Chemistry 4340: General Biochemistry I Syllabus

Instructor: Larry Loomis-Price, Ph.D.

E-mail: LoomisPriceL@uhd.edu; Office Phone: 713–221–5843
Office Hours: Office N650 by appointment only
Tutoring hours: (Library Study Rooms, such as N453) Tuesday from 2:30-3:30
pm & Thursdays from 10-11 am & 2:30-3:30 pm. Mondays from 10-11am,
Room B12-331 (Houston NW).
Lecture Time/Place: Tuesday and Thursday 8:30 AM – 9:45 AM for CRN 21236,
Room A423; 4:00 – 5:15 PM for CRN 21237, Room A425. Monday 10:00
AM – 12:45 PM, Room B12-331 (Houston NW campus).
Credit Hours: 3
Prerequisites: Completion of BIOL 1102, BIOL 1302, CHEM 3201 and CHEM
3301
Required Texts: Fundamentals of Biochemistry; 5 th Ed. by Voet, Voet & Pratt;
Student Companion to Fundamentals of Biochemistry 5 th Ed. by Uzman,
Johnson, Eichberg, Widger, Cornely, Voet, Voet & Pratt

Course Description & Philosophy –

UHD Catalog Description: “Overview of fundamental biochemical principles, topics,

techniques and analytical methods that integrates concepts from previous biology and
chemistry courses to the study of biological molecules. Emphasis is placed on the bioorganic
chemistry and techniques needed to critically and objectively analyze biological molecules and
the fundamental processes that support life. Specifically protein, lipid and membrane structure
and function, enzymatic catalysis and kinetics are emphasized.”

Course Structure: Biochemistry is at the forefront of biological research and modern

medicine, and is the cornerstone of multiple disciplines including: cellular biology, molecular
biology, pharmacology, and toxicology. Biochemistry is an integrative course that requires
students to utilize scientific knowledge obtained throughout their college career. This course
will be a detailed and rigorous overview of fundamental biochemical principles, topics,
techniques and analytical methods that will allow students to integrate and apply concepts
from previous biology and chemistry courses. Topics covered in this course will be detailed
with emphasis on the bioorganic chemistry and techniques needed to critically and objectively
analyze biological molecules and the fundamental processes that support life. Biochemistry is
a calculation-intense discipline. Students will be required to demonstrate competence in
biochemical calculations. Students should use lecture material and specific course learning
outcomes for each chapter as a guide to the material important for exams while using the texts
to supplement understanding of the lectures.
 Biochemistry 4340 Syllabus

Instructor Philosophy on the Course: Biochemistry is required for admission into all Texas
professional schools and most graduate schools for the biomedical sciences. Student
performance in undergraduate biochemistry is often a powerful predictor of success in
graduate and professional programs. Professional and graduate schools often adopt
competency-based performance measures for students where students must demonstrate
proficiencies in what they can accomplish with the curriculum, not what they ‘know’. As such,
CHEM 4340 will be a competency-based course in which students must demonstrate
competency with the material through the successful completion of competency-based
application and critical-thinking problems, not the multiple choice-based ‘knowledge’ exams.
Completion of assigned homework and the ability to apply, integrate and synthesize course
material will be critical for exam preparation. If you do not read the assigned chapters, do
not actively engage the course material, or do not work the assigned problems you are
likely to perform poorly on exams.

Learning Outcomes & Course Objectives–

By the end of Biochemistry, students will meet the following course learning outcomes by
being able to:

1). Articulate the structural features and importance of the hierarchy of protein structure
and describe how it relates to protein function.

2). Apply thermodynamic, kinetic and chemical theory to successfully perform

calculations necessary to understand the molecular behavior of biochemical systems
(especially enzymes) both in vitro and in vivo.

3). Analyze and describe the thermodynamic, mechanistic and kinetic features of
enzymes and other proteins.

Student mastery of course learning outcomes will be facilitated by students successfully

mastering the following content-specific learning outcomes by being able to:

1). Design a protocol to isolate proteins in a mixture based upon physical and chemical
characteristics of proteins, and assess protein purity and structure after isolation.

2). Solve biochemical problems related to thermodynamics, pH, enzyme kinetics and
protein/small-molecule interactions.

3). Explain and critique the most widely accepted theory of protein folding.

4). Describe and recognize the phenomena of biochemical “cooperativity,” enzyme

catalytic strategies, and a variety of protein structure/function relationships.

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 Biochemistry 4340 Syllabus

Student mastery of course and content-specific learning outcomes will be facilitated by

students ultimately capability in meeting the following course objectives by being able to:

1). Relate protein structure, from primary to quaternary structure, to function of a variety
of protein classes, including enzymes, immunoglobulins, transport & structural proteins.

2). Apply isolation and analytical techniques necessary to analyze proteins and other
biological molecules critically.

