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My Teaching: TAing Experimental Biochemistry - 2003-2004 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:
  1. any information that I need to get to students (or would like to make available to students) right now
  2. any comments about the course that I wish to make
  3. a HTMLized version of the intro sheet that I normally give out at the beginning of each semester.
For the 2001-2002 web-page, see For the 2002-2003 web-page, see I am afraid the below is somewhat out of date, at least with regard to the Intro section and below it.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

We are not requiring prelabs, at least for the Tuesday labs. Nor do I plan on requiring them for the Tuesday labs next semester.

Here are most of the SDS and native (activity-stained) gels from the Tuesday lab. I will post any others I get, for either lab section, with some image reworking/improvement on them (the below have already been modified); note that this will need to be on disk (3.5 preferred), not emailed (I don't do attachments). I will be available from Thursday late afternoon on for help with the writeups for the SDS-PAGE/Isoelectric focusing lab reports, including getting the interpretation of the densitometry data out of those computers (note that if you did it on the laptop, I will need to be notified prior to 5:00 PM or so on a given day, so I can get the laptop back from the room it's locked in (I don't have the key).

(If you have problems viewing these, please let me know - I can translate them into other file formats than TIF and JPEG.) In regards to assistance on the SDS-PAGE/IEF lab reports, I can open up the 219 computer room for use of those computers. (Note that the SigmaPlot version on them is 4.01, which can't read SigmaPlot 8.x files!) Moreover, I will usually be in until 1:00 AM or so for consultation and (next week) for turning in the lab report (it's in on a given day provided it's to me before I leave the next morning, unless it comes in after 8:00 AM the next morning). (Note that turning in lab reports via email will not work unless they are in plain text format - as in what Notepad could produce - and since you will need graphs, that won't work. I don't accept Microsoft Word attachments (I don't use an M$ Windoze computer to read email), and whether or not I even let you know that it wasn't accepted will depend on how good a mood I'm in... I really don't like Microsoft!) Call me (732-932-9255 x119) to get let into the building after it's locked up, or throw a stick or something (not a rock!) at my window (the farthest to the right on the front of Lipman).

OK, here are the coomassie and activity-stained IEF gels for Tuesday and Wednesday:

Here's the data that Dr. Chase measured for the positions on the Tuesday Coomassie Blue gel, measured from the top of the gel, using the standards on the right side of the gel: Plot the cm vs pI and see if you get a reasonably smooth curve, then interpolate to get the pIs of the major and minor D-amino-acid oxidase bands (plus the others - Dr. Chase only measured the ones closest to the standards). (You can actually either use these measurements, from the Tuesday coomassie gel, plus your own measurements off of that gel's photo (remember to convert the scaling!) and the Tuesday activity gel, or use the Wednesday gel and the above info to figure out which standards were which from that gel and do your own measurements (while you'll need to do all your own measurements on the Wednesday gels, you will be working with gels that are rather easier to measure!).)

12/05/03: Due to the snow, I'm going to ask Dr. Chase if we can delay the due date of the SDS-PAGE/IEF lab by a couple of days, until Thursday/Friday (for Tuesday/Wednesday labs). [They are delayed; see below for more information.] I am here in Lipman, and probably will be until Sunday morning/afternoon. I will probably be in my office (118) most of that time, but will crash on a couch to sleep at some point!

Here are two more gels:

The non-prestained (single color, only showed up after staining with coomassie blue) standards are the ones given in the lab manual; the carbonic anhydrase band tends to be the heaviest, with two bands moving further than it and two bands not as far (no phosphorylase b protein - she did use one very large protein, but it doesn't seem to have shown up on any of the gels I've seen so far) - that's on page 17 of the lab manual. For the prestained standards, see below. I will be in this evening quite late (until in the morning, really) - call or tap on my window to get in (actually, I suggest calling in any case, to make sure I haven't gone upstairs to take a nap). 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. This isn't an art class...

I'm going home (it's about 4:20 AM) and should be back sometime between 1 and 4 PM.

Well, I overslept by about an hour... sorry about that, but I couldn't get to sleep until after 9 AM! I am here now and available for consultation; I should be available also sometime tomorrow afternoon (4-5 PM is likely). The labs are now due Thursday (for the Tuesday lab) and Friday (for the Wednesday lab), but if they're in later than Friday (including over the weekend), you will not be getting them back at the final and you may be getting a T grade. I will not be available for consultation after Friday - I'll be too busy grading so as to try to get back the reports at the exam, and hopefully be able to put up (on here) some comments on them that may be helpful for the exam (see below for my comments on the exam, BTW).

I have put up above some additional versions of the gels I've scanned so far, namely in JPEG/JPG format as well as TIFF, since some browsers apparently have problems with TIFF. (To print out the gel pictures, bring them up in a web browser - a word processor probably won't do it!)

