Bic 201 Chemistry Of Amino Acids

Additional context

This document provides a foundational overview of acid-base chemistry, a cornerstone of understanding chemical reactions, especially in biological systems like amino acids. The concepts presented build upon the historical development of acid-base theories, starting with the Arrhenius definition, which focuses on the production of hydrogen and hydroxide ions in water. While useful, the Arrhenius theory is limited to aqueous solutions. The document then introduces the Brønsted-Lowry theory, a more comprehensive model that defines acids as proton donors and bases as proton acceptors, expanding the scope beyond water-based reactions. This theory is crucial for understanding how molecules, like amino acids, interact in various chemical environments.

The Brønsted-Lowry theory introduces the concept of conjugate acids and bases, which highlights the reversible nature of proton transfer reactions. This is particularly relevant in biochemistry, where many reactions are reversible and involve the transfer of protons between molecules. Understanding the roles of acids, bases, and their conjugates is essential for predicting the direction and equilibrium of these reactions. For example, the behavior of amino acids, which contain both acidic and basic functional groups, can be predicted using these principles.

In the broader field of chemistry, these acid-base theories are fundamental to understanding various phenomena, including reaction mechanisms, catalysis, and buffer systems. Titration, a common analytical technique, relies on the principles of acid-base neutralization. Moreover, the pH scale, a measure of acidity or basicity, is directly related to the concentration of hydrogen ions and is widely used in various scientific disciplines, including environmental science, medicine, and materials science. These basic principles are taught to all students of chemistry as a core competency.

Bic 201 Chemistry of Amino Acids D.R. I. N. Ezechukwu

Acid-Base Theory

Arrhenius Theory

• Acid with the letters underlined: Any Substance That Ionizes Partially Or Completely In Water To Release Hydrogen (H plus) Ions.

Math summary: This chemical reaction shows hydrogen chloride gas reacting with water. The reaction produces hydrogen ions and chloride ions in an aqueous solution, which is also known as hydrochloric acid.

• Base: Any Substance Whose Dissolution In Water Produces Hydroxide (O.H. superscript negative) Ions.

Math summary: First, solid sodium hydroxide dissolves in water, producing sodium ions and hydroxide ions. Second, sodium metal reacts with water to produce sodium hydroxide and hydrogen gas.

The same also applies to Alkali Metals.

• Acids that contain One Ionizable Hydrogen (such as Nitric Acid/ H.N.O. sub 3 ) are called monoprotic Acids.

• Acids that contain Two Ionizable Hydrogens (such as Sulphuric Acid/ H sub 2.S.O. sub 4 ) are called diprotic Acids.

- Acids that contain Three Ionizable Hydrogens (such as Phosphoric Acid/ H sub 3.P.O. sub 4 ) are called triprotic Acids.

Brønsted - Lowry Theory

• Acid: Any Substance That Can Donate A Proton (H⁺) aka A Brønsted-Lowry Acid is a Proton Donor.

• Base: Any Substance That Can Accept A Proton (H⁺) aka A Brønsted-Lowry Base is a Proton Acceptor.

Image summary:The image is a chemical reaction diagram. It depicts a reversible reaction between ammonia and water. Ammonia acts as a base, and water acts as an acid. The reaction results in the formation of ammonium, which is the conjugate acid, and hydroxide, which is the conjugate base. The reaction shows the transfer of a proton from water to ammonia, leading to the formation of the conjugate acid and base.

Base Acid congugate Acid congugate Base

• conjuagte Acid: The Compound That Is Formed After A Base Has Accepted A Proton.

• conjuagte Base: The Compound That Remains After An Acid Has Donated A Proton.

Image summary:The image is a chemical reaction diagram. It depicts the reversible reaction between ammonia and water. The reaction shows ammonia and water reacting to form ammonium and hydroxide. The diagram illustrates the proton transfer from water to ammonia, resulting in the formation of ammonium and hydroxide ions.

Base Acid conjugate Acid conjugate Base

Limitations

• The Arrenius Theory is limited to reactions involving an aqueous solution.

• the Brunsted - Lowry Theory, although it doesn't require an aqueous solution, it is limited to reactions involving Proton Transfer.

• Both Theories Don't Explain Acidic Behaviour In Substances That Don't Contain Hydrogen (e.g. Boron Trifluoride/B.F..₃). This is covered by the Lewis Theory.

