Ch 8.1 Lecture

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  1. What do jellyfish do?
    produce enzymes that take a substrate and produce light
  2. Characteristics of enzymes? 
    Symbol for reaction rate constant?
    immense catalytic power

    • - lowers Ea
    • - speeds up and makes a reaction easier
    • - enzymes do not change

    Highly specific

    Highly regulated: can produce enzymes in proenzyme form, meaning its sythesized in correct order and almost completely folded. But, one change makes it functional. it is activated when needed

  3. What is the fastest enzyme? Or, one that catalyzes the reaction as fast as possible.
    carbonic anhydrase
  4. What do proteases do?
    break peptide bond by adding a cofactor, which is water

    • They are highly specific for the bond they break 
    • ex: One that breaks the bonds that occur after Lys and Arg
  5. Enzymes do what? What are some examples?
    convert one form of energy to another

    • light--> sugar
    • sugar--> ATP
    • ATP--> mechanical work
    • ATP--> electrical gradients
  6. What is thermodynamics?
    science concerned with the relationship between heat and work
  7. First Law of Thermodynamics: __

    What matters?
    The total energy of a system (whatever we are trying to study/ anything inside a barrier) and its surroundings is constant

    path doesn't matter form A--> B. All that matters are the energies
  8. How to determine change in total energy of a system.

    • Esubb: system when we end the process
    • Esuba: system when we start process
    • Q: heat absorbed by system
    • W: work done by system
  9. With a system alone, what can't we determine?
    we can't determine whether a reaction is spontaneous or nonspontaneous. So, we look at surroundings.
  10. Second Law of Thermodynamics

    When is a system spontaneous if applying this equation?
    A process can occur spontaneously only if the sum of the entrophies of the system and its surroundings increase

    - all entropy increases. 

    if disorder increases, then, yes, its spontaneous
  11. In a system with H2 and O2, by its conerting into water, what is it?
    It is spontaneous. This is because release of heat increases disorder, making it spontaneous. Even though we created a more ordered system, the entropy of the surroundings increaseed
  12. What are the equations for:

    change in total entropy

    change in entropy of srroundings

    a combo of both

    multiplying by T
    dStotal=DSsystem+dSsurroundings (we don't always know DSsurroundings)

    dSsrroundings= dSsystem-dHsystem/T

    dStotal= dSsystem-dHsystem/T

    -TdSsystem= dHsystem-TdSsystem
  13. What is the change in Gibbs free energy?
  14. When does the total entropy increase?

    dSsystem > dHsystem/T

    • or 
    • TdSsystem> dHsystem
  15. When is a reaction spontaneous in terms of the equation?
    dG=dHsystem-TdSsystem <0

    • when dG is negative= spontaneous
    • when dG is positive= nonspontaneous
    • when dG equals 0= equilibrium
  16. Why is the folding of a protein possible if you're going from more disordered to more ordered?
    Although folding is more ordered, hydrophobin amino acids get inside to hide from the water and hydrophilic amino acids reposition themselves outside. If the hydrophobic amino acids remain outside, it causes water to become ordered adn form a cage around them. When inside, water is free to act with bulk water and get more disordered
  17. Under standard conditions, what relationship occurs?
    • a relationship between equilibrium constants and free energy change under standard conditions. Given by:
    • k'eq=10(-Go/1.36)
    • The 1.36 comes from multiplying the 2.303 by the RT
  18. Why did biochemists create the standard conditions? And, what is the symbol?
    biochemists created standard conditions (denoted with a o  sign) for studying the reactions. 

    Then, they added pH of 7, which is denoted by the apostrophe (')
  19. Relationship between K'eq and dGo
    As K'eq increases, dGo  decreases at standard conditions at pH 7
  20. What is the comparison of adding an enzyme?
    Regardless of whether an enzyme is added, the reaction will still have the same equilibrium point/ end point. 

    • What an enzyme does is speed up the reaction. 
    • Therefore, without an enzyme added, it just takes a longer time to reach this equilibrium.
  21. What is free energy? 

    What is dG≠?

    What is the transition state?
    how much free energy is associated with various steps

    that is Gibbs Free energy of activation

    Highest free energy state that a molecule has to go through to be a product
  22. True or False: 

    There is a great deal of free energy associated with the transition state.
  23. Explain energy and how enzymes help in reactions.
    all the weak bonds have energy associated with it. Enzymes help by: 

    • - bringing enzymes closer together
    • - stressing the substrates to make the TS more attainable
  24. Explain the ES complex.
    It is the brief period of time that enzymes comes in to react with the substrate

    E + S --k1--> ES --k2--> E + P

    The ES can continue to convert substrate to product; enzyme not altered
  25. What is the maximal velocity?
    when all are bound together
  26. Why is there a parabolic curve for certain enzymes?
    the reaction velocity goes up but wouldn't reach the max velocity point because not all can react at the exact same time
  27. What are the ways that we proved that an ES complex existed?
    1) the reaction velocity (how much product formed)

    2) taking a look at the active sight only to find that amino acids and prosthetic groups surround the side and have ways of interacting with substrate the best; one ideal substrate that can fit in

    3) Spectrophotometer to see how enzymes change when mixed with substrate

    4) primary sequence of amino acids (6 out of the 29 form the active site and are required for a reaction to take place); the rest of the AAs form the shape that allows them to fit perfectly in the active site
  28. Once in the active site, explain bonding.
    Once in the active site, covalent bonds can form eventually, but not initially. Hydrogen bonds, ionic bonds, hydrophobic interactions, etc. form. The higher the amount of weak interactions that occurs, the better the chance for substrate
  29. What are the two models of enzyme and substrate fitting together?
    lock and key fit

    induced fit
  30. Explain lock and key.
    weak interactions hold the substrate and active site together. The substrate fits perfectly into the active site
  31. Explain the induced fit.
    Only the right substrate will react. The enzyme, prior to binding, has all of the components needed to bind, but it isn't positioned properly. When the substrate comes in, it is fit perfectly in via an induced fit.
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Ch 8.1 Lecture
Test Two
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