CHEM 4341 / BIOL 4341: Biochemistry I

Fall 2016 Syllabus (subject to revisions)

Lecture: Wednesday, 9:00-11:50 am, Bayou 3326

Textbook (required): Nelson and Cox, Lehninger Principles of Biochemistry, 6th ed., W. H. Freeman &
Co., 2013, ISBN-13: 978-1-4292-3414-6.

Instructor: Dr. Arcadius V. Krivoshein, Bayou 3121-36, krivoshein@uhcl.edu, phone (281) 283-3785
Office hours (Bayou 3121-36): Wednesday, 12:00-2:00 pm, or by appointment.

Teaching assistant (TA): Maureen Odhiambo, acquinie@yahoo.com, (832) 517-9092

Prerequisite: at least one semester of Organic Chemistry

Some of the prerequisite material essential for this course is:
Organic chemistry: relevant functional groups and molecules, relevant reactions (including, but not
limited to, hydrolysis and condensation, reduction and oxidation, SN2), weak (non-covalent) interactions
(ionic bonds, van der Waals forces / London dispersion forces, dipole-dipole interactions, hydrogen
bonds), resonance structures, aromatic compounds, stereochemistry, spectroscopy (IR, NMR, UV-Vis),
mass spectrometry, chromatography.
General chemistry: electronegativity, covalent chemical bonds, coordination complexes / coordinate
bonds, weak (non-covalent) interactions, absorption of light and the Beer-Lambert-Bouguer law, rate
and equilibrium constants, the law of mass action (Keq), G and thermodynamics, Le Chatelier principle,
catalysis, electrolytic dissociation, pKa and pH, Henderson-Hasselbalch equation, molar and weight
concentrations, preparation of solutions.

Course description: Biochemistry course is a two-semester sequence. The goals of Biochemistry I

course are: (i) to introduce students to the basic concepts of biochemistry and (ii) to review the key
biomolecules (amino acids, proteins and enzymes, carbohydrates, nucleic acids, lipids, coenzymes,
vitamins, and other physiologically and pharmacologically active small molecules). The relationship
between biological function and chemical structure and reactivity is explored using the fundamental
chemical and physical principles; therefore, a solid working knowledge of general and organic chemistry
is essential. Independent reading of the textbook as well as reading beyond the textbook will be required.

Course objective: to gain an understanding of biologically relevant chemical structures and reactions
and to be able to explain complex biological processes using simple rules of chemistry and physics.
Detailed learning objectives:
1. Know structure and reactivity of amino acids: being able to associate names and structures, know
typical pKa values for -NH2 and -COOH groups, know approximate pKa values of the side chains
2. Understand structure and function of proteins: know function of selected classes of proteins
(myoglobin and hemoglobin, immunoglobulins, receptors, ion channels)
3. Learn the fundamental concepts of enzymology: coenzymes and cofactors, catalytic mechanisms,
Michaelis-Menten kinetics (Vmax, Km, kcat), inhibitors, regulation of enzymatic activity
4. Have a basic knowledge of protein chemistry: protein quantitation (UV spectrophotometry, color
reactions), mass spectrometry, peptide synthesis, Edman degradation, chemical modification of
proteins
5. Know structure, reactivity, and function of carbohydrates
6. Know structure of nucleic acids and its relation to the molecular basis of heredity and gene
expression
7. Know structure, physical properties, and function of lipids and architecture and function of
biological membranes
8. Understand fundamental principles and applicability of biochemical separations: centrifugation,
dialysis and ultrafiltraton, size exclusion chromatography (gel filtration), ion exchange
chromatography, affinity (biospecific) chromatography, SDS-PAGE, isoelectric focusing
9. Being able to do pertinent calculations

Class policies:
Food (including chewing gum) may not be consumed in classrooms; smoking is not permitted.
Violations may result in up to 5 point penalty toward your final grade and disciplinary measures.
Cell phones may not be used in class and students must take them off the tables and ensure they
are turned off or to silent mode. Other electronic devices (such as MP3 players etc.) are also
prohibited. The use of cell phones (including texting) and other electronic devices in class may
result in up to 5 point penalty toward your final grade.
Laptops or tablets/iPads are allowed during the lectures for the purpose of note taking only. Any
other uses (such as surfing the Internet, checking e-mail, watching videos etc.) may result in up
to 5 point penalty toward your final grade.
You are expected to bring a conventional (non-cell-phone-based, non-programmable) electronic
calculator (scientific, with logarithm capability) to tests and the final exam. Use of any other
electronic devices (including cell phones, laptops, tablets/iPads etc.) during tests/exam will
automatically result in an F (zero) grade for that test/exam.
Online quizzes: Online quizzes that are aimed to promote homework will be administered through the
Blackboard. They will be posted on Wednesday evenings and will be due following Tuesdays before
midnight. Late quizzes will not be accepted and will receive an F (zero) grade. Students are
welcome to discuss questions about the quizzes with Dr. Krivoshein during his office hours.
If you experiencing technical difficulties with submitting online quiz on the Blackboard, you need to e-
mail Dr. Krivoshein before the deadline, state the nature of the problem, and list the questions and your
answers.

