Download Monday 10-1 Lecture 1 Q: Thanks for podcasting How can one not

Monday 10-1 Lecture 1
Q: Thanks for podcasting
How can one not? But they are usually delayed by a day while I make sure they are OK
for prime time
Q: Is there anything on the study list that we didn't get to in lecture?
Eventually we will. If we don’t cover something in lecture, it will be removed from the
study list in good time.
Q: Professor you spelled "aging" wrong
Thanks. Any help you can offer in this department is appreciated. I am a houreefic
spellar
Q: How does God play into all this?
In science the challenge is to explain as much as possible with testable, mechanistic
models, that is, using only naturalistic explanations. And looking at the history of
knowledge and technology, it is fair to say far so good: we have incredible medicines,
integrated circuits, string theory, molecular biology, thermodynamics, and best of all,
iPhones. But it is important to realize that science is powerful because it limits itself to
the subset of knowledge that is accessible by hypothesis testing and experimentation. I
believe in many things. I gain a sense of awe, humility and the feeling of being part of
something much bigger than myself when I embrace the idea that hypothesis-driven
experimental science can and will continue to tell us a great deal about the nature of the
universe. But maybe not everything…
Q: Discussions begin Monday Oct 8?
Yes, they do. Although I am right now stranded in JFK airport in New York, and it is
Sunday Oct 7, the sections will start as promised, and I will email you all what they are.
Back home (after getting a friend to pick me up at LAX at 10pm on Sunday….), and the
sections are listed on the course website, http://courses.ucsd.edu/rhampton/bibc102/
Q: What kind of research do u do?
I study what is called protein quality control, by which cells detect and degrade
misfolded and damaged proteins. It is multo bosso
Q: Will there be class the night before thanksgiving break?
I am attempting to develop some alternatives. I will keep you posted.
Q: Your lectures are hella ratchet brah
I think that means I swear too much. I will try to do less of that.
Q: Are we required to memorize all the amino acid structures
No, but you should be able to recognize them. There is a big difference between
recognizing a structure that has been shown to you and drawing one on a blank page.
Although there there might be “tricky” ways to make it difficult for people to recognize a
structure (like adding an extra –CH2- to the lysine (K) chain, or making proline with a
four membered ring), I can promise you I will NEVER do such things. I am not about
TRICKY test questions. Hate that. But knowing the amino acid one letter code, and
being able to recognize the amino acid structures when they are placed in front of you is
very (very) useful. Some are a little tricky by themselves. Like aspartate and glutamate,
which have on –CH2- different from each other, but c’est la biologie…
Q: I can't see the number on the board
The Text Question Number is: 858 914 4945
Q: What do you think of aspartame?
I think Splenda tastes better. Aspartame is a dipeptide, which is sort of cool that is it so
sweet, but it does have methanol esterified to the C-terminus…On the other hand,
Splenda has chorine atoms sigma bonded to carbon, like you see in some pesticides…
Q: Would the covalent bond between Rs influence their functions or not?
I am not sure what you mean by this. In a very few cases, -SH groups form a covalent
bond to each other on different cysteines, and this can be very important.
Q: Why [is] histidine considered positively charged? While it was not "charged"?
His (H) has a pKa (about 6) that makes it an in betweener, easily able to pick up an H+
or let it go. We will see the use of this in the catalytic triad of chymostrypsin.
Q: Can you go over the grading before lecture is over?
I will go over the grading before the midterm. It will all be clear.
Q: Will we be emphasizing particular protein structures more than others? For example
primary vs. Secondary alpha helix?
These things we are mentioning are part of the basic vocabulary of proteins. We won’t
be emphasizing protein structure much at all.
Q: Where can we get the soft reserves?
Q: Where do we buy packets for soft reserves? Online or bookstore
In the Old Student Center, or Student Center A, near Porter’s Pub, also near the
General Store (with all the records and young people in skinny jeans), also near Hi Thai.
Q: what is an isozyme?
Nice! An isozyme is an alternate version of an enzyme encoded by a distinct gene. For
example, there are four versions of hexokinase in humans; each is encoded by a
different gene. They are all isozymes of each other, and thus humans encode four
isozymes of hexokinase. They have different catalytic properties, and are expressed in
different tissues.
Q: Would you be willing to go over photosynthesis in you oh's? Im curious about algae
and biofuels.
I would be happy to talk about PS to you in office hours, especially right after an exam
when no one will be at office hours. Also, if you are interested, there is an enormous
amount of information about photosynthesis on the Internet.
Q: Can u go over cofactor again?
