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BIO401: Biochemistry

Unit 8: Metabolism   Metabolism can be defined by a number of ways, but in the context of this course it is defined as the set of chemical reactions and molecules that occur in which energy is produced for life’s processes. Metabolism includes two complementary sides, anabolism and catabolism; the former breaks down large molecules for energy, while the latter builds large molecules for energy storage. Glycolysis, for example, is the catabolic breaking down of glucose, while gluconeogenesis is the anabolic building of glucose from various other biomolecules. You may have heard of anabolism from steroids, as they are commonly referred to as anabolic steroids. Bodybuilders use them because they encourage the body to undergo unnatural anabolism and build molecules beyond a normal amount. This is a very long and detailed unit, so be sure to spend as much time as needed to learn all of the concepts, especially when you approach the section on metabolic pathways.

Unit 8 Time Advisory
This unit should take you 22 hours to complete.

☐    Subunit 8.1: 1 hour

☐    Subunit 8.2: 1 hour

☐    Subunit 8.3: 3 hours

☐    Subunit 8.4: 2 hours

☐    Subunit 8.5: 3 hours

☐    Subunit 8.6: 2 hours

☐    Subunit 8.7: 2 hours

☐    Subunit 8.8: 2 hours

☐    Subunit 8.9: 2 hours

☐    Subunit 8.10: 1 hour

☐    Subunit 8.11: 1 hour

☐    Subunit 8.12: 2 hours

Unit8 Learning Outcomes
Upon successful completion of this unit, students will be able to:

  • Describe how ATP is generated and used for energy by the cell.

8.1 Importance of ATP   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Metabolism Is Composed of Many Coupled, Interconnecting Reactions" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Metabolism Is Composed of Many Coupled, Interconnecting Reactions" (HTML)
 
Instructions: Read about the importance of ATP in biochemical reactions.  This reading covers all of 8.1.
 
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8.1.1 Universal Currency of Energy   8.1.2 ATP Molecule Energetics   8.1.3 ADP and AMP   8.2 Central Concepts   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 24" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism:"Lecture 24"
 
Instructions: Go to the page in the link and find the set of slides for lecture 24.  This covers all of section 8.2.
 
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8.2.1 Catabolism   8.2.2 Anabolism   8.2.3 Electron Transfer   8.3 Glycolysis   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 25" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 25" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 25.  This covers all of section 8.3 and 8.4.
 
Note: It is very important to keep track of when the products are made during glycolysis, as it is a series of many reactions and only some of these steps result in a product.  Also, remember that there are two molecules of pyruate made per glucose molecule.
 
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8.3.1 Reactants and Products   Note: It is very important to keep track of when the products are made during glycolysis, as it is a series of many reactions and only some of these steps result in a product. Also, remember that there are two molecules of pyruate made per glucose molecule.

8.3.2 Steps from Glucose to Glyceraldehyde 3-Phosphate (G3P) and Dihydroxyacetone Phosphate (DHAP)   8.3.3 Interconversion of DHAP and G3P   8.3.4 Steps from G3P to Pyruvate   8.3.5 Generation of NADH and ATP   8.4 Fates of Pyruvate   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 26" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 26" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 26.  This covers all of section 8.4.
 
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8.4.1 Anaerobic Conversion to Ethanol   8.4.2 Anaerobic Conversion to Lactate   8.4.3 Decarobxylation to Acetyl CoA   8.5 TCA (Tricarboxylic Acid) Cycle   Note: Like glycolysis, there are many steps and you need to keep track of which molecule is made when. Also, other metabolic pathways that you will learn about, such as beta oxidation, will feed into a particular certain stage of the TCA cycle, and it is important not to confuse these feeder pathways.

  • Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 28" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 28" (Microsoft PowerPoint)
     
    Instructions: Go to the page in the link and find the set of slides for lecture 28.  This covers all of section 8.5.
     
    Note: Like glycolysis, there are many steps in the TCA Cycle; you will need to keep track of which molecule is made when.  In addition, keep in mind that some of the other pathways that you will learn about (such as beta oxidation) will feed into a particular stage of the TCA cycle; it is important that you not confuse these feeder pathways.
     
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8.5.1 Reactants and Products   8.5.2 Pyruvate Oxidation and Generation of Acetyl CoA   8.5.3 Inner and Outer Mitochondrial Membranes   8.5.4 Main Reactions Steps to Oxaloacetate   8.5.5 Glyoxylate Bypass   8.6 Gluconeogenesis   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 33" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 33" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 33.  This covers all of section 8.6.
 
