This post is going to be about the Second-Year courses that I took at UBC during Term 2 of the Winter 2010 Session (January 2011 to April 2011), following last term. This will be a detailed version. If you don’t want to read as much, read the summary version. (I actually suggest reading the summary version first.)
Second-year Courses in UBC Sciences (Summary)
Second-year Courses in UBC Sciences – Term 1
First-year Courses in UBC Sciences
Transition: First year to second year
List of my “UBC Academic Stuff” posts (like this one)
This post may not be helpful to everyone in second-year Science, because as one progresses through university, one’s courses or program of study becomes more specialized. I still hope it will be helpful to some who plan to take the same course(s). Also, be aware that course details will change over time.
Second-Year Courses taken:
Please read the summary version of this post if you want to know about MUSC 103 or EOSC 112. There is no detailed version for those courses, sorry.
As always, please feel free to leave a comment or a question and I will answer it as soon as possible. If you ask a question and I reply to it, please reply back so that I know you read my response.
Note: All prices listed in this post were from 2010W, unless otherwise stated.
This course was very different from CHEM 233. Less thinking required, more calculations involved. Many people say it’s an easy course, and after taking it, I can’t say I disagree.
VISTA Quizzes – 15%
Midterm – 15%
Final – 70%
It seems this course is only offered in Winter Session, 2nd term.
There are three main units in this course, and I might argue that there is also another minor unit (Donnan membrane potentials, electrochemistry and colligative properties) but technically it’s part of thermodynamics.
The three main units of the course are thermodynamics, spectroscopy, and kinetics.
Thermodynamics was the first part of this course and it was what the midterm tested (the midterm tested nothing else). Thermodynamics is probably the easiest unit out of the three. Topics in thermodynamics included ideal gas expansion (and compression) as well as internal energy, work, heat, enthalpy, the 3 laws of thermodynamics, and entropy. Questions on thermodynamics mainly focused on how to calculate work, heat, internal energy, enthalpy, and entropy for a given process. Thermodynamics was a bit of review from CHEM 123, but it was overall harder because there was a lot of theory and calculus involved for the derivation of some equations.
We learned about the “rules” of calculations in thermodynamics. For example, when the volume of an ideal gas does not change during a process, then there is no work being done (work = 0). Here is an example problem from thermodynamics that you could encounter on the midterm or final exam.
This question was one of the two thermodynamics questions (not counting colligative properties/electrochemistry/membrane potentials) on the April 2010 CHEM 205 exam.
Here is the answer… according to me anyway:
n = 2 moles
T1 = 27 + 273 = 300 K
P1 = 1 atm
V1 = ?
T2 = ?
P2 = ?
V2 = 2v1
w = -4000 J (work is done by the system, so by definition work is negative)
q = 3000 J (heat is given to the system, so by definition heat is positive)
dU (internal energy, or dE) = w + q
dU = 3000 – 4000
dU = -1000 J
dU = n C (v,m) dT
dT = dU / n C(v,m)
dT = -1000 J / (2 mol * 5R/2)
dT = -1000 J / (2 mol * 5 * 8.314 J/K/mol / 2)
dT = -24.056 K
T2 (T final) = T1 + dT
T2 = 300 K – 24.056 K
T2 = 275.94 K
dH = n C (p,m) dT
dH = (2 mol) * (7R/2) * (-24.056 K)
dH = -1400 J
PV = nRT
V1 = nRT1/P1
V1 = (2 mol)(0.08206 L*atm/K/mol)(300K) / (1 atm) = 49.236 L
V2 = 2V1 = 98.472 L
dS = n C (v,m) ln (T2/T1) + nR ln (V2/V1)
dS = (2 mol) * 5R/2 * ln(275.94K / 300K) + (2 mol) * (8.314 J/K/mol) * ln(98.472L / 49.236 L)
dS = 8.05 J/K
dS (surroundings) = -q/T = -3000J / 300K = -10 J/K
dS (total) = dS + dS (surroundings)
dS (total) = 8.05 – 10
dS (total) = -1.95 J/K
The reaction is non-spontaneous/impossible because dS (total) also known as dS (universe) is negative.
And that is how to do this thermodynamics question. You will definitely encounter this type of thermodynamics question (gas expansion/compression) on the midterm and final, but with different conditions/situations. For example, in another question the process could be adiabatic (q = 0) or isothermic (dT = 0).
Note that I calculated V1 and V2 for finding dS even though I didn’t really have to since V2/V1 = 2 from the question. Also note that when I did calculate V1, I used PV = nRT and for R I did not use 8.314 J/K/mol but I used instead 0.08206 L*atm/K/mol. They are the same thing, they just have different units. I used 0.08206 L*atm/K/mol to calculate volume instead because I wanted my volume units to be liters. If you used 8.314 J/K/mol then you would have to convert pressure from atm (atmospheres) to Pascals (Pa = N/m^2) before plugging numbers in. In that case the units for volume would not be L (liters) but instead cubic meters. It does not matter which units you use (unless they specify in the question), just make sure the units cancel out in the calculations and that way you know that you did things correctly.
The second unit of the course is spectroscopy.
Spectroscopy in CHEM 205 is basically the identification of molecules by looking at how the molecules behave when we shine light on it (that’s a bad definition, but it’s probably enough for our purposes).
The spectroscopy techniques that are covered in CHEM 205 include H-NMR (nuclear magnetic resonance), C-NMR, UV-Vis (Ultraviolet and visible light), IR (Infrared) and mass spectroscopy.
These different techniques are used for identifying different parts of the molecule. H-NMR only looks at the hydrogens, C-NMR only looks at the carbon atoms in the molecule. Mass spectroscopy basically tells you how much the molecule weighs. UV-Vis and IR tell you stuff about what kind of functional groups are present on the molecule, I think.
