Principles of inorganic and organic chemistry




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biochem 107 - introduction to biochemistry

general information and schedule of instruction
Fall, 2010

COURSE DESCRIPTION: Biochem 107 is the first of a 2-semester series of survey biochemistry courses with emphasis on human and clinical relevance, designed to meet the needs of pre-nursing and pre-dental hygiene students, students entering the allied health sciences, and other students who desire a background in biochemistry as it relates to the human body. Biochem 107 begins with a brief but intense survey of the principles of inorganic and organic chemistry (first half of semester); this is followed by a comprehensive survey of biochemistry, including both basic and clinical aspects. Biochemical topics during the first semester include protein structure and function, enzymes, and intermediary metabolism. A 5-6 page research paper is required. The required weekly 2-hour lab (Biochem 107L) consists of dry-lab experiments, demonstrations, problem sets, workshops, and clinical case conference discussions, integrated with lecture material and dealing with topics ranging from basic chemistry to the biochemistry and molecular biology of human diseases. Written lab reports are required for most of the lab exercises. There is no separate grade given for Biochem 107L – lab work is included in your Biochem 107 grade.

Biochem 108/108L is a direct continuation of 107/107L. Topics include lipid metabolism, protein metabolism, molecular and cellular biology, biochemistry of cancer, viruses, and AIDS, and clinical biochemistry and nutrition.

Students can take only Biochem 107, or only Biochem 108 (if they work very hard to do well), but you won’t get the comprehensive survey of biochemistry you’ll have if you take both semesters.

Prerequisites: Students are expected to have completed at least one year of high school chemistry. Students who do not meet this requirement should contact Dr. Toews as soon as possible.

Lecturers: (in order of appearance)

Dr. Arrel Toews 3023 Genetic Medicine Building atoews@med.unc.edu (course director) phone: 843-8727

Elizabeth Pollom 22-062 Lineberger Cancer Center epollom@med.unc.edu
phone: 317- 730-3794

textbook: General, Organic, and Biochemistry, 6th edition (2008) by Denniston, Topping, and Caret. This textbook is available in the UNC Student Stores on the main campus, at downtown bookstores, and on the web. An electronic E-book version is also available.

We also prepare detailed sets of lecture notes and PowerPoint slide sets for each topic. All course materials are available on our course website “INTRO TO BIOCHEM” on BlackBoard (http://blackboard.unc.edu). You should be able to access this site if you’re registered for the course. Read any announcements, then go to “Course Documents” to view this and all other course materials. You will be responsible for downloading this material to your laptop and/or printing it out – we will NOT provide hard copies of any materials. Be sure you have copies of all course materials, including lecture notes and slides, and bring them to each lecture.

Laboratory: Required for this course. Be sure you are registered for a section (401 OR 402) of Biochem 107L. Section 1 meets at 1 PM in 209 Carrington Hall (Nursing School), and Section 2 at 3 PM in the same room each Thursday afternoon. We will go over general lab information during our first lab on Thursday, August 26. This is a real lab session – make sure you show up for it!

All lab material is also online (look in the “LABSTUFF” folder under “Course Documents”), and you will be responsible for downloading/ printing off the lab syllabus and each lab exercise before class. Be sure to bring this material to lab.

Dr. Arrel Toews is also the lab director, and all questions regarding the lab portion of the course should be directed to him or to the lab TAs.

Class Attendance: You are expected to attend all lectures and labs. Absences from lecture or lab sessions are authorized only in the following cases: (1) the student's name appears on the University Infirmary List or the student has a written excuse from her/his doctor stating that the student was indisposed on that date; (2) the student is taking part in a regularly organized and authorized University activity; (3) a death in the family or similar emergency, at the discretion of the Instructor or Course Director.

It is the responsibility of the student to inform the Instructor or Course Director when these exceptions apply, preferably before the absence, otherwise immediately upon the student's return to class.

Roll will be taken approximately once a week during lecture. We do not deduct points for absences from lecture. However, at the end of the semester, students who are on the borderline between two different course grades and who have consistently attended class usually receive the higher grade. See below for an even better reason to regularly attend lectures. Attendance for all lab exercises is mandatory – they cannot be made up at a later date. Unexcused absences from lab result in a grade of zero for that week's labwork.

