Download CHEM 351 • BIOCHEMISTRY I Syllabus • Fall 2016

CHEM 351 • BIOCHEMISTRY I
Syllabus • Fall 2016
INSTRUCTOR
Professor Charles H. Clapp, RB 216
E-mail: [email protected]
GENERAL LEARNING GOALS (Mapped to Chemistry Department Learning Outcomes)
In Chemistry 351, students will:
•Develop the ability to apply chemical principles to understanding the structures and properties of the major
classes of biological molecules. (2, 3)
•Become familiar with major biochemical pathways and develop an understanding of the energetics,
chemical logic, and regulation of these pathways. (2, 3)
•Develop the ability to solve problems requiring the interpretation of biochemical data and the application of
chemical principles to biological problems (2, 3)
•Gain experience using computer graphics to study the structures of biological molecules and learn to access
data in the Protein Data Bank (2, 5).
•Become aware of some important unsolved problems in biochemistry and medicine, and think about how
basic biochemical tools and principles might be used to make headway in addressing these problems. (3, 8)
COURSE FORMAT
There will be three lectures (M W F, 10:00 a.m.) per week. In addition, each student has been assigned to one of
two recitation sections, M, 1–2 p.m. and T, 11 a.m.–12 noon. These sessions will be used to discuss in more
detail material presented in lecture or in readings, to present new material for discussion, and to discuss problem
assignments. It is very important that you attend recitation each week.
The lectures will utilize both PowerPoint and the chalk board. PowerPoint slides for a particular lecture will be
placed on Moodle the day before the lecture. You should print copies of these slides and bring them with
you to class.
There will be no laboratory in CHEM 351. An intensive laboratory course in Biochemical Methods (CHEM
358/BIOL 340) will be offered in the spring semester.
READINGS
th
The textbook for the course is Lehninger Principles of Biochemistry (6 ed.) by D. L. Nelson and M. M. Cox. In
reading the textbook, you should keep in mind that the goal of the course is to develop a conceptual
understanding of biochemistry that you will be able to apply to problem solving. Rather than trying to memorize
all of the factual details, you should ask yourself whether these details fit into a coherent conceptual framework.
When they do not, you should consult the instructor or one of your classmates or raise the point as a question in
recitation. Comments on chapters in the textbook will be posted on Moodle to help you focus your
reading and thinking on the most important points.
The lectures will be designed to be complementary to the reading in the textbook. To optimize your grasp of the
material, you should carefully study both the text and the class notes. I recommend that you read the sections
relating to a particular class prior to that class. After the class, you can then review the reading and reread key
sections that you did not fully understand the first time through. You will then be prepared to start working
problems.
Some important topics will not be covered in class or will only be partially covered in class, and you will be
expected to master the topic from reading and doing problems. I will alert you to these topics as the course
progresses
Some of the topics we will cover are not covered adequately in your textbook. In these cases, the textbook
readings will be supplemented by readings from the biochemical literature. These will be available in electronic
form on Moodle, and I will alert you to them in class.
CHEM 351 • BIOCHEMISTRY I
Syllabus • Fall 2016 • p. 2
PRACTICE PROBLEMS
Since the purpose of the course is to develop a working knowledge of biochemical principles, considerable
emphasis is placed on problem solving. Problems will be assigned regularly. Some of these will be from the
textbook; others will be in the form of weekly problem sets that will be posted on Moodle. It is recommended that
you do them as soon as possible. Most of these assignments will not be collected, but they will be discussed at
the recitation sessions, and a few will be discussed in class. The problems vary considerably in difficulty. Some
are straightforward; others will challenge you to apply ideas presented in class to topics that have not been
covered in class. In some cases problems will be used to introduce new topics. In all cases it is critical that you
make a determined effort to solve these problems before they are discussed in recitation or class. If you have
difficulty, stop by my office, send me an email, or talk about the problem with a classmate. If you do this, your
learning will be active and much more effective than it will be if you simply listen to other people’s solutions.
Answers to the problem sets will be posted on Moodle. I urge you not to consult these answers until you have
worked through the problems thoroughly on your own. If you get stuck on a problem, feel free to contact me, and
I will assist you without giving you the answer. Consulting one of your classmates may also be helpful.
GRADED ASSIGNMENTS
There will be about five short written exercises to be turned in. These will be assigned at least one week before
the due dates. Some of these graded assignments will require the use of JMol, a molecular graphics program.
Other assignments will require you to interpret results from the biochemical literature.
OFFICE HOURS
Biochemistry is a complex subject, and your goal is to understand it at a conceptual level. If you make a
diligent effort to do this, you will have many questions. I am happy to meet with you individually to discuss
your questions. Rather than setting aside specific office hours, I encourage you to see me after class or send
me an e-mail, and we will arrange to meet at a mutually satisfactory time. You are also welcome to stop by
my office without an appointment. If I am there and doing something that can be interrupted, I will be glad to
talk with you.