What you learn in CHEM 205 is about how these techniques work and then how to actually use them. For example, if you isolate some molecule and subject it to spectroscopic analysis, you can get graphs or figures of the H-NMR, C-NMR, UV-Vis, IR, and mass spectrums. From these graphs/figures you can then identify what molecule you have. That is how (or at least one of the ways) researchers confirm the molecule that they purified or made and also how researchers can identify the structure of new molecules that they might have found.
The instructor covered a lot of theoretical stuff on how the spectroscopy techniques work. For example, H-NMR looks at the nature of the nuclei of the hydrogen atoms in the molecule.
In my opinion, the instructor went into detail way too much about spectroscopy and how it is related to quantum physics and the wave particle theory and other stuff even though we really didn’t need to know it. Spectroscopy was therefore probably the most confusing unit for me and I found it very difficult to learn in class as well as the online WebText (see below). After the theoretical stuff of how H-NMR works, we then covered how to identify molecules from H-NMR spectra.
The only thing that is really important to know is how to identify molecules from the spectra; learning the details of exactly how H-NMR and how the H-NMR machine works is not THAT important. All of the practice exam questions and the real final exam questions on spectroscopy were about identifying the molecule from the H-NMR, C-NMR, UV-Vis, IR and mass spectra. So if you know how to identify molecules given the spectra, you will do fine on the spectroscopy questions.
The last unit in the course was kinetics – basically about rates of a reaction. We learned about average rate of reaction, instantaneous rate of reaction (using derivatives), reaction orders, determining rate laws from experimental data (which we did in Chemistry 12), integrated rate laws, half-life (first-order rates), Arrhenius equation, Collision theory (not examinable), reaction mechanisms and steady state approximation, equilibrium, and finally enzymes (examinable but not really focused on). I found this unit to be fairly easy but it probably seemed a bit harder than thermodynamics. Most people were confused by finding the reaction rate of a multistep reaction using something called steady state approximation because there was “a lot of algebra” involved.
In-class Activities and Homework
All the CHEM 205 sections actually had access to “lecture notes” online. What I usually did was that I printed out the lecture notes, usually 4 lecture slides (sometimes 6) per page, and then I would just listen to the prof lecture in class.
This was very convenient because I could pre-read the lecture slides if I wanted to and the professor used the exact same lecture slides, so it was very easy to follow along. Whenever the professor said something important or wrote down something or went through an example problem, I would copy down these notes onto my printed out lecture slides.
I usually did not take that many notes because most of what the professor said was already on the lecture slides, which was good so that I could pay attention to what the prof is saying rather than putting all my effort into copying down notes.
We went through many example problems which were useful for us to test our knowledge and see where we have problems and also how to study since the problems provided in class would be similar to exam-style problems.
We also had three review sessions – one after each unit in the course (thermodynamics, spectroscopy and kinetics). They were pretty useful, basically the professor would just go through a few problems from previous exams or similar problems that the professor came up with, and we were also free to ask questions as well.
Homework in this course was only online VISTA quizzes. We had two tries for each VISTA quiz. There were two different quizzes – theoretical and numerical. The numerical quiz had problems that involved calculations and are probably what would you expect on a midterm or final in CHEM 205. Numerical quizzes were unlimited time up until the due date. The theoretical based questions are not unlimited time and were multiple choice. You could have these kinds of questions on the exams too but to a much lesser extent. There were probably a few quizzes every month, never more than four a month I think. I managed to get perfect on all the quizzes, so I found them pretty easy for the most part, although sometimes I would have to ask my friends for help and on many quizzes I didn’t get perfect on the first try. The hardest quizzes are arguably the theoretical quizzes which did not involve any calculations.
Textbook and WebText
The textbook for this course is called Physical Chemistry for the Biosciences by Raymond Chang. I probably only consulted it like two times. It was for the most part, useless and instead I used the lecture notes (posted on VISTA) to review, as well as the written notes that I took on the printed out lecture notes during class. There are assigned readings from the textbook that are recommended and sometimes recommended problems from the textbook. The textbook is optional, and I shouldn’t have bothered buying it.
That being said, at the beginning of the course, I tried to rely on the textbook a lot because I thought it would be helpful but it really wasn’t, and so afterward I didn’t even touch the textbook for the rest of the term.
Aside from the textbook, there is also a thinner red book or booklet that contains the solutions to the problems in the textbook. I did not buy it. I guess doing the questions in the textbook would have been useful, but apparently I didn’t need the extra practice, judging by my mark on the midterm/final. The problem sets posted on VISTA as well as examples shown in class and the VISTA quiz questions were sufficient practice. Plus, the problems from the textbook weren’t always relevant, although I can’t say for sure because I really only looked at a few, lol.
Another resource is the online WebText which basically contains notes that are compiled or written by someone at UBC I think. They go into a lot of detail in my opinion, and a lot of this detail is confusing and unnecessary, especially the information about derivation and derivatives/integrals and mathematical transforms or whatever. Anyway, I read the online WebText for thermodynamics and it was somewhat useful, but not necessary. I tried to read the WebText for spectroscopy and that totally failed. And so I didn’t even bother reading kinetics. Overall, the WebText was not very helpful and I relied mainly on my lecture notes. A physical copy (printed out version) of the WebText can be bought downstairs in the SUB at Copyright (or whatever it’s called, near the bubble tea place) for $10. I know people that bought it and highlighted stuff in it when they read it.
The resources available on the CHEM 205 VISTA webpage include:
2) Past exams with key
3) Problem Sets
4) VISTA Quizzes
5) General Information, including the syllabus, recommended readings, and the formula sheet
I would recommend to CHEM 205 students to print out the formula sheet. You are allowed to use a formula sheet (they provide you with one) on the midterm and the final exam and so using the formula sheet throughout the course will allow you to get used to using it. You will also find out which formulae they give you and therefore which information you will have to memorize for the exam.
So, how should you study for the course? I actually did quite well in CHEM 205, so I think I have a decent idea.