The prestained standards (multicolor) are as per the ones on Emilia's door, the Kalideoscope standards, namely the ones with the red "X" below them:

Here also is one more (native activity-stained) gel:

When Dr. Chase says to compare the bands you get for the antibody and the bands you get for the coomassie (or, for the native gel, the activity stain), and those you get for measurements via hand and those via the densitometer, the best way I know of to do this is to calculate the Rm/Rfs and corresponding log molecular weights and molecular weights. (Indeed, I don't know how you would do it otherwise - that would be what I would do in doing research myself - but if you can come up with some other way, fine.) Also, in determining what the D-amino-acid oxidase band is, and its molecular weight, you should also be calculating the molecular weight of the other bands (for the SDS gels), partially since given a log scale what looks similar to the eye can be deceptive (again, if it's obvious which one is the D-amino-acid oxidase band, then you are not strictly required to put the info down for the other bands, but I do prefer having it).

In terms of how much writeup of the procedure you should put down, I am not interested in reading 44 copies of the same procedure. Put down any amounts you used, any measurements you made, any way in which the procedure deviated from that in the lab manual, and anything you noticed that was different from what the lab manual said to expect.

If you have already turned your lab in and followed the directions above and in the lab manual, don't worry about the below, except for future reference (e.g., potentially for your future lab work, or even for the exam).

I will be in and available for questions until midnight. After that, I will be grading and not available for questions (or for turning reports into, or for getting let into the building). You can turn reports in over the weekend (before Monday) and they will be counted as being in on Friday - if you can get them into my box (if someone else lets you in or you have a key to the building). I am unlikely to have them graded by the exam if they're in after midnight, however - I'm worried already about having the ones that get turned in on time back at the exam, especially since I seem to be coming down with an infection of some sort!
Please do not put points for your D-amino-acid-oxidase band on your molecular weight graphs, or for your isoelectric focusing graph, if you are using the equation of the line to figure out log(molecular weight) or pI from the distance/Rm/Rf. The lines should only contain points for your standards. (If you've already turned in the lab, don't worry about it.) The only time you would have a marking for a non-standard on such a graph is if you're using the method of drawing a line on the graph between two of the standard values in order to manually figure out the log(molecular weight) or pI from the distance/Rm/Rf.

In regard to what goes on the X axis and what goes on the Y axis, I don't care. I advise people to put the distance/Rm/Rf on the X axis, so that once you get a y=mx+b equation, you can just plug in distances/Rm/Rf to get a log(molecular weight) or pI.

Isoelectric Focusing
Again, you can use either the tuesday or the wednesday lab gels for this. If you use the wednesday lab gels, then you do all your own measurements, including of the standards and of the one or two bands on the activity gel - and use the standards above for the pI values but not the cm. If you use the tuesday lab info, you will be measuring all 5 of the bands on the activity gel, using the main one to get a scaling/conversion factor between the gel picture and Dr. Chase's measurements, and finding the pI of the rest using the graph.

For the tuesday lab data, you will get a pretty broken-up curve. You will need, as Dr. Chase wrote, to interpolate to find the pIs - use more than one line. You may or may not need to do this for the wednesday lab data - it partially depends on which bands one identifies as being which standards.

I am generally seeing the (pre)stained standards as being less accurate than the unstained standards. Do try graphing the (pre)stained stained standards, but the molecular weight values from the unstained standards generally are more accurate.
I will be TAing the Tuesday lab again next term, incidentally - some people have asked about this...

As it wound up, the only labs with things that people should have been told anything about prior to the exam were unfortunately turned in after Friday, so I wasn't able to do any feedback from them. (The lower the molecular weight, the higher the Rm/Rf, people...) I have added a bit to my comments below.


Carotenoid labs:
The carotenoid lab is now due one day later (and may wind up being further extended, but that's up to Dr. Chase). You should pick up from myself, Emilia, Kyle, or Dr. Chase: You may find the site (and the site of use. Other than that, Dr. Chase is the one to ask on carotenoids (although I can help a bit on some aspects, such as the K and K-prime stuff). (He says, BTW, that you only really need to identify the most significant 4 or so carotenoids in each fraction, starting from the right-hand side of the HPLC, although more if you can manage it would be of interest. Anything with a maximum absorbance less than 5 uA is probably not there, as is anything below 4 minutes Rf time (certainly anything below 3 minutes).)
Lipid Labs:
I am available to help with interpretation of your lipid lab results. You will probably need to compare info with another group in order to interpret all of the GC results, such as for peaks that the computer mis-identified or failed to identify (probably due to too tight tolerances for what it will accept, or that the peak was too wide for it to get an accurate retention time). I suggest taking a look at for information on the common names of lipids (don't worry too much if you can't find a common name for stuff that isn't a huge portion of your samples).

