BTC 312 Lecture 1: Amino Acids Structure and Properties - PDF

# Introduction to Amino Acids ## By Dr. Mohamed Attia Ragheb Lecturer of Biochemistry and Molecular Biology ## Content - Introduction - Classification and structure of amino acids - Non-standard Amino Acids - Functions of Amino Acids - Amino acid properties ## Protein Composition ### Introduction In 1839, Dutch chemist GJ Mulder while investigated (elemental analyses) substances such as those found in milk, egg found that they could be coagulated on heating and were nitrogenous compounds. Swedish scientist JJ Berzelius suggested to Mulder that these substances should be called proteins. The term is derived from Greek word Proteios means “primary” or “pre-eminent” because Berzelius thought them to be most important of biological substances. ### In addition to C, H, and O which are present in carbohydrates and lipids, proteins also contain N. The nitrogen content is around 16% of the molecular weight of proteins. Small amounts of S and P are also present. Few proteins contain other elements such as I, Cu, Mn, Zn and Fe, etc. ## Amino Acids - Protein molecules are very large molecules with a high molecular weight ranging from 5000 to 25,00,000. - Protein can be broken down into smaller units by hydrolysis. These small units the monomers of proteins are called as amino acids. - Proteins are made up from 20 such standard amino acids in different sequences and numbers. So, an indefinite number of proteins can be formed and do occur in nature. - Proteins are the unbranched polymers of L- α-amino acids. - The L- α-amino acids has a general formula as shown. ## Amino Acids: Classification The 20 amino acids in proteins encoded by DNA are shown; each can be designated by a three-letter abbreviation and one-letter symbol. They are grouped as per the classification schemes based on: - a) polarity and charge on R groups, - b) structure of side chains, - c) catabolic fate of the amino acid, - d) body's ability to synthesize the amino acid. | Primary amino acid | Three-letter abbreviation | One-letter symbol | |:---|:---|:---| | Alanine | Ala | A | | Arginine | Arg | R | | Asparagine | Asn | N | | Aspartic acid | Asp | D | | Cysteine | Cys | C | | Glutamine | Gln | Q | | Glutamic acid | Glu | E | | Glycine | Gly | G | | Histidine | His | H | | Isoleucine | Ile | I | | Leucine | Leu | L | | Lysine | Lys | K | | Methionine | Met | M | | Phenylalanine | Phe | F | | Proline | Pro | P | | Serine | Ser | S | | Threonine | Thr | T | | Tryptophan | Trp | W | | Tyrosine | Tyr | Y | | Valine | Val | V | ## Based on Polarity and Charge on R Groups Amino acids can be classified into 3 groups depending on their reaction in solution: - A. Non-polar R group - B. Polar but uncharged R groups - C. Charged polar R groups. | Non-polar R groups | Polar but uncharged R groups | Charged polar R groups | |:---|:---|:---| | Alanine | Serine | Negatively charged Aspartic acid Glutamic acid | | Valine | Threonine | Positively charged Lysine Arginine Histidine | | Leucine | Glycine | | Isoleucine | Asparagine | | Phenylalanine | Glutamine | | Tryptophan | Tyrosine | | Methionine | Cysteine | | Proline | The allocation of the 20 amino acids among the three different subgroups is somewhat arbitrary. The following examples illustrate this point: - Tryptophan with its heterocyclic aromatic R group may be thought of as uncharged polar amino acid (not uncharged non-polar amino acid). - Glycine with its smallest R group might as well be classified as non-polar amino acid. - Side chains of tyrosine and cysteine are ionizable, particularly at higher pH values, and so they might be classified as charged polar amino acids. ## Non-polar R group ### A. Non-polar R group : - Eight amino acids are classified as having non-polar side chains (R group). - In proteins these amino acid residues are usually buried in the hydrophobic interior of the biomolecule and are out of contact with water. - Glycine has hydrogen for its R group. - Alanine, valine, leucine and isoleucine have aliphatic hydrocarbon side chains ranging in size from methyl group for alanine to isomeric butyl groups for leucine and isoleucine. | Name | Formula | |---|---| | Glycine (Gly) a-amino acetic acid. | `H-CH-COOH` `NH2` | | Alanine (Ala) a-amino propionic acid | `COO-` `H3N+-C-H` `|` `CH3` | | Valine (Val) a-amino-isovaleric acid | `COO-` `H3N+-C-H` `CH` `/` `H3C CH3` | | Leucine (Leu) a-amino-isocaproic acid | `COO-` `|` `H3N+-C-H` `CH2` `CH` `H3C CH3` | | Isoleucine (Ile) a-amino-ẞ-methyl valeric acid | `COO-` `|` `H3N+ − C-H` `H-C-CH3` `CH2` `CH3` | - Phenylalanine with its phenyl moiety and tryptophan with its indole group contain aromatic side chains, and (together with the aliphatic amino acids) contribute to the