2 - Friday, October 2nd, 2009 Biochemistry 405 Lecture # 02...

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1 Friday, October 2 nd , 2009 Biochemistry 405 – Lecture # 02 Kane Hall 130 10:30- 11:20 am Lecturer: Wim Hol Slide Set #1 The slides shown during the lectures present the prime material to be studied. The handout shows which pages in the book contain background information on the material discussed in the lectures. Topics not covered at all in the slides of a lecture need not to be studied in the book.
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2 Water and Weak Forces in Biopolymers Outline I. Non-covalent forces. II. Physical properties and structure of water III. Hydrogen bonds IV. Hydrophobic interactions V. Covalent and Non-covalent interactions Covalent bonds link atoms in molecules together and are obviously essential. Non -covalent interactions play also a key role in living organisms. Examples are: - The dissolution of salt in water - The three-dimensional structure of proteins - Base-pairing and base-stacking in the DNA double helix - The aggregation of lipids into membrane bilayers - The affinity of sugar molecules for taste receptors - The binding of a medicine to its target protein
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3 Examples of Non-covalent interactions Quite weak Weaker Weakest While covalent bonds range typically between 300 and 500 kJ. mol -1 , non-covalent interactions mentioned above range from 20 (top) to 0.3 (below) kJ. mol -1 Neutral molecules where the center of gravity of the negative charges does not coincide with the center of gravity of the positive charges are said to have a “dipole”. Physical Properties of Water In spite of its simple chemical composition, H 2 O the water molecule is extremely important for life. We will look first at its physical properties and their importance for biochemical processes, and then at its chemical properties.
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4 The Water Molecule The “van der Waals envelope” is the effective “surface of the molecule”. This surface is obtained by making a sphere with a “van der Waals radius” centered on each atom. Two atoms from different molecules rarely come closer together than the sum of their van der Waals radii – with the very important exception of the “hydrogen bond”. Note: The water molecule is non-linear and carries a permanent dipole moment. Water and Hydrogen Bonds (Hydrogen bonds are also called “H-bonds”) = 1.77 Å = 0.965 Å 1 Å = 10 -10 m = 0.1 nm O-O distance: 0.274 nm = 2.74 Å Important: The O-O distance of ~2.74 Å in an H-bond is smaller than the sum of: (i) the O-H covalent bond distance of ~0.97 Å + (ii) the H vdW-radius of ~1.2 A + (iii) the O vdW-radius of ~1.4 A NOTE: H-bond distances are not that precisely the same in each case. The H-bond distance shown is only the approximate average H-bond distance in liquid water Lehninger 4/e Fig 2.1
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5 Water Molecules in Bulk Water The arrangement of water molecules in bulk liquid water is very dynamic. Liquid water consists of a rapid fluctuating, three-dimensional network of hydrogen-
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This note was uploaded on 06/03/2010 for the course BIOL BIO 101 taught by Professor Drumheller during the Spring '10 term at University of Washington.

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2 - Friday, October 2nd, 2009 Biochemistry 405 Lecture # 02...

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