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Exam 1 Review refined

Exam 1 Review refined - Ex am 1 Review Lecture by Lecture...

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Ex am 1 Review: September 21, 2009 Lecture by Lecture Objectives: Lectures 1-5 and 7, and Enzymology Lecture 1 - Intro Thermodynamics o The first law of thermodynamics states that energy is conserved; it can be neither created nor destroyed o According to the second law of thermodynamics, spontaneous processes are characterized by the conversion of order to disorder o All processes increase the entropy—that is, the disorder— of the universe. ΔG = ΔH – TΔS o Understand how to use all components of this equation TABLE 1-3   Variation of Reaction Spontaneity (Sign of  Δ G ) with the Signs of  Δ H  and  Δ S Δ S + The reaction is bot temperatures. The reaction is ent + The reaction is ent above T = Δ H S . The reaction is bot
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o Understand how entropy and enthalpy changes affect Free energy of the system o Know how Entropy is the driving force of many biological reactions Understand the relationship between Free Energy and Equilibrium Constant Understand Steady State
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o Δ G ° is the free energy change of the reaction when all of its reactants and products are in their standard states Understand Open and Closed systems Lecture 2 – Water Concentration = 55.5M, Shape = Bent, Structure is Polar How does water affect biochemical systems? o Protein structure is influenced by water o Hydrogen bonding o Clatherates – “Cages” Compare the ordered structure of ice to liquid water Only 15% difference in bonding. Water has a similar structure in liquid and solid form. H-bonds are stable but in water they are dynamic 10 -12 per second
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Understand different types of bonding interactions and their strengths TABLE 2-1   Bond Energies in Biomolecules Example Bond  O—H C—H C—C   —COO ··· + H 3 N—  
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Example Bond  Understand Electrostatic Interactions between ions and water Ions get solvated in water
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Lecture 3 – Amino Acids Know groups of amino acids. o Nonpolar Gly, Ala, Phe, Leu, Ile, Pro, Met, Trp, Val (GAP LIP MTV) o Polar Cys, Asn, Thr, Tyr, Gln, Ser (CAT TGS) o Charged Acidic
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Asp, Glu Basic Arg, Lys, His o Aromatic Trp, Phe, Tyr Know side chain names and PKa’s for Asp, Glu, Arg, Lys, Tyr, His, and Cys.
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