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  • ELIZABETH NOLAN: We're going to continue

  • where we left off last time.

  • So briefly I'll make a few points about initiation

  • of translation in prokaryotes.

  • And then where we're going to spend the bulk of the time

  • today is with a review of tRNAs and then discussing

  • the aminoacyl-tRNA synthetases, which

  • are the enzymes responsible for loading

  • amino acids onto the three prime end of the tRNA.

  • And these points are important because these process has

  • to happen in order for the amino acids

  • to be delivered to the ribosome, which

  • is where we'll go on Wednesday.

  • So the first questions are, how does initiation happen?

  • So how does this ribosome, 70S ribosome,

  • get assembled with the mRNA and initiator tRNA bound?

  • And then we're going to ask, how do we

  • get an aminoacyl-tRNA, such that the amino acids can

  • be delivered to the ribosome?

  • So first, for initiation in prokaryotes,

  • there's a few steps to this process.

  • We'll just look at these at a basically superficial level

  • of detail.

  • But recall that there are translation factors.

  • And during initiation, there are three initiation factors--

  • so IF 1, 2, and 3--

  • that are required to help assemble the 70S ribosome here.

  • So first in terms of initiation, what happens

  • is that the mRNA needs to bind to the 16S RNA of the 30S

  • subunit.

  • And so I point this out because at this stage in the process,

  • the 70S ribosome isn't assembled yet.

  • So we have the mRNA binding to the small subunit.

  • And this process requires initiation factor 3.

  • And effectively what happens is that the mRNA has

  • a region called the Shine-Dalgarno sequence

  • in prokaryotes, which is the site of ribosome binding.

  • And then upstream of that is a start codon

  • that signals for the start of translation.

  • So if we think about the mRNA of the five prime end,

  • and somewhere there's a sequence that

  • signals for ribosome binding.

  • OK, and then we have our start codon

  • that signals the start of translation.

  • OK.

  • And so this gets translated here.

  • OK, so this start codon pairs with initiator tRNA.

  • And this initiator tRNA is special.

  • One reason why it's special is because the amino acid attached

  • is an N-Formylmethionine OK.

  • So sometimes the initiator tRNA is called f-met tRNA f-met

  • as an abbreviation there.

  • So just as some overview here, what

  • we're seeing in this alignment is

  • a number of the ribosome binding sites,

  • or Shine-Dalgarno sequences in prokaryotes.

  • We have the start codon on that pairs with the initiator tRNA.

  • And here's a schematic depiction of what I've indicated here

  • on the board.

  • OK, so the mRNA binds to the 16S of the 30S subunit.

  • So the 70S is not assembled at this stage.

  • And IF3 is involved, as I said.

  • The Shine-Dalgarno sequence determines the start site.

  • And we determine the reading frame, as well.

  • So here is just an indicating translation of a polypeptide.

  • What happens after that?

  • So after that, it's necessary to assemble the 70S ribosome,

  • have the initiator tRNA in the P site,

  • and have the cell ready to go for translation.

  • And here's just one cartoon overview

  • that we'll use as a description of this process.

  • OK.

  • So what do we see?

  • We've talked about this step so far.

  • We see there's a role for initiation factor 1.

  • And in this cartoon, if we imagine the E site,

  • the P site, and the A site, what we see

  • is that IF1 is binding to the site of the ribosome.

  • And one way we can think about this

  • is that the initiator tRNA has to get to the P site.

  • And so that region is blocked to facilitate the initiator

  • tRNA getting to the P site.

  • OK, we see that initiator tRNA binding to the P site.

  • And this happens via formation of a ternary complex

  • with IF2 and GTP.

  • So initiation factor 2 hydrolyzes GTP.

  • There's an event that results in joining of the two subunits.

  • And there has to be dissociation of these initiation

  • factors for the ribosome to be ready to accept

  • its first aminoacyl-tRNA in the A site.

  • OK, so the outcome of this process

  • here is that we have an assembled 70S

  • ribosome with the initiator tRNA in the P site.

  • The A site is empty, so it can accommodate

  • an incoming aminoacyl-tRNA.

