Dr. David
Mascotti
Office: DSC
W207, Lab W218
Office Hours: MWF 9-10 a.m., T 9-12 a.m.
& available by appointment.
Communications Policy: (Read emails that
I send you and check my webpage at least
once a week
and Canvas frequently.)
Telephone: 397-4216
Email: dmascotti@jcu.edu
Webpage: http://webserv.jcu.edu/chemistry/faculty/mascotti/dmascotti/biochem.html
Course requirements.
Lecture times, MF 11:00 a.m. –
12:15 p.m., W 11:00 -11:50 a.m.
Class location: E346
Text: Essential Biochemistry
by Pratt, C.W. & Cornely, K., 4th edition with WileyPlus access (required)
Course description:
CH 431 is a one
semester overview of general biochemistry. This course is survey course, thus
there will be a large amount of information covered with much less depth than
the one year course (CH435/CH436). We
will cover structural biochemistry of proteins, nucleic acids, lipids and carbohydrates. We will also cover the metabolism of
carbohydrates, lipids, amino acids, purines, and pyrimidines. To help
understand these phenomena, we will follow the flow of matter, energy and
information in living systems. We will outline the universal biochemical
pathways for conversion of substrates and genetic information into cellular
components. We will learn the enzymes responsible for individual steps and
their mechanisms. We will discuss the regulatory systems that integrate and
control these processes.
General Goals
1. To provide the
student a basic and practical understanding of biochemistry (structural
biochemistry) and recognize its relevance in our daily lives.
2. To prepare our
students to meet with success in other chemistry and science courses.
3. To understand the
conceptual organization of the major metabolic pathways and their connections
to one another;
4. To develop the problem solving and
critical analysis skills in the course context;
5. To identify the relevance of
biochemical phenomena to everyday life
6. To prepare our
students for occupations in, and professional programs requiring, a mastery of
General Biochemistry such as Graduate School, Medicine, Dentistry, and
Pharmacy.
This course also contributes to
the Student Learning Goals of the Chemistry Department as:
·
Student
learning goal #2 aligns to Chemistry Department Student Learning Goal l #2 – “Apply their integrative knowledge
of chemistry to solve problems” and to the JCU Academic Learning Goal of “Develop habits of critical analysis
and aesthetic appreciation” and “Apply creative and innovative thinking”.
Learning
Objectives
To explore the
structural aspects of biochemistry, particularly the following:
1.
Amino
Acids
2.
Proteins:
Primary Structure
3.
Proteins:
3D Structure
4.
Protein
Function
5.
Enzyme
Catalysis
6.
Enzyme
Kinetics
7.
Carbohydrates
8.
Lipids
& Membranes
9.
Membrane
Transport
10. Nucleic Acid Structure &
Protein-nucleic Acid Interactions
To
explore the metabolic aspects of biochemistry, particularly the following:
|
1.
Signaling |
|
2.
Carbohydrates |
|
3.
Metabolism
and Bioenergetics |
|
4.
Glucose
Metabolism |
|
5.
The
Citric Acid Cycle |
|
6.
Oxidative
Phosphorylation |
|
7.
Photosynthesis |
|
8.
Lipid
Metabolism |
|
9.
Nitrogen
Metabolism |
|
10. Regulation of Mammalian Fuel
Metabolism |
Learning
Outcomes
Completion
of the course with a passing or better grade will indicate success in the
following learning outcomes:
1.
Knowledge of amino acids and protein structure
2.
Knowledge of protein structure/function
3.
Knowledge of enzyme kinetics including
inhibitors
4.
Knowledge of carbohydrate and lipid chemistry
5.
Knowledge of membrane structure and transport
6.
Knowledge of nucleic acid structure and
protein-nucleic acid interactions
Methods of assessing learning outcomes:
The expected learning goals will be assessed through the use of homework
assignments and/or quizzes, exams, and the final exam.
Absences. Attendance is not mandatory; however,
unannounced quizzes will be given periodically (i.e., "pop" quizzes).
Note: There are no quiz make-ups. Even without this incentive, it has been my
experience that better attendance makes for better grades.
Office Hours. I have a relatively "open door"
policy. If you stop by my office or lab and I'm there, I'll usually make time
to answer short questions. For more lengthy discussions I recommend that you
come in during regularly scheduled office hours (see above) or schedule an
appointment.
Tentative
Grading Policy.
1) four
hour-long 100 point exams
2) quizzes
& assignments (normalized to 100 points)
3) instructor
evaluation (50 points)
4) a mandatory
Final Exam (100 or 200 points, explained below)
Thus, there are 650 or 750 points
total. Grades may be curved, but the
most stringent scale that I will use will be <60% = F, 60-67.99% = D,
68-69.99%=D+, 70-72.99%=C-, 73-77.99% = C, 78-79.99%=C+, 80-82.99%=B-, 83-87.99%
= B, 88-89.99%=B+, 90-92.99%=A-, and 93+% = A.
Make-up Exams. If you know ahead of time that you will miss
an exam and have a valid excuse, I will administer an exam before the regularly
scheduled exam. If you miss an exam due to valid unforeseen circumstances, I
will allow you to count the grade from your final exam as the grade the missed
exam.
Quizzes & Assignments:
“I cannot teach anybody anything. I can only make them think” – Socrates. Based on that premise, any learning that
occurs this semester will be due primarily to your diligent work at
understanding the material. If you stare
at a treadmill, you will not run faster.