I usually printed out the lecture notes posted online before class and skimmed them over as “pre-reading.” A couple times, I read the textbook and WebText for pre-reading by looking at the recommended reading schedule but after a while I realized this wasn’t useful for me personally. You could try it, it could work for you. And if you don’t want to buy the textbook you could just go to the bookstore, take the textbook, and sit down in one of the bookstore chairs and try reading it. Or you could borrow it from the library, I know a few people that did this (I think you’re only allowed to borrow it two hours at a time at UBC though since it’s a course textbook or whatever).
During class, I would write down stuff that the prof said/wrote that I thought were important directly onto the lecture notes that I had printed out. After class I would re-read the lecture notes and try to find things that I wasn’t sure about so that I could think about it or clarify with a friend/the prof.
Topics that are examinable are pretty much completely covered in lecture so if you understand everything from lecture then you won’t need to do extra reading from the textbook or elsewhere, unless you want review or something.
I actually joined a study group for CHEM 205 and it was weekly for two hours. It was good because I got help from others sort of, but most of all it made me keep up with the course material and prevent me from slacking off. Most of the time, I was the one helping other people and you know what they say – teaching is the best way to learn. We usually did the VISTA quiz questions as well as the problem sets posted on the main CHEM 205 VISTA webpage.
There are two different sources of VISTA quizzes. There are VISTA quizzes on the main CHEM 205 webpage and then there are VISTA quizzes on the section-specific CHEM 205 webpage. For us, only the VISTA quizzes on the section-specific CHEM 205 webpage were for marks, while the ones on the main webpage were for extra practice if we wanted it. I looked through them, they weren’t that great and so I didn’t really bother doing them at all.
Problem sets – there are problem sets posted on the main CHEM 205 webpage. I think there are about 7 problem sets in total – 2 for thermodynamics, 1 for electrochemistry, membrane potentials and colligative properties, 3 for kinetics, and at least 1 for spectroscopy. Only the 2 problem sets for thermodynamics were “covered” for the midterm.
The problem sets were useful and I used them as the main source of practice problems. However, some of the problems were not what you would expect on a CHEM 205 exam – for example, the questions that require graphing. The professors said that the VISTA quiz questions are very similar in style to exam questions but nonetheless, the problem set questions were useful for testing general knowledge and I felt that the problem sets still prepared me for the exams. I probably did each problem set 3 – 4 times each. I also read my lecture notes a few times during the course and used them as my main source of information.
As previously mentioned, I did not use the textbook by Chang nor the WebText extensively, and relied on the lecture notes instead. However, the lecture notes were not that great for spectroscopy because they were vague and the professor was supposed to explain stuff in class instead. However, Dr. Bussiere was not very good at explaining spectroscopy to me, and often talked about unnecessary and confusing detailed crap about waves and orbitals and that kind of thing. Instead, I read Organic Chemistry 5/E by Bruice. What, you mean that textbook from CHEM 233? Yeah. If you have the 5th edition (don’t know about the other ones), go look at Chapters 12 and 13. Chapter 12 is called “Mass Spectrometry, Infrared Spectroscopy and Ultraviolet-Visible light Spectroscopy.” Chapter 13 is called “NMR Spectroscopy.” So you mean all the spectroscopy types in CHEM 205 are actually covered in the textbook by Bruice? Yep – instead of paying attention in class, I read the CHEM 233 textbook instead (Organic Chemistry by Bruice) and it worked surprisingly well. Since you’ve probably already taken CHEM 233, you should know that this textbook explains things quite nicely and there are several practice problems available. This textbook told me basically all I really needed to know and there were several useful practice problems as well.
Spectroscopy is something that comes with practice, just like organic chemistry in general. The more practice you get, the easier identifying molecules by their spectra will become and eventually you can identify molecules pretty quickly and with accuracy too.
Past exams and VISTA quizzes – I would do the VISTA quizzes a few times, even after submitting them because the questions are kind of similar to exam questions. There were 3 or 4 past final exams posted on VISTA (there were no midterm exams posted on VISTA) and I probably did each final exam under exam conditions twice each, using a timer. By the end of my final exam study session I was finishing the past exams within an hour (before checking over).
Finally, the VISTA discussion board. I used the VISTA discussion board extensively, more than I have ever had in any other course (I probably should have done this for CHEM 233…). But basically, my posts on the discussion board accounted for like 10 – 20% of all the posts on the section-specific webpage and maybe 10% of all the posts on the main webpage. I made it my goal to answer as many questions as possible from other people and this gave me motivation to keep up with the material and also kind of forced myself to master the material enough to be able to explain the concepts to other people on the board. Again, teaching = learning.
So, in summary for preparation – read lecture notes a few times (and get help if still not understanding stuff), do problem sets and VISTA quizzes a few times each, help people on Discussion board if you are bored… (or ask good questions, too), and do final exams a few times each under exam conditions.
Helpful external resources for spectroscopy
Apparently I was a really bad learner of spectroscopy, so instead of repeatedly trying (and failing) to read and understand the online notes and in-class slides on spectroscopy, I sought out other resources.
I started out by visiting YouTube, specifically this guy’s videos: http://www.youtube.com/watch?v=jRxgX-7FO8g. This video specifically introduces you to H-NMR spectroscopy. He also has videos on mass spectroscopy. Although I found his videos very helpful as a preliminary introduction, they were too introductory and it was insufficient. However, it was still an excellent way to start (for me).
I then proceeded to google some websites to see if any of them could explain spectroscopy better, and found this one: http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/nmr/nmr1.htm which was okay… there was still stuff I couldn’t understand but it was still more helpful than the online notes to be honest. Plus there were some problems at the bottom of the page.
Point is, there are a lot of webpages out there on spectroscopy. Some contain way too much detail and information, and some are mildly acceptable, so go out there and look around if you’re confused by your profs notes. There are also websites (sorry, lost them) that actually predict the spectra based on the chemical formula you can give it, so that’s good for practicing predicting spectra. I also highly recommend reading a textbook like Organic Chemistry by Paula Y. Bruice if you’re still confused and that is what I did since I had the textbook from CHEM 233, and I found it to be easier to understand than many university websites I visited (like the one above).
