COURSE TITLE - Saylor Academy
BIOORGANIC CHEMISTRY
|PURPOSE OF COURSE |
Bioorganic chemistry studies the chemistry of organic biomolecules. It is a rapidly growing interdisciplinary field that combines organic chemistry and biochemistry. Please recall that organic chemistry investigates all molecules that contain carbon and hydrogen, and biochemistry focuses on the network of molecular pathways in the cell. Bioorganic chemistry employs organic chemistry to explain how enzymes catalyze the reactions of metabolic pathways, and why metabolites react the way they do. Bioorganic chemistry aims to expand organic-chemical research on structures, synthesis, and kinetics in a biological direction.
This one-semester course will cover several advanced chemistry topics and will discuss the chemistry behind biological processes. The course begins by introducing you to the mechanisms behind the most common biological chemical reactions (Unit 1). You will then take a closer look at the metabolic processes of biomolecules. You will apply your knowledge of the structural features of organic molecules to biomolecules (Unit 2). The next four units will cover the chemistry of metabolic processes in the cell: lipid metabolism (Unit 3), carbohydrate metabolism (Unit 4), amino acid metabolism (Unit 5), and nucleotide metabolism (Unit 6). The medical significance of the relevant deficiencies of these pathways will be discussed as well.
|COURSE REQUIREMENTS |
In order to take this course you must:
✓ Have access to a computer.
✓ Have continuous broadband Internet access.
✓ Have the ability/permission to install plug-ins or software (e.g., Adobe Reader or Flash).
✓ Have the ability to download and save files and documents to a computer.
✓ Have the ability to open Microsoft files and documents (.doc, .ppt,
✓ .xls, etc.).
✓ Be competent in the English language.
✓ Have read the Saylor Student Handbook.
✓ Have completed the following courses: CHEM101: General Chemistry I, CHEM102: General Chemistry II, CHEM103: Organic Chemistry I, and CHEM104: Organic Chemistry II
|COURSE INFORMATION |
Welcome to CHEM204. Below, please find general information on this course and its requirements.
Course Designer: Marianna Pintér, PhD
Primary Resources: This course is composed of a range of different free, online materials. However, the course makes primary use of the following materials:
- Dr. Joyce Diwan’s Biochemistry of Metabolism
- Dr. Michael W. King’s The Medical Biochemistry Page
- Michigan State University: Dr. William Reusch’s Virtual Textbook of Organic Chemistry
- Salman Khan’s Khan Academy
Requirements for Completion: In order to complete this course, you will need to work through each unit and all of its assigned materials. Please pay special attention to Units 1 and 2, as these lay the groundwork for understanding the more advanced, exploratory material presented in the latter units. You will also need to complete:
- Subunit 1.1 Assessments
- Subunit 1.5.4 Assessment
- Subunit 2.1.1 Assessment
- Subunit 2.1.2 Assessment
- Subunit 2.2.1 Assessment
- Subunit 2.4.1 Assessment
- Subunit 2.4.2 Assessment
- Subunit 2.5.1 Assessment
- Subunit 2.5.2 Assessment
- Subunit 2.6.1 Assessment
- Subunit 2.6.3 Assessment
- The Final Exam
Please note that you will only receive an official grade on your Final Exam. However, in order to adequately prepare for this exam, you will need to work through the problem sets within the above-listed assessments.
In order to pass this course, you will need to earn a 70% or higher on the Final Exam. Your score on the exam will be tabulated as soon as you complete it. If you do not pass the exam, you may take it again.
Time Commitment: This course should take you a total of approximately 139 hours to complete. Each unit includes a “time advisory” that lists the amount of time you are expected to spend on each subunit. It may be useful to take a look at these time advisories and determine how much time you have over the next few weeks to complete each unit and to then set goals for yourself. For example, Unit 1 should take you approximately 26.25 hours to complete. Perhaps you can sit down with your calendar and decide to complete subunit 1.1 (estimated at 4.5 hours) on Monday night; subunit 1.2 (estimated at 3.5 hours) on Tuesday night; subunits 1.3 and 1.4 (estimated at 4.5 hours) on Wednesday night; etc.
Tips/Suggestions: As noted in the “Course Requirements,” there are prerequisites for this course. It may be helpful to review CHEM103: Organic Chemistry I and CHEM104: Organic Chemistry II before you begin this course. If you find the discussion of the clinical significance of metabolism fascinating in this course, you might consider taking BIO305: Genetics.
Please make sure to take comprehensive notes as you work through each resource. These notes will serve as a useful review as you study for your Final Exam.
|LEARNING OUTCOMES |
Upon successful completion of this course, the student will be able to:
• Identify and characterize lipids, carbohydrates, amino acids, and nucleic acids.
• Recognize chiral organic molecules, and explain their biological significance.
• Explain the process of electrophilic and nucleophilic reactions, redox reactions, and enzyme catalyzed reactions.
• Define the role of coenzymes and allosteric regulators in enzyme catalyzed reactions.
• Compare and link terpenoid and steroid biosynthesis.
• Compare and contrast the biosynthesis and the break down of biomolecules in the cell.
• Predict the products of substitution, elimination, condensation, and redox reactions.
• Design enzyme catalyzed reactions that lead to high-energy compound products.
• Explain why certain lipids and amino acids are essential while others are not.
• Determine the significance of fermentation during anaerobic metabolism.
• Explain why certain metabolic pathways are called “cycles.”
• Explain what happens if a eukaryotic cell lacks oxalic acid, ribulose bisphosphate, or ornithine.
• Compare and contrast the Citric Acid Cycle and the Calvin Cycle.
|CONTENT OUTLINE |
UNIT 1: common mechanisms in bioorganic chemistry
Time Advisory: This unit should take you approximately 24.5 hours to complete.
□ Subunit 1.1: 4.5 hours
□ Readings: 2.5 hours
□ Web Media: 1 hour
□ Assessment: 1 hour
□ Subunit 1.2: 4 hours
□ Sub-subunit 1.2.1: 0.5 hour
□ Sub-subunit 1.2.2: 3.5 hours
□ Subunit 1.3: 0.5 hour
□ Subunit 1.4: 2.5 hours
□ Subunit 1.5: 5 hours
□ Sub-subunit 1.5.1: 0.5 hour
□ Sub-subunit 1.5.2: 0.5 hour
□ Sub-subunit 1.5.3: 1 hour
□ Sub-subunit 1.5.4: 1.5 hours
□ Sub-subunit 1.5.5: 1.5 hours
□ Subunit 1.6: 3 hours
□ Subunit 1.7: 3 hours
□ Subunit 1.8: 1 hour
□ Subunit 1.9: 1 hour
The reaction mechanism is the step-by-step sequence of events in a chemical reaction. It includes breaking chemical bonds, describing transition state intermediates, and making chemical bonds. In this unit, you will start with an overview of the functional groups of organic molecules. Next, you will study the mechanisms of nucleophilic substitution, electrophilic addition, condensation, elimination, and redox reactions. The goal is to highlight the fact that these reactions go forward only if the reactants meet specific structural requirements.