This question always comes up early in the class, and always dissipates by a few
lectures because we use if so often that you will learn it by context. But just to be fair, a
cofactor is a molecule or an ion that is associated with a protein that allows it to function.
A beautiful example of a cofactor is the heme group, with a chelated iron, that is
attached to hemoglobin or myoglobin and allows those proteins to bind oxygen.
Q: The date nd time of the final for bibc 102 is diff on the syllabus and tritonlink. Which
one is correct?
Q: Hello! On your syllabus, the final is listed on Dec, 14th, friday from 3-6pm. But
tritonlink said the final is on Thurs, Dec 13th. Which one is true?
FINAL is on THURSDAY DEC 13 at 7PM. Sorry about the confusion.
Wednesday 10-3 Lecture 2
Q: AS ran out of lecture slides. What's up with that?
On it! I now believe they have reprinted them.
Q: Can you do lecture even later on Tuesday so everyone can make it?
That is one alternative I am investigating. You need to understand that it is HARD,
harder than quantumelectrodynamics in ancient Latin, to get a room at UCSD. But I am
tryin’!!
Q: Hey awesome professor! Could you add a section at night like for example after
lecture? Some of us work during the day and can't make it to any of the current ones
That is an interesting idea. About me being Awe-SOME! Just kidding, a night section is
an interesting idea. I will look into it. But see above about rooms…
Q: For the people that can't make the Wednesday before thanksgiving, can't they just
podcast the lecture instead of rescheduling it?
They could indeed, but the ineffable power of the human-to-human learning experience
must be respected as well. We will figure out a solution amenable to all.
Q: is the sigmodial shape of the haemoglobin curve caused by allosteric effects
It is indeed. Stay tuned…
Q: Can you please talk a bit slower?
IwilltryashardasIcan
Q: If hoeger is Walter, would you be Jesse?
For that to be true, I, Randy Pinkman, would have to to wear more oversized hoodies
with lots of skulls and other rock imagery. As Pinkman might say, “this class is BIBC to
the 1 to the 0 to the 2 yo!” But in fact, I believe that Dr. Hoeger is younger than I am.
Q: How did u get kdd for c1e^-Add/C2?
HA! I am so glad you asked this. My handwriting makes that look like kdd, but it is kold.
meaning the rate constant k before the quantity d was subtracted from Ea. knew = kold
x e^d/C2
Q: Enzymes doesn't change equilibrium? Why
The equilibrium is determined by the free energy change between reactants (substrates)
and products. Catalysts including enzymes only change the activation energy of a
reaction, that is, the path that gets the system from substrate to product. This is from
first year chemistry, and review might be useful
Q: Did you have tequila shots on your borthday?
Not for many years... This birthday I went for a long run, and ate some delicious
angelfood cake. Tequila shots: that is your job, my young friends…
Q: can you explain covalent intermediates again?
A covalent intermediate is one of the cases observed in enzyme catalysis, in which the
substrate, or part of it, is transiently made part of the enzyme by covalent attachment. It
is one way an enzyme can create a faster path (lower activation energy) to get to
product. A beautiful example of this is demonstrated in chymostrypsin.
Q: Pizza after the final for real?!?! Movie night?
Well, no movies, but definitely Pizza. Last year we an enterprising TA and I had to
“borrow” a table from a classroom and put the 30 boxes or so out on the plaza, where
many hungry passers by also partook… hopefully we converted some new Metabolites
to our path…
Q: When u say enzymes change the tendency but not the rate of the rxn, does that
mean that the likelihood of the rxn happening does not change? And that the rxn does
not happen more or less often?
I don’t think that is exactly what I said. But what I meant to say, was that enzymes do
not change the degree to which a reaction will go to the right, but only the rate of that
reaction happening.
Q: Where can we find the ligand binding and enzyme catalysis readings?
On the class website. http://courses.ucsd.edu/rhampton/bibc102/ look at readings.
Q: Do the problem sets correspond to a certain number of lectures we cover?
The ones on line do not, they span a number of lectures, but they are in order. However,
I am going to write a second set that does correspond to lectures, just to give that many
more.
Q: Induced fit or lock and key model for ligand binding to substrate?
(I think you mean for substrate binding to enzyme, or ligand binding to protein).
Both can happen. Lock and key implies that the binding site exists independent of the
ligand being present, and this is often the case. Induced fit (as we will talk about in
class) happens when the ligand causes the structure of the enzyme to change to make
a better binding site for the substrate or some other substrate.
Q: What is the difference between binding isotherm and rectangular hyperbola? Thanks
The binding isotherms, and the rate isotherms for that matter, are both specific
examples of the very general graph called a rectangular hyperbola.
Q: What does the double dag in DG double dagger mean?