Finally, here is another great online resource for practice problems for spectroscopy:
Useful information about thermodynamics that people have problems with:
When the volume of an ideal gas does not change during a process, then there is no work being done (work = 0). And when the work is zero, then the internal energy E is equal to the heat q:
q = heat, w = work, E = internal energy
E = q + w (this formula is also known as the law of conservation of energy)
If change in volume = 0, then w = -P dV = 0 (dV is the change in volume = 0 in this case)
E = q + 0 = q
Similarly, if temperature does not change (if the ideal gas process is isothermic), then dT = 0 and so enthalpy and internal energy are zero. The reason for this is because for an ideal gas, enthalpy and internal energy are solely dependent on temperature changes. For an ideal gas, internal energy E and enthalpy H do not depend on whether volume or pressure change or not – E and H are ONLY dependent on temperature for an ideal gas. For a real gas this is not true, but for the most part in the course we only deal with ideal gases.
These formulae are provided on the final exam if I remember correctly:
dH = n C(p,m) dT
dE = n C(v,m) dT
dH is change in enthalpy, dE is change in internal energy, dT is change in temperature, C(p,m) is the molar heat capacity (the m stands for molar) of the substance measured at constant pressure (the p stands for pressure), and C(V,m) is the same thing but measured at constant volume. A very common mistake that CHEM 205 students make is that they assume that they cannot use these two formulae if the process in the problem is not at constant pressure or not at constant volume.
It does NOT matter what the process in the problem is. It could be constant volume (isochoric), constant pressure (isobaric) or NEITHER and these two formulae dH = n C(p,m) dT and dE = n C(v,m) dT STILL APPLY. The reason for this is because C(p,m) and C(v,m) are only constants measured under constant pressure and volume respectively, but can still be used for non-constant pressure and non-volume pressure processes. Therefore, these two formulae explicitly show that H (enthalpy) and E (internal energy) only depend on T (there are no other variables in that equation, assuming ideal gas so that C does not change and assuming the gas doesn’t somehow change in n – number of moles).
For a monoatomic ideal gas, C(v,m) and C(p,m) do not depend on the material (ie. C(v,m) and C(p,m) for Argon gas and for Helium gas would be the same for an ideal gas). Instead, C(v,m) and C(p,m) are constant for any monoatomic ideal gas. For a monoatomic ideal gas, C(v,m) is always equal to 3R/2 and C(p,m) is always equal to 5R/2. (Note that R is called Rydberg’s constant I think, see the formula sheet. R is equal to 8.314 J/K/mol)
For a diatomic ideal gas, you add R to the value of C(v,m) and C(p,m) of the monoatmic ideal gas. So for diatomic ideal gases, C(v,m) = 5R/2 and C(p,m) = 7R/2. An example of a diatomic gas would be oxygen or hydrogen gas because there are two atoms in each molecule.
For a triatomic ideal gas, you just add R again to each of them and C(V,m) would then be 7R/2 and C(p,m) would be 9R/2.
The last mistake I can think of that CHEM 205 students get confused about is about the formula w = -nRT ln (V2/V1). This formula ONLY applies if the following conditions are ALL true:
1) The process involves an IDEAL GAS expansion or compression.
2) The process of expansion or compression is REVERSIBLE. (Reversible is a bit of a complex concept and kind of means that the system is at equilibrium at all steps in the expansion or compression.)
3) The process is ISOTHERMAL.
If one of these conditions is NOT true, then you CANNOT USE THE FORMULA.
Let me show you the derivation:
dw = -P(ex) dV
Work is equal to the external pressure multiplied by the change in volume. ‘ex’ stands for external, P is pressure, dV is change in volume. dw is work, kind of. You can call it change in work I guess..
If the ideal gas process is reversible, then the system is at equilibrium with the surroundings all the time. That is, the pressure of the system (the pressure of the gas) is equal to the external pressure (applied by the surroundings).
P(sys) = P(ex)
We can actually just write P(sys) as P.
P = P(ex)
dw = -P dV
If the process involves and IDEAL GAS, then the ideal gas law PV = nRT applies. (P = pressure, V = volume, n is number of moles of gas, R is a constant, T is temperature).
PV = nRT can be rearranged to: P = nRT/V. Let’s substitute this into our equation.
dw = -P dV
dw = -(nRT/V) dV
This is where some basic calculus comes in. Integrate both sides and integrate the right side from V1 to V2, where V1 is the initial gas volume and V2 is the final gas volume. Recall that integrating 1/x with respect to x gives lnx. Therefore, integrating -nRT/V with respect to V will give -nRT [ ln(V2) – ln(V1) ] since we are integrating from V1 to V2 and -nRT is a constant (the process is isothermal which means T is constant, n is usually always constant, and R is obviously a constant – R = 8.314 J/K/mol).
So we get:
w = -nRT [ ln(V2) – ln(V1) ], or:
w = -nRT ln (V2/V1).
(Recall: lnx – lny = ln(x/y)…)
You are kind of expected to know how to derive such formulae, but the chance that you will have a derivation or integration or differentiation question on the exam is HIGHLY UNLIKELY. You should try to understand the derivations and the calculus if you can though. If you can’t, you can either ask the prof or TA for help, or just ignore the details because there was no derivation or calculus on any of the questions from my midterm and final exam. There was ONE question on it on a previous final but it was the only one and it wasn’t really worth that many marks.
Anyway, back to my main point. You cannot get to the formula w = -nRT ln (V2/V1) if one of the three conditions are NOT met. So remember folks, only use w = -nRT ln (V2/V1) if 1) the gas is an ideal gas, 2) the process is reversible and 3) the process is isothermal.
Average in 2010W was 77% (standard deviation 15%). Several people achieved a perfect grade. 25% of all students achieved an A+. About half of all students achieved 80% or higher. Fail rate quite low at 4%.