If you get on and quit after a minute, you will not run faster. It takes diligence and practice. Maybe someday you will be the Usain Bolt of
Chemistry. Maybe you’ll have a dusty
treadmill. It’s your choice.
With
this thought in mind, I will incorporate the WileyPlus
system (required) for quizzes. These
will allow for three attempts on each quiz to be done on your own time at your
own speed. The goal is to reinforce
class concepts and free up class time to actually go over material instead of
quiz time. The quizzes will have due dates, so please make sure you complete
them by the deadlines! It is hoped that you will get all or nearly all of those
points since you will have three attempts on each quiz and at least several
days to complete each assignment.
Occasionally
I may also administer homework assignments that will be included in this
portion of the overall grade. The average
percentage earned from all quizzes and homework during the semester will be
normalized to 100 to arrive at the grade for that component of the total
grade.
Instructor Evaluation. A
small portion of your grade (50 points) will be based on the degree of your
participation and your attitude in class. In terms of participation, I will
assess your level of attendance, attentiveness, and verbal participation. This
does not mean that you have to say something in every class, but consistent
participation and attention is expected.
Your grade for participation will be based on the frequency and
substance of your comments and on your attentiveness in class. With respect to attitude, I expect students
to display respect for each other and the instructor. Talking to others during
class, leaving cell phones on, unconstructive (or destructive) comments made
during discussions, and tardiness are signs of a poor attitude. In particular,
coming to class late is disruptive and displays disrespect toward the instructor
and classmates.
Student
Behavior. No cell phone activity will be
tolerated during class – including personal texting and web use. It is rude and disruptive to your neighbors
who may actually want to learn the material as well as a potential source of cheating
(see below). Any violations of this policy
will result in a 2% deduction from their overall grade. Multiple violations
will be additive.
Academic Honesty. The John Carroll University statement
of academic honesty can be found in the JCU Undergraduate Bulletin 2019-2020.
Please abide by these rules. Penalties for infractions will be decided in
accordance with the university policy.
Specifically, any act of plagiarism will incur a zero for that
assignment. Repeated plagiarism will
incur a zero for the course. Cell phone
use during any quizzes or exams will incur a penalty of zero for that quiz or
exam. Calculator use during quizzes or
exams will be used for calculations only.
Any stored equations or notes will be viewed as cheating and will incur
a penalty of zero for that quiz or exam.
Students with Disabilities. In accordance with federal law, if you have a
documented disability (Learning, Psychological, Sensory, Physical, or Medical)
you may be eligible to request accommodations from the Office of Services for Students
with Disabilities (SSD). Please contact the Director, Allison West at (216)
397-4967 or come to the office located in room 7A, in the Garden Level of the
Administration Building. Please keep in mind that accommodations are not
retroactive so it is best to register at the beginning of each semester. Only accommodations
approved by SSD will be recognized in the classroom. Please contact SSD if you
have further questions.
Statement on
Inclusiveness. At John Carroll University, we are committed
to fostering a respectful and inclusive campus community. Incidents of bias
which are intentional or unintentional actions against someone on the basis of
an actual or perceived aspect of their identity, including actions that occur
in classrooms, can and should be reported on the Bias Incident Reporting Form,
accessible at http://sites.jcu.edu/bias/. Questions about bias can be directed
to members of the Bias Response Team: Lauren Bowen, Associate Academic Vice
President (bowen@jcu.edu), Bud Stuppy, Director of
Human Resources (cstuppy@jcu.edu) or Danielle Carter, Director of the Center
for Student Diversity and Inclusion (dcarter@jcu.edu).
Make-up
Exams. If you know ahead of time that you will miss an exam and
have a valid excuse (JCU sponsored events), I will administer an exam before
the regularly scheduled exam. If you miss an exam due to valid unforeseen
circumstances, I will allow you to count the grade from your final exam as the
grade the missed exam.
Final
Exam. The final exam is mostly cumulative (includes a small
portion of post-exam 3 material) and mandatory.
This exam will count as 100 or 200 points, whichever is to your
advantage.
|
Exam 1 |
Monday, September 23 |
|
Exam 2 |
Wednesday, October 16
|
|
Exam 3 |
Wednesday, November 13
|
|
Exam 4 |
Tuesday, November 26 |
|
Final Exam |
Friday, December 20 (10-11:50
a.m.) |
Outline of Probable Topics (in probable chronology)
|
Topic |
Chapter |
|
|
The Chemical Basis of Life |
1 |
|
|
Aqueous Chemistry |
2 |
|
|
From Genes to Proteins |
3 |
|
|
Protein Structure |
4 |
|
|
Protein Function |
5 |
|
|
How Enzymes Work |
6 |
|
|
Enzyme Kinetics and Inhibition |
7 |
|
|
Lipids and Membranes |
8 |
|
|
Membrane Transport |
9 |
|
|
Signaling |
10 |
|
|
Carbohydrates |
11 |
|
|
Metabolism and Bioenergetics |
12 |
|
|
Glucose Metabolism |
13 |
|
|
The Citric Acid Cycle |
14 |
|
|
Oxidative Phosphorylation |
15 |
|
|
Photosynthesis |
16 |
|
|
Lipid Metabolism |
17 |
|
|
Nitrogen Metabolism |
18 |
|
|
Regulation of Mammalian Fuel Metabolism |
19 |