It is just an accepted way to designate DG of activation, or the activation energy (I cant
type a delta on the whole-class-emails I send out, so D). It is useful because the DG of
a reaction is distinct from the activation energy, but both are designated by a change in
free energy.. that is, a DG.
Q: Can you explain saturability again
Q: What do you mean by saturable?
Q: Can u explain saturable again?
Saturability refers to a system with a finite number of binding sites, that can be
completely filled. An auditorium with a set number of seats will be saturated when all the
seat are filled, a bank will be saturated with all the tellers always have customers. A
binding protein in solution will be saturated when all of the binding sites are occupied.
An enzyme rate will be saturated with every enzyme is always processing a substrate,
and thus the rate is as high as it can be.
Q: Does the curve with the high k eventually meet with the curve with the low k at the
plateau (when all available proteins are bound to a substrate?
If the binding curve is graphed as fraction of maximal binding (from o to 100 percent)
then yes. If the actual concentration of binding sites is included in the graph, then it
depends on the details of the experiment.
Q: What does V stand for?
It is the rate of the enzyme reaction, usually in concentration/time units. Vo is the initial
rate of an enzyme reaction measured experimentally, RIGHT when all the components
are added, before the enzyme has had a chance to chew up the substrate and before
product has had a chance to build up. Vmax is the maximal rate of the enzyme reaction
being measured as one approaches… ready… saturation.
Q: In a high affinity rxn, is Km very low?
Well, when we are talking about affinity only, we are talking about binding and not
enzyme action, so I think you mean “in a high affinity reaction, is Kd very low?” and the
answer is yes. Meaning, a very low concentrations of ligand, occupancy of the binding
sites is high. In fact, 50% saturation occurs when the ligand concentration equals the
Kd. So the lower the Kd, the lower the concentration of ligand needed to attain 50%
saturation.
Enzymes, because they have the same form of equations, act the same way.
When Km is low, low amounts of substrate are needed to saturate the enzyme. And
when substrate concentration equals Kd, the enzyme is operating at 50% maximal rate,
or ½ saturation.
Q: So rate of change is equal in both directions
The rate enhancement is the same in both directions. And we derived a little equation
showing this. When the activation energy is dropped by d, the rate increases by e to the
d/C2. And that goes for either the forward reaction actvation energy, or the reverser
reaction activation energy.
Q: Should we memorize these equations or will you give them to us?
You should know the Michealis Menton equation. That is absolutely fundamental. The
fancy rate equations you do not need to memorize, but you should know that that whole
things is telling us.
Q: Whose claim to the Iron Throne do you support
I am fan (for obvious reasons) of Tyrion. But I would love to see Arrya gain the thrown.
However, I imagine that She (or he) who has the dragons will win. Bigtime.
Q: You wanna know how you know someone has an iPhone? They tell you.
That is funny, and sadly, somewhat true. In fairness to me, I had just gotten mine, and it
had accidently arrived on the actual day of my birthday. So give a prof a break, yo.
Q: What changes the dissociation constant? Temperature?
Temperature can, so can conditions of the reaction such as ionic strength, pH, etc.
Q: Does catalase exist naturally? Or is it synthetically engineered?
It is a natural enzyme. That is a most fancy question. The weird thing about catalyse is
that simple copper ion can perform its reaction, so one could create a catalase by
appropriate artificial chelators of copper ion. But the enzyme is encoded by a gene, and
there are serveral distinct versions.
Q: Whats the difference between a substrate and a ligand
A ligand is a molecule that binds to a binding site, and nothing happens to its molecular
structure. Drugs that bind to receptors, and neurotransmitters are great examples of
ligands. Substrates are the reactants in an enzyme reaction. As the idea implies, they
are converted by the enzyme into something else through chemistry. So a substrate
may think it is a ligand, in for a moment it is because it binds to the enzyme, but then…
WATCH OUT!
Q: When talking about binding isotherm we call it the protein and the molecule that
binds to it a ligand.. And for an enzyme its a substrate?
Exactamundo. The binding isotherm describes the relationship between the degree of
binding sites occupied and the concentration of ligand in an experiment, and an enzyme
rate isotherm describes the rate of the enzyme’s conversion of substrate into product
and the concentraton of substrate in an experiment
Q: What's an example of a suicide enzyme
Well, I believe you mean what is an example of a suicide substrate. These are
molecules that are treated as substrates by an enzyme and because of the chemistry
that happens to these “trick” substrates, they attack the enzyme and ruin its active site.
