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Amino Acids

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  • 1.Amino Acids

2. Amino acids are one of the first organic molecules to appear on Earth. The isolated amino acids are white crystalline solids. They have high melting and boiling points due to their unique properties of ionic and dipolar in nature. Amino acids are the building blocks of the proteins. 3. Aside from their role in composing proteins, amino acids have many biologically important functions. (1) They are also energy metabolites, and many of them are essential nutrients. (2) Amino acids can often function as chemical messengers in communication between cells. For example, Arvid Carlsson discovered in 1957 that the amine 3-hydroxytyramine (dopamine) was not only a precursor for the synthesis of adrenaline from tyrosine, but is also a key neurotransmitter. (3) Certain amino acids such as citrulline and ornithine, which are intermediates in urea biosynthesis are important intermediaries in various pathways involving nitrogenous metabolism. (4) Although other amino acids are important in several pathways, S-adenosylmethionine acts as a universal methylating agent. Importance of Amino Acids 4. How many amino acids are possible theoretically? Theoretically infinite amino acids 5. Plants have more than 250 non-protein amino acids involved in defenses as secondary metabolites (Swain, 1977). To date, scientists have discovered more than five hundred amino acids in nature, but only twenty-two participate in translation (Gutirrez-Preciado et al., 2010). More than 700 amino acids occur naturally, but 20 of them are especially important. How many amino acids are found in nature? Theanine Ornithine Citrulline Canaline Lanthionine Canavanine 6. Non-standard amino acids are used as (1) Amino acids for Non-Ribosomal Peptide Synthesis (NRPS) system (2) Metabolic intermediates (3) Defense mechanism in plants (4) Others if any What are the role of non-standard amino acids? 7. Essential Non-essential Histidine Alanine Isoleucine Arginine* Leucine Aspartic acid Lysine Cysteine* Methionine Glutamic acid Phnylalanine Glutamine* Threonine Glycine* Tryptophan Proline* Valine Serine* Tyrosine* Asparagine* Selenocysteine (Bock 2000) Pyrrolysine (Srinivasan et al. 2002) Amino acids used for protein synthesis 20100=1.27 x 10130 Are 20 amino acids enough to code for all proteins? 8. Amino acids are electrolytes i.e. they are electric conductive. Due to their dipolar in nature, they are also called zwitterions (or amphoteric behavior). 9. The acid-base properties of amino acids At pH 7, the amino and carboxyl groups are charged. But, over a pH range from 1 to 14, these groups exhibit a series of equilibrium involving binding and dissociation of a proton, reflecting weak acids or bases. Their acid-base properties are important as it influences the eventual properties of proteins, permits methods of identification of different amino acids and dictates their reactivity. The amino group, characterized by a basic pK value of ~9, is a weak base. While the amino group ionizes around pH 9, the carboxyl group remains charged until a pH of ~2 is reached. At this pH, a proton binds neutralizing the charge of the carboxyl group. HA + H2O H3O+ + A- Where HA, the proton donor, is either COOH or NH3 + and A- the protein acceptor is either COO- or NH2. 10. The extent of ionization depends on the equilibrium constant K = [H+][A-]/[HA] And it becomes straightforward to derive the relationship (Known as Henderson-Hasselbalch equation) pH = pK + log[A-]/[HA] 11. Amino acid pK1 pK2 pKR Alanine 2.4 9.9 - Arginine 1.8 9.0 12.5 Asparagine 2.1 8.7 - Aspartate 2.0 9.9 3.9 Cysteine 1.9 10.7 8.4 Glutamate 2.1 9.5 4.1 Glutamine 2.2 9.1 - Glycine 2.4 9.8 - Histidine 1.8 9.3 6.0 Isoleucine 2.3 9.8 - Amino acid pK1 pK2 pKR Leucine 2.3 9.7 - Lysine 2.2 9.1 10.5 Methionine 2.1 9.3 - Phenylalanine 2.2 9.3 - Proline 2.0 10.6 - Serine 2.2 9.2 - Threonine 2.1 9.1 - Tyrosine 2.2 9.2 10.5 Tryptophan 2.5 9.4 - Valine 2.3 9.7 - The pK values for the -carboxyl, -amino groups and side chains 12. Stereoisomerism One of the most important consequences of the asymmetric -carbon is that it gives rise to a chiral centre and the presence of two isomers (mirror image). The two forms are known as L and D amino acids. All naturally occurring amino acids found in proteins belong to the L absolute configuration. The C atom is asymmetric or chiral or optically active molecule except for Glycine. The D and L stereoisomers of any amino acid have identical properties with two exceptions: they rotate plane-polarized light in opposite directions and they exhibit different reactivity with asymmetric reagents. This latter point is important in protein synthesis where D amino acids are effective inhibitors. 