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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:

 

E-mail

Office

Phone

Victor Davidson, Ph.D.

victor.davidson@ucf.edu

Lake Nona 237

6-7111

Steven Ebert, Ph.D.

steven.ebert@ucf.edu

Lake Nona 421

6-7047

Otto Phanstiel, Ph.D.

otto.phanstiel@ucf.edu

BMS annex

3-6545

Ratna Chakrabarti, Ph.D.

ratna.chakrabarti@ucf.edu

BMS annex 107

2-2258

Course Coordinator:

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. 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.

B)

Kaiser, Monty Krieger, Anthony Bretscher , Hidde Ploegh , Angelika Amon , Matthew P. Scott 3) Lehninger Principles of Biochemistry, 5 th 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, 6 th Edition, by James D. Watson

Course Requirements:

Test

Description

Weight toward final grade

4 term

exams

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%

Quizzes/

Assignments

Weekly in class quizzes and assignments will test knowledge acquired from the previous week's 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 else’s 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 another’s work is used or appropriated without any indication of

the source, thereby attempting to convey the impression that such work is the student’s

own.

iv. Any student who knowingly helps another violate academic behavior standards is

also in violation of the standards.

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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.

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SCHEDULE

(Subject to change at the instructors’ discretion)

Lectures 1-10: Monday August 22 Monday Sept. 19

 

Dr. Davidson

SECTION 1:

Biochemical Principles

 
     

Reading Assignments

Assignment/

Date

Format

 

Lecture Content

Quiz

   

BIOCHEMICAL PRINCIPLES

   

a. Water, pH and buffers.

Lehninger Chapters 1.3, 2, 13.1

Mon

8/22/16

F2F

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

Lehninger Chapters 3, 4 and 5

Wed

c. Primary, secondary, tertiary and quaternary structure

8/24/16

F2F

d. Methods of protein characterization

 

Examples of soluble proteins f. Protein folding

e.

Fri

     

8/26/16

Take home assignment 1/Independent study

   

ENZYMES 1

   

a. Principles of catalysis

b. Overview of the types of reactions enzymes catalyze

Lehninger

Mon

F2F

Chapter 6

Assignment

8/29/16

c. Chemical kinetics

1

Due

d. The Michaelis-Menten equation

 

e. Steady-state assay design and analysis

f. Enzyme inhibition

   

ENZYMES 2

Lehninger

 

a. Models for allosteric regulation of enzyme activity

Chapter 6

+

Wed

8/31/16

F2F

b. Posttranslational modifications

c. Methods of enzyme and protein purification

Reaction Mechanisms paper

d. Enzyme reaction mechanisms

Fri

     

9/2/16

Take home assignment 2/Independent study

9/5/16

 

LABOR DAY HOLIDAY

   
   

MEMBRANE PROTEINS AND FAT-SOLUBLE VITAMINS

Lehninger

 

Wed

F2F

Chapter 11

Assignment

9/7/16

a. Properties of membrane proteins

2

Due

b. How proteins interact with membranes

 

4

c. Transporters and channels d. Fat soluble vitamins i. Structures and functions ii. Nutritional requirements
c. Transporters and channels
d. Fat soluble vitamins
i. Structures and functions
ii. Nutritional requirements and
consequences of deficiencies
Take home
Fri
assignment
Vitamins and Metals paper
9/9/16
3/Independent
study
WATER-SOLUBLE VITAMINS AND
MINERALS
a. Water soluble vitamins
i. Structures and functions
Mon
ii.
Conversion to enzyme cofactors
Assignment
F2F
9/12/16
iii. Nutritional requirements and
consequences of deficiencies
3 Due
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
Wed
F2F
9/14/16
c. Multiple roles of key metabolic
intermediates
d. Metabolic hormones
e. The specialized roles of organs and
tissues in metabolism
Mon
EXAM For Section 1
9/19/16
Lectures 11-20: Wednesday Sept. 21 – Monday Oct. 17
Dr. Ebert
SECTION 2:
Metabolism
Date
Format
Lecture Content
Reading Assignments
Quiz
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
Quiz
9/28/16
(B) Lipid biosynthesis and breakdown

5

   

(C)

Lipid metabolites as signaling molecules

   

(D)

Role of Lipids in membranes

Fri

       

9/30/16

On-line

 

Lipids II

Mon

       

10/3/16

F2F

 

Lipids III

   

Nitrogen Metabolism

   

(A)

Introduction to Nitrogen Metabolism

(B)

Urea Cycle

Wed

10/5/16

F2F

(C)

metabolism

Importance of vitamins and co-factors in nitrogen

Quiz

(D)

Biosynthesis & Degradation of Purines and

Pyrimidines

Fri

       

10/7/16

On-line

Nitrogen II

   

Integrated Metabolism

   

(A)

Introduction: Energy demands of different

Mon

F2F

Organs & Tissues

Quiz

10/10/16

(B)

Hormonal regulation of metabolism

(C)

Fasting & Starvation

 

(D)

Metabolic Diseases

Wed

       

10/12/16

F2F

Integrated Metabolism: Regulation

Quiz

Mon

       

10/17/16

 

EXAM for Section 2

Lectures 21-30: Wednesday October 19 - Monday November 14

Dr. Phanstiel

SECTION 3:

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

Date

Format

Lecture Content

Reading Assignments

Quiz

     

Chapter 6. The Structures

 

Wed

DNA Structure, RNA Structure, DNA Topology and Topoisomerases

or DNA and RNA.

