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Amino Acids: Structure, Properties, and
Significance – An Elaborate Treatise
I. Introduction to Amino Acids: The Fundamental Units
of Protein Architecture
Amino acids, often referred to as the building blocks of proteins, are a class of organic compounds of profound biological significance. Their name derives from their characteristic chemical structure, which invariably includes a basic amino group (-NH₂) and an acidic carboxyl group (-COOH) attached to a central carbon atom, known as the alpha-carbon (α-carbon). With the exception of proline (which is technically an imino acid), this general structure holds true for the vast majority of amino acids involved in protein synthesis. Beyond their role in constituting proteins, amino acids are pivotal in a myriad of physiological processes, including neurotransmission, nucleotide biosynthesis, and the generation of metabolic energy. The diversity and versatility of life are, in no small measure, a reflection of the diverse properties of these fundamental molecules. A. General Structure of an α-Amino Acid The quintessential structure of an α-amino acid features a central tetrahedral α-carbon atom covalently bonded to four distinct chemical groups:
- A hydrogen atom (-H).
- An amino group (-NH ₂ ) : This group imparts basic properties to the molecule.
- A carboxyl group (-COOH) : This group imparts acidic properties to the molecule.
- A variable group, known as the side chain or R-group : This is the most distinctive feature of an amino acid. The nature of the R-group determines the unique properties of each individual amino acid, influencing its size, shape, charge, hydrophobicity, and chemical reactivity. There are 20 common R-groups found in proteins, leading to 20 standard amino acids. (Illustration: A diagram here would show the general structure of an L-α-amino acid, clearly labeling the α-carbon, amino group, carboxyl group, hydrogen atom, and the R-group. The tetrahedral arrangement around the α-carbon should be evident.) B. Chirality and Stereoisomerism in Amino Acids With the exception of glycine, where the R-group is a single hydrogen atom, the α-carbon of all other standard amino acids is bonded to four different groups. This makes the α-carbon a chiral center, meaning it is asymmetric. Molecules with a chiral center can exist in two non-superimposable mirror image forms called enantiomers or stereoisomers. These are designated as L- (levo) and D- (dextro) forms, based on their relationship to the configuration of L-glyceraldehyde. ● L-Amino Acids: Virtually all amino acids found in naturally synthesized proteins are of the L-configuration. The reason for this strong biological preference for L-amino acids over D-amino acids is a fascinating subject of evolutionary biochemistry, likely related to the stereospecificity of enzymes involved in protein synthesis and degradation. ● D-Amino Acids: While less common in proteins, D-amino acids are found in some specialized structures, such as bacterial cell walls (e.g., D-alanine and D-glutamate in
peptidoglycans) and certain peptide antibiotics (e.g., gramicidin, valinomycin). Their presence often confers resistance to enzymatic degradation by proteases that are specific for L-amino acids. The L and D nomenclature refers to the absolute configuration around the α-carbon. It should not be confused with the optical activity of the amino acid (levorotatory (-) or dextrorotatory (+)), which refers to the direction in which a solution of the amino acid rotates the plane of plane-polarized light and must be determined experimentally. (Illustration: A diagram here would depict the L- and D-forms of a generic amino acid (e.g., alanine), highlighting them as mirror images. The Fischer projection convention could be used to illustrate this, showing the carboxyl group at the top, R-group at the bottom, and the amino group on the left for L-amino acids and on the right for D-amino acids when the hydrogen is pointing away.) C. Zwitterions and Their Properties In neutral aqueous solution (physiological pH ~7.4), amino acids exist predominantly as dipolar ions, also known as zwitterions (from the German word "Zwitter," meaning "hermaphrodite" or "hybrid"). In this form, the amino group is protonated (-NH₃⁺) and the carboxyl group is deprotonated (-COO⁻), resulting in a molecule with both a positive and a negative charge, yet being electrically neutral overall. The zwitterionic nature of amino acids confers several important properties: ● High Melting Points: Amino acids are crystalline solids with relatively high melting points (often decomposing before melting) compared to analogous amines or carboxylic acids. This is due to the strong electrostatic interactions between the oppositely charged groups in the crystal lattice. ● Solubility in Water: They are generally more soluble in polar solvents like water and less soluble in nonpolar organic solvents like ether or chloroform. The ionic charges enhance interaction with water molecules. ● Amphoteric Nature: Amino acids can act as both acids (proton donors, due to -NH₃⁺) and bases (proton acceptors, due to -COO⁻). This amphoteric behavior is crucial for their role in pH buffering. (Illustration: A diagram showing an amino acid in its non-ionic form, then in its zwitterionic form, indicating the proton transfer from the carboxyl to the amino group.) The study of amino acids is fundamental to understanding the much larger and more complex world of proteins, enzymes, and metabolic pathways. Their individual characteristics, dictated by their side chains, and their ability to polymerize into polypeptide chains, form the basis of structural and functional biology.
