BIOCHEM 501 1st EditionExam # 1 Study Guide Lecture 1 // SEPT 3- Cellular basics- Carbon chemistry and stereochemistry- Free energy and how cells use itCarbon- 4 valence electrons- forms stable bonds with other H, C, O and N atomts- 3 different types of geometries: 109.5, 120, 180 degrees- 3 different depictions of molecules: schematic, ball and stick cartoon, space filling (actual look)Stereochemistry- Chiral molecules- chiral center: 4 different substituents attached to the carbon center- when rotated, it cannot be superimposed on its mirror image- achiral center: carbon center can have the same substituents attached- when rotated, it can be superimposed on its mirror imageEnantiomers: stereoisomers with same chemical formula but different order-MIRROR images of each otherFree EnergySecond Law of Thermodynamics: the tendency in nature to go towards greater disorderEntropy: degree of disorder in chemical systemGibbs Free EnergyG = H - TSH = enthalpy bonding energyS = entropy randomnessEnergetic Coupling: unfavorable process is driven via coupling to a highly favorable oneMechanical example: G > 0  work is done by raising the block up the slopeG < 0  work not done, less potential energy of position, block is sliding down slopeChemical example: ATP breakdown- ATP  ADP + P- Keq = [ADP] [P][ATP]- large Keq means the reaction tends to proceed until almost all reactant has been converted to product- in cells, concentration is far from equilibrium because of the large amount of energy used- G measures the distance of system from equilibrium- G = Standard Free Energy:G = - RTlnKeqLecture 2 // SEPT 5 - Properties of water- Weak interactions between molecules in aqueous solvent- hydrogen bonds- ionic interactions- hydrophobic effect- Ionization of water, weak acids and bases- pH, pKa, Henderson-Hasselbach equationWater- requires much more energy when converting from liquid to gas- has a high melting and boiling points relative to many others- the structure makes it a perfect H bond donor and acceptor- 104.5  - two partial negative pair of electrons- two partial positive H's attached to the Oxygen- has ability to form a lot of H bonds, building up makes it strong- in ICE, water molecules forms an H-bonded network that fully satisfies the H-bonding potential- there are 4 H bonds per water molecule in ice- versus 3.4 H bonds per water molecule in liquid water- makes liquid H2O more dense than ice- when a cup of water has been frozen and the ice level is exactly at the top of the cup. When the ice melts, the water level is below the rim- a linear H bond is stronger than an angled H bond- is an excellent polar solvent- shields ionic interactions by charge-dipole interactions- is a poor solvent for NON-POLAR solvents fatty acids, lipids- hydrophobic components with water reduces the entropy of water and is thermodynamically unstable- hydrophilic head loves water- hydrophobic tail  hates water, cannot mix- so then lipids cluster together, release water molecules to the surrounding water whichraises entropy levels to help molecules get togetherDispersion of lipids by HO  clusters of lipid molecules  micelles Lipids force surrounding HO molecules to become highly ordered only lipids at the edge of cluster forces ordering of water, fewer HO is ordered, so entropy rises all hydrophobic groups are away from HO. ordered shell of HO molecules is minimized and entropy is further increased- is a reactant in hydrolysis and condensation reactions Ionization of water: slight tendency of HO molecules to ionize- HO / H+ + OH-- Keq = 1.8 x 10^-16 = [H+] [OH-][HO]- Kw = 1.8 x 10^-14 at 25 C  the ion product of water- for pure water, [H+] = [OH-]- [H+]^2 = Kw- [H+] = 1 x 10^-7Hydrogen ion concentration- Kw = [H+] [OH-] = 1.8 x 10^-14- can be used for calculating concentrations of H and OH for strong acids and bases- EX: 0.1 M HCl is fully ionized so that [OH-] = 10^-13- biological H ion concentrations vary from 1.5 x 10^-3 to 10^-8It's more convenient to define [H+] in terms of a log scale- pH = -log [H+]- for neutral H2O, pH = -log [1 x 10^-7 ] = 7- EX: pH of 0.1 M HCl is 1Dissociation of weak acids and bases- acids: proton donors or electron pair acceptors- bases: proton acceptors and electron pair donors- weak acids and bases are only partially ionized in water while strong acids and bases are completely ionized- HA / H+ + A- - Ka = [H+][A-] / [HA]- pKa = - log [Ka]Henderson-Hasselbach EquationpH = pKa + log [A-]/[HA]-  pKa = weaker acid stronger base-  pKa = stronger acid weaker base - the covalent bond breaks when ionizing water, not the H bond-EX of pH calculation: what is pH of 0.1 M acetic acid (pKa = 4.76) and 0.1 M of conjugate base sodium acetate?- use HH equation:-pH = pKa + log [A-]/[HA]= 4.76 + log [1]= 4.76- what happens after adding an equal volume of 0.05 M HCl?- [HA] = 0.15 / 2 [A-] = 0.05 / 2pH = 4.76 + log [0.025] / [0.075]= 4.76 - .48 = 4.28Biological buffers:- pH is carefully controlled because activity of enzymes is sensitive to pH- blood plasma ~7.4 - 2 important buffers in blood are phosphate and bicarbonateLecture 3 // SEPT 8- Proteins: the most abundant macromolecules in cells- Amino acids and their properties- Amino acid and peptide isoelectric points- Post-translational modificationsProteins- All are polymers of amino acids (AA)- only 20 AA are defined by the genetic code- can be small (dozens of AA) or large (thousands)- built from 20 α-AA- central alpha carbon, chiral center- all AA in proteins are L-stereoisomers (except glycine because it doesn’t have a chiral center)Amino acids1. Nonpolar, aliphatic R groups-hydrocarbon groups that are hydrophobic1. glycine—smallest 2. alanine—1 hydrocarbon3. proline—only 1 that loops back and connects, 3 hydrocarbons4. valine—has 3 hydrocarbons5. leucine—4 hydrocarbons6. isoleucine—3 hydrocarbons, 1 carbon7. methionine—methylated sulfur in side chain2. Aromatic R groups8. Phenylaline9. tyrosine—can donate/accept a H bond because of the -OH10. tryptophan—can donate/accept H bond because of the NH 3. Polar, uncharged R groups-partial positive and negative charges11. serine12. threonine13. cysteine14. aspargine—has amino group15. glutamine—has amino group4. Positively charged R groups16. lysine17. arginine18. histidine—imidazole group, can turn into an