PHA111 Amino Acids.pptx

MPharm Programme Amino Acids & Peptides Dr. Mark Gray Slide 1 of 27 MPharm PHA111Amino Acids & Peptides Recommended Reading  Bruice: “Organic Chemistry”, 4th Ed. Chapters 23 + 24  Berg, Tymoczko, Stryer: “Biochemistry”  Nelson, Cox: “Lehninger Principles of Biochemistry”  Fersht: “Structure a...

MPharm Programme Amino Acids & Peptides Dr. Mark Gray Slide 1 of 27 MPharm PHA111Amino Acids & Peptides Recommended Reading  Bruice: “Organic Chemistry”, 4th Ed. Chapters 23 + 24  Berg, Tymoczko, Stryer: “Biochemistry”  Nelson, Cox: “Lehninger Principles of Biochemistry”  Fersht: “Structure and Mechanism in Protein Science” Slide 2 of 27 MPharm PHA111Amino Acids & Peptides Proteins in Nature Slide 3 of 27 MPharm PHA111Amino Acids & Peptides Amino Acids • Proteins and many other important biomolecules are made from amino acids. • The amino acids most commonly found in Nature are termed a-amino acids. Slide 4 of 27 MPharm PHA111Amino Acids & Peptides Amino Acids are Chiral • Glycine is the only achiral member of the 20 common amino acids. • The others all exist as the L-optical form. Slide 5 of 27 MPharm PHA111Amino Acids & Peptides Amino acids contain both an acid and a base….. Slide 6 of 27 MPharm PHA111Amino Acids & Peptides The twenty amino acids (i)…… Slide 7 of 27 MPharm PHA111Amino Acids & Peptides The twenty amino acids (ii)…… Slide 8 of 27 MPharm PHA111Amino Acids & Peptides The twenty amino acids (iii)… Slide 9 of 27 MPharm PHA111Amino Acids & Peptides Aromatic Amino Acids are important for visualisation of proteins Slide 10 of 27 MPharm PHA111Amino Acids & Peptides The twenty amino acids (iv)…… Slide 11 of 27 MPharm PHA111Amino Acids & Peptides The twenty amino acids (v)…… Slide 12 of 27 MPharm PHA111Amino Acids & Peptides Each amino acid has a characteristic isoelectric point • Neutral aa side chains • pI = 1/2 (pKaCOOH+pKaNH3+) • Acidic aa side chains • pI = 1/2 (pKaCOOH+pKaR) • Basic aa side chains • pI = 1/2 (pKaR+pKaNH3+) Slide 13 of 27 MPharm PHA111Amino Acids & Peptides Oligopeptides, Polypeptides & Proteins • Aspartame contains two amino acids: it is a dipeptide. O H3N • Oligopeptides contain 2-10 amino acids (residues) and have the following suffixes: di, tri, tetra, penta, hexa, hepta, octa, nona, deca. • Between 10-50 residues they are known as polypeptides (Mw < 5,000). • Proteins usually contain between 50-400 residues (5,000 < Mw < 400,000). N H O O CH3 O Aspartame (Asp-Phe-OMe) O O H3N O O O Aspartic Acid Slide 14 of 27 MPharm PHA111Amino Acids & Peptides H3N O O Phenylalanine Amides: Condensation of Carboxylic Acids and Amines Slide 15 of 27 MPharm PHA111Amino Acids & Peptides A closer look at the peptide bond 121.1° 123.2° 121.9° 115.6° Å 1 5 .33 Å .4 2 1 Å 1.5 1.0 Å Slide 16 of 27 MPharm PHA111Amino Acids & Peptides Peptide bonds have strong Resonance O O N H N H • For most peptides this delocalization energy stabilises the molecule by 75-90 kJ/mol. • Thus, peptides prefer to be in a planar, trans (anti / Z), conformation. Slide 17 of 27 MPharm PHA111Amino Acids & Peptides A Tetrapeptide: • Alanylglutamylglycyllysine. • Name starts at N-terminal AA. • Red colour indicates charged groups at pH7. Slide 18 of 27 MPharm PHA111Amino Acids & Peptides A Pentapeptide: Ser-Gly-Tyr-Ala-Leu • Serylglycyltyrosylalanylleucine Slide 19 of 27 MPharm PHA111Amino Acids & Peptides WEEK 25 Cysteines can be linked via disulphide bonds Slide 20 of 27 MPharm PHA111Amino Acids & Peptides Glutathione: a natural antioxidant • Glutathione: Glu-Cys-Gly • linked via sidechain Glu acid • Forms disulphide in presence of oxidizing agents. • Believed to help against aging and cancer. Slide 21 of 27 MPharm PHA111Amino Acids & Peptides Some medically important small peptides Tyr-Gly-Gly-Phe-Leu Leucine enkephalin Pain Control Tyr-Gly-Gly-Phe-Met Methionine enkephalin Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg Bradykinin Anti-inflammatory Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly-NH2 Vasopressin Controls Blood Pressure Oxytocin Induces Labour Milk Production S S Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2 S S Slide 22 of 27 MPharm PHA111Amino Acids & Peptides Insulin • Insulin is made from two chains of amino acids. • They are linked via disulphide bonds. Slide 23 of 27 MPharm PHA111Amino Acids & Peptides Purification of Peptides & Proteins • Polyacrylamide gel electrophoresis (PAGE) • Agarose: DNA / Large Proteins / Enzyme complexes (larger pores). • Movement determined by mass, shape and charge. • Sodium dodecyl sulphate (SDS) can be used to denature proteins into uniform rods. Slide 24 of 27 MPharm PHA111Amino Acids & Peptides pH electrophoresis profile gives protein isoelectric points pH dependent behaviour of BSA 0.60 0.40 0.20 Velocity (microm/ s) 0.00 4.00 4.50 5.00 5.50 6.00 6.50 7.00 7.50 -0.20 -0.40 -0.60 -0.80 -1.00 -1.20 -1.40 pH pH 4.20 4.56 5.20 5.65 6.30 7.00 Velocity (mm/s) 0.50 0.18 -0.25 -0.55 -0.90 -1.25 Slide 25 of 27 MPharm PHA111Amino Acids & Peptides Homework • Predict the isoelectric point of the unknown peptide below: pH Velocity ( mm/ s) 4.5 -0.1 Slide 26 of 27 MPharm PHA111Amino Acids & Peptides 5 -0.2 5.5 -0.3 6 -0.35 Summary • There are 20 commonly occurring amino acids (AA). • They can be linked together by peptide bonds to produce amides. • Short chains of AA are oligopeptides, polypeptides are larger and proteins largest of all. • When naming sequences of AA we start from the amino terminus. • As well as peptide linkages AA can be linked via disulphide bonds. • Isoelectric points are key to the characterisation and separation of amino acids, peptides and proteins. 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