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BSC 6432 - Biomedical Sciences I

Syllabus and Schedule


Course Description: First semester of a multi-disciplinary course for graduate students. Topics include
principles of biochemical and metabolic reactions, nucleic acid structure and replication and
transcription. Lectures incorporate current scientific findings in the context of biomedical applications.
Prerequisites: 1) Acceptance in the Biomedical Sciences Masters or Ph.D. program, or 2) Biochem I, or
Molecular Biology 1 and 2, or Cell Biology.
Location: CB1-320
Days and Time: Monday/Wednesday/Friday: 7:45 AM to 9:20 AM (See schedule for exact dates for
face-to-face (F2F) instruction and on-line instruction). No F2F classes or exams on Fridays!
Credits: 5
Instructors:
Victor Davidson, Ph.D.
Steven Ebert, Ph.D.
Otto Phanstiel, Ph.D.
Ratna Chakrabarti, Ph.D.
Course Coordinator:

E-mail
victor.davidson@ucf.edu
steven.ebert@ucf.edu
otto.phanstiel@ucf.edu
ratna.chakrabarti@ucf.edu

Office
Lake Nona 237
Lake Nona 421
BMS annex
BMS annex 107

Phone
6-7111
6-7047
3-6545
2-2258

Steven N. Ebert, Ph.D.


Office: BBS 421 (Lake Nona)
Phone: (407) 266-7047
Email: steven.ebert@ucf.edu

Course Materials:
A) Lectures (Powerpoint slides or PDFs) and course materials will be posted on-line at:
http://coursematerial.ucf.edu. The site is password protected. The password will be sent by
email. Each instructor will post their materials within a folder titled with their last name. Please
contact the course coordinator if there are problems accessing the materials.
B) Textbooks recommended for the course are available in the Reserve Room of the Medical School
library at Lake Nona. Textbooks are also available in the Graduate Program Office (HPA 2 rm 312)
for a limited check-out. Other course materials (i.e. review articles) will be posted by instructors.
1) Cell Biology, 2nd Edition, by Thomas D. Pollard, William C. Earnshaw, & Jennifer
Lippincott-Schwartz
2) Molecular Cell Biology, Seventh Edition, by Harvey Lodish , Arnold Berk , Chris A.
Kaiser, Monty Krieger, Anthony Bretscher , Hidde Ploegh , Angelika Amon , Matthew
P. Scott
3) Lehninger Principles of Biochemistry, 5th Edition, by David L. Nelson, Michael M. Cox
Updated August 12, 2016

4) Molecular Biology, 5th edition, by Robert Weaver


5) Molecular Biology of the Gene, 6th Edition, by James D. Watson
Course Requirements:
Test
4 term
exams

Description

Weight toward final grade

Exams will cover material from each section taught by


an instructor. Exam will be taken in class. The last
exam will be during finals week.

80%

Weekly in class quizzes and assignments will test


Quizzes/
knowledge acquired from the previous week's
Assignments
materials. See Schedule.

20%

Course Policies:
A. Student with Special Needs: Students requiring special accommodations are encouraged to
contact Student Disability Services, Administration 149, 823-2371 in the first week of the
semester and complete appropriate documents.
B. Academic Honesty: Cheating on exams or any other form of academic dishonesty is an
offense that will be dealt with as outlined in the Golden Rule. Academic dishonesty in any
form will not be tolerated. Violations of student academic behavior standards are outlined
in The Golden Rule, the University of Central Florida's Student Handbook. See
http://www.ucf.edu/goldenrule/ for further details. For more information, please contact
the Office of Student Conduct at 823-2851. To be clear, any student caught cheating on an
exam will receive zero points and fail the exam. No make-ups will be permitted in cases
where cheating has occurred.
The actual rules (from http://www.osc.sdes.ucf.edu/):
Academic Dishonesty/Cheating
Cheating is a violation of student academic behavior standards. The common forms of
cheating include:
i. Unauthorized assistance: communication to another through written, visual, or oral
means. The presentation of material which has not been studied or learned, but rather
was obtained solely through someone elses efforts and used as part of an examination,
course assignment or project. The unauthorized possession or use of examination or
course related material may also constitute cheating.
ii. Commercial Use of Academic Material: Selling notes, handouts, etc. without
authorization or using them for any commercial purpose without the express written
permission of the University and the Instructor is a violation of this rule.
iii. Plagiarism: whereby anothers work is used or appropriated without any indication of
the source, thereby attempting to convey the impression that such work is the students
own.
iv. Any student who knowingly helps another violate academic behavior standards is
also in violation of the standards.

