The Chemistry of the Cell

Introduction

This chapter explores the chemical foundations of cell biology, focusing on the unique properties of carbon, water, biological membranes, and the synthesis of macromolecules. Understanding these principles is essential for grasping how cells function at the molecular level.

Characteristics of Carbon

Valence and Bonding

• Carbon has a valence of 4, allowing it to form four covalent bonds with other atoms, including hydrogen, oxygen, nitrogen, and sulfur.

• This versatility enables the formation of a wide variety of organic molecules essential for life.

Covalent Bonds

• Single bonds involve one pair of shared electrons, double bonds involve two pairs, and triple bonds involve three pairs.

• Double and triple bonds are more stable and have higher bond energies than single bonds.

Bond Energies

• Bond energy is the amount of energy required to break a bond between two atoms.

• Examples of bond energies (in kcal/mol): C—C: 83, C—N: 70, C—O: 84, C—H: 99, C═C: 146, C≡C: 212

• Higher bond energy means greater stability.

Breaking Covalent Bonds: UV Light

• Ultraviolet (UV) light has enough energy to break covalent bonds, which can damage biological molecules such as DNA.

• Visible and infrared light do not have sufficient energy to break these bonds.

Hydrocarbons

• Hydrocarbons are chains or rings composed only of carbon and hydrogen.

• They serve as the backbone for many biological molecules.

Functional Groups

• Biological molecules often contain functional groups that confer specific chemical properties (e.g., carboxyl, amino, phosphate, hydroxyl).

• These groups determine the reactivity and interactions of molecules.

Stereoisomers

• Stereoisomers are molecules with the same molecular formula but different spatial arrangements of atoms.

• Asymmetric carbons (chiral centers) lead to nonsuperimposable mirror images (enantiomers).

• The number of possible stereoisomers is given by , where n is the number of asymmetric carbons.

Characteristics of Water

Polarity and Hydrogen Bonding

• Water is a polar molecule, with a partial negative charge on oxygen and partial positive charges on hydrogen atoms.

• This polarity allows water molecules to form hydrogen bonds with each other and with other polar molecules.

Cohesion and Surface Tension

• Hydrogen bonding gives water high cohesion, resulting in high surface tension.

• This property allows small organisms to move on the surface of water.

Temperature Stabilization

• Water has a high specific heat and heat of vaporization, meaning it changes temperature slowly and helps stabilize cellular environments.

• This is due to the energy required to break hydrogen bonds.

Water as a Solvent

• Water is the universal solvent in biology due to its polarity.

• Hydrophilic (water-loving) substances dissolve easily, while hydrophobic (water-fearing) substances do not.

• Ions and polar molecules are surrounded by spheres of hydration when dissolved in water.

Selectively Permeable Membranes

Membrane Structure

• Biological membranes are composed of phospholipids, glycolipids, membrane proteins, and sterols (cholesterol in animals, ergosterol in fungi, phytosterol in plants).

• Phospholipids are amphipathic, containing both hydrophilic (polar) heads and hydrophobic (nonpolar) tails.

• This amphipathic nature drives the formation of the lipid bilayer, which is the fundamental structure of cell membranes.

Membrane Permeability

• Membranes are selectively permeable:

  • Small, nonpolar molecules (e.g., O2, CO2) can diffuse freely.

  • Small, uncharged polar molecules (e.g., H2O, ethanol) can pass to some extent.

  • Large polar molecules and ions are generally impermeable and require transport proteins.

Transport Across Membranes

• Ions and most polar molecules require specific transporters (channels or carriers) to cross the membrane.

• Transporters provide hydrophilic pathways or actively move substances across the membrane.

Synthesis by Polymerization of Small Molecules

Macromolecules and Polymerization

• Macromolecules such as proteins, nucleic acids, and polysaccharides are polymers formed by the polymerization of monomers.

• Lipids are also important macromolecules, though not always true polymers.

Types of Macromolecules

• Nucleic acids are informational polymers made of nucleotides.

• Proteins are polymers of amino acids with diverse functions.

• Polysaccharides are polymers of monosaccharides, serving structural and storage roles.

Polymerization Mechanism

• Macromolecules are synthesized by condensation reactions, which join monomers and release water.

• Monomers are often activated by coupling to carrier molecules (e.g., tRNA for amino acids, ADP/UDP for sugars).

• ATP is typically required for activation.

• Polymers have directionality, meaning the two ends are chemically distinct.

Carrier Molecules

• Carrier molecules such as tRNA, ADP, and UDP facilitate the activation and transfer of monomers during polymerization.

Condensation and Hydrolysis

• Condensation reactions build polymers by removing water.

• Hydrolysis reactions break polymers into monomers by adding water.

Self-Assembly and Protein Folding

Forces in Protein Folding

• Protein folding is driven by hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions.

• Hydrophobic groups tend to cluster away from water, stabilizing the protein's interior.

Protein Folding and Chaperones

• Proteins can fold spontaneously into their functional conformations.

• Denaturation is the loss of structure and function; renaturation is the regaining of structure and function under suitable conditions.

• Chaperone proteins assist in the proper folding of other proteins, preventing misfolding and aggregation.

Concept Checks and Applications

Key Questions

• What is an amphipathic molecule? An amphipathic molecule contains both hydrophilic and hydrophobic regions, crucial for membrane structure.

• Why are membranes lipid bilayers? The bilayer arrangement shields hydrophobic tails from water while exposing hydrophilic heads, forming a stable barrier.

• What does selective permeability mean? Membranes allow some substances to cross more easily than others, maintaining cellular homeostasis.

• Drug delivery challenge: Large, polar drugs may require encapsulation in liposomes or conjugation to carrier molecules to cross membranes.

Experimental Observations

• Mixing RNA and coat protein from the same TMV strain forms infectious virions, indicating self-assembly.

• Mixing RNA from one strain with protein from another yields virions with the RNA's strain identity, showing RNA determines viral specificity.

• Coat protein monomers can self-assemble into helical structures even without RNA, demonstrating the inherent self-assembly properties of proteins.