BIOC 3653: Survey of Biochemistry - Biochemistry and Molecular ...

BIOC 3653: Survey of Biochemistry
Fall 2009
Instructor:
Dr. Ben Sandler
348G Noble Research Center
405-744-6194
benjamin.sandler@gmail.com
Chief Teaching Assistant:
Steven Pennington
142J Noble Research Center
steven.pennington@okstate.edu
Teaching Intern:
Edward Van Matre
edward.van_matre@okstate.edu
Lecture: MWF 11:30-12:20PM, Ag Hall 101
Office Hours:
Ben Sandler: MWF 2:30-3:20, 348G NRC, or by appointment.
Review sessions TBA.
Text: Biochemistry: A Short Course, Tymoczko, Berg, and Stryer, 2010. (Required.)
“Skeleton Key” study guides, (by Dr. Sandler, free on the D2L site. Required.)
The Secret Life of Equations, (by Dr. Sandler, free on the D2L site. Recomended.)
Prerequisites:
You are expected to have a working knowledge of algebra, general chemistry, and
organic chemistry. You will need to be able to use logarithms, exponents, and scientific
notation; to rearrange algebraic equations; to balance chemical equations; to understand
the relationships between atomic number, valence, atomic structure, and reactivity; to
calculate pH and use equilibrium constants and ionization constants; to know the
properties (such as reactivity and polarity) of the major chemical functional groups; to
know how to calculate concentration, among other skills. If you feel like you’re rusty on
any of these, you must refresh your memory of these topics before the first exam.
Note: you will not be allowed to use a calculator on exams. Make sure you know how to
calculate simple logarithms (such as log 0.01=?) with pencil and paper.

D2L website:
https://oc.okstate.edu
The D2L site is an essential part of this class. It is your responsibility to check this site
regularly for announcements, homeworks, grades, etc. The Powerpoint files for lectures
will also be posted here. Keep your eye on the site as additional resources are added!
Lecture Videos:
Videos of the lectures will be available through the course website. (Instructions on how
to view these videos will also be posted.)
Homeworks:
Homework problems will be regularly assigned and posted on the D2L website. In
general, they will be assigned on a Friday and due on the following Friday. As usual,
write clearly- unintelligible responses will receive a zero. These homeworks will be spotgraded
(i.e., we will pick a subset of questions to grade on each homework,) and you will
also receive some points for completing all the questions, even if your answers are
incorrect.
You are encouraged to work collaboratively on the homeworks. But, do not copy other
people’s homeworks- even when you work together, your final answer must be your own,
written in your own words.
In order to be considered complete, answers to homework questions must show all your
work, complete with your reasoning and calculations, and be presented in a neat and
organized fashion. Remember, the goal is not merely to learn the material, but also to
learn how to communicate your knowledge effectively.
Exams:
There will be four exams, 50 minutes each, during the semester. You will need to bring
your own orange Scantron sheet to each exam. For some exams, you may also need a
non-programmable, single-line scientific calculator. Be sure to write clearlyunintelligible
responses will get a zero!
All exams are closed-book, closed-notes. Use of any notes, either on paper or on a
calculator, is not permitted and will be considered cheating, and dealt with accordingly.
Use of a calculator on a non-calculator exam will also be considered cheating.
The lowest score on a midterm will be dropped. The final exam will be 2 hours long, and
will cover information from the entire course.
Makeup exams:
There will be no makeup exams. If you miss an exam, it will be given the same grade as
your final exam grade.

Grading Scheme:
Letter grades will be determined using the following scheme. The professor reserves the
right to lower these cutoffs for specific exams, if necessary. Note: the carets are “greater
than” signs. Thus 97 is an A, and 97.1 is an A+.
>97 A+ >77 C+ > 50 F+
>93 A >73 C >30 F
>89.9 A- >69.9 C- 87 B+ >67 D+
>83 B >63 D
>79.9 B- >59.9 D-
Your grade will be a weighted average of your letter grades on exams and assignments.
(To average letter grades, convert them to numbers using 12=A+, 11=A, 10=A-, 9=B+,
etc.) This is why we use the F+ grade: it enables students to pull up their grade if they
fall just below the boundary for passing. Do not use your numerical grades to calculate
your grade in the class! Always convert them to letter grades first, using the scheme
shown above, or using the curved grading schemes posted for curved exams.
Three highest exams of four: 20% each 60%
Homeworks 20 points each 10% total
Comprehensive Final Exam 30%
Total 100%
For example, suppose a student got a 96 (A) on her homework, an 83 (B-), a 78 (C+), a
92 (A-), and a 67 (D) on her midterms, and a 89 (B+) on the final. Her final grade would
be:
0.1 x (A) + 0.6 x (average of B-, C+, and A-) + 0.3 (B+) =
0.1 x (11) + 0.6 (7 + 6 + 10) /3 + 0.3 x (9) = 1.1 + 4.6 + 2.7 = 8.4 = B
If you want to calculate a rough estimate of your current grade, you can do it like this:
[0.1 x (average HW letter grade thus far) + 0.6 x (average of midterm letter grades)]/0.7
= current grade.
Students often want to calculate what grade they must make on the final in order to make
a particular grade in the class. You can calculate that using the following formula and
solving for Y:
0.1 x (HW grade) + 0.6 x (avg of midterm grades) + 0.3 x Y = desired letter grade.

