Skip to main content
Loading Explore guides…
Biophysical chemistry exam review · Acedra
Home
Explore
Chemistry
Biophysical chemistry exam review
Sign in to save
Chat
If YouTube asks you to sign in, open the video on YouTube.
Watch on YouTube
Reload player
Transcript
66 segments
Copy
Hide video
0:01
- I'm Jeff Yarger. I'm a professor of chemistry, biochemistry, and physics at Arizona State University. In the spring semester 2018 been teaching biophysical chemistry, BCH 341, at ASU, and this video is to look over midterm exam number three, which was a take home exam given to students. And to put some context of what this is mainly covering, the topic that this is primarily covering is in biological kind of biochemistry. It's mainly covering introduction to kinetics,
0:41
and electrochemistry.
0:48
Chemistry, or what we would call, most commonly, say like redox chemistry, reduction and oxidation reactions in chemistry, or chemistry of INs, et cetera. And then, you know, the thing about time. So we've, in the first couple exams, covered mainly areas in biological thermodynamics, and now we're moving on and looking at time scales through kinetics and re-looking at thermodynamics through its potentials through electrochemistry as well. Okay, and so, and this was basically
1:19
meant to be similar to a homework set. So a take home exam where they have
1:26
over a day to be able to complete this. Okay, so we won't go through the logistics except to say,
1:37
there were, they answer five questions that I put in a similar vein to what you would see on kind of online quizzes or multiple choice, et cetera, mainly just testing concepts, some simpler calculations or simpler graphing, things you should be able to do in more of a limited time format, and if you've been following the material in basic kinetics and electrochemistry. And then the last one's much more like homework problems, where they're really meant to be multiple step,
2:08
they could be solved in numerous different ways. There's different paths you can find to this solution, really meant to test problem solving and really getting a grasp of real world applications in kinetics and electrochemistry related to biochemistry or biological focused material.
2:28
And so what I'm, you know, these are made available so that the solutions are made available at biopchem.education.
2:44
And then there's a section for BCH341,
2:52
and under there there's a table, and under exams, and like I said, this is exam number three. And I've included the exam, a short set of solutions as well as a full set of solutions. So, what I mainly wanna do in this video is cover more conceptually some of 'em then exact working out, which I provided on the solution set. And this is, what we're looking at is a PDF version of what you can download directly from this website. So the first one you can see, the reactant concentration,
3:26
it's a first order reaction. So I immediately know, you know, it's not gonna be that because first order reaction its rate constant is an inverse seconds, right? So it has to be one of these four, but the rate constant's not negative. So that eliminates two, so I'm down to two before I even start. And I can tell, in fact, that the rate is gonna be significant 'cause it goes from 1.7 molar to .01 molar
3:55
in just a timeframe here of 50 seconds or so. So it's gonna have a fairly decent rate associated with it. Now, you can just do this as, it's gonna be related to the slope of if you take the log of the concentration over versus the time. So I can plot this, and I've done that here, and this is using Google Sheets to plot it. But obviously this is simple enough, since there's only two points, that you could just use, you know, you could just convert these to the LN
4:34
and you could just use Y2 minus Y1 over X2 minus X1 to get the slope as well. And the slope is minus,
4:45
you know, minus the rate constant.
4:49
Next one is just conceptual. We, you know, metallic groups, they're very commonly heme groups and stuff, et cetera. Metallic groups are very common used in biological systems as,
5:03
you know, to catalyze reactions. Proteins are classically enzymes. RNA, to less extent but can be. It's not that DNA can never,
5:15
is not ever known to act as an enzyme, but you would just say in fact they call them DNase enzymes to, there are groups that can, but you would say it's very rare we think of DNA as acting as a catalytic enzyme. So that's, you know, the best answer in this case. Or if, you know, the other one that would be acceptable, is in a sense, none of the above. It's amazing the number of things that can act enzymatically.
5:47
Okay, this is looking, we've looked at several times in this semester about decarboxylation reactions in different forms.
5:54
So this one is being enzymatically catalyzed, so,
6:01
and we're given a whole, so this is given as the table, and so this is enzyme kinetics, we're gonna use Michaelis-Menten enzyme kinetics. So in that we're gonna look at the inverse of the concentration, and we're gonna look at the inverse of its initial velocities as well, and we can plot those. And you know, where it's, you know, it's v max, its one over its v max is gonna be related to where it hits the x axis. And this is gonna, its slope is gonna
6:38
be related to the Michaelis-Menten constant, et cetera.