A famous case is the nerve gas Sarin used in WWI (1914-1917). It is processed as a
substrate by enzyme acetylcholinesterase (AchE), which deactivates the
neurotransmitter acetylcholine, but the IPFP locks onto the enzyme and renders it
inactive. Bad. A more tame version of the same kind of inhibition can be found in the
insecticide malathion, which performs a catalysis-activated destruction of insect AchE,
which is very bad for insects.
Q: We have problem sets?
You have the old set that I recommend using, and new ones I will post each week. The
old ones are longer thought problems and the new ones will be shorter and directly
correspond to the weeks as they go (zooming) by.
Q: So you said chymotrypsin is a protein that cuts protein? What's the diff between
protease and protein?
A protein is ANY sequence of amino acids linked together in a polypeptide chain and
(usually) in a folded functional structure. A protease is on specific type of protein, an
class of enzymes that cut other proteins. BAM!
Q: What's the difference between chymotrypsin and trypsin
Q: What's the difference between chymotrypsin and trypsin
Chymostrypsin and trypsin are both serine proteases that use the serine-based catalytic
triad (like we talked about in detail for chymotrypsin) to cleave proteins at specific sites.
Chymotrypsin cuts proteins at bulky, greasy aromatic residues, resulting in new Cterminus at the bulky residue, while chymotrypsin cuts at positively charged (R or K)
residues. It might be fun to imagine what you would need to do to chymotrypsin to
convert it into trypsin…
Q: How can we recognize peptide bonds?
A peptide bond is an amide bond between two amino acids. If you have not had that in
chemistry yet, it is the covalent bond formed by removing H2O from an amine and a
carboxylic acid. –NH2 + HOOC yields –NH-CO- plus H2O
Q: What's the superscript number above the amino acids
OH good! Glad you asked. It is the position of that amino acid along the polypeptide
chain. Notice that the catalytic triad residues are very near each other in the three
dimensional folded chymotrypsin active site, but are actually distant along the linear
polypeptide chain. THAT is the power of folding and shape.
Q: How much of chymotrypsin rxn do u want us to know? Exact mechanism or general
Q: Should we know the mechanism? and order
See the study list. You do NOT have to know how all the electrons get pushed about.
But you need to know how the reaction cycle procedes, and what each residue of the
catalytic triad is doing.
Q: Can we get the videos?
See the website. There is a whole section of videos. And TONS more on the mightly
internet. http://courses.ucsd.edu/rhampton/bibc102/
Q: Hi professor Hampton… I'm having trouble understanding what you mean by a
binding being in equilibrium. Could you expand on this a little?
Hi! Well, when you mix a protein with a binding site in solution with a ligand that binds to
that site, as long as the ligand is interacting with the protein in a non-covalent manner
(ionic, hydrogen bonds, Van der Walls forces, hydrophobic interactions) then what
happens at the MICROSCOPIC level is that ligands are constantly occupying a binding
site and then exiting. But when the system is in equilibrium the fraction of sites occupied
will be constant, and depend on the ligand concentration. If you look at a SINGLE
protein binding site, you would see ligand coming and going coming and going coming
and going, but the behavior of the system at equilibrium will be a constant fraction of
binding sites occupied at a given ligand concentration.
A useful analogy is a crowded train station (like Union Station in DC, where I was
getting a train a couple days ago). Nearly every seat is occupied, but if you watch one
seat, people will get up, others will take the seat, the person who got up might come
back and sit somewhere else, but the fraction of occupancy is quite high, and
frustratingly constant. Like that. Of course, probably you So Cals have never taken a
train since we all drive everywhere all the time…
Monday 10-08 Lecture 3
Q: Would you consider getting video podcast PLEASE????
I think audio podcasts are a good compromise. I like them for two reasons. First, it
makes editing and control of content do-able for me, and this something I have to be
able to do in order to teach the way I do, as well as just a good idea. Second, use of
audio podcasts with the graphics you have or are seeing is a more active experience.
You have to synthesize the content in an active way.
Q: Can you put some sections on tuesday/thursday please? I have work/class all day
monday Wednesday Friday
Trying. I think it is a good idea, but there are hurdles. I will say that MY office hours
include Tuesday 5-6, and I am somewhat familiar with the material.
Q: What exactly do we have to know about chymotrypsim? Reproduce from memory or
just needa recognize the steps
You need to know the catalytic cycle, and what each amino acid does in that cycle. NO
electron pushing needed, although some people think it helps them understand. SEE
THE STUDY LIST.
Q: What did you call HIV? Its not a catalytic triad but a _____?
The HIV protease is an aspartyl protease, that uses two aspartyl groups, an
unprotonated one (neg charged) and a protonated one. .They do a lovely proton
pushing and pulling dance to make H2O better able to attack the susceptible peptide
bonds. Very boss.
