Amino Acids, Peptides, and Proteins

Overview

Amino acids, peptides, and proteins form a continuous hierarchy: amino acids are the small building blocks, peptides are short chains of amino acids, and proteins are long, usually complex, chains with specific three‑dimensional structures and biological functions. This chapter focuses on their structures, how they are linked, and why their properties are so central in biological chemistry.

Amino Acids

General Structure of α‑Amino Acids

Most naturally occurring amino acids in proteins are α‑amino acids. They share a common “skeleton”:

$$
\mathrm{H_2N{-}CH(R){-}COOH}
$$

• The central carbon is the $\alpha$‑carbon.
• Attached to it are:
• an amino group: $-\mathrm{NH_2}$ (or protonated $-\mathrm{NH_3^+}$),
• a carboxyl group: $-\mathrm{COOH}$ (or deprotonated $-\mathrm{COO^-}$),
• a hydrogen atom,
• a variable side chain: $R$ group.

The $R$ group determines the identity and properties of each amino acid: size, polarity, charge, and reactivity.

Chirality and L‑Amino Acids

For all standard proteinogenic amino acids except glycine, the $\alpha$‑carbon is a chiral center (four different substituents).

• Two possible configurations exist: usually labeled L and D (based on relation to glyceraldehyde).
• Proteins in living organisms almost exclusively use L‑amino acids.
• Glycine has $R = \mathrm{H}$, so its $\alpha$‑carbon is not chiral.

This “homochirality” (same handedness) is crucial for the regular structures that proteins can adopt (helices, sheets).

Classification by Side Chain Properties

The $R$ group determines how amino acids behave in water and how they interact in proteins. Common classifications (for the standard 20 proteinogenic amino acids) include:

Nonpolar (Hydrophobic) Side Chains

These $R$ groups are mostly hydrocarbons and do not form favorable interactions with water:

• Examples: alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), methionine (Met), phenylalanine (Phe), tryptophan (Trp), proline (Pro).
• Often found in the interior of proteins, forming a hydrophobic core.

Proline is structurally special: its side chain loops back and binds to the backbone nitrogen, forming a ring. This “imino” structure restricts flexibility and can kink peptide chains.

Polar, Uncharged Side Chains

These $R$ groups can form hydrogen bonds but are not charged at physiological pH:

• Examples: serine (Ser), threonine (Thr), asparagine (Asn), glutamine (Gln), tyrosine (Tyr), cysteine (Cys).

Important features:

• Ser, Thr, Tyr: side‑chain $-\mathrm{OH}$ groups; can be phosphorylated in regulation of proteins.
• Asn, Gln: side‑chain amides.
• Cys: side‑chain thiol $-\mathrm{SH}$, can form disulfide bonds (see below).

Charged Side Chains

At physiological pH, some side chains carry a positive or negative charge.

• Acidic (negatively charged side chains):
• Aspartic acid (Asp), glutamic acid (Glu).
• Side chains are carboxylate groups $-\mathrm{COO^-}$.
• Basic (positively charged side chains):
• Lysine (Lys), arginine (Arg), histidine (His).
• Side chains contain amino or guanidinium (Lys, Arg) or an imidazole ring (His).

Histidine’s side chain has a $pK_a$ near physiological pH, so it can readily accept or donate a proton. This makes histidine especially important in enzyme active sites.

Special Functional Roles

• Cysteine: two cysteine side chains can oxidize to form a covalent disulfide bridge:

$$
\mathrm{R{-}CH_2{-}SH + HS{-}CH_2{-}R' \rightarrow R{-}CH_2{-}S{-}S{-}CH_2{-}R' + 2\,H^+ + 2\,e^-}
$$

These disulfide bonds help stabilize protein structure.

• Proline: its cyclic structure limits backbone rotation and can disrupt or terminate regular secondary structures like $\alpha$‑helices.

Acid–Base Behavior and Zwitterions

Amino acids are amphoteric: they contain both acidic (carboxyl) and basic (amino) groups. In aqueous solution, they often exist as zwitterions, with internal balancing of charges.

