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My Teaching: TAing Experimental Biochemistry - 2002-2003 webpage
I TA one of the labs in the course
Experimental Biochemistry
(also see
the spring semester course description),
with the professor for that course being
Dr. Theodore Chase,
including supervision of students in the laboratory, helping students with
lab reports, grading of some lab reports, and helping grade the final exams.
Below, you will find:
- any information that I need to get to
students (or would like to make available to students) right now
- any comments about the course that I wish to
make
- a HTMLized version of the intro sheet that I
normally give out at the beginning of each semester.
For the previous semester's web-page, see
http://www.drallensmith.org/teaching/index.old.html. I am afraid the below is
somewhat out of date, at least with regard to the
Intro section and below it.
Information for Current Students
9/9/02:
We are not requiring prelabs, at least for the Tuesday labs.
9/30/02:
The Protein Determination lab is due on
October 11, 2002; I am grading it, so please type it. It is due this much
later than normal because Dr. Kahn will be lecturing that week, in the lab
lecture, on how to use SigmaPlot to do line-fitting, so we concluded that
people should be given some time after that to benefit from said lecture when
doing the lab report. (It is fine if you do the line-fitting via Excel or
another program, BTW.)
11/20/02:
Here are (most/all of) the SDS and native
(activity-stained) gels from the Tuesday lab. I'll do some image
reworking/improvements on them after I've also got the ones from the
Wednesday lab (and after I catch up on sleep... note that I will be
available Wednesday from 12:00 or so to at least midnight to help people
with the enzyme lab; I apologize for not having the protein labs back
yet).
12/7/02:
I am close to being done with the protein
labs; I very much apologize for how long it's taken. (I've had a number of
other things on my mind, but I've still procrastinated on them way too
much... sorry! I do, however, understand procrastination in others - my own
problems in this regard are one reason that I am willing to count lab
reports as being in on time as long as they get to me personally before
morning.) See above for what gel pictures I've been given; I have
not received any from the Wednesday lab - please get them
to me sometime this weekend - Monday at the latest - if at all
possible. (Emailing the pictures will not work. Neither will
emailing me lab reports in any format except plain text (as in what
'Notepad' would produce - not Word format, for instance). I
don't use Micro$oft Windoze computers
to do any more than I absolutely have to, and that definitely includes not
reading email on them (notice all the viruses/worms going around? They're one
reason I don't).) Gavan is supposed to give me the pictures of the
Isoelectric gel sometime on Sunday; given how late this is relative to when
the lab is due (even though there isn't very much to the isoelectric portion
of the lab) I will, once I get authorization from Dr. Chase, be accepting
the isoelectric focusing part of the lab report later than the rest (and
counting it as in on time). I'll let you know how much later. (I'm afraid
that you will pretty certainly not be getting the last lab back before
(unless it's ten minutes before...) the final, no matter when it's turned
in. However, as you can see in my comments below,
from what I've seen past exams are rather more useful for study purposes.)
After I'm done with the protein labs, and have gotten a bit of sleep (it's
3:45PM on Saturday when I'm writing this, I've been here since around
8:45AM on Friday, and was in the day before that helping grade the General
Biochem exam), I will be available to help with the
electrophoresis/isoelectric focusing lab reports, which I am
grading (so please type them, especially if your handwriting is as bad as
mine! A thank you to all who typed the appropriate portions (calculations
need not be) of the protein labs!).
12/8/02:
Due to finding myself falling asleep at the
keyboard, I had to go home and sleep for about 12 hours (longer than I had
intended - my alarm didn't wake me up...) - I apologize to anyone I missed
seeing due to this. I'm now here and available to help with the labs.
Gavin has not yet given me the pictures for the isoelectric gel to post up.
