Biochemistry: A Short Course 3

Protein Structure: Levels and Principles

Primary Structure: Amino Acids are Linked by Peptide Bonds to Form Polypeptide Chains

The primary structure of a protein refers to its unique sequence of amino acids, which are covalently linked by peptide (amide) bonds. These bonds form between the carboxyl group of one amino acid and the amino group of the next, resulting in a linear polymer.

• Peptide Bond: A covalent bond with partial double-bond character, making it resistant to hydrolysis and thus kinetically stable.

• Directionality: Amino acid sequences are written from the amino (N) terminus to the carboxyl (C) terminus.

• Hydrogen Bonding: Each peptide bond contains a hydrogen-bond donor (NH group) and acceptor (CO group), important for higher-order structures.

Example: The sequence Ser-Gly-Ala-Leu represents a tetrapeptide with a specific order of amino acids.

Secondary Structure: Polypeptide Chains Can Fold into Regular Structures

Secondary structure refers to local, regular arrangements of the polypeptide backbone stabilized by hydrogen bonds. The two major elements are the α helix and the β strand/sheet.

• α Helix: A right-handed coil where the CO group of residue i hydrogen bonds to the NH group of residue i+4.

• β Strand/Sheet: Extended polypeptide chains (β strands) align side by side, connected by NH-to-CO hydrogen bonds to form β sheets. Sheets can be antiparallel, parallel, or mixed.

Example: Keratin (hair protein) is rich in α helices, while silk fibroin is composed of β sheets.

Tertiary Structure: Polypeptide Chains Fold into Compact, Asymmetric Structures

Tertiary structure describes the overall three-dimensional shape of a single polypeptide chain, determined by interactions among side chains (R groups) and the polypeptide backbone.

• Hydrophobic Effect: The main driving force for folding is the burial of hydrophobic side chains in the protein's interior, away from water.

• Hydrophilic Residues: These are generally exposed on the protein surface, interacting with the aqueous environment.

• Membrane Proteins: Display an inverse distribution, with hydrophobic residues on the surface to interact with the lipid environment and hydrophilic residues shielded inside.

Example: Myoglobin, a water-soluble protein, has a hydrophobic core and hydrophilic surface.

Quaternary Structure: Multiple Polypeptide Chains Can Assemble into a Single Protein

Quaternary structure arises when a protein consists of more than one polypeptide chain (subunit). The arrangement and interaction of these subunits define the protein's quaternary structure.

• Subunits: Each polypeptide chain is called a subunit; proteins may have identical or different subunits.

• Stabilization: Subunits are usually held together by noncovalent interactions (hydrophobic, ionic, hydrogen bonds).

Example: Hemoglobin is a tetramer composed of two α and two β subunits.

Biochemistry in Focus: Surviving Desiccation

Adaptations to Extreme Dehydration: The Case of Tardigrades

Some organisms, such as tardigrades (water bears), can survive complete desiccation for years and recover upon rehydration. This remarkable ability is of great biochemical interest.

• Trehalose: Many desiccation-tolerant organisms accumulate trehalose, a disaccharide of glucose, which is thought to replace water in hydrogen bonding with biomolecules, thus preventing protein denaturation and aggregation.

Disaccharide	Constituent Monomers	Function
Trehalose	Glucose + Glucose	Protects proteins and membranes during desiccation

$\text{Trehalose structure:}$

$\ce{\underset{Glucose}{C6H12O6} - O - \underset{Glucose}{C6H12O6}}$

• Tardigrades' Unique Strategy: Unlike many organisms, tardigrades have little or no trehalose. Instead, they rely on intrinsically disordered proteins (IDPs) to survive desiccation.

• Experimental Evidence: Deletion of a specific IDP gene in tardigrades (using interference RNA) had no effect under hydrated conditions but drastically reduced survival after dehydration and rehydration.

Example: In experiments, control tardigrades and those with IDP deletion survived equally well when hydrated, but only controls survived desiccation and rehydration.

Problem-Solving Strategies: Protein Folding and Amino Acid Composition

Principles of Protein Folding

Protein folding is primarily driven by the hydrophobic effect, where hydrophobic amino acids cluster in the protein's interior, minimizing exposure to water, while hydrophilic amino acids are exposed on the surface.

• Key Question: To predict protein folding, it is often sufficient to know the ratio of hydrophilic to hydrophobic amino acids, rather than the exact sequence.

• Surface-to-Volume Ratio: Spherical proteins have the lowest surface-to-volume ratio, while elongated or subunit proteins have higher ratios.

• Protein Complexes: Proteins with more hydrophobic residues on the surface may form complexes (e.g., tetramers) to shield these residues from water.

Protein	Hydrophilic:Hydrophobic Ratio	Likely Structure
α	1.8	Spherical (soluble)
β	0.42	Cigar-shaped (less soluble)
δ	1	Subunit of tetramer (hydrophobic surface)

Example: A protein with a high hydrophilic:hydrophobic ratio is likely to be soluble and globular, while one with a low ratio may be membrane-associated or part of a larger complex.

Key Terms

• Primary structure: Linear sequence of amino acids in a protein.

• Peptide (amide) bond: Covalent bond linking amino acids in a polypeptide.

• Disulfide bond: Covalent bond between sulfur atoms of two cysteine residues, stabilizing protein structure.

• φ (phi) angle: Angle of rotation about the bond between the nitrogen and the α-carbon in the polypeptide backbone.

• ψ (psi) angle: Angle of rotation about the bond between the α-carbon and the carbonyl carbon in the backbone.

• Ramachandran plot: Graphical representation of allowed φ and ψ angles in a polypeptide.

• Secondary structure: Local folding patterns (α helix, β sheet) stabilized by hydrogen bonds.

• α helix: Right-handed helical structure stabilized by backbone hydrogen bonds.

• β pleated sheet: Sheet-like structure formed by hydrogen bonding between β strands.

• β strand: Extended polypeptide chain forming part of a β sheet.

• Tertiary structure: Overall 3D shape of a single polypeptide chain.

Additional info: The notes above expand on the brief points in the original material, providing definitions, examples, and context for each level of protein structure and the biochemical adaptation of tardigrades. The tables and equations are reconstructed and clarified for study purposes.