II. Classification of Amino Acids
The 20 standard amino acids that are incorporated into proteins during translation can be classified in several ways, each highlighting different aspects of their structure, function, or metabolic significance. The most common and biochemically informative classification is based on the polarity and chemical nature of their R-groups, as this largely dictates how amino acids interact with each other and with their environment within a protein structure. A. Classification Based on the Chemical Nature of the R-Group (Side Chain Character) This classification system broadly categorizes amino acids into groups with nonpolar, polar uncharged, positively charged (basic), and negatively charged (acidic) side chains.
1. Nonpolar, Aliphatic R Groups
structures and disrupts regular secondary structures like α-helices and β-sheets. It is still considered nonpolar. ○ Illustration: Chemical structure of Proline, highlighting the cyclic structure involving the α-amino nitrogen.
2. Aromatic R Groups These amino acids have side chains containing aromatic rings. They are relatively nonpolar (hydrophobic) but can participate in π-π stacking interactions. Tyrosine and tryptophan are more polar than phenylalanine due to the hydroxyl and indole groups, respectively. All three absorb ultraviolet (UV) light. ● Phenylalanine (Phe, F): ○ Structure: R = -CH₂-C₆H₅ (benzyl group) ○ Properties: Strongly hydrophobic due to the bulky phenyl ring. It contributes significantly to hydrophobic interactions within proteins. Absorbs UV light with a maximum around 257 nm, but less strongly than tyrosine or tryptophan. ○ Illustration: Chemical structure of Phenylalanine. ● Tyrosine (Tyr, Y): ○ Structure: R = -CH₂-C₆H₄-OH (phenyl group with a hydroxyl substituent) ○ Properties: The hydroxyl group makes tyrosine more polar and reactive than phenylalanine. The hydroxyl group can form hydrogen bonds and can be phosphorylated in signaling pathways. It absorbs UV light strongly with a maximum around 274 nm. The pKa of the phenolic hydroxyl group is about 10, so it can be deprotonated at alkaline pH. ○ Illustration: Chemical structure of Tyrosine. ● Tryptophan (Trp, W): ○ Structure: R = -CH₂-C₈H₆N (indole ring attached to a methylene group) ○ Properties: Contains a bulky indole ring, making it hydrophobic. The indole nitrogen can participate in hydrogen bonding. Tryptophan is the largest standard amino acid and absorbs UV light most strongly, with a maximum around 280 nm. It is a precursor for neurotransmitters like serotonin and melatonin. ○ Illustration: Chemical structure of Tryptophan. 3. Polar, Uncharged R Groups These amino acids have side chains that are polar enough to form hydrogen bonds with water or other polar molecules, making them hydrophilic. However, they do not carry a net charge at physiological pH (around 7.4). ● Serine (Ser, S): ○ Structure: R = -CH₂OH (hydroxyl group) ○ Properties: The hydroxyl group makes serine polar and reactive. It can participate in hydrogen bonding and is a common site for phosphorylation (regulating enzyme activity) and glycosylation (attachment of sugar chains). ○ Illustration: Chemical structure of Serine. ● Threonine (Thr, T): ○ Structure: R = -CH(OH)CH₃ (hydroxyl group on a β-carbon) ○ Properties: Similar to serine, with a polar hydroxyl group capable of hydrogen bonding, phosphorylation, and glycosylation. Like isoleucine, threonine has two chiral centers (α and β carbons). ○ Illustration: Chemical structure of Threonine. ● Cysteine (Cys, C): ○ Structure: R = -CH₂SH (thiol or sulfhydryl group)
○ Properties: The thiol group (-SH) is highly reactive and makes cysteine unique. It is significantly more reactive than the hydroxyl groups of serine or threonine. Two cysteine residues can be oxidized to form a disulfide bond (-S-S-), creating a cystine residue. Disulfide bonds are crucial for stabilizing the three-dimensional structures of many proteins, particularly extracellular ones. The thiol group can also bind to metal ions. The pKa of the thiol group is around 8.3, so it can be deprotonated at slightly alkaline pH. ○ Illustration: Chemical structure of Cysteine. ● Asparagine (Asn, N): ○ Structure: R = -CH₂CONH₂ (amide derivative of aspartate) ○ Properties: Contains a polar amide group that can act as a hydrogen bond donor and acceptor. Asparagine is often found on the surface of proteins. It is a site for N-linked glycosylation. ○ Illustration: Chemical structure of Asparagine. ● Glutamine (Gln, Q): ○ Structure: R = -CH₂CH₂CONH₂ (amide derivative of glutamate) ○ Properties: Similar to asparagine, with a polar amide group, but has one more methylene group in its side chain. It can form hydrogen bonds and is often found on protein surfaces. Glutamine is an important nitrogen donor in various biosynthetic pathways. ○ Illustration: Chemical structure of Glutamine.
