Biochemistry Division
Biochemistry graduate students do not have a choice of classes to select from, as you are automatically enrolled in CHEM 5771-Advanced Biochemistry I (aka ‘Core’: as in the core class for all biochemists). The class is 5 credit hours and usually meets MW from 9-11 am, and one hour on Friday. It is supplemented with a one-credit-hour block of time dedicated to "Ethics in the Sciences" (CHEM 5776). The one-credit course does not count towards the required 15 credits for advancement to candidacy. In first semester of Core you will briefly review general nucleic acid and protein structures as well as the thermodynamics of their interactions within the cell. Several of the techniques you will learn about to help understand and probe these interactions will be X-ray crystallography, NMR and several other optical spectroscopic techniques. The class will also spend a fair amount of time on major cellular protein/DNA assemblies. Second semester Core (CHEM-5581- Advanced Biochemistry II) will continue in-depth study of macromolecular complexes. You will also spend a large amount of time on signaling pathways including those involved in immunology, oncogenesis, apoptosis and regulation of the cell cycle. Additionally, there will probably be specific focus on G protein coupled receptors and/or on the MAP Kinase and TGF-b pathways.
You are required to present several times in CORE. At the end of each rotation (see below), you will generally give a Powerpoint presentation of about 15 minutes length to the class. Since the rotations only last about 2 months each, you will probably spend most of the time on the background of the problem you were working on and show a few good data slides. In previous years, an additional presentation was done on a publication of choice in the spring semester. You should know that paper top to bottom as well as several of the works it references.
Finally, in Core you will have to review publications chosen by the instructor and write a ½ to 1 page critique of that paper. Some papers are very good while others are filled with both grammatical and experimental errors. On several of the critiques, I found that doing a literature search on the topic of that paper produced later publications which retract the claims made in the original work. This exercise is designed to get you familiar with reviewing the quality of others' works as well as searching the literature for a multitude of topics.
How to Prepare
Most of the material you will learn in Core is based on current literature and techniques used. Most 1st year students will not have previous knowledge about the use of NMR, X-ray Crystallography or Mass Spectrometry nor the biological pathway/system encountered in the literature, and these are covered in class. There are some basic things you should know, however. For a good review, go back to your college biochemistry textbook (Voet and Voet is a departmental favorite although Stryer and other texts also work) and make sure you are familiar with the following:
-principles behind both DNA and protein helix formation
-how to recognize and draw the 20 amino acids
-a little bit about transcription and translation and some of the basic components of the complexes used for each process
You will generally have time to review each of these before your class exams but often you will find that between class, teaching and rotations that you can only devote so much time to study. Reviewing the basics is good way to ‘give yourself a leg up’ before the year really gets going.
Here is a note from Dr. Rob Kuchta and Dr. Deborah Wuttke, who taught core in the 2003-2004 academic year, about what to prepare for first semester CORE:
In terms of what people should know for the course, these would include:
1. Basic enzyme kinetics
2. Basic thermodynamics
3. Basic organic chemistry (i.e., what you would get in a typical undergraduate course)
4. A general knowledge of protein and nucleic acid structure
5. The 20 amino acids and their functional properties
6. Basic principles of enzyme regulation (phosphorlyation, etc.)
7. The central dogma of gene expression
All of this material would be covered in an undergraduate biochemistry course.
Cumulative Examinations
Biochemistry "cumes" are given 8 times per year and generally have the same topic in any given month. These pass/fail test are given the first Saturday of each month (Sept-Dec and Feb-May) in E1B20 (the basement of Ekeley) from 9:00-10:00 AM. To find out what cumes are being given your year, there is a list on the wall of the mailbox room in Cristol. While some students do not take any cumes during their first year, most students have found it is prudent to at least attempt several of them. You have to pass 6 before you fail 11 and, as you may already know, if you fail one your first year, it only counts as half a fail. You will know which topic is being given and which professor is writing that cume so you can be selective about which ones you want to take. Try and stick to topics that you are familiar with and definitely, definitely ask older graduate students about how hard the professor giving the exam usually grades: some will pass up to 80% of the takers while others tend to fail at least 50%. Additionally, the graduate secretary (Hilary) has copies of previous years' exams on file that you can copy, although these don't have answers to the questions. These are a great way to get a good idea of the questions that will be asked. Professors often use previous cumes as the basis for which questions they will ask and often will ask the same (or very similar) questions. I suggest spending a night or two on your own reviewing a broad range of material then get a group of friends together and go through the old cumes on the Friday before the test. One thing to consider about taking all the cumes your first year: you WILL be swamped and struggle to get everything done that is asked of you. Between your classes, homework, teaching and rotations, it can be too difficult for most students to take every cume and put in a good effort to pass each one. However, three to five attempts should be feasible and will make your 2nd year much easier. The list below shows the topic generally given for each months’ cume:
September- Central Dogma of Gene Expression
October- Enzyme Assays/Binding Assays
November- Thermodynamics
December- Chemical and Biochemical Kinetics (or Enzyme Purification)
February- Enzyme Mechanisms
March- Enzyme Kinetics
April- Cell Signaling/Signaling Pathways
May- Biological Macromolecules (functions, structures and forces)
Presentations/Seminars
Biochemistry students are ‘required’ to attend seminar on Wednesday afternoons. While attendance is not taken, going to these seminars is often quite beneficial in several ways. First, as our department is fairly well funded, we often get excellent speakers that are performing cutting edge research in their fields. This is a great way to meet these individuals and gain some contacts (especially if you volunteer to go to a free lunch with them). Secondly, several of the cumes throughout the year will include questions about the speakers’ talks. By attending the seminar, these cume questions are freebies since they usually only ask about the most important information from the speaker's presentation. Finally, each year the department usually looks to hire 1-2 new faculty. During the spring seminars, you can have a say in who (and what type of research they do) will join the department you’ll be in for the next several years.