Q: Can u talk a little slower. Its hard to follow what ur saying
Tryni’
Q: Will the TAs go over the problem sets each week in section?
They will go over anything you want.
Q: Can we go over the chymotrypsin stuff again? It was all very rushed on Wednesday
Now that you know what the basic questions are, you can own this by figuring it out. It is
actually fairly basic organic chemistry (group transfer by acid catalyzed nucleophilic
attack, followed by hydrolysis).
Q: Is there a difference between substrates and ligands?
A substrate is a molecule that is chemically altered by the catalytic action of an enzyme.
A ligand is a molecule that binds to a specific site in a binding equlibrium, usually on a
protein in our use of the term. Because a substrate often established a rapid binding
equilibrium with an enzyme that is processing it, I suppose it could technically be
considered a ligand, but one almost never hears a substrate being described as such.
On the other hand, an allosteric regulator that is not processed by the enzyme is indeed
a bone fide ligand.
Q: Why is k constant for myo but not constant for hemoglobin?
Q: Why is K constant for myoglobin and not for hemoglobin? And yes I did read
OK! OK! The hemoglobin has a structure that allows this behavior, the myoglobin does
not. The thought is that a simple O2 binding protein based on heme was the ancestor
protein of both, and that a tetrameric, allosteric, cooperative form evolved from the
monomeric myoglobin-type structure.
Q: So with respect to hemoglobin's ability to bind oxygen, does the K increase as it
binds more oxygen? Sorry if this is a stupid question
There are no stupid questions! Hemoglobin’s affinity for O2 increases in high O2
compared to its affinity in low O2. So the virtual Kd gets smaller in high oxygen. That is
because low Kd means high binding affinity.
Q: What does Km stand for?
It is the Michaelis-Menton constant, used in the Michaelis-Menton equation Vo= Vmax
(S/(S+Km)), by which many enzymes’ rate vs substrate behavior can be described. It is
analogous, to the Kd for ligand binding.
Q: Maybe try putting the mic on your other ear?
I am tempted to hide the mic and keep doing it until the replacement ones are the old
style…
Q: What is the definition of cooperativity?
It is another word often used for allosteric behavior, and especially when the substrate S
causes the changes in enzyme behavior. It comes from the poetic idea that S is
cooperating with the enzyme to improve the processing rate at high levels of S. Sort of
like in a busy restaurant, a customer going, “hey! We need some service, NOW!”
Q: Are there more cooperative enzymes than 'boring' ones?
Actually far more enzymes have simple M-M, constant Km behavior. The allosteric
enzymes occupy important positions in metabolism, where large energy drops or
resource branch points exist.
Q: The hill coefficient is the n and not the Km in the equation on the board, right?
That is absolutely right. It is a mathematical “tweek” of S to make its effects on enzyme
behavior match what is observed.
Q: Does a higher hill constant makes a steeper curve?
Yes. When n is 1 (normal, uncooperative enzyme) it takes an 81 fold change is S to go
from 10% rate to 90% rate. When n is 4, the change from 10 to 90 happens over a 3
fold range of S. Van Boss! (Dutch for “Boss!”)
Q: Can you explain what allosteric regulation means?
Q: Can you define allosteric regulation again please?
Allosteric regulation is the widely observed regulation of enzyme rate that occurs when
a molecule binds to a site on the allosteric enzyme distinct from the active site that
causes the enzyme’s processing of substrate to change. Postive regulators increase the
activity of the enzyme, and negative regulators decrease the activity of the enzyme.
One special case that is often seen is when the substrate itself causes activation of the
enzyme. The binding protein analogy is O2 changing the O2 binding behavior of
hemoglobin.
Q: Do all allosteric regulators have a sigmoidal shape (non constand K)
The rate vs S curves of allosteric enzymes are almost always sigmoidal. It is a telltale
sign of such enzymes.
Q: And rosalind franklin!
Perhaps you are referring to the fact that Rosalind Franklin should also have gotten the
Nobel Prize. It is a complex and important story, and very interesting. Many people
share your opinion. To balance out the very skewed and unfair picture of RF painted in
James Watson’s “The Double Helix”, it is great to read the newer biography of RF by
Brenda Maddox: “Rosalind Franklin, the Dark Lady of DNA”. We owe RF a big debt for
her brilliant and critical X ray studies on DNA that led Watson and Crick to realize they
were dealing with an antiparallel helix. But the reality is that the DNA structure Nobel (to
Waston, Crick, and RF’s director Maurice Wilkins) was awarded in 1962, whereas RF
passed away (far too early of cancer) in 1958. Since they don’t give out posthumous
Nobels, it is a moot, but very interesting issue…
Q: When drawing the allosteric regulators, do we have to be specific about where the
activator/inhibitor hit Vo or [s] ..? Im looking at figure 6-34
Q: Can you say again what we need to know about the allosteric regulators graphs?
