Lecture 2 Flashcards
Ligand
Any molecule that binds to any site on a protein; isn’t the active site on a protein, however. When it binds to the protein its structure does NOT get changed. doesn’t have to be the active site of an enzyme, the protein doesn’t even need to be an enzyme?
Kd
Dissociation constant. It is the concentration of L needed for exactly one half of the protein/enzyme population to be saturated at a given concentration of protein/enzyme.
- Is an indication of “fit” of a ligand to its site: the better the fit, the tighter the binding, and the lower the Kd.
isotherm
s
rectangular hyperbola
The shape of the graph that is formed by ligand interactions. An example of a molecule that follows this kind of plot is myoglobin. Hemoglobin, which is allosterically regulated, does not follow this type of graph..
- Occurs when K is constant?
enzyme-substrate complex
e
saturablility
As more ligand is introduced with the same amount of protein present, the more saturated it becomes until it is at its absolute saturation point where every protein is bound to a ligand.
Michaelis-Menten equation
d
Vmax
e
Km
d
kcat
f
turnover number
d
Lineweaver-Burk plot
d
inhibitor
d
competitive inhibitor
Binds to the same place on the protein as our ligand.
- The binding curve still has the L/(L+K) form
uncompetitive inhibitor
e
catalytic triad
d
induced fit
e
cooperativity
Occurs when the concentration of a ligand alters the binding properties of a protein that recognizes it. An example of positive cooperativity is seen in hemoglobin
allosteric enzyme
d
sigmoidal isotherm
d
allosteric inhibitor
Binding of it to one subunit decreases the chance of substrate binding to another subunit of the same enzyme
allosteric activator
Binding of it to one subunit increases the chance of substrate binding to another subunit of the same enzyme
phosphorylation
- Phosphorylation is the addition of a phosphate group to a molecule (typically a protein) by an enzyme ( a protein called a kinase)
- In some cases, adding a phosphate increases activity/activates the molecule, while in other cases, it decreases activity/deactivates it
- Specific amino acids of an enzyme are phosphorylated, so its not just random
- Phosphatases are what remove a phosphate group, and this can also have an activating or deactivating effect, depending on the protein
modification
e
inhibitable (paper)
e
Entropy Reduction Catalysis
- A mechanism of enzyme catalysis
- Decreases the
- Enzymes do this through non-covalent interactions and binding
Acid-Base Catalysis
d
Metal-Ion Catalysis
d
Chymotrypsin
- An example of the covalent intermediate catalysis mechanism
Relationship between change in activation energy and increase in reaction rate
k(new)=K(old) x e^(d/RT)
- When deltaGdagger is lowered by amount d, the rate constant is increased by a factor of e^(d/RT), giving us an exponential relationship
Binding Isotherm
d