4. Positively Charged (Basic) R Groups These amino acids have side chains that are positively charged at physiological pH (typically around 7.4) because their R-groups contain basic functional groups (e.g., amino or guanidinium groups) with pKa values significantly above neutral. They are strongly hydrophilic. ● Lysine (Lys, K): ○ Structure: R = -(CH₂)₄NH₂ (ε-amino group) ○ Properties: Has a long aliphatic side chain terminating in a primary amino group (the ε-amino group). This ε-amino group is protonated (NH₃⁺) at physiological pH (pKa ~10.5), giving lysine a net positive charge. It is often involved in electrostatic interactions, salt bridges, and hydrogen bonding. The ε-amino group is also a site for various post-translational modifications, such as ubiquitination and acetylation. ○ Illustration: Chemical structure of Lysine. ● Arginine (Arg, R): ○ Structure: R = -(CH₂)₃NH-C(NH)NH₂ (guanidinium group) ○ Properties: Contains a complex guanidinium group at the end of its side chain. The guanidinium group is strongly basic (pKa ~12.5) and remains protonated and positively charged over a wide pH range. The positive charge is delocalized over the three nitrogen atoms of the guanidinium group through resonance. Arginine is important in forming salt bridges and hydrogen bonds. ○ Illustration: Chemical structure of Arginine, showing resonance in the guanidinium group. ● Histidine (His, H): ○ Structure: R = -CH₂-C₃H₃N₂ (imidazole ring) ○ Properties: Contains an imidazole ring as its side chain. The pKa of the imidazole group is around 6.0. This means that at physiological pH (~7.4), histidine can exist in both protonated (positively charged) and deprotonated (neutral) forms. This unique property allows histidine to act as both a proton donor and acceptor in
Name 3-Letter 1-Letter R-Group Characteristic
Approx. pKa (R-group) (-CH(OH)CH₃) Cysteine Cys C Thiol (-CH₂SH) ~8.3 (SH) Asparagine Asn N Amide (-CH₂CONH₂)
N/A
Glutamine Gln Q Amide (-CH₂CH₂CONH₂)
N/A
Positively Charged (Basic) Lysine Lys K ε-Amino group ~10.5 (ε-NH₃⁺) Arginine Arg R Guanidinium group ~12. (guanidinium) Histidine His H Imidazole ring ~6.0 (imidazole) Negatively Charged (Acidic) Aspartate Asp D β-Carboxyl group ~3.9 (β-COOH) Glutamate Glu E γ-Carboxyl group ~4.3 (γ-COOH) (Note: The pKa values can vary slightly depending on the chemical environment within a protein.) B. Classification Based on Nutritional Requirements Amino acids are also classified based on whether they can be synthesized by the human body or must be obtained from the diet.
- Essential Amino Acids: ○ Definition: These are amino acids that the human body cannot synthesize de novo at all, or cannot synthesize in sufficient quantities to meet physiological needs, especially during growth or under certain pathological conditions. Therefore, they must be regularly supplied through the diet. ○ List for Humans (9 standard): ■ Histidine (His, H) ■ Isoleucine (Ile, I) ■ Leucine (Leu, L) ■ Lysine (Lys, K) ■ Methionine (Met, M) ■ Phenylalanine (Phe, F) ■ Threonine (Thr, T) ■ Tryptophan (Trp, W) ■ Valine (Val, V) ○ Mnemonic: "PVT TIM HaLL" (Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine). ○ Importance: Deficiency in any essential amino acid can lead to negative nitrogen balance, impaired growth, and various health problems. Protein sources vary in their content of essential amino acids; complete proteins (e.g., from animal sources like meat, milk, eggs) contain all essential amino acids in adequate proportions, while incomplete proteins (many plant proteins) may be low in one or more.
- Non-Essential Amino Acids: ○ Definition: These amino acids can be synthesized by the human body, typically from
common metabolic intermediates or from other amino acids. ○ List for Humans: ■ Alanine (Ala, A) ■ Asparagine (Asn, N) ■ Aspartate (Asp, D) ■ Glutamate (Glu, E) ■ Serine (Ser, S) ○ Note: Proline, Glycine, Cysteine, Tyrosine, and Arginine are often synthesized by the body but sometimes fall into a "conditionally essential" category.
- Conditionally Essential Amino Acids: ○ Definition: These amino acids are normally synthesized by the body but may become essential under specific physiological conditions, such as prematurity in infants, severe illness, trauma, or during periods of rapid growth, when the body's synthetic capacity cannot meet the increased demand. ○ Examples: ■ Arginine (Arg, R): Essential for infants and during times of stress or injury. ■ Cysteine (Cys, C): Can be synthesized from methionine. If methionine intake is insufficient, cysteine becomes essential. Also important for premature infants. ■ Glutamine (Gln, Q): Important for gut health and immune function, demand increases during stress. ■ Glycine (Gly, G): Required for collagen synthesis; demand can be high during rapid growth. ■ Proline (Pro, P): Similar to glycine, important for collagen. ■ Tyrosine (Tyr, Y): Synthesized from phenylalanine. If phenylalanine intake is low or if there's a defect in the enzyme phenylalanine hydroxylase (as in phenylketonuria, PKU), tyrosine becomes essential. Table: Nutritional Classification of Amino Acids (A table would list amino acids under headings: Essential, Non-Essential, and Conditionally Essential, with brief notes on conditions for the latter.) Category Amino Acids Notes Essential Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine
Must be obtained from diet.