(Fig 6-34)
You have been tricked! That graph has almost no information. The S1/2 point is simply
the amount of substrate that gives 50% saturation, and it is NOT equal to any constant
Km, as it is in the case of non-allosteric “standard” enzymes. Really the ONLY thing in
that fancy looking curve is that it is S shaped, and that if you calculated Km for each pair
of points Vo and S by the Michaelis Menton equation, you would be saddened to find
that the Km that resulted was indeed not a constant.
Q: What about the lactose binding?
I believe you must be talking about the Jacob and Monod work on the lac operon
regulation (that eventually got them a Nobel Prize) before most of you were even a good
idea (1961). In their studies, it turns out that lactose is… ready… an allosteric regulator
of a transcriptional inhibitor. When lactose binds to this protein (called LacI), it stops
blocking transcription of a bunch of genes that encoded lactose metabolizing enzymes
and transporters. SWEET! So really there work ushered in the idea of regulation of
protein function by small molecules… allosteric regulation. BAM!
Q: Can you explain he difference between those 3 equations u wrote on the board?
The one with Kd is describing the effect of ligand (L) concentration on the percentage of
sites bound by the ligand at equilibrium. The very similar looking equation with Km is
describing the effect of substrate concentration on the Vo (initial rate) of an enzyme that
displays Michaelis Menton behavior (one of the common, “non allosteric” enzymes”) that
have an unchanging Km. The third equation looks just like the second but there is an
exponent “n” on each S. This is called the Hill coefficient, and it is a mathematical
“tweek” of the Michaelis Menton equation that gives sigmoidal behavior. Note that S
does not actually change, this is purely a mathematical alteration to describe the
sigmoidal allosteric behavior with a K and S. So when n = 1, you have a regular old M &
M enzyme. But when n is different from 1, you have a fancy sigmoidal enzyme. In
nature, n is usually never bigger than 4 for the most sigmoidal enzymes, and as we
discussed above, that causes a big change in the steepness of the curve.
Q: Do allosteric regulators have their own binding sites or do they bind directly to the
substrate? Or can it be both?
They bind to their own sites distinct from the substrate-binding active site, which I think
is what you meant, in your texting frenzy.
Q: Cooperative behavior is sigmoidal. Can you repeat the name of the rectangular
hyperbolic behavior type. The one that acts like the coffee cart...
Sam and Patty (owners of the cart) are going to kill me…. Anyway, the enzymes that
behave with a constant Km, and show the rectangular hyperbolic behavior are usually
called “non-cooperative” “non-allosteric” or Michaelis-Menton enzymes.
Q: The slide that shows tryptophan and tyrosine is missing. Can you please add it
Q: Hello! why are some of the slides that are shown in class missing in the printed
packets?
Q: How come some of the lecture slides are not in our Ted ppt slides?
OOPS. I added that one to clarify, and I will put it in the lecture slide. Mea Culpa!
Q: Why is the point of plotting (1/V) against (1/4)? Where is K in the plot?
You get a straight line with intercepts that immediately tell you 1) you have an M&M
enzyme if there is a line, and 2) what the Km and Vmax are…
Q: Wouldnt forming an ES complex be order so decrease in entropy? So how does a
rxn move forward if thats an unfavorable deltaG?
ES complex formation is part of a whole process that includes S to P change and the
accompanying changes in H, S and G. But even for ligand binding to a site and just
sitting there, sometimes you are right, there is a drop in entropy that is offset by a gain
of released heat (remember that G includes both H and S, critical!) but also sometimes
binding of a ligand to a site causes the release of a great deal of H2O that was
associated with the ligand or the binding site, and the freeing of small molecules like
bound H2O can have a large positive entropy component. It all depends.
Q: The Keq is a ratio of what? Sigh class is over
This is standard first year chemistry. It is the product (mathematical) of the product
(chemical) equilibrium concentrations divided by the product (mathematical) of the
reactant equilibrium concentrations. So, (P1 x P2 x P3…etc)/(R1 x R2 xR3…etc). So
when Rs are very low and Ps are very high, the reaction has gone far to the right and
the DG is very negative…. Stay tuned.
Wednesday 10-10 Lecture 4
Q: How important is it to read the book vs. Reading the articles you tell us to read?
I consider the book a useful and highly information-rich supplement to the lectures and
the readings I write specifically for the class. I strongly suggest reading the
assignments, but the lecture materials and the readings I write are what you are
responsible for. The study list and terms list will tell you exactly what you need to know.