internal hydrophobic interactions of the proteins. They are also responsible for the ultraviolet absorption of most proteins. - Methionine has a thiol ether side chain. - Proline differs from other amino acids in that its side chain pyrrolidine ring. Chemically speaking proline is not an a-amino (-NH2) acid but rather an a-imino (-NH) acid. | Name | Formula | |---|---| | Phenylalanine (Phe) a-amino-ẞ-phenyl propionic acid. | `COO-` `H3N+-C-H` `CH2` | | Methionine (Met) a-amino y-methylthio-n-butyric acid | `COO-` `H3N+-C-H` `CH2` `CH2` `S` `CH3` | | Tryptophan (Trp) a-amino-ẞ-3-indole propionic acid | `COO-` `H3N+-C-H` `CH2` `NH`| | Proline (Pro) Pyrrolidone-2-carboxylic acid | `COO-` `H2N+-C-H` `H2C CH2` `C` `H2` | ## Uncharged Polar R Groups - Side chains of these amino acids are uncharged, and they have polar groups (-OH, -SH, -NH, C=O) that can hydrogen bond to water. - Serine and threonine, for example, bear hydroxylic groups of different sizes. - Tyrosine has a phenolic group (and like phenylalanine and tryptophan is aromatic). | Name | Formula | |---|---| | Serine (Ser) a-amino-ẞ-hydroxy propionic acid | `OH NH2` `H2C-C-COOH` `β` `H` | | Threonine (Thr) a-amino-ẞ-hydroxybutyric acid | `OH` `NH2` `H3C-CH-C-COOH` `β` `α` `H`| | Tyrosine (Tyr) or parahydroxy phenylalanine a-amino-ẞ-parahydroxy phenylpropionic acid |`OH` `NH2` `-CH2-C-COOH` `H` | - Asparagine and glutamine have amide-bearing side chains of different sizes. | Name | Formula | |---|---| | Asparagine (Asn) y -amide of a-aminosuccinic acid | `NH2` `Y` `β` `|` `NH2-C-CH2-C-COOH` `H` | | Glutamine (Gln)-Amide of Glutamic Acid 6-amide of a-aminoglutaric acid |`CONH2` `NH2` `CH2-CH2-C-COOH` `H` | - Cysteine has a thiol group that can form disulphide bond with another cysteine through oxidation of the two thiol groups to form cystine. | Name | Formula | |---|---| | Cysteine (Cys) a-amino-ẞ-mercaptopropionic acid |`SH` `NH2` `CH2-C-COOH` `β` `α` `H` | | Cysteine and cystine | `COOH` `H2N-C-H` `CH2-SH` `Cysteine` + `HS-CH2` `Cysteine` -> 2H `COOH` `H2N-C-H` `CH2-S-S-CH2` `Cystine` | ## Charged Polar R Groups Five amino acids have charged side chains, having acidic or basic groups. These groups can assume respectively, negative or positive charge at physiologic pH values. 1. The basic amino acids have a positive charge on their R group at physiological pH values (because the R groups are protonated). - Lysine has a primary amino group attached to the terminal ε-carbon of the side chain (i.e. butylammonium side chain), which has pK of 11. - Arginine is the most basic amino acid (pK 13) and its guanidine group exists as a protonated guanidinium ion at pH 7.0. - Histidine, which carries an imidazoline ring as the side chain functions as a general acid-base catalyst. This is because with its pK 6.0, it ionizes within the physiological pH range. - In contrast to lysine and arginine, which are fully charged at the physiological pH, histidine is only partially charged; its side chains being weakly basic. | Name | Formula | |---|---| | Lysine (Lys) α- ε-diamino caproic acid | `NH2` `E` `8` `Y` `β` `CH2-CH2-CH2-CH2-C-COOH` `H` `NH2` | | Arginine (Arg) a-amino- 8-guanidino-n-valeric acid | `8` `Y` `NH2` `β` `H-N-CH2-CH2-CH2-C-COOH` `C-NH` `NH2` | | Histidine (His) a-amino-ẞ-imidazole propionic acid. | `NH2` `CH2-C-COOH` `HN` `H` `N` | 2. The acidic amino acids, have negative charge at physiologic pH, e.g. glutamic acid and aspartic acid. Both contain carboxylic acids on their side chains and are ionized at pH 7.0, and as a result, carry negative charges on their ẞ- and y-carboxyl groups, respectively. - In their ionized state, they are referred to as aspartate and glutamate (asparagine and glutamine are, respectively, the amides of aspartic acid and glutamic acid). | Name | Formula | |---|---| | Aspartic acid (Asp) a-amino succinic acid. | `HOOC NH2` `COOH` `CH2-C-COOH` `H` | | Glutamic Acid (Glu) a-aminoglutaric acid | `NH2` `CH2-CH2-C-COOH` `H` | ## Based on Structure of Side Chain - Aliphatic amino acids: - Simple amino acids: Glycine and alanine - Branched chain amino acids: Valine, leucine, isoleucine - Sulphur containing amino acids: Methionine, cysteine - Amide group containing amino acids: Asparagine, glutamine - Hydroxy amino acids: Serine, threonine, tyrosine - Aromatic amino acids: Phenylalanine, tyrosine, tryptophan - Heterocyclic amino acids: Histidine, tryptophan - Dicarboxylic amino acids: Aspartic acid and glutamic acid - Dibasic amino acids: Arginine, lysine - Imino acid: Proline ## Based on Catabolic Fate of the Amino Acid From the viewpoint of their catabolic fate, amino acids may be divided into three categories: those that can give rise to glucose and glycogen, those that can give rise to ketone bodies and those that can give rise to