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Functional Groups in BiomoleculesBy: 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 thefunction 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 otherand the many interactions they undergo between themselves and otherbiomolecules and trace elements in the body; these are termed functional groups 1 and most biomolecules are poly-functional i.e. containing two or more functionalgroups, 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 theirbiological importance.The existence of Carbon Carbon double bond (C=C) groups in fatty acidsespecially the polyunsaturated and the eicosanoids (the precursors of lipidmediators) is of great value to our life. This group has the property of making thealiphatic chain of the fatty acid more polar and of low melting point when comparedto the saturated ones, and also it is the reason that they have the geometricisomerism of cis and trans where cis is the most important so far.

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

Triacyglycerol 2

1 They may be carbon atoms linked together in a special way like the Alkene C=C group2 Triacylglycerol is an ester of Glycerol with 3 fatty acid molecules

cis & trans Fatty acids

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Thioether group (R-S-R) is formed from Sufhydryl (-SH) group and it is found in theamino acid Methionine where it serves as a metal ligand in proteins, and at theanchor points of membrane proteins (Thioether-linked prenyl anchors). Also theheme 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 condensedwith alcohol to form hemiacetal, and with amines to form aldimines which areintermediates in amino acids metabolism.Because of its polarity it tends to form hydrogen bonds and a good example of theseare the hydrogen bonds that occur between the carbonyl carbon and the hydrogenatoms carried on the nitrogen which stabilize the secondary structure in proteins.

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. Thecarboxyl group is involved in the formation of amides and esters through theinteraction with amino group and hydroxyl group respectively. When not involvedin amide or ester formation it is usually found ionized to carboxylate at physiological pH.

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

Carbonyl Group

Carboxyl Group Carboxylate Group

Formation of Hemiacetal

Formation of Hemiketal

Aldehyde Ketone

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

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

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

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

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

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

Ester Group

Thioester Group

Amide Group

Imino Group

Phosphoric Ester Group Phosphoric Anhydride Group

Phosphate Diester Group

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