Non-Essential Alanine, Asparagine, Aspartate, Glutamate, Serine
Can be synthesized by the body. Conditionally Essential Arginine, Cysteine, Glutamine, Glycine, Proline, Tyrosine
Synthesis may be limited under specific physiological conditions (e.g., illness, growth, prematurity). C. Classification Based on Metabolic Fate This classification describes what happens to the carbon skeleton of an amino acid after the removal of its amino group (deamination). The carbon skeletons can be converted into intermediates of glucose metabolism or ketone body formation.
- Glucogenic Amino Acids: ○ Definition: These amino acids are catabolized to pyruvate or one of the
Amino Acid Metabolic Fate Catabolic Products Leading to Fate Threonine Glucogenic & Ketogenic Pyruvate, Acetyl-CoA, and Succinyl-CoA (minor pathway to Glycine + Acetyl-CoA) Tryptophan Glucogenic & Ketogenic Alanine (to pyruvate) and Acetoacetyl-CoA Tyrosine Glucogenic & Ketogenic Fumarate and Acetoacetate Valine Glucogenic Succinyl-CoA This multifaceted classification underscores the diverse roles and properties of amino acids, extending from their structural contributions in proteins to their intricate involvement in metabolic and nutritional physiology.
III. Physicochemical Properties of Amino Acids
The unique structures of amino acids, particularly the presence of the ionizable amino and carboxyl groups, and the diverse nature of their side chains (R-groups), dictate a wide range of physicochemical properties. These properties are crucial for the behavior of amino acids in biological systems, their separation and analysis, and the structure and function of the peptides and proteins they form. A. Acid-Base Properties Amino acids are ampholytes (or amphoteric molecules) because they contain both acidic (carboxyl group) and basic (amino group) functionalities. The R-groups of some amino acids also contain ionizable groups.
- Ionization of Amino and Carboxyl Groups: ○ In aqueous solution, the α-carboxyl group acts as an acid (proton donor) and the α-amino group acts as a base (proton acceptor). ○ The ionization state of these groups, and any ionizable R-group, is dependent on the pH of the solution. ○ Each ionizable group has a characteristic pKa value , which is the pH at which the group is 50% ionized (i.e., 50% in its protonated form and 50% in its deprotonated form). ■ α-Carboxyl groups typically have pKa values in the range of 1.8 to 2.5 (pKa₁). ■ α-Amino groups typically have pKa values in the range of 8.7 to 10.7 (pKa₂). ■ Ionizable R-groups have their own distinct pKa values (pKaR), as listed previously (e.g., Asp ~3.9, Glu ~4.3, His ~6.0, Cys ~8.3, Tyr ~10.1, Lys ~10.5, Arg ~12.5).
- Titration Curves of Amino Acids: ○ A titration curve plots the pH of an amino acid solution against the amount of strong acid or strong base added. These curves reveal the pKa values of the ionizable groups and the buffering regions. ○ For an amino acid with a non-ionizable R-group (e.g., Glycine, Alanine): ■ At very low pH (e.g., pH 1), both the α-carboxyl and α-amino groups are protonated (e.g., ⁺NH₃-CHR-COOH), and the amino acid has a net positive charge (+1). ■ As base (e.g., NaOH) is added, the α-carboxyl group is the first to lose a proton. The midpoint of this deprotonation, where [COOH] = [COO⁻],
corresponds to pKa₁. The amino acid acts as a buffer around this pH. ■ At a pH intermediate between pKa₁ and pKa₂, the amino acid exists predominantly as a zwitterion (⁺NH₃-CHR-COO⁻) with a net charge of 0. This pH is the isoelectric point (pI). ■ As more base is added, the α-amino group loses its proton. The midpoint of this deprotonation, where [NH₃⁺] = [NH₂], corresponds to pKa₂. The amino acid acts as a buffer around this pH. ■ At very high pH (e.g., pH 12), both groups are deprotonated (e.g., NH₂-CHR-COO⁻), and the amino acid has a net negative charge (-1). ■ Illustration: A titration curve for glycine, showing two buffering regions centered around pKa ₁ (~2.34) and pKa ₂ (~9.60), and the isoelectric point (pI ~5.97). ○ For an amino acid with an ionizable R-group (e.g., Glutamate, Lysine, Histidine): ■ The titration curve will show three buffering regions, corresponding to pKa₁, pKa₂, and pKaR. ■ For an acidic amino acid like glutamate (pKa₁ ~2.19, pKaR ~4.25, pKa₂ ~9.67), the R-group carboxyl deprotonates after the α-carboxyl group but before the α-amino group. ■ For a basic amino acid like lysine (pKa₁ ~2.18, pKa₂ ~8.95, pKaR ~10.53), the R-group amino deprotonates last. (Note: Conventionally, pKa values are numbered in increasing order, so for lysine, the α-COOH is pKa₁, α-NH₃⁺ is pKa₂, and ε-NH₃⁺ is pKaR, but sometimes pKa₂ and pKaR might be swapped depending on their values. It's clearer to refer to them by the group they represent). ■ Illustrations: Titration curves for glutamate (showing three inflection points for pKa(α-COOH), pKa(R-COOH), pKa(α-NH ₃⁺ )) and lysine (showing three inflection points for pKa(α-COOH), pKa(α-NH ₃⁺ ), pKa(R-NH ₃⁺ )).
