Lecture%203

Lecture 3 - First problem set BILD1 The Cell Prof Lisa M Boulanger Will be discussed in Sections THIS WEEK Key posted Saturday Problem set 2 posted

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1 BILD1 The Cell Prof. Lisa M. Boulanger 01/6/07 BILD1 - Lecture 3 2 First problem set Will be discussed in Sections THIS WEEK Key posted Saturday Problem set 2 posted Friday ! 01/6/07 BILD1 - Lecture 3 3 Highlights from the previous lecture: Ions are charged and soluble in water, due to ability to form hydrogen bonds Ionic bonds occur between ions (charged atoms) pH = -log[H + ]; acids increase [H + ] van der Waals bonds occur between transiently charged regions of molecules 01/6/07 BILD1 - Lecture 3 4 pH recap (-log 10 [H+]) + (-log 10 [OH-]) = 14 If 10 -3 M H + : (-log 10 [10 -3 ]) + (-log 10 [OH-]) = 14 (-[-3]) + (-log 10 [OH-]) = 14 3 + (-log 10 [OH-]) = 14 [OH-] = 10 -9 01/6/07 BILD1 - Lecture 3 5 4 emergent properties of water: cohesion (H bonds), moderation of temperature (high specific heat), ice floats (H bonds), versatile solvent (H bonds) Molarity of a solution daltons/molecule = grams/mole 1 mole/liter = 1 molar Some chemical reactions can reverse More highlights from the previous lecture: 01/6/07 BILD1 - Lecture 3 6 THIS LECTURE: Determinants and effects of molecular shape Functional groups Carbon: the backbone of biology Building and unbuilding bigger (macro) molecules
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2 01/6/07 BILD1 - Lecture 3 7 Molecular Shape and Function The precise shape of a molecule Is usually very important to its function in the living cell Is determined by the positions of its atoms’ valence orbitals 01/6/07 BILD1 - Lecture 3 8 s orbital Z Three p orbitals X Y Four hybrid orbitals (a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink). Tetrahedron In a covalent bond The s and p orbitals may hybridize, creating specific molecular shapes 01/6/07 BILD1 - Lecture 3 9 Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Natural endorphin (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cel s in the brain. The boxed portion of the morphine molecule is a close match. (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cel recognize and can bind to both endorphin and morphine. Natural endorphin Endorphin receptors Morphine Brain cel Shape affects molecular interactions 01/6/07 BILD1 - Lecture 3 10 Isomers Are molecules with the same molecular formula but different structures and properties Three types of isomers are Structural Geometric Enantiomers H HHH H H H H H H H H H H H H H H H H H H H H H CO 2 H CH 3 NH 2 C CO 2 H H CH 3 NH 2 XX X X CCCCC C C CCC C C C C C (a) Structural isomers (b) Geometric isomers (c) Enantiomers H 01/6/07 BILD1 - Lecture 3 11 Carbon: The Backbone of Biological Molecules All living organisms Are made up of chemicals based mostly on the element carbon The carbon in all organic molecules was originally incorporated into these molecules by plants 01/6/07 BILD1 - Lecture 3 12 The bonding versatility of carbon
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This note was uploaded on 03/26/2010 for the course BENG 110 taught by Professor Schmid-schoenbein during the Spring '08 term at UCSD.

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Lecture 3 - First problem set BILD1 The Cell Prof Lisa M Boulanger Will be discussed in Sections THIS WEEK Key posted Saturday Problem set 2 posted

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