Exams and Grading: There will be 4 scheduled 50-minute lecture exams during the semester. The dates of these exams are shown on the attached schedule. Each exam will consist of approximately 35-45 questions, and will cover material from the lectures, lecture notes, and any assigned reading. Exams may contain multiple choice, matching, true/false, and short answer questions, but questions are usually multiple choice.

Most of the exam answers are computer-graded, so be sure to bring a least two #2 pencils and a good eraser to each exam. We will provide scantron answer sheets – do NOT bring your own answer sheets. Most (perhaps all) of the exams will contain questions on pH, buffers, and biochemical calculations, so bring along a calculator capable of handling logarithms and scientific notation (you'll need this for lab as well).

Lab exams will be given during lab sessions, and details about them are in the lab manual.

Final Exam: Saturday, December 11, 8:00 – 11:00 AM, in Carrington Hall (room to be determined). The final exam is COMPREHENSIVE, i.e., it covers material from the ENTIRE COURSE. It will consist of 100 questions, 80 from the lectures and 20 from lab. Questions will be in the same format as for the 50-minute exams. You will for sure need your calculator for the final. This is very early in the final exam schedule this semester – the time to start preparing for this exam is right now.

Absences from exams: An absence from an exam is excused only under circumstances described above for excused absences from class. Students who miss an exam because they are participating in an authorized university activity must notify the Instructor or Course Director prior to the scheduled exam date. Students who miss an exam due to illness should contact the Instructor or Course Director preferably before (but if not, immediately following) the exam; they will usually be asked to make up the exam within 1-2 days of the originally scheduled date. For students who do not make arrangements to take the make-up exam, their Final Exam grade will be substituted for the missed exam. Students with more than one unexcused absence from an exam will receive a grade of zero for each missed exam except under exceptional circumstances.


The final course grade is calculated as shown below:

Four 50-minute midterm exams (15% each) 60% of total grade
Lab reports, quizzes, and lab exams 20% of total grade
Research paper 5% of total grade
Final exam* (including lab component) 15% of total grade
100%

* Final exam is comprehensive (covers entire course) and has 100 questions, with 20% from lab.

Letter grades and grade points will be assigned with the assistance of a "standardized scoring template." This grading method takes into account the fact that different exams in a course have different averages and standard deviations (variations). This program normalizes the results of all the exams so they each have the same mean and standard deviation; it then recalculates raw test scores to yield equivalent scores (called T-scores) for each student. T-scores for each exam have means of 50 and standard deviations of 10. Grades and grade points are assigned based on these normalized T-scores (how many standard deviations above or below the mean a given exam score is). This is a fairer and more impartial way of "curving" grades than is arbitrary curving by the instructor. If you would like more explanation about all this, see Dr. Toews.

NOTE: Everyone occasionally has a bad day. In recognition of this, we will substitute the score (actually the normalized “T-score”) from your final exam for your lowest 50-minute exam grade if (and only if) doing so will improve your overall average.

Some words to the wise: If you want to get a good grade in this course, you will need to come to lecture, pay attention to what is said, take good notes, study your notes, the textbook, and lecture handouts, and apply yourself in lab. Make sure you don't fall behind. Each lecture builds upon material presented in earlier lectures. Keeping up with the material as it is presented is probably the most important thing you can do to ensure a decent grade. You should plan on devoting 2-4 hours of study time outside of class for each hour of lecture (6-12 hours of studying/week for this course). If you feel yourself falling behind in this course, you'll need to work even harder to catch up before it's too late. Make sure you contact Dr. Toews, your current lecturer, or our other helpers (see below) as soon as you sense yourself getting into trouble – or even if you just have questions. Don’t be shy about asking for help at any time!

We have a number of different types of “help” available, and we encourage you to use them regularly. They are described briefly below.

