Lecture Part 1: Amino Acids, Peptides, and Proteins PDF

Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins)  Amino acids in free form are found in small amounts in liv...

Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins)  Amino acids in free form are found in small amounts in living systems and building units of proteins. Proteins are polymers of amino acids linked together by a “Peptide bond”. About 300 amino acids occur in nature. Only 20 of them enter protein synthesis, specified by genetic code. These DNA-coded amino acids are called primary amino acids.  Amino acids are structures that have an amine and an acid group. Amino acids have a central carbon, the carbon, which has bonded to an amino group, a carboxylic acid, a hydrogen, and a variable side chain designated as the R group. Because of their position on the carbon, the carboxyl and amino groups are called the α-carboxyl and α-amino groups, respectively.  All amino acids are α-amino group. Except proline the amino group is part of a ring structure, therefore, proline does not contain α-amino group (-NH2), but α-imino group (-NH). Page 1 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins)  Each amino acid has four groups attached to α- carbon (C-atom next to COOH). These four groups are: 1. A basic amino group (-NH2). 2. An acidic carboxyl group (- COOH). 3. A Hydrogen atom (-H). 4. A distinctive side Chain (R)  The α-carbon has four different groups attached to it and so is a chiral or asymmetric carbon  The α-carbon of all amino acids is asymmetric, except for glycine  When R is not H, the alpha carbon is asymmetric, giving rise to isomers.  Two possible enantiomers are optically active and represent non-superimposable mirror images: L and D. Unlike sugars )D isomer) At physiological PH (about 7.4), the COOH group is dissociated forming a negatively charged carboxylate ion (COO-), and the amino group is protonated, getting the proton forming a positively charged ion (NH3+) forming a Zwitterion Page 2 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins) Isoelectric point (IEP or PI): is the pH at which the amino acid will be dipolar and carries no net charge (net charge equal to zero) (A) Polarity and Charge on R (C) Catabolic Fate Of The Groups, Amino Acid, Amino Acids Classificiton (D) Body’s Ability To Synthesize (B) Structure of Side Chains, The Amino Acid A. Polarity and Charge on R Groups:- Amino acids can be classified according to the Properties of their side chains as they are: 1. Non-polar amino acids (hydrophobic) sidechains. R is alkyl hydrophobic group, which can’t bind or give off protons, or enter in hydrogen bond formation Methionin Isoleucine Alanine Valine e Glycine Go And Take Vital Part in promoting Mother Language Tryptophan Proline Phenyl Alanine Leucine  If a protein formed from non-polar amino acids and present in aqueous solution, the side chains of such amino acids tend to cluster together in the interior of the protein due to the hydrophobicity of the non-polar R-groups  If the protein is located in a hydrophobic environment as a membrane, the non-polar R-groups are found on the surface of the protein, interacting with the lipid environment. Page 3 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins) 2. Polar amino acids, hydrophilic side chains (uncharged, acidic, or basic). R contains a polar hydrophilic group to form a hydrogen bond with H2O. can be divided into three categories: A. Natural Some Times Cats Try A Growl Serine Threonine Cysteine Tyrosine Asparagine Glutamine A Good Lawyer Aims High Aspartic Acid Glutamic Acid Lysine Arginine Histidine (COO-) (NH3+) B. Acid (Negative charge) C. Basic(Positively charged) (B)Based on the Structure of the Side Chain 1. Aliphatic amino acids :  Branched chain amino acids :- Valine, leucine, isoleucine  Sulfur-containing amino acids: Methionine, cysteine  Amide group-containing amino acids: Asparagine, glutamine  Hydroxy amino acids: Serine, threonine, tyrosine  Simple amino acids: Glycine and alanine 2. Aromatic amino acids: Phenylalanine, tyrosine, tryptophan 3. Imino acid: Proline 4. Heterocyclic amino acids: Histidine, tryptophan 5. Dicarboxylic amino acids: Aspartic acid and glutamic acid 6. Dibasic amino acids: Arginine, lysine (C) Catabolic Fate Of The Amino Acid:- according to metabolic or degradation products of amino acids they may be: 1- Ketogenic amino acids: which give ketone bodies either acetoacetate, one of ketone body, or (acetyl CoA or acetoacetyl CoA) which can be easily converted to ketone bodies. Lysine and Leucine are the only pure ketogenic amino acids 2- Glucogenic amino acids: Which give glucose. They include the rest of the amino acids. These amino acids by catabolism yield products such as pyruvate or TCA cycle intermediates that enter in glycogen and glucose formation. 3- Mixed ketogenic and glucogenic amino acids give both ketonbodies and glucose. These are isoleucine, phenylalanine, tyrosine, and tryptophan Page 4 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins) (A)Aliphatic G. Branched chain (A)Simple G. (H)Heterocyclic G. (O)Aromatic.G (i)Imino.G (A)Sulfur.G (A)Hydroxy G. (A)Sulfur G. (A)Hydroxy G. (A)Amide G. (O)Aromatic.G (D)Dicarboxylic.G (H)Heterocyclic G. (B) Dibasic.G Page 5 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins) D) Body’s Ability to Synthesize the Amino Acid 1. Essential amino acids: cannot be endogenously synthesized, and by dietary intake. Their deficiency affects growth, health, and protein synthesis. Villa HM = Ten Thousands Pound V= valine i= isoleucine l= lysine l = leucine A = arginine* H= histidine* M= methionine T= tryptophan Th= threonine P= phenyl alanine 2. Semi-essential amino acids: These are formed in the body but not sufficiently for body requirements especially in children. Histidine and arginine 3. Non-essential amino acids: These are the rest of the amino acids that are formed in the body in amounts enough for adults and children. Almost all girls go crazy after getting taken Part shopping Part  Properties of amino acids: A -Physical properties:  Solubility: Most of the amino acids are soluble in water and alcohol (polar solvents), but insoluble in nonpolar solvents (benzene).  Melting points: Amino acids generally melt at higher temperatures, often above 200℃. Page 6 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins) B-Chemical properties of amino acids: 1- Reactions due to COOH group - ester formation with alcohols, amide formation with amines and decarboxylation. 2- Reactions due toNH2 group: Transamination, deamination, and reaction with ninhydrin reagent. Ninhydrin reagent reacts with an amino group of amino acids yielding blue colored product. 3- Reactions due to side chain (R): Reactions of SH group: Page 7 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins) Glutamic acid Influences memory Page 8 of 9  Lecture. Jinan Hameed AL-Iraqia University Clinical Biochemistry 2nd stage College of Medicine Lecture Part -1 (Amino acids, Peptides and Proteins) Page 9 of 9