chapter 2 pt 2

Chapter 2 Part 2: Water, Weak Bonds, and the Generation of Order Out of Chaos

• This chapter explores the importance of water and weak bonds in biological systems, focusing on how order arises from seemingly chaotic interactions.

Learning Objectives

• Understand the Second Law of Thermodynamics and its application to hydrophobic molecules.
• Describe the importance of hydrophobic interactions in membrane and protein formation.
• Define pH and understand the pH scale.
• Understand the ion product of water and its calculation.
• Define and identify conjugate acid-base pairs.

2.4 Hydrophobic Molecules Cluster Together

• The Second Law of Thermodynamics dictates that the total entropy of a system and its surroundings always increases in a spontaneous process.
• Entropy is a measure of randomness.
• Hydrophobic molecules are typically nonpolar or uncharged.
• These molecules do not interact with water.
• They cluster together in water, a phenomenon called the hydrophobic effect.
• Clustering releases water molecules, thus increasing entropy and is spontaneous.
• No energy input is required for this process

Membrane Formation

• Phospholipids are amphipathic molecules.
• The hydrophilic head groups of phospholipids interact with water, while the hydrophobic tails cluster together in the interior of the membrane.
• The hydrophobic interactions are stabilized by van der Waals forces.

Protein Folding

• Hydrophobic amino acids cluster together to facilitate protein folding.
• Other interactions like hydrogen bonds and van der Waals forces also play a role in the folding process.

2.5 pH Is an Important Parameter of Biochemical Systems

• pH measures the hydrogen ion concentration of a solution.
• pH = -log[H+]
• pH scale ranges from 0 to 14.
• pH < 7 is acidic, pH = 7 is neutral, and pH > 7 is alkaline.
• Changes in pH can affect ionic bonds and hydrogen bonds, thus altering the structure and function of biomolecules like proteins.

Water Ionization

• Water ionizes to a small extent: H₂O ⇌ H⁺ + OH⁻
• Ion Product of Water (Kw): Kw = [H⁺][OH⁻] = 1.0 x 10⁻¹⁴ M

Conjugate Acid-Base Pairs

• Acids are proton donors, and bases are proton acceptors.
• Conjugate acid-base pairs arise when an acid donates a proton to form its conjugate base, or when a base accepts a proton to form its conjugate acid.
• Example: Acetic acid (CH₃COOH) ionizes to form acetate (CH₃COO⁻) and a hydrogen ion (H⁺).

Buffers

• Conjugate acid-base pairs act as buffers, resisting changes in pH.
• Buffering capacity is greatest near the pKₐ of the weak acid component.
• pKₐ is the pH at which the acid component is half-dissociated

Importance of pH

• Understanding how buffers wok and maintain pH is critical for studying molecules in vitro and understanding cellular processes in vivo, where maintaining pH is essential for cell survival.