BIOC 3713 – Biochemistry I (Biomolecules and Biocatalysis)
Fall 2014
Course description (as quoted from the OSU catalog of courses). “Biochemistry of nucleic acids, proteins, amino
acids, carbohydrates, and lipids with an emphasis on the kinetics, thermodynamics, catalytic and regulatory
strategies of biochemical reactions and energetics. Designed for biochemistry majors.”
Prerequisites. You need to have already taken CHEM 3053 (Organic Chemistry I). You can co-enroll in CHEM
3153 (Organic Chemistry II) while taking BIOC 3713.
You should have a working knowledge of algebra, general chemistry, and organic chemistry. In particular,
you will need to rearrange algebraic equations; to use logarithms, exponents, and scientific notation; to understand
the relationships between atomic number, valence, and reactivity; to balance chemical equations; to calculate
chemical concentrations; to use various reaction constants (equilibrium, kinetic, ionization, and pH); to know the
properties (structures, reactivities, and polarities) of major organic groups; to draw reaction mechanisms using
curved arrow notation.
Professor:
Kevin S. Wilson, Ph.D., Assistant Professor & Academic Advisor
http://biochemistry.okstate.edu/faculty/dr.-kevin-wilson/welcome
Department of Biochemistry & Molecular Biology
Oklahoma State University
Office: Noble Research Center 149 (Phone: 405-744-6810)
[Note: open door to lab. My office is in the back of the lab.]
Office hours: Fridays 1:30-2:30pm (or by appointment)
E-mail: kevin.s.wilson@okstate.edu & Twitter: @kevinswilson66
Graduate teaching assistant:
Xiao Chen
Office: 147 Noble Research Center
Office hours: by appointment
E-mail: xiao.chen@mail.okstate.edu
Course time/place:
Tuesdays & Thursdays 10:30AM - 11:45AM, 320 Ag Hall
Textbooks
1. Biochemistry, 7th Edition (2012); by Berg, Tymockzo & Stryer
2. Student’s Companion to Biochemistry, 7th Edition
Internet resources
(Required)
(Recommended)
(Suggested)
https://oc.okstate.edu OSU Desire2Learn (D2L) website. I will upload the slides for each lecture in Microsoft
PowerPoint format on the D2L website. To open these materials, you will need Microsoft PowerPoint software
(provided freely to all OSU students at http://www.it.okstate.edu/services/). I will also post homework
assignments, exam grades, and other course-related materials on D2L. If you need assistance with D2L, contact
the OSU IT Helpdesk (744-HELP).
http://www.whfreeman.com/biochem6 Publisher of our main textbook. This website has useful text-related
movies, quizzes, flashcards, and web links.
http://biochem.science.oregonstate.edu/biochemistry-free-and-easy E-book written by Dr. Kevin Ahern, a popular
biochemistry professor at Oregon State University. Incidentally, Dr. Ahern grew up in Stillwater and graduated
from Oklahoma State U.
http://www.biology.arizona.edu/biochemistry/biochemistry.html Review of basic chemistry relevant to biology.
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1. Course schedule
Date
Lecture (see D2L)
Quizzes & Exams
Reading (text chapter.section)
Aug 18
1-Introduction
1.1 – 1.2
Aug 20
1-Introduction
1.3 – 1.4
Aug 25
2-Proteins
2.1 – 2.2
Aug 27
2-Proteins
Sept 1
Holiday (no class)
Sept 3
2-Proteins
Sept 8
3-Techniques
Sept 10
3-Techniques
3.4 – 3.6
Sept 15
4-NucleicAcids
4.1 – 4.3
Sept 17
4-NucleicAcids
Sept 22
5-DNAReplication
Sept 24
6-Transcription
Sept 29
7-Translation
30.1 – 30.2
Oct 1
7-Translation
30.3, 30.4, 30.6
Quiz 1
2.3 – 2.4
2.5 – 2.6
HW 1 is due.
HW 2 is due.
3.1 – 3.3
4.4 – 4.7
28.1 – 28.5 (parts)
Quiz 2
Oct 6
29.1 – 29.2
Exam 1
Oct 8
8-MolecularBiology
5.1 – 5.3
Oct 13
8-MolecularBiology
6.1 – 6.3 (parts)
Oct 15
9-Hemoglobin
7.1, 7.2, 7.4
Oct 20
10-EnzymeKinetics
Oct 22
10-EnzymeKinetics
Oct 27
10-EnzymeKinetics
Oct 29
11-EnzymeMechanism
9.1 – 9.4 (parts)
Nov 3
12-EnzymeRegulation
10.1 – 10.4 (parts)
Nov 5
13-Carbohydrates
Nov 10
13-Carbohydrates
Nov 12
14-Membranes
Nov 17
14-Membranes
12.5 – 12.6; 13.1 – 13.2
Nov 19
14-Membranes
13.3 – 13.6
Quiz 3
8.1 – 8.2
8.3 – 8.4
HW 3 is due.
