Chemistry 131: Introduction to Organic and Biochemistry Spring 2018 Chemistry 131 is the second of a 2 quarter series covering the fundamental concepts of inorganic, organic, and biological chemistry and is intended primarily for students in various health-related disciplines. Chem 131 requires completion of Chem 121 or its equivalent, as Chem 131 utilizes the principals developed in Chem 121 as the basis for interpretation of organic and biochemistry. The first half of chemistry 131 takes a functional group approach to organic chemistry, with an emphasis on structure, isomerism, physical properties and reactivity. Straightforward mechanistic details will be provided where important, and a discussion of basic stereochemistry is included. The foundations of IUPAC nomenclature will be established, and expanded as the principal organic functional groups are considered in turn. The second half of chemistry 131 covers the basic physical and chemical aspects of the principal molecules of biochemistry, with a focus on structural macromolecules and those compounds from which energy can be derived. In addition, basic storage, expression and control of cellular information will be introduced. The course will be biased towards mammalian biochemistry, and as such communication and regulatory considerations in complex multicellular systems will also be introduced. This 2 nd and final course in the GOB series will continue to be presented within a framework of practical relevance, providing a chemical scaffold on which to interpret biological phenomena and further health chemistry studies. Instructor: Shane Hendrickson Office: Eller-Fox 3009 Website: http://commons.wvc.edu/shendrickson Phone: (509) 682-6747 e-mail: shendrickson@wvc.edu Official Office hours: M-W 2-4 p.m. 1 Required Text 2 : Fundamentals of General, Organic, and Biological Chemistry, McMurry, Ballantine, et. al. 7 th edition, Prentice Hall (2013). Time & Location Lecture: M, T, Th, F from 8:00 to 8:50 am, Eller-Fox 3015 Laboratory: W from 8:00 9:50 am, Eller-Fox 3018 1 But generally available please see my schedule posted on the commons website 2 The Chem 131 lab experiments are available at the bookstore for $5. You are also required to purchase a pair of chemical safety goggles, also available at the bookstore
Grading: The Grading for Chem 131 will be as follows 3 100 Point Examinations, lowest devalued to 50 points o 2 exams(100 points/exam) + 1 exam(50 points/exam) = 250 points (41.7 %) Final Exam = 100 points (16.7 %) 8 Laboratory Experiments 3 : 8 Labs(20 points/lab) = 160 points (26.7 %) 4 Quizzes, lowest dropped: 3 Quizzes(20 points/quiz) = 60 points (10.0 %) 3 Group Exercises: 3 GE(10 points/ge) = 30 points (5.00 %) Total graded 4 points = 600 Grades will be assigned as a percentage of total points possible, as follows: % Grade % Grade % Grade % Grade >93.0 A 81.0-84.9 B 69.0-72.9 C 57.0-60.9 D 89.0-92.9 A- 77.0-80.9 B- 65.0-68.9 C- < 56.9 F 85.0-88.9 B+ 73.0-76.9 C+ 61.0-64.9 D+ As may be noted from the above, the course is not graded on a Gaussian distribution. I reserve the right to normalize the grades upward if the class average falls below a C+. However, the more likely occurrence will be the assigning of additional problems for extra credit Schedule of Examinations 5 : Section I: Hydrocarbons; Alcohols, Ethers, and Analogs - Monday, 4/24 Section II: Amines; Functional Groups with a Carbonyl Friday, 5/11 Section III: Proteins, Enzymes, & Carbohydrates Friday, 5/25 Section IV: Lipids, Molecular Biology, & Metabolism (Final) Thursday, 6/14 3 You must complete the laboratory experiments to pass the class. Make up labs will not be provided. If you miss 1 lab a literature analysis will be provided to recover lost points. If you miss more than 1 lab they cannot be made up and you should withdraw from the course (drop deadline 5/18, which may be extended at the instructor s discretion) 4 Non-extra credit 5 Questions for the examinations will be based primarily on material covered in lecture, group exercises, and assigned homework. While homework will be regularly assigned, it will not be collected. However, you should expect to find several questions on each exam which bear a remarkable resemblance to previously encountered homework problems.
