CHE 4341-05 S15 Syllabus v.1.0 PDF

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1/9 General Biochemistry (CHE 4341-05) Spring 2015 MWF Syllabus v.1.0 Time: Instructor: Tel:

1:25-2:15 PM Dr. Mark (Devan) Jonklaas 710-2051 (I DO NOT check voice mail!)

Place: Office:

Baylor Science Building (BSB) BSB E 227 Baylor Science Building (BSB) C218

Email: [email protected] ( Best way to contact me. If you email me and I don’t reply, please email me again! Also, PLEASE INCLUDE “CHE 4341-05” in the Subject Heading, so that I know which section you are in (to do this automatically, email me via the Communication tab on the class page on Blackboard [Bb])!)

Course Description: Biochemistry is a modern science that encompasses the intersection of general chemistry, organic chemistry and biology. It is an ever-growing subject whose vital importance only continues to increase as we expand our understanding of the complex and intricate chemical nature of life. It is effectively the study of bio-chemistry, the amazing chemistry of life! Thus we will start our journey delving into primordial life and how it began. In this first step, we will also review certain aspects of Organic and General Chemistry as life IS applied chemistry! We will then examine water, the vital essence indispensable for life. The class’ paintbrush will then take a broad swath, delving into the key chemical “building blocks” of life, the amino acids, nucleotides, carbohydrates, and lipids, along with the more complex, larger biomolecules that these blocks assemble into - macromolecular structures like proteins, DNA and RNA, polysaccharides, and bilayer membranes and the chemical reactions required to join the building blocks together to make the macromolecular structures. Part of our study will involve examining the shapes, functions, chemical reactions, roles, etc, of each type of macromolecular structure. We will also spend substantial time examining enzymes, the incredible “nano-machines” that catalyze the chemical reactions that make life possible – and we will see how enzymes work including understanding their rates and mechanisms along with how they can be inhibited (thus gaining insight into how some medicines work)! In the next chapter of our exploration, we will cover metabolism, zoning in on the main pathways cells use to generate energy by breaking down (catabolizing) nutrients - examining the pathways of glycolysis, the Krebs cycle, and the Electron Transport Chain (ETC) and Oxidative Phosphorylation. Lastly, we will end our adventure by exploring basic molecular biology techniques that overlap with biochemistry, like molecular cloning (genetic engineering), PCR, and DNA sequencing. Goal: In the way a mechanical engineer learns how an engine functions from the smallest cogs and bolts on upwards, this course aims to give Chemistry/Biology/Neuroscience/Pre-Med./Pre-Dent./et al. students a close look “under the hood” at how life is constructed and operates at the molecular level. Apart from the inherent fascination with such an endeavor, insight gained from this course should benefit you as follows: 1) To live as a better steward of you life by understanding how your body function at the “Nano level”; 2) Advising others with this knowledge for the benefit of their health; 3) Being able to critically apply the knowledge learnt to medically help yourself and others both informally (via knowledgeable awareness and advice) and formally as a medical or dental professional. ). Practically, this course also will provide students biochemical knowledge to help them score more highly on the applicable sections of the MCAT (/DAT/etc.) exams, provide pre-health students the background required to excel in their first semester medical (PA/dental/etc.) school medical biochemistry (“molecular medicine”) classes, and provide students going into graduate school in the Biochemical/Biological sciences with a robust foundation in biochemistry for success in their graduate coursework and research. Finally, the information in this course is also intended to prepare students for Topics in Human Biochemistry (CHE 4342) and other upper-level biochemistry classes (e.g. CHE 4327). The breadth of the course is expansive and the course is taught at the very challenging level, befitting a 4000-level science class! Thus, apart from consistently attending class, students should be prepared to spend ~9 hours per week studying for it (or more, if they have had difficulty with the pre-reqs.)!

TEXTBOOK / MATERIALS: Class Textbook: Your main required text: The USA Version of “Fundamentals of Biochemistry,” 4th Ed. by Donald Voet, Judith G. Voet, Charlotte W. Pratt (the “VVP” text or simply the “text”), by John Wiley & Sons, 2012. ( Need 4th Ed., USA version: Because homework problems assigned include the text’s end-of-chapter problems & these can differ between versions, including between the US and international versions of the 4th Ed.!). For different formats & ways the book is available, please see Appendix I.  NOTE: I view these textbooks as important tools designed to complement the Class Lectures and class Lecture Notes. Thus, although the “Assigned Reading” for the class is assigned from content in the text, it may be more advantageous to read the class Lecture Notes that will be posted on Bb ahead of class as a means of completing the “Assigned Reading”! Turning Point Clickers: The class will require the use of a correctly working Turning Point RF LCD or NXT Clickers (Response Cards / Devices), which will be used for attendance, in-class polling, Clicker Quizzes, etc. No other type of Response Card will be acceptable. Response devices can be purchased at the Turning Technologies Online Store