Primary

10/19/16

F2F

Literature Reviews (to be named)

Fri

   

Chapter 7. Genome Structure, Chromatin and the Nucleosome. Reviews to be named.

 

10/21/16

Online

Chromatin Structure

   

Histone and Nucleosomal Structure, Active and Inactive Chromatin (continued)

Chapter 7. Genome Structure, Chromatin and the Nucleosome. Reviews to be named.

Quiz or

Mon

10/24/16

F2F

Study

Guide

Wed

   

Chapter 8. The Replication of DNA. Primary Literature References (to be named).

 

10/26/16

F2F

DNA and Chromatin Replication

6

Fri

 

Completing Replication, Telomeres, Decatenation Completion

Chapter 8 (continued). Reviews on Telomeres, Decatenase and Checkpoints (to be named)

 

10/28/16

Online

     

Chapter 8 (continued) and Primary Literature References to be named.

Quiz or

Mon

10/31/16

F2F

Telomerase, Telomere Hypothesis, T-loops and Telomere Capping

Study

Guide

Wed

   

Chapter 9. The Mutability and Repair of DNA. Recent advances in DNA repair (primary literature references to be named).

 

11/02/16

F2F

Mutability and Repair: Prokarya and Eukary

Fri

   

Chapter 9 and Reviews from Primary Literature to be named.

 

11/4/16

Online

DNA Repair Pathways Specifics

     

Ch. 10. Primary Literature to be named.

Quiz or

Mon

11/7/16

F2F

Double Strand Break Repair.

NHEJ, HR, Epigenetic

Silencing post-repair and Translesion Synthesis

Study

Guide

Wed

 

Site-Specific Recombination, Transposition and V(D)J Recombination

Reviews from Primary Literature to be named.

 

11/9/16

Online

Mon

       

11/14/16

EXAM for Section 3

Lectures 31-40: Wednesday November 16 - Monday December 12

SECTION 4: Gene Regulation (Transcription)

Dr. R Chakrabarti

     

Reading

 

Date

Format

 

Lecture Content

Assignments

Quiz

   

Mechanism of Transcription

   

a.

RNA Polymerase

Wed

11/16/16

F2F

b.Promoters

c.Transcription Initiation

d.

Elongation

   

Regulation of Prokaryotic Transcription

   

a. The lac operon

Fri

Online

b. The ara operon

11/18/16

c. The trp opereon

d. Riboswitches

e. Two component systems

   

Shifts in Bacterial Transcription

   

a. Sigma factor switching

Mon

F2F

b. Infection of E.coli by

Homework 1

11/21/16

bacteriophage Transcriptional Machinery and Gene Regulation in Archaea

Wed

F2F

Eukaryotic RNA Polymerases

   

7

11/23/15

   

a.

Different RNA Polymerases

 

b.

Promoters

c.

Enhancers & Silencers

11/25/16

 

THANKSGIVING HOLIDAY

 
   

General Transcription Factors

 

Mon

 

a. Class II Factors

11/28/16

F2F

b. The Mediator Complex

c. Class I and II factors

   

Transcriptional Activators

 

Wed

 

DNA binding and activating domains

a.

11/30/16

F2F

Homework 2

b.

Functions of Activators

   

Regulation Of Transcription Factors

 
 

a.Coactivators

Fri

12/2/16

Online

b.Ubiquitylation

c.Sumoylation

d.Acetylation

   

Cell-type-specific Transcription and Gene Regulation

 

Mon

12/5/16

F2F

 

a. Viruses

b. Hormone receptor

Homework 3

Role of regulatory RNA (will cover miRNA)

   

Regulation of Primary Response Genes Chromatin Structure and Its Effects on Transcription

 
 

a.

Effects of histones on

Wed

F2F

transcription of class II genes

12/7/16

b. Nucleosome Positioning

c. Histone Deacetylation

d. Chromatin Remodeling

e. Heterochromatin and

Silencing

   

Splicing

 

Fri

Online

 

a. Spliceosomal Splicing

b. Self-Splicing

12/9/16

Capping

Polyadenylation

Mon

     

12/12/16

 

Exam for Section 4

(END OF FALL 2016 SEMESTER)

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