Lecture 1: Protein Chemistry & Amino Acids PDF

Prof. Rania Khalil 1  Proteins are organic compounds found in animals and plants.  Proteins are made up of polymers called polypeptides.  Polypeptides are a polymer chain of three or more amino acids.  peptide bond (amide linkages) is a linkage between the...

Prof. Rania Khalil 1  Proteins are organic compounds found in animals and plants.  Proteins are made up of polymers called polypeptides.  Polypeptides are a polymer chain of three or more amino acids.  peptide bond (amide linkages) is a linkage between the amino group of one amino acid and the carboxyl group of another amino acid to form protein. 2  They are 20 AA responsible for protein structure which consist of: 1. “alpha” carbon (α-C) 2. an amino group (NH2) 3. a carboxylic acid group (COOH) 4. a hydrogen atom (H) 5. a small organic group (R)  All (NH2), (COOH), (H) and (R) groups are attached to the α-C  L-amino acid: are the active amino acid in which the amino group is on the left side configuration.  Only one AA of the 20 is imino acid that contain imino group (NH) (called Proline) 3 aa3 4  Amino acid Function Glycine Supports collagen synthesis; used in sleep aids glutamine Reduces mucositis in chemotherapy patients Tyrosine Precursor for thyroid hormones and dopamine; important for mental health. Histidine Precursor of histamine vasodilator Tryptophan Precursor of serotonin (happiness hormone) Leucine Promotes muscle protein synthesis; useful in recovery Most amino acids enter in structure of body proteins as plasma proteins, tissue proteins and enzymes 5  According to the Chemical structure (number of carbon derived from).  According to the Polarity of the side chain.  According to the Biological (metabolic) value.  According to the Nutritional value. 6  1. Classification according to chemical structure AA Symbol Side chain Additional group Glycine Gly (G) aliphatic - Alanine Ala (A) aliphatic - Serine Ser (S) aliphatic OH Cysteine Cys (C) aliphatic SH Threonine Thr (T) aliphatic Beta OH Methionine Met (M) aliphatic Gamma S-CH3 Aspartate Asp (D) aliphatic COOH Asparagine Asn (N) aliphatic CONH2 Proline Pro (P) pyrolidine ring - Isoleucine Ile (I) aliphatic Beta CH3 Valine Val (V) aliphatic Branched CH3 Arginine Arg (R) aliphatic Delta guanido Glutamate Glu (E) aliphatic COOH Glutamine Gln (Q) aliphatic CONH2 Lysine Lys (K) aliphatic Epsilon NH2 Leucine Leu(L) aliphatic Branched CH3 7  AA Symbol C number Side chain Additional group Phenylalanine Phe (F) 3 aromatic - benzene ring Tyrosine Tyr (Y) 3 aromatic OH benzene ring Tryptophan Trp (W) 3 aromatic - Indole ring Histidine His (H) 3 aromatic - Imidazole ring 8 9 10 11 12 13  Amino acids with nonpolar side chain, hydrophobic  Amino acids with polar uncharged (neutral) side chain, hydrophilic  Amino acids with polar positively charged basic side chain, hydrophilic  Amino acids with polar negatively charged acidic side chain, hydrophilic 14  Amino Acids with Aliphatic R-Groups (Hydrophobicity increases with increasing number of C atoms in the hydrocarbon chain)  Aromatic Amino Acids with benzene ring are relatively nonpolar. Glycine, alanine, methionine, proline, isoleucine, valine, leucine, phenylalanine, tryptophan 15  Neutral amino acids have R groups containing (SH, OH, CONH2), interact with water at physiological pH by H-bond Serine, cysteine, threonine, tyrosine, glutamine, asparagine  Basic amino acids have R groups containing NH2 group. (acidity constant pka>pH 7.4) with positive charge (NH3+) Lysine, arginine, histidine  Acidic amino acids have R groups containing COOH group. (acidity constant pka< pH 7.4) with negative charge (COO-) Aspartate, glutamate 16 17 Semi-essential AA: these are formed in the body in amount enough for adults but not enough for children. They include: arginine and histidine 18 19  Alpha AA Function Non-alpha AA Function Citrulline Participate in urea Beta (β) alanine Enter in structure Ornithine cycle of pantothenic acid vitamin Homoserine Intermediate in Gamma amino Neurotransmitter Homocysteine metabolism butyric acid formed from (GABA) glutamate in brain tissues Cystine (dicysteine) Important for Taurine Occurs in bile protein structure combined with bile acids 20  They are AA found in proteins but formed after protein synthesis Modified amino acid Modification Source Hydroxyproline Hydroxylation Collagen Hydroxylysine N-Methyl lysine Methylation Muscle myosine Methyl histidine γ- Carboxy glutamate Carboxylation Prothrombin 21  Amino acid derived from 2 carbons with aliphatic side chain (Glycine) Amino acid derived from 3 carbons with aliphatic side chain (alanine) Amino acid with aliphatic side chain containing hydroxyl group (Serine) Amino acid with aliphatic side chain containing sulfur group (cysteine) 3 Amino acids with aromatic side chain (phenylalanine, tryptophan, histidine) 22  Amino acid with aromatic side chain containing hydroxyl group (tyrosine) Amino acid with aliphatic side chain containing beta hydroxyl group (threonine) Amino acid with aliphatic side chain containing gamma sulfur methyl (methionine) Amino acid derived from 4 carbons with acidic side chain (aspartate) Amino acid with amide side chain (asparagine) 23  Amino acid with imino side chain (proline) Amino acid with aliphatic side chain containing beta methyl group (isoleucine) Amino acid with aliphatic side chains containing branched methyl group (valine) Amino acids with aliphatic side chains containing delta guanido group (arginine) 24  Amino acid derived from 5 carbons with acidic side chain (glutamate) Amino acid derived from 5 carbons with amide side chain (glutamine) Amino acid derived from 6 carbons with epsilon amino group (lysine) Amino acid derived from 6 carbons with aliphatic side chains containing branched methyl group (leucine) 25  Basic amino acid derived from 5 carbons with aliphatic side chain (Arginine) Acidic amino acid derived from 5 carbons (Glutamate) Neutral amino acid derived from 4carbons with amide side chain (Asparagine) Basic amino acid derived from 6 carbons (Lysine) Neutral amino acid derived from 3 carbons with aromatic side chain (Tyrosine) 26