Molecular Text 3.2

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  1. a.       A protein molecule’s physical interaction with other molecules determines its __. All proteins stick, or __, to other molecules; it can be __ or __. Nevertheless, binding is __
                                                                  i.      The substance bound is a __
    b.      This selectivity is due to __ that allow a close fit between the protein and ligand
    • biological properties
    • bind
    • tight or weak
    • specific

    • ligand
    • weak, noncovalent bonds
  2. a.       The __ has a cavity in the protein surface formed by a particular __, which can come together from different areas of the protein
    b.      Atoms in the interior function to __
    • binding site
    • arrangement of amino acids
    • form a framework that gives the surface its contours and chemical/ mechanical properties
  3. a.       __________enhance __ of amino acid side chains. These interactions fall into two categories. The first is:
                                                                  i.      __ may restrict the access of __ to that protein’s ligand-binding sites
    1.       Important because water does what? If water is excluded, __ between the protein and its ligand form
    • Interactions 
    • chemical reactivity

    • Interaction of neighboring parts
    • water molecules

    forms H bonds that compete with ligands for sites on protein surfaces

    tighter bonding
  4. a.       __________enhance __ of amino acid side chains. These interactions fall into two categories. The second is:
                                                     1.       __ can alter their __

    a.       If negative charges are clumped, the affinity for positively charged ions is increased        
    • Clustering of neighboring polar amino acid side chains
    • reactivity
  5. i.      The surface of each protein molecule has a unique __ that depends on __, as well as their __
    b.      Evolutionary tracing can be used to identify sites in a __ that are the most crucial to the domain’s function
    • chemical reactivity
    • which amino acid side chains are exposed
    • exact orientation relative to one another

    protein domain
  6.                                                               i.      Ex: SH2 domain, which functions in __; it binds the protein containing it to a second protein that contains a __
    • protein-protein interactions
    • phosphorylated tyrosine side chian in a specific amino acid sequence context
  7. Proteins bind to each other in three ways (at least
    •                                                                         i.      A portion of a surface of one protein contacts an extended loop of polypeptide chain on a second protein
    •                                                             ii.      When two alpha helices, one from each protein, pair together to form a coiled-coil
    •                                                           iii.      Precise matching of two rigid surfaces
  8. a.       Antibodies (protiens produced by the __ in response to foreign molecules) bind tightly to their targets, either __ or __; very specific
                                                                  i.      They have two __ that complement the small portion of the surface of the antigen formed by several loops of polypeptide chain
    1.       Changing these loopsà __
    a.       These loops allow __
    • immune system
    • inactivating the target (antigen)
    • marking it for destruction
    • identical binding sites
    • diversity
    • grasping
  9. a.       Strong interactions occur in cells whenever a biological function requires them to __
    b.      A steady state can be reached when the __ equals the __= __ (K) (measures __)
    c.       Though proteins can perform their function simply by binding to another molecule, other proteins use ligand binding as their first step in function
    • remain associated for a long time
    • rate of association of molecules
    • rate of dissociation
    • equilibrium constant
    • strength of binding
  10.                                                               i.      Ex: __, which bind substrates and later convert them to products, act as __that permit cells to make or break covalent bonds in a controlled way
                                                                ii.      Enzymes are grouped by __; each type of enzyme is highly specific 
    • enzymes
    • catalysts 
    • similar chemical reactions
  11. a.       __ is the first step in enzyme catalysis
                                                                  i.      For a protein that catalyzes a chemical reaction (an __), the __ is an essential prelude
    1.       There is a limit to the __ that a single enzyme molecule can process in a given time
    2.       Increase in concentration of substrate does what until what? At that point, it depends on the __ of the enzyme
    a.       The maximum rate divided by the enzyme concentration is called the __
    • Substrate binding
    • enzyme
    • binding of each substrate molecule to the protein
    • amount of substrate
    • increases rate of product formation until it is saturated
    • rapidity
    • turnover number
  12. a.       Another kinetic parameter is __, the concentration of substrate that allows the reaction to proceed at one-half its Vmax
                                                                  i.      Low Km= __
                                                                ii.      High Km= __
    • Km
    • max rate at low concentration of substrate
    • weak binding
  13. a.       Enzymes are effective because:
                                                                  i.      It __ of local substrate molecules at catalytic site and __ for reaction that is to follow
                                                                ii.      Some __ contributes directly to the catalysis
    1.       The __ required to attain the most unstable transition state is the __ for the reaction, and it is the major determinant of the reaction rate
    • increases concentration
    • holds appropriate atoms in correct orientation
    • binding energy
    • free energy
    • activation energy
  14. a.       Enzymes have a much higher affinity for the __ than they have for the stable form. Because this tight binding greatly __, the enzyme __a particular reaction by doing what?
    They not only bind tightly to a __, but they contain __ that alter the __ in those atoms that participate directly in the making and breaking of covalent bonds
    • transition state of the substrate
    • lowers the energies of the transition state
    • accelerates 
    • lowering the Ea that is required
    • TS
    • precisely positioned atoms
    • electron distributions
  15. a.       Enzymes are unique in being able to use__ and __ simultaneously since the framework of the protein binds the __ and __ and prevents them from __
                                                                  i.      __catalyzes the cutting of polysaccharide chains in the cell walls of bacteria; it is a __reaction, which is __ because the free energy of the __is lower than the free energy of the __
                                                                ii.      Sometimes, to reach a __, __must occur to overcome the energy barrier
    • acid and base catalysis
    • acidic and basic residues
    • combining with each other
    • Lysozyme 
    • hydrolysis 
    • energetically favorable
    • severed polysaccharide chain 
    • intact chain
    • transition state
    • distortions
  16.                                                               i.      Conditions are created in the microenvironment of the lysozyme active site that greatly __necessary fo the hydrolysis to take place. Three central steps are: Step One

