Overview
This lecture focuses on how the chemistry of amino acid R groups drives protein folding. It explains the types of bonds involved at each level of protein structure and how the unique sequence of amino acids (specifically their R groups) determines the unique 3D shape and function of each protein. The lecture also touches on the challenges of predicting protein folding and the experimental methods used to determine protein structures.
Levels of Protein Structure and Their Chemical Bonds
Primary Structure
- Defined as the linear sequence of amino acids in a polypeptide chain.
- Amino acids are linked by peptide bonds, which are covalent bonds formed between the carboxyl group of one amino acid and the amino group of the next.
- Peptide bonds are very strong and stable; they are not disrupted by moderate heat, salt, or pH changes typical in biological systems.
- This stability is important because environmental factors that cause protein unfolding usually affect weaker, non-covalent bonds, not peptide bonds.
- Mutations that change the amino acid sequence (and thus the R groups) can alter protein folding and function.
Secondary Structure
- Includes common folding patterns: alpha helices and beta pleated sheets (beta sheets).
- These structures are stabilized by hydrogen bonds formed between backbone atoms (not R groups).
- Specifically, hydrogen bonds form between the carbonyl oxygen (C=O) of one amino acid and the amide hydrogen (N-H) of another.
- In alpha helices:
- Hydrogen bonds form between amino acids that are four residues apart.
- R groups project outward from the helix, making them available for interactions with other molecules or parts of the protein.
- In beta sheets:
- Hydrogen bonds form between adjacent strands of the polypeptide backbone.
- R groups alternate sticking above and below the sheet, creating distinct chemical surfaces.
- The chemistry of R groups influences where secondary structures form but does not directly stabilize these structures.
Chemistry of Amino Acid R Groups and Their Role in Folding
Categories of R Groups
- Nonpolar (Hydrophobic) R groups: Mostly carbon and hydrogen atoms with nonpolar covalent bonds; tend to avoid water.
- Polar (Hydrophilic) R groups: Contain atoms like oxygen and nitrogen that create polar covalent bonds and partial charges; interact well with water.
- Subdivided into:
- Polar uncharged (e.g., serine, threonine, asparagine, glutamine)
- Polar charged (positively charged: lysine, arginine; negatively charged: aspartic acid, glutamic acid)
- Special cases:
- Histidine: Can be positively charged or neutral depending on pH.
- Proline: Unique cyclic structure that restricts backbone flexibility.
Hydrophobic Effect and Protein Folding
- Water is a polar molecule with partial charges, so it interacts favorably with polar and charged R groups.
- Nonpolar R groups do not interact well with water and tend to cluster together inside the protein, away from the aqueous environment.
- This clustering forms a hydrophobic core, which is a major driving force for protein folding and stability.
- The hydrophobic effect is a thermodynamic phenomenon where the system minimizes unfavorable interactions between water and nonpolar groups.
Continuum of Hydrophobicity
- Not all nonpolar R groups are equally hydrophobic.
- For example:
- Glycine and alanine are weakly hydrophobic.
- Isoleucine, leucine, valine, phenylalanine, and methionine are strongly hydrophobic.
- Some polar uncharged amino acids (e.g., serine, threonine, tyrosine) have intermediate properties.
- Understanding this continuum helps explain why some nonpolar residues may be found on the protein surface.
Bonds and Interactions Stabilizing Tertiary and Quaternary Structures
Types of Bonds and Interactions
- Ionic bonds (salt bridges): Form between oppositely charged R groups (e.g., lysine and glutamate).
- Hydrogen bonds: Between polar uncharged R groups or between R groups and backbone atoms.
- Hydrophobic interactions: Nonpolar R groups cluster together to avoid water.
- Van der Waals interactions: Weak, transient attractions due to momentary dipoles from electron movement; contribute to close packing of atoms.
- Disulfide bonds (disulfide bridges):
- Covalent bonds formed between the sulfur atoms of two cysteine residues.
- Formed by an oxidation reaction catalyzed by enzymes.
- Provide strong stabilization, especially in extracellular proteins.
- Not present in all proteins but important for structural rigidity.
Special Notes on Disulfide Bonds
- Disulfide bonds are the only covalent bonds that stabilize tertiary and quaternary structures beyond the peptide backbone.
- Proteins that require rigidity and stability, such as antibodies, often have multiple disulfide bonds.
- Proteins like hemoglobin, which function inside cells, typically lack disulfide bonds in their tertiary and quaternary structures.
Quaternary Structure
- Refers to the assembly of multiple polypeptide subunits into a functional protein complex.
- Subunits are held together by the same types of non-covalent interactions as tertiary structure.
- Disulfide bonds can also link subunits in some proteins (e.g., antibodies).
- Example:
- Hemoglobin has four subunits (2 alpha, 2 beta) held together by non-covalent bonds, no disulfide bonds.
- Antibodies have multiple disulfide bonds linking heavy and light chains and between subunits.
Special Structural Features and Examples
Proline
- Its R group forms a ring that covalently bonds back to the backbone nitrogen.
- This restricts backbone flexibility and introduces kinks.
- Proline is rarely found in the middle of alpha helices but may be found at the ends.
Beta Barrels
- Proteins can form barrel-shaped structures using beta sheets.
- Common in pore-forming proteins in membranes.
Alpha Helices in DNA Binding
- Alpha helices fit well into the major groove of DNA.
- The outward-facing R groups make specific contacts with DNA bases, enabling sequence-specific binding.
Summary of Key Terms
| Term | Definition | |----------------------|---------------------------------------------------------------------------------------------| | Peptide bond | Covalent bond linking amino acids in a polypeptide chain. | | Alpha helix | Spiral secondary structure stabilized by hydrogen bonds between backbone atoms. | | Beta sheet | Pleated sheet secondary structure stabilized by hydrogen bonds between backbone atoms. | | Hydrophobic effect | Tendency of nonpolar R groups to cluster away from water, driving protein folding. | | Van der Waals forces | Weak, transient attractions due to momentary dipoles from electron movement. | | Disulfide bond | Covalent bond between sulfur atoms of two cysteine residues, stabilizing protein structure.| | Tertiary structure | Overall 3D shape of a single polypeptide due to R group interactions. | | Quaternary structure | Assembly of multiple polypeptide subunits into a functional protein complex. |
Action Items / Next Steps
- Watch movies 4.2 and 4.4 to visualize alpha helices and beta sheets and their hydrogen bonding.
- Review the 20 amino acids and practice categorizing their R groups by polarity and charge.
- Practice identifying which types of bonds stabilize each level of protein structure.
- Prepare for practice questions and explore additional resources provided.