Understanding the mechanisms of these reactions is necessary, because they reveal the potential of certain enzymes to speed up similar reactions. Knowledge of reaction mechanisms also provides a basis for the design of pharmaceutical compounds, which manipulate the yield of reactions, and has implications in the treatment of metabolic diseases.
Learning Outcomes:
Upon successful completion of this unit, the student will be able to:
• Explain the processes of electrophilic and nucleophilic reactions.
• Identify redox reactions.
• Predict the products of substitution, elimination, condensation, and redox reactions.
1. Functional Groups in Biological Chemistry
Reading: The Third Millennium Online: James Richard Fromm’s “The Concept of Functional Groups”
Link: The Third Millennium Online: James Richard Fromm’s “The Concept of Functional Groups” (HTML)
Instructions: Please click on the link above, and study this entire webpage, starting at the beginning and continuing until the end of the disulfide group section. The basic structural characteristics of the functional groups are summarized here. Alcohols, aldehydes, ketones, carboxylic acids, amines, mercaptans, and esters are the most commonly discussed bioorganic molecules in this course. While all sugars are alcohols, some of them are aldehydes (reducing sugars) and others are ketones. Amino acids have both amino and carboxylic functional groups; glycerol and fatty acids in fats and phospholipids, as well as the monomers of DNA and RNA, are joined with ester bonds. The amino acid cysteine has a thiol group, which is essential for the stabilization of protein structures with disulfide bridges. Functional groups play an essential role in the active sites of enzymes as well (i.e. the thiol group in the active site of thiol proteases and asparagine in carboxypeptidase).
Reading and note-taking will take approximately 2 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: Classification by Functional Group”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Classification by Functional Group” (HTML)
Instructions: Please click on the link above, and study the “Classification by Functional Group” section on this webpage. It summarizes the reactivity of the functional groups in table format. You may want to return to this table when learning about specific examples of these reactions in later units of this course.
This resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Web Media: Carnegie Mellon University’s “Modern Biology / Biochemistry Flash Tutorials”
Link: Carnegie Mellon University’s “Modern Biology / Biochemistry Flash Tutorials” (HTML)
Instructions: Please click on the link above to access this is a functional group tutorial. You will find a table on this page with the name and the structural formula of non-polar and polar functional groups in the “Functional Groups” column. The “Properties” column provides you with several options to choose from. When you click on an option, the corresponding examples in the “Functional Group” column will be highlighted (i.e. clicking on “non-polar” highlights the methyl and the phenyl groups in the table). Additionally, if you click on one of the properties, the last column will change from “Examples” to “About non-polar,” and you can read a brief description of the non-polar functional groups. Please take your time to carefully study the correlations between the properties, functional groups, and definitions in this tutorial.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Identifying Functional Groups”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Identifying Functional Groups” (HTML)
Instructions: Please click on the link above, read the instructions at the top of the webpage, and complete the assessment to check how well you recognize functional groups. You can check whether your responses are correct or incorrect by clicking on the “Check Answer” button. Please complete the entire quiz before you hit the “View Answers” button to see the complete answer key. This is the first part of the functional groups problem set.
This assessment should take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Identifying Functional Groups”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Identifying Functional Groups” (HTML)
Instructions: Please click on the link above, read the instructions at the top of the webpage, and complete the assessment to check how well you recognize functional groups. You can check whether your response is correct or incorrect by clicking on the “Check Answer” button. Please complete the entire quiz before you hit the “View Answers” button to see the complete answer key. This is the second part of the functional groups problem set.
This assessment should take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Acids, Bases, Electrophiles, and Nucleophiles
1.2.1 Acidity and Basicity
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Acidity and Basicity”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Acidity and Basicity” (HTML)
Instructions: Please click on the link above, and study the “Acidity and Basicity” section on this webpage for a review of acidity and basicity.
This resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
1.2.2 Nucleophilicity and Basicity
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleophilicity and Basicity”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleophilicity and Basicity” (HTML)
Instructions: Please click on the link above, and study the “Nucleophilicity and Basicity Factors in Organic Reactions” and “Acid Base Catalysis” sections on this webpage. Pay particular attention to the definition of Nucleophilicity as well as the figures that show bonding of electrophilic and nucleophilic sites in reactant molecules.
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.
Lecture: Khan Academy’s “Nucleophilicity (Nucleophile Strength)”
Link: Khan Academy’s “Nucleophilicity (Nucleophile Strength)” (YouTube)
Instructions: Please click on the link above, and take notes as you watch this video lecture (14 minutes). The video explains nucleophilicity and how to predict nucleophile strength. Listen to the presentation carefully two or three times until you are able to explain what nucleophilicity is and how to predict nucleophile strength.
Viewing this lecture several times and pausing to take notes should take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Lecture: Khan Academy’s “Nucleophilicity vs. Basicity”
Link: Khan Academy’s “Nucleophilicity vs. Basicity” (YouTube)
Instructions: Please click on the link above, and take notes as you watch the video (13 minutes). Listen to the presentation carefully two or three times as needed until you are able to compare and contrast nucleophilicity and basicity yourself.
Viewing this lecture several times and pausing to take notes should take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
3. Mechanisms: Electrophilic Addition Reactions
Reading: Chemguide: Jim Clark’s “Electrophilic Addition”
Link: Chemguide: Jim Clark’s “Electrophilic Addition” (HTML)
Instructions: Please click on the link above, and study this webpage for a general overview of Electrophilic addition.
Reading and taking notes will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
4. Mechanisms: Nucleophilic Substitution Reactions
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Mechanisms of Nucleophilic Substitution Reactions”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Mechanisms of Nucleophilic Substitution Reactions” (YouTube)
Instructions: Please click on the link above, and study this entire webpage. Note the energy profile of nucleophilic substitutions. Take advantage of the animations that are linked to the SN1 and SN2 substitutions; to access these, press the “Click Here” buttons at the end of the SN1 Mechanism and SN2 Mechanism sections.
