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CHEM204: Bioorganic Chemistry

Unit 6: Nucleotide Metabolism   Nucleotides are building blocks of RNA and DNA.  They are also a part of a number of high energy molecules, including ATP, which is the energy currency in all known cells.  Nucleotides function as cofactors in the regulation of enzyme activities.  A nucleotide is composed of a nitrogenous base, a sugar, and phosphate groups.  In this unit, you will study the biosynthesis and biodegradation of nucleotides. 

Unit 6 Time Advisory
This unit should take you approximately 16.5 hours to complete.

☐    Subunit 6.1: 2.5 hours

☐    Subunit 6.2: 3 hours

☐    Subunit 6.3: 3 hours

☐    Subunit 6.4: 2 hours

☐    Subunit 6.5: 2.5 hours

☐    Subunit 6.6: 3.5 hours

Unit6 Learning Outcomes
Upon successful completion of this unit, the student will be able to:
- Compare and contrast the synthesis and breakdown of nucleotides. - List structural features of ribonucleotides and deoxyribonucleotides.

6.1 Nucleotide Catabolism   6.1.1 Hydrolysis of Polynucleotides   - Reading: University Of Utah: Carol N. Angstadt's "Purine and Pyrimidine Metabolism" Link: University Of Utah: Carol N. Angstadt's "Purine and Pyrimidine Metabolism" (HTML)
 
Instruction: Please click on the link above, and then select "Hydrolysis of Polynucleotides" in the "Topics" section, located on top of the page.  Study the "Hydrolysis of Polynucleotides" section, including the catalyzed reaction, which is revealed when you click on the "Reaction" button.  
 
Studying this resource will take approximately 30 minutes to complete.
                    
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6.1.2 Pyrimidines: Cytidine, Uridine, and Thymidine   - Reading: University Of Utah: Carol N. Angstadt's "Purine and Pyrimidine Metabolism" Link: University Of Utah: Carol N. Angstadt's "Purine and Pyrimidine Metabolism" (HTML)
 
Instruction: Please click on the link above, and then select the "Pyrimidine Catabolism" link in the "Topics" section, located on top of the page.  Study the "Pyrimidine Catabolism" section, including the catalyzed reaction, which is revealed when you click on the "Reaction" button.

 Studying this resource will take approximately 1 hour to
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6.1.3 Purines: Adenosine and Guanosine   - Reading: University Of Utah: Carol N. Angstadt's "Purine and Pyrimidine Metabolism" Link: University Of Utah: Carol N. Angstadt's "Purine and Pyrimidine Metabolism" (HTML)
 
Instruction: Please click on the link above, and then select the "Purine Catabolism" link in the "Topics" section, located on top of the page.  Study the "Purine Catabolism" section, including the catalyzed reaction, which is revealed when you click on the "Reaction" button.
 
Studying this resource will take approximately 1 hour to complete.
 
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6.2 Biosynthesis of Purine Ribonucleotides   - Reading: The Medical Biochemistry Page: Michael W. King's "Introduction" Link: The Medical Biochemistry Page: Michael W. King's "Introduction" (HTML)
 
Instruction: Please click on the link above, and study the "Introduction,” "Purine Nucleotide Biosynthesis," and "Regulation of Purine Nucleotide Synthesis" sections.  In the “Purine Nucleotide Biosynthesis” section, hover your mouse over the abbreviated names of the intermediates (PRA, GAR, FGAR, FGAM, AIR, CAIR, SAICAR, AICAR, and FAICAR) to see their chemical structures.  Note that the inosine monophosphate (IMP) is the primary nucleotide product of de novonucleotide synthesis.  IMP is built on a phosphorylated ribose derivative (PRPP).  Adenosine monophosphate (AMP) and guanosine monophosphate (GMP) are derived from IMP in consecutive reactions of the biosynthetic pathways.  
 
Studying this resource will take approximately 3 hours to complete.
 
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6.3 Biosynthesis of Pyrimidine Ribonucleotides   - Reading: The Medical Biochemistry Page: Michael W. King's "Pyrimidine Nucleotide Biosynthesis" Link: The Medical Biochemistry Page: Michael W. King's "Pyrimidine Nucleotide Biosynthesis" (HTML)
 
Instruction: Please click on the link above, and study the “Pyrimidine Nucleotide Biosynthesis” section.  On the Synthesis of carbamoyl phosphate by CPS I figure, hover your mouse over the reactant (carbamoyl phosphate) and intermediates (CA, DHO, orotate, OMP); doing so will reveal the structure of these molecules.  Please note that UTP is the primary nucleotide product; CTP is synthesized from UTP. Studying this resource will take approximately 3 hours to complete.

