Test Two ID Terms

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  1. binding energy
    Free energy that is the released upon formation of a large number of interactions that take place between a substrate and the enzyme. It establishes substrate specificity and increases catalytic efficiency. This energy is going to help stabilize the transition state and lower the EA so that the reaction can occur.
  2. covalent catalysis
    Catalysis that results in the formation of a covalent bond between a reactive group in the active site that acts as a nucleophile that attacks and the substrate Ex: chymotrypsin
  3. 3. General acid-base catalysis
    Catalysis that involves a molecule other than water acting as the proton donor or acceptorThe molecule that behaves in this matter will shuttle protons from one molecule to another. Ex: Histidine because of the neutral pKa is important and can shuttle/ move protons
  4. 4. Catalysis by approximation
    Usually, when two substrates are involved, they are unlikely to come together. As a result, an enzyme will increase the likelihood that a reaction would occur by bringing the substrates together
  5. Metal ion catalysis
    • A metal will function to make the nucleophile, act as an electrophile to stabilize any charges, and serve as a bridge between enzyme and substrate, increasing binding energy and holding the substrate in a conformation appropriate for catalysis, contributing to binding energy and lower EA
    • Electron poor and positively charged that react with negatively charged groups
  6. Oxyanion hole
    Site that helps stabilize the transition state that precedes the formation of the tetrahedral intermediate in peptide hydrolysis; interacts with the negative charge on the oxygen during proteolysis, more specifically, during the formation of the tetrahedral intermediate in which the oxygen becomes negative 
  7. Scissile bond
    a bond that is available to be broken in a reaction
  8. P loop
    Located in myosin; A loop containing several glycine residues that reacts with the phosphoryl groups of ATP; moves in a way that starts out the chain reaction that gets ADP or ATP out of the active site
  9. EcoRV
    Endonuclease that cleaves the phosphodiester bond between the T and the A at the center of the 5’—GATATC—3’ region; binds to all DNA—cognate and noncognate—with approximately equal affinity, but will only cleave cognate DNA
  10. cofactors
    small that bind to the enzyme and make it more functional by performing an activity the amino acids cannot due; can be metal ions or small, organic molecules called coenzymes, which can be tightly bound (prosthetic groups) or loosely bound (cosubstrates)
  11. apoenzyme
    an enzyme without its cofactor
  12. holoenzyme
    apoenzyme and cofactor
  13. transition state
    The transitory molecular structure at which the particle is not substrate anymore but is not yet product; it is the least stable and most seldom occupied; highest free energy
  14. free energy
    Thermodynamic property that is  measure of useful energy, or the energy that is capable of doing work 
  15. Molecular heterogeneity
    Ability of an enzyme to assume different structures that are slightly different structure that differ slightly in stability 
  16. Heme group
    A molecule that muscles and blood their distinctive red color. It consists of an organic component and a central iron atom. The organic component, called protoporphyrin, is made up of four pyrrole rings linked by methane bridges to form a tetrapyrrole ring. Four methyl groups, two vinyl groups, and two propionate side chains are attached. Iron lies in the center of the protoporphyrin, bonded to the four pyrrole nitrogen atoms. It allows oxygen to bind to the hemoglobin
  17. Distal histidine
    • Histidine that is not located in any of the coordination sites, but it is important in the binding of oxygen. It will cause oxygen to come in at a slant, thereby preventing the binding of other molecules
    • In myoglobin, it donates a hydrogen bond to the bound oxygen molecule so dissipate its superoxide character
    • Binds in a binding pocket on the hemoglobin
  18. proximal histidine
    binds at the fifth coordination site of iron
  19. partial pressure
    how much gas is present in a solution
  20. sequential model
    model taht states that the binding of a ligand to one site in an assembly increases the binding affinity of a neighboring site without fully converting it from T to R
  21. Concerted model
    Model stating that the assembly can exist in only two forms: the T state and the R states; the binding of ligands simply shifts the equilibrium between these two states but does not convert it into R until all sites have oxygen bound and they can all convert together
  22. 2,3 BPG
    Highly anionic compound that is present in RBCs and sits in the center of the tetramer, present in a pocket only in the T form; it prevents the pocket from collapsing and stabilizes the T state so that it does not convert to the R form; it necessitates high oxygen binding in order to convert the T to R; in order for the T-to-R transition, higher oxygen concentrations must be reached
  23. Group-specific reagents
    React with a specific side chain of amino acids; DPIF is an example; do not have exquisite specificity
  24. Affinity labels (reactive substrate analogs)
    Molecules that are structurally similar to the substrate for an enzyme and that covalently binds to active-site residues. They are more specific for the enzyme’s active site
  25. Suicide inhibitors (mechanism-based inhibitors)
    Modified substrates that provide the most specific means for modifying an enzyme’s active site; the inhibitor binds to the enzyme as a substrate and is initially processed by the normal catalytic mechanism, which then generates a chemically reactive intermediate that inactivates the enzyme through covalent modification

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Test Two ID Terms
2014-12-09 03:10:32
Test Two
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