chem 355 syllabus 2011

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					                               Syllabus:
                 Chemistry 355: Advanced Biochemistry
                               Fall 2011

Professor: David Morgan
Office: PSC 3007
Phone: (902) 867-5259
e-mail: dmorgan@stfx.ca


Course website:

        Follow links under http://people.stfx.ca/dmorgan


Office Hours:

        Mondays     3:15 pm – 5:15 pm
        Wednesdays 3:15 pm – 5:15 pm
        Other times by appointment

        During my office hours, you may simply “drop in.”

        If you wish to make an appointment to meet with me at some other time, please use e-
mail. I despise telephones and often ignore them, and I don’t check my voice mail very often. I
am hoping to use Thursdays as my “research day,” and will probably not be available on
Thursdays… but you can always ask.

        A word to the wise: Long experience (mine and others) indicates a strong, positive
correlation between time spent chatting with the professor in his / her office and student
performance in the course. (This is not because professors “play favourites.” )


Text:

        The text you used in Chemistry 255:

        Voet, Voet, and Pratt (2008) Fundamentals of Biochemistry. John Wiley and Sons,
        Hoboken, NJ.

         A variety of other Biochemistry and Organic Chemistry texts will be available on reserve
in the library. It is often worthwhile to look up material in different texts – especially if you find
you are experiencing difficulty “getting it.” Different texts offer different perspectives on the
same material, and sometimes one just plain makes more sense (to you) than another. Also,
practice problems from other texts are very useful.
        Metabolism is, in my view, the organic chemistry of biological molecules and how they
are interconverted by enzymes. Thus, this course is mechanism-intensive. Organic texts are
available for you, therefore, should you wish to brush up on mechanisms (nomenclature, etc).

Lectures:

       Lectures occur during F block, in Immaculata Hall, room 113.

        I do not verify your attendance. (But as with time spent in the professor’s office… so
with class attendance.)


The St. Francis Xavier Univeristy Student Response System (StFXrs):

        A handful of us younger faculty have gotten interested in using computer technology to
assess how well students are “getting” the material – in real time in the classroom. Systems like
this are called “Student Response Systems” or, perhaps more colloquially, “clickers.” Because of
the expense of commercially available response systems, Peter Marzlin in Physics undertook to
write a web-based response system – in house, from the ground up. (I, Darren Derksen, and Shah
Razul also contributed.) I’m planning to -test this system with this class, in preparation for
using it in Chemistry 255 next term.
        As long as you have a device (laptop, tablet, iPhone, Android phone…) that is capable of
interacting with the internet, you’re all set. (Yes, this is a Bring Your Electronic Devices to Class
Policiy. ) Please register yourself in the system using the link below BEFORE class on
Monday:

       http://physics.stfx.ca/StFXrs/studentRegistration.php?course=Chemistry355

Note: there is a cell phone number field. Please do NOT provide this information.

Note: if you don’t have a portable electronic device that fits the bill, please let me know before
class on Monday.

Laboratory:

       Lab occurs during Q1/T1 in the Physical Sciences Centre, room 3066.

        Participation in the lab is essential. You should make every conceivable effort to
participate in every lab. Even if you can not be present for a lab (due to an “excusable absence”
such as a medical or family emergency, or because you are representing the University in an
official capacity – for example, you’re on a sports team) you will, never the less, be responsible
for turning in a lab report.
Lab Reports:

        As befits a course in which you will be implementing experiments the likes of which
have not been perfected over hundreds of person-hours into the boring “canned” labs (with their
predictable results) you have been required to slog through in the past, in this course, your
laboratory reports will have to look and sound more like manuscripts presented for publication in
a professional journal. (You will be purifying and analyzing proteins from yeast, produced in the
early part of the semester, from the beer you brew.) Thus, for this term, you should think of
yourselves as qualified biochemistry professionals, who are isolating proteins out of a brand new
strain of brewer’s yeast (the yeast that grew best in the beer you prepared), characterizing them,
and describing their function to the wider community of biochemists.

       Unless otherwise noted, one lab report is required for every lab experiment.