Studying this resource and note-taking 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. Mechanisms: Nucleophilic Carbonyl Addition Reactions
1. Nucleophilic Addition Reactions
Reading: Chemguide: Jim Clark’s “The Reduction of Aldehydes and Ketones”
Link: Chemguide: Jim Clark’s “The Reduction of Aldehydes and Ketones” (HTML)
Instructions: Please click on the link above, and study this webpage to learn about the reduction of aldehydes and ketones.
This resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Alcohol Formation
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Aldehydes & Ketones”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Aldehydes & Ketones” (HTML)
Instructions: Please click on the link above, and study the “A. Hydration and Hemiacetal Formation” section on this page. Make sure to select “Click Here” at the end of the “Stable Hydrates and Hemiacetals” section, and study these examples. Note that hemiacetals and acetals form when simple sugars undergo a spontaneous rearrangement in an aqueous solution.
Studying this resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
3. Imine (Schiff Base) Formation
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “C. Formation of Imines and Related Compounds”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “C. Formation of Imines and Related Compounds” (HTML)
Instructions: Please click on the link above, and study the “C. Formation of Imines and Related Compounds” section on this webpage. You may wish to click on any embedded hyperlinks to read about associated content. Clicking on the grey “Imine Formation” button opens a new window with an animation of the imine formation reaction. Also, selecting the “Click Here” link at the end of this section of text will take you to a webpage with examples of other carbonyl derivatives.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
4. Acetal Formation
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “B. Acetal Formation”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “B. Acetal Formation” (HTML)
Instructions: Please click on the link above, and study the “B. Acetal Formation” section on this webpage. Note that hemiacetals and acetals form when simple sugars undergo a spontaneous rearrangement in an aqueous solution. You may wish to click on any embedded hyperlinks to read about associated content.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “The Mechanism of Acetal Formation”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “The Mechanism of Acetal Formation” (HTML)
Instructions: Please click on the link above, read the instructions for this assessment, and answer all the questions provided. This exercise will guide you step-by-step through the mechanism of acetal formation. You will receive immediate feedback after each response.
This assessment should take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
5. Conjugate (1, 4) Nucleophilic Additions
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “3. Conjugate Addition Reactions”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “3. Conjugate Addition Reactions” (HTML)
Instructions: Please click on the link above, and study the "3. Conjugate Addition Reactions" section on this webpage. Click on the grey "Nucleophilic Addition" button to view an animation of the reaction mechanism. As needed, click on any embedded hyperlinks to read about associated content.
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.
6. Mechanisms: Nucleophilic Acyl Substitution Reactions
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “1. Acyl Group Substitution”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “1. Acyl Group Substitution” (HTML)
Instructions: Please click on the link above, and study the “1. Acyl Group Substitution” section on this webpage. Select the “Click Here” links to “Mechanism of Ester Cleavage” and “Carbonyl Reactivity and IR Stretching Frequency” for examples and further discussion. Note that ester cleavage is the first step of fat catabolism. As needed, click on any embedded hyperlinks to read about associated content.
Studying this resource and note-taking should take approximately 3 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
7. Mechanisms: Carbonyl Condensation Reactions
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Reactions at the α-Carbon”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Reactions at the α-Carbon” (HTML)
Instructions: Please click on the link above, scroll down to “2. Claisen Condensation,” and read this particular section on this webpage. Press the grey “Structural Analysis” button to highlight the nucleophilic donor and electrophilic acceptor in this reaction. Click on the “Reaction Mechanism” button to display the breaking and forming of chemical bonds. Finally, click on the “Claisen Condensations” button for an example of the general form of Claisen condensation, which is the carbon-carbon bond forming reaction that occurs between two esters.
Studying this resource and note-taking should take approximately 2 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Claisen Condensation”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Claisen Condensation” (HTML)
Instructions: Please click on the link above to access the assessment, and read the instructions at the top of the webpage. On this webpage, you will find five examples of Claisen products. The exercise asks you to identify the enolate donor and carbonyl acceptor of these products from a list. Click on “Check Answers” after you match all products with their donor and acceptor. The “View Answers” button lets you see the correct answers.
This assessment will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
8. Mechanisms: Elimination Reactions
Reading: Purdue University’s Organic Reactions
Link: Purdue University’s “Organic Reactions” (HTML)
Instructions: Please click on the link above, select “Elimination Reactions” in the box at the top of the webpage, and study this entire section.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
9. Oxidations and Reductions
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Oxidation and Reduction Reactions”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Oxidation and Reduction Reactions” (HTML)
Instructions: Please click on the link above, and study the “Oxidation and Reduction Reactions” section on this webpage. Redox reactions are incorporated into both catabolic and anabolic pathways (i.e. into glycolysis and gluconeogenesis).
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Unit 2: BioMolecules
Time Advisory: This unit should take you approximately 35.5 hours to complete.
□ Subunit 2.1: 5 hours
□ Sub-subunit 2.1.1: 2.5 hours
□ Sub-subunit 2.1.2: 1.5 hours
□ Sub-subunit 2.1.3: 1 hour
□ Subunit 2.2: 5 hours
□ Sub-subunit 2.2.1: 2.5 hours
□ Sub-subunit 2.2.2: 2.5 hours
□ Subunit 2.3: 8 hours
□ Sub-subunit 2.3.1: 3.5 hours
□ Sub-subunit 2.3.2: 2 hours
□ Sub-subunit 2.3.3: 2 hours
□ Sub-subunit 2.3.4: 0.5 hour
□ Subunit 2.4: 6 hours
□ Sub-subunit 2.4.1: 2.5 hours
□ Sub-subunit 2.4.2: 3.5 hours
□ Subunit 2.5: 3.5 hours
□ Subunit 2.6: 5 hours
□ Sub-subunit 2.6.1: 2.5 hours
□ Sub-subunit 2.6.3: 2.5 hours
□ Subunit 2.7: 1 hour
Biomolecules are organic molecules synthesized in living organisms. All biomolecules are organic, meaning that they are primarily composed of carbon, hydrogen, nitrogen, and oxygen. Some biomolecules contain other atoms (i.e. phosphorus and/or sulfur). Biomolecules vary in size. Some are large polymeric moles, such as proteins, polysaccharides, and nucleic acids, while others are small, such as metabolites, lipids, and the monomers of the polymers mentioned above.
