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Proteins: Amino acids

Amino Acids: Properties

 

Amino acids are the building blocks of proteins, each one corresponding to one or more DNA codon. They consist of an amine group, a carboxylic acid group, a hydrogen and a group unique to each residue around a central carbon atom. Free amino acids are zwitterions at physiological pH with a proton lost from the carboxy group (COO-) and gained by the amine group (NH3+).

 

 

 

Amino Acids and the Peptide Bond

Amino acids are the building block of all proteins, forming a peptide bond between the amine group of one amino acid and the carboxyl group of the next. In a polypeptide chain, the end with the free amine group is called the N-terminus and the end with the free carboxylic acid the C-terminus.

 

As a biochemist you have to be fluent in the language of amino acids and their qualities should be second nature. In my tutorials, the first thing we do is test each other; we name an amino acid and must list the codes, the properties and an interesting fact. The entire process helps us remember and could be done alone using revision cards.

 

 

 

Aliphatic

Glycine - Gly - G

 

  • The simplest amino acid
    • No chiral centre
      • Hydrophobic
        • Integral for helices and “tight” structures

         

        Alanine - Ala - A

         

        • Hydrophobic
        • Highest propensity to form an alpha helix
        • Particularly inactive – Used as in alanine scanning where each amino acid is sequentially mutated to an alanine as it is not large or polar amino acids therefore will not disrupt the protein structure.

        Valine - Val - V

         

        • Hydrophobic
        • Branched

        Leucine - Leu - L

         

        • Hydrophobic
        • Forms the DNA Binding Motif: Leucine Zipper

        Isoleucine - Ile - I

         

        • Hydrophobic
        • Two chiral centres - the alpha carbon and the first carbon of the R Group (beta carbon)
        • Large

         

        Methionine - Met - M

         

        • Hydrophobic
        • The first amino acid of any protein
        • Sulphur residue

        Proline

          • Forms a link with the amine group of the amino acid backbone
          • Hydrophobic
          • Known as an alpha helix breaker
          • Can be converted to Hydroxyproline which is vital for collagen formation

           

          Aromatic

          Phenylalanine - Phe - F

            • Aromatic - benzene ring R group
            • Hydrophobic
            • Absorbs at 260nm

             

            Tyrosine - Tyr - Y

             

            • Aromatic - Phenol R group
            • Hydrophillic
            • Hydroxyl group means Y residues can be phosphorylated and O-Linked glycosylated
            • The phsophylation of the residues is important in some signalling receptors, specifically the Tyrosine Kinase Receptors such as those for Insulin

            Tryptophan - Trp - W

             

            • Aromatic
            • Hydrophobic
            • Largest amino acid
            • Inodole ring
            • Absorbs at 280nm

             

            Polar, Uncharged

            Serine - Ser - S

             

            • Hydrophillic
            • Hydroxyl group means it can be phosphorylated and o-linked glycosylated

            Threonine - Thr - T

              • Hydrophillic
              • Hydroxyl group means it can be phosphorylated and o-linked glycosylated
              • 2 chriral centres

               

              Cysteine - Cys - C

               

              • Unobscured sulphur group - Disulphide bonds
              • Hydrophilic

              Asparagine - Asn - N

                 

                • Hydrophillic
                • N-link glycosylations
                • Carboxamide group

                 

                Glutamine - Gln - Q

                 

                • Hydrophillic
                • Carboxamide group
                • Can be used in the Kreb's Cycle

                Polar, Acidic

                Aspartate - Asp - D

                   

                  • Carboxyl
                  • Pka 4 – negative at physiological pH

                   

                  Glutamate - Glu - E

                   

                  • Carboxyl
                  • Pka 4.3 – negative physiological pH

                  Polar, Basic

                  Lysine - Lys - K

                   

                  • Hydrophilic
                  • Ubiquitinated
                  • Pka 10 – positive at physiological pH
                  • Amine group

                   

                  Arginine - Arg - R

                   

                  • PKa 12 – positive at physiological pH
                  • Part of urea cycle
                  • Guanidine group

                  Histidine - His - H

                   

                  • Hydrophillic
                  • Pka 6 – ability to change charge at physiological pH eg for conformation change in ph sensitive proteins

                   

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