Water structure, Ionization, pH and Buffers

Why does water have a high heat capacity?

Strong, stable hydrogen bonding between electronegative atoms

Proton donor

Acids, electropositive center

Proton acceptors

Bases, electronegative center

What hydrogen bonding configuration is more stable?

Linear stronger than bent

At what temperature are all hydrogen bonds in water broken?

100^oC, only W1 present, no W5, at equilibrium with steam

What is the difference between a gas and vapor?

Vapor is at lower temperature, collection of water molecules

How many hydrogen bonds will liquid water have on average?

3.4, allows molecules to crowd together more effectively

How many hydrogen bonds will ice have?

4 bonds, more space in structure of ice

Thermal mass

Resistance to changes in temperature

What are the key properties of water?

• High heat capacity

• High boiling point relative to molecular weight

• High viscosity relative to its molecular weight

• Strong interactions with ionic molecules

• Special interactions with nonpolar molecules

How does water affect nucleophilic reactions?

Water deactivates nucleophilic reactions

What conditions are best for a nucleophilic reaction?

Polar organic solvents (DMF or THF)

How does water retard nucleophilic reactions?

Water crowds electron-rich and electron-deficient reactants, thereby deactivating them.

Why is it necessary for water to deactivate nucleophilic reactions in the body?

Prevents uncatalyzed reactions and toxic side reactions to occur, relies on enzymes, which are specific and controllable

How do enzymes increase reactivity so metabolism can proceed under physiologic conditions?

Lowers activation energy for certain reactions

What are the two vital roles of enzymes?

Binding and dehydrating reactant(s) and operating as on/off switches

Why do enzymes bind and dehydrate reactant(s)?

• Increases local concentration of reactants at active sites

• Orients substrate(s) to maximize reactivity

• Stabilizes reaction-transition states

• Makes reactions go much faster

What happens when enzymes are active?

Products are made

Why do we need enzymes to act as on/off switches?

To regulate reactions, minimize toxic side reactions

Hydrolysis

Breaking apart of molecules by H₂O

Autoprotolysis

Proton is transferred between 2 identical molecules: one H₂O acts as a Bronsted acid (proton donor) and the other H₂O acts as a Bronsted base (proton acceptor)

What are the products of a autoprotolysis reaction?

Hydronium ion (H₃O⁺) and Hydroxyl ion (OH^-)

How do protons move in water?

H⁺ never moves freely in water, “hops” from one water molecule to another

Why is proton “hopping” important?

Facilitated proton transfer, allows chain of rigid H-bonds to leave an active site on an enzyme

pH equation

pH = -log₁₀[H₃O⁺]

What is K_w equation?

K_w = [H₃O⁺][OH^-] = 10^-14 M²

Henderson-Hasselbalch Equation

pH = pKₐ + log([A⁻]/[HA])

When pH = pK_a…

[A^-] = [HA]

When pH = pK_a + 1…

[A^-] = 10 x [HA]

When pH = pK_a - 1…

[A^-] = 0.1 x [HA]

On the basic side of pK_a…

[HA] < [A^-]

On the acidic side of pK_a…

[HA] > [A^-]

Why is pH so relevant in biochemistry

Many metabolites have acid or base groups, enzymes have acids/bases in active sites, DNA and RNA are polyelectrolytes

Buffers

Weak acids and weak bases that help stabilize pH, by mixing a conjugate base and weak acid, forms a unit that resists changes in pH

At what pH are buffers most effective?

At a pH close to their pK_a, where there’s an equally large pool of both weak acid and its conjugate base

What are the principal buffers in humans?

Bicarbonate (HCO₃^1-/CO₃^2-), orthophosphate (H₂PO₃^1-/HPO₃^2-), ATP (HATP^3-/ATP^4-), Proteins (P—NH₃⁺/P—NH₂ & R—COOH/R—COO^-)

What enzyme catalyzes the bicarbonate buffer system

carbonic anhydrase