C. Examination Policy: Exam material will be derived from the lectures and corresponding book
sections. Examinations will only be given at the designated times; early exams will not be given.
Cell phones or hats or any electronic gadgets are not allowed in the exam room. All reading
materials MUST be placed inside sealed or closed bags. Other than the exam, pen or pencil, no
other materials are allowed on the desk or in person during the exam. Students are
encouraged to use bathrooms before the start of exams and bathroom breaks during the exam
will be monitored. Students will be seated appropriately to avoid copying but it is the
responsibility of the individual student to avoid any suspicious behavior. Students must avoid
sitting close to study partners or friends because similar responses in exams will be ruled as
"copying" when seated close to each other.
Make-up exams may be allowed under extenuating circumstances with documentation. There
will be no make-up quizzes. Students are responsible for notifying instructors and course
coordinator in the event that they will miss an exam. Make-up exams are not guaranteed and
the decision to allow a make-up exam will be made by the instructors and course coordinator.

SCHEDULE
(Subject to change at the instructors discretion)
Lectures 1-10: Monday August 22 Monday Sept. 19

Dr. Davidson

SECTION 1: Biochemical Principles


Date

Format

Mon
8/22/16

F2F

Wed
8/24/16

F2F

Fri
8/26/16

Mon
8/29/16

Wed
8/31/16

Fri
9/2/16
9/5/16
Wed
9/7/16

Lecture Content
BIOCHEMICAL PRINCIPLES
a. Water, pH and buffers.
b. Types of bonds and interaction
c. Free energy and thermodynamics
d. ATP and its role in energy metabolism
PRINCIPLES OF PROTEIN STRUCTURE
a. Amino acid structures and properties
b. Peptide bonds
c. Primary, secondary, tertiary and
quaternary structure
d. Methods of protein characterization
e. Examples of soluble proteins
f. Protein folding

Reading Assignments

Assignment/
Quiz

Lehninger
Chapters 1.3, 2, 13.1

Lehninger
Chapters 3, 4 and 5

Take home assignment 1/Independent study

F2F

ENZYMES 1
a. Principles of catalysis
b. Overview of the types of reactions
enzymes catalyze
c. Chemical kinetics
d. The Michaelis-Menten equation
e. Steady-state assay design and analysis
f. Enzyme inhibition

F2F

ENZYMES 2
a. Models for allosteric regulation of
enzyme activity
b. Posttranslational modifications
c. Methods of enzyme and protein
purification
d. Enzyme reaction mechanisms

Lehninger
Chapter 6

Assignment
1 Due

Lehninger
Chapter 6
+
Reaction Mechanisms
paper

Take home assignment 2/Independent study

F2F

LABOR DAY HOLIDAY


MEMBRANE PROTEINS AND FAT-SOLUBLE
VITAMINS
a. Properties of membrane proteins
b. How proteins interact with membranes

Lehninger
Chapter 11

Assignment
2 Due

c. Transporters and channels


d. Fat soluble vitamins
i. Structures and functions
ii. Nutritional requirements and
consequences of deficiencies
Take home
Fri
assignment
9/9/16 3/Independent
study

Mon
9/12/16

F2F

Wed
9/14/16

F2F

Mon
9/19/16

Vitamins and Metals paper


WATER-SOLUBLE VITAMINS AND
MINERALS
a. Water soluble vitamins
i. Structures and functions
ii. Conversion to enzyme cofactors
iii. Nutritional requirements and
consequences of deficiencies
b. Essential minerals
c. Metal homeostasis
d. Metals and oxidative stress
INTRODUCTION TO METABOLISM
a. Roles of the major metabolic
pathways
b. Regulation of metabolic pathways
c. Multiple roles of key metabolic
intermediates
d. Metabolic hormones
e. The specialized roles of organs and
tissues in metabolism

Assignment
3 Due

EXAM For Section 1

Lectures 11-20: Wednesday Sept. 21 Monday Oct. 17


SECTION 2: Metabolism
Date
Format
Lecture Content
Carbohydrate Metabolism
(A)
Glycolysis
Wed
(B)
Krebs Cycle
F2F
9/21/16
(C)
Electron Transport Chain & Oxidative
Phosphorylation
(D)
Pentose Phosphate Pathway
Fri
On-line Carbs II
9/23/16
Mon
F2F Carbs III
9/26/16
Lipid Metabolism
Wed
F2F (A) Introduction to Lipids: Structure & Function
9/28/16
(B) Lipid biosynthesis and breakdown

Dr. Ebert
Reading Assignments

Quiz

Quiz

(C) Lipid metabolites as signaling molecules


(D) Role of Lipids in membranes
Fri
On-line Lipids II
9/30/16
Mon
F2F Lipids III
10/3/16
Nitrogen Metabolism
(A) Introduction to Nitrogen Metabolism
(B) Urea Cycle
Wed
F2F (C) Importance of vitamins and co-factors in nitrogen
10/5/16
metabolism
(D) Biosynthesis & Degradation of Purines and
Pyrimidines
Fri
On-line Nitrogen II
10/7/16
Integrated Metabolism
(A) Introduction: Energy demands of different
Mon
Organs & Tissues
F2F
10/10/16
(B) Hormonal regulation of metabolism
(C) Fasting & Starvation
(D) Metabolic Diseases
Wed
F2F
10/12/16
Integrated Metabolism: Regulation
Mon
EXAM for Section 2
10/17/16
Lectures 21-30: Wednesday October 19 - Monday November 14