        Lab reports at or before 11:59:59 pm on the day one week following that on which the
lab session occurred. Late lab reports shall be penalized 3 points per day (or fraction thereof)
they are late. Note that this includes weekend days.

    Lab reports must be submitted electronically. They are to be sent to me as e-mail
attachments, on or before the time they are due, at my e-mail address, above. The digital time
stamp that accompanies your electronic submission shall be considered proof of the time at
which your lab report was submitted. You may submit Microsoft Word, OpenOffice, or pdf files.
If you wish to submit lab reports in some other format please consult with me first.

   Lab reports must be:

      Type-written

      Use the 12 point Arial font for text

      Have uniform 1 inch margins

      Be double-spaced

      Be written in grammatically correct English

               Yep. I mean it. I reserve the right to penalize grammatical errors. Minor
          or occasional grammatical errors will simply be pointed out to you. Major
          grammatical errors will incur penalties ranging from points being taken off
          your grade for the lab in question, up to and including my refusal to grade
          the report until it is resubmitted. In the latter case, the lab will be considered
          late, and will be penalized according to the same policy indicated above for
          late lab reports.

             As for all intellectuals, it is essential for scientists to be able to
          communicate their intellectual activity to the wider community. There are
       no two ways around this, and while it’s popular (in universities) to hear
       people say things like “Oh, I’m majoring in physics because I hate writing,”
       that is complete and utter nonsense, as any of those self same people would
       tell you – five years later – at the end of their graduate school careers when
       they’re writing papers or grant proposals – or in their medical residencies as
       they’re writing patient histories – and so on. So, if you don’t already write
       clear, comprehensible, grammatical English, start learning how to do so
       now.

           No one – NO ONE – no matter how well you write or don’t write –
       should be ashamed to make use of the writing centre. Everyone –
       EVERYONE – can learn to write better all the time. You can find the writing
       centre at:

                      http://www.mystfx.ca/resources/writingcentre/

   Have a descriptive title

          Avoid titles like “Lab Report 1.” Aim instead for something like
       “Michaelis-Menten Treatment of the Kinetics of -Galactosidase in
       Lactase™ Tablets.”

          Use the 18 point, bold, Arial font for titles. If you wish to include a
       sub-title, use either the 14 or 16 point, bold, Arial font. The title should be
       centered left to right.

          No points will be awarded for having an appropriate title, but up to one
       point may be deducted for a really bad title.

   Have your name, the date the lab was carried out and the date the lab report was
    submitted. Your partner’s name (in case you worked with a partner) is not necessary.

             Use the 14 point, bold, Arial font for your name. Use the 14 point Arial
       font (not bold) for the dates. Your names and these dates should be centred
       left to right.

   Have an introductory section

           The introductory section should be about one paragraph in length. It
       should explain the purpose of the experiment and provide an answer the
       question “Why do we as biochemists wish to understand what we are
       testing in this experiment?” Avoid asserting things like “the purpose of
       this experiment is to teach us how to purify aldolase from yeast.” That’s
       thinking like a student. Your challenge is to think like the professionals:
       They would say something like: “Aldolase is a critical enzyme in
       glycolysis… (and explain further)… Yet, few undergraduate biochemistry
       courses investigate this enzyme…. (why might that be?… is that a
       deficiency?... elaborate…) Here, we undertake the purification of aldolase
       from yeast acquired in large quantity from home-brew, and demonstrate
       the feasibility of accomplishing the purification with the inexpensive
       equipment and reagents routinely available in the undergarduate
       biochemistry laboratory.”

           No points will be awarded for an appropriate introductory section, but
       up to two points may be deducted for an inappropriate introductory
       section.

   Have a “Materials and Methods” section

           Just like it sounds, the purpose of this section is to report exactly what
       you did, and exactly how you did it.
           I repeat:
           Just like it sounds, the purpose of this section is to report exactly what
       you did, and exactly how you did it.
           Note that it does not say the purpose of this section is to report the set
       of instructions you were given in the lab manual. Honest scientists report
       exactly what they did, exactly how they did it, and you should do the same
       in this section. Doing this well will be faciliated by taking good,
       comprehensive, notes in your “scribblers” (which I will not look at) as you
       carry out the experiments.

