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Modified on 2013/01/23 16:40 by Ben Fulton Categorized as Uncategorized
Bonds, forces, interactions are always in play
  • Electrostatic interactions
  • Van der Wal forces
  • Hydrogen bonds

Polarity - water segregates nonpolar molecules, contributing to the shape Some molecules are more polar than others

Lipid bilayers - polar on the outside interacting with water, nonpolar on the inside Something that goes through it will probably have a channel that is polar

AZT - needs to have a triphosphate group to work - enzyme that adds the first group is a big pain to work with So it would be nice to give a monophosphate version to patients - unfortunately it is so polar that it can't make it into cells.

Strengths of non-covalent forces that hold molecules together * Hydrophobic: 3 kcal/mol * Hydrogen bonds: 2-5 kcal /mol

Covalent bonds are more like 100 kcal/mol - we take those for granted. Interesting bonds are the weaker ones. But ATP releases energy by breaking them. ATP + H2O => ADP + Pi is delta G ~ 7 kcal/mol

Some definitions

Ligand: something that binds to something else Agonist / Antagonist Free energy = enthalpic contribution - temperature(entropic contribution) delta G = delta H - T(delta S) Reactions of glycolisis - can determine which steps are regulatory based only on the delta G (if it is negative then it's a regulatory step)

Biochem Jan 14 Vocab: Ligand, Agonist/ASntagonist,Activator/Inhibitor,Angstrom,Poloar/NonPolar/Peripheral Membrane Protein Integral,Entropy,Enthalpy,Gibbs Free Energy,ProDrug valacyclovir - 2 parts, acid and base? Have to release heat in order to decrease entropy Keq (K-equilibrium) Can derive delta-G if we know Keq Proton pumps to generate different PH in different parts of the cell Ex. Toll-like receptor - virus creates a double-stranded RNA which is recognized, create a vesicle around it. Pump gets inserted into to the vesicle which lowers the pH and...

Alpha carbon is the central carbon of an amino acid

Both amino group and carboxyl group may lose their protons. Can calculate Ka because HA <=> A- + H+ pKa of Guanine is 9.7 - at that level half the molecules have lost a proton

Ribose - in a high pH environemnt - O will pop off the OH at 2' and create Deoxyribose.

Pick out information from a chemical diagram. Find the alpha carbon, find the peptide bonds. (Find the carbonyl and amino groups?

To calculate the concentration of a protein:
  • epsilon = Molar Extinction Coefficient
    Beer-Lambert law A = epsilon(c)(l)
    calculate C

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