Overall, this course was pretty fun and easy, and I found CHEM 205 to be a GPA booster for me. It definitely seemed difficult at times during the course, especially with the integration and the whole unit of spectroscopy, but after repeated practicing and reviewing I became very familiar with the material and was able to teach other people.
I heard things about how difficult this course would be, and for a large chunk of the course I did feel overwhelmed, but I managed to get back on track before finals rolled around, and my preparation served me well. Biochemistry is in a sense aqueous organic chemistry, and many concepts from CHEM 233 are revisited, mostly reactions at the carbonyl (C=O). However, this course is very different from CHEM 233.
Any reference to “textbook” in this course review is a reference to the custom BIOL 201 textbook, not the commercial textbook by Horton et al., unless otherwise specified.
This course taught me about the chemistry that is “used by cells” in biological processes like how a carboxylate group can be converted into an amide group using ATP. A common theme is looking at which species is a good/better leaving group and in this example it would be phosphate (and ADP) because the negative charge of the phosphate is spread out and phosphate has several resonance structures. If you are still struggling with resonance structures, you’d better learn how to draw all of them properly (and not extra ones) before the exam comes around.
I also learned about the structure of proteins (kind of review), protein folding, and we looked at a few enzymes in detail to understand the mechanisms of the reactions they catalyzed and how enzymes help them to occur. This was a bit intimidating as some mechanisms had like 10 steps or something but after a while it becomes easier to guess which reaction is the next step in the mechanism.
We also went into the energetics (thermodynamics) of both ATP use in biosynthesis and protein folding (looking at Gibb’s free energy change, enthalpy, entropy, etc. There are several equations we use and they’re pretty much the same ones from CHEM 123 or CHEM 205.
Finally, we covered metabolism and looked at the different pathways involved in anabolism and catabolism in the cell like glycolysis and the TCA cycle and the different mechanistic steps and enzymes involved.
List of topics from the textbook:
1. Water and Aqueous Ionization Phenomena (hydroxyl groups being deprotonated, amino groups being protonated in the presence of water, etc.)
2. Protein Structure
i. Structural Aspects of Globular Proteins
ii. Polypeptide Folding and Oligomerization
3. Enzyme Action: Catalytic Mechanism
4. Energy Transfer
i. Basics (definition of energy and work, equilibrium, calculating dG for reactions and what it means)
ii. ATP Use in Biosynthesis (e.g. in protein synthesis)
iii. Mechanisms of ATP Synthesis (oxidative phosphorylation and the ETC, photophosphorylation and chloroplasts, and substrate level phosphorylation)
i. Where We’ve Been and Where We’re Going (ATP, NADPH, enzyme classification, cofactors and coenzymes, vitamins)
ii. Animals (Glycolysis/catabolism, TCA cycle)
iii. Plants (Calvin cycle – fixation and assimilation of carbon, glycolysis and TCA cycle)
iv. Modulation of Enzyme Activity and Metabolic Regulation (inhibitors and activators, Michaelis-Menten and allosteric enzymes).
i. Protein Purification and Characterization (What are the different methods of purifying proteins?)
ii. Quantitative Enzymology (“Describing enzyme function using numbers, empirical enzyme kinetics” and making/interpreting graphs)
Exam-I (Midterm) – 35%
Exam-II (Final) – 50%
Assignments or CSL – 10%
iClicker – 2.5%
Tutorial participation – 2.5%
Exam-I covered lecture topics 1-3 above as well as the first tutorial topic of protein purification. It took place on February 10th.
Exam-II covered everything else basically, and was not cumulative.
CSL is community service learning and may be chosen in lieu of assignments. This is what I chose because I applied for the volunteer position before I knew it could count for marks. Click here for more information and how to apply.
For the first part of the course, the instructor wrote lecture notes on the overhead projector and I copied them down. He also went through many examples to show how to analyze enzymatic mechanisms for example or dG calculations. Finding the isoelectric pH (the pH at which a zwitterion has a net charge of zero – note: a zwitterion is a molecule that can have both positive and negative electrical charges, like an amino acid) is not covered in the custom textbook, only in class. Otherwise, the stuff covered in class was pretty much covered in the custom textbook.
For other parts of the course, instead of writing notes on the overhead, the instructor would show PDF lecture slides. These PDFs are uploaded to VISTA ahead of time and available for downloading only until around 11 pm the day before class.
I preferred when there were written lecture notes because it was very easy to copy things down at the same pace as the professor. Lecture slides were a pain for me personally because I was not fast enough to copy them down, and if I just didn’t copy anything down I tended not to pay as much attention. If you can copy things down fast enough from the PDF slides, great. Otherwise, you can print them out 4 – 6 slides on a page and just write anything extra in the margins or something. There were a few handouts distributed throughout the duration of the course. There were a total of 31 iClicker questions. I would have preferred more, on the scale of a few questions per class because I felt there weren’t enough to really gauge my understanding of the material. However, the iClicker questions were not always simple and thankfully, they were participation only.
There were a total of two assignments, worth a whopping 5% each. The first one was a “review” on buffers and pH calculations. For example, what volume of 0.1 M acetic acid and 0.1 M sodium acetate are needed to make 1 L of 0.1 M buffer solution having a certain pH? There were a total of 10 multiple choice questions and we inputted our answers on a VISTA quiz so it’s easier to mark, I guess. The second assignment was about the same length and was on quantitative enzymology (the second tutorial topic). These assignments can take a long time and it’s highly recommended to check them over multiple times, since they’re worth so much. The assignments are usually given out a few weeks in advance of the due date, which is plenty of time.
There were a total of five tutorial sessions, an hour long each. Basically you go into the tutorial room and sign a sheet to let them know that you showed up and you get 0.5% of your grade each time. Tutorial is optional – the marks for the ones that you don’t go to get added onto your final exam if I remember correctly. Basically, the TAs will go over PDF slides relevant to the tutorial topics (see above) and they also have a few demos and handouts. I wish they had videos of the demos posted on VISTA or something because everyone always crowds around the experiment and people at the back never get to see anything. Then again, I could probably maybe YouTube them anyway. Not that they’re actually important with respect to exam questions. Sometimes you will also get to solve problems together during the tutorial. Tutorial PDF slides are posted online, but I don’t think handouts were. I recommend going to tutorials because it’s free marks plus the material covered there is examinable. If you don’t go to tutorial I guess you can just read the custom textbook.
