Protein Structure and Function Quiz

Protein Structure and Function

• Proteins are polymers of 20 amino acids.
• Amino acid sequence dictates protein shape, which defines function.
• Minor amino acid substitutions may not significantly alter protein function.
• Peptide bonds form via condensation reactions (loss of water).
  • Peptide bonds have partial double bond characteristics, affecting protein flexibility.
• Protein structure is categorized into four levels: primary, secondary, tertiary, and quaternary.

Primary Structure

• Linear sequence of amino acids.

Secondary Structure

• Local folding patterns of polypeptide chains.
• Stabilized by hydrogen bonds along the polypeptide backbone.
• No interaction between R-groups.
• Common secondary structures are alpha-helices (helix-shaped coils) and beta-sheets (folded, pleated sheets).
  • Alpha helices have hydrogen bonds running parallel to the helix axis.
  • Beta sheets can be parallel or antiparallel with hydrogen bonds running perpendicular to the sheets.
  • R-groups extend outward.
  • Important properties such as hydrophobicity (hydrophobic helix) and amphipathic regions (hydrophobic/hydrophilic) influence folding.

Tertiary Structure

• Overall 3D conformation of the entire polypeptide chain.
  • Combination of secondary structures.
  • Stabilized by various non-covalent interactions between R-groups (e.g. hydrophobic interactions, van der Waals forces, ionic bonds, hydrogen bonds) and disulfide bonds.
• Disulfide bonds
  • Covalent bond between two cysteine residues.
  • Forms under oxidized conditions.
  • Can be intermolecular (connecting different polypeptide chains) or intramolecular (within the same polypeptide chain)

Quaternary Structure

• Exists in proteins with multiple polypeptide chains (at least two subunits).
• Represents the arrangement and interactions between all subunits.

Protein Folding

• Protein shape is crucial for function.
• Hydrophobic amino acids usually cluster inward, promoting stability.
• Hydrophilic amino acids typically face outward, maximizing interactions with water.
• Proteins spontaneously adopt the lowest energy conformation.

Enzymes

• Proteins that accelerate chemical reactions.
• Do not alter the overall free energy change of a reaction.
• Provide an alternative pathway with lower activation energy.

Protein Modifications

• Many proteins undergo post-translational modifications, especially in eukaryotes.
  • Disulfide bond formation
  • Hydroxylation (adding a hydroxyl group)
  • Ubiquitination (marking for degradation)
  • Phosphorylation/dephosphorylation (adding/removing a phosphate group)
  • Glycosylation (adding sugar chains)
  • Proteolytic processing (removing portions of the polypeptide) - Important for protein activation and regulation.
• Modifications are often important for regulating protein function.

Example Protein Modifications

• Phosphorylation:
  • Amino acids targeted: Serine, Threonine, Tyrosine.
• Glycosylation:
  • Adds carbohydrate groups, creating more complex structures.
  • Amino acids targeted: Asparagine, Serine, Threonine, Hydroxylysine.
  • Often found on secreted proteins.
• Proteolytic Processing:
  • Removal of polypeptide segments.
  • Frequently found in proteins activated under specific conditions or locations (eg insulin; HIV Envelope).