           This section should be written in the past tense for obvious reasons.

           The length of this section depends on the nature of the experiment you
       are reporting on. Some experiments will require an extensive materials
       and methods section, others will not. If in doubt, write more, not less.

           Up to five points will be awarded for this section. Folks, this section is
       a total no-brainer. Everyone should get these five points on every single
       lab report. The only way you can get less that all five points on this section
       is not to pay attention.

   Have a “Results” section

           Once again, the purpose of this section is just what it sounds like. In
       this section, you report what you observed and measured in the
       experiment. Take note, however, that this section should absolutely not be
       a collection of bullet points, tables, and / or figures. This section may well
       contain tables and figures, but – as with all other sections of the report –
       this section must be written in clear, comprehensible, grammatical
       English, using sentences and paragraphs. You should refer to tables and
       figures in this section as you discuss the corresponding results. (Example:
       “Yeast alcohol dehydrogenase was eluted from the Cibachrom – Blue
       column in elution buffer. SDS-PAGE gels were prepared and stained
       either with Coomassie Blue or silver salts. Figure 1 shows the silver-
       stained gel, Figure 2 shows the Coomassie Blue stained gel.” The figures
       themselves should be clearly labeled and captioned. (Example: An
       appropriate label and caption for Figure 1 would be:

       Figure 1. Silver-stained SDS-polyacrylamide gel of Cibachrom Blue fractions from
       NAD+ elution of alcohol dehydrogenase. Lane 1: (at left) protein molecular weight
       markers. Lanes 2 through 10: fractions one through 9.

           Up to ten points will be awarded for this section. As with the Materials
       and Methods section, if you are in doubt, include more material in this
       section rather than less. As with the Materials and Methods section, this
       section should be a no-brainer: it should be an easy 10 points. Just write
       up what you observed and measured, prepare appropriate figures and
       tables, include appropriate photographs, etc. 10 easy points.

   Have a Discussion section

           The discussion section is pretty much the “meat” of the lab report. Here
      you explain your results. This section is basically your opportunity to show
      off to your professional colleagues (in your case, me) how smart you are,
      and how well you understand the material. While the Results section of
      your lab report describes what you observed and measured, the Discussion
      section is your opportunity to say what it means. In this section you should
      write a minimum of two paragraphs which explain how all your data fit
      together and make sense, if they do. Otherwise, you explain how some of
      your data makes sense, and some of it doesn’t. Here you note things that
      were different, or similar, to what you expected, and why you expected
      what you did; if things were different from what you expected, here you say
      what you’ve learned from that fact. And so on.
           Up to ten points will be awarded for the Discussion section. Note that
      these are the most difficult ten points for you to earn in your lab reports. I’ll
      grade you easy on this section at the beginning of the term, harder on this
      section at the end of the term – the standard for a good Discussion section
      (indeed – a good lab report) will get higher as the term goes on.

   Have a Questions section

           There may be a handful of questions for you to address in the lab
      manual. You should answer these questions in this section. Unless
      otherwise noted, up to two points will be awarded for each question. Unless
      called upon to do something else (like draw a structure or a mechanism)
      write the answers to your questions in clear, comprehensible, grammatical
      English sentences. If in doubt as to whether or not you have answered a
      question completely, write more, rather than less.
        One of my long term goals for Chemistry 355 is the creation of a Journal in which
particularly outstanding lab reports can be published. Towards the end of the term I would like
each of you to choose a lab report on which you performed particularly well, and write it up for
submission to the journal. More on this as the term progresses.

Note: You may (indeed, I strongly encourage you to) work together as you interpret your results
for your lab reports.

Note: Nevertheless, each person must write a lab report independently.

Assignments:

        Assignments will be given out approximately every other week. Assignments will consist
of problems related to material that should be part of your general knowledge, or which has been
previously addressed in class or your readings. Assignments will be due at the beginning of the
class period one week following the date they were given out. Late assignments will not be
accepted and will be scored zero, unless you make prior arrangements with me to hand an
assignment in late. I will make every effort to return graded assignments within one week of
their due date, but will not guarantee my ability to do so.