Quiz

Quiz

Quiz

Dr. Phanstiel

SECTION 3: Nucleic Acid Structure & Function (Quiz or Study Guide exercises are subject to change)
Date

Format

Lecture Content

Wed
10/19/16

F2F

DNA Structure, RNA Structure, DNA Topology and


Topoisomerases

Fri
Online
10/21/16

Chromatin Structure

Mon
10/24/16

F2F

Histone and Nucleosomal Structure, Active and


Inactive Chromatin (continued)

Wed
10/26/16

F2F

DNA and Chromatin Replication

Reading Assignments
Quiz
Chapter 6. The Structures
or DNA and RNA. Primary
Literature Reviews (to be
named)
Chapter 7. Genome
Structure, Chromatin and
the Nucleosome. Reviews
to be named.
Chapter 7. Genome
Quiz or
Structure, Chromatin and
Study
the Nucleosome. Reviews
Guide
to be named.
Chapter 8. The Replication
of DNA. Primary
Literature References (to
be named).

Fri
Online
10/28/16

Completing Replication, Telomeres, Decatenation


Completion

Chapter 8 (continued).
Reviews on Telomeres,
Decatenase and
Checkpoints (to be named)
Chapter 8 (continued) and Quiz or
Primary Literature
Study
References to be named. Guide
Chapter 9. The Mutability
and Repair of DNA.
Recent advances in DNA
repair (primary literature
references to be named).

Mon
10/31/16

F2F

Telomerase, Telomere Hypothesis, T-loops and


Telomere Capping

Wed
11/02/16

F2F

Mutability and Repair: Prokarya and Eukary

Fri
11/4/16

Online

DNA Repair Pathways Specifics

Chapter 9 and Reviews


from Primary Literature to
be named.

Mon
11/7/16

F2F

Double Strand Break Repair. NHEJ, HR, Epigenetic


Silencing post-repair and Translesion Synthesis

Ch. 10. Primary Literature


to be named.

Wed
Site-Specific Recombination, Transposition and V(D)J
Online
11/9/16
Recombination
Mon
EXAM for Section 3
11/14/16
Lectures 31-40: Wednesday November 16 - Monday December 12

Quiz or
Study
Guide

Reviews from Primary


Literature to be named.

Dr. R Chakrabarti

SECTION 4: Gene Regulation (Transcription)


Date

Wed
11/16/16

Fri
11/18/16

Mon
11/21/16

Wed

Format

Reading
Assignments

Lecture Content

Mechanism of Transcription
a. RNA Polymerase
F2F
b.Promoters
c.Transcription Initiation
d. Elongation
Regulation of Prokaryotic Transcription
a. The lac operon
b. The ara operon
Online
c. The trp opereon
d. Riboswitches
e. Two component systems
Shifts in Bacterial Transcription
a. Sigma factor switching
b. Infection of E.coli by
F2F
bacteriophage
Transcriptional Machinery and Gene Regulation
in Archaea
F2F
Eukaryotic RNA Polymerases

Quiz

Homework 1

11/23/15

11/25/16
Mon
11/28/16

Wed
11/30/16

Fri
12/2/16

Mon
12/5/16

Wed
12/7/16

Fri
12/9/16
Mon
12/12/16

a. Different RNA Polymerases


b. Promoters
c. Enhancers & Silencers
THANKSGIVING HOLIDAY
General Transcription Factors
a. Class II Factors
F2F
b. The Mediator Complex
c. Class I and II factors
Transcriptional Activators
a. DNA binding and activating
F2F
domains
b. Functions of Activators
Regulation Of Transcription Factors
a.Coactivators
Online
b.Ubiquitylation
c.Sumoylation
d.Acetylation
Cell-type-specific Transcription and Gene
Regulation
F2F
a. Viruses
b. Hormone receptor
Role of regulatory RNA (will cover miRNA)
Regulation of Primary Response Genes
Chromatin Structure and Its Effects on
Transcription
a. Effects of histones on
transcription of class II genes
F2F
b. Nucleosome Positioning
c. Histone Deacetylation
d. Chromatin Remodeling
e. Heterochromatin and
Silencing
Splicing
a. Spliceosomal Splicing
Online
b. Self-Splicing
Capping
Polyadenylation
Exam for Section 4

(END OF FALL 2016 SEMESTER)

Homework 2

Homework 3