Acids and bases can be classified as proton donors and proton acceptors, respectively. This means that the conjugate base of a given acid will carry a net charge that is more negative than the corresponding acid. In biologically relavent compounds various weak acids and bases are encountered, e.g. the acidic and basic amino acids, nucleotides, phospholipids etc.

Weak acids and bases in solution do not fully dissociate and, therefore, there is an equilibrium between the acid and its conjugate base. This equilibrium can be calculated and is termed the equilibrium constant = K_a. This is also  referred to as the dissociation constant as it pertains to the dissociation of protons from acids and bases.

In the reaction of a weak acid:

HA <-----> A^- + H⁺

the equlibrium constant can be calculated from the following equation:

K_a = [H⁺][A^-]/[HA]

As in the case of the ion product:

pK_a = -logK_a

Therefore, in obtaining the -log of both sides of the equation describing the dissociation of a weak acid we arrive at the following equation:

-logK_a = -log[H⁺][A^-]/[HA]

Since as indicated above -logK_a = pK_a and taking into account the laws of logrithms:

pK_a = -log[H⁺] -log[A^-]/[HA]

pK_a = pH -log[A^-]/[HA]

From this equation it can be seen that the smaller the pK_a value the stronger is the acid. This is due to the fact that the stronger an acid the more readily it will give up H⁺ and, therefore, the value of [HA] in the above equation will be relatively small.

K_eq, K_w and pH

As H₂O is the medium of biological systems one must consider the role of this molecule in the dissociation of ions from biological molecules. Water is essentially a neutral molecule but will ionize to a small degree. This can be described by a simple equilibrium equation:

H₂O <-------> H⁺ + OH^-

This equilibrium can be calculated as for any reaction:

K_eq = [H⁺][OH^-]/[H₂O]

Since the concentration of H₂O is very high (55.5M) relative to that of the [H⁺] and [OH^-], consideration of it is generally removed from the equation by multiplying both sides by 55.5 yielding a new term, K_w:

K_w = [H⁺][OH^-]

This term is referred to as the ion product. In pure water, to which no acids or bases have been added:

K_w = 1 x 10^-14 M²

As K_w is constant, if one considers the case of pure water to which no acids or bases have been added:

[H⁺] = [OH^-] = 1 x 10^-7 M

This term can be reduced to reflect the hydrogen ion concentration of any solution. This is termed the pH, where:

pH = -log[H⁺]

Ampholytes, Polyampholytes, pI and Zwitterion

Many substances in nature contain both acidic and basic groups as well as many different types of these groups in the same molecule. (e.g. proteins). These are called ampholytes (one acidic and one basic group) or polyampholytes (many acidic and basic groups). Proteins contains many different amino acids some of which contain ionizable side groups, both acidic and basic. Therefore, a useful term for dealing with the titration of ampholytes and polyampholytes (e.g. proteins) is the isoelectric point, pI. This is described as the pH at which the effective net charge on a molecule is zero.

For the case of a simple ampholyte like the amino acid glycine the pI, when calculated from the Henderson-Hasselbalch equation, is shown to be the average of the pK for the a-COOH group and the pK for the a-NH₂ group:

pI = [pK_a-(COOH) + pK_a-(NH3⁺₎]/2

For more complex molecules such as polyampholytes the pI is the average of the pK_a values that represent the boundaries of the zwitterionic form of the molecule. The pI value, like that of pK, is very informative as to the nature of different molecules. A molecule with a low pI would contain a predominance of acidic groups, whereas a high pI indicates predominance of basic groups.

Pentose Phosphate Pathway (Hexose Monophosphate Shunt)

The pentose phosphate pathway is primarily an anabolic pathway that utilizes the 6 carbons of glucose to generate 5 carbon sugars and reducing equivalents. However, this pathway does oxidize glucose and under certain conditions can completely oxidize glucose to CO₂ and water. The primary functions of this pathway are:

• To generate reducing equivalents, in the form of NADPH, for reductive biosynthesis reactions within cells.
• To provide the cell with ribose-5-phosphate (R5P) for the synthesis of the nucleotides and nucleic acids.
• Although not a significant function of the PPP, it can operate to metabolize dietary pentose sugars derived from the digestion of nucleic acids as well as to rearrange the carbon skeletons of dietary carbohydrates into glycolytic/gluconeogenic intermediates

Enzymes that function primarily in the reductive direction utilize the NADP⁺/NADPH cofactor pair as co-factors as opposed to oxidative enzymes that utilize the NAD⁺/NADH cofactor pair. The reactions of fatty acid biosynthesis and steroid biosynthesis utilize large amounts of NADPH. As a consequence, cells of the liver, adipose tissue, adrenal cortex, testis and lactating mammary gland have high levels of the PPP enzymes. In fact 30% of the oxidation of glucose in the liver occurs via the PPP. Additionally, erythrocytes utilize the reactions of the PPP to generate large amounts of NADPH used in the reduction of glutathione. The conversion of ribonucleotides to deoxyribonucleotides (through the action of ribonucleotide reductase) requires NADPH as the electron source, therefore, any rapidly proliferating cell needs large quantities of NADPH.

Regulation: Glucose-6-phosphate Dehydrogenase is the committed step of the Pentose Phosphate Pathway. This enzyme is regulated by availability of the substrate NADP⁺. As NADPH is utilized in reductive synthetic pathways, the increasing concentration of NADP⁺ stimulates the Pentose Phosphate Pathway, to replenish NADPH

Clinical significance

Primary hyperparathyroidism is due to autonomous, abnormal hypersecretion of PTH in the parathyroid gland

Secondary hyperparathyroidism is an appropriately high PTH level seen as a physiological response to hypocalcemia.

A low level of PTH in the blood is known as hypoparathyroidism and is most commonly due to damage to or removal of parathyroid glands during thyroid surgery.

Applications of the Henderson-Hasselbalch equation

• Calculate the ratio of CB to WA, if pH is given

• Calculate the pH, if ratio of CB to WA is known

• Calculate the pH of a weak acid solution of known concentration

• Determine the pKa of a WA-CB pair

• Calculate change in pH when strong base is added to a solution of weak acid. This is represented in a titration curve

• Calculate the pI