6:45
So, but we can also just get a sense for this. You know, it's asking what, these are its initial velocities. As you go higher in concentration it gets to be a higher velocity. So again, we can eliminate this one, because, you know, it would fall right here. I mean this is heading towards its maximum velocity. So it has to be over .1.
7:09
Now, so we can eliminate one right off the bat, and you can see, like you've gone up an order of magnitude in concentration, and from here to here, so you could even kind of guess that where this is heading to in this problem even without having to work it directly where I fit this line, get this, and extrapolate to here. And I report both of 'em in case you are asked for that as well.
7:36
Looking at this one it's looking at vitamin C, and we're given the potentials here. And so we can arrange these. This one,
7:48
this potential, and then we can,
7:52
you know, oppose that one. And so we can get the overall EMF of this. And this is kind of keeping in mind that when you, for example, multiply one of these by two or something that we don't end up multiplying the potential by that because it's already accounted for in the constant we use. So, so we don't multiply, but when you do change it, when you move the equation from reactants to products you do change the sign of this. And then we're gonna add these two together. Then we're gonna use that,
8:31
and then it's two electrons, the Faraday constant, adding these two together, which is gonna give the overall Delta G for this. And so we're gonna be able to calculate it.
8:45
In this one, like, we're looking at, again, a type of reaction. And we're gonna be able to look up, again, kind of the same thing, looking up basic electrochemistry looking up their potentials, and being able to combine those to give a combined potential for a specific reaction and then convert it to Delta G. So then once we have that in Delta G form we can tell, you know, when we add, so you know, the standard state's 84, and then we're gonna add this component on to it
9:22
where it's five times pyruvate and 100 times the concentration of this. So it's five here and 100 squared for this
9:34
because there's two. And so that's gonna add this additional component onto it. So after I knew this number right here I knew it would get bigger, so I knew I could eliminate that one and that one, how much bigger, you know, depends on right here. And so we have to do the final calculation to get the result.
9:58
Okay, looking at another biochemical reaction, redox reaction, again, you know, we have tables and these are at both biopchem.education as well as several places where you can look at the potentials, write each of the half reactions to give the full reaction, which were' gonna add these together. Again, when you reverse one of these you reverse the sign. But when you multiply, for example, fro two electrons to four we don't multiply here because it's already accounted for molar amounts,
10:32
and it's accounted for the number electrons in the voltage. Then once we have those voltage we can convert that to an energy using the number of electrons Faraday's constant in the EMF we get from this. And then from there we can convert it to an equilibrium constant. And as soon as we know that it's a positive, or a large negative Delta G we know it's gonna be a positive equilibrium constant, and because it's fairly largely negative it's gonna very largely positive.
11:03
And so that's gonna kind of eliminate a fair number of these and kind of get us down to just a couple even without doing the calculation to figure out what the final one is.
11:16
Okay, this was a homework problem where now we're looking at it at slightly different rates for these parallel reactions of how penicillin is changing with three parallel reactions. And the first thing it's asking for is the percent of each one of these products from these three parallel reactions. And again, I can just look at this right here. So you know, you know, if a slow rate, a faster rate, and an even faster rate. So I'm gonna make mostly, well these are about equal.
11:52
So we'll call this like, you know, 40, you know a little less than 40, 35. And you know, and then, you know less, right? Like basically this is gonna have the most in kind of the 40 some percent range, would be my guess. This is gonna be in the kid of high 40s. This'll be in the low 40s and this'll be in the teens. Just from the ratio of these, before I even calculate it, so I'm gonna take, you know, the amount of one of these, .07, times the sum of all three to give me the percent.
12:27
So once I calculate it and then the percent of two overall three and the percent of three. So (coughing) my initial, what I thought of, you know, as estimates, these are the exact values I calculate out.
