Amino Acid Composition and Classification PDF

1/12/2025 Amino Acid Composition and Classification Dr. Lujain Almohammadi Outline 1-Amino Acid Structure and Properties 2- Classification of Amino Acids 3-Protein classification 4-Protein Structure: Primary to Quaternary 5-Biological Roles of Amino Acids and Proteins...

1/12/2025 Amino Acid Composition and Classification Dr. Lujain Almohammadi Outline 1-Amino Acid Structure and Properties 2- Classification of Amino Acids 3-Protein classification 4-Protein Structure: Primary to Quaternary 5-Biological Roles of Amino Acids and Proteins 1  1/12/2025 Introduction to Amino Acids What are Amino Acids? The building blocks of proteins. Each has three parts: A carboxyl group (-COOH). An amino group (-NH2). A hydrogen atom (-H) A side chain (R group) that makes each amino acid unique. Introduction to Amino Acids The most important amino acids are alpha-amino acids, where the amino (-NH2) and carboxyl (-COOH) groups are attached to the same carbon atom (the alpha-carbon). There are more than 300 amino acids in nature, but only 20 are essential for making proteins in the body. Some amino acids have their amino and carboxyl groups on different carbons (e.g., beta-alanine, gamma-aminobutyric acid). 2  1/12/2025 Classification of Amino Acids Amino acids can be classified based on: 1.Chemical Structure 2.Nutritional or Biological Function 3.Metabolic Fate Classification I - Chemical Structure (based upon: Amino acid side chain ) 1-Nonpolar Aliphatic: Examples: Glycine, Alanine, Valine, Leucine, Isoleucine 3  1/12/2025 Classification I - Chemical Structure 2- Aromatic Amino Acids: Examples: Phenylalanine, Tryptophan (essential), Tyrosine (non- essential) Classification I - Chemical Structure 3-Sulfur containing amino acids 4-Hydroxyl containing amino acids Methionine and threonine are essential amino acid 4  1/12/2025 Classification I - Chemical Structure 5- Acidic amino acids 6- Amidic amino acids All are non-essential amino acid Classification I - Chemical Structure 7- Basic amino acids 8- Imino acid (All Charged & essential amino acids) (non-essential) 5  1/12/2025 Classification II - Nutritional or Biological Classification Based upon: Whether the amino acids can be synthesized in body or not Type Definition Acronym Examples Essential Amino Acids Cannot be synthesized PVT TIM HALL Phenylalanine, Valine, by the body; must be Threonine, Tryptophan, obtained from the diet Isoleucine, Methionine, Histidine, Arginine (semiessential), Lysine, Leucine Non-Essential Amino Can be synthesized by G CATS GAS Glu Glycine, Cysteine, Acids the body; not essential Alanine, Tyrosine, in the diet. Serine, Glutamine, Asparagine, Spartate, Glutamate Semi-Essential Amino Essential during periods Arg (during Acid of growth, stress, or growth/stress) Arginine illness Classification III - Metabolic Fate Based upon: Fate of amino acid inside the body Type Definition Acronym Examples Ketogenic amino Amino acids that LL Leucine, Lysine acids can be converted into ketone bodies Glucogenic Amino Amino acids that All amino acids acids can be converted except Leucine into glucose. and Lysine Mixed Amino Amino acids that PITT Phenylalanine, acids can be converted Isoleucine, into both glucose Tyrosine, and ketone Tryptophan bodies 6  1/12/2025 Uncommon Amino Acids What are they? Not part of the 20 fundamental amino acids. Derived from post-translational modifications or unique synthesis processes. Why are they important? Play critical roles in protein function, structure, and biochemical pathways. Derived from Post-Translational Modifications Name Derived from Function Example 4-Hydroxyproline Proline Stabilizes collagen Found in collagen structure 5-Hydroxylysine Lysine Involved in collagen Found in collagen cross-linking 6-N-Methyllysine Lysine Component of Found in myosin contractile proteins γ-Carboxyglutamate Glutamate Binds calcium in blood Found in prothrombin clotting proteins (clotting factor) 7  1/12/2025 Selenocysteine – The 21st Amino Acid Contains selenium instead of sulfur (derived from serine). Introduced during protein synthesis (not a post-translational modification). Role in Enzymes: Found in active sites of oxidation-reduction enzymes: e.g Glutathione peroxidase Ornithine and Citrulline Both are Intermediate in the urea cycle. Urea cycle Play a key role in nitrogen metabolism Properties of Amino Acids: All Amino Acids Are Alpha Amino Acids Alpha carbon The amino group is attached to the alpha carbon Glycine is the only amino acid without an asymmetric alpha carbon. 8  1/12/2025 Properties of Amino Acids: Optical Activity Alpha Carbon: Asymmetric (except glycine). Forms: 𝐿-Amino Acids: Found in proteins. 