Amino Acids - Lecture Notes PDF

# Amino acids - Amino acids are a group of organic compounds containing two functional groups - amino and carboxyl. - The amino group (-NH₂) is basic while the carboxyl group (-COOH) is acidic in nature. - There are about 300 amino acids occur in nature. Only 20 of them occur in proteins...

# Amino acids - Amino acids are a group of organic compounds containing two functional groups - amino and carboxyl. - The amino group (-NH₂) is basic while the carboxyl group (-COOH) is acidic in nature. - There are about 300 amino acids occur in nature. Only 20 of them occur in proteins. ## Structure of amino acids: - Each amino acid has 4 different groups attached to α-carbon (which is C-atom next to COOH). These 4 groups are: amino group, COOH, Hydrogen atom and side Chain (R). ## THEY ARE CLASSIFIED ACCORDING TO: - **Chemical Structure of Side Chain** - **Polarity of Side Chain** - **Biological Value** - **Nutritional Value** ## Classification of amino acids - **Amino acid classification based on the structure** - The 20 standard amino acids found in protein structure are divided into several distinct groups. - 1. Aliphatic amino acids: - These are monoamino monocarboxylic acids. - This group consists of most simple amino acids. - A) Glycine - Gly - G - B) Alanine - Ala - A - C) Valine - Val - V - D) Leucine - Leu - L - E) Isoleucine - Ile - I - 2. Hydroxyl group containing amino acids: - **Mnemonic**: "OH" Tie Saree Thread - Serine - Ser - S - Threonine - Thr - T - Tyrosine - Tyr - Y - 3. Sulfur containing amino acids: - Cysteine - Cys - C - Methionine - Met - M - 4. Acidic amino acids and their amides: - Aspartic acid - Asp - D - Asparagine - Asn - N - Glutamic acid - Glu - E - Glutamine - Gln - Q - 5. Basic amino acids: - Lysine - Lys - K - Arginine - Arg - R - Histidine - His- H - 6. Aromatic amino acids: - Relatively nonpolar - Absorb ultraviolet light to different degrees - Phe, Tyr and Trp are central molecules in plant metabolism & functions as building blocks of proteins - The three AAA serve as precursors for a variety of plant hormones as auxin and salicylate, as well as for a very wide range of aroma secondary metabolites with multiple biological functions - Phenylalanine - Phe - F - Tyrosine - Tyr - Y - Tryptophan - Trp - W - 7. Imino acids: - Proline containing pyrrolidine ring is a unique amino acid. - It has an imino group (=NH). Therefore, proline is an α-imino acid. ## According to Chemical Structure: - 1) Amino acids with aliphatic side chains: - Aliphatic R groups are nonpolar and hydrophobic - 2) Amino acids with aliphatic branched side chains ## Glycine: - Small, simple amino acid. R - group is hydrogen - It is a non-essential amino acid. - Glycine is an allosteric inhibitor of glutathione synthetase. - Create muscle tissue. - Maintaining healthy central nervous and digestive systems. - Provide protection via antioxidants from some types of cancer. - Almost 1/3 of collagen which keeps the skin and connective tissue firm and flexible. ## Alanine: - It is a non-essential amino acid. Alanine is an allosteric inhibitor of glutathione synthetase. - D-Alanine: is a component of bacterial cell wall. - B-Alanine is found in pantothenic acid. ## Compare the final products of BCAA | Amino Acid | Final Products | Biological Value | |-------------|---------------------|-------------------| | Leucine | acetyl-CoA + acetoacetate | Ketogenic | | Isoleucine | acetyl-CoA + succinyl-CoA | Ketogenic + Glucogenic | | Valine | succinyl-CoA | Glucogenic | ## Metabolic defects of branched chain amino acids - **Maple syrup urine disease:** - The urine of the affected individuals smells like maple syrup or burnt sugar. - **Enzyme defect**: Branched chain α-keto acid dehydrogenase. ## Cysteine: - It is a non-essential amino acid. - Cystine, another important sulfur-containing amino acid, is formed by the condensation of two molecules of cysteine. ## Cystine consists of two disulfide-linked cysteine residues: - Cysteine contains a sulfhydryl group (-SH). - Two cysteines can become oxidized to form a dimmer cystine, which contains a covalent cross-link called a disulfide bond (-S-S-). - Important in the formation and maintenance of the tertiary (folded) structure in many proteins. ## Methionine: - It is an