    reduces the activation energy 

    The enzyme stresses its bound substrate, so that the shape of one sugar more closely resembles the shape of high-energy transition states formed during the reaction
  17.                                                               i.      Conditions are created in the microenvironment of the lysozyme active site that greatly  reduces the Ea of the hydrolysis to take place. Three central steps are: Step Two

    1.       The negatively charged aspartic acid reacts with the C1 carbon atom on the distorted sugar, and the glutamic acid donates its proton to the oxygen that links this sugar to its neighbor. This breaks the sugar-sugar bond and leaves the aspartic acid side chain covalently linked to the site of bond cleavage
  18.                                                               i.      Conditions are created in the microenvironment of the lysozyme active site that greatly  reduces the Ea of the hydrolysis to take place. Three central steps are: Step Three

    1.       Aided by the negatively charged glutamic acid, a water molecule reacts with the C1 carbon atom, displacing the aspartic acid side chain and completing the process of hydrolysis
  19. a.       The active site can also act as a __that brings the substrates together in proper orientation
                                                                  i.      The active site contains __ that speed up a reaction by using __ to alter the distribution of electrons in the substrates
    1.       In addition, when a substrate binds to an enzyme, (what happens), changing the substrate shape, which drive the substrate towards the __
                                                                ii.      Many enzymes participate intimately in the reaction by briefly forming a __ between the __ and __ 

    precisely positioned atoms

    charged groups

    bonds in the substrate often bend

    transition state

    covalent bond

    substrate and a side chain of the enzyme
  20. a.       Proteins use small molecules to perform functions they cannot. These are __, __, or __ 
                                                                  i.      They can be covalently and permanently attached to their protein, becoming an integral part of the protein molecule
    b.      Some chemical reactions catalyzed by enzymes in cells produce __that can be __or __. __ have been developed to preserve the __, allowing __ to the __
    cofactors, prosthetic groups, or coenzymes (organic molecules)



    diffuse out of the cell

    Moelcular tunnels


    rapid procession to the final product

Card Set:
Molecular Text 3.2
2015-01-20 17:46:32
Test One
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