Proteins: Amino Acids and Structure

Introduction

• Proteins are the most abundant and functionally diverse molecules in living systems and are important for every life process.
• Enzymes and polypeptide hormones regulate metabolism, while contractile proteins in muscle permit movement.
• Collagen forms a framework for calcium phosphate deposition in bone.
• Proteins like hemoglobin and plasma albumin shuttle molecules in the bloodstream, while immunoglobulins fight infections.
• Proteins are linear chains of amino acids linked by covalent, peptide bonds.
• Each protein has a specific and unique amino acid sequence.
• This unique sequence defines both its three-dimensional structure and its biological function.

General Nature of Amino Acids

• Only 20 amino acids are involved in the formation of proteins.

• All 20 amino acids found in proteins have a carboxyl group (COOH) and an amino group (NH2) bound to the same carbon atom - the α-carbon.

• Amino acids differ from each other in their side chains or R-groups, attached to the α-carbon.

• The 20 amino acids of proteins are often referred to as the standard, primary, or normal amino acids.

• Standard amino acids have been assigned three-letter abbreviations and one-letter symbols, e.g., glycine has the abbreviated name Gly and symbol letter G.

• All amino acids found in proteins exclusively use the L-configuration.

Classification of Amino Acids

• Amino acids are classified based on several criteria including:
• Chemical nature in solution
• Structure of the side chain
• Nutritional requirement
• Metabolic product
• Nature or polarity of the side chain

Classification Based on Chemical Nature

• Neutral amino acids: These are amino acids which are neutral in solution; they are monoaminomonocarboxylic acids (one amino and one carboxylic group).
• Examples include glycine, serine, phenylalanine, alanine, threonine, tyrosine, valine, cysteine, tryptophan, leucine, methionine, asparagine, isoleucine, proline, and glutamine.
• Acidic amino acids: These are acidic in solution and are monoamino dicarboxylic acids.
• Examples include aspartic acid and glutamic acid.
• Basic amino acid: These are basic in solution and are diamino-monocarboxylic acids.
• Examples include lysine, arginine, and histidine.

Classification Based on Side Chain Structure

• Aliphatic amino acids: Amino acids having an aliphatic side chain, e.g., glycine, alanine, valine, leucine, isoleucine.
• Hydroxy amino acids: Amino acids having a hydroxy group in the side chain, e.g., threonine, serine, tyrosine.
• Sulfur-containing amino acids: Amino acids having sulfur in the side chain, e.g., cysteine, methionine.
• Dicarboxylic acids and their amides: Amino acids with a carboxylic group in their side chain, e.g., glutamic acid, glutamine, aspartic acid, asparagine.
• Diamino acids: Amino acids having an amino group (-NH2) in the side chain, e.g., lysine, arginine, histidine.
• Aromatic amino acids: Amino acids containing an aromatic ring in the side chain, e.g., phenylalanine, tyrosine, tryptophan.
• Imino acids or heterocyclic amino acids: Proline is one of 20 amino acids, and is an imino (-NH) acid not an amino (-NH2) acid like other.

Nutritional Classification

• Essential amino acids: These must be supplied through the diet and there are eight: phenylalanine, methionine, valine, histidine, threonine, arginine, tryptophan, lysine, isoleucine, leucine, with the mnemonic MILL PATH TV.
• Arginine and histidine are semi-essential for child growth, pregnancy, and lactation.
• Nonessential amino acids: These can be synthesized in the human body, therefore, they are not required in the diet.
• Examples include glycine, alanine, proline, tyrosine, serine, cysteine, glutamic acid, aspartic acid, glutamine, and asparagine.

Metabolic Classification

• Glucogenic amino acids: These can be converted into glucose.
• Fourteen of the twenty standard amino acids are classified as glucogenic.
• Ketogenic amino acids: These can be converted to ketone bodies.
• Leucine and lysine are exclusively ketogenic.
• Both glucogenic and ketogenic: These can be converted to both glucose and ketone bodies.
• Isoleucine, phenylalanine, tryptophan, and tyrosine are classified as both glucogenic and ketogenic.

Polarity of Side Chain

• Hydrophilic or polar amino acids dissolve in water, and charged polar amino acids interact electrostatically, whereas uncharged polar amino acids form hydrogen bonds.
• Hydrophobic or nonpolar amino acids dissolve in lipids and avoid aqueous environments.
• They do not gain or lose protons, nor participate in hydrogen or ionic bonds; they promote hydrophobic interactions.

Importance of Amino Acids

• Form of proteins: They are joined to each other by peptide bonds to form proteins and peptides.
• Formation of glucose: Glucogenic amino acids are converted to glucose.
• Enzyme activity: The thiol (-SH) group of cysteine plays a role in enzyme activity.
• Transport and storage of ammonia: Glutamine plays a role in transport and storage of ammonia.
• As a buffer: Free amino acids and some in proteins can act as buffers; histidine can serve as the best buffer at physiological pH.
• Detoxification reactions: Glycine, cysteine, and methionine are involved in the detoxification of toxic substances.
• Formation of biologically important compounds: Specific amino acids can give rise to these.
• Tyrosine forms hormones (e.g., adrenaline, thyroxine) and skin pigment (melanin).
• Tryptophan forms vitamin (niacin).
• Glycine, arginine, and methionine form creatine.
• Glycine and cysteine form bile salts.
• Glycine forms heme.
• Aspartic acid and glutamic acid form pyrimidine bases.
• Glycine, aspartic acid, and glutamine form purine bases.
• β-alanine forms coenzyme-A.