2/9 (https://store.turningtechnologies.com/ ) at a reduced cost, or from the campus bookstore. Our school code for the online store is b2zG. Please put a new battery in your Clicker at the start of the semester and ensure that it is functioning correctly as I will be UNABLE to credit you with a correct response if you don’t have a Clicker or it malfunctions and doesn’t submit the correct one – which will thus result in an absence or zero score on a Clicker Quiz question as a result! Also, please make sure to register your clicker BY THE SECOND CLASS DAY according to the instructions posted in the Syllabus section of Bb: Registration associates the Clicker ID with a name – and thus I will not be able to assign scores or attendance to any unidentified (i.e. unregistered) Clickers! More on Clicker Quizzes is elaborated later on in this Syllabus! Class Website: CHE 4341 on Blackboard (“Bb”): https://my.baylor.edu/webapps/portal/frameset.jsp  There will be TWO Bb pages for each class! The main site will be the combined large (LG) Bb page for ALL 4 of my CHE 4341 sections combined and will contain Course Documents (Class Schedules, Syllabus, Lecture Notes, etc) for ALL sections and will also have the ALL class announcements, etc.! I will also use your individual section’s Bb page, but this will ONLY be for you to see your attendance and Clicker Quiz scores!  VERY IMPORTANT! I communicate extensively with my students via Bb! Thus, it is very important that you check the Bb Announcements (on the LG site) for this class regularly! I will not be responsible for you being unprepared for a class/exam if you fail to read a Bb Announcement concerning it, if the announcement was posted by 5:30 pm the day before the class/exam it is relevant for occurs! (Note: For your convenience, I will also Email class Bb announcements to your Baylor Email address)! Furthermore, I may need to communicate with you on an individual basis via Email: For this reason, please keep your Baylor Email account tidy so that it does not go over quota and can receive Email for the length of the semester! I will not be responsible for you missing an important communication from me if your Inbox cannot receive Email!  Note: There are Bb apps available for many devices, for more on this, see: http://www.baylor.edu/lib/factech/index.php? id=83033 Required Access of Online Multimedia (MM) Content: You will be required to view/watch multimedia (MM) files from the internet! One of the main websites with animations you will be required to watch is the VVP 2nd Ed text’s Student Companion website : http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471214957_BKS_2261____,00.html! This site that has very useful learning resources that include Animated Figures, Interactive Explanations & Guided Explorations of important biochemical concepts. The MM files should will be required to watch are accessed directly from hyperlinks (i.e. links) built into the Class Schedule! (See the Syllabus section entitled “Assigned Reading and Viewing” for more info.)! Facebook: There is a Facebook page for the class, you can access it here: https://www.facebook.com/pages/Jonklaas-GeneralBiochemistry-Baylor-University/616369451717781 I use it to keep up with students after they have finished the class and also to post interesting biochemistry / chemistry relevant information! …and humor, too! POLICIES: Office Hours: MW 2:30-4:45 pm; TR 2:00-4:45 pm; F 2:30-3:30 pm. ( I may sometimes have to change/miss Office Hours due to meetings, etc. - if so, I will attempt to inform you of this via Bb and/or a note on my office door!) Prerequisites: I expect you to know the material covered in two semesters of freshman chemistry & two semesters of organic chemistry. It is likely that you will struggle terribly & earn an “F” if you have not completed the O-Chem. 2 pre-requisite!!!!! Attendance & Tardiness: The Department of Arts and Sciences attendance policy is as follows: “To earn course credit in the College of Arts & Sciences, a student must attend at least 75 percent of all scheduled class meetings. Any student who does not meet this minimal standard will automatically receive a grade of "F" in the course. Any University-related activity necessitating an absence from class shall count as an absence when determining whether a student has attended the required 75 percent of class meetings.” (Ref.: http://www.baylor.edu/artsandsciences/index.php?id=86320). Thus, you cannot miss more than 11 classes (25%), no matter what! Starting on the second class day, attendance will most likely be taken at the start of class using Turning Point clickers (with a fall-back technique being a digital photograph tied to a seating chart, where the seating chart will be constructed also on the 2nd class day)! (Or, if all else fails, on rare occasions using an attendance sheet). Attendance points: You will earn 0.25 points for being present in class when attendance is taken. These points will count towards your Clicker Quiz score (Clicker Quizzes will be elaborated later on in this Syllabus). Thus with 40 classes, a total of 10 points through attendance are available towards your Clicker Quiz score!  I MPORTANTLY,astudent will receive zero attendance points and will be counted as absent if they are tardy and are not present when attendance is taken! However, I also believe in the axiom, “better late than never,” and recommend that you to attend class even if you are late! Class Etiquette: A University classroom should be a place of learning and respect. This respect should be fostered by being on time to class, paying attention to the lecture and addressing your instructor with respect in communication. Please be aware that “private intrusions into a group learning space” (e.g. chatting, texting, puzzle-solving, web browsing, etc.) are selfish acts

