Welcome to Chem 265A ! Biochemistry I Winter 2013

Instructor: Dr. Jacqueline Drak Email: [email protected] (please call me Jacqui) Office: S340E

Office hours: M – 9:30 am -10:30 am (S340E); TWThF- 10:30 pm -11:30 pm Meeting times (or by appointment). You are welcome to stop by to ask questions, work on Lectures: MWF – 8:30 am - 9:20 am (S324) problems, etc. You can also get help in the Science Study Center (S114) every Discussion: W – 9:30 am -10:20 am (S324) day of the week. Lab: T- 8:30 am – 9:20 am (S317)

Contacting me: the best way is probably by email. Please remember that Bellevue College requires us to only communicate by email using the Bellevue College email addresses. Prerequisites: Biol&211 and Chem&261 (or equivalent courses)

Course description This is the first in a two-quarter biochemistry sequence for students preparing to enter the Schools of Pharmacy, Dentistry, Veterinary Medicine, Medicine and undergraduate majors in Chemistry and Biochemistry. The course is divided into two major sections. We begin by reviewing important concepts from biology and chemistry necessary to the study of biochemistry. We introduce amino acids and discuss primary, secondary, tertiary, and quaternary levels of protein structure. We learn about proteins as functional biomolecules via physiologically relevant examples, going into some detail to understand the basis of enzyme catalysis and enzyme kinetics. We discuss biochemical signaling with an emphasis on heterotrimeric G proteins. The second portion of the course primarily covers the principles of metabolism. We study the structure and chemistry of carbohydrates. We discuss glycolysis, the citric acid cycle and glycogen metabolism. We then study the pathways of electron transport and oxidative phosphorylation in eukaryotes. We end the course with a discussion of photosynthesis.

Note: If you require accommodation based on a documented disability, emergency medical information to share, or need special arrangements in case of emergency evacuation, please make an appointment with me as soon as possible. I will do my very best to provide a learning environment that is suitable to your needs. If you would like to inquire about becoming a DRC student you may call 564-2498 or go in person to the DRC (Disability Resource Center) in the reception area in the Student Services Building.

Required Materials: Textbook: Fundamentals of Biochemistry by D. Voet, J. Voet and C. Pratt (3rd edition) A binder for class notes A separate binder (or a section in the class notes binder) for lab work and computer work Course website account (Moodle): Moodle is a course management system that we will use to post course materials, have a discussion forum and many other things (we will not use MyBC). To login, go to http://scidiv.bellevuecollege.edu/moodle. In the login box “create new account” and follow the steps. A confirmation email will be sent to you. Once you have an account , find our class on the main page. To enter you will need an enrollment key, which is “ATPSynthase“. If for some reason you can’t get access to Moodle, contact me ASAP. A basic calculator (you will not be allowed to use your cell phone as a calculator) Soft-side safety goggles with splash guards (available at the bookstore and home improvement stores)

Holidays: Class will not meet on 1/21 and 2/18.

1 Science Division Policy on Cheating : Cheating includes copying answers on tests or assignments, glancing at nearby test papers, swapping papers, stealing, plagiarizing, and illicitly giving or receiving help on exams or assignments -- in short, presenting another's work or ideas as your own. You are expected to conduct yourself with integrity. Academic dishonesty will result in a zero for that assignment and a report to the Dean of Students which may result in suspension or expulsion from the college. If you feel you have been unfairly accused of cheating, you may appeal. Any student found using a cell phone during an exam will automatically get a zero on the assignment.

Studying for this class: From one lecture to the next you should study from the textbook (or from the posted class notes) what will be covered in the next lecture (just follow the detailed schedule on page 3). The expectation is that you will have completed this reading before the next lecture. You are responsible for all material in the reading, including anything not covered in the lecture unless instructed that the material will be omitted. Be aware that the schedule is flexible; attendance in class will keep you up-to-date on the schedule.

Exams: There will be 3 one-hour exams that will take place during the assigned discussion sessions (Fridays) and a comprehensive two-hour final. The dates are on the Tentative Course Calendar (page 4 of the syllabus).  The final exam will not be returned.  The final exam is not optional. If you do not take the final, you will fail! Grade %  You should not expect all problems on tests to be similar to those that you do for homework A 95-100 or to those covered in lecture. A- 90-94  NO make-up exams will be given, except in cases of documented illness or family B+ 85-89 emergency. B 80-84 B- 78-79 Grading: The final grade will be determined as follows. C+ 75-77 C 70-74 3 exams (@ 100 pts each) 300 pts C- 66-69 1 cumulative final (200 pts) 200 pts D 60-65 8 lab reports (@15 pts each) 120 pts F Below 60 10 homework assignments (@10 pts each) 100 pts 720 pts

Re-grading policy: After receiving back any graded paper you have one week from the day it is handed back to submit it for me to recheck the grade. NO exceptions to this policy.

Attendance: I expect that you will make every attempt to be at all lecture meetings. If you miss a class, it is your responsibility to obtain lecture notes, handouts, assignments, announcements, etc. from other classmates or the class website. Please do not email me to ask what you missed.

