Introduction to Biochemical Kinetics – Enzyme Kinetics

Introduction to Biochemical Kinetics – Enzyme Kinetics


– I’m Jeff Yarger, I’m a
professor of chemistry, biochemistry and physics at
Arizona State University. The lecture today we’re gonna cover an introductory lecture
into enzyme kinetics. Which I think of as basically
looking at catalysis chemical catalysis in the
in the biological world. So this is meant to be a follow up on a lecture I gave on chemical kinetics, specifically looking at
now what is very common in the biological world, which is the topic of enzyme kinetics. And so I’d first like to just remind us of general catalysis and
how its effect on kinetics, or the time scale of reaction. We can have catalysis reactions to catalyze a reaction is to do something that speeds up, you know, a reaction. Typically through changing
the activation barriers between a reaction. So it’s not changing
typically the thermodynamics, the overall change in, for example, the energy from the
reactants, the products, that gives free energy of whether something’s spontaneous or not. But just the activation
barriers between the two states to give you, in a sense,
effecting the time scales at which these reactions happen. And so the most common catalyst, and these are whole
areas within the chemical and biochemical sciences, can often be split up into numerous parts. In chemistry it’s usually whether it’s a homogenous
or heterogeneous catalysis. In other words, are you using a surface like a platinum electrode
to do some type of reaction where it’s heterogeneous? The catalytic agent is separate in a sense from what’s being reacted. Some things can regenerate, some things are used as part
of the catalyst, et cetera. This is a whole area of chemical sciences, and a whole line of research goes into creating new catalysts for all sorts of chemically important reaction. Also homogenous reactions where you’re often putting something into the material itself, and it’s homogeneously distributed, and it’s just able to act as a way to get over these intermediates, these high energy activation barriers and allow things to find its
free energy minimum better. Where it’s kind of shown here, un-catalyzed reactions can have very high activation barriers. And it’s usually catalysis
that brings this down and it can do it in a very simple way, or it can do it in complicated ways with multiple intermediates. And you can have heterogeneous
things like surfaces, like platinum surfaces that catalyze, for example, the splitting
of water reaction famously or things that you add to things directly that are homogeneously in the system. And then what we’re here
to mainly introduce today is enzyme kinetics. And so this is in the biological world one of the most common types of catalysts. And so they’re typically,
enzymes are not always but are often proteins. And they often do one of the
most common types you see are these lock and key type enzyme to the substrate. So the substrate could react
to form products on its own. But what this enzyme
substrate complex does is lower this activation
barrier significantly so that the time scale of this
substrate going to product is greatly enhanced through this lock and key type of mechanism. And what are we talking about
as far as some of these? So let’s look at a very simple reaction, something like peroxide
going to water and oxygen. And if you look at it
with no catalyst at all, it happens very, very slowly. So it takes very, very long periods. And as soon as you add a
protein catalyst to this you speed it up, you
know, orders of magnitude and it’s because you’ve
decreased its activation barrier from something like 70 kilojoules per mole all the way down to 8 kilojoules per mole. At room temperature this
thing increases orders of magnitude in speed at
which the reaction happens. So again, we go from something with a very large activation barrier to almost no activation barrier for it to be able to go from
reactants to products in this. And so this is a good example of an enzyme or a protein being used as a catalyst that we then therefor call it an enzyme. And again, like here’s showing you. So you speed up to 10
to the 6 inverse seconds for the one we just showed. But you can see some of these
overall catalytic constants or how much the maximum velocity over normalizing to its initial
substrate concentration. You speed these things up often you know, thousands to
millions of times faster than they happen naturally. This is a critical aspect in most, a lot of reactions in biological reactions are catalytically driven. And in this lock and key type mechanism Michaelis-Menton kinetics
is one of the most commonly followed or the most
common types of mechanisms which this substrate locks into an enzyme to form an intermediate so
that it has a rate constant to this enzyme substrate intermediate. And of course it has a back reaction. And that doesn’t in any way have to be the same rate forward and backwards. And then now this second one
has a rate forward to products. And usually, again, this could
have a back reaction as well it’s just typically this is at a higher, so this is very, very slow with respect to the forward reaction. So it often gets neglected here. In fact that’s primarily what goes into Michaelis-Menton kinetics
is the assumption that this back reaction
is very, very slow. So it’s just looking at
three out of the four potential rate constants and the assumption is, is
that K-2 is much, much smaller than K2, than the forward one. So you don’t have to consider
it backtracking that way. You only have to consider the initial enzyme substrate forming. It can also sometimes un-form, but if it does form this
and does go on to products you don’t have to worry about the products re-reacting with the enzyme back. Okay, when you take
that into consideration, and look at some of the math you can now define these
three rate constants and redefine it as a
Michaelis-Menton constant. And now we get an equation
that we can plot in some way via its maximum velocity and
its Michaelis-Menton constant is usually what we’re looking for versus the substrate concentration
you’re starting with. There’s several ways to look at this because it is complicated. The most common we show here which is to plot the inverse of its velocity versus, or the inverse of its substrate concentration versus the inverse of its
velocity that it’s going at. And then we fit that to a line which we get related to
where it crosses the x-axis its negative inverse of its
Michaelis-Menton constant and it’s related to the maximum velocity that it would have at its
highest concentration. So there are several
other ways I include here that this can be looked at as well to try to get out what
these constants are. And this helps, and then this is directly related to as you saw in the previous slide basically a ratio of the
rate constants for K1 and the back reaction and K2 assuming the back reaction for K2 is slow. So this is one of the
most commonly used methods for looking at enzyme kinetics and what the overall rate
constant this ratio would be in these systems. So hopefully this gives
you an introduction to enzyme kinetics and a practical way of being able to plot and
look at these rate constants when you have enzyme substrates
in biological systems. Thank you.

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