Course Instructor: Dr. Frans Huijing  305-243-6244        fhuijing@miami.edu

Office: 109 Gautier, 1011 NW 15 Street, Miami FL. Permission of instructor needed.

General inquiries should be made to Salome Antezana 305-243-6261, Rm. 116 Gautier.

The purpose of this course is to introduce students to attending research seminars.  There are two goals;

1. to sample current research topics in biochemistry and molecular biology and to connect the material presented to knowledge learned in previous courses.

2. to develop a critical awareness of the factors that go into a good presentation. 

The attitude of students going to the seminars should be a positive one.  The purpose of the seminar is to actively acquire and integrate new information - you should not be a passive state of mind.

For each seminar, a written report is required. For entire course, EIGHT reports are required.  At least SIX of these must be submitted by November 1, 2008. The final reports are due on December  4, 2008. Late submission will reduce your grade. Students can submit their first paper to Dr. Huijing as early as possible for constructive criticism. All papers should be submitted be e-mail. Attach the paper as an MS Word 2003 document. Put your name in the header (not your student number) and be sure to number the pages. Name the files: Lastname-501-S# where # is the number of the seminar (1-8).

Format of the reports:  These need not be longer than 2 pages.  Give the speaker's name, affiliation and seminar title and date. Also, give an indication of the speaker’s status. Is the speaker a well-known researcher or a graduate student giving a dissertation seminar? A summary of the content of the seminar should then be given. If you use sources other than the seminar, for instance for figures (encouraged!!), please give a clear reference to this source. A critique of the seminar should be given. It is important to give YOUR impressions of the seminar.  The following questions will help you to develop a positive and critical approach.

Are the conclusions of the seminar well supported by the data?

Was the question/hypothesis clearly presented, i.e. does the introduction set up the rest of the talk?

For each piece of experimental data presented, were the results clearly discussed (significance, how the data support the original idea, and caveats?).

For the overall presentation, is there a clear linkage of experiments from one to another that builds on a theme? Also, were the slides/illustrations clear and legible?  Did the speaker give a good presentation (clear elocution etc)?

Many times, your paper can be improved by the use of figures.

Which Seminars to attend?     There are a number of weekly seminars at the medical school, which have a biochemical content. Biochemistry seminars will be announced on the department bulletin board in the Cox Science Building. Other seminar announcements can be found on the bulletin board outside room 118 in the Gautier building. I suggest that you contact other basic science departments in the medical school and ask them about their seminar program. Ask if seminar announcements can be sent to students by e-mail. Please make sure that your e-mail address on class web site is up to date. Students will be asked to exercise their own choices in selecting seminars to attend.

The class meets only once, tentatively on Friday, September 5, 2008 or Wednesday September 3 from 11:25 a.m.-1 p.m. in the Gautier Building, room 118. This will be confirmed (or changed) by e-mail. The meeting will introduce the course and we will attend a seminar. Most of the seminars will be on weekdays at noon on the medical campus. Students should not sign up for this course if they cannot attend seminars at the noon hour on the medical campus because of other classes between 11 a.m. and 2 p.m.

STUDENTS REGISTERED FOR THIS COURSE, PLEASE CONFIRM BY E-MAIL THAT YOU WILL BE ATTENDING THE FIRST MEETING.

Students are expected to abide by the University Honor Code.

 Grading Policy

A grade of A will be given to students who get all their papers in on time and who show in their paper that they can connect and integrate information obtained from the seminars to material that they learned in biochemistry, biology, chemistry and any other course that they have taken. The papers should be well written and if possible use illustrations to help the reader.

A grade of C will be given to students who get all their papers in on time and who show in their paper that they can connect but not necessarily integrate information obtained from the seminars to material that they learned in biochemistry, biology, chemistry and any other course that they have taken. The papers should be adequate.

A grade of F will be given to students who do not submit all papers on time.

Grades of B are intermediate between A and C

Grades of D are intermediate between C and F

Prerequisite or co-requisite for this course is BMB 506. The catalog states that this course is a companion course to BMB 506. It is possible to take this course with BMB 506 but I now believe that it is more fruitful to take this course after you finish BMB 506. I will try to change the course description in the catalog.

 This course can be taken more than once.

Scheduled seminars

Monday           noon    Microbiology   starts mid-September?

Tuesday           noon    Cell Biology

Wednesday     noon    Biochemistry Journal Club

Thursday         noon    Pharmacology

Friday              noon    Biochemistry   not every week

Clinical correlation sessions are, in general, not suited for this course.

