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Biochemistry

Biochemistry. Lecture 5. Protein Functions. Binding. +. L. PL. P. Catalysis. Structure. Specificity: Lock-and-Key Model. Proteins typically have high specificity: only certain ligands bind High specificity can be explained by the complementary of the binding site and the ligand.

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Biochemistry

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  1. Biochemistry Lecture 5

  2. Protein Functions Binding + L PL P Catalysis Structure

  3. Specificity: Lock-and-Key Model • Proteins typically have high specificity: only certain ligands bind • High specificity can be explained by the complementary of the binding site and the ligand. • Complementarity in • size, • shape, • charge, • or hydrophobic / hydrophilic character • “Lock and Key” model by Emil Fisher (1894) assumes that complementary surfaces are preformed. +

  4. Specificity: Induced Fit • Conformational changes may occur upon ligand binding (Daniel Koshland in 1958). • This adaptation is called the inducedfit. • Induced fit allows for tighter binding of the ligand • Induced fit can increase the affinity of the protein for a second ligand • Both the ligand and the protein can change their conformations +

  5. Oxygen Binding Proteins

  6. Binding: Quantitative Description • Consider a process in which a ligand (L) binds reversibly to a site in the protein (P) • The kinetics of such a process is described by: the association rate constant ka the dissociation rate constant kd • After some time, the process will reach the equilibrium where the association and dissociation rates are equal • The equilibrium composition is characterized by the the equilibrium constant Ka ka + L PL P kb

  7. Binding: Analysis in Terms of the Bound Fraction • In practice, we can often determine the fraction of occupied binding sites • Substituting [PL] with Ka[L][P], we’ll eliminate [PL] • Eliminating [P] and rearranging gives the result in terms of equilibrium association constant: • In terms of the more commonly used equilibrium dissociation constant:

  8. Oxygen Binding Proteins

  9. Red Blood Cells (erythrocytes)

  10. Two Types of the Immune Systems • Cellular immune system • targets own cells that have been infected • also clears up virus particles and infecting bacteria • key players: Macrophages, killer T cells (Tc), • and inflammatory T cells (TH1) • Humoral “fluid” immune system • targets extracellular pathogens • can also recognize foreign proteins • makes soluble antibodies  • keeps “memory” of past infections • key players: B-lymphocytes and helperT-cells (TH2)

  11. Myosin In Motion! http://www.youtube.com/watch?v=edBRWl1vftc&feature=player_embedded http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter10/animation__myofilament_contraction.html

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