosaccharides

• By the location of the carbonyl group:

  • Aldose: Carbonyl group at the end of the carbon skeleton

  • Ketose: Carbonyl group within the carbon skeleton

• By the number of carbons in the skeleton (triose, pentose, hexose, etc.)

Table: Examples of Monosaccharides

Type	Example	Formula
Triose (3C)	Glyceraldehyde (aldose), Dihydroxyacetone (ketose)	$C_3H_6O_3$
Pentose (5C)	Ribose (aldose), Ribulose (ketose)	$C_5H_{10}O_5$
Hexose (6C)	Glucose, Galactose (aldoses), Fructose (ketose)	$C_6H_{12}O_6$

Disaccharides and Glycosidic Linkages

• Formed by joining two monosaccharides via a glycosidic linkage (covalent bond).

• Examples:

  • Maltose: glucose + glucose

  • Sucrose: glucose + fructose

Polysaccharides: Storage and Structural Roles

• Storage polysaccharides:

  • Starch: Main storage form in plants; composed of α-glucose monomers.

  • Glycogen: Main storage form in animals; highly branched polymer of glucose.

• Structural polysaccharides:

  • Cellulose: Major component of plant cell walls; composed of β-glucose monomers.

  • Chitin: Found in the exoskeleton of arthropods and cell walls of fungi.

Note: The difference between starch and cellulose is the type of glucose monomer and the glycosidic linkage (α vs. β).

Lipids

Characteristics and Types

Lipids are a diverse group of hydrophobic molecules that do not form true polymers. Their unifying feature is their insolubility in water due to a high proportion of nonpolar hydrocarbon bonds.

• Fats (Triglycerides): Composed of glycerol and three fatty acids joined by ester linkages. Serve as energy storage.

• Phospholipids: Major component of cell membranes; consist of a hydrophilic head and two hydrophobic tails.

• Steroids: Characterized by a carbon skeleton with four fused rings (e.g., cholesterol, hormones).

Saturated vs. Unsaturated Fats

• Saturated fats: No double bonds between carbon atoms; solid at room temperature; found in animal fats.

• Unsaturated fats: One or more double bonds (cis or trans); liquid at room temperature; found in plant oils.

• Trans fats: Produced by hydrogenation; associated with increased risk of cardiovascular disease.

Table: Comparison of Fatty Acids

Type	Bonding	Physical State	Source
Saturated	All single bonds	Solid	Animal fats (butter, lard)
Unsaturated (cis)	One or more cis double bonds	Liquid	Plant oils (olive oil, corn oil)
Trans	Trans double bonds (artificial)	Solid/semi-solid	Hydrogenated oils

Proteins

Structure and Function

Proteins are the most diverse macromolecules, accounting for more than 50% of the dry mass of most cells. They are composed of amino acids and perform a wide variety of functions.

• Enzymatic: Catalyze biochemical reactions (e.g., lactase)

• Defensive: Protect against disease (e.g., antibodies)

• Storage: Store amino acids (e.g., casein in milk)

• Transport: Move substances (e.g., hemoglobin)

• Hormonal: Coordinate activities (e.g., insulin)

• Receptor: Respond to chemical stimuli

• Contractile and Motor: Movement (e.g., actin, myosin)

• Structural: Support (e.g., keratin, collagen)

Amino Acids and Peptide Bonds

• Amino acids: Organic molecules with an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable side chain (R group).

• Peptide bond: Covalent bond formed between the amino group of one amino acid and the carboxyl group of another.

• Polypeptides are polymers of amino acids; a protein consists of one or more polypeptides folded into a specific shape.

Levels of Protein Structure

• Primary structure: Sequence of amino acids in a polypeptide chain.

• Secondary structure: Local folding into α-helices and β-pleated sheets, stabilized by hydrogen bonds.

• Tertiary structure: Overall 3D shape of a polypeptide, stabilized by interactions among R groups (hydrogen bonds, ionic bonds, disulfide bridges, van der Waals interactions).

• Quaternary structure: Association of two or more polypeptide chains into a functional protein.

Protein Folding and Denaturation

• Proper folding is assisted by chaperonins.

• Proteins can denature (lose their shape and function) due to changes in pH, temperature, or other environmental factors.

Nucleic Acids

Structure and Function

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

• DNA: Double-stranded helix; stores genetic information; bases: adenine (A), guanine (G), cytosine (C), thymine (T); sugar: deoxyribose.

• RNA: Single-stranded; involved in protein synthesis; bases: adenine (A), guanine (G), cytosine (C), uracil (U); sugar: ribose.

Nucleotides and Nucleic Acid Structure

• Nucleotide: Monomer of nucleic acids; consists of a nitrogenous base, a pentose sugar, and a phosphate group.

• Nucleoside: Nitrogenous base + sugar (no phosphate).

• Nucleotides are joined by phosphodiester bonds between the 3' hydroxyl of one sugar and the 5' phosphate of the next.

• DNA strands are antiparallel and held together by hydrogen bonds between complementary bases (A-T, G-C).

Table: Nitrogenous Bases

Type	Bases	Structure
Pyrimidines	Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA)	Single ring
Purines	Adenine (A), Guanine (G)	Double ring

Key Distinctions and Concepts

• Distinguish between monosaccharides, disaccharides, and polysaccharides.

• Distinguish between saturated and unsaturated fats, and between cis and trans fat molecules.

• Describe the four levels of protein structure and how small changes can affect protein function.

• Distinguish between pyrimidine and purine, nucleotide and nucleoside, ribose and deoxyribose, and the 5’ end and 3’ end of a nucleotide.