(Free Article) Some functional groups and their role in the biochemistry of life:

By: Michael Tran

The lack of polar atoms such as nitrogen (N) or oxygen (O) in alkanes and benzene aromatic rings means that these molecules do not interact much with water. Water is a polar solvent, oxygen gravitates towards “hogging” more of the two hydrogen’s electrons. In figure 1, oxygen is the red sphere-shaped structure, whereas the two hydrogens are the light blue sphere-shaped structures. Because oxygen is more electronegative than hydrogen, oxygen pulls the electrons circling the hydrogens closer to itself.

Figure 0: oxygen is the red sphere-shaped structure, whereas the two hydrogens are the light blue sphere-shaped structures. Because oxygen is more electronegative than hydrogen, oxygen pulls the electrons circling the hydrogens closer to itself.

Alkanes and benzene aromatic rings have nonpolar atoms, which makes them hydrophobic molecules. A hydrophobic compound is one that repels or fails to mix with water. (Breaking up the two parts of ‘hydrophobic,’ we obtain Hydro, meaning water and Phobos, meaning fearing.)

Remember, water is polar, and non-polar atoms do not mix well with it. Therefore, these molecules usually leave the aqueous phase (the homogeneous part of a heterogeneous system consisting of a water portion of a system containing two liquid phases -one phase is of primarily water and the second phase is primarily a liquid immiscible with water). Because there are so many definitions to what unfamiliar words may be, the word immiscible means “not forming a homogeneous mixture when added together,” i.e. it does not mix well together.

Hydrophobic molecules are important in biochemistry because of their ability to “self-assembly.” Not to anthropomorphize atoms and molecules containing no consciousness, but self-assembly here is an emergent property. (An emergent property is one that through a collection of simple interactions, a complex system, usually a structure, forms.) The self-assembly of hydrophobic molecules allows the creation of proteins and cellular plasma membranes. Yes, the proteins and membranes that make up cells, that make up you and me.

Figure 1: the energy required to initiate a chemical reaction is less with an enzyme (blue).

The remaining molecules left are somewhat polar-playing important roles in the catalytic activity of enzymatic reactions (a process used to speed up a chemical reaction).

Figure 2: these four graphs show the activity of different unique enzymes in various pH’s. pH is the abbreviation for “power of hydrogen” or “potential of hydrogen.” pH is a scale used in specifying the acidity and alkalinity of a water-based (liquid-based) solution.

Speaking of polar, imidazole is an organic compound with the chemical formula C 3N 2H 4. The compound is white or colorless, and soluble in water. It produces a basic or alkaline solution when it reacts with a neutral compound. The unique structure is classified as an aromatic heterocycle compound, also known as diazole, containing non-adjacent nitrogen atoms (Figure 3). The amino acid histidine contains imidazole. Imidazole plays a vital role in creating catalytic activity for many enzymes. Another amino acid, arginine, contains the compound guanidium (Figure 4). The amino acid tryptophan contains indole, an important compound for building into many proteins, allowing it to be very biologically active (Figure 5). Indole plays a prominent role in the effects of strychnine (a deadly poison (used in rat poison)) and LSD (a potent hallucinatory agent) (Figure 6 and Figure 7).

Figure 3: these are four ways of representing the same structure known as imidazole.

Figure 4: guanidine, a colorless solid compound which dissolves in most polar solvents.

Figure 5: Indole.

Figure 6: Strychnos nux-vomica, the plant that makes strychnine. This plant is found in southern Asia (India, Sri Lanka, and East Indies) and Australia. Strychnine was used to treat many human ailments before it was found deadly and subsequently banned.

Figure 7: a blotted “microdot” containing LSD.

Originally published at http://moleculardrugs.wordpress.com on June 28, 2020.