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6.4 Biosynthesis of Deoxyribonucleotides   6.4.1 dADP, dGDP, dCTP, and dUDP   - Reading: The Medical Biochemistry Page: Michael W. King's "Formation of Deoxyribonucleotides" Link: The Medical Biochemistry Page: Michael W. King's "Formation of Deoxyribonucleotides" (HTML)
 
Instructions: Please click on the link above, and study the “Formation of Deoxyribonucleotides” section.  Note that thymine deoxynucleotide is not produced in these pathways.  See the next Subunit 6.4.2 dTMP for the pathway making deoxythymidine monophosphate.  
 
Studying this resource will take approximately 1 hour to complete.
 
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6.4.2 dTMP   - Reading: The Medical Biochemistry Page: Michael W. King's "Synthesis of the Thymine Nucleotides" Link: The Medical Biochemistry Page: Michael W. King's "Synthesis of the Thymine Nucleotides" (HTML)
 
Instructions: Please click on the link above, and study the “Synthesis of the Thymine Nucleotides” section.  Note that deoxyuridine monophosphate (dUMP) is needed for the production of deoxythymidine monophosphate (dTMP).  

 Studying this resource will take approximately 1 hour to
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6.5 Salvage of Nucleotides   - Reading: The Medical Biochemistry Page: Michael W. King's "Catabolism and Salvage of Purine Nucleotides" Link: The Medical Biochemistry Page: Michael W. King's "Catabolism and Salvage of Purine Nucleotides" (HTML)
 
Instructions: Please click on the link above, and study the “Catabolism and Salvage of Purine Nucleotides” section, which ends with the "Purine Nucleotide Cycle.”  Note that salvage pathways supply nucleotides for DNA replication, gene transcription, and coenzyme synthesis.  
 
Studying this resource will take approximately 1 hour to complete.
 
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  • Reading: The Medical Biochemistry Page: Michael W. King’s “Catabolism and Salvage of Pyrimidine Nucleotides” Link: The Medical Biochemistry Page: Michael W. King's "Catabolism and Salvage of Pyrimidine Nucleotides" (HTML)
     
    Instructions: Please click on the link above, and study the “Catabolism and Salvage of Pyrimidine Nucleotides” section.  Note that salvage pathways supply nucleotides for DNA replication, gene transcription, and coenzyme synthesis.
     
    This resource will take approximately 1 hour to complete.
     
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  • Reading: The Medical Biochemistry Page: Michael W. King's "Interconversion of the Nucleotides" Link: The Medical Biochemistry Page: Michael W. King's "Interconversion of the Nucleotides" (HTML)
     
    Instructions: Please click on the link above, and study the “Interconversion of Nucleotides” section.  Note that salvage pathways supply nucleotides for DNA replication, gene transcription, and coenzyme synthesis.  
     
    Studying this resource will take approximately 30 minutes to complete.
     
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6.6 Inborn Errors in Nucleotide Metabolism   - Reading: The Medical Biochemistry Page: Michael W. King's "Clinical Significances of Folate Deficiency" Link: The Medical Biochemistry Page: Michael W. King's "Clinical Significances of Folate Deficiency" (HTML)
 
Instructions: Please click on the link above, and study the “Clinical Significances of Folate Deficiency” section.  
 
Studying this resource will take approximately 30 minutes to complete.
 
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  • Reading: The Medical Biochemistry Page: Michael W. King's "Clinical Significances of Purine Metabolism" Link: The Medical Biochemistry Page: Michael W. King's "Clinical Significances of Purine Metabolism" (HTML)
     
    Instruction: Please click on the link above, and study the “Clinical Significances of Purine Metabolism” section.  In the “Disorders of Purine Metabolism” table, select the links to "Gout,” "Lesh-Nyhan Syndrome,” "SCID," and "von Gierke Disease" to learn which dysfunctional molecular pathways are responsible for these diseases.  
     
    Studying this resource will take approximately 2 hours to complete.
     
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  • Reading: The Medical Biochemistry Page: Michael W. King's "Clinical Significances of Pyrimidine Metabolism" Link: The Medical Biochemistry Page: Michael W. King's "Clinical Significances of Pyrimidine Metabolism" (HTML)
     
    Instructions: Please click on the link above, and study the “Clinical Significances of Pyrimidine Metabolism” section.  In the “Disorders of Pyrimidine Metabolism” table, select the link to "OTS Deficiency" to learn which dysfunctional molecular pathways are responsible for these diseases.
     
    Studying this resource will take approximately 1 hour to complete.
     
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