The Molecules of Cells: Structure and Function of Biomolecules

Chapter 3: The Biomolecules in Cells

Organic Compounds

Organic compounds are the foundation of all living organisms, characterized by the presence of carbon and hydrogen atoms. The versatility of carbon allows for a variety of molecular structures, which form the backbone of biological molecules.

• Carbon Skeletons: Can be straight, branched, or arranged in rings; may contain single or double bonds.

• Hydrocarbons: Molecules composed only of hydrogen and carbon (e.g., methane, ethane, propane).

• Isomers: Compounds with the same molecular formula but different structural arrangements, leading to different properties.

Example: Butane (C4H10) and isobutane are isomers with distinct structures and properties.

The Basic Hydrocarbons

Hydrocarbons are the simplest organic molecules and serve as the building blocks for more complex biomolecules.

• Methane (CH4): Simplest hydrocarbon, a single carbon atom bonded to four hydrogens.

• Ethane (C2H6): Two carbon atoms bonded together, each with three hydrogens.

• Propane (C3H8): Three carbon atoms in a chain, each bonded to hydrogen atoms.

The Isomers

Isomers are molecules with the same chemical formula but different structural arrangements, resulting in different chemical and physical properties.

• Example: Butane (CH3-CH2-CH2-CH3) and isobutane (CH(CH3)3).

The Aromatic Hydrocarbons

Aromatic hydrocarbons contain ring-shaped carbon skeletons and often have distinctive aromas.

• Cyclohexane (C6H12): Saturated ring structure.

• Benzene (C6H6): Unsaturated ring with alternating double bonds, known for its stability and aromaticity.

The Chemical Groups

Certain chemical groups, called functional groups, are critical for the function and structure of biomolecules. They influence the chemical reactivity and solubility of organic molecules.

• Hydrophilic (water-attracting) functional groups:

  • Hydroxyl (-OH)

  • Carbonyl (C=O)

  • Carboxyl (-COOH)

  • Amino (-NH2)

  • Phosphate (-OPO32-)

• Hydrophobic (water-repelling) structural group: Methyl (-CH3)

Reactions to Make or Break Polymers

Biological macromolecules are assembled and disassembled through specific chemical reactions involving water.

• Dehydration Reaction: Monomers are joined together by removing a molecule of water, forming polymers.

• Hydrolysis: Polymers are broken down into monomers by the addition of water.

Equation (Dehydration): $\text{Monomer}_1 + \text{Monomer}_2 \xrightarrow{\text{Dehydration}} \text{Polymer} + H_2O$

Equation (Hydrolysis): $\text{Polymer} + H_2O \xrightarrow{\text{Hydrolysis}} \text{Monomer}_1 + \text{Monomer}_2$

Carbohydrates

Carbohydrates are essential biomolecules that serve as energy sources and structural components in cells.

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

• Disaccharides: Formed by joining two monosaccharides via dehydration (e.g., maltose, sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose, chitin).

Example: Two glucose molecules join to form maltose; glucose and fructose combine to make sucrose.

Lipids

Lipids are hydrophobic molecules that play roles in energy storage, membrane structure, and signaling.

• Fats (Triglycerides): Composed of three fatty acids linked to a glycerol molecule.

• Fatty Acids: Hydrocarbon chains (16-18 carbons) with a carboxyl group.

• Unsaturated Fatty Acids: Contain one or more C=C double bonds; fewer hydrogens.

• Saturated Fatty Acids: No double bonds; all carbons saturated with hydrogen.

• Hydrogenation: Process of converting unsaturated fats to saturated fats by adding hydrogen.

• Trans Fats: Produced by partial hydrogenation; associated with health risks.

• Phospholipids: Two fatty acids and a phosphate group attached to glycerol; form cell membranes with hydrophilic heads and hydrophobic tails.

• Steroids: Lipids with four fused rings; cholesterol is a key example, serving as a precursor for other steroids.

Type	Structure	Function
Fat (Triglyceride)	Glycerol + 3 fatty acids	Energy storage
Phospholipid	Glycerol + 2 fatty acids + phosphate	Cell membrane structure
Steroid	Four fused rings	Hormones, membrane component

Example: Cholesterol is essential for animal cell membranes but can cause atherosclerosis at high levels.

Additional info: Anabolic steroids mimic testosterone and are banned due to harmful side effects.

Proteins

Proteins are polymers of amino acids that perform a vast array of functions in cells, including catalysis, transport, defense, and structure.

• Amino Acids: 20 types, each with an amino group (-NH2), carboxyl group (-COOH), and variable R group.

• Peptide Bonds: Covalent bonds formed by dehydration between amino acids.

• Polypeptides: Chains of amino acids; sequence determines protein structure and function.

• Protein Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Hydrogen bonding forms alpha-helices and beta-sheets.

  • Tertiary: Three-dimensional folding due to R group interactions.

  • Quaternary: Multiple polypeptide chains assemble into a functional protein.

• Denaturation: Loss of structure and function due to heat, pH changes, or chemicals.

• Types of Proteins: Enzymes, transport proteins, antibodies, receptors, structural proteins, storage proteins.

Protein Type	Function
Enzyme	Catalyzes chemical reactions
Transport	Moves substances across membranes
Defensive	Antibodies for immune response
Receptor	Receives signals on cell membranes
Structural	Provides support (e.g., collagen)
Storage	Stores amino acids or nutrients

Nucleic Acids

Nucleic acids store and transmit genetic information. They are polymers made of nucleotide monomers.

• Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• Nucleotide Structure: Sugar (deoxyribose or ribose), phosphate group, and nitrogenous base.

• Nitrogenous Bases:

  • Purines: Adenine (A), Guanine (G)

  • Pyrimidines: Thymine (T, in DNA), Uracil (U, in RNA), Cytosine (C)

• Base Pairing: Adenine pairs with Thymine (DNA) or Uracil (RNA); Guanine pairs with Cytosine.

• Polymerization: Nucleotides are joined by dehydration reactions to form polynucleotides.

Equation (Nucleotide Polymerization): $\text{Nucleotide}_1 + \text{Nucleotide}_2 \xrightarrow{\text{Dehydration}} \text{Polynucleotide} + H_2O$

Example: Genes are segments of DNA that code for the amino acid sequence of proteins.