School of Dental Medicine. List of Courses - Academic Year 2012-2013
Molecular Foundations of Medicine. 2012-13
Title:
Molecular Foundations of Medicine (2012-2013)
Department: Physiology and Biophysics and Psychiatry
Course Number: HBC 531
Course Title: Molecular Foundations of Medicine
Course Directors: Nisson Schechter and Raafat El-Maghrabi
Participating Faculty:
Nisson Schechter
Raafat El-Maghrabi
Aaron Neiman
Marie Gelato
Joav Prives
Margaret McGovern
Daniel Bogenhagen
Objective:
Course Objectives
Linked
Institutional
Objective
Patient Care Objectives
ILO3
Develop differential diagnoses based on results of standardized patient
interviews and laboratory data using applied clinical biochemistry principles.
Medical Knowledge Objectives
•
•
•
•
ILO 7
Demonstrate knowledge of and to integrate the vocabularies of
biochemistry, cellular biology, and genetics and be able to apply them to lifelong learning in the medical sciences.
ILO 7
Demonstrate knowledge of the molecular basis of human health and
disease.
Demonstrate knowledge that most human diseases are best described and ILO 7, ILO 9
understood in terms of aberrant metabolism and genetic variation.
Recognize the key regulatory points in metabolic and genetic pathways at ILO7
which existing or yet to be developed therapeutic agents might be expected
to act.
Interpersonal and Communication Skills Objectives
•
•
ILO 13
Demonstrate knowledge of and to integrate the vocabularies of
biochemistry, cellular biology, and genetics and be able to apply them to lifelong learning in the medical sciences.
Description:
Molecular Foundations of Medicine covers fundamental principles and concepts of biochemistry, molecular
biology, cell biology, and human genetics. The material in this course is presented within a framework of
human health and disease. It provides the fundamental building blocks of knowledge for learning about
physiology, pathology, pathophysiology and pharmacology, and, as such, is essential for future physicians
and dentists.
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School of Dental Medicine. List of Courses - Academic Year 2012-2013
Grading:
Examinations
Three multiple choice examinations will be given in Molecular Foundations of Medicine. Each NBMEcustomized exam will cover about one third of the course material and will constitute 24% of the final
course grade. It is important to understand that the amount and extent of information presented during the
course is extensive, and mastering its content will require constant and consistent studying and attention.
All lecture PowerPoint’s are available on CBase beforehand, including some of the assessment quizzes,
PLEASE look them over at least the night before. Ten percent of the final grade is derived from these
assessment quizzes which should serve as an impetus to look at the slides beforehand. In addition,
PLEASE do not wait until exam time to study, but try and review each week’s material in a timely fashion.
All examinations for this course are mandatory. If there are any unusual circumstances which preclude
your attendance at an examination, these must be communicated before the examination to the Office of
the Dean for Academic Affairs as well as to one of the Course Directors.
Discussion Topics
Each student will be randomly assigned three discussion topics from a database that will be posted on this
web site, on which they will write a written report. Each report will account for 4% of the course grade.
They will be graded according to the Discussion Question Guideline. Students are expected to submit
their reports no later than 2 weeks after the topics are covered in lectures. Begin early! The discussion
topics themselves and their assignments (including the specific questions assigned to each student and
the assigned teaching assistants for each question) can be found and downloaded from the CBase
schedule for the introductory lecture. These topics are a platform for learning; they are integrative and
relate to important concepts in biochemistry, molecular biology, and cell biology that are of fundamental
importance to physiology, pathophysiology, and pharmacology. Consequently, although each student is
assigned just three topics to report on in depth, it is worthwhile to become familiar with all of these
questions and to use them a guideline for study and review. While you may discuss your topics with
anyone you wish (and we encourage you to discuss them amongst yourselves and with the course TAs),
the ultimate written product must be your own. We also expect professional behavior to be exhibited
regardless of the resource material that you choose to use in writing these papers. Some of the information
to answer these questions can be obtained from the recommended text books. For additional information,
feel free to use "Google" or other reference materials. The National Library of Medicine website includes
PubMed, which will provide lists of journal articles on specific topics:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi and OMIM (Online Mendelian Inheritance in Man), which
provides clinical descriptions and genetic information about inherited disorders:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM In writing your reports, the format should be as
follows: Title page including the Topic Number, the Student Name, the Date and the Name of the TA
grading the topic. [Please check the document that is posted with the course introduction (1st lecture) to
determine the name of the TA to whom you need to submit each of your questions for grading.]