For a simple amino acid:

• At low pH (strongly acidic): fully protonated, net positive:

$$
\mathrm{H_3N^+{-}CHR{-}COOH}
$$

• At intermediate pH (around physiological, for many amino acids): zwitterion:

$$
\mathrm{H_3N^+{-}CHR{-}COO^-}
$$

• At high pH (strongly basic): more deprotonated, net negative:

$$
\mathrm{H_2N{-}CHR{-}COO^-}
$$

Each amino acid has an isoelectric point $pI$, the pH at which the net charge is zero. This property is important for techniques like isoelectric focusing in protein separation.

Peptides

Formation of the Peptide Bond

A peptide is formed when the carboxyl group of one amino acid reacts with the amino group of another, creating an amide linkage and releasing water (a condensation reaction):

$$
\mathrm{H_2N{-}CHR_1{-}COOH + H_2N{-}CHR_2{-}COOH}
\rightarrow
\mathrm{H_2N{-}CHR_1{-}CONH{-}CHR_2{-}COOH + H_2O}
$$

The newly formed bond $-\mathrm{CO{-}NH}- is called the peptide bond.

Characteristics of the peptide bond:

• Planar: due to partial double‑bond character from resonance between $-\mathrm{C=O}$ and $-\mathrm{C{-}N}$.
• Restricted rotation: this limits the conformations of the peptide backbone.
• Typically in the trans configuration (the $\alpha$‑carbons on opposite sides of the bond), minimizing steric clashes.

Directionality of Peptides

A peptide chain has two ends:

• N‑terminus: free amino group (or modified derivative) at one end.
• C‑terminus: free carboxyl group (or modified derivative) at the other end.

By convention:

• Sequences are written from N‑terminus to C‑terminus.
• Example: a tripeptide made from alanine, glycine, and serine in that order is written as Ala-Gly-Ser.

The order of amino acids (sequence) is essential; Ala-Gly-Ser and Ser-Gly-Ala are different molecules with different properties.

Oligopeptides and Polypeptides

Based on length (not strictly defined, but generally):

• Dipeptide: 2 amino acids.
• Tripeptide: 3 amino acids.
• Oligopeptide: a short chain (e.g., up to about 10–20 residues).
• Polypeptide: longer chain of amino acids (tens to hundreds).

Biologically, compounds are often called “peptides” when relatively short and “proteins” when long enough to adopt stable, functional three‑dimensional structures. However, “polypeptide” and “protein” are closely related terms and sometimes used interchangeably.

Biologically Active Peptides

Short peptides can act as signaling molecules, hormones, or toxins. A few examples (structures are not detailed here, focus is on the peptide nature):

• Glutathione (GSH): a tripeptide (γ‑Glu–Cys–Gly) involved in redox regulation.
• Oxytocin and vasopressin: cyclic nonapeptides (9 amino acids) with hormone functions.
• Many peptide hormones and neurotransmitters are derived by cleavage of longer precursor polypeptides.

These examples show that even short amino acid chains can have highly specific biological roles.

Proteins

From Polypeptide to Protein

A protein is a polypeptide (often one or several chains) that folds into a specific three‑dimensional shape and performs a defined biological function.

Key points:

• The linear sequence of amino acids (primary structure) fully determines the final folded structure under physiological conditions.
• Folding is driven by interactions among side chains and with the surrounding environment (e.g., water, membranes, ions).

Levels of Protein Structure

Primary Structure

The primary structure is the linear amino acid sequence of the polypeptide chain, written from N‑terminus to C‑terminus.

Example notation:

• Met-Ala-Ser-Lys-Val-...

The specific order of amino acids encodes all information required for higher‑level structures.

Secondary Structure

Secondary structures are regular, repeating patterns stabilized mainly by hydrogen bonds between backbone $-\mathrm{C=O}$ and $-\mathrm{N{-}H}$ groups.

