lecture 9 Flashcards
What is required of any protein to bind to a ligand?
Ligand needs to be the right size and shape
Requires the right volume and high enough amount of weak interactions between it and the molecule it binds to to stabilize it and resist thermal jolting.
needs to withstand the thermal energy/motion the molecule experiences.
Binding of glucose to GLUT 1
NOT ENZYME: R groups in the 12 alpha helices stabilize the glucose molecule as it passes through - R groups or backbone atoms rotate interact with functional groups on glucose in the best way, this rotation opens the passage to the cell. Weak interactions that can’t hold too tight or won’t let glucose pass all the way, ligand specificity illustrated in only taking B glucose
Lactose to Lactase
affinity for enzyme highest in TS, substrate binds to active site, causes enzyme to change shape to induce fit, this change stresses bond and takes lactose into TS, bond breaks, products have low affinity for enzyme and are released.
When is a protein called an enzyme?
both protein and substrate changes shape
how is an enzyme different from a transport protein like Glut 1 or a channel protein
in a transport protein, only the protein changes conformation. In an enzyme, both the protein and the substrate change conformations, which is what puts substrate into high energy state
What is the difference between a ligand and a substrate
Both bind to proteins but substrates get catalyzed
-Substrates are the reactants in enzymatic reactions. When the enzyme lactase hydrolyzes the disaccharide lactose in to sucrose and fructose, lactose is the substrate.
-Ligand is a generic term for substances that bind to receptors. When the hormone insulin binds to its receptors, it is acting as a ligad
What is an active site
An active site is the location of an enzyme that a substrate binds. The active site must have the correct shape and exposed R groups to bind to the substrate - the R groups form interactions, most commonly Hydrogen bonds, with the substrate. Remember, this is “induced fit” so the enzyme’s active site does not perfectly match the substrate.
When an enzyme binds a substrate, when is the binding affinity highest
At the transition state. As the interactions between the substrate and enzyme increase and get closer to the conformation of the transition state, the affinity of the enzyme increases. Affinity is highest at transition state
In general terms, what does an active site do to a substrate?
Changes the substrates conformation to put strain on its bonds.
How does this help an enzyme lower activation energy?
Moves the reactant into a higher energy conformation, reducing the amount of energy the system needs to overcome the activation energy
What are the key metrics, with units, of enzyme reactions? What do they mean, and how do we measure them?
Km - [substrate] that has the enzymes half occupied - units depend on what is being measured -eg- nmol/ml
Vmax - rate/velocity - - - how fast an enzyme works, units = depend, i think we used absorbance/sec?
½ Vmax - half Vmax, rate where enzyme is half occupied with substrate.
What are the two main reaction conditions that can be manipulated to accelerate or slow down an enzymatic reaction
Temperature and pH
How does a competitive inhibitor inhibit an enzyme
A competitive inhibitor binds to the enzyme’s active site and stops it from binding to the substrate. However, if the substrate concentration becomes high enough, the chance of a substrate particle binding when the inhibitor comes off is higher, which results in the enzyme being able to continue toward its maximum velocity.
the Michaelis-menten plot, how does it compare to a normal curve? (competitive)
The curve has a less steep growth, but the line reaches the same hight as the original, non-inhibited enzyme.
How does this affect Km and Vmax (competitive)
The Km gets larger, which indicates that the affinity of the enzyme decreased, and the Vmax stays the same because the enzymes can still work at their maximum capacity, it just takes longer to get there. Km increase means that enzyme needs fore substrate to be half occupied