Difficulty and Exam Preparation
This course proved to be really quite an interesting course and “opened my eyes” to many things about Biology that I really didn’t know… probably the most useful/informative course of the term. This was one of my courses where I was going into it knowing absolutely nothing about what to expect and therefore a bit intimidated, but honestly it really wasn’t too bad but obviously you still need to put the work into reading and practicing problems. The exams focused more on my ability to synthesize information and apply concepts rather than memorizing random info.
The types of questions on the exam included one word answers, explanations for certain observations, calculations, arrow-pushing mechanisms, graph interpretation, fill in the blank for those long metabolic pathways, resonance structures. Basically all kinds of stuff, and mostly application/explanation stuff too.
How to prepare?
Other than the stuff about calculating isoelectric pH (pH I), everything’s covered in the textbook as far as I remember. So all you really need to do is:
1) Do the recommended readings from the custom textbook. You don’t need to follow the online schedule exactly, just keep up in small sections at a time.
2) Attend lecture. Write notes.
3) Review your notes and the textbook readings especially. Get help from office hours if needed.
4) Do the problem sets on schedule and get help during the tutorial sessions. There are special tutorial sessions just for problem set help. Do not put off doing the problem sets. They are actually long sometimes and can take like 5 hours each. And don’t look at the answer key until you’ve seriously attempted a problem because that really won’t help you.
5) Read the relevant sections in the custom textbook again and make sure you are able to meet the learning objectives which are posted online for each topic.
6) Do the problem set a second time. A third time if you have time and want to become more familiar with it. Some exam questions are very similar to the problem set questions. After all, one of the learning objectives is to be able to do the problem set questions LOL. Make sure you didn’t skip the tutorial problem set like I did.
7) Do the practice exam available on VISTA without looking at the answer key. Make sure you have your “reference material” printed out so that you become familiar with it because you will be using the same one during the midterm/final. It’s kind of like a formulae sheet, except better perhaps.
In short, if you read the custom textbook a few times and do the problem sets a few times each before the midterm/final then you should be good for exams. I only read the textbook maybe once and did the problem sets once for the midterm and didn’t even look at the practice midterm. So I got around 70% on the midterm. But for the final I read the textbook like 3 times and did the problem sets 3 – 4 times each and let’s just say my final mark was very significantly higher.
The course average was 72% (standard deviation 15%) which is pretty much the same as BIOL 200 in 2010W. About 9% of all students achieved an A+. About a third of all students achieved 80% or higher. Fail rate 9%.
I think the people who have trouble with this course don’t really understand concepts fully enough to apply them to new situations and are too reliant on memorization. And they might also not be becoming familiar enough with the problem set questions. Also in courses where actual thinking and application is encouraged over memorization, cramming is harder and doesn’t really work as well, so keep up.
I already mentioned the usefulness of the custom textbook (top picture, referred to as textbook in previous sections). There is also an optional textbook called Principles of Biochemistry 5th ed. by Horton et al. This is an optional commercial textbook and is sold in the Bookstore for $170.60 used, $76.75 (prices checked in January 2012). I mentioned in some comments that it was not offered to us last year and the truth is that indeed, it was not listed by the Bookstore officially. However, I realize now that it was mentioned on VISTA as a recommendation for anyone wanting a commercial textbook to read. Therefore, I do not think it would be that useful to get because it really isn’t necessary, and I’m assuming that the course material did not change that much within a year. So if I were you taking the course this term, I probably wouldn’t get it. I would just get the custom textbook package which is sold by MISA for $30.
Custom textbook package (incl. chemistry supplement booklet and problem set booklet): $30
I found a lot of the material in this course to be useful for me to learn as a student in Microbiology because it’s like the very basics of environmental microbiology that every microbiologist should know and in fact the first few chapters are somewhat review from BIOL 112.
This course started out pretty straightforward but I admit that the “second part” of the course really confused me and was what made the course seem quite difficult to me in the end.
This course has a lot to do with diversity in prokaryotes and you’re supposed to appreciate that for many given processes or structures, there is a wide range of diversity in different prokaryotic groups/families. Sometimes you will be expected to compare them. This means that when you learn about something like metabolism, you’ll be learning about the various types of metabolism and which types of prokaryotes do which type of metabolism.
1) Introduction to Bacterial and Archael Diversity
-domains of life
-why and how the small subunit ribosomal RNA is used to study the evolutionary distances/relationships between organisms
-prokaryotic diversity and horizontal gene transfer, how to name new bacteria/archaea
2) Prokaryotic Structure and Locomotion
-shape size, cell composition
-descriptions of common features like the cytoplasmic membrane, peptidoglycan (and its synthesis), capsules, pili, flagella
-Gram negative vs. Gram positive structure in bacteria
-chemotaxis (a behaviour exhibited as a result of sensing a chemical concentration difference in the environment)
3) Prokaryotic Genomes and Gene Expression
-chromosome and nucleoid structure
-transcription and translation in prokaryotes
-promoters and gene expression transcriptional regulation, operons (think lac operon)
-genomes, genome sizes of different prokaryotes
4) Prokaryotic Cell Division and Reproduction
-introduction to the different proteins and systems that different bacteria use to accomplish cell division, like FtsZ
-how different bacteria divide, especially if they have different shapes
5) Antibiotics and Antibiotic Resistance in Bacteria
-what are antibiotics, really?