  • And the E site or exit site is also empty.

  • So that's the main take home for initiation.

  • And that's the extent to which we're

  • going to discuss it within this class.

  • So in order to get to the elongation cycle,

  • we need to get the aminoacyl-tRNA into the A site.

  • And that's going to require the help of EF-Tu, so elongation

  • factor Tu.

  • Before we discuss how elongation factor

  • Tu is going to help deliver that aminoacyl-tRNA,

  • we need to talk about how we get the aminoacyl-tRNA

  • in the first place.

  • So what is the tRNA structure, just as a review

  • to get everyone up to speed.

  • How are amino acid monomers attached to the tRNA?

  • And how is the correct amino acid attached?

  • So this is an aspect of fidelity,

  • which came up as a concept last week in lecture.

  • And so we'll look at the mechanism

  • of aminoacyl-tRNA synthetases to see

  • how is the correct amino acid attached,

  • and then what happens if the wrong amino acid is selected.

  • Are there mechanisms to correct that?

  • And if it's not corrected, what are the consequences here?

  • So moving forward with that, we're

  • going to focus on the tRNAs and addressing those questions.

  • So just as a review, so we can think

  • about tRNA secondary structure, which is often

  • described as cloverleaf.

  • So we have a five prime end.

  • The tRNA has several arms.

  • OK.

  • So we have a D arm.

  • This arm here has the anticodon that pairs

  • with the codon of the mRNA.

  • We have a variable arm, this arm here.

  • And we have this three prime end here,

  • where the amino acids get attached.

  • So this, in terms of base numbering,

  • we have C74, C75, A76 here.

  • OH.

  • This is often called the CCA acceptor stem.

  • And the amino acids are attached here.

  • I'm going to abbreviate amino acid

  • as AA via an ester linkage.

  • And these ester linkages are important for the chemistry

  • that happens in the ribosome.

  • OK.

  • So we can imagine just if we have abbreviating the tRNA

  • structure like this and if we think about the sugar of A76--

  • bless you.

  • OK.

  • We have one prime, two prime, three prime here.

  • This type of connectivity here.

  • And this is abbreviated throughout as amino acid tRNA,

  • aa in general terms, or the three-letter abbreviations,

  • like what we saw for f-met tRNA f-met with the initiator tRNA

  • here.

  • So here's a schematic of a tRNA secondary structure with a bit

  • more detail than what I show you on the board.

  • And something we need to keep in mind

  • is even though we often draw the tRNA in this cloverleaf type

  • depiction, it has tertiary structure.

  • And so it's very important to think about this structure

  • as we think about how the tRNAs enter the various sites

  • of the ribosome.

  • OK.

  • So this structure is L-shaped.

  • And I like this depiction here because regions

  • of the secondary structure are color

  • coded with the corresponding regions

  • of this tertiary structure here.

  • OK, so we see the shell shape of an L,

  • rather upside down here, where we have the CCA acceptor stem

  • over here and the anticodon arm and anticodon region down here.

  • So what is a consequence of this structure?

  • The tRNA is quite narrow.

  • So we're thinking about 20 to 25 Angstroms in width.

  • And if we think about this in the context of the ribosome

  • and the peptidyl transferase center,

  • 3 tRNAs need to fit into that catalytic center

  • during the elongation cycle.

  • So it makes sense that they're relatively narrow.

  • This allows three to fit there.

  • So as we think about the translation process

  • and also think about some of the translation factors,

  • we want to keep this type of structure in mind here.

  • Here's just another view of that,

  • with some additional descriptions

  • of the overall structure.

  • And this includes the numbering of the tRNA bases

  • within that structure here.

  • Just a point to make, this won't be a major focal point

  • in the course, but do keep in mind

  • that tRNA contains many post-transcriptionally modified

  • bases, so you'll see an example of that in problem set one.

  • Up to 25% of the bases can be modified.

  • Typically, we see about 5% to 20% of them modified here.

  • OK, you're not responsible for these structures,

  • these modified structures, in the context of this class.

  • So the key question for today is how

  • are amino acids attached to the tRNA, as shown here?