The discussion topic title should be written out at the beginning of the paper.
The discussion report should include 3 to 4 pages of discussion (12 point, double spaced, 1 inch margins,
and page numbering centered at the bottom of each page except the title page).
All references should be cited using an Author-Date format, as is used in the Journal of Neuroscience. For
example, "Tetrahydrocannibinol has a significant role as a neurotransmitter in the addicted brain (Weed,
1978),"or "These observations are in agreement with those of Hash and Dope (1979) and of Hemp et al.
(1980),"or with multiple references, in chronological order: "Earlier reports (Blunt and Dull, 1979, 1981;
High et al., 1980; Munchey, 1982,1984).... "
References (which MUST BE primary research references) should be listed on a separate page or
pages following the discussion topic report. The list of references should also be typed, double spaced,
and in alphabetical order according to the surname of the first author. In two-author papers with the same
first author, the order is alphabetical by the second author's name. In three-or-more-author papers with the
same first author, the order is chronological. The name of the author(s) should be followed by the date in
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School of Dental Medicine. List of Courses - Academic Year 2012-2013
parentheses, the full title of the paper as it appeared in the original together with the source of the
reference, the volume number, and the first and last pages. Do not number the references. Examples are
shown below:
Journal article
Weed MJ (1978) Tetrahydrocannibol and you. Acta Artifacta 391: 85-100.
Book
Hemp T, Hash N, Dope R (1980) Reefer redux. San Francisco: Haight Street Press.
Chapter in a Book
Munchey Q (1982) Up in smoke. In: Puff the Magic Dragon (Blunt RU, ed), pp102-105. New
York: Bong Books.
Performance as measured by In-Class Assessment Quizzes (Turning Point Technology).
At most of the lectures in the course, instructors will be using the Turning Point Technology (clickers) to
test your learning in a real-time fashion. This will be totally at the discretion of the lecturer, without
advance notice. As mentioned above, your cumulative score on these quizzes will account for 10% of the
final course grade. If you are not present for a lecture which contains TPT questions, you will lose the
opportunity to achieve these points.
Objective Structured Clinical Examination (OSCE)
All students are required to participate in three OSCE's to be held in the Clinical Skills Center. These
simulations will involve clinical scenarios linked to the course material previously covered in class. The
OSCE quizzes will account for a total of 6% of the final course grade.
Summary of Grading for Molecular Foundations of Medicine
This course is graded according to a scale of Honors, High pass, Pass, and Fail for Medical Students, and
letter scored (A, B, C & F) for Dental Students. Failing grades of students who subsequently pass the
remediation exam will be changed to a grade of Low pass. Professional behavior is expected at all times in
examinations, in answering of study questions and in interactions with faculty, TAs and peers. It is
important to note that your average for Exams #1, #2 and #3 must be at least 65% for medical students
and 55% for dental students in order to pass the course. In addition, your overall average must be at least
65% for medical students and 55% for dental students.
Grade cutoffs for medical students: Honors requires 91% or above Passing is 65% to 90.9%
Grade cutoffs for dental students A requires 81% or above
B requires 73% to 80.9%
C is 55% to 72.9%
Grades will be calculated based on the following: Exam #1, 24%
Exam #2*, 24%
Exam #3*, 24%
*General review type questions reflecting material from previous exam will constitute about 30% of the
questions on Exam #2 and 3.
Assigned Discussion Question #1, 4%
Assigned Discussion Question #2, 4%
Assigned Discussion Question #3, 4%
In class performance (quizzes) 10%
OSCE's 6% total; 2% for each of 3 simulation/quizzes.
