Term
| How many amino acids can DNA code for? |
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Definition
| 20, anything else has to be modified from those 20. |
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Term
| Can life use D, L, or both forms of amino acids? |
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Definition
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Term
| There are 3 main groups of amino acids, what are they? |
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Definition
| Hydrophobic, polar, charged |
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Term
| What's special about proline? |
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Definition
| It's a secondary amino acid, it's *cyclic*, and it's good for making turns. |
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Term
| Residue vs. amino acid, difference? |
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Definition
| Residue refers to an AA within a protein, and amino acid refers to a free amino acid. |
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Term
| What's special about a peptide bond? |
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Definition
| It's got resonance, so it's a partial double. Thus more RIGID. |
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Term
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Definition
| At least 3 AAs linked together. |
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Term
| What makes a polypeptide a protein? |
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Definition
| When it take on a function and structure. |
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Term
| Primary structure, what is it? |
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Definition
| The simple sequence of AARs in a protein |
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Term
| Secondary structure, what is it? |
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Definition
| The arrangement of H-bonds among aminos and carboxyls NOT PART OF R GROUPS |
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Term
| How do AARs arrange to make an alpha-helix? |
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Definition
| Every 4th AAR makes an H-bonds |
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Term
| Membrane proteins, what kind of AARs will you see on the membrane side of the protein? |
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Definition
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Term
| What's a multipass membrane protein? |
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Definition
| A protein, probably helical, where one chain makes more than one pass through the membrane. Each pass is probably about 16 AARs. |
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Term
| Tertiary structure, what's the deal? |
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Definition
| Interactions among the R-groups: ionic bonds, H-bonds, covalent (sulfide bridges), hydrophobic interactions. These interactions bend and twist the secondary structure (a-helix, b-sheet, random coil). |
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Term
| What's quaternary structure? |
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Definition
| Interactions between distinct polypeptide subunits of a protein. |
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Term
| Heterodimers, homotetramers, what's the naming convention? |
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Definition
| If all of the subunits are identical, it's homo, if some are different, it's hetero. Second part is number of subunits. |
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Term
| What's special about the energetics of an enzyme catalyzed reaction? |
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Definition
| They make reactions happen FASTER by lowering *activation energy*, but they cannot alter total energy change (delta G). They do this by creating more favorable chemical micro-environments. |
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Term
| Competitive inhibition, what's the deal? |
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Definition
| Enzyme 1 uses A as a reaction substrate. Inhibitor B also fits the active site, but doesn't work in the reaction. Increasing [B] lowers reaction velocity. Increasing [A] compensates for velocity loss. |
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Term
| What's noncompetitive inhibition? |
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Definition
| Enzyme 1 uses A as substrate. Inhibitor C fits into ANOTHER site on the enzyme, and causes a conformation change inactivating it. Isn't competing with A. Increasing [A] doesn't compensate for lowered velocity. |
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Term
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Definition
| They ADD phosphate to their substrate. This can either activate OR deactivate an enzyme. |
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Term
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Definition
| They DEphosphorylate their substrates. This can either activate OR deactivate an enzyme. |
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Term
Protein study:
First you break up the cells, how? |
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Definition
Mortar/Pestle
Sonicate
"French Press"
Osmotic Shock
Blender
*All of these generate HEAT, so are performed in the COLD. Also, buffers are used to keep proteins from denaturing. |
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Term
Protein study:
How do you isolate proteins from lysed cells? |
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Definition
Crude filtration (cheese cloth)
Centrifuge (if target is a cytosolic protein)
Centrifuge by density with a sucrose gradient (good for larger thing like organelles) |
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Term
Protein Study:
How does chromatography help? |
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Definition
| You can use ion exchange resins. If you have a negative target protein, use a positive resin. It will bind to the resin, and you can gradually salt it out once the other gunk is through the column. Must be cautious to avoid denaturing the proteins. |
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Term
Protein study:
How does gel filtration work? |
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Definition
| You use gel beads of controlled size. Proteins larger than the bead pores pass rapidly between the beads. Protein smaller than the pores go more slowly through the bead pores. |
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Term
Protein Study:
How does affinity chromatography work? |
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Definition
| You run size sorted proteins through a matrix that has custom antibodies or a substrate bonded to it. VERY specific in some cases. |
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Term
Protein study?
How do you test purity of your protein isolate? |
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Definition
| You can run an SDS-page gel electrophoresis that sorts the proteins by size. You can run a pH gradient column that sorts protein by their isoelectric point. Better yet, you can combine a pH gradient with a gel and get much better resolution. |
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