  • And in order for that to happen, there's

  • a family of enzymes called aminoacyl-tRNA synthetases,

  • or abbreviated aaRS.

  • OK, so this name tells you right away, synthetase,

  • that these enzymes use ATP.

  • And these enzymes catalyze the attachment

  • of amino acids to the three prime OH,

  • or sometimes two prime OH, of the tRNA here for that.

  • And so we're going to consider this overall reaction.

  • And then we're going to think about the reaction

  • mechanism and experiments that were done to give support

  • to the mechanism that we see.

  • So all aminoacyl-tRNA synthetases

  • require ATP and hydrolyze ATP to AMP and PPI.

  • And so they catalyze this overall reaction

  • where we have an amino acid monomer.

  • We have the tRNA that encodes this--

  • that is for this amino acid.

  • ATP to give us the aminoacyl-tRNA AMP and PPI.

  • So if the ATP is being hydrolyzed to AMP and PPI,

  • what phosphate is being attacked?

  • So we saw on Friday there's the alpha, beta,

  • and gamma phosphates of ATP.

  • OK, pardon?

  • AUDIENCE: Beta.

  • ELIZABETH NOLAN: Beta.

  • Any takers?

  • AUDIENCE: Alpha?

  • ELIZABETH NOLAN: Any takers?

  • Gamma?

  • Yeah, so it's alpha.

  • If you're getting AMP, it's attack at alpha.

  • If you're getting ADP, it's attack at gamma here.

  • OK, so P alpha is next door to the ribose of the nuc--

  • there.

  • Yeah.

  • OK.

  • So if we consider this overall reaction, how does it work?

  • Just before that, one other observation

  • I just want to point out, if we're

  • thinking about these enzymes and asking

  • what is it that they recognize of the tRNA,

  • so we have the anticodon.

  • And that goes in hand-in-hand with the identity

  • of the amino acid.

  • Just keep in mind that it's not just the anticodon.

  • So here we're seeing an example of an aminoacyl-tRNA synthetase

  • with its tRNA bound.

  • And we see that there's many contacts between the tRNA

  • and this enzyme here.

  • OK, so here we have the amino acid end, the anti-codon end,

  • and all throughout here.

  • So what is the mechanism to get us where we need to go?

  • We have our overall reaction that I'll put up on the board,

  • just to keep it straight as we move forward.

  • So amino acid plus ATP plus the tRNA for that amino acid.

  • Aminoacyl-tRNA synthetase to give us the aminoacyl-tRNA

  • plus AMP plus PPI.

  • So let's consider a mechanism.

  • This is going to be a two-step mechanism.

  • And so in the first step of this mechanism,

  • we have the amino acid plus ATP.

  • And we have formation of an OAMP intermediate.

  • Plus PPI here.

  • So this intermediate is called an amino adenylate.

  • Adenlyate because adenosine here.

  • And we need to think about why this intermediate might form.

  • Why would we propose this in a mechanism?

  • And then in step two--

  • we'll come back to that in a minute--

  • we can take our amino adenlyate, have our tRNA,

  • this is the three prime end here.

  • We can have attack with release of AMP.

  • OK, so here we have the ester linkage at the three prime end,

  • like what we see on that board here,

  • to give us our aminoacyl-tRNA.

  • OK, so we see in step one, there's

  • formation of this amino adenylade intermediate.

  • And in step two, there's transfer

  • of the amino acid monomer to the three prime end of the tRNA

  • here.

  • So why might these enzymes go through that OAMP intermediate?

  • What needs to happen for this chemistry to occur?

  • AUDIENCE: You need a more activated reading group

  • to have that acyl substitution form an ester

  • from a carboxylate.

  • ELIZABETH NOLAN: Right.

  • We need to activate the CO2H group there.

  • So this affords that.

  • So what might be another possible mechanism, right?

  • Imagine you're the experimentalist

  • and you've combined your eighth amino acid ATP

  • tRNA and this enzyme you've isolated in a test tube.

  • And you see you've got this as a product.

  • And this as a product.

  • And you're wondering how did we get from reactants to products?

  • This is one possibility.