Agarose gel pictures, in 3 different formats:


The brightest band should be the 1636 band; the 506/517 band should be the second-brightest after that, unless it's covered over by the dye marker.

I will put up blot pictures if given them; please do give copies to me so that I can do so. Here are the ones that I have been given so far:

Do NOT yank on the side door(s) to try to get them to pop open. Doing so damages the doors. If I catch anyone doing so, I will see to it that they are:

  1. Flunked from the course;
  2. Brought up on charges for damaging Rutgers property; or
  3. Both.

Yes, I'm here over break, and available for some limited assistance on the plasmid labs - I will be available for a lot more assistance after the break, but this week, I need to catch up on sleep/laundry/etcetera! I suggest emailing me to schedule something; I am in this morning but probably not this afternoon, for instance.

I am not feeling very well (congestion (resulting in earaches), sore muscles, etcetera), but will endeavour to be as available as possible for help on the plasmid lab, which I am grading. A few things:

Here are another couple of blot/membrane pictures:

A few other things:

I am probably mostly going to be around in the evenings, although not for that much longer tonight (only an hour or so longer). Hopefully, I'll be feeling better by this weekend or so...

The Plasmid lab is now due (for both lab days) on Friday, April 2nd (and will be counted as in on Friday if you can get it to someone who can sign it over the weekend; note that I cannot read attachments and may not receive them, so don't try sending labs to me as a Microsoft Word file or similar).

I am feeling slightly better, and should be able to be here tonight until midnight or so, then on Saturday again in the afternoon/evening.

Please let me know what letter of plasmid your group had if a picture from your gel or blot/membrane is on this webpage. I will be here until midnight or so (let me know if you're planning on coming later than 9 or 10, or I might leave earlier than that; I'm still needing more sleep than normal...), and again on Sunday.

I'll be here tonight until around midnight; I may be busy around 8:00 or so, however. Here are a few more blot/gel images:

Here are some RNA gels:

And here are the RNA standards:

I have still not received any Wednesday RNA gel pictures - come in and give them to me, even if you think you don't have anything. If necessary, if I have taken a look at your gel (including on Tuesday during the lab) and concluded it wasn't usable, you may use the below, 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:

(in the appropriate file format for the names; the .tif one is the highest-quality, but is also the largest-size and is not as portable as some of the other formats). Going from left to right, the first lane is the standards (see above); 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 if you use this gel, you will need to do either a by-hand curve fitting for the standards, or figure out a way to get an accurate curve from them on a computer (for the latter, and possibly the former, you will need to use the E. coli rRNA sizes as additional standard bands). You may therefore wish to use another gel.

The due date for the RNA lab will be pushed back - we are not sure by exactly how much as yet, however (possibly until this Friday?). (Dr. Chase is grading it, BTW.) Peter Anderson is currently working on the computer connected to the Photodyne (gel camera) - that hard drive may have some (more-)usable gel pictures on it.

Update: Sigh... the hard drive on the computer connected to the gel camera is a paperweight (defunct). Use either:

Either is fine, as long as you interpret it properly (as well as possible). The lab is (currently) due Friday.


I am discovering that other equations than the above do not actually fit Rosa's gel very well (as in well enough for bands to be clearly identifiable as 18S, 5.8S, 5S, or whatever)... and that some of the RNA gels from Tuesday give sufficiently curved lines that it may be best (at least to make Dr. Chase happy, since he's the one grading it) to use the above equation to fit them also. Note also that it appears that, despite what it says on page 2 of the lab manual, plants have 25S rRNA, not 28S, which has a smaller size. Since the lab manual got this wrong, you should not be penalized for saying 28S, but you may find it easier to fit the bands using 25S instead of 28S (25S is smaller).

The Sequencing lab is now due Monday, April 26 (4/26/04).

I am pleased to report that every lab group on Tuesday got something (even if only a faint band) in their 1/1000 dilution for PCR, and all got strongly present bands in all lesser dilutions (and, in a few cases, even in the 1/1000 dilution). Both standards also worked. The first standard is the same as the 1KB ladder for the plasmid lab; the second standard is shown below:

This is an Omega-X174 DNA phage cut with HaeIII, BTW; we are pleased that it worked (mostly) despite the marker being several years old (one reason we ran it along with another marker). The pictures that I have so far are as follows, including which PCR primers they used:

(The sequencing lab is now due Tuesday/Wednesday, depending on class period, since I won't be able to start working on the plasmid labs until at least Thursday of this week.) PCRs on Wednesday likewise worked out well, I am pleased to say. One group did have the problem of first not putting the EtBR in the gel, then not putting enough of it in the samples. OTOH, while their gel is not usable (due to the lower standards - in the region of the PCR'd DNA - not being visible), it does show the value of putting (enough) EtBR in the samples/standards instead of in the gel. EtBR produces a fog in the end of the gel near the wells, which is rather of a headache to compensate for afterward (as I've been learning with my attempts at processing the gel pictures); try comparing their gel to those of others, particularly in the versions prior to combining (during which I removed as much of the fog as I was able to do). The groups (with primer info if I have it) and their gels:

