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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
The Saylor Foundation 1
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
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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
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Readings: 2.5 hours
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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.
1.1
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)
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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
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“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
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webpage above.
1.2
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
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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.
1.3
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.
1.4
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
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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.
1.5
Mechanisms: Nucleophilic Carbonyl Addition Reactions
1.5.1 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.
1.5.2
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.
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1.5.3
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.
1.5.4
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
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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.
1.5.5
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.
1.6
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.
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1.7
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.
1.8
Mechanisms: Elimination Reactions
Reading: Purdue University’s Organic Reactions
Link: Purdue University’s “Organic Reactions” (HTML)
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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.
1.9
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
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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
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Sub-subunit 2.4.1: 2.5 hours
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Sub-subunit 2.4.2: 3.5 hours
 Subunit 2.5: 3.5 hours
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 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.
2.1
Chirality and Biological Chemistry
2.1.1
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
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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.
2.1.2
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.
The Saylor Foundation 15
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.
2.1.3
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.
2.2
Biomolecules: Lipids
2.2.1 Triacylglycerols, Waxes, and Phospholipids
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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.
2.2.2
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
The Saylor Foundation 17
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.
The Saylor Foundation 18
2.3
Biomolecules: Carbohydrates
2.3.1 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.
2.3.2
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
The Saylor Foundation 19
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.
2.3.3
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.
2.3.4
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 Nacetylneuraminic.
Studying this resource will take approximately 30 minutes to complete.
The Saylor Foundation 20
Terms of Use: Please respect the copyright and terms of use displayed on
the webpage above.
2.4
Biomolecules: Amino Acids, Peptides, and Proteins
2.4.1 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 αAmino Acids,” “3. The Isoelectric Point,” and "4. Other Natural Amino
Acids," and read these sections in their entirety. In the “2. Natural αAmino 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.
2.4.2
Peptides and Proteins
Reading: John W. Kimball's Biology Pages: “Proteins”
Link: John W. Kimball's Biology Pages: “Proteins” (HTML)
The Saylor Foundation 21
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.
2.5
Biomolecules: Nucleic Acids
2.5.1 DNA: Deoxyribonucleic Acid
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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.
2.5.2
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
The Saylor Foundation 23
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.
2.6
Biomolecules: Enzymes, Coenzymes, and Coupled Reactions
2.6.1 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 Saylor Foundation 24
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.
2.6.2
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.
2.6.3
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
The Saylor Foundation 25
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.
2.7
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
The Saylor Foundation 26
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.
3.1
Triacylglycerol Turnover
3.1.1 Triacylglycerol Hydrolysis
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Lipoproteins:
Lipid Digestion & Transport”
The Saylor Foundation 27
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.
3.1.2
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.
3.2
Triacylglycerol Catabolism: The Fate of Glycerol
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Glycolysis and
The Saylor Foundation 28
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.
The Saylor Foundation 29
Terms of Use: Please respect the copyright and terms of use displayed on the
webpage above.
3.5
Terpenoid Biosynthesis
3.5.1 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.
3.5.2
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.
Terms of Use: Please respect the copyright and terms of use displayed on
The Saylor Foundation 30
the webpage above.
3.5.3
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.
3.6
Steroid Biosynthesis
3.6.1 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.
3.6.2
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"
The Saylor Foundation 31
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.
3.7
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.
The Saylor Foundation 32
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.
4.1
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.
The Saylor Foundation 33
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.
4.2
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
The Saylor Foundation 34
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.
4.3
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.
4.3.1
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.
4.3.2
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.
4.4
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.
The Saylor Foundation 35
Terms of Use: Please respect the copyright and terms of use displayed on the
webpage above.
4.5
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.
4.6
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.
4.7
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.
The Saylor Foundation 36
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.
4.8
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.
4.9
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.
The Saylor Foundation 37
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 αamino 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 nonessential 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.
