Professional Documents
Culture Documents
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
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
Description
80%
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
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
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
F2F
Lehninger
Chapter 11
Assignment
2 Due
Mon
9/12/16
F2F
Wed
9/14/16
F2F
Mon
9/19/16
Assignment
3 Due
Dr. Ebert
Reading Assignments
Quiz
Quiz
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
Fri
Online
10/21/16
Chromatin Structure
Mon
10/24/16
F2F
Wed
10/26/16
F2F
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
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
Wed
11/02/16
F2F
Fri
11/4/16
Online
Mon
11/7/16
F2F
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
Dr. R Chakrabarti
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
Homework 2
Homework 3