Attendance:
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School of Dental Medicine. List of Courses - Academic Year 2012-2013
Consistent attendance at this course, while not mandatory, is highly recommended. Although learning
styles and preferences differ, those who choose not to attend class often miss out on the emphasis which
the lecturers give to key principles. Transcripts of lectures are not always accurate and can never fully
convey the sense of importance that the lecturer is trying to transmit about particular topics. Just as
importantly, attendance will provide you with a better chance to get to know the faculty and for the faculty
to get to know you through formal and informal interactions during and surrounding the lectures. Coming
together as a group will also help you to developing a sense of esprit de corps and professional identity.
Given these advantages of class attendance, we hope to see your smiling faces early and often.
Recommended Texts:
The suggested text books for Molecular Foundations of Medicine are:
1. Principles of Biochemistry. (Lehninger). 5th edition. Nelson and Cox, Published by Freeman.
2. Molecular Biology of the Cell (5th edition) by Alberts et al. Published by Garland Science.
3. Medical Genetics, by Jorde, Carey, Barmshad, and White. Published by Mosby.
4. Lippincott's Illustrated Reviews-Biochemistry. 5th edition.
These can be purchased at the Medical School Bookstore. These books may be on reserve at the
Medical School Library however, we urge you to obtain your own copies for use during the course as well
as for future reference. If you have other up to date text books in graduate level biochemistry or cell
biology you might consider using them. However, students who chose to use other textbooks are
responsible for coordinating the lectures with those texts.
Outline or summary books are not recommended as primary textbooks for Molecular Foundations of
Medicine, since they do not lend themselves to understanding concepts and are more useful as review
books for professional exams, only after the course material has been thoroughly assimilated.
Additional Notes:
COURSE DIRECTOR'S CONTACT INFORMATION
Nisson Schechter, Ph.D.
Office: HSC-T10, Room 034
Phone: 444-1368
Fax: 444-7534
E-mail: nisson.schechter@stonybrook.edu
M. Raafat El-Maghrabi, Ph.D. Office: BST-T6 Room 170 Phone: 444-3049
Fax: 444-3432
E-mail: raafat.el-maghrabi@stonybrook.edu
Miscellaneous:
LIST OF 2012 TA'S AND THEIR E-ADDRESSES
Joseph.caputo@hsc.stonybrook.edu brendan.carr@hsc.stonybrook.edu
Christopher.chandler@hsc.stonybrook.edu
Oren.factor@hsc.stonybrook.edu
Rachel.feder@hsc.stonybrook.edu
Vy.han@hsc.stonybrook.edu
Arjun.iyer@hsc.stonybrook.edu
Pavel.mazirka@hsc.stonybrook.edu
Jeremy.miyauchi@hsc.stonybrook.edu
Shula.schechter@hsc.stonybrook.edu
Andrew.smith@hsc.stonybrook.edu
Daniel.talmasov@hsc.stonybrook.edu
Daniel.ventarola@hsc.stonybrook.edu
Keith.willner@hsc.stonybrook.edu
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School of Dental Medicine. List of Courses - Academic Year 2012-2013
Schedule:
Date
08/27/2012
08/27/2012
Duration
55 min
55 min
08/28/2012
55 min
08/28/2012
55 min
08/31/2012
55 min
08/31/2012
55 min
09/04/2012
55 min
09/04/2012
55 min
09/05/2012
55 min
09/05/2012
55 min
09/07/2012
55 min
09/07/2012
55 min
09/10/2012
55 min
09/10/2012
55 min
09/11/2012
09/11/2012
55 min
55 min
09/12/2012
55 min
09/12/2012
55 min
09/14/2012
55 min
09/14/2012
55 min
09/17/2012
115 min
09/18/2012
55 min
09/18/2012
55 min
Title
Course Introduction
Amino Acids: the building blocks of
proteins.
Primary and Secondary Structures
of Proteins I: The peptide bond, the
alpha helix and beta sheets.
Primary and Secondary Structures
of Proteins II
Protein misfolding and disease:
Sickle cells & Prions
Alzheimer's disease; another bad
protein?
Introduction to Enzyme Kinetics:
mechanisms of catalysis
Enzyme Inhibition: feedback
regulation and pharmacological
targeting.
Myoglobin/Hemoglobin; the
allosterism of Oxygen transport
Allosterism
Type
Lecture
Lecture
Introduction to Carbohydrates: NonEnzymatic Glycation and Disease.