essential amino acid. - In genetic code methionine is coded by codon AUG. This codon is called start codon. Methionine is the first amino acid used to build a protein chain. ## Lysine: - It is an essential amino acid. These are strongly polar. - Require for the manufacture of carnitine -> proper fat metabolism - Crosslink in collagen and elastin -> proper collagen and elastin function - Depend on lysloxidase which requires copper - Copper deficiency can result in imperfections in collagen or elastin ## Arginine: - It is a semi-essential amino acid. - It contains guanidino group and is monocarboxylic acid. - It is an intermediate in urea cycle and is precursor for nitric oxide. ## Histidine: - It is a semi-essential amino acid. - It contains imidazole ring. ## According to Polarity of Side Chain: | Group | Amino Acid | |-------------|----------------| | Nonpolar | Glycine(Gly) | | | Alanine(Ala) | | | Valine(Val) | | | Leucine(Leu) | | | Isoleucine(Ile) | | | Methionine(Met) | | | Tryptophan(Trp) | | | Phenylalanine(Phe) | | | Proline | | Polar | Serine(Ser) | | | Threonine(Thr) | | | Cysteine(Cys) | | | Tyrosine(Tyr) | | | Asparagine(Asn) | | | Glutamine(Gln) | | Electrically Charged | Aspartic Acid(Asp) | | | Glutamic Acid(Glu) | | | Lysine(Lys) | | | Arginine(Arg) | | | Histidine(His) | ## According to the nutritional value: | Category | Amino Acid | Amino Acid | Amino Acid | Amino Acid | Amino Acid | Amino Acid | |-----------------|----------------|----------------|-------------|-------------|-------------|-------------| | Obtained from Nutrition | Leucine | Methionine | Isoleucine | Phenylalanine | Valine | Histidine | | | Lysine | Threonine | Tryptophan | Arginine | | | | Synthesized by the Body | Alanine | Glutamine | Glycine | Asparagine | Proline | Serine | | | Glutamic acid| | | | Aspartic Acid| Tyrosine | | Cysteine | | | | | | - **Amino acid in human body** ## 3. Nutritional classification of amino acids: - **A) Essential or indispensable amino acids:** - The amino acids which cannot be synthesized by the body and need to be supplied through the diet are called essential amino acids. - They are required for proper growth and maintenance of the individual. - **The 10 essential amino acids are** - 1. Arginine - Semi-essential - 2. Valine - 3. Histidine - Semi-essential - 4. Isoleucine - 5. Leucine - 6. Lysine - 7. Methionine - 8. Phenylalanine - 9. Threonine - 10. Tryptophan - **Mnemonic**: PTV TIM HALL, PVT TIM HALL, AVHILLMPTT - **B) Non - essential amino acids:** - The body can synthesize about 10 amino acids to meet the biological needs, hence they need not be consumed in the diet. - These are glycine, alanine, serine, cysteine, aspartate, asparagine, glutamate, glutamine, tyrosine, and proline. ## Based on their metabolic fate: - The carbon skeleton of amino acids can serve as a precursor for the synthesis of glucose (glucogenic) or fat (ketogenic) or both. - From metabolic veiw point, amino acids are divided into three groups ## According to Biological Value: | Category | Amino Acid | Amino Acid | Amino Acid | Amino Acid | Amino Acid | Amino Acid | Amino Acid | Amino Acid | |-----------------|-------------|-------------|-------------|-------------|-------------|-------------|-------------|-------------| | Nonessential | Alanine | Arginine | Asparagine | Aspartate | Cysteine | Glutamate | Glutamine | Glycine | | | Proline | Serine | | | | | | | | Essential | Histidine | Methionine | Threonine | Phenylalanine | Tryptophan | Valine | | | - **They are classified to**: - 1) **Pure ketogenic**: that give ketone bodies only in the body. - 2) **Mixed glucogenic & ketogenic**: that give ketone bodies and glucose. - 3) **Pure glucogenic**: that give glucose only. ## Amino acid metabolism and central metabolic pathways - **20 amino acids are converted to 7 products:** - pyruvate - acetyl-CoA - acetoacetate - α-ketoglutarate - succinyl-CoA - oxalacetate - fumarate ## New amino acids: - In addition to 20 L - amino acids that take part in protein synthesis, recently two more new amino acids are described. They are: - 1. Selenocysteine - 21st amino acid - 2. Pyrrolysine - 22nd amino acid ## Properties of amino acids: - **Physical properties:** - **Solubility**: Most of the amino acids are soluble in water and insoluble in organic