The Saylor Foundation 38

5.1
Identify the toxic amino acid breakdown product, which is converted to a less
toxic product during the Urea Cycle.
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.
5.2
Deamination of Amino Acids
5.2.1 Transamination of Amino Acids
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid
Catabolism: Nitrogen”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid
Catabolism: Nitrogen” (HTML)
Instruction: Please click on the link above, select “Transaminase (Amino
Transferase)” under the “Contents of this page” heading, and study this
section up until “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.
5.2.2
Oxidative Deamination of Glutamate
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid
Catabolism: Nitrogen”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid
Catabolism: Nitrogen” (HTML)
Instruction: Please click on the link above, select the “Deamination of
amino acids" link under the “Contents of this page” heading, and study this
The Saylor Foundation 39
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.
5.3
The Urea Cycle
Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid
Catabolism: Nitrogen”
Link: Rensselaer Polytechnic Institute: Joyce J. Diwan’s “Amino Acid Catabolism:
Nitrogen” (HTML)
Instruction: Please click on the link above, select the links to “Urea Cycle” and
“Other Roles of Urea Cycle Intermediates” under the “Contents of this page”
heading, and study these sections in their entirety.
Studying this resource will take approximately 2 hours to complete.
Terms of Use: Please respect the copyright and terms of use displayed on the
webpage above.
5.4
Catabolism of Amino Acid Carbon Chains
Reading: The Medical Biochemistry Page: Michael W. King’s “Introduction to
Amino Acid Metabolism. Essential versus Non-Essential Amino Acids: Inborn
Errors in Amino Acid Metabolism”
The Saylor Foundation 40
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.
5.5
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.”
5.6
Biosynthesis of Essential Amino Acids
5.6.1 Introduction
Reading: BioMed Central: BMC Genomics; R. L. M. Guedes et al.’s
“Amino Acids Biosynthesis and Nitrogen Assimilation Pathways: A Great
Genomic Deletion during Eukaryotes Evolution”
Link: BioMed Central: BMC Genomics; R. L. M. Guedes et al.’s “Amino
Acids Biosynthesis and Nitrogen Assimilation Pathways: a Great Genomic
Deletion during Eukaryotes Evolution” (HTML)
Instructions: Please note that this reading is optional. Please click on the
link above, and 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.
5.6.2
Threonine and Lysine
The Saylor Foundation 41
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.
5.6.3
Isoleucine, Valine, and Leucine
Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis
of Amino Acids"
Link: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of
Amino Acids" (HTML)
Instructions: Please click on the link above, scroll down about half way to
the "Branch Chain Amino Acids" heading, and 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.
5.6.4
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.”
The Saylor Foundation 42
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.
5.6.5
Histidine
Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis
of Amino Acids"
Link: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of
Amino Acids" (HTML)
Instructions: Please click on the link above, scroll down toward the end of
the webpage to the "Histidine" heading, and 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.
5.6.6
Methionine
Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis
of Amino Acids"
Link: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of
Amino Acids" (HTML)
Instructions: Please click on the link above, scroll down toward the end of
the webpage to the "Methionine" heading, and 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.
5.7 Clinical Significance of Amino Acid Metabolism
Reading: The Medical Biochemistry Page: Michael W. King's "Urea Cycle
Disorders"
The Saylor Foundation 43
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.
The Saylor Foundation 44

6.1
List structural features of ribonucleotides and deoxyribonucleotides.
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.
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 complete.
Terms of Use: Please respect the copyright and terms of use displayed
on the webpage above.
6.1.3
Purines: Adenosine and Guanosine
Reading: University Of Utah: Carol N. Angstadt's "Purine and
Pyrimidine Metabolism"
The Saylor Foundation 45
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)
The Saylor Foundation 46
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.
The Saylor Foundation 47
Terms of Use: Please respect the copyright and terms of use displayed
on the webpage above.
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)
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.
6.6
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
The Saylor Foundation 48
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.
The Saylor Foundation 49