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Functional group modification for conjugation

 
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10/01/2013

Functional group modification for conjugation

Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. Functional groups are attached to the carbon backbone of organic molecules. They are less stable than the carbon backbone of organic molecule and they are more likely to participate in chemical reactions. Each type of functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule. Functional groups are necessary to have in bioconjugation chemistry.

Common Biological Functional Groups

Six common biological functional groups are: hydrogen, hydroxyl, carboxyl, carbonyl, amino, phosphate, and methyl. Table below contain chemical class and functional group available for conjugation.

Chemical class Group Formula Structural Formula Prefix Suffix
Acyl halide Haloformyl RCOX haloformyl- haloformyl

-oyl
Alcohol Hydroxyl ROH hydroxy- -ol
Aldehyde Aldehyde RCHO oxo-

-al
Aldehyde * Alkyl RH alkyl-

-ane
Aldehyde * Alkenyl R2C=CR2 alkenyl-

-ene
Aldehyde * Alkynyl RC≡CR' alkynyl- -yne
Amide Carboxamide RCONR2 carboxamido- amide
Amines Primary amine RNH2 amino- -amine
Secondary amine R2NH amino- -amine
Tertiary amine R3N amino- -amine
4° ammonium ion R4N + - ammonio-- -ammonium
Azo compound Azo (Diimide) RN2R'   azo-

-diazene
Toluene derivative Benzyl RCH2C6H5 RBn benzyl- 1-(substituent)toluene
Carbonate Carbonate ester ROCOOR   alkyl carbonate
Carboxylate Carboxylate RCOO− carboxy- -oate
Carboxylic acid Carboxyl RCOOH carboxy- -oic acid
Cyanates Cyanate ROCN cyanato- alkyl cyanate
Thiocyanate RSCN thiocyanato- alkyl thiocyanate
Ether Ether ROR' alkoxy alkyl alkyl ether
Ether Ether RCOOR'   alkyl alkanoate
Haloalkane Halo RX halo alkyl halide
Hydroperoxide Hydroperoxy ROOH   hydroperoxy alkyl hydroperoxide
Imine Primary ketimine RC(=NH)R imino- -imine-
Secondary ketimine RC(=NR)R imino- -imine
Primary aldimine RC(=NH)H imino- -imine
Secondary aldimine RC(=NR')H imino- -imine
Isocyanide Isocyanide RNC   isocyano- alkyl isocyanide
Isocyanates Isocyanate RNCO isocyanato- alkyl isocyanate
Isothiocyan ate RNCS isothiocyanat o- alkyl isothiocyanate
Ketone Ketone RCOR' keto-, oxo -one
Nitrate Nitrate RONO2   nitrooxy-, nitroxy alkyl nitrate
Nitrile Nitrile RCN cyano- alkanenitrile alkyl cyanide
Nitrite Nitrite RONO   nitrosooxy alkyl nitrite
Nitro compound Nitro RNO2 nitro-
Nitroso compound Nitroso RNO   nitroso-
Peroxide Peroxy ROOR peroxy- alkyl peroxide
Benzene derivative Phenyl RC6H5 phenyl- -benzene
Phosphine Phosphino R3P   phosphino- -phosphane
Phosphodies ter Phosphate HOPO (OR)2 phosphoric acid di(substituent) ester di(substituent)
hydrogenphosphate DNA
Phosphonic acid Phosphono RP(=O) (OH)2 haloformyl phosphono- substituent
phosphonic acid
Phosphate Phosphate ROP(=O) (OH)2 haloformyl phospho-  
Pyridine
derivative 		Pyridyl RC5H4N

4-
pyridyl (pyridin-4-yl)
3-
pyridyl (pyridin-3-yl)
2-
pyridyl (pyridin-2-yl)		 -pyridine
Sulfide   RSR'     di(substituent) sulfide
Sulfone Sulfonyl RSO2R' sulfonyl- di(substituent) sulfone
Sulfonic acid Sulfo RSO3H sulfo substituent sulfonic acid
Sulfoxide Sulfinyl RSOR' sulfinyl- di(substituent) sulfoxide
Thiol Sulfhydryl RSH mercapto-, sulfanyl- -thiol
Functional group *formula Family of molecules Example Properties of functional group
Amino Amino Amino Glycine (an amino acid)
Amino		 Acts as a base tends to attract a portion to form
Carbonyl Carbonyl Aldehydes Acetaldehyde
Acetaldehyde		 Acetaldehyde especially react with compounds of form HR2 to produce larger molecules with form
  Ketones Acetone
Acetone		  
Carbonyl Carbonyl Carboxylic Acids Acetic acid
Acetic acid		 Acts as an acid - tends to lose a proton to form
Hydroxyl Hydroxyl Alcohols Ethanol
Ethanol		 Highly polar to make compounds more soluble through hydrogen bonding with water
Phosphate Phosphate Organic phosphates 3-Phosphoglyceric acid
3-Phosphoglyceric acid		 When several phosphate groups are link together breaking O- P bonds between them releases large amounts of energy
Sulfhydryl Sulfhydryl Thiols Cysteine
Cysteine		 When present in proteins, can form disulfide (S-S) bonds that contribute to protein structure
In these structure formulas *R* stands for the rest of the Molecules.

Table 3-1. Important Functional Group in Biological Molecules
Group Structure Properties Type of Molecules
Hydrogen (-H) Hydrogen (-H) Polar or nonpolar, depending on which atom hydrogen is bonded to ; involved in condensation and hydrolysis Almost all organic molecules
Hydroxyl (-OH) Hydroxyl (-OH Polar, involved in condensation and hydrolysis Carbohydrates, nucleic acids, alcohols, some acids, and steroids
Carboxyl (-COOH) Carboxyl (-COOH) Acidic; negatively charged when H+ dissociable, involved in peptide bonds Amino acids, fatty acids
Amino (-NH2)) Amino Basic may bond additional H+ becoming positively charged; involved in peptide bonds Amino acids, nucleic acids
Phosphate (-H2PO4) Phosphate Acidic; up to two negative charges when H+ dissociates; links nucleotides in nucleic acids; energy-carrier group in ATP Nucleic acids, phospholipids
Methyl (-CH3) Methyl Nonpolar, tends to make molecules hydrophobic Many organic molecules especially common in lipids