Week 6 Flashcards
Enthalpy
the total energy in a system
Entropy
the tendency for ordered things to become random
Free Energy (G)
refers to the amount of energy that is available in a system to use
If Product (P) has less free energy than the starting reagents (A and B), the ∆G for this reaction is –
Exergonic which means energy (or heat) is released and the reaction will go forward spontaneous
If P has more free energy than A and B, the ∆G is +
endergonic (which means energy need to be added for reaction to occur) and the reaction will not spontaneous occur
∆G predicts the…
direction of the reaction but doesn’t affect the rate at which the reaction occurs.
Transition state
when the substrate is mid-way through the transition to product
when do molecules have the highest potential energy
When in transition state/point
Rate of reaction dependent on….
activation energy. The smaller the activation energy the quicker the reaction will occur
Function of enzymes
speed chemical reactions by lowering the activation energy
what molecule drives endergonic reactions?
ATP
energetically favorable reactions
the free energy of the reactants is grater than the free energy of the of the product. Therefore, G is negative and the reaction con occur spontaneously
energetically unfavorable reactions
G would be positive if the reaction occurred and the universe would become more ordered. So the reaction can only occur if coupled to a second energetically favorable reaction
Active site
Site where chemical reaction takes place
Contains functional groups that are actively involved in the reaction
Stabilization of an enzyme
Additional bonds form with the enzyme to stabilize the substrate in its transition state. This is how enzymes lower the activation energy.
Substrate binding involves…
formation of non covalent bonds and interactions with amino acids from enzymes or cofactors (hydrophobic, electrostatic, and Hbonds)
Enzyme-substrate specificity
extremely high specificity due to the chemical shapes/interactions within the substrate binding site
lock and key mechanism
substrate binding site creates a 3-D shape that is complementary to the substrate
Enzyme AAs, cofactors, etc interact with substrate via non-covalent interactions
induced fit mechanism
Substrate binding to the enzyme induces a conformational change. Helps to reposition functional groups to promote reaction
Activation energy
energy required to raise substrate energy to the transition state
Coenzymes
non-protein organic molecules (vitamins).
Activation transfer coenzymes
Form covalent bond with substrate then activate it for transfer
Oxidation reduction coenzymes
similar to activation-transfer, but no covalent bond is formed. Functional groups accept or donate electrons
metal ions
electrophiles. involved in substrate binding, stabilizing anions, donate/accept electrons in redox reactions
inhibitors
compounds that decrease the rate of an enzymatic reaction
Covalent inhibitors
form covalent bond with functional groups in the active site
transition state analogs inhibitors
Bind more tightly to enzyme than substrate to products
the velocity of all reaction is dependent on what?
Substrate concentration
substrate saturation are found in which reactions?
enzymes catalyzed reactions
Michaelis-Menten Equation
E+S ES E+P
Assumes enzyme will let go once the product its formed and will go on to grab more substrate
Rate of product formation
is dependent on 2 constants (Km and Vmax) and on the amount of substrate available at that time point
Km
1/2 Vmax. allows us to compare affinities
Km values for enzymes
are typically just above [S] in the cell, so that the enzyme rate is sensitive to small changes in [S]
Catalytic constant/ Turnover number
Kcat = Vmax / [E]total
measured in units per sec
irreversible inhibitors
decreases amount of enzyme available
Reversible inhibitors
can diffuse away at a significant rate.
Competitive, non competitive, uncompetitive
Competitive inhibitors
inhibitor binds to substrate-binding site.
Km is increased. Vmax is the same
non-competitive inhibitors
Inhibitor binds enzyme someplace other than s-site. Vmax is lowered. Km is the same
uncompetitive inhibitors
inhibitor only binds to the ES complex. both the Vmax and Km will decrease but the slope stays the same.
Lineweaver-Burk transformation
plotting the velocity vs substrate concentration gives us hyperbolic curve
Y intercept = 1/Vmax
X intercept = -1/Km
slope is Km/Vmax
feedback loops
as product forms, apparent rate of enzymes decreases
genetic regulation
Activation of gene expression, increased enzyme (protein) production
Allosteric modification
Binding of regulators to sites outside of the active site (allosteric sites) induces conformational. Doesn’t follow Michaelis mention/ yields a sigmoidal shape
Cooperativity in allosteric enzymes
Substrate binding in one subunit increases the chance of substrate binding in another
Allosteric inhibitors
tend to bind more tightly to T state
Allosteric activators
tend to bind more tightly to R state
covalent modification
Extremely common way to quickly adjust activity of enzymatic reactions. Usually reversible.