PEER TUTORS for Biochem 107: We have five peer tutors available to help you. They were excellent students in this course last year, so they are excellent sources of help for you this year. Peer tutoring involves drop-in one-on-one assistance with any specific questions/problems (no appointment needed – just stop by). Peer tutoring is FREE – there is no charge for this help!! You can find Biochem 107 peer tutors on Tuesday and Wednesday evenings from 6-9 PM in 206 Dey Hall (on the main campus near Wilson Library). These sessions will begin on September 7/8. The full schedule, including any changes in room numbers is online at The Learning Center.

Peer tutors are listed below:
Tuesday nights Wednesday nights

Rachel Stowe stower@email.unc.edu Rebecca Kabatchnik becca10@email.unc.edu
Laura Borders lborders@email.unc.edu Jane Held mheld@email.unc.edu
Kelsey Knight knightkm@email.unc.edu


There will also be "help sessions" with the lab TAs immediately following each lab session. A TA will be on hand to answer any of your questions from lab.

Dr. Toews will also hold informal review/help sessions on Tuesday afternoons (beginning at 2 PM) in Carrington Hall (room to be determined). These sessions are student-driven and unstructured – anything from either lecture or lab is fair game, and we usually stay as long as needed to get things cleared up. This is a group effort where we help each other understand things.

Don't even think about trying to learn everything just before an exam. It cannot be done. Because of the highly integrated complex nature of biochemistry, you’ll do best if you have a good overall understanding of what is going on. Attempting to "cram" your brain with individual specific biochemical facts just before an exam is especially futile and dangerous.

Students who find themselves in difficulty in the course at any time should contact Dr. Toews (or Liz Pollom) to set up a friendly chat. Don’t forget about all the other resources we have to help you as well. We will do all we can to help you along, but in the end, it is all up to you. Lots of time and hard work will be required, but in the end, it will all (hopefully) be worth it.

the university's honor SYSTEM and HONOR code: You are reminded that the Honor Code, which prohibits things like lying, cheating, stealing, and interfering with the welfare and educational opportunities of others, must be strictly observed. Remember that we are all on our honor to be good citizens of the University community. This is the correct way to live your life in general anyway, so be sure you do that. See your instructor or the Undergraduate Bulletin if you are unsure of how these codes apply.

RESEARCH PAPER: A research paper is required and it will account for 5% of total course grade. This 5-6 page paper will require a good bit of thought, preparation, organization, and good writing. It will be graded rigorously in a number of categories, including quality of content (scientific and otherwise), information searching and retrieval, quality and appropriateness of illustrative materials, general organization and overall thought, composition (grammar, syntax, flow), and quality of references (at least 2 from the internet, with an appraisal of their value/reliability, and at least 2 from printed books/journals). We will post a list of general topic areas, as well as some specific suggestions within them, but finding your own unique topic (within the general topic areas) is even better. You will need to get your specific topic approved by either Dr. Toews or Liz Pollom, who will both be happy to assist you in coming up with a suitable topic. You will be given more specific information on these papers soon after class begins. We will also devote part of a lab exercise to online searching strategies for web and printed reference sources.

This paper will be due on Monday, November 15 at 5 PM. Handing your paper in early is a very good strategy that will be much appreciated by those grading it.

A word to the wise: Don’t put this off until the last minute (or last day or even last week). Think carefully, choose a good topic, start your research and writing activities early, put real effort into them, go through several drafts, and be sure the final product is something you (and Dr. Toews!) will be proud of.

These reports will be graded rigorously and you will do well to put some genuine effort into them. The 5% of your grade accounted for by this paper might end up playing a very important role in your final course grade.

biochem 107 lecture and lab schedule - FALL, 2010

Dr. Arrel Toews, Course Directoratoews@med.unc.edu; 843-8727

All lectures in Carrington Hall, Auditorium #9; 9:00-9:50 AM.