Academic dishonesty or misconduct:
Students are, as always, expected to follow the rules. Academic dishonesty or
misconduct is defined in the OSU Policy and Procedures letter 2-0822. If you are found
to have engaged in dishonesty or misconduct, the punishment will be at minimum an F on
an exam or assignment, up through an F in the course or worse.
Disabilities:
If you have special needs, please contact Dr. Sandler as soon as possible so that we can
work with you and the Office of Disabled Student Services (326 Student Union) to
provide reasonable accommodations for you.
How to Make an A in This Class:
Biochemistry is very different from many of the courses you’ve taken before. You need
to learn a great deal of material, and understand how it all fits together. The ability to
think and problem solve will be very important, not only because your exams will ask
you “puzzle questions” about biochemistry, but because that kind of thinking will help
you to organize and understand all of the facts that you need to learn. Merely being able
to “plug and chug” an equation or memorize a graph will not enable you to do well in
this class! It is essential that you genuinely understand what the material means. I have
written some course materials, available through the D2L site, that will help you do this.
Make flash cards for all the facts that you encounter in class, with a question on one side,
and the answer on the back. Many students have found it helpful to make a second set of
flash cards, each of which has a diagram on one side, and an annotated copy of the same
diagram on the back. (For example, it might have a picture of the Citric Acid Cycle on
the front, with explanations on the back of what’s going on at each step.) Or, make “idea
maps” showing how the ideas are connected together. (I will show you some of these in
class, and will increasingly leave it to you to make your own as the class goes on.) Use
construction paper to make tokens indicating different biomolecules, and use these tokens
to act out the processes you learn about in class.
Many students assume that they can do badly on the midterms and bring their grade up if
they do well on the final. This generally will not work, because the final only counts for
30% of your grade. Don’t wait until the last minute to do well in this course!
What to Study:
You are only required to read the sections of the textbook that are covered in lecture.
Exam questions will be taken from the lectures and Skeleton Keys, not from the textbook.
Attendance:
Attendance is strongly encouraged, but regular attendance is not required. For paperwork
purposes, we will be taking roll every day starting on the second Wednesday, until
roughly the midpoint of the semester. Only sign your own name! If one student is
caught having signed in another, they will both receive a zero on two exams.

Student learning outcomes for BIOC3653
Below are listed some major learning outcomes for this course.
1. Students, given the Henderson-Hasselbalch equation, will able to perform pH
calculations, predict the charge and protonation state of biomolecules in physiological
solution, and describe their behavior and function in terms of their state.
2. Students will master the basic principles of protein structure. They will be able to
recall, identify, and sketch all 20 amino acids, and classify them according to their
properties, including the special properties of glycine, alanine, proline, and cysteine.
They will be able to recall, define, and identify primary, secondary, tertiary, and
quaternary structure. They will be able to recognize the alpha helix and beta sheet in
both two- and three-dimensional representations of backbone traces and ribbon diagrams.
Students will be able to recall and produce a written explanation of the principles of
several techniques of protein purification, based on the properties of proteins. They will
be able to recall and explain, in writing, the rationale behind experiments that use these
techniques, including the purification of both novel and cloned proteins.
3. Students will master the basic principles of nucleic acid structure and function. They
will be able to recall and identify the differences between purines and pyrimidines, and
between bases, nucleosides, and nucleotides. They will be able to recall, list and describe
the differences between DNA and RNA, and explain the ways these differences affect the
function and behavior of nucleic acids. They will be able to recall and produce written
explanations of the principles of techniques for manipulating RNA and DNA.
4. Students will be able to produce a written explanation of how biological systems use
randomness and selection to produce new information. They will be able to recognize
features of biochemical systems as products of divergent or convergent evolution.
5. Students will master the principles of Gibbs Free Energy. Students will be able to
make both quantitative and qualitative predictions of the outcome of a reaction, or of the
distribution of conformational states of an enzyme, given either qualitative or quantitative
information about the thermodynamics of the system. This includes being able to
perform calculations involving ∆G, ∆G o , and ∆Eo, once given the equations. Students
will be able to explain, in writing, where the energy comes from to drive given enzymatic
reactions or changes in protein conformation.
7. Students will be able to recall and explain in writing the significance of kcat, Vmax,
and Km for enzyme kinetics. They will be able to recall and explain in writing the
mechanisms of inhibition of competitive, uncompetitive, and noncompetitive inhibitors,
and how these mechanisms result in their effects on the kinetic parameters.

