Biochemistry II

In this course, we will read, analyze and discuss original research papers involving modern molecular and biochemical methods. These papers will be chosen to cover a variety of topics of high current interest. Papers will range from topics such as the discovery and reconstitution of essential biological pathways to disease mechanisms through fundamental principles of genomic organization and control. In all cases, the emphasis will be on underlying biochemical mechanisms and experimental approaches. The class periods will involve a mixture of discussions (both in large and small groups) and interactive problem solving and analyses.

The advantages of teaching a course based on the scientific literature are many:

The first block will focus on critical analyses of papers. We will start with paper anatomy and the peer review process to set the stage of the nuts and bolts of publishing work. You will also present a paper in preparation for your final grant presentation (see below). Together we will discuss and dissect strengths and weaknesses of papers which will allow you to propose future directions in preparation for your final grant proposal (see below) and grant panel critique. We will examine seminal genomics papers and current therapeutics papers as key examples. You will analyze our papers and write short assignments developing critical thinking skills, as well as begin choosing and preparing your grant proposal sections.

The second block will focus on scientific application and significance. As such, we will read and discuss papers that use biochemistry for purposes related to energy and materials science. These discussions will allow us to think ‘outside the box’ of some traditional uses of biochemistry, and will help you to formulate your own application/ justification for your final grant proposal (see below).

Attendance and Participation: Because this class depends on interactions, attendance is expected, as are regular contributions to the class discussions. If you will be unable to attend a class, notify us in advance by email or voicemail. Anyone who is present every day and is involved in the class meets expectations; deductions will be made if a student is not contributing to discussions and/or for unexcused absences. The specific grading scheme is as follows:

3 = Class participation is exceptional. The student is well-prepared for class and makes thoughtful, clear, and concise points; initiates highly intellectual discussions.

2 = Class participation is good. The student is mostly prepared for class and makes mostly clear points; successfully engages in intellectual discussions.

1 = Class participation is minimal. The student is not prepared for class and makes minimal contributions to class discussion.

0 = No class participation. The student does not engage at all, or is absent from class.

Weekly Writings: There will be at least one writing assignment each week for the first block. The writing assignments will focus on analysis (goals 1-4). Writings involve exercises such as analyzing or commenting on the strengths and weaknesses of a scientific paper, suggesting further experimental approaches, or considering the broader implications of some finding. Grades will be given based on whether the student met the expectations of the assignment, using a scale of 0- 3 as follows:

3 = Exceeds goal. Performs the task at the level expected of a professional in the field. There are no significant errors or misunderstandings, the work is clear and comprehensive, and it demonstrates sophisticated thinking (insight, analytical ability, integration etc…).

2 = Meets goal. The work is performed with minimal errors or misunderstandings and is of overall good quality. It could be improved, however, with increased analysis, integration, sophistication or rigor.

1 = Approaches goal. The guidelines of the assignment were followed and the work shows evidence of progress towards meeting the goal. Nevertheless, it may be unclear, partially incorrect, or reflect misunderstandings.

0 = No evidence of achieving goal. The work was either not done, or done so poorly that one cannot discern sufficient progress towards achieving the goal.

Grant Proposal Writings: Writing is an extremely important component of this course, and this is reflected in the points designated for writing assignments.

“Writing clearly, correctly, and concisely is essential to success in chemistry, and in this electronic age chemists are writing more than ever before. Recently, after surveying many companies, including major employers of trained chemists, the National Commission on Writing suggested that employers perceive college graduates as ill-prepared to do the kind of writing necessary in the modern workplace, where writing clearly and cogently is not only a threshold skill but also vital to career advancement.”

(A Short Guide to Writing about Chemistry by Davis, Tyson, Pechenik, 2010)

One piece of your final grant proposal will be due each Tuesday. This will give you the opportunity to get feedback, and encourage you to continuously work on this final project. The grant proposal writing assignments will be graded out of 10 points, and evaluated on clarity, concise wording, proper scientific language, and scientific accuracy, among other things. Excessive errors in spelling and grammar will result in a lower grade. Please look over the grading rubric for the final proposal to familiarize yourself with writing expectations.

