Biochemistry of the cell, NSC13                                                       Fall 2013

 

Instructor:    Todd Smith, Science 110

Days/Time:   Tuesday & Thursday, 11:30-12:50

Credits:          4 credits        

Text:               Biochemistry, 7^th ed., Berg, Tymoczko & Stryer

 

 

Course Description

Biochemists once debated the nature of proteins: their composition, structure, and function. Now we know many extraordinary details of the shapes of proteins and how they function. For example, how they help our bodies acquire nutrients from food, use those nutrients for fuel, and carry oxygen to our tissues. In particular, researchers have revealed the intricacies of how a protein’s structure is related to its function. In this course we will employ an evolutionary perspective as we discuss major topics such as amino acids, proteins and protein structure, bioenergetics, enzymes and enzyme function. We will also study major metabolic pathways and their key control points. Our goals are for you to develop a thorough understanding of how enzymes work and to be familiar with key metabolic pathways and how they are controlled. 

 

The course will include class discussions and group projects based on the text and primary literature, homework assignments, a 5-page paper and take-home exams (including a final exam).

 

Prerequisite:  General Chemistry I and II

Co-requisite:  Laboratory in Biochemical Techniques, NSC425

 

Goals of the course

Through this course students will:

• Learn to apply principles of general and organic chemistry in the context of biological systems
• Become familiar with the molecular components of living systems
• Learn how these molecular components interact in a controlled and organized manner
• Learn the general principles that govern the myriad of interactions between cellular components
• Hone their writing and problem-solving skills, develop their ability to work collaboratively, and increase their facility with analytical software

 

Grading Policy

Students are expected to attend all lectures and to come to class prepared to discuss all reading assignments. 

 

There will be two take-home exams during the semester, weekly homework assignments, a research paper, and a final exam. The paper and take-home exams are worth 100 points each, each homework is 20 points each, and the final exam is worth 100 points. The grade received in the course will be the ratio of points earned over points possible: 90% & above = A, 80-89% = B, 70-79% = C, 60-69% = D. Diligent and conscientious participation in class and on assignments will boost borderline grades to the higher grade.

 

If extenuating circumstances will prevent you from taking an exam notify me as soon as possible so that we can make alternative arrangements for administering the exam.

 

Paper assignment – due Friday, 11/25/13

The topic for your paper is synthetic biology:  the attempt to engineer complex biological systems. An extreme example would be the complete construction of a novel type of cell. Some researchers feel this approach will provide new sources of low-cost fuels, whereas others worry about unforeseen ecological consequences or the creation of biological weapons. What do you think? You must take a clear position in your paper and defend that position based on your research:  either support the attempt to create new types of cells, or express serious reservations. In your paper you must cite at least two secondary sources (i.e., textbooks) from the Rice-Aron Library, and at least two articles from peer-reviewed scientific journals to develop your argument for or against the construction of synthetic cells.

            The citation format you should use is that of the Council of Science Editors, as described at: http://library.osu.edu/help/research-strategies/cite-references/cse/ .

 

Assignment                                                                                due dates

• Topic, research questions & 3 sources                         9/19, in class

• Paper outline or concept map, with argument           10/18, in class

• Final paper                                                                          11/25, in class

 

 

Policy on Academic Integrity

Students must understand Marlboro College’s Policy on Academic Integrity. This policy defines plagiarism and describes consequences for students who commit plagiarism and is described in detail in the Marlboro College Handbook.

            The Marlboro College library hosts several resources for students on the proper use and citation of sources, including a Library Guide called “Creating Citations,” which also contains a link to Handling Sources: a Guide for Marlboro College Writers.  These are excellent resources and students should take some time to explore them.

 

 

 

 

 

 

 

 

Course schedule – approximate

 

Week of	Week	Topic	Text chapter
9/2	0	Intro class: themes and goals; Chemical principles in biochemistry; biochemistry and the unity of life.	1, 2
9/9	1	Protein composition, structure, and function; Librarian & research for papers on Thursday	2
9/16	2	Protein structure, continued. Paper topic, etc. due Wednesday 9/19	2
9/23	3	Structural biology – a brief intro to crystallography & NMR.	6
9/30	4	Evolution and bioinformatics	6
10/7	5	Hemoglobin as a model of protein function; Free energy; enzyme kinetics, and the Michaelis-Menten equation Exam 1 – take-home on Fri. 10/11	7, 8
10/14	6	Catalytic strategies – structure of an active site Paper outline & argument – Friday 10/18	8, 9
10/21	7	Hendricks Days – no class Tuesday Regulatory strategies for enzyme control	10
10/28	8	Membranes and membrane proteins	12 & 13
11/4	9	Coupled reactions are a key biochemistry concept; Transduction - signaling across membranes	14, 15
11/11	10	Glycolysis – a metabolic pathway	16
11/18	11	The central role of the Citric Acid Cycle Exam 2 - take-home on Friday 11/22	17
11/25	12	Oxidative phosphorylation: electron transport chain, Peter Mitchell & chemiosmosis	18
		Thanksgiving – no class Thursday
12/2	13	Fatty acid metabolism occurs through b-oxidation Papers due Monday, 12/2	22
12/9	14	Regulation of metabolism - integrating metabolic pathways	27
12/12, 13		Reading days
12/13		Final exam – take-home on Friday, 12/13