MEES 680 - Cell and Molecular Biology for Environmental Scientists - Genes to Ecosystems

Meets Monday and Wednesday - Lectures 8:00AM to 10:00AM with 20 minute discussions.  Lectures & Discussions end at 9:55AM.  We meet in the Columbus Center Room 2041

Course will be available by IVN and will be web-based using CourseForum. 

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Prerequisites: Undergraduate biochemistry and/or cell biology 

Instructors: Allen R. Place, Rose Jagus, Tsetso Bachvaoff, Paul Gugger, Louis Plough

Suggested texts: Cell biology by the Numbers, Ron Milo & Ron Phillips, Illustrated by Nigel Orme

Atomic Evidence. David S. Goodselll

Phylogenetic trees made easy.  Barry G Hall. 

If you need a classic textbook, both of these are available as electronic downloads. 

Course Organization: There will be two written examinations available on CourseForum, weekly homework assignments, one assignment on molecular phylogenetic analysis and a final project.  We will discuss several recent papers in class. 

Grading:

First Exam:                                       10%
Second Exam:                                   10%
Student Paper Discussion:                 15%
Phylogeny Assignment:                     15%
Project:                                             20%
Attendance/Participation:                 30%

Syllabus: 

The Cogs in the Machinery of Life - A Gallery of Size, Shape & Charge

August 29, Lecture 1: AP: Molecules of Life

August 31, Lecture 2: APL Carbohydrates and Lipids 

September 5, Labor Day - No Class

September 7, Lecture 3: AP: Amino Acids

September 12, Lecture 4: AP: Nucleic Acid and Metabolites

The Machinery of Life - Making DNA, Making RNA, Making Proteins, Making Membranes, Making a Cell

September 14, Lecture 5: AP: Chromatic and Nucleus

September 19, Lecture 6: AP: Protein Sorting & Trafficking 

September 21, Lecture 7: RJ: Making DNA

September 26, Lecture 8: RJ: Making RNA

September 28, Lecture 9: RJ: Transcriptional Regulation & Splicing 

October 3, Lecture 10: RJ: Organelles

October 5, Lecture 11: RJ: Translation Part 1

October 10, Lecture 12: RJ: Translation Part 2

October 12, Lecture 13: RJ: Non-coding RNAs

October 17, Exam 1: The exam will place on CourseForum on October 17 at 8:00AM, answers must be uploaded by October 18 at 8:00AM

Are the Cogs and Machinery Shared and How do you know? 

October 19, Lecture 14: TB: Next generation DNA sequencing 

October 24, Lecture 15: TB: Bioinformatics and computational biology, sequence alignments, protein structure alignments, orthologues, paralogues, gene duplication, lateral gene transfer, data mining, phylogenetic trees, molecular versus physical taxonomy 

October 26, Lecture 16: TB: Comparing Sequences and Making Phylogenetic Trees

Variation in the Machinery

October 31, Lecture 17: LP&PG: Using Variation for Population Studies

November 2, Lecture 18: LP&PG: Population and Landscape Genomics

November 7, Lecture 19: AP: Lateral and Horizontal Gene Transfer

November 9, Lecture 20: RJ: Symbiosis and Parasitism

November 14, Lecture 21: Microbiomes - Environmental and Gastrointestinal 

Manipulating and Detecting the Machinery - The Researcher's Toolbox

November 16, Lecture 22: RJ: Basic molecular biological tools, Part I 

November 21, Lecture 23: RJ: Basic molecular biological tools, Part II

November 24, Thanksgiving NO CLASSES

November 28: Exam 2: The exam will place on CourseForum on November 28 at 8:00 AM, answers must be uploaded by November 29 at 8:00 AM.

Modifications to the Machinery

November 30, Lecture 2: RJ: Phosphorylation

December 5, Lecture 25: AP: Ubiquitnation, sumolaytion, etc. 

December 7, Student Project Presentations