In Organic Chemistry, you learned about organic compounds; this unit will focus on carbohydrates, lipids, amino acids, and nucleic acids that occur in the cell. In Organic Chemistry, you also learned about stereoisomerism; this unit will focus on stereoisomers that are produced by the cell, including chiral molecules and cis-trans isomers. You may recall that some reactions involving organic compounds produce specific stereoisomers. The stereoselectivity of reactions in the cell is more pronounced, because enzymes that catalyze biochemical reactions are chiral themselves. Only one enzyme enantiomer exists in the cell and has biological activity. Life on Earth is chiral.
Learning Outcomes:
Upon successful completion of this unit, the student will be able to:
• Identify and characterize lipids, carbohydrates, amino acids, and nucleic acids.
• Recognize chiral organic molecules, and explain their biological significance.
• Recognize chiral organic molecules, and explain their biological significance.
• Compare and contrast the progress of chemical reactions with and without catalysis.
• Define the function of coenzymes.
• Design enzyme catalyzed reactions leading to high-energy compound products.
1. Chirality and Biological Chemistry
1. Enantiomers
Lecture: Khan Academy’s “Introduction to Chirality,” “Chiral Examples 1,” and “Chiral Examples 2”
Link: Khan Academy’s “Introduction to Chirality,” “Chiral Examples 1,” and “Chiral Examples 2” (YouTube)
Instructions: Please click on the links above, and take notes as you watch these videos in their entirety (7 minutes, 12 minutes, and 11 minutes, respectively). Listen to these lectures carefully two or three times until you are able to explain what chirality is and how to recognize a chiral molecule. Note that chirality is dependent on the presence of at least one carbon atom, which binds to four different functional groups.
Viewing these lectures several times and pausing to take notes should take approximately 2 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Optical or Chiral”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Optical or Chiral” (HTML)
Instructions: Please click on the link above, read the “Introduction to Chiral or Optical Isomers,” and then answer all of the quiz questions in the “Chiral or Optical Isomers” column of the table on a separate piece of paper. Then, click on the drop-down menu next to each question to check your answers. Note that chiral compounds are also called “optical isomers” or “optically active” substances, because the isomers have the ability to rotate the plane of the polarized light. Optical activity is measured in polarimeter, and some microscopes are equipped with polarimeter as well.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Diastereomers, Epimers, and Meso Compounds
Web Media: Khan Academy’s “Stereoisomers, Enantiomers, Diastereomers, Constitutional Isomers, and Meso Compounds”
Link: Khan Academy’s “Stereoisomers, Enantiomers, Diastereomers, Constitutional Isomers, and Meso Compounds” (YouTube)
Instructions: Please click on the link above, and take notes as you watch the video (14 minutes). Listen to the presentation carefully two or three times until you are able to explain what diastereomers are and how to recognize a chiral molecule and a diastereomer. Note that diastereomers include cis-trans isomers, non-enetiomeric chiral compounds, and epimers; epimers have more than one chiral center, but differ only in one; and meso compounds have an internal plane of symmetry.
Viewing this lecture several times and pausing to take notes should take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Cis – Trans Isomers of Alkenes”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Cis – Trans Isomers of Alkenes” (HTML)
Instructions: Please click on the link above, read the introductory information on the webpage, and then on a separate piece of paper, answer all of the quiz questions at the end of the webpage. Finally, click on the drop-down menu next to each question to check your answers.
This assessment should take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
3. Prochirality
Reading: International Union of Pure and Applied Chemistry: A. D. McNaught and A. Wilkinson’s Compendium of Chemical Terminology, 2nd ed.: “Prochirality”
Link: International Union of Pure and Applied Chemistry: A. D. McNaught and A. Wilkinson’s Compendium of Chemical Terminology, 2nd ed.: “Prochirality” (HTML)
Instructions: Please click on the link above, and study this entire webpage. Take advantage of the “Interactive Link Maps” on the bottom of the page; in particular, make sure to select the links to “First Level,” “Second Level,” and “Third Level.”
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Biomolecules: Lipids
1. Triacylglycerols, Waxes, and Phospholipids
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Lipids”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Lipids” (HTML)
Instructions: Please click on the link above, and study the “1. Fatty Acids,” “3. Fats and Oils,” “4. Waxes,” and “5. Phospholipids” sections on this webpage. Click on the link to “Unusual Fatty Acids” in section “1. Fatty Acids.” Also, select any embedded hyperlinks to examine lipid models. Note that fatty acids may have double bonds. The waste majority of naturally occurring unsaturated fatty acids are cis isomers; trans-fats are byproducts of industrial vegetable oil solidifying methods. Trans-fat consumption coincides with an increased rate of cardiovascular disease.
Studying this resource and taking notes will take approximately 2 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Fatty Acids”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Fatty Acids” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, answer all quiz questions in the “Fatty Acids” column of the table. Then, click on the drop-down menu next to each question to check your answers.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Other Lipids: Terpenoids, Steroids, and Prostaglandins
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Lipids”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Lipids” (HTML)
Instructions: Please click on the link above, scroll down to “Prostaglandins Thromboxanes & Leukotrienes,” “Terpenes,” and “Steroids,” and read these sections in their entirety. Click on any embedded hyperlinks to read about associated content, such as information about lipid models, and click on the grey “Toggle Structures” button to reveal additional structural formulas. Note that the arachidonic acid is an ω-6 fatty acid; it is an essential fatty acid, which is necessary for prostaglandin and leukotriene production.
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.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Prostaglandins”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Prostaglandins” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, answer all of the quiz questions in the “Prostaglandins” column of the table. Then, click on the drop-down menu next to each question to check your answers.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Steroids”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Steroids” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, answer all of the quiz questions in the “Prostaglandins” column of the table. Then, click on the drop-down menu next to each question to check your answers.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
3. Biomolecules: Carbohydrates
1. Carbohydrate Stereochemistry
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Carbohydrates”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Carbohydrates” (HTML)
Instructions: Please click on the link above, and study the “1. Glucose” and “3. Ketoses” sections on this webpage. Please note the number of optical hexose isomers, including diastereomers. Make sure to click on any embedded links to read about associated content.
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.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Carbohydrate Quiz”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Carbohydrate Quiz” (HTML)
Instructions: Please note that this assessment is optional. Please click on the link above to access the assessment, and read the instructions at the top of the webpage. Basically, you should click on a graphic link in the “Static Graphic Image” column to view the structural formula of a carbohydrate compound. On a separate piece of paper, identify the compound and determine whether it is an alpha or a beta epimer. Finally, click on the drop-down menus labeled “Answer” to reveal the correct answer to the quiz question.