Make-up Examinations & Late Work Policy Make-up exams will be considered only if you approach me before the scheduled exam with an exceptional, documentable excuse. Documentation is mandatory before a makeup examination will be provided. If you miss an exam and have not notified me beforehand you will receive a zero for that exam. As one quiz is dropped, make-up quizzes will not be provided. Due to time constraints, make-up examinations will not be given for poor test performance. Late work is assessed a 20 % penalty for each calendar day it is late; that is, a 10 point assignment turned in 3 days late has a maximum value of 4 points. After 5 days the assignment has no point value. Any assignment turned in after the assignment has been returned to the rest of the class has no point value Labs are normally due at the beginning of the following lab session. Labs not turned in at the start of the session will be assessed a 5 % penalty Excusal from Final In the event a student need only pass the final with a C to receive an A for the course, he or she is excused from taking the final examination. Since the total number of graded (non-extra credit) points in the course is 600,.93(600) = 558 points are required for an A. As a C passing score for the final is 70, 488 points (558 70) accumulated prior to the final is required to have the examination waived. While this corresponds to 97.6 % of graded points, opportunities for extra credit exist and having the final waived is a real possibility for the dedicated student. All other work must be turned in prior to the final and the 3 rd and final quiz must receive a passing mark to exercise this option. Behavior You are primarily students who have elected to pursue professional careers in the health sciences. As such, little needs be said concerning behavior since the expectation is you will conduct yourselves accordingly. You should be mindful of creating distractions, as they only impede your fellow students opportunity for success. Please note that questions are never considered distractions, but must be limited to the topic at hand. As a courtesy to others, cell phones or other portable electronic devices should be turned off, or switched to vibrate in the event an emergency call is anticipated. Laptop computers are encouraged, but only as a learning aid for the day s topic. Students using laptops for anything but the day s topic will be assessed a 5 point penalty. Texting in class is not allowed and students found doing so will also be penalized 5 points no exceptions. Cheating will not be tolerated under any circumstances. My standing policy is to give a score of 0 for any exam a student is caught cheating on. As each exam is worth ca. 15%, of the total points, and the division of letter grades roughly corresponds to 10% of the total points available, cheating on an exam will cost you no less than 1.5 letter grades. A quiz in which a student has been caught cheating cannot be dropped, nor will an exam in which cheating has occurred be devalued by half (see grading section above) Disabilities Students with disabilities who believe they may need academic adjustments, auxiliary aids or services to fully participate in course activities or meet course requirements are encouraged to register with Disability Support Services, Rm 2133 in Wenatchi Hall. (509) 682-6854.
Tentative Schedule of Lecture Topics Week 1 Section I: Hydrocarbons; Alcohols, Ethers, and Analogs Monday, 4/02 Course Introduction; Organic Chemistry, Organic Transformations, and the Functional Group Approach; Names of the First 10 Straight Chain Alkanes (12.1-12.2) HW 1 Out Tuesday, 4/03 Functional Groups Continued (12.2) Wednesday, 4/04 Lab 1: Check in; Preparation of a Hand Cream Thursday, 4/05 Alkanes; Structural Isomers; Drawing Organic Structures; The Shapes of Organic Molecules (12.3-12.5) Friday, 4/06 Naming Alkanes; Physical and Chemical Properties of Alkanes (12.6-12.8) Week 2 Monday, 4/09 Group Exercise 1 Tuesday, 4/10 Cycloalkanes, Cis-Trans Isomerism in Cycloalkanes; Halogenated Alkanes and the concept of the Leaving Group (12.9, 14.10) Wednesday, 4/11 Lab 2: Organic Families Thursday, 4/12 Alkenes & Alkynes, Structure, Nomenclature, cis-trans Isomerism, and Physical Properties (13.1-13.4) HW 2 Out Friday, 4/13 Physical and Chemical Properties of Alkenes, Radical Mediated Polymerization (13.5-13.7) Week 3 Monday, 4/16 Quiz 1 Tuesday, 4/17 Aromatic Definition, Structure, Nomenclature, Isomerism, and Reactivity (13.8-13.10) Wednesday, 4/18 Lab 3: Organic Nomenclature Thursday, 4/19 Alcohols, Ethers and Sulfur Analogs: Structure, Nomenclature, & Physical Properties (Chapter 14) HW 3 Out Friday, 4/20 Alcohols, Ethers and Sulfur Analogs: Reactivity (Chapter 14)