8. Students will be able to recall and describe in writing, using standard conventions, the
structures and roles of carbohydrates in cells. They will be able to describe, in writing,
how differences in the structures of these molecules result in differences in their
properties and roles.
9. Students will be able to recall and describe in writing, using standard conventions, the
structures and roles of lipids and membranes in cells. They will be able to describe, in
writing, how differences in the structures of these molecules result in differences in their
properties and roles.
10. Students will be able to recall, recognize, list, and explain important features held in
common by a range of signal transduction pathways.
11. Students will be able to recall and explain in writing how carbohydrates, lipids, and
proteins are broken down by the body, how energy is extracted from them, and how that
energy is stored as ATP.
12. Students will be able to recall, list, and explain in writing the differences between
lipid synthesis and breakdown.
13. Students will be able to recall and define in writing a number of important
biochemical terms.

Tentative Lecture, Quiz, and Exam Schedule, Fall 2009
DATE Topic Chapter HW due
AUG.
Mon. 17 Introduction. Assessment Quiz. 1-2
Wed. 19 Chemistry review. Protein composition and structure 3,4
Fri. 21 Protein composition and structure 3,4
Mon. 24 Exploring proteins and proteomes 38, pg 602-608
Wed. 26 Exploring proteins and proteomes 38, pg 602-608
Fri. 28 DNA and RNA 32, pg 520-525
Mon. 31 Exploring genes and genomes 32, pg 520-525
SEP.
Wed. 2 Exploring evolution and bioinformatics HW1
Fri 4.
Exploring evolution and bioinformatics
Mon. 7
HOLIDAY
Wed. 9 Exam 1 (Chapters 1-6)
Fri. 11 Basic concepts on enzyme action 5
Mon. 14 Kinetics and regulation 6
Wed. 16 Mechanisms and inhibitors 7
Fri. 18 Mechanisms and inhibitors 7
Mon. 21 Hemoglobin, an allosteric protein 8
Wed. 23 Carbohydrates 9
Fri. 25 Lipids and cell membranes 10, pg 156-164 HW2
Mon. 28 Signal-transduction pathways 12
Wed. 30 Introduction to metabolism 14, & pg 301-306
OCT.
Fri. 2 Exam 2 (Chapters 7-12, 14)
Mon. 5 Glycolysis 15
Wed. 7 Glycolysis and gluconeogenesis 15, 16
Fri. 9
FALL BREAK
Mon. 12 Glycolysis and gluconeogenesis 16
Wed. 14 The citric acid cycle 17
Fri. 16 The citric acid cycle 18
Mon. 19 The citric acid cycle 18
Wed. 21 Oxidative phosphorylation 19
Fri. 23 Oxidative phosphorylation 19, 20
Mon. 26 Oxidative phosphorylation 20 HW3
Wed. 28 The light reactions of photosynthesis 21
Fri. 30 The light reactions of photosynthesis 21
NOV.
Mon. 2 Exam 3 (Chapters 15-18)
Wed. 4 Glycogen metabolism 23
Fri. 6 Glycogen metabolism 24
Mon. 9 Fatty acid metabolism 26
Wed. 11 Fatty acid metabolism 26,27
Fri. 13 Fatty acid metabolism 27
Mon. 16 Protein turnover and amino acid catabolism 31 HW4
Wed. 18 Protein turnover and amino acid catabolism 31
Fri. 20
Integration of metabolism
Mon. 23 Exam 4(Chapters 19, 21-23, 27)
Wed 25, Fri. 27
THANKSGIVING
Nov 30-Dec 4
Dead week: Review
Fri. 11
10:00-11:50 FINAL EXAM