Baseline test: A baseline test aimed at determining student preparation and knowledge of prerequisite
material will be administered on Jan 20. The test will be graded and returned to you, but its score will
not count toward your course grade. However, this baseline test it mandatory - a student who misses it,
will receive a 5% grade penalty for the subsequent in-class test, unless the absence was due to
circumstances beyond his/her control, and a written proof has been provided to Dr. Krivoshein.
Circumstances beyond students control: sickness, family emergency, military duty, jury duty.

In-class tests: 30-35-min tests will be given at the beginning of lecture every other week on the days
specified in the lecture schedule. These tests will emphasize understanding of basic laws, reactions, and
phenomena, as well as the ability to do pertinent calculations and will be composed of: (i) long answer
questions (about one-page answer with drawings will be required); (ii) short answer questions (a few
sentences will be required as an answer); (iii) multiple choice questions; (iv) numerical problems. Some
of the questions from previous tests will be repeated (in the same or modified form) in subsequent tests.
Graded tests will be available for pick up and discussion in Dr. Krivosheins office by appointment
starting 9 am on Fridays; they will be brought to class the following Wednesday.
Final exam: cumulative.
Absence policy for tests and exams: Attendance of in-class tests and the final exam is mandatory. As
a rule, no make-up tests or exams will be given. A student who misses not more than two tests due to
circumstances beyond his/her control and provides a written proof to Dr. Krivoshein, will be given no
grade for those tests; the overall grade will be determined based on grades for other tests. Missed final
exam will result in Incomplete grade for the entire course.

Lecture attendance: Timely arrival is expected. Lecture slides will be posted on the Blackboard after
the lectures. However, it is important to keep in mind that lecture slides are just visual aids for the
lectures, but not the lectures themselves; if you missed a lecture, it is your responsibility to get lecture
notes from your classmates. Attendance of lectures is strongly suggested (but not required).

Academic Honesty: The UHCL Honesty Code requires students to be honest in all their academic
activities and not to tolerate dishonesty. For first incident of cheating (including plagiarism and
falsification of records), the assignment (exam, test, online quiz etc.) will receive an F (zero) grade. An
additional incident of cheating will result in an F grade for the entire course. See UHCL Academic
Honesty Policy (http://prtl.uhcl.edu/dean-of-students/files/academic-honesty-policy.pdf).
Disabilities: In accordance with federal law, it is the Universitys policy to comply with the Americans
with Disabilities Act. If you believe that you have a physical, learning, or psychological disability that
requires an academic accommodation, contact the Disability Services office
(http://prtl.uhcl.edu/disability-services/accommodations).

Dropping the course. Before dropping this course, you are encouraged to talk to the instructor, Dr.
Krivoshein, or to your faculty advisor. The instructions for dropping a class can be found here:
http://prtl.uhcl.edu/eservices/students/academics/DropaClass.pdf. You should be aware of the 6 Drop
Rule (http://prtl.uhcl.edu/registrar/6-drop-rule).

Evaluation:
Online quizzes 30 course points (lowest grade will be dropped)
In-class tests 40 course points (lowest grade will be dropped)
Final exam 30 course points

The course points (maximum 100) will be converted to the letter grade according to this table:
Letter Grade Course points Grade points per semester hour
(GPA equivalent)
A 90 4.000
A- 87-90 3.667
B+ 83-86 3.333
B 79-82 3.000
B- 75-78 2.667
C+ 71-74 2.333
C 67-70 2.000
C- 63-66 1.667
D+ 59-62 1.333
D 55-58 1.000
D- 51-54 0.667
F <51 0.0

Grade appeals: Students should first discuss concerns about grading and other academic issues with the
instructor, Dr. Krivoshein. If this fails to resolve the matter, then meet with the Chair of the Department,
Dr. Magdy Akladios. If no resolution results, the student may submit a written appeal - one that states
clearly the case that the grade inaccurately reflects your performance - to the Associate Dean, Dr. Ju H.
Kim. Ultimately, the appeal may go to the Dean, Dr. Zbigniew J. Czajkiewicz, who makes the final
determination in the matter. You must file the appeal within 45 days of the grade assignment.
Lecture schedule (relevant chapters in the textbook are given in parentheses)

Date Topic
Aug 24 Introduction; Baseline test
Aug 31 The foundations of biochemistry (ch. 1), Water (ch. 2)
Sep 7 Amino acids, peptides, and proteins (ch. 3); Test
Sep 14 The three-dimensional structure of proteins (ch. 4)
Sep 21 Protein function: oxygen-binding proteins, immunoglobulins (ch. 5); Test
Sep 28 Protein function: receptors, ion channels, signal transduction (pp. 418-427, 433-453, 464-470)
Oct 5 Enzymes (ch. 6); Test
Oct 12 Enzymes (ch. 6)
Oct 19 Purification and characterization of proteins; Test
Oct 26 Carbohydrates and glycobiology (ch. 7)
Nov 2 Nucleotides and nucleic acids (ch. 8); Test
Nov 9 Lipids (ch. 10)
Nov 16 Biological membranes and transport (ch. 11); Test
Nov 23 Thanksgiving no lecture
Nov 30 Special topic; Test
Dec 7 Final exam