Structure determination by elemental composition
Analysis of the structure of organic compounds often begins with determining the element ratio. When investigating an equimolar mixture consisting of two different $\alpha$-amino acids, their exact formulas can be established based on the proportion of atoms.
For example, if quantitative analysis reveals that there are exactly 3 nitrogen atoms per 8 carbon atoms, this provides a crucial clue for decoding. Since the basic backbone of a standard amino acid contains one nitrogen atom in the $\alpha$-position, the presence of an additional, third nitrogen atom in a two-molecule mixture indicates that the side chain of one of the acids contains an extra nitrogen-containing group. Such calculations require precise correlation of molar ratios.
Specific chemical properties of side chains
The chemical behavior of a molecule is largely determined by the nature of its side chain. Let us consider two important examples demonstrating unique properties:
- Oxidation of cysteine: This molecule contains sulfur. Under the action of molecular iodine, cysteine residues undergo an oxidation reaction. As a result, they cross-link with each other via a strong covalent bond, forming disulfide bridges. The product of such a reaction is called cystine.
- Tyrosine reactions: The side chain of this compound includes a phenolic ring with a hydroxyl group. Unlike ordinary alcohols, the phenolic hydroxyl possesses pronounced acidic properties. Due to this, tyrosine is capable of interacting with strong alkalis, such as sodium hydroxide (NaOH), to form salts.
Peptide analysis and identification
A key process is hydrolysis—the cleavage of peptide bonds. It can occur in an alkaline medium (yielding products in a KOH solution) or in an acidic medium (for example, yielding hydrochloric acid salts for a dipeptide composed of lysine and phenylalanine). During hydrolysis, the total mass of the products always exceeds the mass of the starting peptide due to the addition of water.
Comprehensive identification of an unknown dipeptide (containing, for example, tyrosine, lysine, phenylalanine, serine, or glutamic acid) relies on a series of tests:
- Action of sodium bicarbonate ($NaHCO_3$): If gas evolution ($CO_2$) is observed upon adding an excess of the reagent, this indicates the presence of free carboxyl groups, which is characteristic of glutamic acid.
- Xanthoproteic test: Interaction with nitric acid ($HNO_3$). A positive result signifies the presence of aromatic structures, such as in tyrosine or phenylalanine.
- Mass evaluation: An increase in mass following hydrolysis confirms the presence of peptide bonds.
Organic synthesis of amino acids
The synthesis of complex structures from simple molecules is an important aspect of chemistry.
- Synthesis from dicarboxylic acids: A chain of transformations starting from succinic acid and leading to the formation of an amino acid is possible. Following synthesis, a check is always performed: does the resulting compound belong to proteinogenic (protein-ogenic) amino acids?
- Synthesis with reagent limitations: A more challenging task is obtaining alanine propyl ester using exclusively propanal as the starting material (without applying any other organic reagents). This requires constructing both the acid (alanine) and alcohol parts of the future ester from propanal.
Briefly: answers to topical questions
Which amino acids give a positive xanthoproteic test?
A positive xanthoproteic test is given by amino acids containing aromatic side chains. Such amino acids include:
- Phenylalanine (L-phenylalanine) — contains an aromatic ring.
- Tyrosine (L-tyrosine) — contains an aromatic ring.
- Tryptophan (L-tryptophan) — contains an aromatic ring.
The mechanism of the reaction involves the nitration of the aromatic side chains of amino acid residues with nitric acid, resulting in the formation of yellow-colored products.
Which proteinogenic amino acids contain a sulfur atom in their side chain?
Sulfur-containing proteinogenic amino acids have a sulfur atom in their side chain:
- Cysteine (L-cysteine) contains a thiol (sulfhydryl) group in its side chain $-CH_2SH$.
- Methionine (L-methionine) contains a thioether group in its side chain $-CH_2CH_2SCH_3$.
Which amino acids are classified as monoaminodicarboxylic (acidic)?
Monoaminodicarboxylic (acidic) amino acids are those containing two carboxyl groups. This group includes:
- Aspartic acid (L-aspartic acid) contains an additional carboxyl group that provides a negative charge.
- Glutamic acid (L-glutamic acid) contains an additional carboxyl group that provides a negative charge.
In acidic solutions, one $-COOH$ group participates in zwitterion formation, while the second ionizes, releasing hydrogen ions.
Which proteinogenic amino acids are basic (contain an additional amino group)?
Basic (cationogenic) proteinogenic amino acids are those that contain additional amino groups or other nitrogen-containing groups that confer a positive charge. They include:
- Lysine (L-lysine) contains an additional amino group (diaminomonocarboxylic acid).
- Arginine (L-arginine) contains a guanidino group.
- Histidine (L-histidine) contains an imidazole ring.
These amino acids determine the alkaline properties and positive charge of proteins.
Which amino acids contain a hydroxyl group in their side chain?
Hydroxy amino acids and certain aromatic amino acids contain a hydroxyl group ($-OH$) in their side chain. They include:
- Serine (L-serine) contains a hydroxyl group in its aliphatic side chain ($-CH_2OH$).
- Threonine (L-threonine) contains a hydroxyl group in its aliphatic side chain ($-CH(OH)CH_3$).
- Tyrosine (L-tyrosine) contains a phenolic hydroxyl group in its aromatic side chain.
These amino acids belong to the hydrophilic (polar) uncharged amino acids.
To remember the xanthoproteic test: "Nitric acid seeks rings" — $HNO_3$ reacts with aromatic side chains (tyrosine, phenylalanine).
Class and exam questions
Why is the mass of peptide hydrolysis products always greater than the mass of the peptide itself?
During hydrolysis, the peptide bond is cleaved, and water elements are added to the resulting molecular ends. The mass increases by exactly the mass of the reacted water.
How to prove the presence of a glutamic acid residue in a peptide?
Glutamic acid contains an additional carboxyl group. Upon addition of sodium bicarbonate, this group reacts with the release of carbon dioxide ($CO_2$).
What specific reaction does tyrosine undergo with alkalis?
Due to the acidic properties of the phenolic hydroxyl in its side chain, tyrosine is capable of reacting with sodium hydroxide (NaOH), unlike aliphatic alcohols.
What else to study on this topic
- Calculation of product masses in the alkaline hydrolysis of peptides in a KOH solution.
- Algorithm for calculating amino acid formulas based on the carbon-to-nitrogen atom ratio.
- Determining whether synthesized acids belong to the class of proteinogenic acids.
- Mechanism of disulfide bridge formation during the oxidation of cysteine with iodine.
- Multistage synthesis of alanine propyl ester using propanal as a starting material.
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Other topics in "Chapter 18. Major Classes of Bioorganic Compounds"
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