Two common types:

• $\alpha$‑Helix:
• Right‑handed coil.
• Intrachain hydrogen bonds stabilize the helix (e.g., between residue $i$ and residue $i+4$).
• Side chains project outward from the helix.
• $\beta$‑Sheet:
• Formed by alignment of sections of polypeptide chains (parallel or antiparallel).
• Hydrogen bonds between neighboring strands.
• Side chains alternate above and below the sheet.

Loops and turns connect these elements and provide flexibility and surface accessibility.

Tertiary Structure

Tertiary structure is the overall three‑dimensional arrangement of a single polypeptide chain, including how helices, sheets, and loops are packed together.

Stabilizing forces include:

• Hydrophobic interactions: nonpolar side chains cluster inside the protein, away from water.
• Hydrogen bonds: between side chains and/or backbone atoms.
• Ionic interactions (salt bridges): between oppositely charged side chains.
• Disulfide bonds: covalent links between cysteine residues, particularly important in secreted and extracellular proteins.
• Van der Waals interactions: close packing of atoms.

Tertiary structure determines the shape of:

• Binding sites for ligands or substrates.
• Active sites in enzymes.
• Interfaces for interacting with other biomolecules.

Quaternary Structure

Some proteins consist of more than one polypeptide chain (subunit). The spatial arrangement of these subunits is the quaternary structure.

• Subunits can be identical (homomultimer) or different (heteromultimer).
• Example: hemoglobin consists of four subunits (two α and two β chains).

Subunit association allows cooperative effects and regulation (e.g., changes in one subunit affecting others).

Protein Functions

Proteins carry out a wide variety of roles in biological systems. A few main categories:

• Enzymes: catalyze chemical reactions with high specificity and rate enhancements.
• Structural proteins: provide mechanical support (e.g., collagen in connective tissue, keratin in hair).
• Transport and storage: move or store small molecules or ions (e.g., hemoglobin transports oxygen; ferritin stores iron).
• Signaling and regulation:
• Hormones and receptors.
• Transcription factors regulating gene expression.
• Movement: motor proteins (e.g., myosin, kinesin) convert chemical energy into motion.
• Immune defense: antibodies recognize and bind foreign molecules (antigens).

In all these functions, structure–function relationships are central: changing the amino acid sequence (mutation) can alter folding and hence function.

Protein Denaturation and Renaturation

Denaturation is the loss of a protein’s native three‑dimensional structure, often with loss of function. Causes include:

• Heat
• Extreme pH
• Organic solvents
• High concentrations of salts or certain chemicals (e.g., urea)

Denatured proteins can:

• Precipitate or aggregate.
• Sometimes, under mild conditions, refold back into their native state upon removal of the denaturing agent (renaturation), showing that the primary structure encodes the folding information.

Post‑Translational Modifications (Conceptual Overview)

After synthesis, many proteins undergo chemical modifications that fine‑tune their properties, localization, or activity. Examples (without detailed mechanisms):

• Phosphorylation: usually on Ser, Thr, Tyr side chains; central in signaling.
• Glycosylation: addition of carbohydrate chains; important in membrane and secreted proteins.
• Disulfide bond formation: oxidation of cysteine pairs.
• Cleavage: removal of signal peptides or activation by cutting precursor polypeptides into active forms (common in hormones and digestive enzymes).

These modifications allow a single polypeptide sequence to have multiple functional states.

Summary

• Amino acids are α‑amino carboxylic acids with variable side chains that determine their individual properties.
• They can act as zwitterions and are classified by side chain polarity and charge; special residues like cysteine and proline have distinctive structural roles.
• Peptide bonds link amino acids into peptides and polypeptides, giving directional chains (N‑ to C‑terminus).
• Proteins are folded polypeptides with hierarchical structures (primary to quaternary) dictated by their sequences.
• The three‑dimensional structure of proteins underlies their diverse biological functions, and changes in sequence, environment, or chemical modifications can modulate or disrupt their activity.