DATE Day Lecture # Topic Lecturer

Aug. 25 W 1 Orientation/Matter and Energy Dr. Toews
Aug. 26 Th Lab 1 Orientation; Units, Basic Calculations Dr. Toews
Aug. 27 F 2 Elements and the Periodic Table Dr. Toews

Aug. 30 M 3 Compounds and Chemical Bonds Dr. Toews
Sept. 1 W 4 Water, Solutions, and Gases Dr. Toews
Sept. 2 Th Lab 2 Online and library searching; Graphing Dr. Toews
Sept
. 3 F 5 Chemical Reactions and Kinetics Dr. Toews

Sept. 6 M Labor Day Holiday (no class)
Sept. 8 W 6 Chemical Equilibria Dr. Toews
Sept. 9 Th Lab 3 Biochemical Calculations; Solutions Dr. Toews
Sept. 10 F Review (# 1-6) Dr. Toews

Sept. 13 M EXAM 1 (# 1-6) Dr. Toews
Sept. 15 W 7 Acids, Bases, and Salts Dr. Toews
Sept. 16 Th Lab 4 Acid, base, & pH workshop Dr. Toews
Sept. 17 F 8 Buffers Dr. Toews

Sept. 20 M 9 Organic Chemistry I Dr. Toews
Sept. 22 W 10 Organic Chemistry II Dr. Toews
Sept. 23 Th Lab 5 Workshop on Functional Groups; Models Dr. Toews
Sept. 24 F 11 Organic Chemistry III Dr. Toews

Sept. 27 M 12 Chemistry of Life I Dr. Toews
Sept. 29 W 13 Chemistry of Life II Dr. Toews
Sept. 30 Th Lab 6 Bio-macromolecules; Basic biochemical Rx Dr. Toews)
Oct. 1 F Review (# 7-13) Dr. Toews

Oct. 4 M EXAM 2 (# 7-13) (Dr. Toews)
Oct. 6 W 14 Amino Acids and Peptides Dr. Toews
Oct. 7 Th Lab 7 Spectrophotometry (Dr. Toews)
Oct. 8 F 15 Protein Structure and Function Dr. Toews

Oct. 11 M 16 Enzymes: How they work Liz Pollom
Oct. 13 W 17 Regulation of Enzyme Activity Liz Pollom
Oct. 14 Th Lab 8 LAB MIDTERM EXAM (Dr. Toews)
Oct. 15 F 18 Clinical Applications of Enzymes Liz Pollom
Mini-Case Conference

Oct. 18 M 19 Nucleotide Metabolism I: Folate and

1-C Metabolism Liz Pollom
*Oct. 20 W 20 Nucleotide Metabolism II: nucleotide
synthesis & chemotherapy Liz Pollom *
Oct. 21 Th FALL BREAK
Oct. 22 F FALL BREAK

Oct. 25 M 21 Nucleotide Metabolism III: nucleotide

degradation and its associated diseases Liz Pollom
Oct. 27 W Review (# 14-21) Dr. Toews
& Liz Pollom
Oct. 28 Th Lab 9 Cancer Chemotherapy Case Conference Liz Pollom
Oct. 29 F EXAM 3 (# 14-21) Dr. Toews
& Liz Pollom

Nov. 1 M 22 Overview of Metabolism & Bioenergetics Dr. Toews
Nov. 3 W 23 Carbohydrate Structure & Chemistry Dr. Toews
Nov. 4 Th Lab 10 Enzymes & Disease Case Conference Dr. Toews
Nov
. 5 F 24 Digestion, Absorption, & Blood Glucose Dr Toews

Nov. 8 M 25 Insulin, Glucagon, & Diabetes Dr. Toews

Nov. 10 W 26 Glycogen Metabolism Dr. Toews
Nov. 11 Th Lab 11 Serum Glucose Assay Dr. Toews
Nov. 12 F 27 Glycolysis Dr. Toews

Nov. 15 M 28 Citric Acid (Krebs) Cycle Dr. Toews
RESEARCH PAPER DUE BY 5 PM
Nov. 17 W 29 Oxidative Phosphorylation; ETS Dr. Toews
Nov. 18 Th Lab 12 Diabetes Case Conference Dr. Toews
Nov. 19 F 30 * Gluconeogenesis; PPP; Overall
Integration of Metabolism Dr. Toews