- Isoelectric Point (pI): ○ Definition: The isoelectric point (pI) is the specific pH at which an amino acid molecule has no net electrical charge, meaning the number of positive charges equals the number of negative charges. At this pH, the amino acid exists predominantly as a zwitterion. ○ Significance: ■ At its pI, an amino acid is least soluble in water because the lack of net charge reduces its interaction with polar water molecules and increases aggregation. ■ At its pI, an amino acid does not migrate in an electric field, a principle used in electrophoretic separation techniques like isoelectric focusing. ○ Calculation of pI: ■ For amino acids with non-ionizable R-groups: The pI is the average of pKa₁ and pKa₂. pI = (pKa₁ + pKa₂) / 2 Example: Glycine, pI = (2.34 + 9.60) / 2 = 5. ■ For amino acids with acidic R-groups (e.g., Aspartate, Glutamate): The pI is the average of the two pKa values that flank the zwitterionic form (i.e., pKa₁ and pKaR). pI = (pKa₁ + pKaR) / 2 Example: Glutamate, pI = (2.19 + 4.25) / 2 = 3. ■ For amino acids with basic R-groups (e.g., Lysine, Arginine, Histidine):
is known or can be estimated. This is the basis for the Beer-Lambert Law (A = εcl, where A is absorbance, ε is the molar absorptivity or extinction coefficient, c is concentration, and l is path length). ○ This method is rapid and non-destructive but can be affected by other substances that absorb UV light (e.g., nucleic acids, which absorb strongly at 260 nm). D. Solubility The solubility of amino acids in various solvents is influenced by several factors:
- Polarity of the Solvent: ○ Amino acids, being zwitterionic at physiological pH, are generally soluble in polar solvents like water and ethanol due to the favorable electrostatic interactions and hydrogen bonding between the charged groups of the amino acid and the polar solvent molecules. ○ They are poorly soluble in nonpolar organic solvents such as benzene, hexane, or ether.
- Nature of the R-Group: ○ The polarity of the R-group significantly affects solubility. Amino acids with polar R-groups (e.g., Ser, Thr, Asp, Glu, Lys, Arg, His, Asn, Gln) are more soluble in water than those with nonpolar, hydrophobic R-groups (e.g., Ala, Val, Leu, Ile, Phe, Met, Pro, Trp).
- pH of the Solution: ○ Solubility in water is minimal at the isoelectric point (pI) because the net charge on the amino acid is zero, reducing its interaction with water and promoting aggregation through intermolecular electrostatic attractions between the zwitterions or hydrophobic interactions. ○ At pH values above or below the pI, the amino acid carries a net negative or positive charge, respectively. This increased charge enhances its interaction with water molecules, leading to increased solubility. For example, glutamic acid is least soluble at its pI of 3.22; its solubility increases at pH < 3.22 (becomes positively charged) and at pH > 3.22 (becomes negatively charged). E. Other Physical Properties ● Taste: Amino acids vary in taste. Some are sweet (e.g., Gly, Ala, Ser), some are bitter (e.g., Arg, Leu, Ile, Val, Phe, Trp), some are tasteless (e.g., Met), and one, glutamate (as monosodium glutamate, MSG), is responsible for the "umami" (savory) taste. ● Density: Amino acids are generally denser than water. ● Amphiphilicity: While some amino acids are clearly hydrophilic and others hydrophobic, some, particularly those with longer aliphatic chains and a polar group (like lysine), can exhibit amphiphilic properties, having both hydrophilic and hydrophobic regions. These physicochemical properties are not just academic details; they are fundamental to the methods used to isolate, identify, and quantify amino acids, and they underpin the complex structures and diverse functions of proteins.
IV. Chemical Reactions of Amino Acids
Amino acids can undergo a variety of chemical reactions characteristic of their functional groups: the carboxyl group (-COOH), the amino group (-NH₂), and the specific R-group (side chain). These reactions are important for amino acid analysis, peptide synthesis, protein modification, and understanding metabolic pathways.
