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CHEM204: Bioorganic Chemistry

Unit 5: Amino Acids and Metabolism   Amino acids are biomolecules that contain an amine group and a carboxylic acid group.  They also contain a side chain that varies depending on the amino acid.  In α-amino acids, the amino group is on the carbon next to the carboxyl group; α-amino acids are the building blocks for protein synthesis.  Amino acids also play vital roles in coenzymes.  In some living organisms, including humans, not all amino acids can be synthesized.  Essential amino acids are amino acids that cannot be synthesized by an organism in sufficient amounts, because the biosynthetic pathway is absent or not efficient enough.  Thus, essential amino acids must come from the diet of the organism.  
           
In this unit, you will learn about amino acid catabolism and biosynthesis.  The first step of amino acid catabolism is the removal of the amino group and the elimination of the toxic NHproduct from the cell.  Next, the carbon chain of the amino acid is used in a variety of biosynthetic pathways.  Note that it can also be used as an energy source during starvation.  Amino acids are split into two major groups depending on whether an organism can synthesize them or not.  Non-essential amino acids can be synthesized by the cell in sufficient amounts; essential amino acids cannot be synthesized and must come from the diet.  In this unit, you will study the biosynthesis of amino acids that are non-essential and those that are essential for humans.

Unit 5 Time Advisory
This unit should take you approximately 22.5 hours to complete.

☐    Subunit 5.1: 2.5 hours

☐    Subunit 5.2: 2.25 hours

☐    Subunit 5.3: 2.5 hours

☐    Subunit 5.4: 2.5 hours

☐    Subunit 5.5: 2.5 hours

☐    Subunit 5.6: 6.75 hours ☐    Subunit 5.6.1: 3 hours

☐    Subunit 5.6.2: 0.75 hour

☐    Subunit 5.6.3: 0.75 hour

☐    Subunit 5.6.4: 0.75 hour

☐    Subunit 5.6.5: 0.75 hour

☐    Subunit 5.6.6: 0.75 hour

☐    Subunit 5.7: 3.5 hours

Unit5 Learning Outcomes
Upon successful completion of this unit, the student will be able to:
- Explain why certain amino acids are essential and others are not. - Explain why ornithine is essential in the Urea Cycle. - Compare and contrast the biosynthesis and the break down of amino acids in the cell. - Identify the toxic amino acid breakdown product, which is converted to a less toxic product during the Urea Cycle.

5.1 Protein Degradation   - Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Protein Degradation” Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Protein Degradation” (HTML)
 
Instruction: Please click on the link above, and study this entire webpage to learn about protein degradation.  
 
Studying this resource will take approximately 2 hours and 30 minutes to complete.
 
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5.2 Deamination of Amino Acids   5.2.1 Transamination of Amino Acids   - Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid Catabolism: Nitrogen” Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid Catabolism: Nitrogen” (HTML)
 
Instruction: Please click on the link above, select “Transaminase (Amino Transferase)” under the “Contents of this page” heading, and study this section up until "Essential amino acids."
 
Studying this resource will take approximately 45 minutes to complete.
 
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5.2.2 Oxidative Deamination of Glutamate   - Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid Catabolism: Nitrogen” Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid Catabolism: Nitrogen” (HTML)
 
Instruction: Please click on the link above, select the “Deamination of amino acids" link under the “Contents of this page” heading, and study this section up until “Urea Cycle.”  
 
Studying this resource will take approximately 45 minutes to complete.
 
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  • Reading: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Oxidative Deamination Reaction” Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook:Oxidative Deamination Reaction” (HTML)
     
    Instruction: Please click on the link above, and study this entire webpage.  Click on the embedded hyperlink to “Transamination and Deamination” to visit an interactive page where you can investigate transamination and deamination reactions simultaneously.  You can also investigate the individual reactions of this metabolic pathway by moving the cursor over the arrows of this metabolic pathway.  
     
    Studying this resource will take approximately 45 minutes to complete.
     
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5.3 The Urea Cycle   - Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid Catabolism: Nitrogen” Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid Catabolism: Nitrogen” (HTML)
 
Instruction: Please click on the link above, select the links to “Urea Cycle” and “Other Roles of Urea Cycle Intermediates” under the “Contents of this page” heading, and study these sections in their entirety.  
 
Studying this resource will take approximately 2 hours and 30 minutes to complete.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

5.4 Catabolism of Amino Acid Carbon Chains   - Reading: The Medical Biochemistry Page: Michael W. King’s “Introduction to Amino Acid Metabolism. Essential versus Non-Essential Amino Acids: Inborn Errors in Amino Acid Metabolism” Link: The Medical Biochemistry Page: Michael W. King’s “Introduction to Amino Acid Metabolism. Essential versus Non-Essential Amino Acids: Inborn Errors in Amino Acid Metabolism” (HTML)
 
Instruction: Please click on the link above.  Under the heading of this page, you will find a table of contents.  Please, focus on the "Amino Acid Catabolism" section of the table of contents.  Click on the links to the following topics "Glutamine/Glutamate and Aspartate/Asparagine,” "Alanine,”  "Arginine,” Ornithine and Proline,: "Serine,” "Threonine,” "Glycine,” "Cysteine,” "Methionine,” "Valine, Leucine, Isoleucine,” "Phenylalanine and Tyrosine,” "Lysine,” "Histidine," and "Tryptophane" to study the breakdown pathways of these amino acids.
 
