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Biochemistry Exam 2
| Term | Definition |
|---|---|
| isoelectric point (pI) | specific pH at which a protein or molecule has a net overall charge of zero |
| isoelectric focusing | laboratory separation technique where proteins migrate through pH gradient in electric field until they reach their pI |
| x-ray crystallography | method of determining 3D protein structures by analyzing diffraction pattern created when x-ray is shot through protein crystal |
| 2D NMR | technique used to determine protein structures in solution by identifying protons that are close together in 3D space |
| peptide bond resonance | phenomenon giving the peptide bond partial double-bond character, making it rigid, planar, and unable to rotate |
| phi and psi angles | rotatable single bonds on either side of central alpha carbon in peptide backbone that dictate protein folding |
| Ramachandran plot | graph mapping the favored angle combos in a protein, highlighting regions for alpha helices and beta sheets |
| alpha helix hydrogen bonding | primary stabilizing force of an alpha helix, occurring entirely between amide groups in peptide backbone |
| 3.6 amino acids | exact number of amino acid residues it takes to complete one turn of alpha helix |
| alpha helix side chains | all amino acid side chains point outward from helix center |
| proline in helices | amino acid considered unfavorable in alpha helices because its rigid structure forces a bend in chain |
| disulfide bond | strong covalent bond formed by oxidation of adjacent side chains utilized to lock keratin structures in place |
| beta sheets | secondary structure held together by backbone H-bondswith alternating side chains |
| anti-parallel beta sheets | beta sheet with adjacent strands running in opposite directions allowing for stable H-bonds |
| parallel beta sheets | beta sheet with adjacent strands running in same direction causing skewed H-bonds |
| beta turn | secondary structure that reverses peptide chain direction utilizing glycine and proline |
| disulfide bond | covalent bond formed by oxidation of two cysteine residues |
| chaperone protein | protein that provides environment for other proteins to fold correctly |
| amyloid beta | protein that exposes hydrophobic patches when misfolded and is associated with Alzheimer's disease |
| stationary vs. mobile phase | stationary phase is fixed (silica gel) to slow solutes, while mobile phase is fluid (solvent) to carry mixture |
| cation exchange chromatography | separation method using negative stationary phase to slow positive proteins |
| anion exchange chromatography | separation method using positive stationary phase to slow negative proteins |
| size exclusion chromatography | separation method using porous beads that allows large molecules to elute first and small molecules to elute last |
| antibody | Y-shaped protein molecule produced by the immune system, consisting of heavy and light chains, that binds to specific antigens |
| antigen | specific target molecule or structure that an antibody recognizes and binds to |
| variable domain | specific regions at the tips of the antibody's "y" shape that differ between antibodies and allow them to bind to unique antigens |
| constant domain | uniform base region of an antibody that remains the same across all antibodies of a certain class and is recognized by the immune system |
| sandwich ELISA | assay where a target antigen is captured between a primary antibody bound to a surface and a secondary antibody linked to a detectable enzyme marker |
| western blot | lab technique where proteins are separated by size on a gel and then probed with specific antibodies to detect the presence of a target protein |
| immunoprecipitation | purification technique that uses targeted antibodies to capture and pull a specific protein out of a complex lipid mixture |
| immunoflourescence | microscopic imaging technique that uses fluorescently tagged antibodies to visualize the exact location of specific proteins within a cell |
| enzyme | biological catalyst, usually a protein, that significantly speeds up a chemical reaction by lowering its activation energy |
| activation energy | initial energy required to initiate a chemical reaction and reach the high-energy transition state |
| transition state | highest-energy, unstable intermediate phase of a chemical reaction where old bonds are breaking and new bonds are forming |
| transition state stabilization | primary mechanism of enzyme catalysis; enzyme forms tight bonds with the transition state, lowering overall activation energy |
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hlr2326