-looking at specific antibiotics and how they function and which cellular functions they target/inhibit
-a list of many different antibiotics, their functions, and which organisms/diseases they can target…. yay memorization
-mechanisms by which bacteria develop resistance to antibiotics
-types of mutations (insertion, deletion, base substitution)
-transformation, transduction and conjugation (horizontal gene transfer)
6) Prokaryotic Nutrition
-types of nutrients
-using nutrients for energy, electrons, etc
-organisms can be classified by their nutritional requirements (e.g. chemolithoautotroph… /groans)
7) Prokaryotic Metabolism
-ATP, NADPH, oxidative phosphorylation, catabolism, anabolism
-differences in metabolism between different organisms, for example between lithotrophs and heterotrophs
-energy sources and TEAs for different (kinds of) organisms
-assimilation of elements from the environment
8) Growth and Environment
-growth rate, exponential growth, limits to growth
-how different groups of prokaryotes grow
9) Food Borne-Illness and Control of Bacterial Growth in the Food Industry
10) Life on the rocks
-a few of the ways by which prokaryotic metabolism negatively impacts the environment from the human point of view, such as bacteria producing lots of acid at mining sites resulting in metal run off and the death of fish and other wildlife
11) Bacteria and Archaea on the Farm
-bacterial and archaeal processes that occur on farms that help/hurt agricultural processes
-nitrification, denitrification, microorganisms that live in the rumen of cows
12) Cleaning-up with Prokaryotes
-covers the use of prokaryotes to treat sewage, clean up oil spills, etc.
iClicker – 10%
Assignments – 10%
Exam-I (midterm) – 30% on Ch. 1-5
Exam-II (final) – 50% on Ch. 6-12
The iClicker grades are based on both correctness and participation. I don’t know the weighted ratios but I would say something like 50:50. One must achieve an overall passing grade for both exams together in order to pass the course. According to the general information sheet, grades in MICB 201 are not scaled.
In-class Activity and Assignments
Slides are posted online before lecture. Some of the slides are absolutely gigantic in file size (like 50 Mb per lecture) which is pretty ridiculous, but I usually printed them to PDF again using a program called pdf995 and that usually reduced the file size significantly. Slides are only available up until a certain time, just like in BIOL 201. That means that you should download them and save them before they are removed!
I usually printed out the lecture slides (4 slides per page) and then I wrote notes directly on them in class. The instructor just went over the powerpoint slides that were posted and sometimes wrote extra notes on the overhead. There were also clicker questions; about 30-40 were asked during the term. They were moderate in difficulty and discussion was allowed, so sit beside a smart person lol. The answers to clicker questions are not posted online.
Assignments are worth 10% of the grade and they are generally fairly straightforward, but make sure you check over because it is easy to make mistakes that will cost you marks. Like using the wrong units. There are not many assignments, which means each assignment is actually worth a lot (some are 2% of your entire grade).
Exams and Tips
Exams are in multiple choice format, and a practice exam was distributed via VISTA for both the midterm and final. The format of the exams will be just like the practice exams, and the questions themselves are similar to the iClicker questions asked in class.
There were also “Chapter problems” available on VISTA for each chapter of the textbook. Frankly, I didn’t do any of them (I don’t think they’re multiple choice anyway) but they might have been helpful for the later chapters (Ch. 6 onwards).
To review for exams, I made a word document and pasted the learning objectives in it. Then, I went through my lecture notes and textbook (mostly the textbook) to answer the learning objectives. This ensured that I met the learning objectives on which the exam would be based. I found this to be extremely helpful with respect to the midterm and ended up getting the highest mark in the class. However, it didn’t work that well with respect to the final (but I didn’t give myself a lot of time to review anyway). You can view these documents that I made for the first four chapters:
Chemistry 235 is a lab course offered in both terms of the Winter Session, and it is offered in the Summer Session as well. It is mandatory for many Life Sciences students and “accompanies” the lecture course CHEM 233 (but not really). Labs are 3 hours a session, once a week. A TA or the prof will introduce you to the lab, and talk about which equipment is necessary and things like that. This takes 20 – 30 minutes, most of which is a waste of time because you already prepared yourself by reading the lab manual… although occasionally there are helpful hints and tips. Regardless, I think the “pep talk” is 99% useless. Before the talk, you might get a quiz. After the talk, you get started on the lab right away and rush to beat people for communal supplies! The point of CHEM 235 is really to 1) introduce you to basic techniques in Chemistry, and 2) test your ability to learn and perform them in the laboratory. You’ll probably forget the bulk of the material once you leave this course, so overall it’s not a very useful course, but it can be fun, especially watching other people break glassware and stuff like that. The smell and sensation of diethyl ether and acetone on the skin is quite interesting… you’ll know what I’m talking about once you’re done with this course.
Lab results (prep work done in the manual, any homework, and lab results) – 40%
Lab Quizzes and Exams (there is a two-part final exam – one is practical and the other is theoretical, both at the end of the term) – 50%
Technique (basically what your TA thinks of your “skills” in the lab) – 10%
Although this post is supposed to be detailed, I’m not going to go into too much detail with each experiment because the lab manual describes it well enough, plus you’ll need to read it anyway.
The order that you do your experiments in may not be the same as someone else who is taking the course in another section.
The experiments I performed were as follows:
Purifying a compound based on differences in solubility of solids in a given solvent system. Remember the filter paper for the Buchner funnel because I forgot lol. Questions on the quiz may be something like, “What characteristics are desired for a recrystallization solvent?”
2) Melting point determination and thin layer chromatography
Allows identification of compounds. Also allows for determination of how pure a compound is based on the range of the melting point.
Liquid-liquid extraction is used for separating mixtures based on the differences in the solubility of the components in two immiscible solvents (e.g. water and octane).
4) Identification of Unknowns
Basically, you’re given a mixture of two unknown compounds. You have to perform extraction to separate them, and then recrystallize to purify them further, and then perform melting point tests and compare the values to the reference pages in the lab manual. Then you write a report showing your findings and concluding which compounds you think you have. This takes 3 lab periods and basically tests how much you’ve learned from the individual recrystallization, extraction, and melting point labs.
5) Synthesis of Amyl Acetate
Esterification is a concept you learn in organic chemistry and basically, when you add something like acetic acid and an alcohol together, you can make an ester!