Lewis Theory

• Acid: Species That Accepts A Pair of Electrons.

• Base: Species That Donates A Pair of Electrons.

• The reaction Bewteen A Lewis Acid & A Lewis Base will produce a Coordinate Covalent Bonded Compound called an Addition COMPOUND/an Adduct.

Image summary:The image is a chemical reaction diagram. It illustrates the formation of a coordinate covalent bond between a Lewis acid and a Lewis base. The diagram shows a Lewis acid and a Lewis base reacting to form a product with a coordinate covalent bond. A specific example of this reaction is shown, where ammonia, which acts as a Lewis base, reacts with boron trifluoride, which acts as a Lewis acid, to form an ammonia-boron trifluoride adduct. In this reaction, ammonia donates an electron pair to boron trifluoride, resulting in the formation of a coordinate covalent bond between the nitrogen and boron atoms.

Acids

• Act as Proton Donors

• Are Electron Pair Acceptors

• Dissociate In Water To Release Hydrogen/H plus or minus Ions:

■ Strong Acids Dissociate Fully In Water (eg Sulphuric Acid), While Weak Acids Partially Dissociate In Water (Carboxylic Acids).

Bases

• Act as Proton Acceptors

• Are Electron Pair Donors

• Dissociate In Water To Release Hydroxide/O.H. minus Ions:

■ Strong Bases Dissociate Fully In Water (eg Sodium Hydroxide), While Weak Bases Partially Dissociate In Water (Ammonia).

Strengths Can Be Determined By The Acid or Base Dissociation Constant The Acid Dissociation Constant (K sub a) Is The Ratio Of The Concentration Of The Dissociated Form Of An Acid To The Concentration Of The Undissociated Form.

• Strong Acids Have Higher Ka Values, while Weak Acids Have Lower Ka Values.

Image summary:The image is a chemical equation. It illustrates the reaction of hydrogen chloride in water. Hydrogen chloride in gaseous form reacts with water to produce hydrogen ions and chloride ions in aqueous solution. This reaction shows the dissociation of hydrogen chloride into its constituent ions when dissolved in water, forming hydrochloric acid.

Image summary: The image is a chemical reaction diagram. It depicts hydrogen chloride reacting with water. The reaction yields a hydronium ion and a chloride ion. The diagram suggests that hydrogen chloride donates a proton to water, forming hydronium, and becomes a chloride ion in the process.

Math summary: This describes the acid dissociation reaction of an acid in water. It then calculates the acid dissociation constant by dividing the product of the concentrations of the conjugate base and hydronium or hydrogen ions by the concentration of the acid.

Where:

K = Acid Dissociation Constant

Math summary: The concentration of dissociated hydrogen ions is calculated. Also defined are the concentration of the conjugate base of the acid and the concentration of the undissociated form of the acid.

The Base Dissociation Constant (K sub b) Is The Ratio Of The Concentration Of The Dissociated Form Of A Base To The Concentration Of The Undissociated Form.

• Strong Bases Have Higher K sub b Values, while Weak Bases Have Lower K sub b Values.

Math summary: The equation calculates the base dissociation constant. It divides the product of the concentration of the protonated base and hydroxide ions by the concentration of the base.

Where:

Code summary: The code defines terms related to base dissociation. It explains that Kb is the base dissociation constant, [OH-] is the concentration of dissociated hydroxide ions, [BH+] is the concentration of the conjugate acid of the base, and [B] is the concentration of the undissociated form of the base. The input is the definition of each term and the output is the explanation of what each term means.

pH and Buffers

pH Scale

• The concentration of hydrogen ions is commonly expressed in terms of the pH scale.

• A Low pH corresponds to High Hydrogen Ion Concentration, while A High pH corresponds to Low Hydrogen Ion Concentration.

- Acids Lower the pH value of a solution as they increase the Concentration of Hydrogen Ions. In contrast, Bases Raise the pH value as they Lower the Concentration of Hydrogen Ions.

- Most biological fluids are within the pH range of 6 – 8, with Pure Water having a neutral pH of 7.

Image summary: The image is a diagram that illustrates the pH scale. It shows the range of pH values from zero to fourteen, with corresponding hydrogen and hydroxide ion concentrations. The diagram also indicates the acidic, neutral, and basic regions of the pH scale. The hydrogen ion concentration is higher in the acidic region and lower in the basic region, while the hydroxide ion concentration is lower in the acidic region and higher in the basic region. The neutral region has a balance of hydrogen and hydroxide ions.

