| Term | Definition |
|---|
| covalent bond | strongest bond |
| hydrogen bond | H shared between electron negative atoms |
| VDW interactions | charge distribution. Greatest attraction 2-3A. |
| polar molecule | electric dipole. Hydrophilic. |
| nonpolar molecule | Hydrophobic |
| acid | donates H+ from solvent |
| base | accepts H+ from solvent |
| weak acid | strong conjugate base, good buffering |
| weak base | strong conjugate acid, good buffering |
| pH | =-log[H+] = pKa + log([A-]/[HA]) |
| pKa | pH at which [conjugate acid]=[conjugate base] |
| bicarbonate buffer system | H+ + HCO3- <--> H2CO3 <--> H20 + CO2 |
| zwitterion | dipolar amino acid ion |
| amino acid chirality | predominantly L isomer (CCW) |
| nonpolar residues | on inside of amino acid |
| polar residues | on outside of protein |
| porin | exception. Hydrophobic outside and hydrophilic inside. |
| b-Mercaptoethanol | used w/ urea to reduce covalent disulfide bonds, denature protein. |
| cooperative transition | simultaneous, collective displacement or change of protein state |
| cumulative selection | retentian of partly correct intermediates |
| ab initio predictions | predictions of 2/3* structure by amino acid sequence |
| knowledge-based predictions | camino acid sequences compared to known proteins |
| spongiform encephalopathy | prion (misfolding) propagation. Neurodegenerative disorder. |
| Creutzfeldt-Jakob disease | TSE. prion (misfolding) propagation. Neurodegenerative disorder. |
| scrapie | TSE in sheep. prion (misfolding) propagation. Neurodegenerative disorder. |
| BSE | bovine spongiform encephalopathy. Mad cow disease. prion (misfolding) propagation. Neurodegenerative disorder. |
| scurvy | lack of Vitamin C. can't hydroxylate collagen. |
| collagen composition | >33% glycine, ~20% proline or hydroxyproline, some lysine |
| differential centrifugation | can be used to purify proteins |
| dialysis | separates larger molecules from smaller molecules |
| column (gel) chromatography | gel filtration discriminates proteins based on size. Larger = faster. |
| affinity chromatography | purifies and separates based on binding affinity to a molecule. Best way to separate. |
| effectiveness of purification | judged based on yield and activity of protein |
| SDS-PAGE | electrophoresis separates based on molecular mass |
| isoelectric focusing gel | separation based on isoelectric point (pI) by making a pH gradient |
| ninhydrin | react with a protein to denature it into amino acids |
| Edman degradation | tells amino acid sequence |
Combine with other sets
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