6) Grignard Reaction
A synthesis reaction that involves the Grignard reagent, which is a strong base and thus a strong nucleophile.
Heating a substance until it vaporizes, condensing the resulting vapours by cooling, and then collecting the condensate/distillate. This allows for purification of liquids that have different boiling points.
I often get the question: “Does it matter if I take CHEM 235 with CHEM 233 in the same term or not?” And my answer is no. The knowledge you get from CHEM 233 that is used in CHEM 235 is a very small part of the course, and it’s improbable that you’ll forget the concept if you take CHEM 235 in the second term. Besides, that’s what prep work is for.
You’ll be using something called a West condenser for many of the experiments. A West condenser is merely an apparatus that allows water to flow through the ‘outside’ so that it can keep it cool and condense any gas formed in the middle of the tube. As such, there will be two tubes attached to the West condenser — one for water going in from a tap, and the other for water going out into the sink. Always put these tubes over some kind of bar, otherwise they will fall onto the hot plate and BURN. And you’ll probably get an angry TA who will dock marks from you.
Prep work, Assignments and Exams
Prep work is done before each lab. Usually prep work is done directly in the lab manual and it’s just fill in the blank or do some calculation that they teach you how to do. It’s basically to show that you actually read the introductory pages to the experiment. They can ask you to define terms, or give the chemical hazards for the certain chemicals you’ll be using, and other basic things. All the answers are in the lab manual. Another part of the prep work is the viewing of online videos, which are quite helpful and very convenient. I find it important to be able to know exactly what your hands will be doing in the lab because constantly referring to your lab book is a waste of time.
I took about 2 – 3 hours to prepare for each experiment, which consisted of reading the lab manual for the experiment a few times (or enough so that I knew what I was going to be doing), watching the relevant videos online (see below), and doing any necessary prep work directly in the lab manual. Sometimes I wrote out my own procedure based on the lab manual so that it would be easier to follow.
For the Grignard reaction lab and the esterification lab (synthesis of an ester like amyl acetate), you might need to hand in an extra assignment that shows your understanding of the theory behind esterification. This is a difficult assignment because it is tricky and most people do not get high marks on it… so be careful and check with as many people as possible if you can. The terminology and the wording of the questions in particular need paying attention to.
In addition to the regular prep work, for the “Identification of Unknowns” lab (which is actually 3 lab sections long), you will need to submit a report. Thankfully, the criteria and format is all in the lab manual, so all you need to do is follow it very closely. Feel free to take a look at the one I wrote: Exp. 6: Separation and Identification of Unknown Compounds. Aside from getting a chunk of marks off because my two compounds were WRONG, I pretty much got 100% on this lab report.
As I said earlier, there are two exams near the end of the term, and both are before the official last day of school. The first is a practical exam, where you’ll be asked to set up apparatus to do an experiment. This may be anything from rotovap (easiest) to fractional distillation (hardest). You don’t know what you’ll be asked to do until the exam begins, so essentially you’ll have to prepare to be able to do all of them and only in a small amount of time (5 minutes?). However, it’s pretty straightforward and by this time in the term you’ll be hopefully quite familiar with the techniques. Do not forget the boiling chip. Do not forget the boiling chip. Do not forget the boiling chip. (A boiling chip is a small, uneven rock-like object that is used to make liquids boil “smoothly.”)
The second exam is the theoretical exam, which consists of true/false questions as well as short answer questions and is one hour long. The instructor gave us helpful tips to narrow down what the exam would be asking during the last lab session. The questions were fairly straightforward though, and similar to the quiz questions. If you want to narrow down your studying, make sure you focus on the learning objectives at the beginning of each section of the lab manual — you should be able to answer each of them. However, there is a lot of material, which makes it a memorization exam (sigh).
Do not forget the boiling chip if you need to use one. And if you forget, don’t add it to the flask if the liquid is already hot, otherwise it will overflow… you have to wait for it to cool down.
In extraction, remember to remove the top of the separatory funnel before you try to let liquid out. Otherwise, always try to keep your hand/fingers over the top of the flask to ensure that the lid doesn’t pop out and you lose all your sample. Finally, don’t overmix it or vigorously shake it at anytime, because some solvents can become ‘miscible’ because they emulsify or something like that, and then you won’t be able to extract anything… which is what happened to me.
Don’t leave things boiling on the hot plate… sadly this happens to a lot of people, and one time all the liquid in my flask evaporated because I was busy doing something else and forgot. It was just water though lol (thank goodness).
When you turn off the tap that is connected to the West condenser (or the vacuum), do it slowly so that if you find out you’re turning it the wrong way, you can just reverse the direction without any harm. Often, people turn it off too quickly but it turned out they turned the wrong way (ie. turned the water on even more) and this meant that water sprayed everywhere, glass being broken, samples being lost, etc.
The boiling chip. Don’t forget it. Even on practical exam day.
CHEM 235 is pretty straightforward — all the experiments are pretty much spelled out for you in the lab manual, so all you really need to do is read it a few times before the lab and then follow it religiously while using common sense in the lab. The lab TAs are generally helpful. The average for this course is about 70% and the highest mark across all sections in a given year is generally around 90%.
Lab goggles are mandatory, you can borrow them for $1 in the lab per session.
Lab coats are mandatory, make sure it is 100% cotton unless you want it to stick to your skin when it’s on fire. Buy this as soon as possible because they sell out fast – costs $30 at the bookstore. Discount bookstore might carry these too.
Lab manual can be purchased from the bookstore – costs $24.
The lab manual comes with CDs with the videos on them. However, they are all accessible online here: http://www2.chem.ubc.ca/courseware/235/index.html – see the bottom right of the page for the links to the videos. I recommend viewing them more than once, unless you watched them for a previous lab.
As always, please feel free to leave a comment or a question and I will answer it as best as I can and as soon as possible. If you ask a question and I reply to it, please reply back so that I know you read my response.