Math summary: The first equation calculates pH as the negative logarithm of the hydrogen ion concentration. The second equation calculates pOH as the negative logarithm of the hydroxide ion concentration.

How To Read A pH Scale:

for Acids: When the concentration of H plus ions in a solution is 10 to the power of negative 14, the pH is 14 and Vice Versa.

• for Bases: When the concentration of O.H. to the power of negative 1 ions in a solution is 10 to the power of negative 1, the pH is 14 and Vice Versa.

• If the pH Value Is Greater Than 7, The Solution is Basic.

• If the pH Value Is Equal To 7, The Solution is Neutral.

• If the pH Value Is Lower Than 7, The Solution is Acidic.

Buffers

• Buffers are Solutions Which Resist Changes in pH Either When Small Amounts of An Acid or Base Are Added or When The solution Is Diluted.

• They work by accepting Hydrogen Ions from Solutions with Excess Ions in & by donating Hydrogen Ions to solutions whose ions have been depleted.

• The amount of acid or base that can be added without causing a large change in pH is referred to as Buffering Capacity.

• Since many metabolic reactions are accompanied by the release or uptake of Protons, most Intracellular Reactions are buffered. This is possible through Blood.

• Normal Blood pH is around 7.3 - 7.45 & it is able to maintain its pH through certain components of its Buffer System:

Hemoglobin

■ Phosphate

Bicarbonate

The Phosphate Buffer System

Math summary: This expression represents a reversible chemical reaction. It shows dihydrogen phosphate converting into a proton and hydrogen phosphate.

Consists of H sub 2 P O sub 4 to the power of negative 1, H plus Donor, and H P O sub 4 to the power of negative 2, H plus Acceptor

•This Phosphate Buffer Pair tends to resist changes in pH between 5.9 - 7.9

•When blood pH falls, H.P.O. sub 4 super 2 minus of the buffer combines with excess H super plus to form H sub 2 P.O. sub 4 super minus. In contrast, when Blood pH rises, H sub 2 P.O. sub 4 super minus dissociates to release H.P.O. sub 4 super 2 minus and free Hydrogen ions.

•Is maximally effective in providing buffering power in Intracellular fluids.

The Bicarbonate Buffer System

• This is the Principal Buffer in Blood Plasma.

• Consists of H sub 2 C-O sub 3 (Proton Donor) & H.C.O. sub 3 to the power of negative 1 (Proton Acceptor)

• In this buffer system, the acid is formed from dissolved carbon dioxide and Water.

Math summary: This expression shows the reversible reaction of carbon dioxide and water to form carbonic acid, facilitated by carbonic anhydrase. Carbonic acid then dissociates into a hydrogen ion and a bicarbonate ion, demonstrating an equilibrium.

•When Blood pH falls, bicarbonate combines with excess hydrogen to form carbonic acid. Carbonic acid then decomposes to form dissolved carbon dioxide, which is later exhaled from the lungs.

• In contrast, when Blood pH rises, dissolved C-O₂ combines with water to form H₂C-O₃, which dissociates to release H.C.O.₃⁻ & free Hydrogen Ions.

Introduction to Amino Acids

• There are approximately 300 Amino Acids present in various animals, plants, and microbial systems. But only 20 Amino Acids are coded by D.N.A. to appear in proteins.

• Cells produce proteins with strikingly different properties and activities by joining the same 20 amino acids in many different combinations and sequences.

- This indicates that the properties of proteins are determined by the physical & chemical properties of their monomer units, The Amino Acids.

• Therefore, Amino Acids Are The Basic Structural Units of Proteins.

Amino Acid Structure

Image summary: The image is a structural diagram. It illustrates the general chemical structure of an amino acid, highlighting the key functional groups attached to a central carbon atom. The diagram shows an amino group, a carboxyl group, a hydrogen atom, and a side chain (R-group). The structure indicates that amino acids, the building blocks of proteins, share a common backbone with a variable side chain that determines the specific properties of each amino acid.

• Amino Acids consist of An Amino Group (-N.H.₂), A Carboxyl Group (-C.O.O.H.), A Hydrogen Atom (H) and A Variable Side Chain/R Group.