A. Reactions due to the Carboxyl Group (-COOH) The carboxyl group behaves like a typical carboxylic acid.
- Salt Formation (with bases): ○ The carboxyl group can react with bases (e.g., NaOH, KOH, metal hydroxides, or amines) to form salts. ○ R-CH(NH₂)-COOH + NaOH → R-CH(NH₂)-COO⁻Na⁺ + H₂O ○ This is a fundamental acid-base reaction.
- Esterification (with alcohols): ○ In the presence of an acid catalyst (e.g., dry HCl gas), the carboxyl group can react with alcohols to form esters. The amino group must usually be protected first, or protonated by the acid catalyst, to prevent it from reacting. ○ R-CH(NH₃⁺)-COOH + R'OH --(HCl)--> R-CH(NH₃⁺)-COOR' + H₂O ○ Esters of amino acids are often more volatile than the parent amino acids and are used in some analytical procedures (e.g., gas chromatography after derivatization). They are also important intermediates in peptide synthesis.
- Decarboxylation: ○ Amino acids can be decarboxylated (lose CO₂) to form primary amines. This reaction can occur chemically (e.g., by heating) or, more significantly, enzymatically in biological systems. ○ R-CH(NH₂)-COOH --(Enzyme/Heat)--> R-CH₂NH₂ (amine) + CO₂ ○ Biological Examples: ■ Histidine → Histamine (mediator of allergic response and inflammation) ■ Glutamate → γ-Aminobutyric acid (GABA) (inhibitory neurotransmitter) ■ Tryptophan → Tryptamine (precursor to serotonin) ■ DOPA (Dihydroxyphenylalanine) → Dopamine (neurotransmitter)
- Amide Formation (including Peptide Bond Formation): ○ The carboxyl group can react with ammonia or amines to form amides. The most important amide formation involving amino acids is the peptide bond , where the α-carboxyl group of one amino acid reacts with the α-amino group of another. This will be discussed in detail in Section V. ○ R-CH(NH₂)-COOH + R'-NH₂ → R-CH(NH₂)-CO-NH-R' + H₂O (Amide)
- Reduction to Alcohols: ○ The carboxyl group can be reduced to a primary alcohol (-CH₂OH) using strong reducing agents like lithium aluminum hydride (LiAlH₄). This reaction is not common in biological systems but is used in organic synthesis. ○ R-CH(NH₂)-COOH --(LiAlH₄)--> R-CH(NH₂)-CH₂OH B. Reactions due to the Amino Group (-NH ₂ ) The α-amino group behaves like a typical primary amine.
- Salt Formation (with acids): ○ The amino group can react with acids (e.g., HCl) to form ammonium salts. ○ R-CH(NH₂)-COOH + HCl → R-CH(NH₃⁺Cl⁻)-COOH
- Acylation: ○ The amino group can be acylated by reaction with acid anhydrides (e.g., acetic anhydride) or acyl halides (e.g., acetyl chloride) to form N-acylamino acids (amides). ○ R-CH(NH₂)-COOH + (CH₃CO)₂O (acetic anhydride) → R-CH(NHCOCH₃)-COOH + CH₃COOH ○ This reaction is often used to protect the amino group during chemical synthesis.
nitrous acid (formed from NaNO₂ + HCl) to liberate nitrogen gas and form an α-hydroxy acid. The volume of N₂ gas can be measured (Van Slyke method) to quantify amino acids. R-CH(NH₂)-COOH + HNO₂ → R-CH(OH)-COOH + N₂ + H₂O Proline and hydroxyproline, being secondary amines, form N-nitroso derivatives instead of liberating N₂. C. Reactions involving both Amino and Carboxyl Groups
- Chelation with Metal Ions: ○ Amino acids can form chelate complexes with metal ions (e.g., Cu²⁺, Co²⁺, Mn²⁺). The metal ion binds to both the α-amino group and the α-carboxyl group, forming a ring structure. ○ This property is utilized in some chromatographic separation methods. D. Reactions due to the Side Chain (R-group) The diverse R-groups of amino acids exhibit specific chemical reactivities. These reactions are crucial for protein structure, enzyme catalysis, and post-translational modifications.
- Reactions of the -SH group (Cysteine): ○ Oxidation to form Disulfide Bonds (Cystine): This is one of the most important reactions of cysteine. The thiol groups of two cysteine residues can be oxidized (e.g., by O₂, mild oxidizing agents like iodine) to form a disulfide bond (-S-S-), linking the two cysteines into a single cystine residue. 2 R-SH (Cysteine) + [O] → R-S-S-R (Cystine) + H₂O Disulfide bonds are covalent bonds that play a critical role in stabilizing the tertiary and quaternary structures of many proteins, particularly extracellular proteins (e.g., antibodies, insulin). They can be cleaved by reducing agents (e.g., β-mercaptoethanol, dithiothreitol). ○ Alkylation: The thiol group is a strong nucleophile and can be alkylated by reagents like iodoacetate or iodoacetamide. This reaction is often used to block cysteine residues and prevent disulfide bond formation during protein sequencing or analysis. R-SH + I-CH₂COO⁻ → R-S-CH₂COO⁻ + HI ○ Reaction with Heavy Metals: Thiol groups have a high affinity for heavy metal ions (e.g., Hg²⁺, Pb²⁺, As³⁺), forming mercaptides. This is the basis for the toxicity of some heavy metals, as they can inactivate enzymes by binding to essential cysteine residues. ○ Reaction with Ellman's Reagent (DTNB): 5,5'-Dithiobis(2-nitrobenzoic acid) reacts with free thiol groups to release a yellow-colored thiophenolate anion, which can be quantified spectrophotometrically at 412 nm. This is used to determine the number of free cysteine residues in a protein.
