BIOC 3713 - Biochemistry I - Biochemistry and Molecular Biology ...

BIOC 3713 - Biochemistry I (Biomolecules and Biocatalysis) - Fall 2011
Instructor:
Lectures:
Text:
Kevin S. Wilson, Ph.D.
Assistant Professor & Academic Advisor
Department of Biochemistry & Molecular Biology
Oklahoma State University
kevin.s.wilson@okstate.edu @kevinswilson66
http://biochemistry.okstate.edu/faculty-research-1/kevin-wilson
Tuesdays & Thursdays 10:30AM - 11:45AM, 348B NRC
Biochemistry, 6 th Edition (2007); by Berg, Tymockzo & Stryer (Required)
Student’s Companion to Biochemistry, 6 th Edition (Recommended)
Office Hours: Tuesdays 12:00PM - 1:00PM (Additional times by appointment; mobile: 405-385-3900)
Teaching office: 142G Noble Research Center (405-744-6707)
Teaching Assistant:
Steven Pennington
steven.pennington@okstate.edu
TBA and by appointment
Prerequisites: CHEM 3053 and CHEM 3153. 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.
Course Description: 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.
Internet Resources:
https://oc.okstate.edu OSU Desire2Learn (D2L) website. Look for course materials listed in “BIOC 3713-
Biochemistry I”.
http://www.whfreeman.com/biochem6 Useful text-related movies, quizzes, flashcards, and web links
http://www.biology.arizona.edu/biochemistry/biochemistry.html Review of basic chemistry relevant to biology
I will upload the slides for each lecture in Microsoft PowerPoint format on the D2L website. To open these
materials, you will need to have 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 to access D2L, contact the OSU IT Helpdesk (744-HELP) without delay.
Extracurricular 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.
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BIOC 3713 (Fall 2011): Tentative Schedule of Lectures and Exams
Date Lecture Text (chapter.section)
Aug 23 1. Introduction. Chemistry review. Assessment quiz. 1.1 – 1.4
Aug 25 2. Protein composition and structure 2.1 – 2.3
Aug 30 3. Protein composition and structure 2.4 – 2.6
Sept 1 4. Exploring proteins and proteomes 3.1 – 3.3
Sept 6 5. Exploring proteins and proteomes 3.4 – 3.6
Sept 8 6. DNA, RNA, and the flow of genetic information 4.1 – 4.2
Sept 13 7. DNA, RNA, and the flow of genetic information 4.3 – 4.4
Sept 15 Mid-Exam 1 (Lectures 1–7; Text 1.1–4.4)
Sept 20 8. Introduction to RNA synthesis 4.5, 4.7, 29.1
Sept 22 9. Introduction to protein synthesis 4.6, 30.1
Sept 27 10. Introduction to protein synthesis 30.2 – 30.4
Sept 29 11. Exploring genes and genomes 5.1 – 5.2
Oct 4 12. Exploring genes and genomes 5.3 – 5.4
Oct 6 13. Exploring evolution and bioinformatics 6.1 – 6.3
Oct 11 14. Exploring evolution and bioinformatics 6.4 – 6.5
Oct 13 Mid-Exam 2 (Lectures 8–14; Text 4.5–6.5, 29.1, 30.1–30.3)
Oct 18 15. Hemoglobin: Portrait of a protein in action 7.1 – 7.2
Oct 20 16. Hemoglobin: Portrait of a protein in action 7.3 – 7.4
Oct 25 17. Enzymes: Basic concepts and kinetics 8.1 – 8.3
Oct 27 18. Enzymes: Basic concepts and kinetics 8.3 – 8.6
Nov 1 19. Catalytic strategies 9.1 – 9.4
Nov 3 20. Regulatory strategies 10.1 – 10.4
Nov 8 Mid-Exam 3 (Lectures 15–20; Text 7.1–10.4)
Nov 10 21. Carbohydrates 11.1 – 11.4
Nov 15 22. Lipids and cell membranes 12.1 – 12.3
Nov 17 23. Lipids and cell membranes 12.4 – 12.6
Nov 22 24. Membrane channels and pumps 13.1 – 13.3
Nov 24
Thanksgiving (no class)
Nov 29 24. Membrane channels and pumps 13.4 – 13.6
Dec 1 26. Signal transduction pathways 14.1 – 14.5
Dec 6 Mid-Exam 4 (Lectures 21–26; Text 11.1 – 14.5)
Dec 8
Review
Dec 13
Final Exam (Cumulative): 10:30AM in 348B NRC
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Exams: There will be four 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 previous page indicates the topics that will be covered on each mid-term exam. The
final exam will be cumulative, covering all material.
To give you an idea of what you can expect, the exam questions will resemble the homework assignments.
Questions 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. To receive credit, you must respond both intelligibly and legibly to each
question. During each exam, you will not be permitted to use any outside information, including your textbook,
paper notes, computers, phones, etc. A calculator will only be allowed on certain exams, which I will indicate to
you.
Your top three exam scores will be used in computing your final grade for the course. There will not be any
makeup exams. If you miss an exam, your grade will be determined from your remaining three exams.
Homework: To give you exercise your understanding of biochemistry, I will assign approximately five sets of
homework problems. I will announce these assignments and post them on D2L.
You are encouraged to work together in study groups on these problems. However, your answers to these problems
should be written in your own words. Problems that involve calculations should include all of your reasoning to
arrive at your numerical answer.
Attendance: Your attendance of the lectures is important for you to effectively master biochemistry. Although
attendance is not strictly required, I am required to report attendance history, so I will take a daily class roll.
Starting the second week of class, I will circulate a list of names. You will sign beside your own name. Make sure
you sign in every day, and only sign your own name.
Grading Scheme:
points
total points
3 mid-term exams (top scores): 200 600
5 homework assignments: 20 100
final exam: 300 300
course: 1000
You must earn at least 900 points to make an A,
at least 800 points to make a B,
at least 650 points to make a C, and
at least 500 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.
Therefore, 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 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
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experimental techniques that are used to obtain some of the facts that described in the text. The homework
assignments are designed particularly to exercise your reasoning skills. You will likely see similar problems on the
exams.
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. For the exams, you should remember
biochemical structures and mechanisms, by drawing them on a blank sheet of paper repeatedly from memory.
Finally, practice the assigned problems and explore the suggested resources on the internet, to gain a deeper
perspective of biochemistry. Strive to understand the underlying chemical and physical logic of biochemistry, and
you will do very well in this course.
Learning Objectives: As a preview, I have listed below some of the major things that you will learn in this course.
Many concepts and terms may not make sense to you now. They should become very clear to you by the end of this
course.
1. Using the Henderson-Hasselbalch equation, determine the charge and protonation state of biomolecules in
physiological solution, 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.
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.
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Syllabus Attachment: The faculty of OSU is very concerned about your success as a student. The following link
provides answers to questions most often asked by students:
http://academicaffairs.okstate.edu/faculty-a-staff/46-syllabus-attachment
A copy of the BIOC 3713 course syllabus and the OSU Syllabus Attachment are posted on D2L for your
convenience.
The following points bear repeating …
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 (without exception). For additional information,
see: http://academicintegrity.okstate.edu/ .
Note: 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.
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 29 Last day to add a course or drop a course with no grade, without instructor permission, and
100% refund.
Sept 2 Last day to add or drop a course with grade of W, with instructor permission, and 50%
Refund.
Nov 11 Last day to drop a course with automatic grade of W, 50% refund.
Dec 2 Last day to withdraw from all courses with an assigned "W" or "F".
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