The value can be derived from the rules of diffusion as shown in Figure 3 and is known as the diffusion-limited rate. For a protein-sized enzyme and a small molecule substrate the diffusion-limited rate constant takes the value of roughly s -1 M An enzyme approaching this limit can be described as optimal with respect to its ability to perform a successful transformation on every encounter provided by random diffusion.
How well does the characteristic enzyme do? Figure 2C shows that the median value is about s -1 M -1 , about 4 orders of magnitude lower than the diffusion limit. This difference can be partially explained by the liberal nature of the diffusion limit that does not depict all the issues related to binding and by noting that for many enzymes there might not be a strong selective pressure to optimize their kinetic properties.
Moreover, the rate might be compromised in many cases by the need for recognition and specificity in the interaction. The value of KM in conjunction with the diffusion-limited-on-rate can be used to estimate the off rates for bound substrate. The goal of the simple estimate is to find the time scale over which a substrate that is bound to the enzyme will stay bound before it goes back to solution usually without reacting , the so called off rate koff.
An approximation for the koff is the product of this kon and the KM. This gives only a taste of the idealized case; the actual measured values for off-rates or residence times are revealed by enzymologists keeping them busy and confronted with a plethora of surprises. An analogous estimate for the off-rate can be considered for interactions between signaling molecules and for transcription factors binding to DNA with characteristic time scales from milliseconds to tens of seconds or even longer.
A striking quantitative insight into the possibilities and rate of interactions at the molecular level can be gleaned from a clever interpretation D.
Say we drop a test substrate molecule into a cytoplasm with a volume equal to that of a bacterial cell. If everything is well mixed and there is no binding, how long will it take for the substrate molecule to collide with one specific protein in the cell? We make use of one of our tricks of the trade which states that in E. This allows us to estimate that every substrate molecule collides with each and every protein in the cell on average about once per second.
As a concrete example, think of a sugar molecule transported into the cell. Within a second it will have an opportunity to bump into all the different protein molecules in the cell. The high frequency of such molecular encounters is a mental picture worth carrying around when trying to have a grasp of the microscopic world of the cell.
Enzymes are highly selective catalysts, meaning that each enzyme only speeds up a specific reaction. The molecules that an enzyme works with are called substrates. The substrates bind to a region on the enzyme called the active site. In the lock-and-key model, the active site of an enzyme is precisely shaped to hold specific substrates. V max reflects how fast the enzyme can catalyze the reaction.
Click on the image at right to see how high V max and low V max enzymes compare. V max is given by the asymptote to the velocity curve as the substrate concentration is extrapolated to infinity. Notice that K m stays constant for the two enzymes described here. Michaelis Constant K m : Enzymes have varying tendencies to bind their substrates affinities.
An enzyme's K m describes the substrate concentration at which half the enzyme's active sites are occupied by substrate.
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