3). Draw conclusions from experimental data to best describe modern theories of
protein biochemistry.

4). Apply understanding of molecular biochemistry to specific topics in whole organism

physiology

Student success and competency with these learning outcomes and course objectives will be
assessed via consistent participation in classroom activities, completion of assigned
homework, and passing of regular in-class exams as well as the summative and cumulative
final exam.

Assessments & Course Grade–

Student Assessment – Participation, Homework, In-class Exams, and the Final Exam:
Your grade for this course will be assigned from a possible total of approximately 950 points
earned throughout the semester. The totals may be modified as necessary.

Participation*: Regular attendance of class sessions is strongly correlated with success in

college courses. In light of this fact, attendance will be monitored in various ways to encourage
students to attend and participate in every class. The lowest grade will be dropped.
 A participation grade will be assigned: 88 points*. (*Monday section, see handout)

Homework, Assignments*: Problems from the textbook, student companion and instructor-
designed questions will be assigned. The required homework problems are designed to
enhance your understanding of material. Many, but not all will reflect the style of questions on
the exams. Homework will be collected and a completion grade will be assigned. Homework is
due at 4:00 PM on the assigned date*. Homework may be turned in at the beginning or end
of class, or during discussion sessions only. Homework will NOT be accepted at my office, or
electronically. Late homework turned in before the next class period will not be graded, but will
be awarded up to half credit. The lowest homework grade will be dropped.
 Assignment grade: 110 points*.

Exams: Four competency-based exams will be administered periodically throughout the

semester, each worth 150 points. The exams will test student understanding and application of
the lecture material and assigned homework, as well as student ability to apply this material to
new experimental situations. All exams are closed-book and closed-notes, but formulas will be
given to you. The lowest exam grade will be dropped. A cumulative/summative 300 point

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 Biochemistry 4340 Syllabus

competency-based final exam will be administered at the end of the semester. The final exam
is absolutely required for this course. If you do not take the final exam, you will fail the course.
For all exams you will only be allowed to have a calculator (without a lid). Bonus point
questions are likely on all exams!

Participation @ 88 points total (drop the lowest)

+ Homework @ 110 points total (drop the lowest)
+ 4 exams @ 450 points total (drop the lowest)
+ 1 final exam @ 300 points total_____________
948 Total Points

Note: You must complete all regular exams and the final exam during the times/section for
which you are enrolled. If you are enrolled in the morning section, you must complete your
exams with the morning section. If you are enrolled in the afternoon section, you must
complete your exams with the afternoon section. Exceptions by prior arrangement only.

Make-Up Exams: There will be no opportunity to make up exams!!! The lowest exam
score will be dropped. Missing more than one exam will result in a score of “0” for each exam
missed beyond the first. If you arrive tardy to an exam – after a classmate has already turned
in their exam – you will not be allowed to take the exam.

Grading Scale and Policy: I DO NOT BELIEVE IN STANDARD BELL CURVES FOR
GRADING. Bell curves for grading force students to compete with each other for a few “A’s”. In
addition, with bell curves if one student performs better than the rest then the average student
suffers. I do not want you competing with each other for grades. The following grade scale will
be used. NOTE: minor changes in exact total points for the class are expected, this is a guide
only.

Grading Scale-
849 – 948 pts. (> 90%) =A
755 – 848 pts. (80% – 89.5%) =B
660 – 754 pts. (70% – 79.5%) =C
565 – 659 pts. (60% – 69.5%) =D
0 – 564 pts. (less than 59.6%%) =F

This grading scale benefits YOU!!! Everyone has the opportunity to earn an “A” in this class,
no matter how his/her classmates score. If everyone in the class accumulates > 849 points,
then the whole class gets an “A”. If you do not earn the points, you do not earn the grade.

Extra credit: There will be four extra-credit opportunities offered during the semester, for a
maximum total of 20 points. These will be explained during class and posted on Blackboard.
No other extra credit will be offered.

NOTE: You must log into Blackboard the first week of class and take a short syllabus
familiarity quiz. No homework or participation grades will be assigned until you have
completed this quiz with a grade of 90% or higher.

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 Biochemistry 4340 Syllabus

Course Policies–

Attendance: Attendance in this course is mandatory. Each lecture meeting comprises a

significant portion (4%) of the total course material and is worth 4 points*.
1) Students will be required to sign a role sheet as they enter the classroom each
day to confirm their attendance (1-2 pts). Students will fill out a “One Minute
Paper” at the end of each class (2-3 pts). You may attend any section without
prior permission, but must complete all the requirements below*.
2) Students that arrive more than 10-minutes late to class will not be allowed to sign
the role sheet and lose the attendance points. If you do not sign-in within the
first ten minutes, do not ask to sign the role sheet at the end of class.
3) Students will be required to ask and answer questions in class regularly using a
“One-Minute Paper” (1MP) format. Failure to turn in the complete, required
response will result in loss of credit for that class period.
4) Each student is allowed one unexcused absence without penalty. After one
missed class, students will lose 4 points per day missed*. At the instructor’s
discretion ONLY, this loss may be waived for a medical/family emergency, legal
issue, or other documented extenuating circumstances approved by the
Department of Natural Sciences. This will require approved, written
documentation of the excused absence immediately upon returning to class.