Q: How does it feel to win the Nobel Prize in chemistry?
I’ll be pretty good! You can ask Roger Tsien, who is a professor in UCSD Chemistry and
Biochemistry Dept, and won (for his work with optical proteins such as GFP) a few years
ago.
Q: What does isotherm mean?
It is a curve generated at constant temperature. All of our binding and enzyme rate
curves are isotherms, because the measurements are done at constant temperature.
Q: Can you post the lyrics on the website?
Q: Can you post the lyrics to your rap on the class site?
Q: Can you post the lyrics to your rap on the website? It was a little hard to hear.
I will. You can put them to your own cheesy Wal Mart Organ GangstaBeat® track to sing
along.
Q: You said ATP hydrolysis (forward rxn) is like running a half marathon. What was the
analogy you used for the reverse reaction?
That is not exactly what I said. I said that when we start depleting stores of ATP, like
when we exercise a lot, mechanisms kick in to run that hydrolysis reaction backwards,
using energy from glucose or fat oxidation to do so. You will become an expert in these
processes.
Q: The dude next to me smells really bad. Like really really really
Give him a hug, encourage him to take better care of himself.
Q: HNNNNNNNNGH
(Probably from the dude…)
Q: How does water exist at 55M? How can you concentrate or dilute water?
Water sitting in a vessel at room temp exists at a concentration of 55moles/l, that is, 55
molar. Water is famously incompressible, so it is hard to make it more concentrated with
pressure.
Q: You mentioned THC in the first class. Out of pure curiosity how does THC work with
the human brain?
THC (tetrahydrocannabinol) is a plant-made, high affinity
THC
(low Kd) ligand for the cannabinoid receptor expressed
on many neurons in the brain. The cannabinoid receptor
is one of the large class celebrated in Wed 10/10’s
Nobel Prize for chemistry, given to Bob Lefkowitz and
Brian Kobilka for their work showing how this class of
receptors work. The crazy thing is that we produce our own powerful version of THC,
poetically called anandamide, just like we produce natural versions of ligands for the
opiate receptor. These “endocannabinoids” are important in mood control, reward,
appetite regulation, and a host of other high brain functions. Recent studies in
exercising animals indicate that the endocannabinioids may be as or more important in
the “runners high” that drive mammals to endurance exercise. I have included a picture
of THC. It makes you wonder why a plant would produce such a molecule…
Q: [Are] the problem sets set up for each week?
I am now putting up a problem set for each lecture, attempting to do it very soon after
the lectures. They are listed on the class website, in the PROBLEM SETS section as
“Fa 12 Short, Lecture-associated Problem Sets”. The is a growing list of problem sets,
with a small collection for each lecture. The lectures are separated with page breaks, so
it is easy to print out lone lectures if you desire. A corresponding growing answer sheet
will be found at a link right below this, soon…
Q: How does luciferase differ from hrp used in western blotting?
Well, the luciferase enzyme catalyzes the oxygen dependent reaction (also requiring
ATP) that alters the substrate luciferin to make light. The HRP (horseradish peroxidase)
reaction that many of us use to visualize proteins on immunoblots works by producing a
reactive oxygen species that reacts with the synthetic molecule luminol. This is a purely
chemical reaction, but the generation of the reactive oxygen species is catalyzed by an
enzyme. So some similarities but very different.
Q: Why is for example, CH4 more/less oxidized than CO2? How was that determined?
And what does it mean when you say CH4 has less e's to give up?
Well, the CH4 has electrons it can give up when reacting with O2 and being so oxidized.
The balanced reaction is
CH4 + 2 O2 —> C02 + 2H2O
One way to view the electron transfer it by removal of H- (hydrides) and H+ (protons)
from CH4, which are then transfered to the neutral O atoms. That particular route shows
the movement of negative charges from the electron-rich CH4 to electron-hungry O2.
Another way is to strip the CH4 of all atoms, producing neutral C, 4H+ and 4e-, and then
produce the water from O atoms and the CO2 from the C combining with neutral O
atoms as well. Both show loss of electrons from CH4 (oxidation) and gain of electrons
by O2 (reduction). Redox, yo!
Q: Can you explain the part with the business end and hydrogen transfer again?
What I mean (and we will go over this again) by “the business end” of a cofactor, is that
small moiety, or functional group that actually does the chemistry. Even though the
NAD+ molecule is very big and fancy, the small six-membered, nitrogen containing ring
that I emphasized in class is where all the chemistry is happening.
Monday 10-15 Lecture 5
Q: Will the lecture before thanksgiving be uploaded on podcast?