𝐷-Amino Acids: Found in some bacterial products. Exception: Glycine is not optically active. D and L forms of alanine are mirror images Properties of Amino Acids : Amphoteric Nature Amino acids have both acidic (COOH) and basic (NH2) groups. Can act as both acids and bases depending on the pH. Isoelectric Point (pI) H At pI, amino acid has no net charge. COOH is negatively charged and NH2 is positively charged. H3+N C COO- Zwitterion: A molecule with both positive and negative charges. CH3 Zwitterion of Alanine 9  1/12/2025 Effects of pH on Amino Acid Behavior At Low pH (Acidic): At Neutral pH (Around pI): High hydrogen ion (H⁺) concentration. Amino acid exists as a zwitterion: Both amino and carboxyl groups are NH3⁺ (positively charged) and protonated: COO⁻ (negatively charged). NH2 → NH3⁺ Overall charge: Neutral. COOH remains COOH. Overall charge: Negative. Overall charge: Positive. At High pH (Basic): Low hydrogen ion (H⁺) concentration. Both amino and carboxyl groups lose protons: NH3⁺ → NH2. COOH → COO⁻. Overall charge: Negative. Beyond Proteins: Amino Acid Functions In addition to their role as building blocks of proteins and peptides, amino acids serve variety of functions. Amino Acid Function Glycine Detoxification and Synthesizes heme Methionine Methyl donor in metabolism Synthesizes thyroid hormones (T3, T4), Tyrosine epinephrine, norepinephrine, and melanin Synthesizes niacin (Vitamin B3) and Tryptophan serotonin Histidine Synthesizes histamine Aspartate and Glutamine involved in pyrimidine synthesis Glycine, Aspartic Acid, Glutamine Involved in purine synthesis 10  1/12/2025 Summary- Amino acids at a glance ‫لإلطالع‬ Protein Classification and Conformation 11  1/12/2025 Introduction to Proteins and Biologically Active Peptides Proteins (polypeptides) are polymers of amino acids, linked by peptide bonds. Their structure and function are dictated by the sequence of amino acids. They play crucial roles in various biological processes. peptides range in size from two to many thousands of amino acids. Biological activities are not always related to size or molecular weight. Very Small Peptides Even small peptides can have significant biological effects. Example: Aspartame (dipeptide L-aspartyl-L-phenylalanine methyl ester), a low-calorie artificial sweetener. 12  1/12/2025 Examples of Small Peptides Peptide Amino acids Function Example of effects Oxytocin 9 Stimulates uterine contractions during Plays a crucial role in labor childbirth. and milk ejection. Bradykinin 9 Inhibits inflammation and mediates Reduces tissue pain. inflammation. Thyrotropin-Releasing 3 Stimulates the release of thyroid- Helps regulate thyroid Factor stimulating hormone (TSH) from the function. pituitary. Glutathione 3 Antioxidant, protects cells from Crucial for cellular oxidative stress. detoxification. Amanitin (toxic peptide) 8 Inhibits RNA polymerase in cells, leading Responsible for the toxicity to cell death. of certain mushrooms. Gramicidin A (antibiotic) Varaiable Disrupts bacterial cell membranes, Used as an antibiotic against leading to bacterial cell death. bacterial infection Slightly Larger Peptides and Oligopeptides Peptide Amino Acids Functions Example of effects Insulin 51 Regulates glucose metabolism by Regulates and controls promoting glucose uptake in cells. blood sugar levels. Glucagon 29 Raises blood glucose levels by Opposes insulin to stimulating glycogen breakdown. increase blood glucose levels during fasting. Corticotropin 39 Stimulates the adrenal cortex to Regulates the body's release cortisol in response to stress response and stress. immune function 13  1/12/2025 Proteins – Definition and Role Proteins are long chains of amino acids with specific sequences. Their structure is directly influenced by the gene sequence. Even a single amino acid change can alter function (e.g., sickle cell anemia Classifications of Proteins Proteins can be classified based on: 1-Function 2-Shape 3-Composition Classification Based on Shape Globular Protein Fibrous protein compact, water Description: Spherical, Description: Linear, structural, insoluble in soluble, less stable, biologically active. water, more stable. Examples: Examples: Insulin: Hormone regulating glucose Keratin: Protein in hair, wool, skin. metabolism. Collagen: Connective tissue protein. Myoglobin: Oxygen storage in muscle. Elastin: Found in lungs and arteries. Antibodies: Immune response proteins. Myosin: Muscle protein. Enzymes: Catalysts for biochemical reactions. 