The due date for the lab will be pushed back by at least a day, more for the
isoelectric focusing part (although this means I may not have them back at
the exam, I'm afraid). Here is some info on the standards (unstained -
without the different colors - until you put the Coomassie Blue on them)
used in the SDS gels (THIS IS DIFFERENT FROM THE INFORMATION EARLIER
- SORRY ABOUT THAT! I had not gotten the info from Emilia that I thought I
had...):
- Pictures (3 different formats - .tif is preferable, but is large
and not usable by all browsers):
- Molecular weights:
- 250,000 Daltons
- 150,000 Daltons
- 100,000 Daltons
- 75,000 Daltons
- 50,000 Daltons - Darker band
- 37,000 Daltons
- 25,000 Daltons
- 15,000 Daltons
- 10,000 Daltons
12/9/02:
Below are the Tuesday and Wednesday Isoelectric Focusing gels. (This would
have taken less time if Gavin had sent them to me via some other means than
email and in some other format than PowerPoint... imagine trying to read
such an email on, say, eden.rutgers.edu. Gavin is still to be thanked for
his help on this, however - none of us realized the headache that happened
with the image transfer, and it seems to have been caused by how he was
improving the pictures with info (like the pIs of the standards!)
that you'll need.) The gel picture (gels from both classes - for "Thursday",
read "Tuesday"), in 2 different formats:
Dr. Chase has your protein labs and will be handing them out at General
Biochem lecture this afternoon. In regard to the due date on the
Electrophoresis/Isoelectric labs, we're rather limited in how much we can
push it back, but:
- All of the lab but the Isoelectric focusing part
will be due:
- Tuesday People: Wednesday, Dec 11th
- Wednesday People: Thursday, Dec 12th
- The Isoelectric Focusing part will be due:
- Tuesday People: Thursday, Dec 12th
- Wednesday People: Friday, Dec 13th
I will not accept any labs turned in Monday or later. I may
well limit exactly how late on the weekend I will accept labs turned in, and
will almost certainly not have them back for you at the exam if
they are turned in late. However, I will be here as much as possible this
week (and weekend, if need be - I hope not) to help you do them. (I do have
a NJ driver's license to go get (my current one is from Alabama, and I can't
register a car here with it), which will take up half a day or so from
what I've heard...)
12/10/02:
As it turns out, you can use the
prestained (with the different colors) standards for helping figure out the
molecular weight (Rm vs log(molecular weight), rather) standard curve. The
values in the manual are correct for those, as it turns out - it's the same
tube of standards that we were using last year. I will put up a picture ASAP of
the colors for each one, and/or you can come by and take a look. In regard
to who had which sample in which lane in the isoelectric focusing gels,
here's the info I have so far (if you know more, please
email me):
- Tuesday Lab:
- Standard A?
- ?
- Jenna + Johanna + Yiannos
- ?
- Darius + Tomas + Michelle + Nitya
- Lynda + Tracey + Dee
- ?
- Standard G?
- Wednesday Lab:
- Emelia's Standards
- S + R
- P E A
- K D F
- V K M
- E E M
- E M J
- ?
Incidentally, regarding the gels/blots and the mention of "drawings" - you
do not have to do full drawings of any of them, if
you have a picture and you have drawn on it where the bands
are that you measured.
12/16/02:
In response to people's questions:
- The exam is in Ruth Adams room 001 (the lecture hall).
- I expect to have the electrophoresis/isoelectric focusing lab
reports ready to hand back at that time, at least for those turned
in by Friday or so... if I am left undisturbed this evening
and night!
Good luck on the exams, BTW...
3/11/03:
Below are the pictures from Tuesday lab; I'll do some work on sharpening
them up (sorry about not having done this already, but dissertation research
proposal work does have to have a higher priority...):
3/13/03:
OK, here are the cleaned-up versions (in TIFF, GIF, and JPEG formats):
4/5/03:
I am in (room 118 in Lipman, usually) and available for a limited
amount of helping people with the plasmid lab (I hadn't anticipated being in
this evening, but my cold makes it inadvisable for me to do much talking due
to a sore throat developing (keep that in mind when coming by for my
assistance - I suggest email if at all possible!), so I'm in). See below for how to get in touch with/locate me (making
very sure to read over the information on emailing me carefully so
you don't send email to an address where it will get mistaken (by a program)
for spam... I have taken
precautions against this happening for email from Rutgers
computers, but other email accounts are another matter entirely). The
plasmid lab is due, essentially, anytime before Monday, if you didn't get
that info. If people did not get a copy of the 1 Kb DNA
Ladder, the standards, it is available at 1kbLadder.png or 1kbLadder.gif on this server. Note that the 1636 Kb
band is likely to be brighter than the bands above and below it, although
the 1018 band can be easier to locate in some circumstances.