  • Maybe there's also a possibility of a concerted mechanism

  • where there's no intermediate like the one I'm showing you

  • here.

  • These are just things to keep in mind

  • when thinking about reactions.

  • This two-step mechanism is the accepted mechanism

  • for the amino aceyl tRNA synthetases.

  • And so what we're going to think about

  • are what are the experiments that were done

  • to support this mechanism here.

  • So what are the things we need to think about?

  • And so we're going to think about this

  • by examining one aminoacyl-tRNA synthetase as a paradigm.

  • And this is the one for a isoleucine here.

  • OK, so what are the experiments that

  • need to be done to characterize this reaction

  • and determine mechanism?

  • OK.

  • So one thing we need to confirm is reaction stoichiometry.

  • So there's a stoichiometry up in what I've written above.

  • But experimentally, that needs to be determined.

  • So one, reaction stoichiometry.

  • And so how can we think about this?

  • We can think about the equivalence of the amino acid.

  • So in this case, isoleucine.

  • How many equivalents of isoleucine?

  • And presumably, this isoleucine binds to the enzymes.

  • We can think about it of equivalence

  • of isoleucine bound.

  • And we also see that ATP is consumed, right?

  • That's hydrolyzed to AMP and PPI.

  • So how many equivalents of ATP are consumed in this reaction?

  • What else do we want to know?

  • We need to know something about kinetics.

  • So what are rates of formation?

  • What is the rate of formation of the product,

  • the aminoacyl-tRNA, and since I've

  • told you this intermediate forms,

  • what is the rate of formation of the intermediate?

  • And since this is an intermediate,

  • it's something transient.

  • So we need to think about how are we as experimentalists

  • going to detect this intermediate over the course

  • of this reaction.

  • It forms and decays in order to get product here.

  • So rates of formation.

  • And so we have formation of our product, which in this case--

  • and then formation of the intermediate, which

  • I'll just abbreviate Ile-AMP.

  • And what else would we like to know?

  • We can figure out how, in addition

  • to rate of formation of the product and the intermediate,

  • we can think about the rate of transfer of Ile

  • from the intermediate to the tRNA.

  • So what this tells us is that we need

  • a way to look for or detect the intermediate.

  • Here.

  • So imagine let's just have a hypothetical situation.

  • If we find the intermediate, that tells us

  • something about the reaction.

  • If we don't find the intermediate,

  • what can we conclude?

  • Pardon?

  • AUDIENCE: That there was no intermediate?

  • ELIZABETH NOLAN: So that's one possibility.

  • Are there other possibilities if our method doesn't

  • let us detect the intermediate?

  • AUDIENCE: Second step is to test.

  • ELIZABETH NOLAN: Can it be hard to detect an intermediate?

  • It can be very hard, right?

  • So they don't always--

  • there aren't around all the time very much

  • or in very abundant quantities.

  • So if it's not detected, could it be there?

  • Yeah, it might be there.

  • And the method just didn't allow for it to be seen.

  • So you always need to keep that possibility in mind.

  • This will be a case where there is

  • a robust method that allows us to detect

  • this type of intermediate.

  • But always keep that in mind.

  • OK, so first thinking about reaction stoichiometry.

  • We're not going to go over the experiments that

  • were done to define this.

  • I'll just tell you some facts that result

  • from some experimental studies.

  • So this isoleucine aminoacyl-tRNA synthetase

  • binds 1 equivalent of isoleucine as indicated

  • in the overall reaction.

  • And it consumes one equivalent of ATP,

  • also as shown in this overall reaction,

  • to make one equivalent of the aminoacyl-tRNA.

  • OK and these stoichiometries were determined experimentally.

  • So now we need to think about points two and three

  • to characterize the reaction kinetics.

  • So what experiments were done?

  • So there are several different sets

  • of experiments, some of which we're familiar

  • with from 7.05 or 5.07 and others that will be new

  • and presented in more detail in recitation this week

  • and next week.

  • So we can imagine doing steady state kinetic experiments,

  • as well as pre-steady state kinetic experiments.