both. They are called the glucogenic, the ketogenic, and both glucogenic and ketogenic amino acids, respectively. | Nonessential | Glucogenic | Glucogenic and Ketogenic | Ketogenic | |---|---|---|---| | Alanine Arginine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Proline Serine | Tyrosine | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Essential | Isoleucine Leucine Phenyl-alanine Lysine Tryptophan | | | | | | | | | | | | | | | | | | ** Glucogenic amino acids are amino acids that can be converted into glucose via gluconeogenesis** **Ketogenic amino acids are amino acids that form acetyl CoA or acetoacetyl CoA ** - Form glucose precursors - Important in gluconeogenesis - Form precursors for ketone bodies - Important in Ketogenesis - Include most essential and non-essential amino acids - Include exclusively lysine and leucine ## Based on Essentiality Nutritionally, amino acids are classified into 3 classes: a. **Essential amino acids:** These are the ones which are not synthesized by the body and must be taken in diet. They include valine, leucine, isoleucine, phenylalanine, threonine, tryptophan, methionine and lysine. b. **Non-essential amino acids:** They can be synthesized by the body and may not be the requisite components of the diet. They include Alanine, aspartic acid, asparagine, glycine, glutamic acid, glutamine, cysteine, proline, seine, and tyrosine. c. **Semi-essential amino acids:** These are growth promoting factors since they are not synthesized in sufficient quantity during growth. They include arginine and histidine. They become essential in growing children, pregnancy and lactating women. | Nonessential | Essential | Glucogenic | Glucogenic and Ketogenic | Ketogenic | |---|---|---|---|---| | Alanine Arginine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Proline Serine | Histidine Methionine Threonine Valine | Tyrosine | Isoleucine Leucine Phenyl-alanine Lysine Tryptophan | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ## Non-standard Amino Acids 1. **Non-standard amino acids found in proteins:** These amino acids are produced by specific modification of a primary amino acid residue after the polypeptide chain has been synthesized. They are important, and in most cases, essential for the function of the protein. Hydroxylation, methylation, acetylation, carboxylation and phosphorylation are some common modifications, though more elaborate modifications are found in some amino acid residues. Some examples of modified amino acids are: - hydroxylysine and hydroxyproline in collagen, - methylhistidine in muscle proteins, - phosphoserine in casein and certain enzymes, - γ-carboxyglutamic acid in prothrombin and other calcium-binding proteins, - pyroglutamic acid as the N-terminal amino acid in thyrotropin and several proteins. 2. **Non-standard amino acids not found in proteins:** Termed non-protein amino acids, they occur in free state in cells, e.g. ornithine and citrulline that are intermediates of urea cycle. The most abundant amino acid in human organism, taurine, also occurs in a free state in bile and plays an important role in fat digestion and absorption. 3. **Biologically active amino acids:** These amino acids are used for functions other than protein synthesis. Examples: - a) as chemical messengers for communication between cells, e.g. glycine, dopamine (tyrosine derivative), γ-aminobutyric acid GABA (glutamate derivative), - b) as local mediator of allergic reactions, e.g. histamine (histidine derivative), - c) as a hormone, e.g. thyroxine (another tyrosine derivative). 4. **D-Amino acids:** They are components of bacterial polypeptides that are widely distributed as constituents of bacterial cell walls. They are also found in many bacterially produced peptide antibiotics, including valinomycin and gramicidin A. ## New Amino Acids In addition to 20 L-amino acids that take part in protein synthesis, recently two more new amino acids described. They are: A. **Selenocysteine - the 21st amino acid** Selenocysteine occurs at the "active site" of several enzymes. Examples include: - Thioredoxin reductase - Glutathione peroxidase which scavenges peroxides, - De-iodinase that converts thyroxine to triiodothyronine - Glycine reductase - Selenoprotein P, a glycoprotein containing 10 selenocysteine residues, found in mammalian blood. It has an antioxidant function and its concentration falls in selenium deficiency. B. **Pyrrolysine - the 22nd Amino Acid** Recently it has been claimed as 22nd amino acid by some scientists. The STOP codon UAG can code for pyrrolysine in some bacteria. ## Functions of Amino Acids Apart from being the monomeric constituents of proteins and peptides, amino acids serve a variety of functions. - a) Some amino acids are converted to