Some things regarding the instructions on page 26-28 on the Report:
- You do need to give me a circular map (one for each
lane - except the standards - and one for the entire plasmid as
you've reconstructed it), since there's no realistic way that you
can reconstruct the "linear sequence of the insert" (or, rather, the
restriction sites in the insert) without it - so don't bother with a
seperate linear map, just give me the circular form (all you have
to do with the vector part is label it vector and give how many BP
it is).
- I don't advise using semilog graph paper, at least if the
relationship between log molecular weight and distances appears to
be reasonably linear - human drawing is too inaccurate, although it
can be better at accomodating weird curves than a computer is unless
the computer is very well programmed.
- For the instructions in #9, ignore the references to
digoxigenin-labelled standards.
- For #11:
- Tell me what the equation is that you used to convert from the
blot measurements to the gel measurements (physical measurements
on the gel will generally not correspond (in non-relative
distances) to measurements on the blot). I don't advise people to
try converting to the physical gel measurements, BTW -
that's a waste of time; just be sure that you convert your blot
measurements to the same set of measurements as you use for the
standards. I really don't even care what the physical gel
or blot distances were - just the distances on the photographed
gel and the distances on the photographed blot.
- Tell me the data points you used to get the conversion
equation (I have a program that I can use for getting the
conversion equation if you tell me the distances to be used for
the conversion) - note that I am finding this matters quite a bit,
and it is preferable that you use points from both sides of the
gel if at all possible (to allow for distortions in how the gel
ran, such as one side moving faster than the other).
- See about figuring out where the probe bound (not to what
"sequence" the probe bound to (you don't have the
plasmid's sequence (yet))) in relation to your restriction map -
note that you will almost certainly be somewhat unsure on this,
especially since we are also - by comparing what showed strongly
on the blot, and not on the gel (which corresponds to the
restriction fragments that the probe bound strongly to), to what
showed strongly on the gel, and not on the blot (which is what
the probe did not bind strongly to).
- The standards are not in kbp (kilo-base-pairs), but in bp
(base-pairs) and you should be working in bp; working in kbp is
a bit silly with a plasmid of less than 10,000 bp.
- If your gel picture is reasonably clear, a photocopy
with the bands you used outlined is sufficient to fulfill
the requirement for a "drawing" - this isn't an art class.
The same is true of the blot. (Just turning in the blot, however, is
not sufficient, as Dr. Chase states.)
4/6/02:
I'll be in until at least 1 AM or so. Keep in mind that you're working with
a log scale - so a minor error, difference in measurement due to fuzziness
of the band, etcetera can easily make a big difference in the estimated BPs
- as in 800 BPs or so. Another factor is that the smaller bands tend to have
a better measurement of their size than do the larger bands (the standard is
more reliable and not so blurred together), so the linear band may not be as
accurate an estimate of the size of the entire plasmid as the sizes of the
fragments put together.
4/8/02:
Unless I hear otherwise from Dr. Chase, the due date is now today, due to
the snow yesterday. The one person who got hers in yesterday (plus the other
person who hasn't been able to complete it due to her lab partner not making
the data available - if it isn't due to illness, he's not going to
be happy with the grade he gets) will be getting extra credit. I'm available
today, keeping in mind that I'm still congested and can't talk for long
without getting a sore throat, but I am feeling somewhat more energetic than
I was last week. A few things to note:
- In the description of what is needed for the report that
Dr. Chase gives, that description is not in the
actual order that you (will almost certainly) need to do the actual
procedure in - it's what makes sense as how the final report is set
up. The sequence for dealing with the gel and blot pictures I
suggest it is as follows:
- Measure the distances of the bands on the gel and blot
pictures, preferably on as enlarged a picture as you can
get, with the zero point being the well for that lane (if
possible).
- Figure out which bands on the gel and which bands on the
blot clearly correspond to each other. Come to me
(or do a least-squares equation yourself) to
figure out an equation for taking a blot distance and
getting out the equivalent gel distance, using said
corresponding bands. Note down and include in your final lab
report the bands used for constructing the equation as well
as the equation itself. Put into the table for the blot
values both the original blot measurement and the equivalent
gel measurement. The blot measurements are of use in
determining where the probe bound (see below) and, if a band
showed up on both the gel and the blot, confirming that the
band in question seems "real".