  • And the general aims here are, one,

  • to determine the rate of aminoacyl-tRNA formation,

  • to determine the rate of amino adenylate formation,

  • so this intermediate-- and again, we

  • need a method to detect the intermediate.

  • And at the end of the day, we'd like

  • to know what is the rate determining step.

  • So a method that is commonly employed

  • for these types of studies involves

  • the use of radioactivity.

  • And we'll just go over a few points about radioactivity now

  • to help with understanding these experiments.

  • And you'll hear more about this method in recitation this week.

  • So the experiments I'm going to tell you about

  • are going to involve the use of radio isotopes like C14, P32.

  • And the question is, why do we like

  • to use radio isotopes in biochemical experiments?

  • And they're really excellent probes.

  • It's the bottom line.

  • And one reason for that is that if you can use a radio isotope

  • like C14 or P32, it's introducing

  • minimal perturbation into your system.

  • So you're not needing to attach a fluorophore whether it be

  • a small molecule or a protein.

  • You're not modifying the structure

  • of a component of your system.

  • So the overall size and the chemical properties

  • are maintained when you use different isotopes

  • of the same element.

  • And some of the ones we'll see today

  • are, for instance, C14 labeled isoleucine, P32 labeled ATP.

  • They have the same chemical properties

  • as the unlabeled forms, and same size.

  • The other point to make is that we

  • can detect very small amounts of radioactivity in a sample.

  • And you'll see some of those calculations

  • and how to do them in recitation this week.

  • So we can detect small amounts, and that's

  • good for looking for something like an intermediate.

  • And there's readily available techniques

  • for quantifying radioactivity in a sample.

  • So if you see nomenclature like this,

  • the NX nomenclature indicates the radioisotope

  • in this sample.

  • And I'll just say in passing here,

  • we all know the isotopes are atoms

  • bearing the same number of protons but different numbers

  • of neutrons.

  • And radioactive isotopes have an unstable nucleus,

  • which means there's a radioactive decay.

  • And typically-- well, we often use beta emitters

  • in biochemical studies.

  • And that's what you'll see today.

  • So what are some of the experiments?

  • We're first going to consider looking at the steady state

  • kinetics to ask what do we learn in the steady state.

  • So from our steady state experiments,

  • we're able to get our Kcat and our Km

  • and the catalytic efficiency, which is the Kcat over Km.

  • We're going to compare our Kcat values or turnover today.

  • So experiment one is to monitor formation of product.

  • So how is this done?

  • This reaction is done by taking C14 labeled

  • isoleucine and unlabeled tRNA and watching

  • for transfer of that radio label to the tRNA.

  • And so what comes from these studies

  • is a Kcat on the order of 1.4 per second.

  • And now we have a way to detect this amino adenylate

  • intermediate.

  • And we'll talk about that assay in a minute,

  • after we get through this comparison.

  • We do a steady state experiment to monitor

  • formation of this amino adenylate intermediate.

  • And this assay also uses radioactivity.

  • And it's called ATP PPI exchange assay.

  • And we'll go over how this works in a minute.

  • So the results of these experiments

  • give a Kcat on the order of 80 per second.

  • So what does this comparison tell you?

  • These values are quite different, correct?

  • So we're seeing that this ATP PPI exchange assay

  • is telling us that ATP PPI exchange, which

  • is a measure of formation of this intermediate,

  • is about 60-fold faster than formation of product here.

  • That's an important observation to have.

  • So how are we going to figure this out?

  • How are we going to see this intermediate?

  • That's the question we need to ask next.

  • And so we need to go over this ATP PPI exchange assay.

  • And this is an assay that will come up again in module 4

  • when we talk about the biosynthesis

  • of non-ribosomal peptides.

  • So we'll return to this type of assay and data many times.

  • So the question is, if we have this reaction, OK,

  • how do we detect this?

  • OK, it's not so easy.

  • And we need an assay.

  • And this is some of the background

  • towards the development of this assay.

  • So we need to suppose that our amino acid and ATP react

  • with the aminoacyl-tRNA synthetase

  • in the absence of tRNA.

  • And that's indicated by step one, more or less.

  • But that doesn't show it experimentally.