• All substituents in the Amino Acid are attached/bonded to A Central Tetrahedral Carbon Atom known as The α-Carbon.

alpha-Amino acids in peptides and proteins (except Proline) contain alpha-Carboxylic Acid (alpha-C O O H) and alpha-Amino (alpha-N H subscript 3) functional groups.

• The R Group is what distinguishes one amino acid from another & determines its chemical properties.

• R Groups vary in Structure, Size & Electric Charge. They also influence Solubility of Amino Acids in water.

• Glycine Is The Simplest Amino Acid with "H" as its R Group.

• Proline is unique among the standard Amino Acids in that It doesn't have a free alpha-Amino Group. Instead, its alpha-Amino Group is linked to 2 Carbon Atoms that is The alpha-Carbon and A Side Chain Carbon Atom.

• The 20 Amino Acids are assigned Three Letter Abbreviations & One Letter Denotations. These are used as short hand to indicate Composition and Sequence of Amino Acids in Protein.

Table 1 summary: The table presents the full name, three-letter abbreviation, and one-letter abbreviation for each of the twenty standard amino acids.

Physical Properties of Amino Acids

• Amino Acids Are Colorless, Crystalline Solids. They are Colourless because They Do Not Absorb Visible Light. Though Phenylalanine, Tyrosine & Tryptophan Absorb U.V. Light.

• Although some Amino Acids are Tasteless, Some Possess Taste:

Glycine, Alanine, Serine, Valine, Tryptophan, Histidine & Proline are Sweet in Taste

■ Isoleucine & Arginine are Bitter in Taste

• Amino Acids Have Very High Melting Points (greater than 200 degrees Celsius)

• All Are Soluble In Water & Alcohol but Insoluble In Non-Polar Solvents (like Benzene).

Chemical Properties of Amino Acids

• Free amino acids/Amino Acids in Solutions exist largely as dipolar Ions or Zwitterions (German for “Hybrid Ions”).

• A Zwitterion carries an Equal Number of Positively & Negatively Charged Groups. The Net Charge of the entire molecule is Zero.

• The pH at which an amino acid has no net charge is known as its isoelectric Point (pl).

• Amino acids are amphoteric in nature that is They have Both Acidic and Basic Groups (their Amine Group/Basic & their Carboxylic Group/Acidic).

• At Acidic pH, the alpha amino group is fully protonated and Positively Charged, yielding N.H. sub 3 plus minus C.H. sub 2 minus C.O.O.H.

• At Alkaline pH, amino acids exist primarily as the Negatively Charged/Anionic N H sub 2 minus C H sub 2 minus C O O superscript minus Species.

Stereochemistry of Amino Acids

• When all 4 sides of the Central Tetrahedral alpha Carbon possess a uniquely different functional group, it gives rise to a phenomenon known as stereoisomerism.

• With the exception of Glycine, whose side chain is Hydrogen, all the 19 other common Amino acids are Chiral.

• The term "Chiral" indicates that there are four different constituents bonded to the alpha carbon, making the alpha Carbon Asymmetric.

• Since the α Carbon is asymmetric, there exists 2 Possible, Non-Superimposable, Mirror Images of the Amino Acids.

• These 2 Forms are possible due to a property known as Optical Activity - The Ability To Rotate In Plane Polarized Light.

• Clockwise Rotation is known as Dextrorotation and Anti-Clockwise Rotation is known as Levorotation.

• When the Amino Group stays on the Left side of the amino acid, then it looks like an L-shaped Amino Acid. D - shaped Amino Acids are mirrored images of L-shaped amino acids, with the Amino Group on the Right side of the Amino Acid.

• Stereochemistry mainly emphasizes the configuration of Amino Acids at the alpha Carbon atom, having either D or L isomers. All naturally occurring proteins from all living organisms consist of L alpha Amino Acids. D alpha amino acids are found in Polypeptide Antibiotics.

Image summary: The image is a structural representation of L-amino acid and D-amino acid molecules. The figure presents two molecules that are mirror images of each other. The position of the amino group distinguishes the two molecules.