Failure to attend class and make contact with the instructor to adequately explain your
absence by the 10th class calendar day of the semester will result in your being dropped
administratively from this course. Being administratively dropped from this course may affect
your enrollment status and/or your financial aid eligibility.

Office Hours: My office hours are a time for you to seek individual help and advice. I will have
two different kinds of office hours.
One set will be reserved for homework-related questions and problem solving
(discussion groups). I will keep these office hours in large library study rooms or the science
conference room to maximize space and allow us to talk without disturbing other instructors
and students.
The other set will be for individual questions involving logistics of the course, exams,
and course material not related to homework. These will be by appointment only and the
length of time allowed for them may be limited on any given day by the number of students
who sign up.
Finally, I will use the Blackboard Learning system extensively. Everything I hand out in
class will be available on Blackboard. Answers to Homework problems and on-going grades in
the course will ONLY be available on Blackboard. I will start discussion threads periodically to
answer questions about Homework and during the period before the examinations. You MUST
sign into Blackboard and complete the quiz about this syllabus before you will be
awarded ANY grades in this course. Do so before the end of the third class period
(Tuesday, January 23).

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 Biochemistry 4340 Syllabus

Academic Dishonesty: All students are subject to the UHD Academic Honesty Policy (Policy
03.A.19) and all University-wide policies set forth in the University Catalog and Student
Handbook. Cheating in any form will not be tolerated. Students are obligated to have read and
understand all of the academic honesty violations listed in this policy. The UHD Academic
Honesty Policy (Policy 03.A.19) can be found at http://www.uhd.edu/about/hr/PS03A19.pdf.
Students that are caught cheating will fail the exam or exercise; no exceptions. In particular,
possession of any electronic device (other than an approved calculator or digital watch) at any
exam will result in a “0” for that exam regardless of whether or not the device was used during
the test. This includes cell phones and smart watches. Leave them in your backpacks.

Disabled Students: The University of Houston-Downtown complies with Section 504 of the
Rehabilitation Act of 1973 and the Americans with Disabilities Act of 1990, pertaining to the
provision of reasonable academic adjustments/auxiliary aids for students with a disability. In
accordance with Section 504 and ADA guidelines, UHD strives to provide reasonable
academic adjustments/auxiliary aids to students who request and require them. If you believe
that you have a documented disability requiring academic adjustments/auxiliary aids, please
contact the Office of Disability Services, One Main St., Suite 409-South, Houston, TX 77002.
(Office) 713-226-5227 (Website) www.uhd.edu/disability/ (Email) disabilityservices@uhd.edu.
You must do this prior to the first exam in order to have needed accommodations applied to the
exam. Do not procrastinate!

Electronic devices in class: You may record my lectures if you wish, however all of the
lectures are posted on-line, in narrated form. Cell phones must be turned off and put away
during lectures. Students who disregard this policy will be asked to leave. I discourage use of
laptop computers in class except for students with certified accommodations (see above). For
many reasons, using a computer to take notes is often inferior to taking notes by hand (see:
https://www.npr.org/2016/04/17/474525392/attention-students-put-your-laptops-away). If you
firmly believe that you have the skill and discipline to use a computer in class, you may do so,
with explicit permission, and only if you sit in the front row of the classroom. I may withdraw
this permission at any time, including during class, at my sole discretion.

Course Withdrawal: Dropping or withdrawing from this course is per University policy.
Instructors are not obligated to give grades of IP (In Progress) or I (Incomplete), and I will not
do so.

Letters of Recommendation: Your completion of this course does not entitle you to a letter of
recommendation. A letter of recommendation should come from someone that knows you well,
and can speak to a majority of your strengths and weaknesses. Taking a single class from a
faculty member does not allow the faculty member to get to know a student sufficiently well. In
order for me to consider writing a student a letter of recommendation, the student must
minimally: have done well (grades of A or B) in at least two courses that I teach, or you must
have performed well in one of my courses and participated in one or more significant
extracurricular activities with me, such as undergraduate research.

THE GRADING SCALE AND SCHEDULE OF THIS SYLLABUS/COURSE MAY BE

ALTERED AT ANY TIME TO MORE EFFECTIVELY MEET THE NEEDS OF THE
STUDENTS!!!