- Reactions of the Hydroxyl Group (-OH of Serine, Threonine, Tyrosine): ○ Esterification: The hydroxyl groups can be esterified with acids. A biologically crucial example is phosphorylation , where a phosphate group (from ATP) is transferred to the hydroxyl group, catalyzed by protein kinases. R-OH + ATP --(Kinase)--> R-O-PO₃²⁻ + ADP Phosphorylation of Ser, Thr, and Tyr residues is a major mechanism for regulating protein activity and signal transduction. ○ Glycosylation: Sugars can be attached to the -OH of Ser or Thr (O-linked glycosylation), forming glycoproteins. ○ Oxidation: Under strong conditions, hydroxyl groups can be oxidized.
- Reactions of the Phenolic Group (Tyrosine): ○ Nitration: Tyrosine can be nitrated with nitric acid to form 3-nitrotyrosine. This modification is sometimes observed under conditions of oxidative stress. ○ Iodination: Tyrosine residues can be iodinated to form monoiodotyrosine and
diiodotyrosine. This is a key step in the synthesis of thyroid hormones (thyroxine and triiodothyronine) in the thyroid gland. ○ Millon's Reaction: A specific test for tyrosine (and other phenolic compounds). Heating with mercuric nitrate in nitric acid gives a red color.
- Reactions of the Indole Group (Tryptophan): ○ Hopkins-Cole Reaction (Glyoxylic Acid Reaction): Specific for tryptophan. Tryptophan reacts with glyoxylic acid in the presence of concentrated sulfuric acid to give a purple-violet colored ring. ○ Oxidation: The indole ring is susceptible to oxidation. N-formylkynurenine is an oxidation product. ○ Tryptophan can be modified by various reagents, e.g., N-bromosuccinimide (NBS) can specifically oxidize the indole ring.
- Reactions of Basic Groups (Amide of Asn/Gln, ε-Amino of Lysine, Guanidinium of Arginine, Imidazole of Histidine): ○ Hydrolysis of Amides (Asn, Gln): The amide groups of asparagine and glutamine can be hydrolyzed to the corresponding carboxylic acids (aspartate and glutamate) and ammonia, especially under acidic or basic conditions or enzymatically (e.g., by asparaginase, glutaminase). ○ Modifications of Lysine's ε-Amino Group: This group is highly reactive and can undergo acylation (e.g., acetylation, succinylation), methylation, ubiquitination, and reaction with aldehydes (e.g., forming Schiff bases). These modifications are important in regulating protein function, stability, and localization. ○ Sakaguchi Reaction: Specific for the guanidinium group of arginine. Arginine reacts with α-naphthol and sodium hypobromite (or hypochlorite) in alkaline solution to give a red color. ○ Pauly Reaction: Histidine (and tyrosine) react with diazotized sulfanilic acid in alkaline solution to form a red-colored azo dye.
- Reactions of Acidic Groups (Aspartate, Glutamate): ○ These side-chain carboxyl groups can undergo reactions similar to the α-carboxyl group, such as esterification and amide formation, though usually requiring more specific conditions or enzymatic catalysis in biological systems. These reactions highlight the chemical versatility of amino acids, which is essential for their diverse roles in biological systems, from forming the structural framework of proteins to participating directly in catalytic processes and signaling pathways.
V. Peptide Bond Formation: The Linkage of Life
The peptide bond is the fundamental covalent linkage that connects amino acids together to form peptides and proteins. Understanding its formation, structure, and properties is crucial for comprehending protein architecture and function. A. Definition and Structure of the Peptide Bond (-CO-NH-) A peptide bond is an amide bond formed between the α-carboxyl group (-COOH) of one amino acid and the α-amino group (-NH₂) of another amino acid. During this reaction, a molecule of water is eliminated. O O H // // | R₁-CH-C-OH + H-N-CH-R₂ → R₁-CH-C-N-CH-R₂ + H₂O
■ In the cis configuration , the α-carbon atoms are on the same side of the peptide bond. This is sterically less favorable and occurs much less frequently. ○ Most peptide bonds in proteins (over 99%) are in the trans configuration. ○ An important exception is peptide bonds preceding a proline residue (X-Pro bonds, where X is any amino acid). Due to the cyclic nature of proline, the steric hindrance difference between trans and cis for X-Pro bonds is less pronounced. Consequently, about 5-10% of X-Pro peptide bonds are found in the cis configuration, which can introduce significant kinks or turns in the polypeptide chain. ○ Illustration: Diagrams comparing the trans and cis configurations of a peptide bond, highlighting the positions of the α-carbons and R-groups.