Classification of the 20 Common Amino Acids

The 20 Common Amino Acids Are Classified:

• Based On Their R Groups/Side Chains

• Based On Their Metabolism

• Based On Nutritional Requirements

Classification Based on R Groups/Side Chains:

1. Classification Based On The Structure Of The Side Chains

2. Classification Based On Polarity & Charge Of The Side Chains:

• Amino Acids With Non-Polar, Aliphatic Side Chains (Hydrophobic)

• Amino Acids With Non-Polar, Aromatic Side Chains (Hydrophobic)

• Amino Acids With Polar, Uncharged Side Chains (Hydrophilic)

• Amino Acids With Positively Charged Side Chains (Basic)

• Amino Acids With Negatively Charged Side Chains (Acidic)

Table summary:The table presents a list of amino acids, categorized by their R groups (nonpolar, aliphatic; polar, uncharged) and their chemical structures.

Classification Based on the Structure of the Side Chains

• Simple Side Chains: Glycine & Alanine

• Branched Side Chains: Valine, Leucine & Isoleucine

• Side Chains With A Hydroxyl Group (-O.H.): Threonine & Serine

• Side Chains Containing Sulphur: Cysteine & Methionine

• Side Chains With An Amino Group: Asparagine & Glutamine

• Dicarboxylic Side Chains: Aspartic Acid & Glutamic acid

• Dibasic Side Chains: Arginine

• Aromatic Side Chains: Phenylalanine, Tyrosine & Tryptophan

1. Amino Acids With Non-Polar, Aliphatic Side Chains (Hydrophobic)

Image summary: This image is a collection of structural chemical diagrams of seven amino acids with nonpolar, aliphatic R groups. The diagrams show Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, and Methionine. There are variations in the structure of the R groups attached to the central carbon atom. Glycine has the simplest structure with only a single hydrogen atom as its R group, while others have more complex hydrocarbon chains or cyclic structures.

• aliphatic: Open-Chain Compounds, whether Straight or Branched, that Contain No Rings of Any Type

• Glycine has the Simplest Side Chain & It's the Only Non-Chiral Amino Acid.

• Alanine has a Methyl Side Chain, while Valine, Leucine & Isoleucine have Branched Side Chains. Leucine & Isoleucine have Isomeric Butyl Side Chains.

• Proline is unique among the standard Amino Acids in that It doesn't have a free alpha-Amino Group. Instead, its alpha-Amino Group is linked to 2 Carbon Atoms (i.e. The alpha-Carbon and A Side Chain Carbon Atom).

2. Amino Acids With Non-Polar, Aromatic Side Chains (Hydrophobic)

Image summary:The image is a structural diagram. It shows the chemical structures of three amino acids with aromatic R groups: phenylalanine, tyrosine, and tryptophan. The diagram highlights the differences in the R groups of these amino acids, specifically the phenyl ring in phenylalanine, the phenol ring in tyrosine, and the indole ring in tryptophan. The diagram suggests that the different chemical properties of these R groups contribute to the unique functions of these amino acids in proteins.

• Are Relatively Bulky

• Able To Absorb U.V. Light

3. Amino Acids With Polar, Uncharged Side Chains (Hydrophilic)

Image summary:The image is a set of chemical structure diagrams. The diagrams show the chemical structures of several polar, uncharged amino acids. Specifically, the image shows the structures of Serine, Threonine, Cysteine, Asparagine and Glutamine. The R groups of Asparagine and Glutamine are similar, with Glutamine having an additional methylene group. Serine and Threonine also share similarities, with Threonine containing an additional methyl group.

• Serine & Threonine have Hydroxylic R Groups and can bond with Hydrogen to form Water.

- Cysteine has a Thiol Group that often forms a Disulfide Bond with another Cysteine Molecule, through Oxidation of their Thiol Groups, to form the Dimeric Compound called Cystine (This is important for the stability of many proteins).

4. Amino Acids With Positively Charged Side Chains (Basic)

Image summary:The image is a diagram that depicts the chemical structures of three positively charged amino acids. The diagram showcases the molecular structures of Lysine, Arginine and Histidine. The diagram indicates that all three amino acids have positively charged R groups. The amino acids differ in the composition and arrangement of atoms within their respective R groups, leading to variations in their overall charge distribution and chemical properties.

• Lysine, underlined, has butylammonium side chain.

- Histidine possesses a Unique Imidazole Side Chain, which allows it to function as a Versatile Acid-Base Catalyst. This is because, at physiological pH values, the Imidazole Ring can readily accept or donate protons. Thus, Histidine is an Amino Acid that most often makes up the Active Sites of Protein Enzymes. The Imidazole Ring can also contribute to The Stability of Protein Structures.

