ࡱ> JLEFGHI bjbjߍ 0 [8YZ">+(<+<+<+, 6 9@BBBBBB,eznM;,,M;M;n><+<+>>>M;<+<+@>M;@>>fLpDФ|Ƹ.>D,)0YDߠ>ߠD>DXM;M;M;nn>M;M;M;YߠM;M;M;M;M;M;M;M;M; x:   BIOORGANIC CHEMISTRY PURPOSE OF COURSE Bioorganic chemistry studies the chemistry of organic biomolecules. Itis a rapidly growinginterdisciplinary fieldthat 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  HYPERLINK "http://www.saylor.org/site/wp-content/uploads/2012/05/Saylor-StudentHandbook.pdf" Saylor Student Handbook. Have completed the following courses:  HYPERLINK "http://www.saylor.org/courses/chem101/" CHEM101: General Chemistry I,  HYPERLINK "http://www.saylor.org/courses/chem102/" CHEM102: General Chemistry II,  HYPERLINK "http://www.saylor.org/courses/chem103/" CHEM103: Organic Chemistry I, and  HYPERLINK "http://www.saylor.org/courses/chem104/" CHEM104: Organic Chemistry II COURSE INFORMATION Welcome to CHEM204. Below, please find general information on this course and its requirements. Course Designer: Marianna Pintr, 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 Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/MB1index.html" Biochemistry of Metabolism - Dr. Michael W. Kings  HYPERLINK "http://themedicalbiochemistrypage.org/" The Medical Biochemistry Page - Michigan State University: Dr. William Reuschs  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/intro1.htm" Virtual Textbook of Organic Chemistry - Salman Khans  HYPERLINK "http://www.khanacademy.org/" 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  HYPERLINK "http://www.saylor.org/courses/chem103/" CHEM103: Organic Chemistry I and  HYPERLINK "http://www.saylor.org/courses/chem104/" 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  HYPERLINK "http://www.saylor.org/courses/bio305/" 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. Functional Groups in Biological Chemistry Reading: The Third Millennium Online: James Richard Fromms The Concept of Functional Groups Link: The Third Millennium Online: James Richard Fromms  HYPERLINK "http://www.3rd1000.com/chem301/chem301a.htm" 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 Reuschs Virtual Textbook of Organic Chemistry: Classification by Functional Group Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/react1.htm#rx3" 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 Universitys Modern Biology / Biochemistry Flash Tutorials Link: Carnegie Mellon Universitys  HYPERLINK "http://telstar.ote.cmu.edu/biology/supplements/functional-group/" 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 Reuschs Virtual Textbook of Organic Chemistry: Identifying Functional Groups Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Questions/General/functgrp2.htm" 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 Reuschs Virtual Textbook of Organic Chemistry: Identifying Functional Groups Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Questions/General/functgrp.htm" 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. Acids, Bases, Electrophiles, and Nucleophiles 1.2.1 Acidity and Basicity Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Acidity and Basicity Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/react1.htm#rx1b" 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 Reuschs Virtual Textbook of Organic Chemistry: Nucleophilicity and Basicity Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/react3.htm#rx10" 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 Academys Nucleophilicity (Nucleophile Strength) Link: Khan Academys  HYPERLINK "http://www.khanacademy.org/science/organic-chemistry/v/nucleophilicity--nucleophile-strength" 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 Academys Nucleophilicity vs. Basicity Link: Khan Academys  HYPERLINK "http://www.khanacademy.org/science/organic-chemistry/v/nucleophilicity-vs--basicity" 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. Mechanisms: Electrophilic Addition Reactions Reading: Chemguide: Jim Clarks Electrophilic Addition Link: Chemguide: Jim Clarks  HYPERLINK "http://www.chemguide.co.uk/mechanisms/eladd/whatis.html#top" 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. Mechanisms: Nucleophilic Substitution Reactions Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Mechanisms of Nucleophilic Substitution Reactions Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/alhalrx2.htm" 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. Mechanisms: Nucleophilic Carbonyl Addition Reactions Nucleophilic Addition Reactions Reading: Chemguide: Jim Clarks The Reduction of Aldehydes and Ketones Link: Chemguide: Jim Clarks  HYPERLINK "http://www.chemguide.co.uk/mechanisms/nucadd/reduce.html#top" 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. Alcohol Formation Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Aldehydes & Ketones Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/aldket1.htm#rx1" 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. Imine (Schiff Base) Formation Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: C. Formation of Imines and Related Compounds Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/aldket1.htm" \l "rx1b" 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. Acetal Formation Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: B. Acetal Formation Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/aldket1.htm#rx1a" 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 Reuschs Virtual Textbook of Organic Chemistry: The Mechanism of Acetal Formation Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Questions/MechPrb/actlmech.htm" 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. Conjugate (1, 4) Nucleophilic