Kyle says the PCR lab is now due 2 weeks from the final lab (in other words, May 4th and 5th for Tuesday and Wednesday, respectively). For analyzing the PCR lab bands, we have noticed that the older of the two standards did not come out completely matching how it is supposed to look. Use the 1KB standards to create an initial standards graph, determine the weights of the older standards using that graph, and then use whichever ones of those match how it is supposed to look to help (along with the 1KB ladder) in creating a new standards graph with more points (especially helpful if the 1KB ladder lacks (reliable) bands around where your PCR products show up). (It is likely that the differences are due to some of the standard fragments (restriction fragments of a bacteriophage's DNA) coming back together over time. When we next use this standard, we will heat it immediately prior to use to denature any such binding of standards together.)

When the PCR lab says (on page 8) "Assuming the PCR worked perfectly, making 225 [2^25] copies", read instead "Assuming the PCR worked perfectly, making 235 [2^35] copies", since we ran the PCR machine for 35 cycles, not 25.

In regard to the sequencing lab:

I am intending to be here until 1 or 2 AM today, and again tomorrow (Sunday) from noon until 1 or 2 AM again.

Here are Michael and Barbara's PCR gel pictures:

A couple of things:

I got less than 4 hours of sleep last night. I'm going home and going to bed. I will hopefully not be back in before noon or so Sunday...

I am in, but should not be disturbed if at all possible. I am hoping that I can grade the plasmid labs that were in on time by Monday, but this won't be possible if too many people disturb me. (Note that disturbing me unnecessarily is going to cause me to be in a bad mood when I grade your lab report!)

I have the following people's plasmid labs graded (and you should be able to pick them up, although it's possible I may need to borrow them back if I discover some problem with the grading scheme I made up):

So far as I know, these are all but one of the ones that were in on time, although some that were not in on time will not be counted as being late due to legitimate excuses. (Kyle has the lipid labs that were gotten to him for regrading ready to hand back, BTW.) I will probably be in sometime late this afternoon or early this evening; I am writing this at approximately 6:15 AM.

I have some more plasmid labs graded, and hope to have all of them done by tomorrow morning (or, really, later this morning; it is currently 12:20 AM on 5/6/04). FYI from Dr. Chase:

The Experimental Biochemistry exam is Monday, May 10, 8-11 AM, in Heldrich 106 (that's the DC Chemistry building, officially renamed, since Ms. Heldrich gave $1 million to renovate it, but no one pays attention).

The following plasmid labs are graded and can be picked up (this list includes the one above):

They are currently in my office (118); after I leave today (after the General Biochem exam), they will be with Dr. Chase in his office.

All but one lab group's plasmid labs are graded. Currently, the mean is 95.5; the median is 97; the lowest is 78; and the highest is 108. (These numbers include extra credit bonuses and subtractions for lateness.) I have started on the sequencing labs but do not have any ready to hand back as yet (I have to grade enough to make sure the grading scheme I put together will work, and have to have them around in case I need to go back and make changes to the grading scheme).

5/9/04 (3:00 AM):
All sequencing labs that were turned in to me on time have been graded (plus one lab turned in 4/28/04 but excused):

You can pick them up from my office (they're on top of the green computer), if I'm in or someone with a key is in. If you have turned your (plasmid or sequencing) lab in, you can email me for answers to the questions for purposes of studying for the exam. I will probably be coming in this evening, judging by my current sleep cycles, and will try to email everyone who asks ASAP. Kyle has some PCR labs graded, and if yours is not among them but you have turned the PCR lab in, you can email him for a copy of a well-done lab report to study by. A couple of comments on the plasmid labs:


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 for old exams with answers (at the bottom of the page). For the spring semester, I generally put together a question (either on plasmid assembly or on dideoxynucleotide sequencing).) 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; I can personally recommend Dr. William Sofer - Bill Sofer - as a teacher, although like everyone else he's human and does have limits to his patience, which are sometimes reached around exam times for Genetics/Molecular Genetics if 300 people are bombarding him with requests for grade changes...), 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.

I am willing to spend quite a bit of time giving assistance, as you can see from the scheduling comments above. Some (as expressed in one anonymously-made comment) may be concerned about whether or not the people I work with are doing enough on their own:

Intro Sheet

Tuesday Lab

My background: My primary background is in biology, specifically molecular genetics. I am mainly qualified for this lab due to:

  1. prior lab experience, especially with DNA; and
  2. having TAed it before (this will be my 5th or 6th time for the fall 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 and my need for sleep, 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, 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:

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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