5. Amino Acids With Negatively Charged Side Chains (Acidic)

Image summary: The image is a structural representation of two negatively charged amino acids. The image shows the chemical structures of Aspartic Acid and Glutamic Acid. Both amino acids share a similar core structure, but Glutamic Acid has an additional methylene group in its side chain compared to Aspartic Acid.

• Aspartic Acid & Glutamic Acid are negatively charged at pH above 3.

• They are referred to Aspartate & Glutamate in their Ionized State.

• The Carboxylic Acid on their Side Chains give them their Acidic/Proton Donating Properties.

Classification Based on Metabolism

• Amino Acids can be classified as being Ketogenic or Glucogenic based on the type of intermediates that are formed during their breakdown.

- Ketogenic Amino Acids are Amino Acids that can be broken down into Acetyl-CoA, which can then be used to synthesize Ketone Bodies (An alternative Source of Energy for The Body when Glucose is scarce).

• Glucogenic Amino Acids are Amino Acids that can be broken down to yield Pyruvate or One of The Intermediates of The Citric Acid Cycle. These Intermediates can then serve as Substrates for the Formation of Glucose Through Gluconeogenesis.

Purely Ketogenic Amino Acids

Ketogenic & Glucogenic Amino Acids

■Isoleucine

■Phenylalanine

■Tyrosine

■Tryptophan

Purely Glucogenic Amino Acids

Table summary: The table presents a list of amino acids. It includes both essential and non-essential amino acids, covering a range of structures and properties.

Classification Based on Nutritional

Requirements

Definition

Essential Amino Acids: Amino acids that the human body cannot synthesize on its own and therefore must be obtained through the diet. They are crucial for various bodily functions, including muscle growth, energy production, and immune function.

- Essential Amino Acids are Amino Acids that cannot be synthesized by Humans. They must be Obtained Through Diet. They are vital for Muscle Growth, Energy Production & Immune Function.

Definition

Non-Essential Amino Acids: Amino acids that the human body can synthesize in sufficient quantities. They are important for protein synthesis, tissue repair, and overall metabolic function.

• NON-Essential Amino Acids are Amino Acids that can be synthesized by Humans in the Body in Suffucient Quantities. They are important for Protein Synthesis, Tissue Repair & Overall Metabolic Function.

Definition

Semi-Essential Amino Acids: Amino acids that can be synthesized by the body but not in sufficient amounts during periods of growth, stress, or illness, making dietary intake necessary. Critical for children, pregnant women, and those recovering from surgery.

SEMI-Essential Amino Acids are Amino Acids that can be synthesized by the body, but not in sufficient Amounts During Periods of Growth, Stress or Illness, making Dietary Intake Necessary. They are critical for Children, Pregnant Women & Those Recovering From Surgery.

Essential Amino Acids

■Leucine ■Isoleucine ■Lysine ■Threonine ■Methionine ■Phenylalanine ■Tryptophan ■Valine

Semi-Essential Amino Acids

Non-Essential Amino Acids

■Glycine ■Alanine ■Proline ■Serine ■Cysteine ■Tyrosine ■Asparagine ■Glutamine Glutamic Acid Aspartic Acid

General Reactions of Amino Acids

Decarboxylation

■ The Removal of a Molecule of Carbon Dioxide (C O subscript 2) from The Carboxyl Group to form An Amine. Eg Histidine to Histamine, Glutamate to gamma AminoButyric Acid/gaba

Image summary: The image is a chemical reaction diagram. The diagram depicts a molecule undergoing a transformation where a carboxyl group is removed, indicated by the release of carbon dioxide. This transformation results in a shorter carbon chain attached to the core molecule, suggesting a decarboxylation reaction.

Image summary: The image is a chemical reaction diagram. The diagram depicts the decarboxylation of glutamate by the enzyme glutamate decarboxylase. The reaction involves the removal of a carboxyl group from glutamate in the form of carbon dioxide, resulting in a different molecule. The product molecule has a shorter carbon chain compared to glutamate due to the loss of the carboxyl group.

2. Amide Formation

■ A Carboxylic Group of An Amino Acid (other than alpha -Carboxyl Group) will combine with Ammonia to form a corresponding Amide. Eg Aspartate & Glutamate will combine with Ammonia to form Asparagine & Glutamine respectively.

