Biochemistry Week 2 notes
Biochemistry Week 2 notes CHEM 3653 - 001
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This 6 page Class Notes was uploaded by Lauran Notetaker on Monday February 15, 2016. The Class Notes belongs to CHEM 3653 - 001 at University of Oklahoma taught by Dr. Paul A. Sims in Winter 2016. Since its upload, it has received 22 views. For similar materials see Biochemistry in Chemistry at University of Oklahoma.
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Date Created: 02/15/16
January 26, 2016 A container has a volume of 1.0 x 10^3 cm^3. What is the volume of this container in um^3? 1.0 x 10^15 um^3 1cm = 10^4 um 10^4 x 10^4 x 10^4 = 10^12um +10^3 = 10^15um (1 cm^3 over 10^12um^3) Exponential Equation A=A_o_e^+or-kt - (decay) + (growth) Hydrogen bonds 1 angstrom allows overlap 2.8 angstrom does NOT allow overlap Example of noncovalent bond L + M LM can be intermolecular (same molecule) hormone binding to receptor gene How to convert kJ to kCal 4.184 J/cal or kJ/kCal Value of gas constant R=1.987 cal K * mol H2O has a melting point and boiling point than NH3 and CH4 Photosynthesis: hv 6CO2 + 6H2O C6H12O6 + 6O2 water - “matrix of life” - allows delivery - cleansing of the cells *Make sure to know what an Angstrom (Å) is and ho to calculate the diameter of a “spherical” and “cubical” water molecule 10^10 Å 1m 1.5Å 1.2Å 1.2Å H2O = 1.2Å + 1.2Å + 1.5Å = 4.2Å 4 hydrogen bonds per water molecule O2 taken in when breathing, is added to Electron Transport Chain to come out as CO2 Water is a polar molecule n-pentane is a non-polar molecule Hydrophobic Effect “Cages” of H-bond linked water molecules about a non-polar solute - have to constrain molecules cage when submerged in water, not favored energetically - get shoved together then can form Van der Waals which offer up more H2O to solution - Entropy process CH4 in H2O (polar) CH4 in C6H6 (favored because both are non-polar) “like dissolves like” Delta S must be positive because of the increase in entropy Solubility of amphipilic molecules Polar Head Non- polar tail Acid-Base Chemistry pH = -log [H+] False pH = - log a^H+ True a^H+ = [H+] (activity coefﬁcient)^H+ pH = -log [H+] assuming a is 1, for solutions this is a good assumption What is the pH of a 0.1M solution of HCl? -log[0.1M] = 1 [H+] (M) [OH-] (M) Where the axises cross is where they are neutral Henderson-Hasselbalch pH = pKa + log [A-] [HA] HA H+ + A- 0 = log [A+] log1 = 0 [HA] 4.26 = 4.76 + log [A-] [HA] [A-] = 10^(pH - pKa) [HA] [A-] = 10^(4.26 - 4.76) [A-] = 0.32 fA = [A-] = 0.32 = 0.24 [HA] + [A-] 1 + 0.32 January 28, 2016 Acids and Bases handout Pk1 Pk2 Pk3 (about 2) (about 6.8) (about 13) H3PO4 H2PO4^- HPO4^2- PO4^3- Pk1 - half of H3PO4 and half of H2PO4^- H2PO4^- (between Pk1 and Pk2) - 1.0 completely H2PO4^- Pk2 - half H2PO4^- and half H2PO4^2- H2PO4^2- (between Pk2 and Pk3) - 1.0 completely H2PO4^2- Pk3 - half H2PO4^2- and half PO4^3- PO4^3- - 1.0 completely PO4^3- Amino acids titration curves Pi - pH at which the net charge of the molecules is zero Chapter 5 - Amino acids DNA will have a net-charge because of the phosphate backbone histones - positive charged proteins Ionic strength - I = 1/2 (sigma) M_i_Z_i_^2 i DNA Seperation In an agarose gel, the anion (-) wants to go to the Anode (+) the smaller it is the faster it moves SDS Page - separates proteins - it heats samples, denatures and adds SDS detergent - Anion wants to go to Anode DNAs wrap around histones Chapter 3 - The Energetics of Life Luciferin + ATP + O2 oxyluciferin AMP + PPi + light Quantum mechanics Microscopic Statistical Mechanics Bridges Microscopic functions of state are path independent 1st Law of Thermodynamics DeltaE sys + DeltaE sur = 0 usually we focus on the system DeltaE sys = q + w 2nd Law of Thermodynamics DeltaS total = DeltaS sys + DeltaS sur > 0 DeltaS = qrev T S = kBlnW or kBlnOmega “you can’t break even” 3rd Law of Thermodynamics lim S=0 T->0k “you can’t get out of the game” Not all processes that are spontaneous are exothermic Ex. Ice melting DeltaS total = DeltaS sys + DeltaS sur DeltaS total = DeltaS sys - DeltaH sys / T -TDeltaS total = -TDeltaS sys +DeltaH sys DeltaG = DeltaH - TDeltaS negative - spontaneous, favorable positive - nonspontaneous, unfavorable Reaction Quotient: DeltaG = DeltaG not + RTlnQ equilibrium: DeltaG = 0 and Q = Keq DeltaG not = -RTlnKeq nm
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