3/9 that are invariably distracting to your peers and/or the instructor! In particular, I am extremely sensitive to distracting noises during class: Thus for the sake of an undiverted lecture that benefits everyone, please refrain from conversing (unless part of a directed discussion) in class and have cell phone, watch, etc. alarms/alerts/ringers on silent as well! As I like to use the 5 minutes right before class starts in preparation to start on time, I also ask that you please refrain from talking to me about any class matters until the end of class (or Email me with your question well in advance instead)! Homework (Hwk): Hwk will be posted on Bb in the Assignments section and is intended to help students prepare for biochemical calculations of the type that will be on class exams! However, Hwk will NOT be collected or graded – though suggested Hwk due dates are listed on the Class Schedule to help students keep an adequate pace and to help motivate you to keep up with your coursework, I WILL NOT answer questions concerning an Hwk assignment past 1 class day after its due date in the most current Class Schedule! NOTE: Students should not take an exceptionally long time on Hwk problems and answers to Hwk assignments are provided and students are expected to look at the answers if/when an Hwk problem takes too long: What is important is that by doing the Hwk, students learn how to work problems like those in the Hwk - because similar problems could be present on the corresponding class Exam and/or the Final Exam! For this reason, Hwk assignments may be done collaboratively/with a tutor, as long as a student is truly learning how to solve such problems for an exam! Furthermore, because I strongly believe that we learn in the process of attempting to solve problems, I will not help you with answering Hwk questions until you have exhausted all possible resources available to help you figure out the answer for yourself (e.g. by you’re your working backwards from the answers first, by watching any Video Lectures provided to help with Hwk, etc.). Syllabus Quiz: My desire is that all students achieve paramount success in the class: As a result, the course Syllabus is intended to be a detailed explanation of requirements a student must be mindful of in order to not hinder their achievement. Thus, there will be a ~4 minute, 5 point multiple choice quiz on the contents of this Syllabus at the start of the 2nd class day. The 5 points from the Syllabus Quiz will not count as part of your regular class total but will count as bonus/extra-credit points towards your overall class score! Assigned Reading & Assigned Viewing (of Online MM Content): Because of the level of difficulty & the scope of the course, its material is presented at a brisk pace. Thus in order to properly follow along, assigned materials are to be completed before the start of the class next for which they are assigned. Assigned Reading includes any content in the “Boxed sections” of the text within the assigned reading pages! The Assigned Viewing of Online MM Content (Assigned Viewing) refers to the complete viewing of online multimedia (MM) content linked to in the Class Schedule. All Assigned Viewing content is required material that could be on class exams - even though it may NOT be covered in class due to the time constraints of the course! Vi de oLe c t ur e s( No t e :The s ea r edi s t i nc tf r o mt heAs s i gne dVi e wi ng ! ) :Ce r t ai nma t e r i a l( pr e domi na nt l yr e vi e wma t e r i a l f r o m Ge n. Che m.a ndOChe m. )wi l lno tbec o v e r e di nc l a s sbutwi l li ns t e a dbepo s t e do nl i nei nt hef o r mo fVi de o Le c t ur e s( a l o ngwi t ht hea c c o mpa ny i ngLe c t ur eNo t e st ha twi l lbepo s t e do nBb) .Vi d e oLe c t ur e sa r en o t e di nt heCl a s s Sc h e d u l eb yt h et i t l e“ VI DEOLECTURE”a n ds ho u l db ewa t c h e ddi r e c t l ya f t e rt h ec l a s sf o rwhi c ht h e ya r el i s t e d .Fo re a c h Vi d e oLe c t u r e , t h el i nk ( s )t oi ta n di n s t r uc t i o n sonh o wt oa c c e s si twi l lb ep o s t e da saBbAnno unc e me nt .Vi de oLe c t ur e c o nt e nti si mpo r t a nta ndc o ul ds ho wupo ne x a msand/ o rt heFi na l ! Ce r t a i nVi de oLe c t u r e swi l lbeus e f ulf o rc ompl e t i ng Hwka s s i g nme nt sa n dwi l lb en o t e da ss uc h ! Structure Quizzes (SQuizzes): There will be 6 SQuizzes as shown in the Class Schedule. These will occur over the first 8-10 minutes of class and will focus on your memorization and recollection of specific biochemical molecules and/or metabolic pathways. Because ample time in now provided between classes, those tardy for a Structure Quiz (SQz) will not be given additional time to complete it (but if you have a University acceptable verifiable excuse for being tardy, PLEASE inform me of it BEFORE starting the quiz)! Instructions for each SQz, along with sample questions for it will be posted on Bb! Each SQz will be worth 30 points and your Clicker Quiz score (explained in the paragraph below) will count as an additional SQz score, amounting to a total of 7 SQz scores available – where your lowest 2 SQz grades will be dropped, thus making SQz scores worth 150 points towards your overall grade. Because SQuizzes are an important way of preparing for an Exam, it is advisable that you attend and attempt every SQz! You will only be allowed to make-up a SQz missed due to a University accepted excused absence! Clicker Quizzes: These will be taken using your Turning Point clickers and can be any of all of the following: 1). Pop Quizzes at the start-of-class based on the Assigned Reading / Viewing*; 2). Pop Quizzes at the start of class based on the previous Class Lecture; 3). In-class Quizzes over the presented Lecture material. Clicker Quizzes will be of varied points and will count 30 points towards your class grade with at least 35 Clicker Quiz points available, with the extra 5 (or more) points intended to help anyone who misses a Clicker Quiz due to absence or tardiness! As a result of these extra points being available, you will NOT be able to make up any missed Clicker Quizzes for whatever type of absence or tardiness. In addition, as previously noted, attendance quiz points will contribute 10 points towards your Clicker Quiz grade (thus you can earn 10 of your 30 Clicker Quiz points simply by coming to class on time)! Your Clicker Quiz score will be capped at a maximum of 30 points and will count towards a Structure Quiz score (for more on Structure Quizzes, see the next paragraph)! As noted earlier, Clickers MUST be