Image summary: The image is a reaction diagram. It shows the conversion of Aspartate to Asparagine. This reaction requires Ammonia and ATP. ATP is converted to AMP and PP during this reaction. The reaction indicates that Aspartate is aminated to form Asparagine, utilizing ammonia and consuming ATP.

Image summary: The image is a chemical reaction diagram. It illustrates the conversion of glutamate to glutamine. The diagram shows glutamate as a reactant and glutamine as the product. The reaction requires ATP and ammonium and is catalyzed by glutamine synthetase. The reaction also produces ADP and inorganic phosphate as byproducts. Glutamine synthetase facilitates the addition of ammonia to glutamate, forming glutamine.

3. Transamination

■ The alpha -Amino Group of an Amino Acid is transferred to an alpha -Keto Acid to form a corresponding New Amino Acid & New Keto Acid. This reaction is essential for Amino Acid Degradation & Synthesis of Non-Essential Amino Acids.

Image summary: The image is a reaction scheme. It depicts the transamination reaction, which involves the conversion of an amino acid and an alpha-keto acid into a new alpha-keto acid and a new amino acid, respectively. The reaction is catalyzed by transaminase. The amino group from the amino acid is transferred to the alpha-keto acid, resulting in the formation of a new amino acid and a new alpha-keto acid. The reaction is reversible.

Image summary: The image is a chemical reaction diagram. It depicts the reversible reaction catalyzed by alanine transaminase, where alanine and alpha-ketoglutarate are converted into pyruvate and glutamate. Alanine and alpha-ketoglutarate are the initial reactants while pyruvate and glutamate are the products of the reaction. The reaction involves the transfer of an amino group from alanine to alpha-ketoglutarate, resulting in the formation of pyruvate and glutamate.

4. Oxidative Deamination

- The Removal of An Amino Group From An Amino Acid To Produce A Corresponding Keto Acid & Ammonia. This reaction is essential because it liberates Ammonia for Urea Synthesis & generates Keto Acids for Gluconeogenesis.

Image summary:The figure is a chemical reaction diagram. It shows the reversible reaction between Glutamate and alpha-ketoglutarate, catalyzed by the enzyme glutamate dehydrogenase. In this reaction, Glutamate, along with water, is converted into alpha-ketoglutarate and ammonium. NAD+ is converted to NADH + H+ in the forward reaction. The reaction can also proceed in the reverse direction, converting alpha-ketoglutarate and ammonium back into Glutamate and water, with NADH + H+ being converted back to NAD+.

5. Condensation/Peptide Bond Formation

■ The alpha -Carboxyl group of one Amino Acid reacts with the alpha -Amino Group of another Amino Acid to form a Peptide Bond, with the elimination of a Water Molecule. Proteins are made by polymerisation of Amino Acids through Peptide Bonds.

Image summary:The image is a chemical structure diagram. It illustrates the formation of a peptide bond between two amino acids. The diagram shows two amino acids on the upper side combining to form a dipeptide on the lower side, with the release of a water molecule. The peptide bond is formed between the carboxyl group of one amino acid and the amino group of the other. The process is a dehydration reaction, where water is removed.

Detection of Amino Acids

Reaction With Ninhydrin

• Ninhydrin acts as an Oxidizing Agent. It oxidizes alpha amino acids to release C-O sub 2, Ammonia and An Aldehyde.

• The now Reduced Ninhydrin then reacts with the liberated Ammonia, resulting in the formation of a Purple Pigment called Ruhemanns Purple which absorbs light at 570 nanometers (Imino Acids like Proline give off a Yellow Colour).

• Since the terminal amines of Lysine residues in peptides located in fingerprints react with ninhydrin, this test is most widely used to Detect Fingerprints.

The Ninhydrin Test

Image summary: This is a structural diagram. The diagram depicts a chemical compound. The compound consists of a benzene ring fused to a five-membered ring containing two carbonyl groups and two hydroxyl groups attached to a single carbon atom. The compound is likely an organic molecule with both aromatic and aliphatic characteristics.

Definition

Analyte: A substance whose chemical constituents are being identified and measured.

Ninhydrin 2,2-dihydroxyindane-1,3-dione C₅H₈O₂ M.W = 178.143 g/mol The Ninhydrin test is a chemical test for presence of amines or α-amino acids in a given analyte.

A deep blue-purple color indicates the presence of ammonia, primary/secondary amines, or amino acids in the analyte.