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 Biochemistry 4340 Syllabus

Tentative Course Schedule, Tuesday and Thursday, Main Campus –

Date Topic Assigned Reading Assignment Due

Jan 16 & 18 Principles of Biochemistry Chap 1, Section 1, 2
Properties of Water, pH Chap 2, all but 2C
Jan 23 & 25 Properties of Water, buffers Chap 2, Section 2C Homework 1
Amino Acid Structure Chap 4, Section 1
Jan 30 & Amino Acid Properties Chap 4, finish Homework 2
Feb 1 Primary Structure Chap 5, Sections 1,4
Feb 6 & 8 Protein Structure, Secondary Chap 6, Section 1 Homework 3
EXAM 1
Feb 13 & 15 Protein Structure, 3ry and 4ry Chap 6, Section 2&3
Protein Purification, Part 1 Chap 5, Section 3
Feb 20 & 22 Protein Folding Chap 6, Section 4, 5 Homework 4
Protein Purification, Part 2 Chap 5, Section 2
Feb 27 & Protein Structure & Function: Chap 7, Section 3 Homework 5
Mar 1 Antibodies & Receptors Chap 13, Section 2
EXAM 2 parts A&B only
Mar 6 & 8 Biochemical Chap 1, Section 3 Homework 6
Thermodynamics
Mar 13 & 15 Spring Break – NO CLASS
Mar 20 & 22 Protein Catalysis, Intro Chap 11, Section 1-3 Homework 7
Catalysis Tools
Mar 27 & 29 Catalysis Mechanisms Chap 11, Section 5 Homework 8
EXAM 3
Apr 3 & 5 Enzyme Kinetics Chap 12, Section 1 Homework 9
Apr 10 & 12 Enzyme Inhibition Chap 12, Section 2&3 Homework 10
& Regulation
Apr 17 & 19 Protein Function: Muscles Chap 7, Section 2 Homework 11
EXAM 4
Apr 24 & 26 Protein Function: Chap 7, Section 1
Hemoglobin Cooperativity
May 1 Reading Day/Final Review session
May 3, 8, 10 FINAL EXAM Date TBA

Unless indicated otherwise, all readings are in the course textbook (Fundamentals of
Biochemistry)

Final Exam–

The meeting times and dates for the final exams are set by the University and are posted on
the UHD website at a later date. The final exam is absolutely required for this course. If
you do not take the final exam, you will absolutely fail the course. You must take the
final exam for the section in which you are enrolled. No exceptions.

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 Biochemistry 4340 Syllabus

Tentative Course Schedule, Wednesdays, Houston NW Campus –

Date Topic Relevant Reading Assignments Due*

Jan 22 Principles of Biochemistry Chap 1, Section 1, 2
Properties of Water, pH Chap 2, all but 2C
Jan 29 Properties of Water, buffers Chap 2, Section 2C Lectures/Quizzes
Amino Acid Structure Chap 4, section 1 3 & 4 (all parts)
Feb 5 Amino Acid Properties, Chap
and 4, finish L/Q 5 & 6
Primary Structure Chap 5, Sections 1,4
Feb 12 Protein Secondary Structure Chap 6, Section 1 L/Q 7
EXAM 1
Feb 19 Protein Structure, 3ry & 4ry Chap 6, Section 2&3 L/Q 8 & 9
Protein Purification, Part 1 Chap 5, Section 3
Feb 26 Protein Folding Chap 6, Section 4, 5 L/Q 10 & 11
Protein Purification, Part 2 Chap 5, Section 2
Mar 5 Protein Structure & Function: Chap 7, Section 3 L/Q 21 & 22
Antibodies & Receptors Chap 13, 2 (A&B)
EXAM 2
Mar 12 Biochemical Chap 1, Section 3 L/Q 12 a&b
Thermodynamics
Mar 19 Spring Break – NO CLASS
Mar 26 Protein Catalysis, Intro Chap 11, Section 1-3 L/Q 13 & 14 a&b
Catalysis Tools
Apr 2 Catalysis Mechanisms Chap 11, Section 5 L/Q 15
EXAM 3
Apr 9 Enzyme Kinetics Chap 12, Section 1 L/Q 16 & 17
Apr 16 Enzyme Inhibition Chap 12, Section 2, L/Q 18 a&b & 19
& Regulation 3
Apr 23 Protein Function: Muscles Chap 7, Section 2 L/Q 20
EXAM 4
May 30 Protein Function: Chap 7, Section 1 L/Q 23 & 24
Hemoglobin Cooperativity
TBA FINAL REVIEW
TBA FINAL EXAM (normal class time and location)

*Assignments are due at 1:45 pm on Monday, except for those noted otherwise.
Unless indicated otherwise, all readings are in the course textbook (Fundamentals of
Biochemistry, 5th edition; use of other texts, such as the 4th edition will be discussed in class)

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