Describe the three charge properties of amino acids and how they influence biochemical interactions within the body.

Question

Amino acids can be broken into three distinct groups based on net charges: positively charged, negatively charged, and neutral. With these charges – or lack of charges – come special properties that affect the interaction of each amino acid with other amino acids and molecules in the body.

For example, just like with magnets, two positive amino acids would repel another, and two negative and positive amino acids would attract another. Additionally, neutral (uncharged) amino acids would have no interaction with either a positively or negatively charged amino acid.

Because of these properties, positive and negative sections of amino acids, called residues, are often found on portions of molecules that physically interact with other molecules. If a residue is not supposed to interact with other molecules, it will most likely have no charge and be neutral.

Answer 1

These charges are also very important in enzyme mechanism

We have serine, tyrosine, and threonine, the residues with the -OH distally on the R group. While not charged, they are partially charged due to the electronegativity between oxygen and hydrogen. These groups participate in the clefts of enzymes and can catalyze reactions by participating as the nucleophile due to the lone pairs of electrons on the oxygen. Additionally and perhaps more importantly they are subject to substitution by phosphorylation on the surface of proteins. This is a control mechanism known as a molecular switch. They can either turn proteins or a pathway on or off, or even fine tune the kinetics of its function.

The acidic and basic residues are also involved in the reactive clefts of enzymes, that behave like the acid - base reactions of organic chemistry. You can often find combinations of acid-base residues for example histidine and aspartate or glutamate, to help catalyze a stable transition state, so a nucleophile such as serine can participate in an energetically favorable way in an enzymatic reaction. Chymotrypsin is an example of this.

Hydrophobic interactions are a result indirectly of charged property, because the aqueous environment which is charged promote the hydrophobic association. Proteins that have leucine/ isoleucine zippers are an example of this. Hydrophobic patches on the outside of globular proteins are often the site where some other hydrophobic patch associates with. Thus scaffolds of molecules can be fastened together with hydrophobic patches.