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PROTEINS

Objectives

  • Classify proteins according to function, solubility, and composition.

  • Illustrate how amino acids are linked to form the four levels of structure in proteins.

  • Identify the various forces of attractions that stabilize each level of protein architecture.

Introduction to Proteins

  • Origin of the term: From the Greek word proteios meaning "first of rank."

  • Prevalence: Proteins are the most abundant biomolecule in cells.

  • Definition of Polypeptides: A single linear chain of amino acids.

  • Definition of Proteins: Comprised of one or more polypeptide chains folded into specific conformations.

  • Molecular Weight of Proteins: Generally expressed with a molecular weight (MW) of at least 10,000 Da (Daltons).

Molecular Weight (MW) of Proteins

  • Measurement Units: Mass is expressed in Daltons (Da or D), a unit approximately equal to that of a hydrogen atom.

CLASSIFICATION OF PROTEINS

Classification According to Composition

  • Simple Proteins: Yield only amino acids upon hydrolysis.

  • Conjugated Proteins: Composed of simple proteins bonded with non-protein substances.

Types of Conjugated Proteins

  • Nucleoproteins: Combinations of nucleic acid and protein.

  • Glycoproteins: Composed of carbohydrates and proteins.

  • Lipoproteins: Combinations of lipids and proteins.

  • Phosphoproteins: Proteins associated with phosphate groups.

  • Hemoproteins: Proteins that include heme groups.

  • Flavoproteins: Containing flavin nucleotides.

  • Metalloproteins: Containing metal ions.

Classification According to Biological Function

  • Enzymes: Serve as biological catalysts catalyzing biological reactions.

  • Transport Proteins: Carry specific molecules or ions from one organ to another.

  • Nutrient and Storage Proteins: Mobilized by the body for building blocks or energy.

  • Defense Proteins: Protect organisms against foreign invasion.

  • Contractile or Motile Proteins: Facilitate cell and organism movement, shape changes, or contraction.

  • Structural Proteins: Provide support as filaments, cables, or sheets, enhancing strength and protection.

  • Regulatory Proteins: Regulate physical or cellular activities.

Classification According to Shape

  • Globular Proteins:

    • Shape: Polypeptide chains coiled into a compact spherical form.

    • Properties: Soluble in water and mobile within cells.

    • Examples: Amylase, hemoglobin.

  • Fibrous Proteins:

    • Shape: Polypeptide chains arranged side-by-side in long filaments.

    • Properties: Insoluble in water and mechanically strong.

    • Functions: Primarily structural and protective.

    • Example: Collagen.

Classification According to Solubility

  • Albumins:

    • Solubility: Soluble in water and dilute aqueous solutions.

    • Example: Egg albumin, lactalbumin in milk.

  • Globulins:

    • Solubility: Soluble in dilute salt solutions but insoluble or sparingly soluble in water.

    • Example: Ovomucin of egg, myosin of muscle.

  • Glutellins:

    • Solubility: Soluble in dilute solutions of acids and bases.

    • Example: Glutellin from wheat and oryzenin from rice.

  • Albuminoids:

    • Solubility: Insoluble in most solvents, including water, salt solutions, dilute acids, alkalis, and alcohol.

    • Example: Keratins of hair, collagen of bones.

  • Prolamins:

    • Solubility: Soluble in 70-80% alcohol (and others in 50-90%), insoluble in water, neutral solvents, or absolute alcohol.

    • Example: Zein from corn.

LEVELS OF PROTEIN ARCHITECTURE

Hierarchy of Protein Structure

  • Primary Structure:

    • Definition: The linear sequence of amino acids from the N-terminus to the C-terminus.

    • Significance: Determinative for protein structure and function.

  • Case Study:

    • Normal Hemoglobin:

    • Amino Acid Sequence: Contains traditional amino acids.

    • Functionality: Each molecule does not associate, allowing each to carry oxygen efficiently.

    • Sickle-Cell Hemoglobin:

    • Mutation: Glu6 replaced by Val.

    • Functionality: Molecules interact and crystallize into fibers, significantly reducing capacity to carry oxygen leading to a sickle shape in red blood cells.