HW 4 is due.
8.5 – 8.6
11.1 – 11.2
11.3 – 11.4
Quiz 4
Nov 24
12.1 – 12.4
Exam 2
Nov 26
Thanksgiving (no class)
Dec 1
15-SignalTransduction
Dec 3
16-Review
14.1
Final Exam
Dec 8 (10:00am – 12)
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2. Course activities
Lectures. I will present summaries of each chapter in the textbook. These presentations will include a combination
of my lectures to you (from electronic PowerPoint files, available on D2L, and the chalkboard), and your questions
and responses in class.
The textbook mainly serves as a reference to reinforce and clarify the classroom presentations. You are strongly
advised to attend class regularly, since classes will include non-electronic material (not on D2L), quizzes, and
homework assignments that are due.
Homework. To exercise your understanding of biochemistry, I will assign four homework exercises, which will
come from my own questions as well as selected problems in the textbook. Your homework assignments will be
submitted at various class periods throughout the semester.
Homework assignments will provide opportunities for you to earn extra-credit points. From each
assignment, only one question will be graded. You will receive half-credit (10 points) for simply doing the
homework, and full-credit for correctly answering the graded question. To receive credit, homework must be
submitted at the beginning of class (dates to be announced later), in hardcopy form (no electronic submissions).
Quizzes. There will be four quizzes that will encourage you to keep up with studying biochemistry between the
exams. They will take place at the end of the lecture (on the dates indicated), requiring approximately 15 minutes of
time.
Quizzes will be graded, and like homework, they will provide opportunities for you to earn extra-credit points.
Therefore, the quizzes can only help improve your course grade. Their format will be a combination of shortanswer questions. No make-ups will be allowed on missed quizzes.
Exams. There will be two mid-term exams during the semester, during regular class time. These exams will test
you primarily on material that was covered in my lectures and homework assignments. They may also include some
material from the textbook.
The format of all exams will largely include questions that will ask you to recall specific facts such as
definitions, names, chemical structures, and reactions. They will test your understanding of biochemistry and your
ability to reason and compute solutions of biochemical problems, given specific information. During each exam,
you will not be permitted to use any outside information, including your textbook, paper notes, computers, phones,
etc. You will be allowed to use a calculator (non-programmable) on mid-term exams #1 and #3, and on the final
exam. The mid-term exams will cover material as indicated in the course schedule (see page 2). The final exam will
cover all material in the course. Note that the final exam will start at 10am on Dec 8.
If you miss an exam, you will only be allowed to make it up if you provide a legitimate excuse from a
physician (if you are sick or incapacitated), pre-approved university event (such as athletics), or car mechanic (if
your car is wrecked).
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3. Course grading scheme
points (each)
Exam 1 and Exam 2:
Final Exam:
points (sub-total)
300
400
600
400
points (sub-total):
1000
Extra credit
4 quizzes:
4 homework exercises:
20
20
80
80
points (grand total)
1160
You must earn: at least 900 points to make an A,
at least 800 points to make a B,
at least 700 points to make a C, and
at least 600 points to make a D.
How to earn an A in this course. Biochemistry is a challenging subject to master. It combines reasoning skills in
chemistry, mathematics, and logic with the complexity of biology at the molecular level. Fundamentally, living
processes do obey the laws of chemistry and physics. This is the particular power of learning biochemistry.
To master biochemistry and to earn an A, you should study regularly and attentively, as in other courses.
Try to read the assigned sections on the text before each lecture. Review your notes promptly after class, re-read the
text, and be sure to see me if your have unresolved questions or need clarifications. You should remember
biochemical structures and mechanisms, by drawing them on a blank sheet of paper repeatedly from memory. The
homework assignments are designed particularly to exercise your reasoning skills. The quizzes are designed to test
your knowledge of biochemistry. The exams are designed to test your cumulative comprehension of biochemistry.
On the exams, you will likely see similar questions from the homework and quizzes. Strive to understand the
underlying chemical and physical logic of biochemistry, and you will do very well in this course.
4. Course learning objectives
This course will build up from atoms to building blocks (amino acids, nucleotides, sugars, and lipids) of biological
polymers (proteins, nucleic acids, carbohydrates, and fats). Ultimately, biochemistry has to be presented in the
context of cells, organs, and organisms. While it is almost impossible to remember every fact in the text and
lectures, I do expect you to know important chemical structures, reactions, and biochemical pathways. I will points
these out to you in lectures as the course progresses, so that you will know what to study in preparation for each
exam. More importantly, you should strive to understand the chemical logic of biological molecules and reactions.