Additions Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: 3. Conjugate Addition Reactions Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/special2.htm#top4d" 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. Mechanisms: Nucleophilic Acyl Substitution Reactions Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: 1. Acyl Group Substitution Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/crbacid2.htm#react1" 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. Mechanisms: Carbonyl Condensation Reactions Reading: Michigan State University: William Reusch s Virtual Textbook of Organic Chemistry:  Reactions at the -Carbon Link: Michigan State University: William Reusch s Virtual Textbook of Organic Chemistry:   HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/crbacid3.htm#react5" Reactions at the -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 Reuschs Virtual Textbook of Organic Chemistry: Claisen Condensation Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Questions/Match/claisen.htm" 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. Mechanisms: Elimination Reactions Reading: Purdue Universitys Organic Reactions Link: Purdue Universitys  HYPERLINK "http://chemed.chem.purdue.edu/genchem/topicreview/bp/3organic/organic.html" 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. Oxidations and Reductions Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Oxidation and Reduction Reactions Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/react1.htm#rx2b" 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 Biomoleculesare organic moleculessynthesized 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. Chirality and Biological Chemistry Enantiomers Lecture: Khan Academys Introduction to Chirality, Chiral Examples 1, and Chiral Examples 2 Link: Khan Academys  HYPERLINK "http://www.khanacademy.org/science/organic-chemistry/v/introduction-to-chirality" Introduction to Chirality,  HYPERLINK "http://www.khanacademy.org/science/organic-chemistry/v/chiral-examples-1" Chiral Examples 1, and  HYPERLINK "http://www.khanacademy.org/science/organic-chemistry/v/chiral-examples-2" 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. Ophardts Virtual Chembook: Optical or Chiral Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/209optical.html" 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. Diastereomers, Epimers, and Meso Compounds Web Media: Khan Academys Stereoisomers, Enantiomers, Diastereomers, Constitutional Isomers, and Meso Compounds Link: Khan Academys  HYPERLINK "http://www.khanacademy.org/science/organic-chemistry/v/stereoisomers--enantiomers--diastereomers--constitutional-isomers-and-meso-compounds" 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. Ophardts Virtual Chembook: Cis Trans Isomers of Alkenes Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/209cistrans.html" 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. Prochirality Reading: International Union of Pure and Applied Chemistry: A. D. McNaught and A. Wilkinsons Compendium of Chemical Terminology, 2nd ed.: Prochirality Link: International Union of Pure and Applied Chemistry: A. D. McNaught and A. Wilkinsons Compendium of Chemical Terminology, 2nd ed.:  HYPERLINK "http://goldbook.iupac.org/P04859.html" 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. Biomolecules: Lipids Triacylglycerols, Waxes, and Phospholipids Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Lipids Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm" \l "fatacid"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. Ophardts Virtual Chembook: Fatty Acids Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/551fattyacids.html" 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. Other Lipids: Terpenoids, Steroids, and Prostaglandins Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Lipids Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm#prstgl" 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 -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. Ophardts Virtual Chembook: Prostaglandins Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/555prostagland.html" 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. Ophardts Virtual Chembook: Steroids Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/556steroids.html" 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. Biomolecules: Carbohydrates Carbohydrate Stereochemistry Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Carbohydrates Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/carbhyd.htm#carb1" 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. Ophardts Virtual Chembook: Carbohydrate Quiz Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/544carbohydrateQUIZ.html" 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. Monosaccharide Anomers Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Carbohydrates Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/carbhyd.htm#carb1" 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. Disaccharides and Polysaccharides Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Carbohydrates Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/carbhyd.htm#carb1" 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. Sugar Derivatives Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Carbohydrates Sugar and Polysaccharides Link: Rensselaer Polytechnic Institute: Joyce J. Diwan's " HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/sugar.htm#deriv" 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. Biomolecules: Amino Acids, Peptides, and Proteins Amino Acids Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Proteins, Peptides, & Amino