Information & Policies

Course Syllabus

Download hardcopy of the Syllabus (.doc)


Instructor:
William W. Metcalf
B415 C&LSL
244-1943
metcalf@illinois.edu
Office Hours: Mondays 4:00-5:00 PM or by appointment

Teaching Assistant:
Divyanshi
Learning Center, Burrill Hall
divyans2@illinois.edu
Office Hours: Wednesdays 8:50-9:50 AM or by appointment

Description:
The course examines the biochemical and physiological adaptations that allow microbes to compete and succeed in diverse environments. Emphasis is placed on the role of metabolism in the living organism and on the specific evolutionary advantages conferred by different metabolic stragtegies.

Grading:
Option I: An initial grade based on 400 total points will be assigned after the third exam. If the student is satisfied with this grade, then the Final Exam is not required.
3 exams = 300 points
6 problem sets = 60 points
10 muddiest points = 10 points
1 quiz = 30 points
Total 400 points

Option II: If the student is not satisfied with the initial grade, the final exam may be taken. In this case, the grade will be based on 600 total points. The percentage score required to achieve each grade will be identical to that used for Option I. You cannot lower the initial grade by taking the final.
3 exams = 300 points
6 problem sets = 60 points
10 muddiest points = 10 points
1 quiz = 30 points
Final exam = 200 points
Total 600 points

Problem Sets:
Six problem sets will be given over the semester, two for each third of the course. Each will be worth 10 points. Grading will be based on whether an effort was made to solve the problems, not on whether the right answer was obtained. Partially complete homework will receive partial credit. Problem sets will be due at midnight on the dates indicated below. They can be turned in during class, or in my mailbox in B103, CLSL, or via email. If submitted by email, your answers must be compiled into a single PDF document. "Cut and paste" answers from other sources will not receive credit. Answers will be posted online after the due date. Fully completed, late homework will be accepted prior to the last day of class, but will only be worth 5 points each. No partial credit will be given for late homework.
February 2 Problem set #1
February 14 Problem set #2
March 6 Problem set #3
March 25 Problem set #4
April 10 Problem set #5
April 26 Problem set #6

Help Sessions:
Help sessions will be held prior to the due date for each problem set and exam. All help sessions will be at 5 PM in Burrill 140.
Thursday, Feb 1 Problem Set #1 Help Session 5PM, 140 Burrill
Tuesday, Feb 13 Problem set #2 Help Session 5PM, 140 Burrill
Thursday, Feb 15 Exam 1 Help Session 5PM, 140 Burrill
Tuesday, Mar 5 Problem Set #3 Help Session 5PM, 140 Burrill
Thursday, Mar 21 Problem Set #4 Help Session 5PM, 140 Burrill
Tuesday, Mar 26 Exam 2 Help Session 5PM, 140 Burrill
Tuesday, Apr 9 Problem Set #5 Help Session 5PM, 140 Burrill
Thursday, Apr 25 Problem Set #6/Exam 3 Help Session 5PM, 140 Burrill

Muddiest Point:
Students often feel that certain topics covered in class are not well explained or confusing. When this occurs, please write a short email of 1-2 sentences asking that this be explained again. Send these to me (metcalf@illinois.edu) with the subject heading "Muddiest point". Each Monday at the beginning of class the most commonly asked question(s) will be discussed. To encourage participation in this feedback exercise, these will be worth 1 point each, up to a maximum of 10 points. You can submit as many questions as you like, but you will receive credit for a maximum of one point per week (i.e. you can't submit ten questions in the last week of class to improve your grade).

Quiz:
One quiz covering material you should have learned previously in prerequisite courses will be given during class on Friday, Jan 26. The answers are available online prior to the quiz.

Exams:
All exams will be taken during class on the dates indicated below. Questions will be in essay/problem solving format. Makeup Exams will not be given, if you miss an exam you must take the final, which will then count the same as a regular exam. Grading option II is not available if you miss a test.

Exam Schedule:
Exam I February 16
Exam II March 27
Exam III April 29

This is a tentative schedule and may change depending on the pace of lectures.

Optional Final Exam:
Friday, May 10, 1:30-4:30 PM, Burrill Hall, room 140


Web Site:
http://www.life.illinois.edu/mcb/424

The web page will contain lecture outlines, problem sets and problem set answers. Important: the lecture outlines are NOT meant as a substitute for class notes. If you rely on these as your sole source of class material, you are unlikely to do well on the exams.