Biochemistry is very much an experimental science, still under rapid development. You will hear about
experimental techniques that are used to obtain some of the facts that are presented in the textbook.
1. Using the Henderson-Hasselbalch equation, determine the charge and protonation state of biomolecules in
physiological solutions, and describe their behavior and function in terms of their state.
2. Master the basic principles of protein structures. You will be able to recognize and sketch all 20 amino acids,
and classify them according to their properties. You will be able to recognize and define the folding of proteins
in terms of their primary, secondary, tertiary, and quaternary structures. You will be able to define protein
folding in terms of the rotational conformation of the polypeptide backbone and interactions of the amino acid
residues. You will be introduced to a variety of experimental techniques for studying structure and function of
proteins, including types of chromatography, electrophoresis, mass spectrometry, X-ray crystallography, and
NMR spectroscopy.
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3. Master the basic principles of nucleic acid structure and function. You will be able to recognize and sketch the
bases, pairing, and backbone of nucleic acids. You will be able to recognize and describe the differences
between DNA and RNA in both structure and function in living cells.
4. Be introduced to the flow of genetic information. You will learn about the genetic code, the biochemical
machineries that transcribe DNA into RNA, and translate RNA into protein. You will be introduced to a variety
of experimental techniques for sequencing genomes, cloning genes, and regulating gene expression in bacteria
and eukaryotic cells.
5. Be introduced to genetic sequence analysis and evolution. You will learn about bioinformatic computations,
which are used to classify life forms, identify genes, predict protein structure and function, and identify
mutational differences that are correlated to human health and disease.
6. Visualize and understand how the conformational flexibility of proteins regulates their functions. You will
study several case examples, including hemoglobin, myoglobin, myosin, and metabolic enzymes.
7. Analyze and quantify the kinetics of enzyme reactions. You will learn about mechanisms of enzyme inhibition
and regulation.
8. Analyze catalytic mechanisms of enzymes. You will study several case examples, including trypsin,
chymotrypsin, carbonic anhydrases, restriction enzymes, and ATPases.
9. Master the basic principles of the structure and function of carbohydrates and lipids.
10. Be introduced to the components and organization of cell membranes. You will learn about phospholipids,
membrane proteins, ion channels, and ATPase pumps.
11. Be introduced to signal-transduction pathways. You will learn about hormone receptors, GTPase amplifiers,
and cAMP second messengers. You will study a few case examples, including insulin and Ras pathways, and
correlate defects in them to diabetes and cancer.
12. This course will cover a large territory of information, which will lay the groundwork for tackling many
specialized areas of biological science. Therefore, you should strive to understand how biomolecules work
together to carry out the myriad tasks in cells. Hopefully, you will begin to see the unifying chemical logic that
underlies life in all of its great diversity. That is the most important lesson to glean from this course.
5. Other important information
Research Opportunities. Undergraduate Research in Biochemistry (BIOC 4990): 1-6 credits, up to a maximum of
10. You can contribute toward a real, ongoing research project within a laboratory of the Department of
Biochemistry & Molecular Biology. Responsibilities: 1 credit = minimum of 3 hours of lab work per week for an
entire semester. You would normally work under supervision of a graduate student. Your project would culminate
with a presentation of the results of your project to the professor and other lab members.
The following points bear repeating …
Syllabus Attachment. The faculty of OSU is very concerned about your success as a student. For further
information see: http://academicaffairs.okstate.edu/faculty-a-staff . A copy of the BIOC 3713 course syllabus and
the OSU Syllabus Attachment are posted on D2L for your convenience.
Academic integrity. Academic dishonesty or misconduct is defined in the Oklahoma State University Policy and
Procedures Letter 2-0822. You should become familiar with this document as a matter of self-interest. There is
absolutely no tolerance for academic dishonesty or misconduct. For further information, see:
http://academicintegrity.okstate.edu/ . If you are caught plagiarizing on homework or cheating on an exam, the
minimum penalty will be zero points for that document, and it will not be dropped from your score for the course.
Violations may extend to receiving an “F” for the course, or suspension from OSU.
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Disabilities. If you have special needs, please contact the Office of Student Disability Services (315 Student Union;
http://sds.okstate.edu) as soon as possible, and we will provide reasonable accommodations for you.
Important dates
Aug 26
Aug 30
Nov 8
Non-restrictive Add/Drop deadline. Last day to add a course or drop a course with no
grade. Does not require instructor permission. 100% refund.
Restrictive Add/Drop deadline. Last day to add a course, or to drop a course with no
grade attached. Requires instructor permission. 50% refund.
W Drop deadline. Last day to drop a course with grade of W. Requires advisor signature.
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