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Functional Groups in Biomolecules

By: Fakhereddin Babiker Ali Musa The purpose of biochemistry is the chemical explanation of biological phenomena; in other words is to find the relation between form and function. For the achievement of that goal; isolation, structure elucidation and analysis of the function of various biomolecules are the corner-stones of biochemistry. Biomolecules are principally compounds of carbon, and some other elements that constitute the live parts of them by influencing their behavior towards each other and the many interactions they undergo between themselves and other biomolecules and trace elements in the body; these are termed functional groups1 and most biomolecules are poly-functional i.e. containing two or more functional groups, which imply different properties to the molecule or macromolecule that carries them. In a quick review we will go through them and give some highlights to their biological importance. The existence of Carbon Carbon double bond (C=C) groups in fatty acids especially the polyunsaturated and the eicosanoids (the precursors of lipid mediators) is of great value to our life. This group has the property of making the aliphatic chain of the fatty acid more polar and of low melting point when compared to the saturated ones, and also it is the reason that they have the geometric isomerism of cis and trans where cis is the most important so far.

cis & trans Fatty acids

The Hydroxyl (R-OH) group in biological systems has a lot of advantages to the physical and chemical behavior of biomolecules. By their ability to form hydrogen bonds they increase the solubility but, sometimes they impart rigidity to the system for instance the hydroxylation of proline in collagen. It is found almost in all biomolecules. It can also be converted to (e.g. Adlehydes and Ketones, Carboxylic acids and Esters). Glycerol and Sphingosine are examples of biologically important Alcohols.

Triacyglycerol2
1 2

They may be carbon atoms linked together in a special way like the Alkene C=C group Triacylglycerol is an ester of Glycerol with 3 fatty acid molecules

Ether group (R-O-R) on other hands is not very common in biological molecules, and it is confined to the phospholipids family the plasmalogen group which constitutes 10% of the brain and muscle phospholipids.

Plasmalogen

The Amino group (RNH2, R2NH, and R3N) is found abundantly in biomolecules as amino acid, amino sugar, and amino alcohol, where it offers basic properties to them. And it is usually positively charged at physiologic pH (=7.4).

Amino Acid

Glucosamine (Amino Sugar)

Sphingosine (Amino Alcohol)

Also it is found in some important amines in the body like Choline, Ethanolamine, Dopamine, Histamine, etc... Many are derived from amino acids. Sulfhydryl group or Thiol group (-SH) is one the most polar groups in biomolecules and a powerful nucleophile among the 20 amino acids side chains. It is found in the amino acid Cysteine and it forms a crucial part of many important biomolecules like; Glutathione where it acts as a buffer that stabilizes the red blood cell proteins where Hemoglobin stands on top of them. It can also be oxidized to disulfide. Disulfide group(R-S-S-R) which is formed by oxidation of Sulfhydryl group; is undoubtedly very important in stabilizing tertiary and quaternary structures of proteins (e.g. Insulin, Oxytocin, Vasopressin, Calcitonin and many others).

Thioether group (R-S-R) is formed from Sufhydryl (-SH) group and it is found in the amino acid Methionine where it serves as a metal ligand in proteins, and at the anchor points of membrane proteins (Thioether-linked prenyl anchors). Also the heme is covalently bounded to the protein through thioether linkage. Carbonyl group forms adehydes and ketones and can be part of other functional groups like Carboxylic acids, Amides, Esters, and Thiesters. And can be condensed with alcohol to form hemiacetal, and with amines to form aldimines which are intermediates in amino acids metabolism. Because of its polarity it tends to form hydrogen bonds and a good example of these are the hydrogen bonds that occur between the carbonyl carbon and the hydrogen atoms carried on the nitrogen which stabilize the secondary structure in proteins.
Carbonyl Group Aldehyde Ketone

Carboxyl group is found in amino acids and fatty acids the building blocks of proteins and lipids respectively. In proteins (namely enzymes) the carboxlate (parent base) terminal is found at the active site for binding substrates. The carboxyl group is involved in the formation of amides and esters through the interaction with amino group and hydroxyl group respectively. When not involved in amide or ester formation it is usually found ionized to carboxylate at physiological pH.
Carboxyl Group Carboxylate Group

Hemiacetal group is only found in sugars, and it occurs by condensation of a carbonyl group of an aldehyde and a hydroxyl group. Similarly there is a hemiketal group which happens by condensation of a carbonyl group of a ketone and a hydroxyl group.

Formation of Hemiacetal

Formation of Hemiketal

Ester group is formed by the condensation of a carboxyl group and a hydroxyl group. It is found in lipids, some derivatives of sugars.

Ester Group

Thioester is a high energy group, and usually present in metabolic pathways as an energy-rich intermediate. Also found in membrane proteins, but far less strong than the daughter thioether and are easily cleaved by the action of hydrolases. Thioester happens also with acyl carrier protein and Acetyl-CoA is a well known thioester.

Thioester Group

Amide group is formed by the condensation of a carboxyl group and an amino group. It happens between amino acids, and usually found in peptides and proteins where it takes the name "peptide bond".

Amide Group

Imino group or Schiff's base is found in many biomolecules, for instance the amino acid proline is an imino acid rather than amino acid, and the rare imino tautomer of adenine.
Imino Group

Phosphoric Ester group or Phosphoryl group Phosphoric Anhydride group or Diphosphate ester group again are involved in high energy bonds found in energy nucleotides like ATP. Also found in metabolic intermediates.

Phosphoric Ester Group

Phosphoric Anhydride Group

Phosphate Diester group is found in polynucleotides and nucleic acids backbone.

Phosphate Diester Group

Bibliography
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