This assessment will take approximately 2 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Monosaccharide Anomers
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Carbohydrates”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Carbohydrates” (HTML)
Instructions: Please click on the link above, scroll down to “4. Anomeric Forms of Glucose,” “5. Cyclic Forms of Monosaccharides,” and “6. Glycosides,” and read these sections on this webpage. Note that the cyclic anomers are hemiacetals. Make sure to click on any embedded links or any links labeled “Click Here” for further discussions on associated content.
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.
3. Disaccharides and Polysaccharides
Reading: Michigan State University: William Reusch’s “Virtual Textbook of Organic Chemistry: Carbohydrates”
Link: Michigan State University: William Reusch’s “Virtual Textbook of Organic Chemistry: “Carbohydrates” (HTML)
Instructions: Please click on the link above, scroll down to “7. Disaccharides” and “8. Polysaccharides,” and study these sections on this webpage. Make sure to click on any embedded links or any links labeled “Click Here” for further discussions on associated content.
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.
4. Sugar Derivatives
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Carbohydrates – Sugar and Polysaccharides”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan's "Carbohydrates – Sugar and Polysaccharides" (HTML)
Instructions: Please click on the link above, and study the description of the four diagrams in the “Sugar Derivatives” section. It may help to reproduce the diagrams, sketching these yourself, to better understand the structure of each sugar: sugar alcohol, sugar acid, amino sugar, and N-acetylneuraminic.
Studying this resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
4. Biomolecules: Amino Acids, Peptides, and Proteins
1. Amino Acids
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Proteins, Peptides, & Amino Acids”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: "Proteins, Peptides, & Amino Acids” (HTML)
Instructions: Please click on the link above, scroll down to “2. Natural α-Amino Acids,” “3. The Isoelectric Point,” and "4. Other Natural Amino Acids," and read these sections in their entirety. In the “2. Natural α-Amino Acids” figure, compare the structures of tyrosine, cysteine, lysine, and aspartic acid.
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.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Review of Characteristics and Properties of Amino Acids”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Review of Characteristics and Properties of Amino Acids” (HTML)
Instructions: Please click on the link above, and on a separate piece of paper, complete the questions in the “Polar or Non-Polar” and “Acidic, Basic, or Neutral” columns. After you have identified each structure, you can check whether your responses are correct by clicking on the drop-down menus marked “Answer.”
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Peptides and Proteins
Reading: John W. Kimball's Biology Pages: “Proteins”
Link: John W. Kimball's Biology Pages: “Proteins” (HTML)
Instructions: Please click on the link above, and study this entire webpage. Next, follow the links at the bottom of this page to learn “How Proteins Get Their Shape,” “Primary Structure,” “Secondary Structure,” “Tertiary Structure,” and “Quaternary Structure.” Please take advantage of the many embedded links on this page.
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.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Proteins - Introduction”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Proteins – Introduction” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, complete the two quiz sections in the “Proteins – Introduction” column. Finally, select the “Answer” drop down menu to view the correct answer.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Amino Acid Peptide Bonds”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Amino Acid Peptide Bonds” (HTML)
Instructions: Please click on the link above, read the text, and on a separate piece of paper, complete all quiz questions in the “Amino Acid Peptide Bonds” column. You can check whether your responses are correct by clicking on the “Answer Graphic” link.
This resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
5. Biomolecules: Nucleic Acids
1. DNA: Deoxyribonucleic Acid
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleic Acids”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleic Acids” (HTML)
Instruction: Please click on the link above, scroll down to “2. The Chemical Nature of DNA” and “4. The Secondary Structure of DNA,” and read these sections on this webpage. Please note that the backbone of the nucleic acid polymer is made of phosphodiester bonds. Make sure to click on any embedded links to read about associated content and explore any interactive figures in the text.
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.
Assessment: University of Arizona: The Biology Project’s “Nucleic Acids and the Genetic Material – Problem Set 1”
Link: The University of Arizona: The Biology Project’s “Nucleic Acids and the Genetic Material – Problem Set 1” (HTML)
Instructions: Please click on the link above, and complete this multiple choice quiz from questions 8-15. Clicking on a response will lead you to a tutorial page where your response will be accepted, if it is correct. If you make a mistake, you will find a short explanation on the page. In this case where you have selected an incorrect answer, please return to the problem, and try answering the question again.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright ant terms of use displayed on the webpage above.
2. RNA: Ribonucleic Acid
Reading: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleic Acids”
Link: Michigan State University: William Reusch’s Virtual Textbook of Organic Chemistry: “Nucleic Acids” (HTML)
Instructions: Please click on the link above, and study the “3. RNA, a Different Nucleic Acid” section on this webpage. Click on the “Components of Nucleic Acids” table to reveal the structure of a short RNA polymer.
This resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “DNA and RNA Introduction”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “DNA and RNA Introduction” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, complete the two quiz sections in the “DNA and RNA Introduction” column. You can check whether your responses are correct by selecting the “Answer” drop down menu.
This resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
6. Biomolecules: Enzymes, Coenzymes, and Coupled Reactions
1. Enzymes
Reading: National Center for Biotechnology Information’s Bookshelf: Sunderland (MA): Sinauer Associates: G. M. Cooper’s The Cell: A Molecular Approach, 2nd edition: “The Central Role of Enzymes as Biological Catalysts”
Link: National Center for Biotechnology Information’s Bookshelf: Sunderland (MA): Sinauer Associates: G. M. Cooper’s The Cell: A Molecular Approach, 2nd edition: “The Central Role of Enzymes as Biological Catalysts” (HTML)
Instruction: Please click on the link above, and read the entire webpage to learn about the central role of enzymes as biological catalysts. Note that this reading also covers the topic outlined in sub-subunit 2.6.2.
Reading and note-taking 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.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Role of Enzymes in Biochemical Reactions”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Role of Enzymes in Biochemical Reactions” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, complete the quiz questions in the “Role of Enzymes in Biochemical Reactions” column. You can check whether your responses are correct by clicking on the drop-down menu “Answer” boxes.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Enzyme Inhibitors”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Enzyme Inhibitors” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, complete the quiz questions in the “Enzyme Inhibitors” column. You can check whether your responses are correct by clicking on the drop-down menu “Answer” boxes.