Section II: Amines; Functional Groups with a Carbonyl Week 4 Monday, 4/23 Examination I Tuesday, 4/24 Amines: Structure, Nomenclature, & Physical Properties; Heterocyclic Amines (15.1-15.3) HW 4 Out Wednesday, 4/25 Lab 4: Reactions of Organic Compounds Thursday, 4/26 Amine Reactivity, Amine Salts, Alkaloids (15.4-15.6) Friday, 4/27 Aldehydes, Ketones, and Analogs: Structure, Nomenclature, & Physical Properties (16.1-16.4) HW 5 Out Week 5 Monday, 4/30 Mental Health I No Class (Bonus Exercise Available) Tuesday, 5/01 Aldehydes, Ketones, and Analogs: Reactivity (16.5-16.7) Wednesday, 5/02 Lab 5: Esters and Aspirin Thursday, 5/03 Carboxylic Acids and Derivatives: Structure, Nomenclature, & Physical Properties (17.1-17.3) HW 6 Out Friday, 5/04 Carboxylic Acids and Derivatives: Reactivity (17.4-17.7) Week 6 Monday, 5/07 Quiz 2 Tuesday, 5/08 Advising NO DAY CLASSES Wednesday, 5/09 Lab 6: Biochemistry Potluck Thursday, 5/10 Carboxylic Acids and Derivatives: Physical Properties and Reactivity Continued; Phosphoric Acid Derivatives (17.8) Friday, 5/11 Examination II
Section III: Proteins, Enzymes, and Carbohydrates Week 7 Monday, 5/14 Tuesday, 5/15 Introduction to Biochemistry; Protein Structure and Function; Amino Acids and Properties; Chirality & Handedness in Amino Acids (18.1-18.6) HW 7 Out Hierarchical Structure of Proteins; Structural Classification of Proteins; Protein hydrolysis vs. Protein Denaturation; Mutation & Protein Structure - Sickle Cell Anemia (18.7-18.12) Wednesday, 5/16 No Lab Lecture Instead (in 3018) Quiz 3 Enzyme Catalysis; Enzyme Cofactors; Enzyme Classification; Mechanisms of Enzyme Activity (19.1-19.4) HW 8 Out Thursday, 5/17 Factors Affecting Enzyme Activity; Enzyme Inhibition & Regulation; Vitamins (19.5-19.10) Friday, 5/18 Mental Health II No Class (Group Exercise 2 Available Online) Last to Withdraw or Change to Audit Week 8 Monday, 5/21 Tuesday, 5/22 Wednesday, 5/23 Thursday, 5/24 Friday, 5/25 Carbohydrate Introduction, Fischer Projections, & Stereoisomerism (21.1-21.4) HW 9 Out Monosaccharides, Cyclization of Monosaccharides, Physical and Chemical Properties of Monosaccharides (21.5-21.6) Lab 7: Carbohydrates and Lipids Acetal Formation: Disaccharides & Polysaccharides; Cellular Recognition, Dietary Polysaccharides (21.7-21.9) Examination III
Section IV: Lipids, Molecular Biology, and Metabolism Week 9 Monday, 5/28 Tuesday, 5/29 Wednesday, 5/30 Thursday, 5/31 Friday, 6/01 Memorial Holiday Lipid Classification and Structure, Fatty Acids & Their Esters (Triglyceride Formation); Properties of Fats and Oils (23.1-23.3) HW 10 Out Lab 7: Carbohydrates and Lipids Continued Reactions of Triglycerides; Membrane Lipids Membrane Structure; Membrane Transport (23.4-23.5, 23.7-23.8) Lipid Chemical Messengers; Bile Salts (23.6, 23.9) Introduction to Nucleic Acids and Heredity; Components of Nucleic Acids; Structure of DNA; DNA Replication and Repair (25.1-25.6) HW 11 Out Week 10 Monday, 6/04 Group Exercise 3 Tuesday, 6/05 Classes of RNA; Genes; Introduction to Gene Expression & Transcription; Post-Transcriptional Processing (25.7-25.8) Wednesday, 6/06 Lab 8: Soap (& Checkout) Thursday, 6/07 The Genetic Code, Translation and Protein Synthesis (25.9-25.10) Friday, 6/08 Genomics and Gene Regulation - Mutations, Mutagens, and Genetic Diseases; Recombinant DNA & Gene Therapy; The Polymerase Chain Reaction; DNA Sequencing (Chapter 26) HW 12 Out Week 11 Monday, 6/11 Quiz 4 Tuesday, 6/12 Bioenergetics Introduction, Role of Mitochondria, Principal Compounds of the Common Metabolic Pathway; The Citric Acid Cycle; Oxidative Phosphorylation, Electron Transport and the Chemiosmotic Pump; ATP Yield & Uses (Chapter 20) Wednesday, 6/13 Finals Thursday, 6/14 Final Examination from 8 to 10 am in Eller-Fox 3015 Friday, 6/15 Finals