Acids Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: " HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/proteins.htm#aacd1" Proteins, Peptides, & Amino Acids (HTML) Instructions: Please click on the link above, scroll down to  2. Natural -Amino Acids,  3. The Isoelectric Point, and "4. Other Natural Amino Acids," and read these sections in their entirety. In the  2. Natural -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. Ophardts Virtual Chembook: Review of Characteristics and Properties of Amino Acids Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/562review.html" 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. Peptides and Proteins Reading: John W. Kimball's Biology Pages: Proteins Link: John W. Kimball's Biology Pages:  HYPERLINK "http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Proteins.html" 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. Ophardts Virtual Chembook: Proteins - Introduction Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/565proteins.html" 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. Ophardts Virtual Chembook: Amino Acid Peptide Bonds Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/564peptide.html" 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. Biomolecules: Nucleic Acids DNA: Deoxyribonucleic Acid Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Nucleic Acids Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/nucacids.htm#nacd1" 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 Projects Nucleic Acids and the Genetic Material Problem Set 1 Link: The University of Arizona: The Biology Projects  HYPERLINK "http://www.biology.arizona.edu/molecular_bio/problem_sets/nucleic_acids/08q.html" 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. RNA: Ribonucleic Acid Reading: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry: Nucleic Acids Link: Michigan State University: William Reuschs Virtual Textbook of Organic Chemistry:  HYPERLINK "http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/nucacids.htm#nacd1" 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. Ophardts Virtual Chembook: DNA and RNA Introduction Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/580DNA.html" 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. Biomolecules: Enzymes, Coenzymes, and Coupled Reactions Enzymes Reading: National Center for Biotechnology Informations Bookshelf: Sunderland (MA): Sinauer Associates: G. M. Coopers The Cell: A Molecular Approach, 2nd edition: The Central Role of Enzymes as Biological Catalysts Link: National Center for Biotechnology Informations Bookshelf: Sunderland (MA): Sinauer Associates: G. M. Coopers The Cell: A Molecular Approach, 2nd edition:  HYPERLINK "http://www.ncbi.nlm.nih.gov/books/NBK9921/" 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. Ophardts Virtual Chembook: Role of Enzymes in Biochemical Reactions Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/570enzymes.html" 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. Ophardts Virtual Chembook: Enzyme Inhibitors Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/573inhibit.html" 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. 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. Coupled Reactions and High-Energy Compounds Reading: National Center for Biotechnology Informations Bookshelf: W. H. Freeman: Berg et al.s Biochemistry, 5th edition: Metabolism Is Composed of Many Coupled, Interconnecting Reactions Link: National Center for Biotechnology Informations Bookshelf: W. H. Freeman: Berg et al.s Biochemistry, 5th edition:  HYPERLINK "http://www.ncbi.nlm.nih.gov/books/NBK22439/" 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. Ophardts Virtual Chembook: Electron Transport Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/596electransport.html" 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. Test Your Understanding on the Structures of Biomolecules Assessment: Yakima Valley Community College: J. Lovelands Name the Biomolecule Link: Yakima Valley Community College: J. Lovelands  HYPERLINK "http://www2.yvcc.edu/Biology/109Modules/Modules/Biomolecules/NameTheBiomolecule.html" 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. Triacylglycerol Turnover 3.1.1 Triacylglycerol Hydrolysis Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Lipoproteins: Lipid Digestion & Transport Link: Rensselaer Polytechnic Institute: Joyce J. Diwans HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/lipoprot.htm"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. Diwans Lipid Catabolism: Fatty Acids & Triacylglycerols Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fatcatab.htm" 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. Triacylglycerol Resynthesis Reading: James Hutton Institute: William W. Christies Triacylglycerols Link: James Hutton Institute: William W. Christies  HYPERLINK "http://lipidlibrary.aocs.org/lipids/tag2/index.htm" 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. Triacylglycerol Catabolism: The Fate of Glycerol Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Glycolysis and Fermentation Link: Rensselaer Polytechnic Institute: Joyce J. Diwans HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/glycolysis.htm"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. Diwans Lipid Catabolism: Fatty Acids & Triacylglycerols Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fatcatab.htm" 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 -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. Diwans Fatty Acid Synthesis Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fasynthesis.htm" 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. Terpenoid