Chapter 4 – Protein Structure and Function (Expanded Study Guide)

🔹 Introduction: Why Proteins Matter

• Proteins are the most versatile and essential macromolecules in living systems.

• They are responsible for:

  • Structure: giving cells shape (cytoskeleton, extracellular matrix).

  • Catalysis: enzymes accelerate chemical reactions up to a million times faster than without them.

  • Transport: move molecules across membranes or through the bloodstream.

  • Signaling: hormones and receptors allow cells to “talk” to each other.

  • Defense: antibodies neutralize pathogens, toxins disable competitors.

  • Movement: motor proteins power muscle contraction, cilia/flagella beating, and intracellular transport.

• Without proteins, cells could not build, maintain, or regulate themselves.

🔹 1. Shape and Structure of Proteins

1.1 Amino Acids: The Building Blocks

• 20 standard amino acids differ only in their side chains (R-groups).

• Common features:

  • Backbone: repeating –N–C–C– atoms.

  • N-terminus (amino group) and C-terminus (carboxyl group) give proteins directionality.

• Side chain properties determine protein behavior:

  • Hydrophobic (e.g., Val, Leu, Ile) → cluster inside proteins.

  • Hydrophilic polar (e.g., Ser, Thr, Gln) → interact with water.

  • Charged (e.g., Lys, Glu, Asp) → form salt bridges, stabilize structure.

📌 Key point: The amino acid sequence (primary structure) alone contains all the information needed for folding and function.

1.2 Protein Folding

• Proteins fold spontaneously into shapes of lowest free energy.

• Stabilized by weak noncovalent bonds:

  • Hydrogen bonds (e.g., between backbones or side chains).

  • Electrostatic attractions (charged groups).

  • Van der Waals forces (close packing of atoms).

  • Hydrophobic effect: nonpolar side chains bury inside to avoid water.

• Chaperone proteins assist folding:

  • Some bind and stabilize partly folded chains.

  • Others form “isolation chambers” (like a folding box) to prevent aggregation.

• Denaturation: heat or chemicals (e.g., urea) unfold proteins.

• Renaturation: some proteins can spontaneously refold if conditions allow → shows sequence dictates structure.

1.3 Hierarchy of Protein Structure

1. Primary – exact amino acid sequence (polypeptide chain).

   • Example: Insulin has a fixed sequence identical in all human molecules.

2. Secondary – local folding patterns.

   • α helix: coiled structure stabilized by H-bonds every 4th amino acid.

   • β sheet: strands hydrogen-bond side by side (parallel or antiparallel).

3. Tertiary – full 3D conformation of one polypeptide, including loops, turns, and side chain interactions.

4. Quaternary – multiple polypeptides assemble into a functional complex.

   • Example: Hemoglobin (α2β2 tetramer).

1.4 Structural Motifs

• α Helices:

  • Common in membrane proteins: hydrophobic side chains face lipid bilayer, backbone H-bonds shielded inside helix.

  • Coiled-coil: two helices twist around each other, hydrophobic stripes align (keratin, myosin).

• β Sheets:

  • Provide rigidity (silk fibroin).

  • Amyloid fibrils: stacked β sheets; stable but pathological (Alzheimer’s, prion diseases).

1.5 Domains and Assemblies

• Protein domains: independently folding units (40–350 amino acids).

  • Example: Catabolite activator protein (CAP) has a cAMP-binding domain and a DNA-binding domain.

• Quaternary assemblies:

  • Dimers (CAP protein).

  • Tetramers (neuraminidase, hemoglobin).

  • Filaments (actin).

  • Tubes (microtubules).

  • Spheres (viral capsids).

1.6 Fibrous vs. Globular Proteins

• Globular proteins:

  • Compact, irregular shapes.

  • Mostly enzymes, antibodies, signaling proteins.

• Fibrous proteins:

  • Elongated, strong.

  • Provide support in cells/tissues.