Studying this resource will take approximately 2 hours and 30 minutes to complete.
 
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5.5 Biosynthesis of Nonessential Amino Acids   - Reading: The Medical Biochemistry Page: Michael W. King's "Introduction to Amino Acid Metabolism. Essential versus Non-Essential Amino Acids. Inborn Errors in Amino Acid Metabolism." Link: The Medical Biochemistry Page: Michael W. King's "Introduction to Amino Acid Metabolism. Essential versus Non-Essential Amino Acids. Inborn Errors in Amino Acid Metabolism." (HTML)
 
Instruction: First, click on the link above, and study the "Essential versus Non-Essential Amino Acids" section, which provides a list of these amino acids.  Next, return to the table of contents at the beginning of the webpage, and select the links to and study the following sections: "Glutamate and Aspartate,” "Alanine and the Glucose-Alanine Cycle,”  "Cysteine,” "Tyrosine,” "Ornithine and Proline,” "Serine,” "Glycine," and "Aspartate/Asparagine and Glutamate/Glutamine."  Please note that these are the non-essential amino acids for humans.   
 
This resource will take approximately 2 hours 30 minutes to complete.
 
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5.6 Biosynthesis of Essential Amino Acids   5.6.1 Introduction   - Reading: BioMed Central: BMC Genomics; R. L. M. Guedes et al.’s “Amino Acids Biosynthesis and Nitrogen Assimilation Pathways: A Great Genomic Deletion during Eukaryotes Evolution” Link: BioMed Central: BMC Genomics; R. L. M. Guedes et al.’s “Amino Acids Biosynthesis and Nitrogen Assimilation Pathways: a Great Genomic Deletion during Eukaryotes Evolution” (HTML)
 
Instructions: Please note that this reading is optional.  Please click on the link above, and study the entire article.  Note that essential amino acids are not essential for all taxa.  Research suggests that mutations disrupting certain biosynthetic pathways for amino acids may persist as long as an organism can take in the missing amino acid in the diet.  
 
This resource will take approximately 3 hours to complete.
 
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5.6.2 Threonine and Lysine   - Reading: University of Wisconsin-Madison: Timothy Paustian’s “Synthesis of Amino Acids” Link: University of Wisconsin-Madison: Timothy Paustian’s “Synthesis of Amino Acids” (HTML)
 
Instructions: Please click on the link above, scroll down about 1/3 of the way to the “Threonine/lysine” section, and study this section, which describes the biosynthesis of threonine from oxaloacetate through aspartate semialdehyde as well as the biosynthesis of lysine from threonine.  
 
Studying this resource will take approximately 45 minutes to complete.

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5.6.3 Isoleucine, Valine, and Leucine   - Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" Link: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" (HTML)
 
Instructions: Please click on the link above, scroll down about half way to the "Branch Chain Amino Acids" heading, and study this entire section.  Isoleucine, valine, and leucine are branch chain amino acids. 
 
Studying this resource will take approximately 45 minutes to complete.
 
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5.6.4 Tryptophan, Phenylalanine, and Tyrosine   - Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" Link: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" (HTML)
 
Instructions: Please click on the link above, scroll down about half way to the "Aromatic Amino Acids" heading, and study this entire section.  Phenylalanine, tyrosine, and tryptophan are aromatic amino acids. 
 
Studying this resource will take approximately 45 minutes to complete.
 
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5.6.5 Histidine   - Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" Link: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" (HTML)
 
Instructions: Please click on the link above, scroll down toward the end of the webpage to the "Histidine" heading, and study this entire section, which describes the biosynthesis of histidine from PRPP through AICAR and imidazolglycerol phosphate.
 
This resource will take approximately 45 minutes to complete.
 
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5.6.6 Methionine   - Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" Link: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" (HTML)
 
Instructions: Please click on the link above, scroll down toward the end of the webpage to the "Methionine" heading, and study this entire section, which describes the biosynthesis of methionine from oxaloacetate through homoserine, using cysteine as a sulfur donor.
 
This resource will take approximately 45 minutes to complete.
 
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5.7 Clinical Significance of Amino Acid Metabolism   - Reading: The Medical Biochemistry Page: Michael W. King's "Urea Cycle Disorders" Link: The Medical Biochemistry Page: Michael W. King's "Urea Cycle Disorders" (HTML)
 
Instruction: Please click on the link above, and study this entire webpage.  Click on the enzyme names (red) in the diagram of the urea cycle to read more about the diseases.
 
Studying this resource will take approximately 2 hours to complete.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

  • Reading: The Medical Biochemistry Page: Michael W. King's "Defects in Amino Acid Metabolism" Link: The Medical Biochemistry Page: Michael W. King's "Defects in Amino Acid Metabolism" (HTML)
     
    Instruction: Please click on the link above, select the links to "Alkaptonuria,” "Maple Syrup Urine Disease, MSUD," and "Phenylketonuria,” and study these sections in their entirety.
     
    Studying this resource will take approximately 1 hour and 30 minutes to complete.
     
    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.