- Dipole Moment: ○ The peptide bond has a significant dipole moment. The carbonyl oxygen has a partial negative charge (δ⁻), and the amide nitrogen has a partial positive charge (δ⁺) due to resonance and the electronegativity difference. ○ This polarity allows peptide bonds to participate in hydrogen bonding, particularly the C=O oxygen as a hydrogen bond acceptor and the N-H hydrogen as a hydrogen bond donor. These hydrogen bonds are crucial for stabilizing secondary structures like α-helices and β-sheets.
- Hydrogen Bonding Capability: ○ The carbonyl oxygen (C=O) of each peptide bond is a good hydrogen bond acceptor. ○ The amide hydrogen (N-H) of each peptide bond (except when the amino acid is proline) is a good hydrogen bond donor. ○ This hydrogen bonding potential is fundamental to the formation of regular secondary structures in proteins. D. Peptides: Dipeptides, Tripeptides, Oligopeptides, Polypeptides Chains of amino acids linked by peptide bonds are called peptides. ● Dipeptide: Two amino acids linked by one peptide bond. ● Tripeptide: Three amino acids linked by two peptide bonds. ● Oligopeptide: A short chain of amino acids, typically containing 2 to 20 residues. ● Polypeptide: A longer chain of amino acids, typically containing more than 20 residues. Proteins are composed of one or more polypeptide chains. A polypeptide chain has a defined sequence of amino acids. E. Nomenclature of Peptides
- N-terminus and C-terminus: ○ A polypeptide chain has directionality because its ends are different. ○ The end with the free α-amino group (not involved in a peptide bond) is called the amino-terminus or N-terminus. ○ The end with the free α-carboxyl group is called the carboxyl-terminus or C-terminus. ○ Peptide sequences are conventionally written and read from the N-terminus to the C-terminus (left to right).
- Naming Conventions: ○ Peptides are named as derivatives of the C-terminal amino acid. ○ For all amino acids except the C-terminal one, the suffix "-ine," "-an," "-ic acid," or "-ate" is changed to "-yl."
○ Example: A tripeptide composed of Alanine, Glycine, and Serine, in that order from N- to C-terminus (Ala-Gly-Ser), would be named Alanyl-glycyl-serine. ○ Three-letter or one-letter abbreviations are commonly used: ■ Ala-Gly-Ser or A-G-S F. Biological Significance of Peptides Beyond being constituents of proteins, many small peptides have distinct and important biological activities: ● Hormones: ○ Insulin: A polypeptide hormone (51 amino acids in two chains) regulating glucose metabolism. ○ Glucagon: A polypeptide hormone (29 amino acids) that raises blood glucose levels. ○ Oxytocin: A nonapeptide hormone involved in uterine contraction and milk ejection. ○ Vasopressin (Antidiuretic Hormone, ADH): A nonapeptide hormone regulating water reabsorption in the kidneys. ○ Adrenocorticotropic hormone (ACTH): A peptide hormone (39 amino acids) that stimulates the adrenal cortex. ● Neurotransmitters/Neuromodulators: ○ Enkephalins (e.g., Met-enkephalin, Leu-enkephalin): Pentapeptides that act as natural analgesics (pain relievers) by binding to opioid receptors. ○ Endorphins: Longer peptides with opioid activity. ○ Substance P: An undecapeptide involved in pain transmission. ● Antioxidants: ○ Glutathione (γ-glutamyl-cysteinyl-glycine): A tripeptide that plays a crucial role in protecting cells from oxidative damage. It is unusual because the peptide bond between glutamate and cysteine involves the γ-carboxyl group of glutamate, not the α-carboxyl group. ● Antibiotics: ○ Gramicidin S: A cyclic decapeptide antibiotic. ○ Bacitracin: A cyclic peptide antibiotic. ● Toxins: ○ Amanitin (e.g., α-amanitin): A cyclic octapeptide from Amanita phalloides mushrooms, a potent inhibitor of RNA polymerase II. ○ Conotoxins: Peptides from cone snails, often targeting ion channels. ● Food Additives/Sweeteners: ○ Aspartame (Aspartyl-phenylalanine-1-methyl ester): An artificial sweetener. The peptide bond, therefore, is not merely a structural link but the foundation upon which the vast diversity of peptide and protein functions is built.
VI. Non-Standard Amino Acids and Derivatives
While the 20 standard amino acids are encoded by the universal genetic code and incorporated into proteins during translation, there are many other amino acids and amino acid derivatives that play important biological roles. These can be broadly categorized into:
- Amino acids that are metabolic intermediates or have other functions but are not typically found in proteins.
- Amino acids that are found in proteins as a result of post-translational modification of