Writing assignments will be reviewed using Turnitin, an online program that is used to detect plagiarism. You will have the opportunity to submit your assignments to Turnitin prior to submitting them for grading. In this way, you will learn what gets ‘flagged’ by the program and may constitute plagiarism. Your use of this program is optional, but highly recommended. As stated below, academic dishonesty will not be tolerated. Assignments reflecting any sort of academic dishonesty will be automatically submitted to the judicial board for review.

Weekly Presentations: Each week a pair of students will be responsible for preparing an oral presentation of a paper we are reading. The presentations should be brief (roughly 10-15 min) and focused, and will serve as a launching point for discussion. You will turn in your powerpoint presentation. You will be evaluated on presentation depth of understanding, clarity, and style. In addition, you will be given feedback on your presentation for continued improvement over the course of the semester and in preparation for your grant proposal presentation.

Grant Proposal: Your final semester-long project will be a formal grant proposal. You will chose one primary paper and write a grant proposal expanding on a specific aspect of that paper (i.e. a new direction with proposed experiments, a parallel set of experiments in a new organismal system chosen for a specific purpose, etc.) We will help you to focus the scope of your proposal. This will be a semester-long assignment; the final grant proposal will be due at the end of the semester with deadlines for individual sections throughout the semester. Further details are provided in the Grant Proposal handout.

Final Presentation: There will be a final presentation to accompany the grant proposal at the end of the semester. Each student will give a 15 minute presentation with 5 minutes for questions explaining the background and significance of their proposal, as well as their specific aims and proposed research plans. These presentations will be peer-evaluated. Each presentation will be ‘scored’ on whether or not it should be funded. The 5 top-scoring proposals will receive bonus points and be invited to present again during finals week in our ‘Proposal Face-Off!’ The final winner will receive additional bonus points and a prize! We will provide snacks and beverages for the competition.

We take into account progress over the semester. We typically expect students to have more trouble meeting the goals early in the semester, but as their skills develop, they can meet the goals more easily. Demonstrating full ability to meet the goals at the end of the semester carries a lot of weight in the grading.

In compliance with Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act, reasonable accommodation will be provided to students with documented disabilities on a case-by-case basis. Students must register with Student Disability Services with the Office of Academic Support Services (607-274-1005, TDD 607-274-7319, acssd @ithaca .edu) and provide appropriate documentation to Ithaca College before any academic adjustment will be provided.

All the work in this class must be your own, unless stated otherwise. For many of the assignments, it is expected that you will discuss ideas with your classmates. Nevertheless, the final work must be your own, and must reflect your own analysis and interpretation. Confirmed instances of academic misconduct will result in a zero for that assignment/quiz and referral to the school judiciary system. Please refer to the Student Handbook for a detailed description of the policies regarding student academic conduct. If you have a question about what constitutes plagiarism, refer to the following web site: http://www.ithacalibrary.com/sp/subjects/BPR.

Diminished mental health, including significant stress, mood changes, excessive worry, or problems with eating and/or sleeping can interfere with optimal academic performance. The source of symptoms might be related to your course work; if so, please speak with me. However, problems with relationships, family worries, loss, or a personal struggle or crisis can also contribute to decreased academic performance. Ithaca College provides cost-free mental health services through the Center for Counseling and Psychological Services (CAPS) to help you manage personal challenges that threaten your personal or academic well-being. In the event I suspect you need additional support, expect that I will express to you my concerns and the reasons for them. It is not my intent to know the details of what might be troubling you, but simply to let you know I am concerned and that help (e.g., CAPS, Health Center, Chaplains, etc.), if needed, is available. Remember, getting help is a smart and courageous thing to do -- for yourself and for your loved ones.

Student input is highly valued and is important to maintain high quality instruction. Course evaluations are required. You may get a ZERO for an assignment if not completed by the due date. The evaluation will be submitted online to the department Administrative Assistants.

Professor:	Maki Inada, Biology Department	Kathryn Cole, Chemistry Department
Office:	156 CNS	364 CNS
Telephone:	274-1274	274-7104
Email:	minada@ithaca.edu	kcole@ithaca.edu
Office Hours:	Tuesday, Thursday 2-3:00, or by appointment	MWF 9am-10am or by appointment