Nov. 22 M Review (# 22-29) Dr. Toews

Nov. 24 W NO CLASS

Nov. 25 Th THANKSGIVING HOLIDAY
Nov. 26 F THANKSGIVING HOLIDAY

Nov. 29 M EXAM 4 (# 22-29) Dr. Toews
Dec. 1 W 31 * Amino Acid Metabolism I: Overview, Dr. Toews
Protein dig’n; Catabolism of C-skeletons Dr. Toews
Dec. 2 Th Lab 13 Amino Aciduria (PKU) Case Conference Dr. Toews
Dec. 3 F 32 * Amino Acid Metabolism II: N-elimination;
Urea cycle; non-protein AA uses Dr. Toews

Dec. 6 M Course Review Dr. Toews
Dec. 8 W Course Review Dr. Toews & Liz Pollom
Dec. 9 Th Optional Review/Help Session Dr. Toews

Dec. 11 SAT FINAL EXAM (8:00 AM – 11:00 AM)

* This lecture, just before Fall Break, covers important topics that will not be covered again. Cut out early at your own risk!! And yes, a good day to take roll.

* These two lectures are not covered by a mid-term exam, so there will be some added emphasis on these topics on your final exam (more questions/topic than for the others).

NOTE: The final exam is comprehensive, and covers material from both lecture and lab.

course resources

Material on Blackboardhttp://blackboard.unc.edu

All course materials are available online on our “INTRO TO BIOCHEM” course website on BlackBoard. Look under “Course Documents” for folders for each unit/lecturer and for lab (LABSTUFF). We will NOT be providing paper copies of any course materials – you will need to download these files to your laptop (and print them if you like). Be sure to bring them and/or your laptop to class and lab. Most of the .ppt slide sets are animated, and so best viewed in the “SlideShow” mode on your computer. It’s also a good idea to print out the .ppt slide sets – in PowerPoint, go to File/Print/Handouts/4 per page/scale to fit.

Wireless access in NOT guaranteed in Carrington Hall, so I strongly suggest you download all required files onto your laptop before coming to class/lab.

2009 Exams from both lecture and lab are also available on this website. Look in the “EXAMS” folder (or the LABSTUFF folder for lab exams). These exams are very useful review/study tools, and you are urged to make use of them.

Answer keys to our 2010 midterm exams will also be posted at this site.

Material on Reserve – Health Sciences Library: (ask at the front desk)

An Introduction to Chemistry for Biology Students” by Sackheim – A very simple, programmed-learning book potentially useful as a primer for those rusty on their general and organic chemistry. Also available for optional purchase (but 4 copies on reserve). Older (used) editions are just a good as the latest version.

Essentials of Chemistry” by Burns - A simplified introduction to college chemistry with some nice figures and diagrams – maybe useful to look through if you’re intimidated or scared about chemistry in general.

General, Organic, and Biochemistry, 5th ed. by Denniston, Topping, & Caret” (previous edition of our textbook). The Student Study Guide/Solutions Manual from the 5th edition is also on reserve – it has some useful chapter outlines, problems, and solutions to exercises.

Where’s Arrel?? How to find Biochem 107/108 Faculty

T
o find Dr. Toews:
My office is in the new Genetic Medicine Building (3023; 3rd floor). This building is south of Mason Farm Road, near the Ambulatory Care Center of UNC Hospitals (a bit southwest of the big Hospital Parking Decks). In most instances, it will be easier for us to meet in the coffee shop in the Health Sciences Library (much closer to Carrington Hall than the GM building, plus I’m usually good for a free latte or ice-cold Pepsi-Cola!). Just see me before/after class, send an email (atoews@med.unc.edu) or call (843-8727) so we can work things out.

Dr. Fried (Biochem 108) is also on the 3rd floor of the Genetic Medicine Building.
Liz Pollom (Biochem 107 & 108) lives in the Lineberger Cancer Center (22-062).

A searchable campus map can be found online at: http://www.maps.unc.edu/MapBook/Index.asp

A section of that map is shown at right – it shows most of the relevant locations.

Carrington Hall () is also shown in this panel. The Health Sciences Library is also worth noting.
The Genetic Medicine Building ( * ) is south of the Lineberger Cancer Center ( * ). If you want to come and see me in the GM Building, I will be happy to give you more specific directions as well – it is not a bad walk from South Campus.

\NURSES\107\2010\SYLL-BIOC 107-2010.doc


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