5.1: Introduction
- Page ID
- 88920
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)By definition, all catalysts accelerate chemical reactions, including enzymes. But enzymes and inorganic catalysts differ in important ways (Table 5.1).
Table 5.1
Enzymes vs Inorganic Catalysts
| Inorganic Catalysts | Enzymes |
|---|---|
| e.g., Ni, Pl, Ag, etc. | e.g., pepsin, trypsin, ATP synthase, ribonuclease, etc |
| increase rxn rate | increase rxn rate |
| unchanged at end of rxn | unchanged at end of rxn |
| non-specific | highly specific |
| rigif, inflexible | flexible - can undergo allosteric change... |
| cannot be regulated | can be regulated |
In this chapter, we look at the properties and mechanism of action of enzymes. These include allosteric change (induced fit, enzyme regulation), energetic events (changes in activation energy), and how enzymes work in open and closed (experimental) systems.
Most enzymes are proteins; a few are RNAs. All enzymes are long flexible polymers that fold into intricate shapes, able to recognize and tightly bind specific target molecules. In contrast, inorganic catalysts are rigid, weakly binding many molecules and catalyzing many random reactions. The specificity of an enzyme lies in the structure and flexibility of its active site. We will see that the active site of an enzyme undergoes conformational change during catalysis.
The structural flexibility of enzymes also explains their ability to respond to metabolites in a cell, metabolites which indicate the cell’s biochemical status. When such regulatory metabolites bind to an enzyme, the resulting conformational changes can speed up or slow down the catalytic rate of the reaction—a phenomenon called allosteric regulation. As you might imagine, changing the rate of a biochemical reaction can change the rate of an entire biochemical pathway—and ultimately the steady-state concentrations of products and reactants in that pathway.
To understand the importance of allosteric regulation, we’ll look at how we measure the speed of enzyme catalysis. As we consider the classic early twentieth-century enzyme kinetic studies of Leonor Michaelis and Maud Menten, we’ll focus on the significance of the Km and Vmax values that they derived from their data. But before we begin our discussion, remember that chemical reactions are by definition reversible. The action of catalysts, either organic or inorganic, depends on this concept of reversibility.
Either now or when you are done reading this chapter, see if you can explain in your own words the relationship between catalysis and the inherent reversibility of chemical reactions.
Finally, let’s give a nod to recent human ingenuity that enabled enzyme action to turn an extracellular profit! You can now find enzymes in household cleaning products like spot removers and detergents, where they function to digest and to remove stains caused by fats and pigmented proteins. Enzymes added to meat tenderizers also digest (hydrolyze) animal proteins down to smaller peptides. Enzymes can even clean a clogged drain!
When you have mastered the information in this chapter, you should be able to:
1. describe how the molecular flexibility of protein and RNA molecules make them ideal biological catalysts.
2. compare and contrast the properties of inorganic and organic catalysts.
3. explain why catalysts do not change equilibrium concentrations of a reaction conducted in a closed system.
4. compare the activation energies of catalyzed and un-catalyzed reactions and explain the roles of allosteric effectors in enzymatic reactions.
5. discuss how allosteric sites interact with an enzyme's active site and explain the concept of the rate limiting reaction in a biochemical pathway.
6. write simple rate equations for chemical reactions.
7. write the possible rate equations for equations for catalyzed reactions.
8. distinguish between Vmax and Km in the Michaelis-Menten kinetics equation.
9. state what Vmax and Km say about the progress of an enzyme catalyzed reaction.
10. interpret enzyme kinetic data and the progress of an enzyme-catalyzed reaction from this data.
11. more accurately identify Leonor Michaelis and Maud Menten!