Biology 485 Syllabus (Fall, 2001) 
Macromolecular Structure  
Homepage URL: www.clunet.edu/BioDev/marcey/biol485/bio485syl.htm

 

David Marcey  

116 Ahmanson   493-3263
e-mail: marcey@clunet.edu
Office Hours or availability for
appointment: see DM's schedule


 


 
about the course...

Subject Material:

The elaborate interplay of a variety of macromolecules underlies the mechanisms that govern cell function. This advanced, 2 unit seminar course deals with the structure-function relationships of these macromolecular machines. It is intended that students emerge from this course with a deep understanding of the principles that govern macromolecular structure and the functional consequences of these principles. See learning goals, below. This course assumes a good understanding of basic molecular biology. See DM if you think you might require some remedial reading in this area.

Course Format:
This is a seminar class in which students must assume responsibility for their own learning. Students will come to class prepared to discuss the reading assignment for the week. Lectures will focus on teaching the methods that students will employ to construct a web-based tutorial on a macromolecule, chosen with input from DM.

Text: 

Introduction to Protein Structure, 2nd edition - Branden & Tooze (BT)
Additional Reading:
Journal Articles on the structure of macromolecules

Supplemental Learning Material:

You will also be provided additional learning aids that are accessable on the WWW or on the local CLU network. See linked resources, below. 

Grading:

The grade for this class will be determined solely by the quality of the completed web tutorial and on the quality of an oral presentation delivered in public.

The WWW tutorial construction assignment involves building a molecular tutorial in an HTML (HyperText Markup Language) document. You may choose your own molecule in consultation with DM. You will need to learn the RasMol/Chime scripting language to build your tutorial. Instruction on tutorial construction will be provided in the first few weeks of class. More information on the project assignment can be found here.

Academic Honesty and Class Conduct:

It is you responsibility to know the guidelines of the university regarding academic honesty and class conduct. READ THE SECTION ON ACADEMIC HONESTY in the CLU COURSE CATALOG to familiarize yourself with the CLU policies, as this course will follow these guidelines. Please be reminded that if you use the words of another person, whether or not you scientifically cite the source in your text, you also must use quotes around those words. It is important to learn to use your own writing to present ideas and syntheses of ideas. You should read the CLU guide to avoiding plagiarism!

Learning Disabilities:

If you have a disability and therefore may have need for some type of accommodation(s) in order to participate fully in this class, please feel free to discuss your concerns in private with me AND BE SURE TO CONTACT the learning center.

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learning goals & assessments...

Goals 

Assignments & Assessment 

To learn about: 

  • structure/function relationships of macromolecules 

reading, course lectures, discussions,

web project 
To learn to use the hypertextual medium of the World Wide Web as a way to present ideas.

web project 

To hone written and oral communication skills.

web project and class discussions

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course schedule...
DATE   TOPICREADINGASSIGNMENTS
Aug 28  Introduction to Course  
Sep

4

Basic Principles of Protein Structure

Chapters 1 & 2

explore PDB
Sep 

11

Motifs, Structures, Folding - Web page fomat

Chapters 3-6

work on molecule of choice
Sep

18

Tutorial construction

 

pick molecule
Sep 

25

Nucleic Acid Structures

Chapter 7, read articles on molecule of choice

one page write up on molecule
Oct 

2

DNA recognition

Chapter 8, read articles on molecule of choice

 
Oct

9

Transcription Factor Binding

Chapter 9, read articles on molecule of choice oral presentation to the class of key structural features of the molecule of choice
Oct 

16

Transcription Factor Families

Chapter 10, read articles on molecule of choice

 
Oct 

23

Catalysis

Chapter 11, read articles on molecule of choice

first drafts due
Oct

30

Membrane Proteins

Chapter 12, read articles on molecule of choice

 
Nov 

6

Signal Transduction

Chapter 13, read articles on molecule of choice

 
Nov

13

Fibrous Proteins

Chapter 14, read articles on molecule of choice

second drafts due
Nov

20

Immune System Molecules

Chapter 15, read articles on molecule of choice

 
Nov 27 Practice Talk   prepare talks
Dec

4

Presentation of Project

  final projects due

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linked resources... (clicking on the links below will open new browser windows)

The Online Macromolecular Museum - (see the WWW links section)

RasMol Manual (detailed) - RasMol Manual (beginner's introduction)

Scripting Tutorial

Chime Manual - Chime Tutorials

An Article on Molecular Modeling Freeware

Protein Structure at ExPASy (see the "autopsy of a PDB file" - Chapter 11)

Info Page on the Macromolecular Tutorial Assignment 

Pedro's Biomolecular Research Tools

Virtual Library: Biochemistry and Molecular Biology

 

 

 

 

 

 

 

 

more coming soon.... 

  linked resourceslearning goalscourse scheduleabout the course