       You may work together on assignments and lab reports. But, to be clear, this means that
you may discuss problems with each other, work them out together, think through them together,
teach each other how to do them, etc. To be clear, this does not mean that you may hand in
assignments which are de facto, or actual, copies of each others work. Every individual is
required to hand in an assignment that reflects his or her personal understanding of the meaterial
– even if you have arrived at that understanding collectively. As a rule of thumb: you may
discuss the material with each other out loud; you must write your answers independently.

        Regarding this last point, please note that I take academic integrity very seriously in
general, and that I take the integrity of the scientific enterprise particularly seriously. Thus, as in
all your other classes at St. FX, in this class I require you to be bound by the university’s
Academic Integrity Policies and Procedures. Why? Science is a process in which we absolutely
rely on our fellow scientists to honestly report what they did and observed, and faithfully present
their reasoning to the rest of us. Errors and mistakes happen in science all the time. Errors and
mistakes are – in large part – how we learn to do better next time. Errors and mistakes are not
unethical, just human. Fraud and cheating are rare in science (though not as rare as they should
be); they are unethical, and they are deeply contradictory to the spirit of scientific inquiry. I
charge you to hold yourselves to the highest standards of academic integrity in this course, in all
your other courses, and throughout your personal and professional lives.
Exams:

       There will be two midterm exams and one final exam. Midterm exams are tentatively
scheduled for Wednesday, October 19th and Wednesday, November 16th. Midterms will take
place during the usual class time. I will make every effort to return graded exams one week
following the date they were written, however, I will not guarantee my ability to do so.

        I will conduct at least one review session before each exam, possibly more. If there is a
general feeling among you that regular review sessions would be useful (in the secnd half of the
term) I am prepared to make arrangements for weekly or bi-weekly review sessions.
Participation in review sessions is completely optional.

         Students with a documentable academic or other official university-sanctioned activity
that conflicts with an exam time will be permitted to take the exam at another time. If you are in
this situation, you must make arrangements with me at least one full week in advance, by e-mail.
This ensures that we each have a record of the arrangements we make with each other.

       Students who are registered with the Tramble Rooms should inform me to that effect as
soon as possible, and will be permitted to arrange their exam times and locations with the
Tramble Rooms.


Grading:

        StFXrs1                             5%
        Assignments:                        10 %
        Mid-term 1:                         20 %
        Mid-term 2;                         20 %
        Lab:                                20 %
        Final:                              25 %


Course Content:

        We will discuss carbohydrate metabolism in depth beginning with glycolysis, the Kreb’s
cycle, and oxidative phosphorylation. We will finish off this part of the course with a look at
alcoholic and lactic acid fermentation. Except for the level of depth with which we examine the
subject matter, this will largely be review for you.

       We will proceed from there to gluconeogenesis (which has the opposite effect of
glycolysis) and examine how each of these pathways can be made thermodynamically favourable
even though they go in opposite directions.



1
 Everyone starts out with 2.5 % out of the available 5 %. Every question you answer correctly gets you closer to 5
%. The exact value of each question depends on the total number of questions asked over the term.
       We will finish our study of carbohydrates by looking at glycogen metabolism and –
importantly – the manner in which it is regulated.

        We will probably study either the biosynthesis of lipids or the biodegradation of lipids, as
well as basics of lipid chemistry. If time permits, we may study both aspects of lipid chemistry,
but this is unlikely.

       We will look at some of the simpler pathways in amino acid biosynthesis and degradation
in depth; we will at least glance at some of the more complex of these pathways. Additionally,
we will look at how amino acids serve as the building blocks of a variety of hormones, signalling
molecules, and other biologically active small molecules.

        Having done all this, there will be a few days left in the term. I haven’t chosen what to do
with those days yet. Some possibilities are: a survey of photosynthesis, nucleotide and
nucleobase metabolism, some biochemistry that’s made headlines recently, or a quick tour
through an advanced area of biochemistry. I would be pleased to take suggestions from you in
this regard.

				
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