solvents. - **Melting points**: Amino acids generally melt at higher temperatures, often above 200°C. - **Taste**: Amino acids may be sweet( Gly, Ala, Val), tasteless (Leu) or bitter (Arg, Ile ). - **Monosodium glutamate** is a salt of glutamic acid. It is employed as a flavoring agent in food industry to increase taste and flavor. - **Optical properties**: All amino acids except glycine possess optical isomers due to the presence of asymmetric carbon atom. - **Amino acids as ampholytes**: Amino acids contain both acidic (-COOH) and basic (NH₂) groups. They can donate a proton or accept a proton, hence amino acids are regarded as ampholytes. ## Zwitter ion or dipolar ion: - **Zwitter ion** is a **hybrid molecule** containing positive and negative ionic groups. - The amino acids rarely exist in a neutral form with free carboxylic and free amino groups. - In **strongly acidic pH**, the amino acid is **positively charged** (cation). - In **strongly alkaline pH**, the amino acid is **negatively charged** (anion). ## Acid-base properties of amino acids: - The presence of a carboxyl group and an amine group mean that amino acids have both acidic and basic properties. - **When acting as an acid**, the COOH group loses a H⁺ ion: - H₂NCHRCOOH + OH^- -> H₂NCHRCOO^- + H₂O - **When acting as a base**, the NH₂ group gains a H⁺ ion: - H₂NCHRCOOH + H⁺ -> H₃N⁺CHRCOOH - **Each amino acid** has a characteristic pH at which it carries both positive and negative charges and exists as a zwitter ion. - **Isoelectric pH** is defined as the pH at which a molecule exists as a zwitter ion or dipolar ion and carries no net charge. - pH at which amino acids exist as the zwitterion (neutral) and carries no net charge. Thus, the molecule is electrically neutral. - The pI value can be calculated by taking the average pK values corresponding to the ionizable groups. For example, leucine has two ionizable groups, and its pI value can be calculated as follows. ## Chemical properties: - The general reactions of amino acids are mostly due to the presence of two functional groups namely carboxylic (-COOH) and amino (-NH₂) group. - **Reactions due to -COOH group**: - 1. Amino acids form salts (-COONa) with bases and esters (-COOR') with alcohols. - **Reactions due to -NH₂ group**: - The amino groups behave as bases and combine with acids to form salts. ## Decarboxylation: - Amino acids undergo decarboxylation to produce corresponding amines. - e.g., histamine, tyramine, γ-amino butyric acid (GABA) from the amino acids histidine, tyrosine, and glutamate respectively. ## Reaction with ammonia: - The carboxyl group of dicarboxylic amino acids react with NH₃ to form amide. - Aspartic acid + NH₃ -> Asparagine - Glutamic acid + NH₃ -> Glutamine ## Transamination: - Transfer of an amino group from an amino acid to a keto acid to form a new amino acid is known as transamination. ## Oxidative Deamination: - The amino acids undergo oxidative deamination to liberate free ammonia. ## Importance of Amino Acids: - When proteins are digested or broken down, amino acids are left. The human body uses amino acids to make proteins to help the body: - Break down food - Grow - Repair body tissue - Perform many other body functions - Amino acids can also be used as a source of energy by the body. - Tryptophan → serotonin. - Aspartate, glutamine → pyrimidines. - Glycine, aspartate, serine → purines. - Glycine, cysteine → detoxificant. - Methionine → transfer methyl group. - Glutamate → GABA. - Tyrosine → dopamine. ## Questions: - How would you classify amino acid? - What are the major physical and chemical properties of Amino acids? - What is meant by glucogenic and ketogenic amino acid? - Niacin is formed by which of the following amino acids? - Thyroid hormone is formed by which of the following amino acid? - Which of the following amino acid is used for the formation of catecholamine? ## Fill in the Blanks: - Small amino acids - ___, ___, ___ - Branched amino acids - ___, ___, ___ - Sulfur amino acids - ___, ___ - Aromatic amino acids - ___, ___, ___ - Melanin is formed by ___ (amino acids) - ___ AMINO ACID used in the formation and maintenance of the tertiary (folded) structure in many proteins. - Methionine is coded by codon ___ - ___ amino acids are called as an aromatic amino acids.