Integrated SequencePhysics Chemistry Organic Biology

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Special points of emphasis


Periodic Properties

The Chemical Bond

Functional Groups in Organic Chemistry


Chemical Thermodynamics and the Equilibrium State


Acids and Bases

Organic Acids and Bases

In aqueous solution, carboxylate anions are stabilized both by the electron delocalization corresponding to resonance as well as solvation by water.

Electronegative substituents, particularly those bonded to the α carbon, such as in trifluoroacetic acid, significantly increase the acidity of a carboxylic acid because of stabilization by induction.

Acids and Bases

Organic Acids and Bases

Bioenergetics and Cellular Respiration

Integration of Metabolism

Carboxylic acids are centrally important in biochemistry. Many important substances of oxidative metabolism are carboxylic acids, such as pyruvic acid or lactic acid.

The pH environment in which most biological processes occur is close to 7. Most carboxylic acids have ionization constants on the order of Ka = 10-5 (pKa = 5). This means that in the biochemical context, these substances exist much more prominently as their carboxylate conjugate bases.

Do you remember why you know this? The Henderson-Hasselbalch equation tells us that a weak acid with a pKa equal to 5 within a pH environment of 7 will exist 100 to 1 in the conjugate base form.

Because the more common physiological form is the carboxylate anion, biochemists much more commonly refer to 'pyruvate' and 'lactate' than to 'pyruvic acid' or 'lactic acid'.

Organic Acids and Bases


The Digestive System and Nutrition

While all amino acids contain a carboxyl group bonded to the central carbon, in peptide bond formation, this carboxyl group becomes part of an amide linkage and loses its ionizability.

Aspartic acid and glutamic acid, however, possess carboxyl groups in their side chains. Here's an interesting discussion involving aspartic acid representative of the kinds of issues that may arise in an MCAT passage:

A protease is a digestive enzyme designed to break down proteins. The acid protease, pepsin, contains two aspartate residues within its active site. This leads to an interesting control mechanism for pepsin activity in addition to the zymogenic control mechanism everyone is familiar with (Pepsin is stored as the inactive precursor pepsinogen ('zymogen' is the name for an inactive enzyme precursor)). The additional interesting control mechanism for pepsin is that it only functions within the acidic environment of the stomach. For the enzyme to be active, one of the side chains of aspartate must be ionized, the other not. This means that the optimum pH of pepsin is quite acidic, close to the pKa of the side-chains. Can you reason why the pH must be near the pKa using Henderson-Hasselbalch?

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