Please check the web pages of the different basic science departments for seminar announcements.

FH

Faculty: Dr. Frans Huijing   109 Gautier Building, Medical Campus        305-243-6244
              Dr. Tina Wenz          301 Lois Pope Building, Med. Campus         305-243-4232

General inquiries: Salome Antezana, 117 Gautier Building Medical Campus, 305-243-6261.
E-mail addresses: fhuijing@miami.edu          TWenz@med.miami.edu   santezan@med.miami.edu

Time:     8:00-9:15 a.m. Tuesdays and Thursdays.      Place: Room LC 130 Coral Gables Campus
and         3:35-4:25 p.m. Wednesdays (section NH).    Place: Room PHY 108 Coral Gables Campus
Exams will be given in a different room. Please watch for announcements.
Textbook: Berg, Tymoczko and Stryer, Biochemistry, 2006 6^th edition Freeman plus iClicker. Please register your clicker online before the first class (August 27).

This course is intended for Biochemistry undergraduate majors and for graduate students in chemistry, biology and other sciences. It requires previous knowledge of biochemistry such as taught in our course BMB 258. Students who are not in the above-mentioned categories need permission of the instructor to take this course. Students who do not have the prerequisite courses (especially CHM 202 C or better) will be dropped from this class.

The course consists of two parts. One is taught concurrently with BMB 401. It is a general biochemistry course that will be part review for the students who took BMB 258 but it will use different applications and reinforce the connection with organic chemistry. Organic chemistry was not required for BMB 258.
Students who already took BMB 401 are not eligible for BMB 506. They should discuss alternatives with Dr. Huijing. The Wednesday tutorial section can be taken for BMB 511 credit.

The second part of the course will introduce the students to areas of protein structure and function, metabolism and molecular biology that are not normally covered in a general biochemistry course. Emphasis will be on retrieval and use of information rather than on memorizing it. Students will show that they can recover and use information from books, journals and on-line databases in weekly homework assignments and three papers or PowerPoint presentations on assigned topics. Class attendance and participation is mandatory. Participation in the weekly group-homework is mandatory. The instructor reserves the right to refuse to accept the papers of students who do not attend and participate in class and those who do not participate in the group homework.

Examples of topics that may be discussed in lectures and be the subject of student work are listed below.

Exams and grading. Students will take all four exams in the BMB 401 class. The grades on these exams will constitute 80% of the grade in BMB 506. The remaining 20% will be the grade for the three required papers. Homework will be corrected and marked from poor to excellent. This will provide feedback to the students to tell them if they are using the right methods and finding the proper sources.  Homework is a prerequisite for writing the papers. Failure to do the homework or to hand it in on time can cause a reduction of the grade by 20%.

Homework and papers will only be graded if they are handed in when they are due. Please mark the dates of the exams (see the handout for BMB 401) and the due dates of the papers on your calendar. Most homework assignments, papers and presentations must be submitted by e-mail. In some cases a written or printed copy is required at the time of the class. If you cannot be in class, for instance because of a major religious holiday, send me the paper by e-mail well before the due date. If you do not intend to participate in class discussions and get your assignments in on time, please drop this class. Drop dates are September 12 and October 24.

This honors class is intended for students who get satisfaction from learning new concepts, especially if they can collect the facts needed to understand these concepts themselves.

It is expected that students will do well in the 401 portion of this course. After all, that is part review. Students should attend those lectures and take all exams on time. The grades on the papers and homework for the Wednesday afternoon sessions cannot be used to improve a poor performance on the Tuesday/Thursday section of the course.

Students are expected to abide by the University Honor Code.

Incomplete grades will not be given except for unusual, serious circumstances such as hospitalization. In that case a date will be set for completion of the grade. Completing that work late will result in a reduction of grade.

Topics for the papers will be assigned by lottery. Below is a list of possible topics for the first paper but these can be changed or eliminated and new topics may be added.

Tentative topics for the first paper (topics to be assigned by lottery):

Enzymes that have more than one different activity                 

G-proteins

Transport proteins (e.g. for glucose, iron, vitamins, fatty acids, hormones)

Enzymes that bind all or part of the substrate covalently during the reaction catalysis

Lipid-linked proteins (properties, synthesis, location, function and degradation)

Active sites that are formed by two or more subunits.