This assessment will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Coenzymes
Note: Please note that this topic is covered by the reading assigned below sub-subunit 2.6.1. In particular, please review the “Coenzymes” section of the reading. Note that coenzymes are essential for the activity of many enzymes.
3. Coupled Reactions and High-Energy Compounds
Reading: National Center for Biotechnology Information’s Bookshelf: W. H. Freeman: Berg et al.’s Biochemistry, 5th edition: “Metabolism Is Composed of Many Coupled, Interconnecting Reactions”
Link: National Center for Biotechnology Information’s Bookshelf: W. H. Freeman: Berg et al.’s Biochemistry, 5th edition: “Metabolism Is Composed of Many Coupled, Interconnecting Reactions” (HTML)
Instruction: Please click on the link above, and read this entire text. Please note that anabolic reactions invest energy into building complex molecules, and this energy is provided by catabolic reactions.
Reading and taking notes should take approximately 2 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Assessment: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Electron Transport”
Link: Elmhurst College: Charles E. Ophardt’s Virtual Chembook: “Electron Transport” (HTML)
Instructions: Please click on the link above, read the introductory text, and on a separate piece of paper, complete the quiz questions in the “Electron Transport” column. You can check whether your responses are correct by clicking on the drop-down menu “Answer” boxes.
This assessment should take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Test Your Understanding on the Structures of Biomolecules
Assessment: Yakima Valley Community College: J. Loveland’s “Name the Biomolecule”
Link: Yakima Valley Community College: J. Loveland’s “Name the Biomolecule” (HTML)
Instructions: Please click on the link above to access the assessment. You will find the structural formula of a biomolecule in the center of the page and the names of 14 biomolecule groups on the right side. Drag and drop the name of the biomolecule into the black box under the structural formula. You will receive immediate feedback. If your answer is correct, the next structural formula will appear and you can choose again. If you make a mistake, it will be marked “Incorrect,” and you can try again. You can also bypass a structural formula if you do not know the answer by clicking on the “Next” button at the top. This website has a large database, so expect to see different structural formulas and several different structures for the same compound groups.
This assessment will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Unit 3: lipid metabolism
Time Advisory: This unit should take you approximately 20.5 hours to complete.
□ Subunit 3.1: 2.5 hours
□ Subunit 3.2: 1 hour
□ Subunit 3.3: 2 hours
□ Subunit 3.4: 3 hours
□ Subunit 3.5: 5 hours
□ Sub-subunit 3.5.1: 2 hours
□ Sub-subunit 3.5.2: 1.5 hours
□ Sub-subunit 3.5.3: 1.5 hours
□ Subunit 3.6: 1.5 hours
□ Subunit 3.7: 5.5 hours
The term “lipid” refers to a broad group of hydrophobic biomolecules. This family of compounds includes fats, waxes, steroids, fat-soluble vitamins (such as vitamins A, D, E, and K), and phospholipids, just to name a few. While most lipids are hydrophobic, some are amphiphilic, meaning that they possess a hydrophilic head and a hydrophobic tail. This property enables them to form vesicles and membranes in aqueous environments. Hydrophobic chemicals can be dissolved into the membrane. The primary biological functions of lipids in living organisms include plasma membrane building, energy storage, enzyme regulation, and signaling. This unit explains the biosynthesis and biodegradation of lipids.
Learning Outcomes:
Upon successful completion of this unit, the student will be able to:
• Explain lipid transport within the cell.
• Compare and contrast fatty acid biosynthesis and fat catabolism in the cell.
• Compare and link terpenoid and steroid biosynthesis.
• Explain why certain lipids are essential and others are not.
1. Triacylglycerol Turnover
3.1.1 Triacylglycerol Hydrolysis
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Lipoproteins: Lipid Digestion & Transport”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Lipoproteins: Lipid Digestion & Transport” (HTML)
Instruction: Please click on the link above, and select the “Lipid Digestion” under the “Contents of this page” heading, read this entire section, and study the structures with the figures provided.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Lipid Catabolism: Fatty Acids & Triacylglycerols”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Lipid Catabolism: Fatty Acids & Triacylglycerols” (HTML)
Instruction: Please click on “Fatty Acids & Triacylglycerols” under the “Contents of this page” heading, read the text in this section, and study the structures in the figures provided.
Studying this resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Triacylglycerol Resynthesis
Reading: James Hutton Institute: William W. Christie’s “Triacylglycerols”
Link: James Hutton Institute: William W. Christie’s “Triacylglycerols” (HTML)
Instruction: Please click on the link above, and study the “1. Biosynthesis of Triacylglycerols” and “5. Triacylglycerol Metabolism in Plants and Yeasts” sections on this webpage.
Studying this resource should take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
1. Triacylglycerol Catabolism: The Fate of Glycerol
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Glycolysis and Fermentation”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Glycolysis and Fermentation” (HTML)
Instruction: Please click on the link above, select the “Glycolysis Pathway” link under the “Contents of this page” heading, scroll down to the “4. Aldolase” section, and read this entire section. Glycerol is converted to dihydroxyacetone phosphate (see sub-subunit 3.1.1 of this course), which in turn is an intermediate of glycolysis. Thus, glycerol can be used in the glycolytic pathway.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
3.3 Triacylglycerol Catabolism: Fatty Acid Oxidation
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Lipid Catabolism: Fatty Acids & Triacylglycerols”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Lipid Catabolism: Fatty Acids & Triacylglycerols” (HTML)
Instruction: Please click on the link above, and study the “b-Oxidation Pathway” and “ATP Production” sections on this page. Note that “b-Oxidation” is generally called β-oxidation.
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.
3.4 Fatty Acid Biosynthesis
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Fatty Acid Synthesis”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Fatty Acid Synthesis” (HTML)
Instruction: Please click on the link above, and study this entire webpage. Chain elongation is a series of Claisen condensations and redox reactions catalyzed by multi-subunit fatty acid synthesis.
Studying this resource will take approximately 3 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
5. Terpenoid Biosynthesis
1. The Mevalonate Pathway To Isopentenyl Diphosphate
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Cholesterol Synthesis”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Cholesterol Synthesis” (HTML)
Instruction: Please click on the link above, and then select the “HMG-CoA formation and conversion to mevalonate” link under “Contents of this page,” and study this section. The section ends with the production of mevalonate.
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.