Secondary Structure

  • Definition: Spatial arrangement of amino acid residues nearby in the linear sequence.

  • Characteristics: Common patterns include regular folding of the polypeptide backbone.

  • Major Interactions: Stabilized by hydrogen bonds between peptide bonds.

  • Common Secondary Structures:

    • α-Helix:

    • Structure: Tightly wound around an imagined longitudinal axis.

    • Rise per Turn: Rises by 5.4 Å per turn; approximately 1.5 Å rise between amino acid residues; each turn contains roughly 3.6 amino acid residues.

    • Orientation: Can be right-handed (counterclockwise) or left-handed (clockwise).

    • Stability: Stabilized by hydrogen bonds; usually found in globular proteins.

    • R Groups: Protrude outward; bulky side chains are less common in helices, while Gly and Pro destabilize the structure.

    • β-Pleated Sheet:

    • Structure: Polypeptide chains are extended into a zigzag configuration rather than a helix.

    • Interaction: Zigzag chains lie side by side, stabilized by hydrogen bonds.

    • Appearance: "Pleated" formation due to alternating positions of α-carbons.

    • Collagen Helix:

    • Structure: Three polypeptide chains super-twisted around each other.

    • Properties: Around 3 amino acid residues per turn with a repeating peptide sequence: Gly-Pro-Hyp (hydroxyproline).

Tertiary Structure

  • Definition: Overall three-dimensional arrangement of all atoms in the protein.

  • Importance: Result of folding into specific 3D shapes, determining unique binding sites.

  • Common Interactions Stabilizing Tertiary Structure:

    • Hydrophobic Interactions: Non-polar residues tend to cluster in the protein’s interior.

    • Hydrogen Bonding: Between side groups or peptide bonds.

    • Electrostatic Interactions: Between charged side chains (e.g., —COO⁻ of aspartate and glutamate, and ε-NH₃⁺ of lysine).

    • Disulfide Bridges: Formed by covalent bonds between two cysteine residues, providing additional stabilization.

Quaternary Structure

  • Definition: Organization of subunits (polypeptide chains with tertiary structure) in multimeric proteins.

  • Stabilization: Subunits are held together by non-covalent interactions.

  • Types: Can be homo-multimers (same type of subunits) or hetero-multimers (different subunits).

  • Stability: Multimeric/Oligomeric proteins exhibit more stability than individual subunits.

    • Example: Hemoglobin is an oligomeric protein comprising four polypeptide chains and a heme group.

Protein Folding

  • Description: The process through which proteins acquire their three-dimensional shape, crucial for their function (e.g., formation of binding sites).

  • Influence of Amino Acid Sequence: The folding pattern is dictated by the specific amino acid sequence of the protein, which minimizes the free energy of the molecule, thus enhancing stability.

    • Aqueous Environments: Polypeptide chains fold so that hydrophobic side chains are buried internally while polar side chains remain on the exterior.

Role of Molecular Chaperones in Protein Folding

  • Assistance in Folding: Protein folding can be facilitated or stabilized by molecular chaperones.

Implications of Misfolded Proteins

  • Consequences of Misfolding: Misfolded proteins must be targeted for degradation.

  • Associated Diseases: Accumulation of misfolded proteins is linked to diseases such as Alzheimer’s, Parkinson’s, Mad Cow disease, and senile dementia.

PROTEIN DENATURATION

Definition of Protein Denaturation

  • Description: Denaturation involves alterations to the secondary, tertiary, and quaternary structures of proteins.

  • Primary Structure Preservation: The primary structure (peptide bonds) remains intact during denaturation, as peptide bonds are not easily disrupted.

Effects of Denaturation

  • Biological Activity: Denaturation can lead to a reduction or complete loss of protein function.

  • Agents of Denaturation:

    • Physical Agents: Heat and extreme pH levels.

    • Chemical Agents:

    • Strong acids and bases.

    • Heavy metal cations (e.g., Pb²⁺, Hg²⁺).

    • Alkaloidal reagents (e.g., trichloroacetic acid).

    • Organic solvents (e.g., ethanol, acetone).

Reference

  • S Nelson and Cox. "Lehninger's Principles of Biochemistry," 4th ed.