Biosynthesis The Mevalonate Pathway To Isopentenyl Diphosphate Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Cholesterol Synthesis Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/cholesterol.htm" 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. The Deoxyxylulose Pathway to Isopentenyl Diphosphate Reading: National Center for Biotechnology Informations PubMed: Proceedings of the National Academy of Sciences of the United States of America: Felix Rohdichs 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 Informations PubMed: Proceedings of the National Academy of Sciences of the United States of America: Felix Rohdichs  HYPERLINK "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC149876/" 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 webpage above. Conversion of Isopentenyl Diphosphate to Terpenoids Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Cholesterol Synthesis Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/cholesterol.htm" 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. Steroid Biosynthesis Synthesis of Squalene and its Conversion to Lanosterol Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Cholesterol Synthesis Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/cholesterol.htm" 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. Conversion of Lanosterol to Cholesterol Reading: Rensselaer Polytechnic Institute: Joyce J. Diwan's "Cholesterol Synthesis" Link: Rensselaer Polytechnic Institute: Joyce J. Diwan's " HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/cholesterol.htm" 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. Clinical Significance of Lipid Metabolism. Reading: The Medical Biochemistry Page: Michael W. Kings Clinical Significance of Fatty Acids Link: The Medical Biochemistry Page: Michael W. Kings  HYPERLINK "http://themedicalbiochemistrypage.org/fatty-acid-oxidation.php#clinical" 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. Kings Clinical Significance of Lipoprotein Metabolism Link: The Medical Biochemistry Page: Michael W. Kings  HYPERLINK "http://themedicalbiochemistrypage.org/lipoproteins.php#clinical" 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. Digestion and Hydrolysis of Complex Carbohydrates Reading: University of Virginias Chapter 7: Carbohydrates Link: University of Virginias  HYPERLINK "http://web.virginia.edu/Heidi/chapter7/chp7.htm" 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 Goodmans Interconversion of Sugars Link: University of Kansas Medical Center: Scott Goodmans " HYPERLINK "http://www.kumc.edu/AMA-MSS/Study/carbohydrates.htm#interconversion" 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. Diwans Glycogen Metabolism Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/glycogen.htm" 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. Glucose Catabolism: Glycolysis Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Glycolysis and Fermentation Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/glycolysis.htm" 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. Transformations of Pyruvate Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Pyruvate Dehydrogenase & Krebs Cycle Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/krebs.htm" 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. 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. 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. The Citric Acid Cycle Reading: Clackamas Community College: Sue Egglings Citric Acid Cycle Link: Clackamas Community College: Sue Egglings  HYPERLINK "http://dl.clackamas.edu/ch106-06/citric.htm" 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-Gyrgyi 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. Glucose Biosynthesis: Gluconeogenesis Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Gluconeogenesis Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/gluconeo.htm" 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. The Pentose Phosphate Pathway Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Pentose Phosphate Pathway Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/pentose.htm" 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. Oxidative Phosphorylation Reading: The Medical Biochemistry Page: Michael W. Kings Biological Oxidations Link: The Medical Biochemistry Page: Michael W. Kings  HYPERLINK "http://themedicalbiochemistrypage.org/oxidative-phosphorylation.php" 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. Photosynthesis: The Reductive Pentose Phosphate (Calvin) Cycle Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Calvin Cycle Photosynthetic Carbon Reactions Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/dark.htm" 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. Clinical Significance of Carbohydrate Metabolism Reading: The Medical Biochemistry Page: Michael W. Kings Glycogen Storage Diseases Link: The Medical Biochemistry Page: Michael W. Kings  HYPERLINK "http://themedicalbiochemistrypage.org/glycogen.php#clinical" 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. Kings Metabolic Disorders Associated with the PPP Link: The Medical Biochemistry Page: Michael W. Kings  HYPERLINK "http://themedicalbiochemistrypage.org/pentose-phosphate-pathway.php#disorders" 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 acidsarebiomolecules that contain an amine group and a carboxylic acid group. They also contain a side chain that varies depending on the amino acid. In -amino acids, the amino group is on the carbon next to the carboxyl group; -amino acids are the building blocks for protein synthesis. Amino acids also play vital roles incoenzymes. 