2. The Deoxyxylulose Pathway to Isopentenyl Diphosphate
Reading: National Center for Biotechnology Information’s PubMed: Proceedings of the National Academy of Sciences of the United States of America: Felix Rohdich’s “The Deoxyxylulose Phosphate Pathway of Isoprenoid Biosynthesis: Studies on the Mechanisms of the Reactions Catalyzed by IspG and IspH Protein”
Link: National Center for Biotechnology Information’s PubMed: Proceedings of the National Academy of Sciences of the United States of America: Felix Rohdich’s “The Deoxyxylulose Phosphate Pathway of Isoprenoid Biosynthesis: Studies on the Mechanisms of the Reactions Catalyzed by IspG and IspH Protein” (HTML)
Instruction: Please click on the link above, and read this entire publication. Focus on the “Experimental Procedures,” “Results,” and “Discussion” sections as well as “Figure 1: The deoxyxylulose phosphate pathway of isoprenoid biosynthesis.”
Studying this resource will take approximately 1 hour and 30 minutes to complete.
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3. Conversion of Isopentenyl Diphosphate to Terpenoids
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Cholesterol Synthesis”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Cholesterol Synthesis” (HTML)
Instruction: Please click on the link above, and select "Conversion of mevalonate to isoprenoid precursors" under the “Contents of this page” heading, and study the four images in this section.
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.
6. Steroid Biosynthesis
1. Synthesis of Squalene and its Conversion to Lanosterol
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Cholesterol Synthesis”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Cholesterol Synthesis” (HTML)
Instruction: Please click on the link above, and then select “Synthesis of squalene and its conversion to lanosterol” under the “Contents of this page” heading. Study the pathway summary image in this section, starting with the text after the heading “Squalene Synthase” to the end of the section.
Studying this resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Conversion of Lanosterol to Cholesterol
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan's "Cholesterol Synthesis"
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan's "Cholesterol Synthesis"
Instruction: Please click on the link above, and then select the "Conversion of Lanosterol to Cholesterol" link under the “Content on this page” heading. Read this section up until “Isoprenoids,” focusing specifically on the first image of the section. Then, under the “Content on this page,” click on "Regulation of cholesterol synthesis and pharmaceutical intervention," and study the entire section.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
3. Clinical Significance of Lipid Metabolism.
Reading: The Medical Biochemistry Page: Michael W. King’s “Clinical Significance of Fatty Acids”
Link: The Medical Biochemistry Page: Michael W. King’s “Clinical Significance of Fatty Acids” (HTML)
Instruction: Please click on the link above, and read the entire “Clinical Significance of Fatty Acids” section. Also, select the hyperlinks to “MCAD Deficiency” and “Refsum Disease” to read about associated content.
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 “Clinical Significance of Lipoprotein Metabolism”
Link: The Medical Biochemistry Page: Michael W. King’s “Clinical Significance of Lipoprotein Metabolism” (HTML)
Instruction: Please click on the link above, and read the “Clinical Significances of Lipoprotein Metabolism,” “Lipoprotein(a) and Atherogenesis,” and “Pharmacologic Intervention” sections in their entirety. Select the link to the “Aspirin Page” from the “Pharmacologic Intervention” section to read about associated content.
Studying this resource will take approximately 3.5 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Unit 4: carbohydrate metabolism
Time Advisory: This unit should take you approximately 23 hours to complete.
□ Subunit 4.1: 5.5 hours
□ Subunit 4.2: 2 hours
□ Subunit 4.3: 2 hours
□ Subunit 4.4: 2 hours
□ Subunit 4.5: 2 hours
□ Subunit 4.6: 2 hours
□ Subunit 4.7: 3 hours
□ Subunit 4.8: 2 hours
□ Subunit 4.9: 2.5 hours
Carbohydrates have the general formula CnH2nOn. Autotrophs synthesize carbohydrates (i.e. plants synthesize simple sugar from carbon dioxide and water through photosynthesis). The central simple carbohydrate is glucose, because it is delivered by the circulatory system as an energy source to all cell types in most multicellular organisms. Carbohydrates may be stored in polysaccharide form (i.e. glycogen and starch, converted to energy or used as building blocks in a variety of biosynthetic pathways). Other polysaccharides (i.e. chitin and cellulose) are structural and used for cellular support. This unit explains the major catabolic and anabolic pathways of carbohydrate metabolism.
Learning Outcomes:
Upon successful completion of this unit, the student will be able to:
• Identify the biological pathway which leads to the synthesis of ATP in all living cells investigated so far.
• Determine the significance of fermentation during anaerobic metabolism.
• Describe the effect of allosteric regulators on the activity of phosphofructokinase in glycolysis.
• Explain why certain metabolic pathways are called “cycles.”
• Explain what happens in a eukaryotic cell and lacks oxalic acid or ribulose bisphosphate.
• Compare and contrast the Citric Acid Cycle and the Calvin Cycle.
1. Digestion and Hydrolysis of Complex Carbohydrates
Reading: University of Virginia’s “Chapter 7: Carbohydrates”
Link: University of Virginia’s “Chapter 7: Carbohydrates” (HTML)
Instruction: Please click on the link above, scroll down to “7.4 Polysaccharides,” and study this entire section. Glucose and the metabolic intermediates of glycolysis are an energy source that all cells can use. Complex carbohydrates are hydrolyzed, and simple sugars are converted to glucose in the vertebrate liver.
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: University of Kansas Medical Center: Scott Goodman’s “Interconversion of Sugars”
Link: University of Kansas Medical Center: Scott Goodman’s "Interconversion of Sugars” (HTML)
Instruction: Please click on the link above, and study this section on “Interconversion of Sugars.” Note that only glucose and the metabolic intermediates of glycolysis are used to produce energy.
Studying this resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Glycogen Metabolism”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Glycogen Metabolism” (HTML)
Instruction: Please click on the link above, and study this entire webpage. Please note that animal cells store glucose in glycogen. Glycogen is a glucose polymer. Glycogen synthesis and glycogen breakdown are reciprocally regulated as blood sugar levels are changing.
Studying this resource will take approximately 3 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Glucose Catabolism: Glycolysis
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Glycolysis and Fermentation”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Glycolysis and Fermentation” (HTML)
Instruction: Please click on the link above, and read the entire webpage for information on the glycolysis pathway, fermentation, and regulation of glycolysis. Please note that this resource also covers the topic outlined in sub-subunit 4.3.1.
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.
3. Transformations of Pyruvate
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Pyruvate Dehydrogenase & Krebs Cycle”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Pyruvate Dehydrogenase & Krebs Cycle” (HTML)
Instruction: Please click on the link above, and read the entire webpage to learn about pyruvate dehydrogenase and the Krebs cycle. Please note that this reading also covers the topic outlined in sub-subunit 4.3.2.