13. Amino acids: Enantiomer (Stereoisomer) The amino, carboxyl, hydrogen and R groups are arranged tetrahedrally around the central - carbon. 14. Amino acid classification Non-polar (hydrophobic): Ala, Ile, Leu, Phe, Pro, Trp, Val Positively charged: Arg, His, Lys Polar, but uncharged: Asn, Gln, Ser, Thr Negatively charged: Asp, Glu Thiol group: Cys, Met Uncharged: Gly Aromatic: Phe, Trp, Tyr 15. Chemical and physical properties of amino acids Glycine is the simplest amino acid. It is the only one in the table that is achiral i.e. lacks an asymmetric centre and does not occur as R/S isomers, possess little intrinsic chemical reactivity, has conformational flexibility. Glycine (Gly or G) Amino acids having hydroxyl groups Serine (Ser or S) Threonine (Thr or T) Generally phosphorylated, strong nucleophile in the presence of His, Asp. 16. Aliphatic amino acids Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Inactive side chain, hydrophobic 17. Acidic or Negatively charged amino acids Aspartic acid (Asp or D) Glutamic acid (Glu or E) Negative charge under physiological conditions, exhibit chemical reactions including esterification with alcohols or coupling with amines, chelators of divalent metal ions. Asparagine (Asn or N) Glutamine (Gln or Q) Amino acids having amino groups Unreactive group that is polar and acts as hydrogen bond donor and acceptor, labile at alkaline pH or extreme temperature being deamidated to form the corresponding acidic side chain. 18. Basic or Positively charged amino acids Lysine (Lys or K) Arginine (Arg or R) Most basic side chain of Arg (pK=12). Lysine is strong basic and interacts with negatively charged atoms. Lys can also go methylation, acetylation, arylation and acylation. One of the most popular lysine modifications involves adding a nitrobenzene derivative (colored). Methylation preserves the positive charge on the side chain. In fungi, trimethylated lysine residues are found as natural components of proteins. One of the most important reactions occurring with Lys is the reaction with aldehydes to form a Schiff base. The reaction is important within the cell because pyridoxal phosphate reacts with amino group of Lys and is found in the many enzyme's active site. 19. Amino acids containing sulfur Methionine (Met or M) The sulfur atom of methionine can be oxidized to form first a sulfoxide and finally a sulfone derivative. This form of oxidative damage is known to occur in proteins and the reaction scheme involves progressive addition of oxygen atoms. The sulfur atom of Met is readily methylated using methyl iodide in a reaction that is often used to put label on Met via 13C. Sulfur of Met interacts with heavy metal complexes particularly those involving mercury and platinum such as K2PtCl4 or HgCl2 and these have proved extremely useful in the formation of isomorphous heavy atom derivatives in protein crystallography. One of the most important reactions of Met involves cyanogen bromide a reagent that breaks the polypeptide chain on the C-terminal side of Met by sequestering the carbonyl group of the next peptide bond in a reaction involving water and leading to formation of a homoserine lactone. This reaction is used to split polypeptide chains into smaller fragments for protein sequencing. 20. The thiol group ionizes at alkaline pH (~8.5) to form a reactive thioate anion (S-). This thiolate anion reacts rapidly with many compounds, but the most importantly includes other thiols or disulfides in exchange type reactions occuring at neutral to alkaline pH. A common reaction of this type is between Cys and Ellmans reagent (Dithionitrobenzoic acid DTNB). The aromatic disulfide unergoes exchange with reactive thiolate anions forming a colored aromatic thiol nitrothiobenzoate. The benzoate anion absorbs intensely at 416 nm allowing the concentration of free thiol groups to be accurately estimated in biological systems. Thiols are oxidized by molecular oxygen in reactions catalyzed by trace amounts of transition metlas including Cu and Fe. More