Biological role and general characteristics of proteins
Proteins are polymers whose structural units are the 20 $\alpha$-amino acids. Biochemistry follows the strict principle of "Structure determines Function": each protein molecule possesses a unique spatial configuration ideally suited to perform a specific task.
An individual set of proteins in the body is of paramount importance. It determines:
- Human phenotypic features.
- The presence of hereditary diseases (in case of errors in the genetic code).
- Predisposition to various diseases.
Structure of $\alpha$-amino acids
All proteinogenic amino acids share a unified structural layout. At the center of the molecule lies the $\alpha$-carbon atom, to which the main functional groups and a unique side chain are attached.
Under physiological conditions, these functional groups are ionized:
- The $\alpha$-amino group carries a positive charge ($-NH_3^+$).
- The $\alpha$-carboxyl group carries a negative charge ($-COO^-$).
The third component is the radical ($R$) attached to the same $\alpha$-carbon atom. Amino acids differ from each other exclusively in the structure, size, and physicochemical properties of their radicals.
Classification of radicals and their solubility
The physicochemical properties of radicals determine the ability of amino acids to hydrate, that is, to interact with water molecules and dissolve in them.
1. Hydrophilic radicals These radicals actively interact with water due to charged or polar groups:
- Anionic groups: carboxyl group ($-COO^-$).
- Cationic groups: amino group ($-NH_3^+$), imino group ($=NH^+$), and guanidino group ($-NH_2-C=NH_2^+$).
- Polar uncharged groups: hydroxyl group ($-OH$), amide group ($-CONH_2$), and thiol/sulfhydryl group ($-SH$).
2. Hydrophobic radicals These groups are incapable of hydration. Non-polar hydrophobic radicals include methyl groups ($-CH_3$), aliphatic chains, and aromatic rings.
Formation of the peptide bond and structure of peptides
Amino acids are linked into linear polymers (proteins) via a peptide bond.
The mechanism of its formation involves the chemical interaction between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another amino acid. This process is accompanied by the elimination of a single water molecule ($H_2O$).
As a result, a peptide backbone is formed — a long chain of repeating $-NH-CH-CO-$ groups. Side chains (radicals $R_1, R_2, R_3...$) project outward from this backbone. Each individual monomer within such a chain is called an amino acid residue.
Any peptide has two distinct ends:
- N-terminus (N-terminal residue): contains a free $\alpha$-amino group.
- C-terminus (C-terminal residue): contains a free $\alpha$-carboxyl group.
Unique properties of proline
Among the 20 protein monomers, proline occupies a special place. According to chemical classification, it is not an amino acid, but an imino acid.
The radical of proline forms a closed ring: it is simultaneously bonded to both the $\alpha$-carbon atom and the imino group. Due to this cyclic structure, the peptide bond formed by the imino group of proline differs significantly from standard ones — the nitrogen atom within the peptide group completely lacks hydrogen.
Briefly: answers to topical questions
Which specific amino acids are classified as hydrophobic?
Hydrophobic (non-polar) amino acids are those whose radicals contain aliphatic hydrocarbon chains or aromatic rings without polar groups. These include:
- Alanine (Ala) — contains an aliphatic radical.
- Valine (Val) — contains an aliphatic radical.
- Leucine (Leu) — contains an aliphatic radical.
- Isoleucine (Ile) — contains an aliphatic radical.
- Phenylalanine (Phe) — contains an aromatic ring.
- Tryptophan (Trp) — contains an aromatic ring.
- Methionine (Met) — contains a non-polar thioether group.
- Proline (Pro) — is a cyclic imino acid.
Which proteinogenic amino acids contain a hydroxyl -OH group in their radical?
The hydroxyl group (-OH) in the side radical is contained in the following proteinogenic amino acids:
- Serine (Ser) — radical is -CH₂OH; classified as a hydroxy amino acid.
- Threonine (Thr) — radical is -CH(OH)CH₃; classified as a hydroxy amino acid.
- Tyrosine (Tyr) — contains a hydroxyl group in its radical; classified as an aromatic amino acid.
Serine, threonine, and tyrosine are categorized in sources as hydrophilic uncharged (polar) amino acids.
Which amino acids have an additional carboxyl group in their radical (acidic amino acids)?
An additional carboxyl group in the side radical is present in hydrophilic anionic (acidic) amino acids:
- Aspartic acid (Asp) — a carboxy amino acid.
- Glutamic acid (Glu) — a carboxy amino acid.
Sources indicate the carboxyl group -COOH / -COO⁻ for their radicals, which is why they are classified as negatively charged hydrophilic amino acids.
Which amino acids contain a sulfur atom?
A sulfur atom is part of the following sulfur-containing amino acids:
- Cysteine (Cys) — radical is -CH₂SH, contains a thiol/sulfhydryl group.
- Methionine (Met) — radical is -CH₂CH₂SCH₃, contains a thioether group.
- Cystine is mentioned in the literature among sulfur-containing amino acids; disulfide bonds are formed by cysteine residues to yield cystine.
To avoid confusion about the direction in which proteins are read, remember: read it the way you read the word "NaChalo" (from start to finish) — from the N-terminus to the C-terminus.
Class and exam questions
In what state are the functional groups of amino acids in the body?
Under physiological conditions, they are ionized: the $\alpha$-amino group turns into a cation ($-NH_3^+$), and the $\alpha$-carboxyl group turns into an anion ($-COO^-$).
What is the peptide backbone?
This is the central axis of the polypeptide chain, consisting of repeatedly recurring chemical groups $-NH-CH-CO-$, to which side chains are attached.
Why is proline called an exception among amino acids?
Because it is an imino acid. Its side chain forms a ring by bonding with the imino group, which means that the nitrogen atom in the resulting proline peptide bond lacks a hydrogen atom.
How do hydrophilic amino acids differ from hydrophobic ones?
Hydrophilic amino acids have anionic, cationic, or polar groups in their side chains and are capable of hydration. Hydrophobic ones contain nonpolar hydrocarbon chains or rings and avoid water.
What else to study on this topic
- Mechanisms of genetic determination of amino acid sequences in DNA
- Association of phenotypic features with the structure of specific proteins
- Impact of amino acid substitutions on the development of hereditary diseases
- Spatial organization of the peptide backbone and formation of protein structures
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