Introduction to Glycobiology:
Mannose 6-Phosphate and I-Cell
Disease.
Introduction to Metabolism: The role
of Phosphate Bond Energy,
Coenzymes, and Vitamins in
Biochemical Reactions.
Glycolysis: The Fate of Glucose in
Liver, Muscle, and Brain.
Regulation of Glycolysis
Pyruvate Oxidation and the TCA
Cycle
Electron Transport and Oxidative
Phosphorylation: The Fate of NADH
& FADH2 and the Synthesis of ATP
Glycogen metabolism and the
Glycogen Storage Diseases
Gluconeogenesis: The Synthesis of
Glucose from Non-glucose
Precursors.
Pentose Phosphate Pathway and
the Role of Glutathione in Health
and Disease.
Rosh Hashanah!!!!
Lecture
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Nisson Schechter
Lecture
Nisson Schechter
Lecture
Nisson Schechter
Lecture
Nisson Schechter
Lecture
Lecture
Nisson Schechter
Nisson Schechter
Lecture
Nisson Schechter
Lecture
Nisson Schechter
Lecture
Nisson Schechter
Lecture
Nisson Schechter
Other
Structure and Oxidation of Fatty
Acids I
Structure and Oxidation of Fatty
Acids II
Lecture
Nisson Schechter,
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
| Page 33
Lecture
Lecture
Lecture
Lecture
Lecture
Lecture
Lecture
Lecture
Lecture
Instructor
Nisson Schechter
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
School of Dental Medicine. List of Courses - Academic Year 2012-2013
09/19/2012
120 min
OSCE 1-MANDATORY
Simulation
09/21/2012
60 min
Lecture
09/21/2012
60 min
Synthesis and Storage of Fatty
Acids
Membrane Lipids
09/24/2012
480 min
First Customized NBME exam
Exam
09/25/2012
55 min
Lecture
09/25/2012
55 min
Lecture
Nisson Schechter
09/26/2012
115 min
Ubiquitin-Mediated Proteolysis: The
Kiss of Death.
Nitrogen Metabolism: The Fate of
NH2 Groups and NH4+.
Yom Kippur
Nisson Schechter,
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Nisson Schechter,
Raafat
El-Maghrabi
Nisson Schechter
Other
09/28/2012
55 min
Lecture
09/28/2012
55 min
Lecture
Nisson Schechter
10/02/2012
55 min
Lecture
Nisson Schechter
10/02/2012
55 min
Lecture
Nisson Schechter
10/03/2012
55 min
Lecture
10/03/2012
55 min
Lecture
Raafat
El-Maghrabi
Marie Gelato
10/05/2012
55 min
Lecture
Nisson Schechter
10/05/2012
55 min
Lecture
Nisson Schechter
10/08/2012
55 min
Lecture
Nisson Schechter
10/08/2012
55 min
Lecture
Nisson Schechter
10/09/2012
55 min
Degradation and synthesis of Amino
Acids I
Degradation and synthesis of the
amino acids II
Nucleic Acids: Synthesis and
Degradation
Nucleic Acids: Synthesis and
Degradation
Glucose Transport, Insulin action
and Diabetes
The Pathogenesis of Type I and
Type II Diabetes mellitus
Review and Integration of
Metabolism
Review and Integration of
Metabolism
Cholesterol; structure, synthesis and
regulation.
Cholesterol; structure, synthesis and
regulation II.
Lipid transport: Lipoproteins
Nisson Schechter,
Raafat
El-Maghrabi
Nisson Schechter
Lecture
10/09/2012
55 min
Hyperlipidemias. Dad or Big Mac?
