BIBC 100. Structural Biochemistry

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1 BIBC 100 Structural Biochemistry

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3 Papers- Dialogue with Scientists Questions: Why? How? What? So What?

4 Dialogue Structure to explain function Knowledge Food Molecular Medicine Farming Fine Chemicals(drugs) Diagnosis / Therapy

5 Red Blood Cell Dimensions (1Å = m) Bacterium Macromolecule [protein] Small molecule [glucose] m µm Å Limit of light microscopy High resolution EM C-C Bond X-rays/NMR

6 Today Interactions in Biology Uniqueness of Water Protein primary structure: 20 amino acid repertoire The peptide unit Proteins have unique sequence specified by genes Sequence determines 3-D structure, and function

7 The Bread and Butter of the Course Structure Basis of Molecular Function Intervention Structure Control Function

8 Why Structural Biology? Form and Function Structure to understand Vital Function How? Process: Description of Structure Dissection of Function

9 Protein Data Bank (PDB) Where? San Diego Super Computer (SDSC) What? Structures 89,212 as of 03/26/ Molecule of the Month - PDB 101Tutorial - Interactive

10 Nature Nature is: Selective And Conservative Unity and diversity

11 All cells share some common features

12 Dogma - Proteins [proteios] = of the first rank] Function { Structure Energetics Dynamics Energy Interaction * {Protein Protein} Order Living matter evades the decay to equilibrium

13 The Uniqueness of Water as the biological solvent Influences all molecular interactions Why? Polarity (charge) Cohesiveness (order) Hydro/dehydration reactions Electron transfer reactions Proton transfer reactions Origin of Cavities : Creation of water-free microenvironments

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18 Importance of Hydrogen Bonds Source of unique properties of water Structure and function of proteins Structure and function of DNA Structure and function of polysaccharides Binding of substrates to enzymes Binding of hormones to receptors Matching of mrna and trna I believe that as the methods of structural chemistry are further applied to physiological problems, it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature. Linus Pauling, The Nature of the Chemical Bond, 1939

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20 Reversible Molecular Interactions in biology Electrostatic ~3Å 3-7 kcal/mole Hydrogen Bonds ~3Å 3-7 kcal/mole Van der Waals 3Å ~1 kcal/mole A covalent bond (e.g. C-C) A photon (green light) 1.5Å ~80 kcal/mole ~60 kcal/mole

21 Physics of Noncovalent Interactions Noncovalent interactions do not involve sharing a pair of electrons. Based on their physical origin, one can distinguish between: Ionic (Coulombic) Interactions Electrostatic interactions between permanently charged species, or between the ion and a permanent dipole Dipole Interactions Electrostatic interactions between uncharged, but polar molecules van der Waals Interactions Weak interactions between all atoms, regardless of polarity Hydrophobic Effect Complex phenomenon associated with the ordering of water molecules around nonpolar substances Attractive (dispersion) and repulsive (steric) component

22 Examples of Noncovalent Interactions

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25 The Hydrophobic Effect Refers to the association or folding of nonpolar molecules in the aqueous solution Is one of the main factors behind: protein folding protein protein association formation of lipid micelles binding of steroid hormones to their receptors Does not arise because of some attractive direct force between two nonpolar

26 Low solubility of hydrophobic solutes can be explained by entropy Bulk water has little order: high entropy Water near a hydrophobic solute is highly ordered: low entropy Low entropy is thermodynamically unfavorable, thus hydrophobic solutes have low solubility.

27 Water surrounding nonpolar solutes has lower entropy

28 Origin of the Hydrophobic Effect (1) Consider amphipathic lipids in water Lipid molecules disperse in the solution; nonpolar tail of each lipid molecule is surrounded by ordered water molecules Entropy of the system decreases System is now in an unfavorable state

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30 Origin of the Hydrophobic Effect (2) Nonpolar portions of the amphipathic molecule aggregate so that fewer water molecules are ordered The released water molecules will be more random and the entropy increases All nonpolar groups are sequestered from water, and the released water molecules increase the entropy further Only polar head groups are exposed and make energetically favorable H bonds

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33 Levels of Structure in Protein Architecture Sequence structure function Primary: amino acid sequence Secondary: Folding motifs (α,β) Tertiary: Packing of secondary structures domains Quaternary: Packing of several polypeptide chains

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35 Sequence-Structure relation Amphipatic β- strand: Polar = P Non-polar = N Sequence: NPNPNPNPNP. Alignment: Strand Sequence # 1- I S A R F S V C 2- L E M T A K G C P P P Motif suited to create hydrophobic cavities

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