An orange-yellow color indicates the presence of Imino-acids (such as Proline).

When no color change is observed, there are no amino acids in the analyte.

Image summary:The image shows chemical reaction diagrams. The first diagram illustrates the reaction between ninhydrin and an amino acid to form a blue-purple complex, along with other products. The second diagram shows the reaction between ninhydrin and an amine group to form a similar blue-purple complex. The third diagram depicts the reaction between ninhydrin and proline to form a yellow complex. The reaction of ninhydrin with amino acids and amines produces a blue-purple complex, while the reaction with proline yields a yellow complex.

Sanger's Reaction

• The purpose of this test is to Identify the N-Terminal Amino Acid of a Polypeptide Chain.

- When a protein is treated with Sanger's Reagent (1-Fluoro-2,4-Dinitrobenzene/F.D.N.B.), the reagent reacts with the free Amino Group of the N-Terminal Amino Acid, causing the N-Terminal Amino Acid to be labeled with a Yellow Compound (A Dinitophenyl Group).

• The resulting D.N.B.-Labeled Protein is hydrolyzed into its constitutent Amino acids, allowing for the detection of the yellow D.N.B.-Labeled Amino Acid through Chromatography.

Image summary: The image is a chemical reaction diagram. The diagram illustrates the reaction between an amino acid and FDNB, also known as Sanger's reagent. The reaction produces DNB-amino acid and hydrogen fluoride. The DNB-amino acid product is a result of the amino group of the amino acid bonding with the FDNB reagent, releasing fluoride as hydrogen fluoride.

Edman's Reaction

• This test is also used for N-Terminal Protein Sequencing.

- Unlike with Sanger's Reagent, Edman's Reagent labels & cleaves one Amino Acid Residue at a time from the N-Terminus without hydrolyzing/destroying the rest of the Polypeptide, allowing the process to be repeated to sequence up to 30 - 50 Residues.

• When a protein is treated with Edman's Reagent (Phenylisothiocyanate/P.I.T.C.), the reagent reacts with the free Amino Group of the N-Terminal Amino Acid, under Alkaline conditions, to form a Phenylthiocarbamyl Derivative.

• Then, under Acidic conditions, that derivative is cleaved to release its Phenylthiohydantoin form (P.T.H.-Amino Acid), allowing for its detection through Chromatography.

• The rest of the Peptide then undergoes the same procedure again.

N-terminal sequencing cycle:

Image summary:This figure is a schematic diagram. The figure illustrates the Edman cycle, a chemical process used to determine the amino acid sequence of a peptide or protein. The Edman cycle involves the sequential removal and identification of amino acid residues from the N-terminus of a peptide. The process starts with the reaction of the peptide with phenylisothiocyanate, followed by cleavage and HPLC separation. The rest of the peptide goes through the cycle again. This cycle allows for the identification of each amino acid in the sequence, providing valuable information about the protein's structure and function.

Xanthoproteic Test

• This Test is used for the Detection of Aromatic Amino Acids (Tyrosine, Tryptophan & Phenylalanine) in a Protein solution.

• Here, Amino acids react with Concentrated Nitric Acid to give a Yellow Colour that becomes Orange on Addition of Excess Ammonia.

Million's Test

• This Test is for Tyrosine & Phenylalanine.

• Amino Acids, when boiled with few drops of Million's Reagent, give off a Brick Red Colour with Precipitation.

Rosenhein's Test

• This is a Test for Tryptophan.

• A Protein Solution containing Tryptophan reacts with Rosenhein's Reagent & Concentrated Sulphuric acid to give a Purple Ring.

Sulphur Test

• This is a Test for Cysteine.

• Here, A Protein Solution containing Cysteine reacts with Sulphur to produce a Black Colour.

• Methionine, although containing Sulphur, does not Give A Positive Result because Its Thioether Linkage is More Difficult to Break.

Say

• This Test is for Arginine.

• Free Arginine or Arginine residues in Proteins react with α-Naphthol & Alkaline Hypobromite to give a Bright Red Colour.

Pauly's Test

This is a Test for Histidine & Tyrosine.

• Pauly's Reagent (Diazo-Benzene Sulfonic acid) reacts with the Imidazole Group of Histidine to give a Cherry Red Colour.

• The same reagent will give an Orange-Red Colour after reacting with the Phenol Group of Tyrosine.

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