Lecture
10/10/2012
55 min
Atherosclerosis
Lecture
10/10/2012
55 min
Review of Atherogenesis
Lecture
10/11/2012
55 min
Lecture
10/11/2012
55 min
10/12/2012
55 min
Lecture
10/12/2012
10/15/2012
10/15/2012
10/16/2012
55 min
55 min
55 min
55 min
Bile Acids, Bile Pigments, Heme
synthesis and Porphyrias
Steroid Hormone Synthesis in the
Adrenal Cortex
The Cell Cycle - Growth Control and
Cancer
Structure and Replication of DNA
Chromatin and Epigenetics
DNA repair and disease
Chromosomes, Telomeres and
Raafat
El-Maghrabi
Raafat ElMaghrabi
Raafat
El-Maghrabi
Raafat ElMaghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Aaron Neiman
Lecture
Lecture
Lecture
Lecture
Aaron Neiman
Aaron Neiman
Aaron Neiman
Aaron Neiman
| Page 34
Lecture
Lecture
School of Dental Medicine. List of Courses - Academic Year 2012-2013
10/16/2012
10/17/2012
10/17/2012
10/19/2012
55 min
55 min
55 min
120 min
10/22/2012
55 min
10/22/2012
55 min
10/23/2012
55 min
10/23/2012
55 min
10/24/2012
55 min
10/24/2012
55 min
10/26/2012
Cellular Sensescence
Structure and Synthesis of RNA
Transcriptional Regulation
RNA Processing
OSCE 2
Lecture
Lecture
Aaron Neiman
Lecture
Aaron Neiman
Lecture
Aaron Neiman
Lecture
Joav Prives
Lecture
Joav Prives
115 min
Protein Synthesis I - mRNA
translation
Protein Synthesis II - Regulation of
Translation
Protein targeting: Organellar
Transport
Protein Targetting: Vesicular
Transport
Biochemistry of Ligand- and
Voltage- Gated Channels
Biochemistry of Voltage-Gated
Channels
Eid ulAdha
Aaron Neiman
Aaron Neiman
Aaron Neiman
Nisson Schechter,
Raafat
El-Maghrabi
Aaron Neiman
Other
10/29/2012
510 min
Second Customized NBME Exam
Exam
11/06/2012
11/06/2012
11/07/2012
55 min
55 min
55 min
Cytoskeleton
Intermediate filaments and disease
Introduction to Cell Signaling
Lecture
Lecture
Lecture
11/07/2012
55 min
G Protein Coupled Receptors.
Lecture
11/12/2012
55 min
Lecture
11/12/2012
55 min
Lecture
Nisson Schechter
11/13/2012
55 min
Lecture
Aaron Neiman
11/13/2012
11/14/2012
11/14/2012
55 min
55 min
55 min
Lecture
Lecture
Lecture
Nisson Schechter
Aaron Neiman
Aaron Neiman
11/16/2012
55 min
Non-receptor and Receptor tyrosine
kinases: Cancer
Apoptosis: Programed cell death
and cancer.
RNAi: Interfering with Gene
Expression
Toxins: Ribosylation in Disease
Mitosis
Meiosis Gametogenesis and
Fertilization
Human Genetics-1
Nisson Schechter,
Raafat
El-Maghrabi
Nisson Schechter,
Raafat ElMaghrabi
Aaron Neiman
Nisson Schechter
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Nisson Schechter
Lecture
11/16/2012
55 min
Human Genetics-1
Lecture
11/19/2012
55 min
Human Genetics-2
Lecture
11/19/2012
55 min
Human Genetics-2
Lecture
11/20/2012
55 min
Human Genetics-3
Lecture
11/20/2012
55 min
Human Genetics-3
Lecture
11/21/2012
60 min
Fasting for Thanksgiving!
Other
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat ElMaghrabi
Somnus Morpheus
| Page 35
Lecture
Lecture
Lecture
Simulation
School of Dental Medicine. List of Courses - Academic Year 2012-2013
11/21/2012
11/28/2012
55 min
55 min
Other
Lecture
120 min
On the road home!
Mitochondrial Dysfunction in
Disease
Mitochondrial Dysfunction in
Disease II
OSCE 3
11/28/2012
55 min
12/03/2012
12/05/2012
60 min
Human Genetics 4
Lecture
12/10/2012
60 min
Metabolic Genetics
Lecture
12/10/2012
60 min
Other
12/14/2012
240 min
Genetics of Metabolism........the
meaning of life.....42!
Final Customized NBME Exam
SOM
| Page 36
Lecture
Simulation
Exam
Thomas Turkey
Daniel
Bogenhagen
Daniel
Bogenhagen
Nisson Schechter,
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Raafat
El-Maghrabi
Nisson Schechter,
Raafat
El-Maghrabi