carbohydrates and are called as glucogenic amino acids. - b) Specific amino acids give rise to specialized products, e.g. - Tyrosine forms hormones such as thyroid hormones, (T3, T4), epinephrine and norepinephrine and a pigment called melanin. - Tryptophan can synthesize a vitamin called niacin (B vitamin).and serotonin. - Glycine, arginine and methionine synthesize creatine. - Glycine and cysteine help in synthesis of Bile salts. - Glycine, cysteine and glutamate synthesize glutathione. - Histidine changes to histamine on decarboxylation. - Pyrimidines and purines use several amino acids for their synthesis such as (aspartate and glutamine for pyrimidines) and (glycine, aspartic acid, Glutamine and serine for purine synthesis). - c) Methionine acts as "active" methionine (S-adenosylmethionine or SAM) and transfers methyl group to various substances by transmethy - d) Methionine and Cysteine are sources of sulfur. ## Properties of Amino Acids ### A. Isomerism: - All amino acids except glycine are optically active and exist in D and L isomers. In D-amino acids - NH2 group is on the right hand while in L-amino acids it is oriented to the left. Natural proteins of animals and plants generally contain L-amino acids. D-amino acids occur in bacteria. ### B. Amphoteric Nature and Isoelectric pH: - The -NH2 and -COOH groups of amino acids are ionizable groups. Further, charged polar side chains of few amino acids also ionise. Depending on the pH of the solution these groups act as proton donors (acids) or proton acceptors (bases). This property is called as amphoteric and therefore amino acids are called as ampholytes. - At a specific pH the amino acid carries both the charges in equal number and exists as dipolar ion or "Zwitterion". - At this point the net charge on it is zero, i.e. positive charges and negative charges on the protein/amino acid molecule equalizes. - The pH at which it occurs without any charge on it is called pI or isoelectric pH. - On the acidic side of its pI amino acids exist as a cation by accepting a proton and on alkaline as anion by donating a proton. - It plays a key role in the separation of amino acids, peptides and proteins by altering the pH of the medium (e.g. PAGE). - The isoelectric pH (pI): is the pH midway between pKa values on either side of the isoelectric species. pI = (2.3+9.1)/2 = 5.7 - At pH 4, which one of the following sentence is true: Knowing that pK₁=2.3 and pK2=9.1 - a. Form I is higher than Form II - b. Form II is higher than Form I - c. Form I equal Form II - d. None of them Note: Not conditional to write pI in this type of questions, so you will calculate it from the given pK₁ and pK2 to answer the question ### C. Physical Properties: - They are colorless, crystalline substances, more soluble in water than in organic solvents. Tyrosine is soluble in hot water. They have high melting point usually more than 200°C. They have sweet taste (glycine, alanine, valine), tasteless (leucine), or bitter taste (glutamate). ### D. Chemical Properties #### I. Due to Carboxylic (-COOH) Group 1. Formation of esters: They can form esters with alcohols. The COOH group can be esterified with alcohol. 2. Reduction to amino alcohol: This is achieved in presence of lithium aluminium hydride. 3. Formation of amines by decarboxylation: Action of specific amino acid decarboxylases, dry distillation or heating with Ba(OH)2 or with diphenylamine evolves CO2 from the COOH group and changes the amino acid into its amine. 4. Formation of amides: Anhydrous NH3 may replace alcohol from its combination with an amino acid in an amino acid ester so that an amide of amino acid and a molecule of free alcohol is produced #### II. Due to Amino (-NH2) Group 1. Salt formation with acids: The basic amino group reacts with mineral acids such as HCl to form salts like hydrochlorides. 2. Formation of acyl derivatives: Amino group reacts with acyl anhydride or acyl halides such as benzoyl chloride and give acyl amino acids like benzoyl glycine (hippuric acid). Incidentally, this is one of the mechanisms of detoxication in which glycine is used. 3. Oxidation: Potassium permanganate or H2O2 oxidises the NH₂ group and converts the amino acid into imino acid which reacts with water to form NH3 and a-ketoacid. 4. Reaction with HNO2: Like other primary amines, the amino acids except proline and hydroxyproline react with HNO2 (nitrous acid) libering N₂ from NH2 group. This forms the basis of Van Slyke's method for determining -NH2 group (Nitrogen). 5. Specific color reactions: Reactions with Ninhydrin, Millon's test, Sakaguchi test, Hopkins-Cole test are discussed under properties of proteins.

BTC 312 Lecture 1: Amino Acids Structure and Properties - PDF

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