12:44
Then after that it tells me what the temperature dependence is of starting with this first one right here. So starting with it at a specific temperature of 22. And now redoing that looking at how the rate changes at different temperatures, and as expected it's getting a larger rate, meaning it'll have a positive activation barrier. So now it's asking me to use the Arrhenius equation to calculate the activation barrier in pre-exponential factor. You'll see if you just plot the temperature
13:15
versus the rate constant it's not linear. I don't expect it to be. It should go exponentially. So I need to get this in a form, if I'm gonna fit this, it's much easier to fit to a linear form; however, you could fit this to an exponential if you prefer. Or put it in the, sometimes the easier thing to do is just to put it logarithmically. So logarithmically one over temperature, inverse temperature versus the logarithm. Now it's a line and I can fit that line to this equation.
13:47
I've also just blown up this component here to show you what that fit looks like. And (coughing) I've also used a linear fit function in Google. And you see that the equation is just a little different. In other words, the linear regression it used gave a little different values. So this'll vary a little bit depending on what you use as far as your linear regression algorithm. But you'll get in this kind of ballpark for the activation energy and pre-exponential constant.
14:19
And you can see the pre-exponentials where it hits right here. And the activation energy is related to the slope over, over r, so.
14:32
Okay, so we know the half life is 22,000 seconds.
14:38
And we're asking for not, when half of it's decomposed, but only 25% is decomposed. There's 75% left of the initial value. So if it takes 22,000 seconds for half of it and we're only looking for about a quarter of it, you know, this is gonna be on the order of 11,
14:58
you know, on the order of 11,000. Not exactly because this is not halving linearly. But that just gives me an estimate. I expect it to be somewhere on the order of 11,000 seconds-ish, you know? Plus or minus a few thousand. So that just helps me when I'm gonna actually work the problem. So I know, again, what the half life is, so that I can get a rate constant. And now I can look at it when there's 75% of the initial amount, with respect to that first order rate constant
15:28
and solve and I get an answer of 9,130.
15:33
Which is kind of what I was in the right ballpark. Again, like the point here is that it's often very helpful to just read the problem and have an intuitive guess, or kind of an approximation of what you expect the answer is, so that if you miss a sign or do something like miss a variable or just calculate something wrong and it gets way off. You'll say, oh let me go back and just make sure I didn't. The number one thing, you know, often people, myself included miss when I try to work a problem
16:03
is a sign or just one little input parameter wrong, which can change things drastically. And I think it's very important that we just have an intuition going in so that when our intuition is not met, we can either, a, try to conceptually understand the problem better, or b, go back and look and make sure we haven't made a silly mistake.
16:26
Okay, we looked at a parallel reaction. Now we're looking at a sequential one. So you must react A to form this intermediate first to then form products. And you'll see that this constant is eight times as fast as this one. (coughing) So if this one is .4 inverse seconds, KA is, then this one's eight times smaller. So it's .05. And so I, in a sense, I can already kind of estimate. Again, if I was looking at what these concentrations are, as a function of time, it's gonna start,
17:06
if we start with this being all here, you know, this is a first order rate constant. It's in inverse seconds. So it's gonna decay like that, you know. Because this, because this builds up slowly, eight times slower, it means you're gonna build this up. So if it was at the same rate it might do something like that and then the products come up. But this one's gonna build up high and then the products are gonna come like that. So I already have an estimate. And this'll build, if this was say,
17:39
now not eight times but say 100 times, you know, slower, then it would build up even more, right? And even faster, so that's kind of where I'm expecting this to look like. So I made, again, a Google Sheet, and so this is your intermediate, this is your initial A, and this is your products that are formed, and you can come in here and change these rates based on these equations it'll redo these ratios and re-plot this for you. And you can get a thing in exact time
18:09
and how any seconds, how fast A decays, how the products go up and how these intermediates change, et cetera. You can take a derivative to get this or you can just plot it based on knowing the equations here. And you can also just kind of drop a line here or blow it up and it's basically around six seconds is where you get a maximum in the amount of I. So if you made this, say if it was only twice (voice muffled) the maximum and I would stretch out, you know, much further, et cetera,
18:40
which is what our homework. It was just two times, KI was just two times that, and so it stretched out this way and decreased here.