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. Protein Degradation Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Protein Degradation Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/protease.htm" 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. Deamination of Amino Acids Transamination of Amino Acids Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Amino Acid Catabolism: Nitrogen Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/amino.htm" 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. Oxidative Deamination of Glutamate Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Amino Acid Catabolism: Nitrogen Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/amino.htm" 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. Ophardts Virtual Chembook: Oxidative Deamination Reaction Link: Elmhurst College: Charles E. Ophardts Virtual Chembook:  HYPERLINK "http://www.elmhurst.edu/~chm/vchembook/632oxdeam.html" 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. The Urea Cycle Reading: Rensselaer Polytechnic Institute: Joyce J. Diwans Amino Acid Catabolism: Nitrogen Link: Rensselaer Polytechnic Institute: Joyce J. Diwans  HYPERLINK "http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/amino.htm" 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. Catabolism of Amino Acid Carbon Chains Reading: The Medical Biochemistry Page: Michael W. Kings Introduction to Amino Acid Metabolism. Essential versus Non-Essential Amino Acids: Inborn Errors in Amino Acid Metabolism Link: The Medical Biochemistry Page: Michael W. Kings  HYPERLINK "http://themedicalbiochemistrypage.org/amino-acid-metabolism.php#intro" 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. 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. Biosynthesis of Essential Amino Acids 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  HYPERLINK "http://www.biomedcentral.com/1471-2164/12/S4/S2" 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. Threonine and Lysine Reading: University of Wisconsin-Madison: Timothy Paustians Synthesis of Amino Acids Link: University of Wisconsin-Madison: Timothy Paustians  HYPERLINK "http://lecturer.ukdw.ac.id/dhira/Metabolism/aminoacids.html" 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. Isoleucine, Valine, and Leucine Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" Link: University of Wisconsin-Madison: Timothy Paustian's " HYPERLINK "http://lecturer.ukdw.ac.id/dhira/Metabolism/aminoacids.html" 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. 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 " HYPERLINK "http://lecturer.ukdw.ac.id/dhira/Metabolism/aminoacids.html" 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. Histidine Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" Link: University of Wisconsin-Madison: Timothy Paustian's " HYPERLINK "http://lecturer.ukdw.ac.id/dhira/Metabolism/aminoacids.html" 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. Methionine Reading: University of Wisconsin-Madison: Timothy Paustian's "Synthesis of Amino Acids" Link: University of Wisconsin-Madison: Timothy Paustian's " HYPERLINK "http://lecturer.ukdw.ac.id/dhira/Metabolism/aminoacids.html" 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. 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 " HYPERLINK "http://themedicalbiochemistrypage.org/ureacycledisorders.php" 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 " HYPERLINK "http://themedicalbiochemistrypage.org/aminoaciddiseases.php" 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 Nucleotidesarebuilding 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 anitrogenous 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. 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 " HYPERLINK "http://library.med.utah.edu/NetBiochem/pupyr/pp.htm" 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. 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 " HYPERLINK "http://library.med.utah.edu/NetBiochem/pupyr/pp.htm" 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. Purines: Adenosine and Guanosine Reading: University Of Utah: Carol N. Angstadt's "Purine and Pyrimidine Metabolism" Link: University Of Utah: Carol N. Angstadt's " HYPERLINK "http://library.med.utah.edu/NetBiochem/pupyr/pp.htm" 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 " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#intro" 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 " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#pyrimidine" 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 " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#dntp" 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 " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#thymine" 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. 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 " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#salvage" 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 " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#interconversion" 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. 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 "HYPERLINK "http://themedicalbiochemistrypage.org/vitamins.php" \l "fclinical"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. 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King's " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#puriclin" 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 " HYPERLINK "http://themedicalbiochemistrypage.org/nucleotide-metabolism.php#pyrimclin" 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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