  • So in the absence of tRNA, this amino acid and ATP

  • react with the enzyme and they form the aminoacyl AMP

  • intermediate and PPI.

  • And they do this reversibly.

  • OK, so the reversibility of this reaction

  • is key for ATP PPI exchange to work.

  • So if this occurs and they do this reversibly,

  • therefore we can deduce formation of the aminoacyl AMP.

  • If we add radio labeled PPI, the amino acid, and ATP

  • to the enzyme and we see that radio labeled phosphorus

  • from the radio labeled PPI incorporate into ATP.

  • That's only going to happen if this chemistry is reversible.

  • And bear in mind, we can detect very small quantities

  • with radioactivity.

  • So it's not that it has to be reversible

  • to some large degree.

  • We're relying on the detection of this radio label.

  • So how does this work chemically?

  • Let's take a look.

  • OK, so imagine here we have our ATP.

  • We have our amino acid.

  • And we have our enzyme.

  • And step one, we have binding.

  • So there's some ATP binding site to the enzyme and some site

  • for the amino acid to bind.

  • And I'm leaving magnesium out of this depiction,

  • but remember that magnesium and ATP come together.

  • Now what?

  • Step two, OK, we're going to have

  • a chemical step where we have formation

  • of the amino adenylate and PPI.

  • And they currently are bound to the enzyme.

  • We have step three.

  • So imagine in this step our PPI is released.

  • And this is another key aspect of this assay.

  • So what does this mean?

  • We now need to think about going backwards.

  • If the PPI is released and we spike this reaction with radio

  • labeled PPI and work our way backwards,

  • will the radio label end up here in the ATP?

  • OK.

  • So this is going to be going backwards.

  • We've left off with this enzyme with the amino adenylate bound.

  • We have the PPI that was released.

  • And then we spike this reaction with our radio labeled

  • or hot PPI.

  • So then what happens?

  • Step four, working backwards.

  • Imagine that some of the radio labeled PPI binds.

  • Then what?

  • Working backwards another step.

  • 32 P ATP and the amino acid.

  • And then we have release here.

  • OK, so then the question is, can you detect this?

  • And so if you can detect some incorporation of this radio

  • label into the ATP, that indicates

  • that this enzyme worked through that type of intermediate.

  • AUDIENCE: So are PPI not also sometimes

  • [INAUDIBLE] and then if you had some competing hypothesis where

  • it made ATP and ADP, then your PPI would maybe sometimes

  • turn into just a single radio label

  • phosphate that could then have the same reverse reactions

  • as the [INAUDIBLE]?

  • ELIZABETH NOLAN: Yeah.

  • So whether you initially end up with PPI or PI

  • is going to depend on how the ATP is hydrolyzed.

  • And so you could imagine maybe there

  • could be some background ATP hydrolysis

  • that gives ADP and PI in this type of assay.

  • That's something you always need to look out for.

  • For the purpose of this, let's assume

  • that we're not having some background problem in terms

  • of the ATP source, and also that the enzyme is specific in terms

  • of what it's doing to the ATP.

  • But yeah, certainly background ATP hydrolysis

  • can be a problem.

  • So how will this be detected?

  • And how will you know the radio label is associated with ATP

  • and not something else in your mixture?

  • AUDIENCE: [INAUDIBLE]

  • ELIZABETH NOLAN: Pardon?

  • AUDIENCE: [INAUDIBLE]

  • ELIZABETH NOLAN: No.

  • So we're going to look at the radioactivity.

  • So this will come up more in recitation this week.

  • But we need to be able to measure radioactivity by, say,

  • scintillation counting here.

  • But what's also needed is a separation

  • because you need to know where that signal's coming from.

  • You need to know it's coming from ATP

  • and, say, not a background from however much of the PPI

  • you introduced.

  • Or if you have no idea what's going on with your chemistry,

  • maybe the data are going to tell you it's not this mechanism.

  • So you need to have a separation.

  • So how might you separate ATP from all

  • of these other components?

  • AUDIENCE: Based on affinity column.

  • ELIZABETH NOLAN: Some affinity column.

  • So I like the column.

  • But we're not going to have some sort of tag on the ATP.