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.
1. Conversion of Pyruvate to Lactate or Ethanol
Note: This topic is covered by the reading assigned below subunit 4.2. Please focus on the “Fermentation” section, and study the description of the two pathways in this section.
2. Conversion of Pyruvate to Acetyl CoA
Note: This topic is covered by the reading assigned below subunit 4.3. In particular, focus on the “Roles of acetyl-coenzyme A” section.
4. The Citric Acid Cycle
Reading: Clackamas Community College: Sue Eggling’s “Citric Acid Cycle”
Link: Clackamas Community College: Sue Eggling’s “Citric Acid Cycle” (HTML)
Instruction: Please click on the link above, and study the entire webpage. Note that the Citric Acid Cycle is also called the Szent-Györgyi – Krebs Cycle.
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.
5. Glucose Biosynthesis: Gluconeogenesis
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Gluconeogenesis”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Gluconeogenesis” (HTML)
Instruction: Please click on the link above, and study the entire page to learn about gluconeogenesis.
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.
6. The Pentose Phosphate Pathway
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Pentose Phosphate Pathway”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Pentose Phosphate Pathway” (HTML)
Instruction: Please click on the link above, and study this webpage to learn about the pentose phosphate pathway.
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.
7. Oxidative Phosphorylation
Reading: The Medical Biochemistry Page: Michael W. King’s “Biological Oxidations”
Link: The Medical Biochemistry Page: Michael W. King’s “Biological Oxidations” (HTML)
Instruction: Please click on the link above, and study the text in its entirety to learn about biological oxidations.
Studying this resource will take approximately 3 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
8. Photosynthesis: The Reductive Pentose Phosphate (Calvin) Cycle
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Calvin Cycle – Photosynthetic Carbon Reactions”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Calvin Cycle – Photosynthetic Carbon Reactions” (HTML)
Instruction: Please click on the link above, and study this entire webpage to learn about the Calvin Cycle.
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.
4. Clinical Significance of Carbohydrate Metabolism
Reading: The Medical Biochemistry Page: Michael W. King’s “Glycogen Storage Diseases”
Link: The Medical Biochemistry Page: Michael W. King’s “Glycogen Storage Diseases” (HTML)
Instruction: Please click on the link above, and study this section and the “Table of Glycogen Storage Diseases.”
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.
Reading: The Medical Biochemistry Page: Michael W. King’s “Metabolic Disorders Associated with the PPP”
Link: The Medical Biochemistry Page: Michael W. King’s “Metabolic Disorders Associated with the PPP” (HTML)
Instruction: Please click on the link above, and study the “Metabolic Disorders Associated with the PPP” section, as well as the “Chronic Granulomatous Disease” and “Erythrocytes and the Pentose Phosphate Pathway” sections that follow.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
Unit 5: amino acid metabolism
Time Advisory: This unit should take you approximately 20 hours to complete.
□ Subunit 5.1: 2.5 hours
□ Subunit 5.2: 2 hours
□ Subunit 5.3: 2 hours
□ Subunit 5.4: 4 hours
□ Subunit 5.6: 6 hours
□ Sub-subunit 5.6.1: 3 hours
□ Sub-subunit 5.6.2: 0.5 hour
□ Sub-subunit 5.6.3: 0.5 hour
□ Sub-subunit 5.6.4: 1 hour
□ Sub-subunit 5.6.5: 0.5 hour
□ Sub-subunit 5.6.6: 0.5 hour
□ Subunit 5.7: 3.5 hours
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. Amino acids that should be taken by the diet because the biosynthetic pathway is absent or cannot produce enough are call essential amino acids.
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 NH3 product 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.
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.
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.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
2. Deamination of Amino Acids
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 “Chime Exercises.”
Studying this resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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 by moving the cursor over the arrows in these enzyme catalyzed reactions.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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 to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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, and read the entire webpage. To cover this topic, please focus on the “Amino Acid Catabolism” column of the table that appears at the top of the webpage to study the breakdown pathways of these amino acids. Note that this resource also covers the topic outlined for subunit 5.5.
Studying this resource will take approximately 4 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
5. Biosynthesis of Nonessential Amino Acids
Note: This topic is covered by the reading assigned below subunit 5.4. In particular, focus on the text below the section “Essential versus Non-Essential Amino Acids.”
6. Biosynthesis of Essential Amino Acids
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 read 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.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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”
Instructions: Please click on the link above, scroll down about 1/3 of the way to the “Threonine/lysine” section, and read 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 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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 read this entire section. Branch chain amino acids are isoleucine, valine, and leucine.
Studying this resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
4. Tryptophan, Phenylalanine, and Tyrosine (4)
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 read this entire section. Make sure to read these sections that describe each of these amino acids: “Phenylalanine,” “Tyrosine,” and “Tryptophan.”
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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 read this entire section, which describes the biosynthesis of histidine from PRPP through AICAR and imidazolglycerol phosphate.
This resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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 read this entire section, which describes the biosynthesis of methionine from oxaloacetate through homoserine, using cysteine as a sulfur donor.
This resource will take approximately 30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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.
Unit 6: nucleotide metabolism
Time Advisory: This unit should take you approximately 15.5 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: 1.5 hours
□ Subunit 6.6: 3.5 hours
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.
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.
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.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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 complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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, FAICAR) to see their chemical structures. Note that the inosine monophosphate (IMP) is the primary nucleotide product of de novo nucleotide 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.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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)
Instruction: 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 sub-subunit 6.4.2 dTMP for the pathway making deoxythymidine monophosphate.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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)
Instruction: 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 complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
6. 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)
Instruction: Please click on the link above, and study the “Catabolism and Salvage of Purine Nucleotides” section. Pay particular attention to the figure of 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.
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 "Interconversion of the Nucleotides"
Link: The Medical Biochemistry Page: Michael W. King's "Interconversion of the Nucleotides" (HTML)
Instruction: 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 20-30 minutes to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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)
Instruction: 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.
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 "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 molecular pathways are disabled by these 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 "Clinical Significances of Pyrimidine Metabolism"
Link: The Medical Biochemistry Page: Michael W. King's "Clinical Significances of Pyrimidine Metabolism" (HTML)
Instruction: 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 molecular pathway is disabled by this disease.
Studying this resource will take approximately 1 hour to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.
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