- Figure out what band on the standards (on the gel) is
which, keeping in mind that the 1636 band is typically
brightest. Use this bp (not kbp) information (note that
506,517 on the standards is actually 2 bands, one with 506
bp and one with 517 bp - not one band from a
506,517 bp fragment, which would be huge...) and the
distances of those standard bands to get the plot that Dr.
Chase discusses (except that you only put the standard bands on
this plot, not any others) and a log(bp) = slope*distance +
intercept equation (y = mx + b, where y is log(bp) and x is
distance) - alternatively, you may actually find that if the
plot you get is curved, it works better to use a slightly
different equation (I'm still examining this... feel free to
experiment, as long as what you wind up using is at least as
accurate as the "standard" equation and you explain the
equation that you use). Plug the other gel band distances,
including the blot distances converted into gel distances,
into this equation to get out a log(bp) value, then take the
antilog to figure out how many bp (not kbp) each band
represents.
- For each lane except lane 1 and the standards (lane 6),
create a miniature plasmid (circular, not linear) drawing,
as with a normal plasmid map. If a particular lane is giving
you headaches (more so than normal...), go on to another
lane and later use the data from the other lanes to figure
out the problematic lane(s). If you are getting more than
one distance between sites (as in one distance from the gel
and one distance from the blot), put down both distances as
a range (500-600, for instance).
- Put together the plasmid maps for each lane into one
large plasmid map of the entire plasmid. There will be some
uncertainty, particularly about the exact lengths; report
the reasonable range of possible lengths of plasmid between
the restriction sites.
- Using information from what is visible on the blot but
not on the gel and vice-versa (note that most of the
standard will not be visible on the blot; neither will the
RNA), figure out where on the plasmid (between what
restriction sites) the probe hybridized to (or at least
hybridized to most strongly).
- Do not try to label anything on the drawing except for
RNA. Label things in a column in the table that you make up (you can
make up either one table for both the gel and blot values, or two
seperate tables for each), as one of:
- RNA
- Standard
- Supercoiled (plasmid)
- Relaxed (plasmid)
- Linear (intact plasmid, with only one cut)
- Restriction Fragment (plasmid with more than one cut,
producing at least 2 fragments)
("Unknown" or "?" may also be an acceptable category, especially if
I can't tell what it is...) While the restriction
fragments, like the standard bands, are linear in conformation, it
is most useful to treat each of these as a seperate category.
- I am seeing very few cases where the "linear" band is visible in
lane 1. Use lane 2 instead to get it. Lane 1 is more useful for
figuring out what, in the other lanes, is actually supercoiled
(undigested) and relaxed (partially digested/broken), not a
restriction fragment (unless a restriction fragment band happened to
be in the same place as the supercoiled/relaxed band, which is
unfortunately possible).
4/11/03:
I will be in and available this weekend, with the exception of Saturday
evening/night. Afternoons and (except for Saturday) evenings/nights are
preferable. Note that, in calculating the concentration of DNA, the lab
manual has a clarity problem in that if you used 2.5 ul of sample with 2 ml
of water in the cuvette, it should be a dilution factor of 800, not 400, at
least for figuring out the nucleic acid concentration from the absorbance
(but a dilution factor of 400 is correct for the fluorescence
measurement). (Don't worry about this on your lab report if you've already
turned it in, since I hadn't noticed it until now...) Things seem to have
worked despite this, interestingly enough. (BTW, regarding the RNA gels, I
will put up previous ones for people to analyze (since their own didn't
work) once I get more plasmid lab reports in or someone who has turned their
plasmid lab in requests it.)
4/13/03:
The questions:
- Appropriate concentrations are not of that much
importance for the first and third parts of the question - think
about how restriction enzymes work, and that they leave
complementary sticky ends (and that you can't ligate things back
together if the sticky ends aren't complementary). The answer to the
second question is simpler than it looks, and can indeed be done in
terms of concentration.