18:54
Okay, this was another one based on homework where we're looking at a specific antiseptic and infected. One of the reasons it doesn't get used very much is because of its interactions with DNA. And we're looking at its dimerization rate. It gives several rates and we're asked to calculate. So,
19:16
this is another one where you can almost, just by knowing what the two rates are that the forward reaction is an order of magnitude faster than the dimerization back (coughing) kinetics. It gives you immediate since, you know, if you have a certain concentration of the monomer you're gonna have less of the dimer and so I have an expectation, and sure enough I do have less of the dimer and I can calculate the exact rate, et cetera, for this.
19:51
Then I'd given an equation that helps define how long it takes to get to equilibrium, in a sense a kinetic component to this, and it gives an intuition feel. So you calculate out a value for a rate, and if you inverse that you get about .21 microseconds.
20:13
And generally that's good enough for the answer. Generally, full relaxation is considered five times the rate constant, which is so full relaxation in about one microsecond. So, and basically the answer's correct here if you just get somewhere between .1 and one, you know, microsecond. You know, it's really about getting in the right order of magnitude ballpark for what the relaxation rate or how long it takes to get back to equilibrium for this system.
20:45
Okay, this is one out of Jim Allen's book, where he gave a small window of potential. I increased the window of potential and just asked for us to look for the midpoint, which often there are tables of values that show the midpoint for a bunch of very common biological redox reactions. (coughing) Which are very common in biochemistry to help define which one it could be. Again, you can just look at this and tell, like it drops through .5 right here, somewhere between 600 and 700,
21:20
more or less equally between these, so you're gonna get a value of about 650 millivolts, or .65. And if you look at the table in this book you'll see that there's only kind of one suggested protein in that range. So this is actually plotting it where you can see it falls here. And you can see where it falls through .5 is right there. So you know, 640, 650 millivolts.
21:48
And if you look at the table, that defines kind of a specific one in that table.
21:56
And then finally, one that I would call is just a very introductory question, but so critical that we're able to look at which is just, you know, an overall ionic strength. You know, almost every biological solution we work with, it's almost critical to understand what it's ionic strength is. And the ionic strength, or the amount of ions in solution, can often dictate how biological molecules, how they're activated, how they react, their kinetics, their thermodynamics, et cetera.
22:28
So, and you know it's critical, even though it's a fairly basic calculation to be able to do. And this is one that it meant to hopefully be a little more real world, in that looking at multiple different salts in kind of an interstitial fluid. (coughing) This can be considered more complicated if you remove the assumption that all of these are co-soluble at these molarities, which you'll actually find might not actually be a good assumption. But if we make the simple assumption
22:58
that all of these will go into solutions as ions, meaning, you know, magnesium chloride will completely dissociate into magnesium two plus and chlorine minus ions where there'll be twice as many chlorines, et cetera. And we do that for all of 'em. Then we can calculate. Now again, you can just look at this and say, you know, the ionic strength for, you know, any pair or any salt, like sodium chloride has to be at least the concentration of the combined salt itself.
23:29
And it can often be more, especially when it's dissociating into multiple moles of things. Or it has a lot of charge, right? Or that it's divalent, trivalently charged. So I can at least put a lower bound. There's 80, so another 20, so 100, 110 170.
23:49
You know, it has to be above 170 millimolar, you know? Kind of by definition, so. And given that a fair number of these are doubly charged, you know, magnesium, you know calcium sulfate is two minus, you know, et cetera. That indicates and, you know, some of 'em are gonna have multiple ions like chlorine, there'll be two for every one magnesium, et cetera, means this is probably gonna go up, you know, a factor of two as well, would be kinda my initial guess.
24:19
And sure enough, when you do the calculation that's your kind of gut estimate is bores out to be about true.
24:29
Instead of writing this all out as just the sum over each one of the cation and anions, and et cetera in this kind of long form I think it's always useful to do it kind of step by step for each one of the salts in solution just and then add them all together at the end, just 'cause that way if you make a mistake, too, it's pretty obvious when you look at it individually. So that gets us through the problems we did for the take home exam three and kind of some estimates and working through
25:02
some of the concepts and intuitions for the problems. I hope this video was helpful, and you find these type of general problems come up a lot in all sorts of applications in biochemistry. So hopefully the concepts will ring through when you're working a lot of different problems in both basic kinetics and redox, or electrochemistry and biological systems. Thank you.
Here to help you learn
Sign in to keep a private conversation with your course tutor.
Ask me anything about the material…
Sign in to chat