OTHER SUGGESTIONS
The amount of material to be covered in the course is considerable, and the pace will therefore be fast. In
addition, the course is designed so that topics build on what has been taught earlier. It is important that you
make a determined effort to avoid falling behind. I expect that the reading, practice problems and written
assignments will require at least eight hours per week outside of class.
As indicated above, if you study and think about the course material carefully and critically, you are likely to have
many questions. An excellent way to clarify your understanding is to discuss these questions with your classmates.
GRADING
There will be three hour exams and a final exam.
The hour exams will be given at 10:00 a.m. on
the days listed at right:
1. Wednesday, September 21
2. Wednesday, October 19
3. Wednesday, November 16
There will also be two or three short quizzes. They will be announced at least one week in advance. The first
quiz will be on Wednesday, September 9.
Grades will be
computed in
two ways:
I. Hour exams.................................... 48%
Graded assignments & quizzes ..... 20 %
Final exam ..................................... 32%
II. Two best hour exams .................... 32%
Graded assignments & quizzes .... 20%
Final exam ..................................... 48%
The higher of the two computed numerical grades will be used in determining your letter grade. No make-up hour
exams will be given; students who miss an hour exam will have their grades computed by the second method.
ACCESS STATEMENT
Any student who may need an accommodation based on the impact of a disability should contact Heather
Fowler, Director of the Office of Accessibility Resources, at 570-577-1188 or [email protected], who will help
coordinate reasonable accommodations for those students with documented disabilities.
CHEM 351 • BIOCHEMISTRY I
Syllabus • Fall 2016 • p. 3
TENTATIVE LECTURE OUTLINE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
Mon 22 Aug
Wed Aug 24
Fri Aug 26
Mon Aug 29
Wed Aug 31
Fri Sept 2
Mon Sept 5
Wed Sept 7
Fri Sept 9
Mon Sept 12
Wed. Sept 14
Fri. Sept 16
Mon Sept 19
Wed Sept 21
Fri Sept 23
Mon Sept 26
Wed Sept. 28
Fri Sept 30
Mon Oct 3
Wed Oct 5
Fri Oct 7
Mon Oct 10
Wed Oct 12
Fri Oct 14
Mon Oct 17
Wed Oct 19
Fri Oct. 21
Mon Oct 24
Wed Oct 26
Fri Oct 28
Mon Oct 31
Wed Nov 2
Fri Nov 4
Mon Nov 7
Wed Nov 9
Fri Nov 11
Mon Nov 14
Wed Nov 16
Fri. Nov 18
39
40
41
42
Mon Nov 28
Wed Nov 30
Fri Dec 2
Mon Dec 5
Cells. Molecules and Energy
Water and Aqueous Solutions
Intro. to Peptides and Proteins
Amino Acids
Primary Structure. Mass spectrometry
Mass spec (cont). Solid-phase synthesis
Three-dimensional Structure
Quiz 1 Quaternary Structure
Protein Folding
Collagen. Post-translational Modification. Myoglobin
Hemoglobin. Allosteric Regulation
Allosteric regulation (cont.). Sickle-Cell Hemoglobin
Enzyme Catalysis and Kinetics
Exam I
Enzyme Kinetics (cont.), Inhibition
Serine Proteases
Acetyl Cholinesterases, Nerve Agents, Cysteine Proteases
Aspartyl and Metalloproteases
Kinases
Synthetases. Allosteric Regulation of Enzymes
Carbohydrates
Fall Break
Carbohydrates and Glycoproteins
Nucleic Acids. Structure and Conformation
Polymerases, Nucleases and Ligases
Exam II
Lipids and Membranes
Membrane Proteins
Receptors. Signalling
Bioenergetics
Biological Redox Reactions
Glycolysis
Metabolism of Pyruvate
Citric Acid Cycle
Oxidative Phosphorylation
Oxidative Phosphorylation
Gluconeogenesis
Exam III
Regulation of Carbohydrate Metabolism
Thanksgiving Break
Fatty Acid Oxidation
Pentose Phosphate Pathway
Glycogen Synthesis and Breakdown
Regulation of Glycogen Synthesis and Breakdown. Wrap up
Chapter 1
Chapter 2
3.1–3.3
3.1
3.4
3.4
4.1–4.3
4.3
4.4
pp. 127–130, 157–163
5.1
5.1
6.1–6.3
6.3
pp. 214–218, 231-232
pp. 218–219, 219-220
pp. 206–207
6.5
7.1
7.1–7.3, pp. 221–223
8.1, 8.2
8.3, pp. 1013–1014, 1024
Chapter 10
11.1–11.3
12.1–12.3, 12.12
13.1–13.3
13.4
14.1
14.3, 16.1–16.2
16.2
19.1–19.2
19.1–19.2
14.4
15.1, 15.3, 16.3, 19.3
17.1–17.3
14.5
15.4–15.5
15.5, 12.2