- Page three of the introduction mentions a bacterium whose DNA is
being pelleted (to remove the chromosomal DNA, the size of which is
what you need to know for the question); assume it is
E. coli, even though it doesn't say the species.
- Don't worry about the Boehringer blocking agent; assume that
it's the same thing as sheared (randomly chopped up) salmon sperm
DNA. Note that in this case, it isn't a question of "what might you
see if you didn't do this?" - it's a question of "what did we see
because this (the procedure mentioned in the first part) answer to
the first question) didn't work very well", and that Dr. Chase wrote
the lab assuming that the blot would only show parts of the plasmid
from which the probe DNA was derived. This didn't happen. Think
about what happens when randomly-chopped-up pieces of DNA (the
sheared salmon sperm DNA) get added to the blot, which has a lot of
DNA bound to it, some of which is complementary to - and thus binds
tightly to - the probe, and some of which the probe is no more
complementary to than it (the DNA on the blot) is to the sheared
salmon sperm DNA.
- Most people seem to get this one. Please let me know if there's
anything unclear about it.
- He's referring to the hybridization procedure, after you've
added the probe but before you add the dye. The hybridization we're
trying to make stringent is the one between the probe and the DNA on
the blot (as per what I said above, we didn't succeed in making it
very stringent - this actually wound up helping us, since the blot
is more sensitive than the gel for plasmid DNA).
RNA:
None of the RNA gels (at least on Tuesday, and for most
people on Wednesday) turned out very well - or, actually, for anything other
than the standards, with anything at all usable I'm afraid. (Given the
consistency of this, it's pretty clear that this wasn't something you did
that caused this (in most cases - some were a bit worse than others). We'll
be looking at the procedure for ways to make sure this doesn't happen again
- while RNA is notoriously difficult to work with, nobody
having usable results on an entire day should not be normal. I can
say that it looks like the liquid nitrogen preserved the RNA better than the
dry ice; instead of the RNA getting chopped up, we instead seem to have had
more problems with too much DNA being left in, as seen by the
bright wells.) We are therefore going to provide all of you with a picture
of a gel of previous results (to be precise, by Rosa, a past student of
Dr. Chase's). This picture is available as
RNAGel.tif, RNAGel.jpg, RNAGel.png, and RNAGel.gif
(in the appropriate file formats for the names; the .tif one is the
highest-quality, but is also the largest-size and is not as portable as the
other two formats). Going from left to right, the first lane is the
standards (the same ones as you got - see rnastd.jpg if you didn't get a copy); the second lane
is RNA from another plant; the third lane is how the cabbage leaves you
worked with should have turned out; and the fourth lane is from
E. Coli RNA. The (unfortunately faint) black rectangles close
to the top, with thin bright lines right below them in some cases, are the
wells. Note that you don't need to worry about what the physical distance
was on the original gel, just on the picture. You can use the end of the
picture (away from the wells) as the "dye front". You should use
the 2 bands from the E. coli rRNA (in the rightmost lane) along
with the info in the introduction to the lab on prokaryotic rRNA sizes to
get a sufficiently accurate standards graph. Dr. Chase may want you to use a
curve instead of a line for the standards (I'd say to do this only for the
portion of it that is curved, with a computer equation line being used for
the rest, or else figure out an equation on SigmaPlot for the curve);
however, ask him, not me, especially since I'm not grading this lab.
- Unless you are using semilog graph paper (if for some reason you
wish to do this, it's allegedly available from the Cook/Douglass
bookstore), you do not need to label the graph in kilobases vs
distance, you need to label it in log kb vs distance.
- Ask Dr. Chase how much of the procedure he wants written up (I
suspect he will want more than I had asked for in the earlier version
of this writeup - sorry!)
- You can use the equation of the line to get the log kb (and convert
that into kb) instead of measuring off the graph, provided you look
at the equation of the line to make sure it makes sense... at least,
you can do this for the portion of the line that isn't a curve, or
with an equation for the entire line including the curve.
You are supposed to measure and report on the bands in the other
plant's RNA, and are expected to discuss them if they correspond with bands
from either the Napa Cabbage or the E. coli RNA. The RNA sizes for
eukaryotic rRNA (except for the smallest of them) are not given in the lab
manual, partially so you aren't adjusting your measurements to fit them!
However, you probably do need this info in order to answer the question
regarding whether bands are explained by rRNA (at least to answer the
implied question of which bands are explained by rRNA...) -
I suggest doing a web search, or come to me or Dr. Chase after you've already
calculated your band sizes. Also read carefully over the material regarding
mitochondrial and chloroplast rRNA. (The origins of mitochondria and
chloroplasts, which people normally think of as simply parts of cells, is
of definite interest in an evolutionary/genetics sense, BTW, including
for my own research.)