  • Collagen: triple helix; forms fibrils with tensile strength like steel (in tendons, skin).

  • Elastin: cross-linked meshwork; allows tissues like skin and lungs to stretch and recoil.

1.7 Stabilization by Disulfide Bonds

• Covalent S–S bonds between cysteine side chains.

• Stabilize extracellular proteins (where environment is harsher).

• Example: Lysozyme in tears/saliva retains antibacterial function due to disulfide reinforcement.

🔹 2. How Proteins Work

2.1 Binding to Ligands

• Every protein binds specific ligands at its binding site.

• Specificity arises from complementary shape and chemical interactions.

• Examples:

  • Antibodies bind pathogens.

  • Hexokinase binds glucose and ATP.

  • Actin monomers bind to form filaments.

2.2 Antibodies

• Y-shaped proteins made by immune system.

• Bind antigens (foreign molecules) with extreme specificity.

• Each antibody has two identical binding sites formed by loops of polypeptides.

• Humans can produce billions of different antibodies, allowing recognition of nearly any pathogen.

2.3 Enzymes

• Biological catalysts that speed up reactions by stabilizing the transition state.

• Do not alter equilibrium, only reaction rate.

• Examples:

  • DNA polymerase → copies DNA.

  • Protein kinase → adds phosphate to proteins.

  • Pepsin → digests proteins in stomach.

2.4 Regulation and Switching

• Allosteric proteins: change shape when ligands bind at regulatory sites.

• Phosphorylation:

  • Carried out by kinases, reversed by phosphatases.

  • Acts as an on/off switch.

• GTP-binding proteins:

  • Active when bound to GTP, inactive with GDP.

  • Function as molecular timers (e.g., Ras in signaling).

2.5 Motor Proteins

• Convert ATP hydrolysis → mechanical work.

• Examples:

  • Myosin: muscle contraction.

  • Kinesin: transports organelles along microtubules.

  • Dynein: powers cilia/flagella movement.

2.6 Protein Machines

• Large complexes of multiple proteins working in cycles.

• Example: Ribosome synthesizes proteins.

• Require energy input (ATP/GTP) for coordination.

🔹 3. How Proteins Are Controlled

• Gene expression: controls quantity of proteins made.

• Protein degradation: proteasomes remove misfolded/unneeded proteins.

• Compartmentalization: ensures proteins act in correct cellular location.

• Feedback inhibition: metabolic product inhibits earlier enzyme (negative regulation).

• Positive regulation: product stimulates another enzyme.

• Covalent modifications: phosphorylation, acetylation, ubiquitination.

• Phase separation: proteins form liquid-like compartments (e.g., stress granules).

🔹 4. How Proteins Are Studied

• Purification:

  • Centrifugation separates components by size/density.

  • Chromatography (ion-exchange, gel-filtration, affinity) isolates specific proteins.

• Mass spectrometry: measures peptide fragment masses to deduce sequence.

• X-ray crystallography: high-resolution 3D structure.

• NMR spectroscopy: solution structures for small proteins.

• Cryo-electron microscopy (Cryo-EM): powerful for large complexes, near-atomic resolution without crystallization.

🔹 5. Historical Highlights

• 1838: Mulder coined “protein”.

• 1894: Fischer’s lock-and-key model of enzyme action.

• 1951: Pauling & Corey proposed α helix and β sheet.

• 1955: Sanger sequenced insulin (first protein sequence).

• 1960: Kendrew & Perutz solved first 3D protein structures (myoglobin, hemoglobin).

• 1970s–2010s: NMR, mass spectrometry, and cryo-EM revolutionized protein science.

🔹 6. Key Takeaways

• Sequence dictates structure, structure dictates function.

• Proteins are stabilized by noncovalent bonds + hydrophobic forces.

• Misfolded proteins → serious diseases (Alzheimer’s, prion diseases).

• Proteins are regulated at multiple levels: expression, modification, degradation, localization.

• Modern methods allow us to visualize proteins at atomic detail.