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8.6.1 Carbon Sources   8.6.2 Main Reaction Steps to Glucose   8.7 Glycogen   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 34" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 34" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 34.  This covers all of section 8.7.
 
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8.7.1 Glycogen and Liver Storage   8.7.2 Glycogenolysis   8.8 Oxidative Phosphorylation   8.8.1 Electron Transfer   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 29" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 29" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 29.  This covers all of section 8.8.1-8.8.3.
 
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8.8.2 Complex I, II, III, IV   8.8.3 Coenzyme-Q (Co-Q)   8.8.4 ATP Synthase and Chemiosmosis   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 30" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism:  "Lecture 30" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 29.   This information covers sections 8.8.4 and 8.8.5.

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8.8.5 Oxygen as Final Electron Acceptor   8.9 Pentose Phosphate Pathway   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 33" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 33" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 33.   This information covers all of 8.9.

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8.9.1 Oxidative Phase   8.9.2 Non-oxidative Phase   8.10 Fatty Acid Breakdown   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 35" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 35" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 35.   This information covers all of 8.10.

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8.10.1 Lipolysis and Free Fatty Acids (FFA)   8.10.2 Triacylglycerols (TAG)   8.10.3 ?-oxidation of FFA   8.10.4 Ketone Bodies   8.11 Fatty Acid Synthesis   8.11.1 Reactions from Acetyl-CoA to Palmitate   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 36" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 36" (Microsoft PowerPoint)
 
Instructions: Go to the page in the link and find the set of slides for lecture 36.
 
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8.11.2 Insulin and Leptin   - Reading: NCBI Bookshelf’s version of W.H. Freeman(publisher), Berg, Tymoczko, and Stryer (authors) Biochemistry 5th Edition: “Section 22.5 Acetyl Coenzyme A Carboxylase Plays a Key Role in Controlling Fatty Acid Metabolism”

Link: Reading: NCBI Bookshelf’s version of W.H. Freeman(publisher),
Berg, Tymoczko, and Stryer (authors) Biochemistry 5<sup>th</sup>
Edition: “[Section 22.5 Acetyl Coenzyme A Carboxylase Plays a Key
Role in Controlling Fatty Acid
Metabolism](http://www.ncbi.nlm.nih.gov/books/NBK22381/)”  

 Instructions: Read the entire webpage.  
  

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  • Reading: NCBI Bookshelf’s version of W.H. Freeman(publisher), Berg, Tymoczko, and Stryer (authors) Biochemistry 5th Edition: “Section 30.2 Food Intake and Starvation Induce Metabolic Changes”

    Link: NCBI Bookshelf’s version of W.H. Freeman(publisher), Berg, Tymoczko, and Stryer (authors) Biochemistry 5th Edition: “Section 30.2 Food Intake and Starvation Induce Metabolic Changes

    Instructions: Read the first section of this webpage and the section titled “30.3.3 Caloric Homeostasis: A Means of Regulating Body Weight”
     

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8.12 Protein Breakdown   8.12.1 Ubiquitin and Proteasome   - Reading: Baldwin-Wallance College: Cell Biology: "The Ubiquitin System" Link: Baldwin-Wallance College: Cell Biology: "The Ubiquitin System" (HTML)
 
Instructions: Read through the information about ubiquitination of proteins.
 
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8.12.2 Amino Acid Deamination   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The First Step in Amino Acid Degradation Is the Removal of Nitrogen" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The First Step in Amino Acid Degradation Is the Removal of Nitrogen" (HTML)
 
Instructions: Read this webpage to learn how amino acid deamination occurs.
 
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8.12.3 Ketone Bodies   - Reading: Wikipedia: "Ketone Bodies" Link: Wikipedia: "Ketone Bodies" (PDF)
 
Instructions: This entry will explain the importance of ketone bodies.
 
Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikipedia version of this article here (HTML).

8.12.4 Reaction Steps to Urea   - Reading: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 38" Link: University of Arizona: Dr. Miriam Ziegler’s Biochemistry 460 Proteins and Metabolism: "Lecture 38" (Microsoft PowerPoint)
 
Instructions: Click on the link above and find the link for the lecture 38 slides in order to view them in their entirety.
 
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