14  1/12/2025 Classification Based on Function Hemoglobin Enzymes (e.g., (oxygen Lactase, transport),T Pyruvate kinase). ransferrin Transport Function Catalytic Function Proteins that Enzymes speed up transport molecules biochemical across the body reactions. Storage function Defense Function Store vital Proteins involved in molecules for later immune defense. use. Immuno- Myoglobin globulins. (store (anti- oxygen), bodies) Ferritin. More Functions of Proteins Function Function Structural Function Buffering Function - Provides structure, strength, and elasticity. - Plasma proteins act as buffers to maintain pH balance - Examples: Collagen, Keratin. - Examples: Albumin, Haptoglobin. Nutrient Function Gene Expression - Provides nutrients for biological systems. - Involved in gene regulation and packaging. - Examples: Casein, Albumin. - Examples: Histones, Nucleoproteins. Infective Agents Regulatory Function - Prions act as infective proteins causing disease. - Controls physiological processes through protein hormones. - Examples: Prions. - Examples: Insulin, Hormone receptors. 15  1/12/2025 Classification Based on Composition Simple proteins Proteins composed only of amino acids. E.g. Albumins and Globulins Derived proteins Proteins derived from simple or complex proteins after hydrolysis or denaturation. E.g. Casein and Peptones Complex Proteins Proteins made from amino acids combined with non-protein parts (lipids, carbohydrates, nucleic acids, metals). E.g. Glycoproteins and Metalloproteins Conformation of Proteins Proteins have unique three-dimensional structures, known as their conformation. Their function is determined by this structure. Proteins have four structural levels: Primary, Secondary, Tertiary, Quaternary. 16  1/12/2025 Primary Structure The sequence of amino acids in a polypeptide chain. Held together by peptide bonds. Determines the protein’s final structure and function. The protein sequence is read from left to right. It starts with the N-terminal amino acid (free amino group). It ends with the C- terminal amino acid (free carboxyl group). The remaining amino acids in the chain are called amino acid residues. Secondary Structure Local folding of the polypeptide chain into structures like: Alpha helix: Right-handed spiral, stabilized by hydrogen bonds. Beta sheet: Extended structure with hydrogen bonds between chains. 17  1/12/2025 Secondary Structure: α-helix The α-helix is a spiral structure with peptide bonds coiled tightly inside and side chains sticking out. It is a right-handed helix (coils turn clockwise), which is more stable than the left-handed version. There are 3.6 amino acids per turn of the helix. α-helices are usually found inside the protein structure. The α-helix is stabilized by hydrogen bonds within the chain (intra-chain). These bonds are weak individually, but together, they help keep the helix stable Secondary Structure: β-pleated sheet β-pleated sheet: A more extended structure than the α-helix. The structure is pleated because the C-C bonds are tetrahedral and can't be straight. Stabilized by hydrogen bonds between NH and C=O of adjacent peptide segments. The segments may run in the same direction (parallel β-sheet) or in opposite directions (antiparallel β-sheet). Beta bends (U-turns in the chain) are stabilized by disulfide bridges. In an antiparallel β-sheet, the chains are oriented in opposite directions, and the amino acid side chains alternate above and below the plane of the sheet. Hydrogen bonding occurs between different chains (interchain bonding) 18  1/12/2025 Tertiary Structure The overall 3D folding of a protein. The protein's tertiary structure is influenced by covalent bonds (such as disulfide bridges) and noncovalent bonds (including hydrophobic forces, ionic bonds, and hydrogen bonds). Hydrophobic side chains are in the interior, hydrophilic side chains are on the exterior. Quaternary Structure Quaternary structure refers to the arrangement of multiple polypeptide chains in a protein. Not all proteins have a quaternary structure. Each polypeptide chain is called a subunit, and it has its own primary, secondary, and tertiary structure. The polypeptide chains are held together by the same forces that stabilize tertiary structure. Monomer: 1 subunit Dimer: 2 subunits Tetramer: 4 subunits Example: Insulin is made up of two subunits, linked by two disulfide bridges. 19  1/12/2025 The quaternary structure of Insulin A homopolymer is made up of identical subunits. A heteropolymer is made up of different subunits. Insulin is a heteropolymer The quaternary structure of haemoglobin: Haemoglobin is a tetramer made up of two identical dimers, (αβ)₁ and (αβ)₂, where the numbers refer to dimer 1 and dimer 2. Within each dimer, the two polypeptide chains are tightly held together, primarily by hydrophobic interactions 20  1/12/2025 Summary Proteins are classified based on: Function (e.g., enzymes, transport, structural). Shape (globular vs. fibrous). Composition (simple, complex, derived). Protein Structure Levels: Primary: Amino acid sequence. Secondary: Folding into α-helices and β-pleated sheets. Tertiary: 3D shape formed by interactions. Quaternary: Assembly of multiple subunits (e.g., haemoglobin). Key Takeaway: Protein structure determines its function—classification helps us understand their diverse biological roles. 21