Suggested (not required) Text:
The physiology and biochemistry of prokaryotes, by David White, Oxford University Press


Other Useful (but older) Texts:
Biology of the Prokaryotes, edited by Joseph W. Lengeler, Gerhart Drews and Hans Schlegel , 1999, Blackwell Science Bacterial Metabolism, by Gerhard Gottschalk, 1985, Springer-Verlag

Reading:
Periodic reading will be assigned as the course progresses. These will be from a variety of sources, including the recommended text cited above. Where ever possible I will attempt to have links for these readings on the course web site.

Tentative Course Schedule

Date Day Topic Assignment
1/17 Wednesday Class policies/Introduction to Microbial Diversity
1/29 Friday Introduction to Microbial Diversity
1/22 Monday Phylogeny/Classification of Prokaryotes
1/24 Wednesday Phylogeny/Classification of Prokaryotes
1/26 Friday Basic Microbial Physiology/Glycolysis Quiz in class
1/29 Monday Basic Microbial Physiology/Glycolysis
1/31 Wednesday Thermodynamics and Glycolysis
2/1 Thursday Problem Set 1 Help Session 5PM, 140 Burrill Hall
2/2 Friday Pyruvate Oxidation and TCA Cycle Problem Set #1 Due
2/5 Monday Electron Transport
2/7 Wednesday Electron Transport
2/19 Friday Energetics of Redox Reactions/ATPase
2/12 Monday Energetics of Redox Reactions/ATPase and Biosynthesis and Metabolic Diversity
2/13 Tuesday Problem Set 2 Help Session 5PM, Burrill 140
2/14 Wednesday Biosynthesis and Metabolic Diversity and Anaplerotic reactions Problem set #2 Due
2/15 Thursday Exam 1 Help Session 5PM, 140 Burrill
2/16 Friday Exam #1, in class
2/19 Monday Anaplerotic reactions
2/21 Wednesday Anaplerotic reactions/Catabolism of Polymers
2/23 Friday Catabolism of Polymers
2/26 Monday Catabolism of Polymers
2/28 Wednesday Catabolism of Polymers/Hydrocarbons/Anaerobic World
3/1 Friday Hydrocarbons/Anaerobic World/Fermentation I
3/4 Monday Fermentation I
3/5 Tuesday Problem Set 3 Help Session 5PM, 140 Burrill
3/6 Wednesday Fermentation I/Fermentation II Problem Set #3 Due
3/8 Friday Fermentation II/Fermentation III
3/11 Monday No Class, Spring Break
3/13 Wednesday No Class, Spring Break
3/15 Friday No Class, Spring Break
3/18 Monday Fermentation III
3/20 Wednesday Fermentation III/Decarboxylation Phosphorylation
3/21 Thursday Problem Set 4 Help Session 5PM, 140 Burrill
3/22 Friday Decarboxylation Phosphorylation/Anaerobic respiration: denitrification
3/25 Monday Anaerobic respiration: denitrification/Q&A Problem Set #4 Due
3/26 Tuesday Exam 2 Help Session 5PM, 140 Burrill
3/27 Wednesday Exam #2, in class
3/29 Friday Anaerobic respiration: metals
4/1 Monday Anaerobic Respiration: Sulfur
4/3 Wednesday Anaerobic Respiration: Sulfur/Acetogenesis
4/5 Friday Acetogenesis
4/8 Monday Acetogenesis/Methanogenesis
4/9 Tuesday Problem Set 5 Help Session 5PM, Burrill 140
4/10 Wednesday Methanogenesis/Syntrophy Problem Set #5 Due
4/12 Friday Syntrophy/Anoxic Ecosystems
4/15 Monday Aerobic Methanotrophs/Methylotrophs
4/17 Wednesday Aerobic Methanotrophs/Methylotrophs/Chemolithotrophy
4/19 Friday Chemolithotrophy
4/22 Monday Photosynthesis I
4/24 Wednesday Photosynthesis I/II
4/25 Thursday Problem Set 6/Exam 3 Help Session 5PM, Burrill 140
4/26 Friday Photosynthesis II Problem Set #6 Due
4/29 Monday Exam #3, in class
5/1 Wednesday Grades/ICES on-line
5/10 Friday Optional Final, 1:30 - 4:30 PM Burrill Hall, room 140