  • That might be a problem for that enzyme.

  • But your notion is correct in the sense

  • that we'll use some sort of chromatography

  • in order to separate.

  • OK, so maybe HPLC, how many of you

  • have used an HPLC or at least know what one is?

  • AUDIENCE: [INAUDIBLE].

  • ELIZABETH NOLAN: Right.

  • So typically looking at UV vis.

  • But you can imagine hooking up an HPLC to a detector that

  • allows you to do scintillation counting and some sort

  • of column that will allow you to look for ATP.

  • Is all of the ATP going to be radioactive in this assay?

  • No.

  • So again, we can detect small quantities.

  • And as long as there's a little bit of reversibility,

  • we can see this here.

  • OK, so what's critical in this assay

  • is the reversibility of steps 3 and 4.

  • What would happen in this assay if the PPI is not released?

  • AUDIENCE: [INAUDIBLE].

  • ELIZABETH NOLAN: Right.

  • Under the conditions, or if for some reason

  • the PPI is not released, we're not

  • going to see this exchange reaction.

  • We're going to have a readout that doesn't give us this.

  • Does that mean this didn't form?

  • No.

  • OK, so there's many caveats and details

  • that you need to think through when thinking about a reaction

  • and then the experiment is done to test this.

  • So in the case of these aminoacyl-tRNA synthetases,

  • these ATP PPI exchange assays work well.

  • And these assays can be used to get steady state kinetic

  • parameters, to get Kcat, Km, Kcat over Km, which

  • is where this type of value comes from, in this case here.

  • So back to these analyses up here, what they're telling us

  • is that formation of this amino adenylate intermediate

  • is about 60-fold faster than formation of the product.

  • OK.

  • And what we all want to recall when

  • thinking about steady state experiments

  • is that they're set up with a great excess of substrate

  • and with the enzyme concentration.

  • The reaction is zero order in respect to substrate.

  • And you'll have some additional notes

  • about that in your recitation materials this week for review.

  • So something else biochemists like

  • to do when looking at reactions and understanding reaction

  • mechanisms is to look in the pre-steady state.

  • And this came up briefly in lecture 1 as a method.

  • And again, you'll hear more about it

  • in recitation over the next two weeks.

  • In these experiments, the goal is

  • to look at the very first, early moments of a reaction.

  • And they're set up quite differently.

  • So limiting substrate is used.

  • There's no turnover, so huge contrast

  • to what we know about steady state experiments.

  • And one of the goals is to look at the formation

  • and consumption of intermediates here.

  • So this type of chemistry often happens on a fast timescale.

  • You can imagine millisecond timescale here,

  • which means that we need a special apparatus that has fast

  • mixing capabilities, because there's no way for one of us

  • to do this on our own with our pipette.

  • And so the type of experiment or apparatus

  • used is called a stop flow.

  • And I just show one depiction of a stop flow apparatus here.

  • You'll get some other variations on this theme in the recitation

  • notes.

  • OK, but effectively what happens is

  • that you have two drive syringes, a and b,

  • and each of these syringes will contain certain components

  • of your reaction.

  • And this stop flow has a drive motor and a stop syringe.

  • And it effectively allows you to rapidly mix

  • the components of these syringes in a mixer, shown here.

  • And then you either have some way to detect product--

  • so maybe if you can use optical absorption,

  • you have a UV vis detector or a fluorescence detector.

  • Or in other cases what you'll do is

  • you'll punch the reaction at a certain time point.

  • So you need a third syringe not shown here with a quencher.

  • So you can imagine if you're working with an enzyme,

  • maybe you quench by addition of acid or base, something

  • that will denature and precipitate that enzyme.

  • And then you can take that sample

  • and analyze it in some way that fits in terms of what

  • you need to detect there.

  • So this type of methodology was used in order

  • to monitor transfer of isoleucine to its tRNA.

  • And so where we'll pick up in lecture on Wednesday

  • is the design of that experiment in terms of what will we

  • put in each syringe, and then what

  • are the results of those experiments?

  • And ultimately, what does that tell us about rates of transfer

  • here?

  • That's where we'll continue.

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