Chapter 1 - Biochemistry PDF

Preview

Summary

Download Chapter 1 - Biochemistry PDF

Description

CHAPTER 1 

What is the net charge on ATP? -At what pH? 

The answer to this question depends on the pH of the solution



At pH 7 (majority net charge is -4 BUT co-exists with some -3 charge; however with presence of Mg+ the -4 & -3 net charge are in equilibrium)

**Need to know the 20 amino acids & structures 

Thermodynamics of Protein Folding Primary  Secondary  Tertiary  Quaternary The Gibbs Free Energy Function G= S H T G

H-T

S

Entropy Enthalpy Temperature (Constant) Free Energy Change

In order for Delta G to proceed spontaneously, it has to be negative In order for Delta G to equal 0, it has to be in equilibrium Covalent Bonds: Strongest bonds; Formed by the sharing of a pair of electrons between adjacent atoms Non-Covalent Bonds: Weaker; However are crucial for biochemical processes such as the formation of a double helix 1. Electrostatic: A charged group on one molecule can attract an oppositely charged group on another molecule An attractive interaction has a negative energy o E = kq1q2/Dr2 E= energy of electrostatic interaction (negative = attraction, positive = repulsion) q= Atomic charge (-1, +1, +2, etc) D= Dielectric constant (80 for water) r= distance between the two atoms k= a constant

2. Hydrogen Bonds: HBD: Electronegative Atom that is bonded to Hydrogen (atom is tightly linked) HBA: Electronegative atom that want the Hydrogen to remain stable (atom is loosely linked) These interactions are fundamentally electrostatic interactions Figure 1.9. The electronegative atom to which the hydrogen is covalently bonded too pulls electron density away from the hydrogen atom, which thus develops a partial positive charge. Thus, the hydrogen atom can interact with an atom having a partial negative charge through an electrostatic interaction 3. Van Der Waals Forces: Figure 1.10. As two atoms approach each other the energy between the two molecules is most favored at the Van Der Waals CONTACT DISTANCE. Due to electron-electron repulsion, the energy rises rapidly as the atoms approach closer than this distance 4. The Hydrophobic Effect: Biochemical reactions take place in water Water is a polar solvent; a dipole is present Figure 1.11. Water loves to interact with itself to make hydrogen bonds Figure 1.12. The hydrophobic effect is due to the increase in entropy ( S = positive) that occurs when hydrophobic regions aggregate in an aqueous environment When two non-polar molecules come together, some of the water molecules are released, allowing for them to interact freely with bulk water Two forces driving the reaction – Van Der Waals & Hydrophobic Effect The Double Helix Is An Expression of the Rules of Chemistry Figure 1.13. Electrostatic repulsion between formal negative charges on phosphate groups that are brought together by the high dielectric constant of water and presence of Na+ and Mg2+ H = Positive Figure 1.14. Adjacent base pairs are stacked up on each otherand so many atoms in each base pair are sepaated by their Van Der Waals contact distance. The base stacking and associated Van Der Waals interactions are nearly optimal in a double helical structure H = Negative Sample Question (WIR) Q: Given the above, would heating the solution to greater than 25 degree Celsius tend to favor ssDNA or dsDNA?

A: ssDNA Ionization of Guanine proton at position N1: GH G-+ H+ The most susceptible proton to be dissociated as the base is added is the N-1 proton Generic Expression for Acid Dissociation: AH A- + H+ H + = H 3O + pH = -log[H+] At pH 7, [H+] = 1 x 10-7 M At pH 3, [H+] = 1 x 10-3 M Acid Dissociation reaction HA  H+ + AKeq = [Product] / [Reactants] Ka is the Keq for an acid dissociation reaction Ka = [H+] [A-] / [HA] pKa = -logKa What happens when pH = pKa? pH = pKa -log [H+] = -log ([H+] [A-] / [HA]) [H+] = [H+] [A-] / [HA] [A-] = [HA]

*50% protonated when the pH = pKa

Henderson Hasselbalch Equation—Pg. 16 Ka = [H+] [A-] / [HA] log [Ka ]= log ([H+] [A-] / [HA]) log [Ka ]= log [H+] + log [A-] / [HA] -log [H+] = -log [Ka ] + log [A-] / [HA] pH = pKa + log [A-] / [HA] 1. pKa is constant for any reaction (known) 2. For any given pH you can calculate the percent ionized and vice versa 3. Special case at 50% ionized

Note: The pH of Double Helical structures in DNA is suppose to be at pH=7; however when adding a base, and the pH rises, the double helical structure dissociate Figure 1.17-A Buffer in Action As you drop drops of the acid, you can see that the change in pH is minimal. Q: Why does the pH decrease gradually in the middle of the titration? A: When hydrogen ions are added to this solution, they react with the acetate ions to form acetic acid. This reaction consumes some of the added hydrogen ions so that the pH does not drop. Hydrogen ions continue reacting with acetate ions until essentially all the acetate ions are converted to acetic acid. After this happens, the added protons are free in solution so the pH has a sharp decline. Figure 1.18 Q: What is the pKa of Acetic Acid? A: 4.7 Natural buffers present in blood: Inorganic phosphate [Picture], 1mM Carbonic Acid/Bicarbonate ion, 10mM...