Disulfide bond formation, breakage and rearrangement

No writing credit
This course cannot be taken for writing credit. The goal is to write brief, concise papers of about 500 words plus figures and references. Since you are describing the work of others, you will tend to use their words also. Give proper credit to the original authors. Provide a reference mark in the text and at the end of the paper give the complete reference, including page numbers or give the exact address of the web page. Provide a working link to the web page (test the link!).  Common knowledge needs not to be cited but web pages are not common knowledge. Do not only read abstracts of papers. They are often too concise. Read the introduction and at least part of the discussion.

The first paper will be an actual paper written in MS Word. Save it as a Word 2003 document. I cannot read .docx documents. The second ‘paper’ will be a clear PowerPoint presentation with at least 10 slides. We will discuss this in class and I will give examples of a good presentation. I will decide on the format of the last paper later.

STUDY STRATEGIES for BMB 401  or

How to Get a Good Grade in Biochemistry?

Adapted from Dr. John Makemson    BCH 3033  makemson@fiu.edu

2.      Next, do the Practice questions and some of the End of Chapter Problems without looking at the answers. If you have difficulty, get it resolved NOW. By doing this you are building upon your knowledge and making problem solving so much easier.

3.      Next take out a piece of paper and review the material with the book, notes, etc. CLOSED. To some students this is a paper lecture (but this may be the most important study activity you will do). When you are finished, check what you did in the lecture with your notes and book to see if you have everything correct. This is a great learning experience. Now you are almost ready for the next lecture.

4.      Before the Exam, calmly review the material, do some of the practice problems and tests at the textbook website. Now you don't have to cram and be anxious or get into some psychological frenzy about Biochemistry. It is much better to get a good night’s rest and eat a healthy breakfast than it is to cram for a Biochemistry exam at the last minute. Your performance on the exam is directly affected by your health and readiness, so prepare in advance and maintain your health to show us what you know! This is because at this point you know you have obtained a good understanding and facility with biochemistry. Further you will most likely observe your classmates who are next to throwing a fit trying to cram. Here is your opportunity to tutor them, because if you know it, you can now teach it to your fellow students...which is a real solid way of developing confidence in what you know.

5.      Getting a Good Grade comes directly from effective Learning. The major expense in doing this is your time, it is one of the most valuable possessions you have and if you have done 1-4 above it will pay off! Your grade equals time well spent.

Comments from Students Who Got Good Grades - comments from student course evaluations.

1.      Take a light load with Biochemistry. This is a heavy duty course, much more than you expect. Be honest with yourself in what you can handle. If you are, it will save you much anxiety and having to repeat the course.

2.      Tape record the class - Listen carefully to what the Prof. says - this is what WILL BE TESTED.

3.      Go through the notes and figures, make up questions for yourself, when preparing for the test, take you own test. This is the absolute best way to make sure you understand the concepts it will sharpen your attention to details not paid close attention to before.

4.      Start reviewing for a test 7 days before the test.

5.      Attitude: try not to learn the material just for the tests, it never works. Go in with the desire to get a solid understanding...it will make your life easier when prepping for the MCAT, and in medical school, etc.

6.      If you ever have a question or you have missed something in lecture go ASK THE PROF, he taught the stuff - he should know the answer.

Here's How to get a Low Grade. See if this is your strategy. I hope not!!

1.      Come to all lectures unprepared. It is so much fun to see things you never thought of before and do not understand during the lectures. Very little of these lectures will be retained and almost no learning will occur. This is the best way to make lectures useless.

2.      Do not attend the lectures. You get to sleep in and do not have to trek across the campus to the Learning Center. Of course you also do not get your “money’s worth” for your tuition dollars, miss out on the in class discussion, and do not benefit from your professor’s efforts to produce lucid and enlightening lectures about fundamental mechanisms of living systems.

3.      Put off studying to the last minute, say, the day before the exam. It impressive how much material there is! You will find that at this time it is too late to do any critical reading in the text. Just try to memorize the facts, facts you can know much about and facts that will not help you at all in problem solving. Stay up late doing this wonderfully non-productive studying, do it overnight so you will really be messy. This can get some degree of sympathy from your friends. However, then when you flunk and have to repeat the course, you will even get more sympathy.

You can make your life easier by recognizing similarities. For instance three of the four reactions of the fatty acid oxidation spiral are identical to three of the reactions of the citric acid (Krebs) cycle. A second example is the fact that glutamine often acts as a donor of nitrogen or amino groups. Two of the nitrogens of the purine ring, the amino group of guanine and the amino group of glucosamine all come from the amide nitrogen of glutamine. Draw metabolic maps. See how different pathways are related and connected.