4/25/03:
Since most people didn't have results for the PCR gel (probably because of
too much RNA and plasmid DNA instead of genomic DNA in their samples), we're
putting up the one gel that worked, and a PCR try and gel that the Wednesday
Lab TA, Maria Cruz, got:
- JLY group from Tuesday:
- Maria:
In regard to Maria's picture:
- The bottom lane is a (positive) control (to make sure the PCR
machine was working);
- The next two lanes (going up) are from a couple of the groups (H
and M, I believe);
- The next three lanes are a 1:10 dilution, a 1:100 dilution, and
a 1:1000 dilution, using the D (not A) group as a basis;
- The topmost lane is a 1kb standard ladder (see
above);
- The primers used for D were F27 and R1522.
Use whichever one of these you want - check with the JLY (Johanna Lynda
Yiannos) group if you want to use their gel picture and have questions
on it.
4/29/03:
The sequencing labs are due tomorrow, 4/30/03, by 6:00 PM, in Maria Cruz's
mailbox in Lipman Hall. The PCR labs are due next Monday, May 5th, by 6:00
PM, again in Maria Cruz's mailbox in Lipman Hall. There are a couple of
changes to the PCR data above; please take a look at
that.
4/30/03:
I am afraid I misinformed some people regarding the RNA standard bands. Do
not skip over the 1.35 band in the standards; it does indeed
appear. The heaviest two bands (7.46 and 9.49) are, however, merged into the
band at the top (closest to the wells).
I am not enthused about the amount of memorization required for the
final exam. (Dr. Chase is not of the opinion that it is that heavy on
memorization - but he has an extremely good memory, so perhaps does
not fully realize how difficult memorization can be, especially for those of
us like me who have a bad memory. Incidentally, I recommend studying old
exams as the best way to do OK on the final - see
http://aesop.rutgers.edu/~dbm/tedchase.html
for old exams with answers (at the bottom of the page).) My disapproval of
memorization where not absolutely necessary is one reason that I don't give
in-class, closed-book quizzes except on safety matters - things that people
do need to know things off the tops of their heads, to
avoid endangering anyone. (I have a particular concern with regard to
harming other people - speaking from my
political/
ethical viewpoint, if someone harms
themselves when they knew
or could have known if they'd bothered to find out the danger,
that's their business (I find it unfortunate - I don't like
seeing people harm themselves - but freedom comes with responsibilities).
Unfortunately, the legal system in the US, and other governmental regulatory
means in most of the rest of the world, don't agree, and I do try to avoid
either getting other people in trouble or fighting fights I can't win
(yet).)
People frequently say that the lab takes more time than a 2.5 credit course
should. You are correct; Dr. Chase and I agree with you. Unfortunately, it
appears to be University policy, probably due to the various humanities
departments lobbying, to not count laboratory hours as much as classroom
hours - even if the laboratory in question has, like Experimental Biochemistry,
lab reports that require lots of time outside of class. On the other hand, do
realize that this is one of the more thorough biochemistry (and related areas)
laboratory courses that undergraduates might ever take, and definitely gives
people lots of experience - experience that has meant the difference between
getting a job and not getting a job for some.
I have suggested to Dr. Chase that the Rutgers Genetics course (as variable in
quality as I've heard it is - some report it being better-taught in the
summertime, BTW), or some equivalent, be prerequisites or
corequisites for the second semester of Experimental Biochemistry - and may
suggest this also for the second semester of General Biochemistry - in light
of the many people coming to me needing help on what I, as a geneticist,
would consider very basic aspects of the plasmid, RNA, sequencing, and PCR
labs. While this would take too much wrangling to get through for next year,
he is planning on adding a strong recommendation for such a course to the
description of Experimental Biochemistry in the course catalog.
Tuesday Lab
My background: My primary background is in biology, specifically
molecular genetics. I am mainly qualified for this lab due to:
- prior lab experience, especially with DNA; and
- having TAed it before (this will be my 5th or 6th time for the spring
labs).