Conduct: Rudeness, tardiness, chatter during lecture, and disrespect make learning difficult for everyone around you, and will not be tolerated. This also applies to cellular phones and beepers; turn these devices off during class. If you must leave before class ends take your seat towards the side of the lecture room.

How to do well in this class (the Do’s): Attend all lectures; participate in class; be respectful of others, turn in all required work on time; study; come well prepared for the labs and ask what you don’t understand. What to do about what you don’t understand? You can ask me, a classmate or another chemistry teacher at the Science Study Center (S114). Students receiving a grade of C or lower in the class are eligible for individual tutoring through the Academic Success Center. The course moves very fast, so do your best not to get behind!

2 Homework: There will be one homework assignment per week. I will assign the homework on Monday and collect it the next Monday. Homework will be thoroughly graded. The questions and problems on the homework are excellent practice for the exam. The homework key will be posted on Moodle.

Laboratory sessions:  You should come to lab with the proper attire and with safety goggles. You need to keep the goggles on from the time the chemicals are out until they are put away.  The laboratory portion of Chemistry 265 is worth 120 points. There are 8 labs worth 15 points each. Some of the labs are computer exercises and some are “real” labs.  To print the lab handouts go to our Moodle site and you will find a section that has all the labs. Print the correct lab handout before the corresponding lab and bring it to the lab.  You need to read and understand the experiment’s handout before you come to the lab.  Remember that attendance to the lab is mandatory: the lab is an integral part of this course.  There are no make-up labs (no exceptions).

What follows is a detailed list of the topics we will cover, with chapter numbers and pages from our textbook.

Chapter # Page Number of lectures Topic (textbook) numbers The structure of the cell.Thermodynamics’ review 1 1-19 1 (and 1st discussion session) Water, acid-base, buffers 2 22-36 1 Amino acids 4 74-89 2 Protein isolation and purification 5 91-103 1 Primary structure of proteins and chemical evolution 5 104-120 1 Secondary structure of proteins; collagen; globular proteins 6 125-140 1 Tertiary structure of proteins; protein stability; quaternary structure 6 140-161 1 Protein folding; molecular chaperones; conformational diseases 6 161-172 1 Hemoglobin and myoglobin function; abnormal hemoglobins 7 176-197 2 Introduction to enzymes; catalytic mechanisms 11 322-339 1 Lysozyme; serine proteases 11 339-360 1 Enzyme kinetics 12 363-375 1 Enzyme inhibition; control of enzyme activity 12 375-393 1 Biochemical signaling: hormones; receptor tyrosine kinases 13 405-425 1 Biochemical signaling: Tyrosine kinase based signaling 13 428-442 1 Introduction to metabolism 14 448-469 1 Thermodynamics of phosphate compounds; redox reactions 14 469-482 Discussion session Monosaccharides; polysaccharides. 8 219-232 1 Glycosaminoglycans; glycoproteins 8 232-242 1 Glycolysis I 15 485-504 1 Glycolysis II: metabolic regulation and control 15 504-520 1 Glycogen metabolism 16 530-545 1 Control of glycogen metabolism 16 545-560 1 Citric acid cycle 17 567-583 1 Regulation of the citric acid cycle 17 583-590 1 Electron transport and control 18 596-618 1 Oxidative phosphorylation 18 618-637 1 Energy metabolism: integration and energy specialization 22 791-809 1 Photosynthesis 19 641-675 1

“Science, my lad, is made up of mistakes, but they are mistakes which it is useful to make, because they lead little by little to the truth.” ― Jules Verne.

3 Tentative Course Calendar MONDAY TUESDAY WEDNESDSAY THURSDAY FRIDAY 1/2 1/3 1/4 Chapters 1 & 2 Chapter 4

1/7 1/8 1/9 1/10 1/11 Chapter 4 ChemDraw 1 Chapter 5 Chapter 5

1/14 1/15 1/16 1/17 1/18 Chapter 6 ChemDraw 2 Chapter 6 Chapter 6 Last day to withdraw w/o a W 1/21 1/22 1/23 1/24 1/25 NO CLASS Protein Chapter 6 Chapter 7 quantitation Exam1 1/28 1/29 1/30 1/31 2/1 Chapter 7 Size exclusion Chapter 11 Chapter 11 chromatography

2/4 2/5 2/6 2/7 2/8 Chapter 12 Cellobiase 1 Chapter 12 Chapter 13 Enzyme kinetics

2/11 2/12 2/13 2/14 2/15 Chapter 13 Cellobiase 2 Chapter 8 Last day to withdraw Enzyme kinetics Exam 2 with a W Chapter 8

2/18 2/19 2/20 2/21 2/22 NO CLASS ChemDraw PDB Chapter 15 Chapter 15

2/25 2/26 2/27 2/28 3/1 Chapter 16 Metabolic Pathways Chapter 16 Chapter 17 Chart work

3/4 3/5 3/6 3/7 3/8 Chapter 17 ChemDraw PDB Chapter 18 Chapter 18 ATP Synthase Exam 3

3/11 3/12 3/13 3/14 3/15 Chapter 22 Review Chapter 19 Chapter 19

3/18 3/19 3/20 Final Exam 7:30 am – 9:20 am

4