Modified or Nonstandard Amino Acids

• Cystine provides stability to the three-dimensional structure of proteins via disulfide bridges.
• Hydroxyproline and Hydroxylysine are necessary for collagen formation of connective tissue.
• Desmosine and Isodesmosine are formed by oxidation and crosslinking of four lysine side chains, found in connective tissue protein, elastin
• Gamma Carboxyglutamate is formed by carboxylation of glutamic acid side chains in clotting proteins (e.g., prothrombin).
• Selenocysteine has a structure similar to cysteine, containing the trace element selenium in place of sulfur.
• It can form Glutathione peroxidase, Deiodinase and Glycine reductase.

Optical Properties

• Naturally occurring amino acids are optically active, existing in D and L forms, which are mirror images, except for glycine, which is optically inactive.
• These forms are stereoisomers, optical isomers, or enantiomers.
• At pH 7.4, all amino acids have the same L-configuration and hence L-α-amino acid

Ionization of Amino Acids

• Acid/base behavior: Amino acids behave as both acids and bases in solution.
• Amphoteric properties: Amino acids are amphoteric, forming zwitterions at their isoelectric pH.

Biologically Important Peptides

• Peptides are polymer chains of amino acids.

• Two amino acid molecules are covalently joined with a peptide bond by dehydration, resulting in a dipeptide.

• Polypeptides are formed when many amino acids join together; proteins are polypeptides with thousands of amino acids, or even multiple polypeptides

• Glutathione (GSH) is a tripeptide (γ-glutamyl – cysteinyl - glycine) containing glutamate, cysteine and glycine, which is found in all mammalian cells except neurons.

• Glutathione exists as either the reduced (GSH) or oxidized (G-S-S-G) form.

• The sulfhydryl (-SH-) group of glutathione is primarily responsible for its properties, including acting as a redox buffer to regulate the cell and protecting enzymes

• Thyrotropin Releasing Hormone (TRH) is a hypothalamic hormone stimulating thyrotropin release.

• Oxytocin is a 9-amino acid hormone that stimulates uterine contractions.

• Vasopressin is a 9-amino acid hormone that increases blood pressure and acts as an antidiuretic.

• Gastrin is a local hormone that stimulates gastric juice production.

• Angiotensin II is a vasoconstrictor that elevates arterial pressure and promotes aldosterone synthesis.

• Bradykinin is a vasodilator that contains 9 amino acid residues and stimulates pain receptors.

• Insulin is a pancreatic hormone with two polypeptide chains (30 and 21 amino acids) that regulates blood glucose.

• Glucagon is a pancreatic hormone of 29 residues that opposes the action of insulin.

Classification of Proteins

• Proteins are classified by their functions:
• Catalytic proteins (enzymes) act as enzymes.
• Transport proteins transport substances.
• Storage proteins serve as storage forms.
• Contractile proteins form the contractile system of skeletal muscle.
• Structural proteins provide structural support.
• Defense proteins provide defense against foreign substances.
• Regulatory proteins regulate physiological activity.
• Based on Physical and Chemical Properties, proteins are classified as simple proteins (hydrolyzed into amino acids), conjugated proteins (with non-protein substances), and derived proteins.

Protein Structure

• Primary: the amino acid sequence forming the protein’s backbone. Amino acids join by peptide bonds (α-carboxyl and α-amino groups)
• Secondary: regular folding and twisting due to hydrogen bonding.
• An alpha-helix is stabilized by hydrogen bonds, has an optimal N-O distance of 2.8 Å, and an axial distance of 1.5 Å and has 3.6 amino acid residues per turn of helix.
• Glycine and proline destabilize helices.

Hemoglobin (Hb)

• Only in red blood cells (RBCs) and transports O2 from the lungs to the tissues
• Hb A consisting of two α and two β chains held by noncovalent interactions;
• Each chain has 141-146 amino acid residues and stretches of α-helical structure.
• Several forms exist:
• Adult Hb A1 (α2β2) is the major form (90 – 95%).
• Adult Hb A2 (α2δ2) is a minor form (2%).
• Fetal Hb F (α2γ2) is present up to the first year.
• Embryonic hemoglobin (α2ε2) occurs in early life.
• Glycosylated Hb A1c is present at 3-5% in normal individuals, but can be increased greatly with diabetes mellitus.
• In abnormal, structural mutations result in replacement of single amino acid residues, and regulator mutations affect the rate in synthesis peptide chains.
• Examples: Hb S, Hb М, НЬ С, НЬ D.
• Sickle Hemoglobin (Hb S):
• In Hb-S α-chains are normal.
• In both β-chains glutamic acid in 6th position is replaced by valine with formula has formula a2b2A6val for sickle hemoglobin
• Thalassemias result from impaired synthesis of a single Hb-chain, due to Repressed or unregulated.
• alpha-chain are repressed and compensatory increase in synthesis of other chains and β-chains either ẞ-chains or y-chains results.
• Beta-chain is decreased or absent and divided into two types:
• beta thalassemia minor if they defective beta globin chain and beta-thalassemia if both genes are defective.