4/9 correctly registered and functional for you to receive credit on an Attendance and Clicker Quiz! Obviously, since Clickers will be used for attendance and Clicker Quizzes it is IMPERATIVE that students bring their Clickers to every class: For any given class day, a student forgetting to bring their Clicker or participating with an unregistered clicker will amount to them being counted as ABSENT and/or receiving a ZERO grade on that day’s Attendance and Clicker Quiz! *Note: There shall be no start-of-class Pop Quizzes over the Assigned Reading / Viewing on Structure Quiz days! Regular Exams: Frequency, Facts and Format: There will be 4 Regular Exams worth 100 points each, as noted in the Class Schedule. Exams, in general, will explicitly be over material covered since after the previous Exam but will implicitly draw on knowledge of older material. For a listing of material that an Exam will explicitly cover, please see the Class Schedule. Exams will be divided into 2 parts: A Multiple Choice Question (MCQ) section (that may also potentially contain matching and/or true or false [T/F] questions) worth 75 points (usually 40 questions at 1.875 points per question); and a Short Answer (SA) question section worth 25 points. Sample Exam Questions: (1.) Sample MCQs (collected from previous Exams) will also be posted on Bb: For the benefits & reasons to why these should ALL be attempted, see the point about them in the Appendix IV “HELPFUL TIPS FOR SUCCEEDING IN THIS CLASS:” It is STRONGLY recommend that students give themselves ample time to work over all the Sample MCQs posted for a particular Exam before taking it! However & importantly, the sample MCQs posted will NOT be the MCQs that will be on the Exam (i.e. the Exam MCQs will almost invariably be different from the sample MCQs posted)! (2.) Sample Short Answer (SA) Questions: The SA Question section will comprise of mainly of Structure/Mechanism and Calculation based questions, though it could also include a few regular 1-2 sentence answer and/or fill in the blank type questions. Calculation based SA questions for an Exam will be similar to those in the corresponding Hwk. The main content that you will be required to study/memorize for ...