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BIO401: Biochemistry

Unit 4: Enzymes   Enzymes are extremely important to life; toxins that destroy enzymes are almost always lethal. Enzymes, as you already know, speed up chemical reactions. While this may seem trivial, without the right chemical reactions life could not happen. Because enzymes function in the context of chemical reactions, they are classified in a system according to the type of reaction occurring, and we will cover each of these six classes. You will also learn about the thermodynamics and kinetics of enzymes, and how all enzymes share a similar pattern of energetics regardless of function. Lastly, you will learn what regulates their activity, as we do not “turn on” every enzyme all the time.

Unit 4 Time Advisory
This unit should take you 14 hours to complete.

☐    Subunit 4.1: 2 hours

☐    Subunit 4.2: 2 hours

☐    Subunit 4.3: 3 hours

☐    Subunit 4.4: 1 hour

☐    Subunit 4.5: 2 hours

☐    Subunit 4.6: 2 hours

☐    Subunit 4.7: 2 hours

Unit4 Learning Outcomes
Upon successful completion of this unit, students will be able to:

  • Explain how enzymes function as catalysts.
  • Describe the different classes of enzymes.
  • Describe how enzymes are regulated.

4.1 Enzymes as Catalysts   - Reading: Carnegie Mellon Open Learning Initiative: Modern Biology: "Enzyme Kinetics" Link: Carnegie Mellon Open Learning Initiative: Modern Biology: “Enzyme Catalysis” and “Enzyme Kinetics” (HTML)
 
Instructions: Review how enzymes serve to increase the rate of a reaction.  Click on the link and then on “Enter Course” to access each page.
 
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4.1.1 Rate Enhancement   4.1.2 Energy Transfer   4.2 Six Major Classes   - Reading: Cliffs Notes: Biochemistry: "Six Types of Enzyme Catalysts" Link: Cliffs Notes: Biochemistry: "Six Types of Enzyme Catalysts" (HTML)
 
Instructions: Understand the six types of enzyme catalysts. This covers subunits 4.2.1-4.2.6.
 
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4.2.1 Oxidoreductases   4.2.2 Transferases   4.2.3 Hydrolases   4.2.4 Lyases   4.2.5 Isomerases   4.2.6 Ligases   4.3 Thermodynamics   - Reading: University of Arizona: Biochemistry 462a: "Enzyme Mechansims" Link: University of Arizona: Biochemistry 462a: “Enzyme Mechansims" (HTML)
 
Instructions: Read through how enzymes function.  This covers subunits 4.3.1-4.3.4.
 
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4.3.1 Direction   4.3.2 Free-Energy Change   4.3.3 Transition State Formation   4.3.4 Enzyme Active Site   4.4 Michaelis-Menten (M-M) Model   - Web Media: Rensselaer Polytechnic Institute: Biochemical Engineering: "Enzyme Kinetics Simulation" Link: Rensselaer Polytechnic Institute: Biochemical Engineering: "Enzyme Kinetics Simulation" (HTML)
 
Instructions: Understand the concept of Michaelis-Menten kinetics by using the simulation tool on this page.  This covers subunits 4.4.1-4.4.4.
 
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4.4.1 M-M Equation   4.4.2 Vmax   4.4.3 Km   4.4.4 Kcat   4.5 Enzyme Inhibition   4.5.1 Competitive   - Reading: University of Arizona: Biochemistry 460: "Enzymes: Competitive Inhibition Notes" Link: University of Arizona: Biochemistry 460: "Enzymes: Competitive Inhibition Notes" (PDF)

 Instructions: Go to the link and find the lecture notes entitled
"Enzymes: Competitive Inhibition Notes."  

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4.5.2 Non-Competitive   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Enzymes Can Be Inhibited by Specific Molecules" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Enzymes Can Be Inhibited by Specific Molecules" (HTML)
 
Instructions: Read how noncompetitive enzyme inhibition works.  This also covers subunits 4.5.3 and 4.5.4.
 
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4.5.3 Uncompetitive   4.5.4 Transition State Analog   4.6 Coenzymes   Note: Many vitamins are essential to our diet simply because they are essential for some enzymes to function. Some vitamins are water-soluble, while others are not. This is why some vegetables are more nutritious raw than boiled, because immersing them in water washes away water-soluble vitamins. Please be sure to know which vitamins are water-soluble and which are fat-soluble.

  • Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Vitamins Are Often Precursors to Coenzymes" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Vitamins Are Often Precursors to Coenzymes" (HTML)
     
    Instructions: Read about vitamin cofactors.  This covers all of unit 4.6.
     
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4.6.1 Water-Soluble Vitamins   4.6.2 Fat-Soluble Vitamins   4.7 Regulation   4.7.1 Enzyme Production   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Recurring Motifs in Metabolic Regulation" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Recurring Motifs in Metabolic Regulation"(HTML)
 
Instructions: Read about enzymatic regulation.  This covers subunits 4.7.1-4.7.3.
 
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4.7.2 Compartmentalization   4.7.3 Inhibition and Activation   4.7.4 Post-Translational Modification   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Covalent Modification Is a Means of Regulating Enzyme Activity" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Covalent Modification Is a Means of Regulating Enzyme Activity" (HTML)
 
Instructions:  Read how various modifiction of proteins affect their function.
 
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