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Exam 1- BICH 410
| Question | Answer |
|---|---|
| What is the letter symbol for Enthalpy? | H |
| Endothermic | H > 0 |
| Exothermic | H < 0 |
| What is the letter symbol for Entropy? | S |
| Final state is more ordered than initial state in entropy? | S < 0 |
| Final state is less ordered than initial state in entropy? | S > 0 |
| What is the letter symbol for Free Energy? | G |
| Equation for Free Energy | G = H - TS |
| Exergonic | (delta)G < 0, High energy to low energy, spontaneous |
| Endergonic | (delta)G > 0, Low energy to high energy, non spontaneous |
| Free Energy Change Equation | (delta)G = (delta)H - T(delta)S |
| (delta)G = (delta)H - T(delta)S < 0 | Spontaneous |
| (delta)G = (delta)H - T(delta)S > 0 | Non spontaneous |
| Free Energy Change depends on | Characteristic, Concentration, Stoichiometry, Temp |
| Standard Free Energy Change Symbol | (delta)G° |
| Standard Free Energy Change Equation | (delta)G° = -RT ln Keq |
| Biochemists Standard State Equation | (delta)G = (delta)G°’ + RT ln ([P]/[R]) |
| Keq >> 1 | (delta)G is large and negative, highly favorable |
| Keq << 1 | (delta)G is large and positive, highly unfavorable |
| Hydrophilic | LOVE water! Polar and Ionic Compounds |
| Hydrophobic | Hate water. Non polar Compounds |
| What is Enthalpy-Entropy Compensation? | Loss of bonds ((delta)H > 0) but increase in disorder ((delta)S > 0) |
| Amphipathic Molecules | Hydrophobic and Hydrophilic |
| What is neutral pH? | 7.0 |
| Equation to find pH | pH = -log (H+) |
| Relation between H+ and pH | Lower the H+, higher the pH |
| Relation between OH- and pH | Lower the OH-, lower the pH |
| Relation between H+ and OH- | Lower the H+, higher the OH- |
| Equation to find pOH | pOH = -log (OH-) |
| pH + pOH should always equal what? | 14 |
| Which is the proton donor? Acid or Base? | Acid |
| Which is the proton acceptor? Acid or Base? | Base |
| Equation to find pKa | pKa = -log(Ka) |
| Henderson-Hasselbalch Equation | pH = pKa + log ((A-)/(HA)) |
| Titration Curve Axis’s | pH vs amount of strong base added |
| What is the Inflection Point? | Point which enough base has been added to neutralize 50% of acid |
| What is the Equivalence Point? | Point which enough base has been added to exactly neutralize the acid |
| Monoprotic Acid is what? | One dissociable proton with 2 possible ionic forms |
| Diprotic Acid is what? | Two dissociable protons with 3 possible ionic forms |
| Triprotic Acid is what? | Three dissociable protons with 4 possible ionic forms |
| The buffer is at what point on titration curve? | Where the titration curve becomes flat |
| Alanine | Ala, A |
| Arginine | Arg, R |
| Asparagine | Asn, N |
| Aspartic Acid | Asp, D |
| Cysteine | Cys, C |
| Glutamic Acid | Glu, E |
| Glutamine | Gln, Q |
| Glycine | Gly, G |
| Histidine | His, H |
| Isoleucine | Ile, I |
| Leucine | Leu, L |
| Lysine | Lys, K |
| Methionine | Met, M |
| Phenylalanine | Phe, F |
| Proline | Pro, P |
| Serine | Ser, S |
| Threonine | Thr, T |
| Tryptophan | Trp, W |
| Tyrosine | Tyr, Y |
| Valine | Val, V |
| Which AA have 3 acid-base groups (due to their ionizable side chains)? | Lys, Arg, His, Glu, Asp, Cys, Tyr, Ser, Thr |
| Polar Side Chains | Hydrophilic |
| Non polar Side Chains | Hydrophobic |
| Cationic | Low pH, ALL ionizable groups protonated |
| Anionic | High pH, ALL ionizable groups deprotonated |
| Charge range for AA with no charge on R group? | +1 -> -1 |
| Charge range for AA with positive charge on R-group? | +2 -> -1 |
| Charge range for AA with negative charge on R-group? | +1 -> -2 |
| Equation to find Isoelectric Point (pI) | pI = 1/2 (pKi + pKj) |
| How are AA Residues named? | Drop the “ine” and add “yl” |
| Charge characteristics of Peptides | pKa free carboxyl = 3.5, pKa free amino = 8.5 |
| Charge characteristics of Free AA | pKa alpha carboxyl = 2, pKa alpha amino = 9 |
| Homomultimeric Protein | Composed of multiple polypeptides that are identical |
| Heteromultimeric Protein | Composed of multiple polypeptides that are unique |
| What is the protein purification strategy? | Isolate, Detect (UV or Bradford Assay), Assay Protein Activity, Separation Techniques (Salting Out, Ion Exchange, Hydrophobic Interactions, Gel Filtration, Affinity Chromatography), Quantitation |
| Salting Out | Use low salt concentration -> Unwanted proteins, Use high salt concentration -> Target protein |
| Ion Exchange | Separate by charge. action/Anion Exchange |
| Hydrophobic Interactions | Purifies Non-polar molecules |
| Gel Filtration | Separate by size or MW, High MW (1st off) -> Middle MW -> Smallest MW (last off) |
| Endopeptidases | Enzymes that hydrolyze an internal peptide bond |
| Exopeptidases | Enzymes that hydrolyze N-term/C-term residues (external peptide bond) |
| Protein Sequencing | Determines order of AA in chain; 2 Methods: Edman Degradation and Mass Spec |
| Protein Structure Levels | 1 -> 2 -> motifs -> domains -> 3 -> 4 |
| Secondary Structure 3 Main | alpha helix, beta sheet, beta turn |
| Tertiary Structure Morphology | Globular and Fibrous |
| Oligomers (Proteins with >1 subunit) | Dimer (2 subunits), Trimer (3 subunits), Tetramer (4 subunits), Homodimer (Same), Heterodimer (Different) |
| Domains | Tertiary Structure that results from a combination of secondary structres |
| What interactions stabilize tertiary structures? | Hydrophobic and Electrostatic Interactions, Hydrogen Bonds, Chemical Crosslinking |
| What does denaturation mean? | Unfold |
| What disruptions cause proteins to unfold? | Heat, pH, detergents, chaotropic agents |
| When will proteins unfold? | When (delta)G = 0 |
| Below denaturation temp -> | Protein folded |
| Above denaturation temp -> | Protein unfolded |
| Protein folding types | Hierarchical and Hydrophobic Collapse |
| Molecular Chaperons | 2 classes: Hsp70 Family and Chaperonins |
| Protein Folding Diseases | Sickle Cell Anemia, Alzheimer’s, Creutzfeldt-Jacob, Hereditary Emphasema, Cystic Fibrosis |
| Sickle Cell Anemia | Hemoglobin - Deformation of erythrocytes |
| Alzheimer’s | Beta amyloid peptide - Plaques form in neural tissue |
| Creutzfeldt-Jacob | Prion - Plaques for in neural tissue |
| Hereditary Emphasema | Alpha 1-antitrypsin - Slow folding allows elastase to destroy lung tissue |
| Cystic Fibrosis | CFTR - Folding intermediates are not stable and are degraded |
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