potent oxidants such as performic acid oxidize the thiol groups to a sulfonate (SO3 2-) and this reaction has been exploited as a method of irreversibly breaking disulfide bridges to form two cysteic acid residues. More frequently, disulfide bonds are broken by mercaptoethanol or dithiothreitol, dodium borohydride or molecular hydrogen. Cysteine (Cys or C) The sulfur group of Cys is more reactive than that of Met. Functional group of Cys is called Thiol, sulfhydryl or mercapto. It is the most reactive side chain found amongst the 20 naturally occuring amino acids undergoing many chemical reactions with diverse reagents. For example, some enzyme use Cys in their active site. It can also form disulfide bonds. 21. Proline (Pro or P) Unique side chain that covalently bonds with the backbone nitrogen atom to form a cyclic pyrrolidine ring with groups lacking reactivity. One of the few reactions involving prolyl side chains is enzyme-catalyzed hydroxylation. Hisdine (His or H) pK of around 7.0. In its ionized state, it has positive charge whilst in the unionized state the side chain remains neutral. Experimental evidence suggests that the hydrogen atom is usually located on the NE2 nitrogen but upon further protonation, it moves to ND1 nitrogen. Thus, it exists in resonance between two nitrogen atoms. The unprotonated nitrogen of the uncharged imidazole ring is a potent nucleophile and has a capacity for the hydrogen bonding. 22. Aromatic amino acids Phenylalanine (Phe or F) Tyrosine (Tyr or Y) Tryptophan (Trp or W) They absorve UV light and are responsible for the absorbance and the fluorescence of proteins frequently measure between 250 and 350 nm. In this region, the molar extinction coefficients (an indication of how much light is absorbed at a given wavelength) of Phe, Tyr and Trp are not equal. Trp exhibits a molar extinction coeff. ~four times that of Tyr and ~28 times greater than Phe. Almost all spectrophotometric measurements of a proteins absorbance at 280 nm reflect the intrinsic Trp content of that protein. At equivalent molar concentrations, proteins with a high number of tryptophan residues will give a much larger absorbance at 280 nm when compared with proteins possessing a lower Trp content. 23. Amino acid Properties Phenylalanine The aromatic ring of Phe is chemically inert and thus resistant to chemical modification. However, it forms pi-pi interactions with other aromatic rings. Tyrosine It is more reactive than Phe due to the presence of OH group. Nucleophiles such as nitrating agents or activated forms of iodide react with tyrosine side chains in proteins and change the acid-base properties of the ring. Tryptophan The indole side chain is the largest side chain occurring in proteins and is responsible for most of the intrinsic absorbace and fluorescence. As a crude approximation, the molar extinction coeff. Of a protein at 280 nm may be estimated by adding up the number of Tryp residues found in the sequence and multiplying by 5800. Spectroscopic properties of the aromatic amino acids Amino acid Absorbance Fluorescence max (nm) (M-1 cm-1) max (nm) Quantum yield Phe 257.4 197 282 0.04 Tyr 274.6 1420 303 0.21 Trp 279.8 5600 348 0.20 24. Detection, identification and quantification of amino acids and proteins The concentration of a protein solution is calculated using the data in Table and Beer- Lamberts Law A280 = 280 x c x l (where A: absorbance, : molar absorptivity coeff, c: concentration in moles dm-3 and l: light path length normally 1 cm). The specific optical rotation of selected amino acids L-amino acid [ ]D (H2O) L-Amino acid [ ]D (H2O) Alanine 1.8 Isoleucine 12.4 Arginine 12.5 Leucine -11.0 Cysteine -16.5 Phenylalanine -34.5 Glutamic acid 12.0 Threonine -28.5 Histidine -38.5 Tryptophan -33.7 25. Amino acid composition in proteins Based on the UnitProtKB/trEMBL database (release no.: 2013_06 on 29th May 2013) It contains 3,55,02,518 sequence entries and 11,38,44,40,438 amino acids. Amino acid Frequency (%) Alanine 8.66 Arginine 5.43 Asparagine 4.09 Aspartate 5.33 Cysteine 1.23 Glutamine 3.98 Glutamate 6.19 Glycine 7.09 Histidine 2.20 Isoleucine 6.00 Amino acid Frequency (%) Leucine 9.96 Lysine 5.26 Methionine 2.47 Phenylalanine 4.03 Proline 4.65 Serine 6.63 Threonine 5.55 Tryptophan 1.30 Tyrosine 3.03 Valine 6.79 26. Legend: gray = aliphatic, red = acidic, green = small hydroxy, blue = basic, black = aromatic, white = amide, yellow = sulfur