Getting in touch: The best means of getting in
touch with me is to come by
Lipman Hall
room 118/119, then try Lipman Hall 202 (the
SGI computer lab). (If the
building
is locked up, try the phone number given below - use the 119 number first in
that case.) The second best is to email me (see below
for the address), since I check my email several times most days. (Note the
points on my tutorials page about not sending
me email that's something other than plain text.) The third best is to call
me at 932-9255 extension 119 (202 if that doesn't work). (Do not assume that
I'll receive voicemail; only use this method if I (or someone else) answers the
call.) The fourth best is to put a note in my box; it is on the first floor of
Lipman Hall. (By the way, if you are turning in a lab report other than
directly to a TA or to Dr. Chase, be sure to get someone - a secretary,
professor, graduate student, whoever, just someone other than another
undergraduate - to sign and date it so we don't have to count off for
lateness (or for any more lateness than you should have been counted off
for).
Office Hours: I will try to let you know what times I
will be available; the best thing to do is to simply ask whether I
will be available at a given time - people who've had me before can tell you
that I am willing (unless other obligations, including my own academics,
conflict) to work with people at quite odd times and/or for very long hours.
Quizzes: My quizzes have as their primary purpose encouraging you to
have read over the lab before you come in and making sure that you
know, in particular, safety-related information. I do not expect you
to have memorized all of it; my own memory isn't that good, and I will
generally consult the lab manual before answering questions - but I
will have read over the lab. I expect you to know in general terms
what we are supposed to be doing that day and about any safety
precautions that you need to take, particularly those which can affect
other people. I may - I generally don't unless I get inspired or feel
that you aren't reading over things - give you a take-home,
open-library quiz (or at least a question or two, if not a full quiz)
that is for the next week's lab, again mainly to encourage you to read
it over. Except for take-home quizzes and safety quizzes, given the
prelabs you are being asked to do, I will not ask for any further
quiz-taking.
Subjective Grade: How I do the subjective grade is to note down when
you do something good, and when you do something bad. I will fix a
particular starting grade, and doing something bad will decrease your
subjective grade below this; doing something good will increase it
above this. The starting grade and amount up/down will be determined
by whatever gives a final mean of 85 and a high of 100. Examples of
good and bad things:
- Good things:
- asking an intelligent question;
- giving an intelligent answer on a quiz;
- giving an amusing answer on a quiz;
- typing a take-home quiz;
- typing lab reports, particularly the ones that I grade (which
are the gel electrophoresis and isoelectric focusing ones for the
Spring Semester);
- doing significantly more work than other people;
- giving a good answer to the questions on a lab that I grade;
- helping someone else in the lab (especially someone not your lab
partner);
- cleaning up messes that you didn't create;
- doing extra work because of things that aren't your fault;
- pointing out problems to us (especially if you provide the
solution also);
- for the Spring Semester, choosing to do the Carotenoid lab
(generally considered harder but more interesting - there have been
exceptions to this, depending on sources of material chosen,
however) if most people are choosing to do the Lipid lab
- Bad things:
- asking a question that makes it apparent that you haven't
read over the lab;
- doing something that makes it apparent you haven't read over the
lab (more off for this than the first - if you don't know
something, do ask);
- coming in more than 15 or so minutes late without an
adequate excuse (this may also result in your missing a quiz -
which you will not be able to make up without a good
excuse for coming in that late);
- leaving a mess that I or Emilia have to clean up
(particularly the latter, if she has cause to complain to me);
- doing significantly less work than your lab partners;
- doing something that irritates your lab partners (unless you
and they come to me and/or Dr. Chase and explain the problem and we
decide you're in the right)
I normally find I have more +'s than -'s by the end of a
semester. This means that those who do get significant minuses (e.g.,
a lab group a bit back that left lots of gunk in the pig kidney
centrifuge bottles...) will get a rather low subjective grade, and
that those who simply don't do much either positive or negative won't
get a particularly good one.
Nametags: I have problems remembering people's names (including close
friends, BTW!), especially in a class of 20+ people. This sometimes
causes problems with assigning subjective grades. Something I'm trying
out this year is to have everyone fill out and wear a nametag. These
should be left in the lab, to avoid losing them. At least for the fall
semester, if you forget to wear it, that will be subjective points off; if
you lose yours, that will be even more subjective points off
- especially since I bought them with my own money!
Curving: I normally will try to curve to a mean of 85 and a high of
100. On lab reports and quizzes, I'll circle the final grade that
you'll get for each of them. Such curving does not include extra
credit points or points taken off for lateness.
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