BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
v STRUCTURE
£ There are only 20 (among >300 different AAs [amino acids] described in nature) are commonly found as constituents of mammalian proteins
• These are the only AAs that are coded for by DNA
• These AAs are used for the synthesis of proteins by the mRNA-directed process that occur on ribosomes
• Other AAs exist for which there is no genetic code
§ example, in the urea cycle or in proteins where they are generated by posttranslational modifications (such as
hydroxyprolone in collagen)
• Selenocysteine
§ It is known as the 21st amino acid
§ It is unique in that a serine residue is converted to selenocysteine while attached to a transfer RNA.
§ Selenium is a necessary metal ion for certain enzymes, such as glutathione peroxidase
£ Each aa has:
• An alpha carboxyl group, and a primary alpha amino group
§ Except: Proline, has a secondary amino group (nitrogen is part of ring)
§ At physiologic pH, it is dissociated, forming negatively charged carboxylate ion (-COO-) [pKa ~ 2] , and the amino group
is protonated (-NH3+) [pKa ~ 9]
• Positive charges are present on the side chains of the acidic amino acids, arginine, lysine, and histidine at pH 7
• Negative charges are present on the side chains of the acidic amino acids, aspartate and glutamate at pH 7
§ Almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not
available for chemical reaction except for hydrogen bond formation.
• Hydroxyl groups found on serine and threonine can form hydrogen bonds
• A distinctive side chain ("R group"): bonded to the α-carbon atom.
§ Except: Glycine, does not have a side chain. Its α-carbon contains two hydrogens
§ It is useful to classify the aas according to the properties of their side chains
§ Proline
• It differs from other aas
• Differ in its side chain, and α-amino N form a rigid (five-membered ring structure)
• Has secondary amino group - refers to "imino acid"
• The unique geometry of proline contributes to the formation of the fibrous structure of collagen and often
interrupts the α-helices found in globular proteins.
, BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
• AA Isomers
§ The α-carbon of an amino acid is a chiral, or optically active carbon atom (attached to four different chemical groups
[asymmetric])
• Except glycine. (Its α-carbon has two hydrogen substituents)
§ AAS with an asymmetric center at the α-carbon can exist in two forms, designated D and L
• The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers.
• All AAS found in proteins (except Glycine) are of the L configuration
• Glycine is not optically active; thus, it is neither D nor L
• D-amino acids are found in some antibiotics and in bacterial cell walls.
v STRUCTURE
£ There are only 20 (among >300 different AAs [amino acids] described in nature) are commonly found as constituents of mammalian proteins
• These are the only AAs that are coded for by DNA
• These AAs are used for the synthesis of proteins by the mRNA-directed process that occur on ribosomes
• Other AAs exist for which there is no genetic code
§ example, in the urea cycle or in proteins where they are generated by posttranslational modifications (such as
hydroxyprolone in collagen)
• Selenocysteine
§ It is known as the 21st amino acid
§ It is unique in that a serine residue is converted to selenocysteine while attached to a transfer RNA.
§ Selenium is a necessary metal ion for certain enzymes, such as glutathione peroxidase
£ Each aa has:
• An alpha carboxyl group, and a primary alpha amino group
§ Except: Proline, has a secondary amino group (nitrogen is part of ring)
§ At physiologic pH, it is dissociated, forming negatively charged carboxylate ion (-COO-) [pKa ~ 2] , and the amino group
is protonated (-NH3+) [pKa ~ 9]
• Positive charges are present on the side chains of the acidic amino acids, arginine, lysine, and histidine at pH 7
• Negative charges are present on the side chains of the acidic amino acids, aspartate and glutamate at pH 7
§ Almost all of these carboxyl and amino groups are combined through peptide linkage and, in general, are not
available for chemical reaction except for hydrogen bond formation.
• Hydroxyl groups found on serine and threonine can form hydrogen bonds
• A distinctive side chain ("R group"): bonded to the α-carbon atom.
§ Except: Glycine, does not have a side chain. Its α-carbon contains two hydrogens
§ It is useful to classify the aas according to the properties of their side chains
§ Proline
• It differs from other aas
• Differ in its side chain, and α-amino N form a rigid (five-membered ring structure)
• Has secondary amino group - refers to "imino acid"
• The unique geometry of proline contributes to the formation of the fibrous structure of collagen and often
interrupts the α-helices found in globular proteins.
, BIOCHEMISTRY | PROTEIN STRUCTURE AND FUNCTION | AMINO ACIDS | NOTED BY FAKHRY (IG @SFAKHRYM)
• AA Isomers
§ The α-carbon of an amino acid is a chiral, or optically active carbon atom (attached to four different chemical groups
[asymmetric])
• Except glycine. (Its α-carbon has two hydrogen substituents)
§ AAS with an asymmetric center at the α-carbon can exist in two forms, designated D and L
• The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers.
• All AAS found in proteins (except Glycine) are of the L configuration
• Glycine is not optically active; thus, it is neither D nor L
• D-amino acids are found in some antibiotics and in bacterial cell walls.
