Protein Structure, Properties, and Functions
Protein Structure and Properties
Primary Structure
The primary structure of proteins is the linear sequence of amino acids. This simplest structure is crucial because it determines higher-level structures. The peptide bond’s planarity causes amino acid rotation around the alpha carbon, resulting in a zigzag pattern. The variety of possible sequences is virtually unlimited.
Secondary Structure
The secondary structure is the spatial arrangement of the amino acid sequence, a direct result of alpha carbon rotation. Common structures include the alpha-helix and beta-sheet (folded sheet). Collagen helix is another example.
Alpha-Helix
In an alpha-helix, the polypeptide chain coils due to twists around each amino acid’s alpha carbon. Intrachain hydrogen bonds between the NH group of one peptide bond and the C=O group of the fourth amino acid maintain this structure. The rotation is clockwise, with approximately 3.6 amino acid residues per turn. Amino acid radicals point outwards. Proline and hydroxyproline can disrupt alpha-helix formation.
Beta-Sheet (Folded Sheet)
Some proteins maintain a zigzag primary structure and associate through interchain hydrogen bonds. All peptide bonds participate in these cross-links, increasing stability. Polypeptide chains can be arranged parallel (N-C orientation) or antiparallel (alternating N-C and C-N). Radicals alternate on either side of the sheet. Antiparallel arrangements are more compact.
Collagen Helix
Collagen, found in tendons and connective tissues, has a rigid structure. Its high proline content prevents the formation of alpha-helices or beta-sheets. Individual chains wind clockwise, forming a triple helix with no intrachain hydrogen bonds.
Tertiary Structure
The tertiary structure describes how the native protein folds in space. This stability arises from interactions between distant amino acid R-groups:
- Hydrogen bonds between peptide groups
- Electrostatic attractions between oppositely charged groups
- Hydrophobic attractions and van der Waals forces between aliphatic or aromatic radicals
- Disulfide bridges between cysteine residues
Large proteins often have compact units called domains (50-300 amino acids) connected by flexible hinges. Domains are stable and may contain alpha-helices or beta-sheets.
Quaternary Structure
This structure applies to fibrous and globular proteins composed of two or more polypeptide chains (subunits, monomers, or protomers). These subunits are linked by weak bonds (hydrogen bonds, van der Waals forces, and disulfide bonds).
Protein Properties
Solubility
Solubility depends on hydrophilic R-groups on the protein’s surface forming hydrogen bonds with water. Fibrous proteins are insoluble; globular proteins are soluble.
Denaturation
Denaturation breaks bonds, disrupting secondary, tertiary, and quaternary structures. Peptide bonds remain intact, causing the protein to adopt a filamentous form. Under certain conditions, denaturation is reversible.
Specificity
Proteins exhibit specificity at various levels. The most important is specific function (minor amino acid sequence changes can cause loss of function) and species specificity (some proteins are unique to a species). Homologous proteins perform similar functions in different species.
Buffering Capacity
Proteins are amphoteric, acting as acids or bases to absorb pH changes.