I will make sure it is! In fact, both of them.
Q: CSB 110 doesn't exist
You are CORRECT! It is CSB 001. CSB stands for Cognitive Sciences Bldg. Usual
class time, this smaller room since many will come to the 9:30-10:50 class on Tuesday
Nov 20, 110 Peterson.
Q: If we invite you to a party will you come rage with us?
I would have to dust off my binky and bone up on my e-fueled hacky sack. M’raging
days are long over…
Q: You're a marathon runner, right? Did you run the Nike marathon in SF yesterday?
It is a beautiful race, but it is a Woman’s Marathon. I am this weekend running The
Bethlehem Hat Trick, in Pennsylvania. It is a 5K (3mi) and 10K (6mi) on Saturday, and a
½ Marathon (13.1 miles) on Sunday. Then I fly back to teach you good people.
Q: Does the reduced form have no double bonds besides the ketone?
I am not sure what you are talking about. This is the one problem with the text-quests.
There is a time lag…
Q: How is NAD+ designed to carry a hydride ion? How is FAD designed to carry
individual electrons
These molecules have an evolved structure that makes them good carriers of electrons.
NAD+ is good at picking up H-, also written as 2e + H+, however you want to describe it.
I find it easy to describe NAD+ reduction as that carrier acquiring a H- (hydride). The
cool thing is that the oxidized form (NAD+) is aromatic but charged, while the reduced
form (NADH) is non-aromatic but neutral. This way there is no huge advantage of either
form, and this is a good way to be an electron carrier. Not hard to pick up H-, not hard to
let it go… FAD is evolved to pick up 2e but can do so either one or two electrons at a
time, and the finally reduced form is FADH2. Also, one often (not always) sees FAD
picking up electrons by removing two H. radicals to create a double bond. .
Q: R u married? And have kids?
I am married to science and teaching, and you are my kids! But I do have two cars, like
a family…
Q: Are the problem sets indicative of the problems we will get on the midterm/final?
They are a very (VERY) good study aid. Have a look at the previous midterms and see
for yourself. That does not mean that there will never be problems that are distinct from
the problem sets, but you can see for yourself that most problems are similar.
Q: I think fructose is pronounced "frooctose"... (fructose (ˈfrʌktəʊs, -təʊz, ˈfrʊk)
It turns out either way is fine, and I have heard FRUK more often than FROOK, but both
are acceptable. The remarkable video “Sugar: the Bitter Truth” mentions fructose like 80
times, and they use fruk- as opposed to froook. But both are accepted.
Q: I'm amazed by phosphorylation modification. (yeahh nerd buddy). but why
phosphorus? i mean there are many other elements on the periodic table, why
phosphorus play such an important role, can it be replaced by other element that have
similar chemical properties?
Evolution is a combination of what works and what can be arrived at by selectable
accident. Phosphorous and phosphate fits the bill. It is a great way to store chemically
releasable ΔG, and it is readily available. Now that PO4 is so enmeshed in metabolism,
signaling and energy storage, it could not be replaced, but it is possible that in some
other living world, a distinct element that acts similarly could be involved.
Q: is the beta structure of glucose more stable than the alpha due to steric hinder?
It turns out that the beta structure is more stable, that is, the one with the OH pointing
up. It is only a teeny bit more stable, with the equilibrium ratio in water being about 2:1
beta to alpha.
Q: On the slide it says your anomeric carbon is carbon #5 and I do not understand
why...
Q: Why is the anomeric carbon not @ carbon #1?
I am not sure why this has been asked a few time in the texts.
But I am glad! On the slide showing anomers, I marked the 5
carbon with a little green arrow, which I have reproduced here. Perhaps people thought
this was the anoeric carbon. But I simply marked carbon 5 to allow students (and me) to
keep track of the different carbons as you go between ring and open. It is true that the 1
carbon shows the two different anomeric forms.
Q: What is dehydrogenase again?
A dehydrogenase removes hydrogen from a substrate, and thus causes oxidation of
that substrate. In the case of GAPDH, an H- is removed to NAD, thus forming NADH,
and so oxidizing glyceraldehyde 3 –P.
Q: Most of what you have covered is in the reading as well right?
Yes, especially Glucose Glycolysis and Krebs.
Q: What's the line on the bottom of the cost hanger model?
We will get to it, and it is covered in GG&K. The bottom right of the coat hanger is G3P,
so the first enzyme coming from that is GAPDH.
Q: Omg all this sugar stuff... HNNNNNNNGH
Total…
Q: Tomorrow is National Boss Day. I think you should celebrate
It passed in my lab without a wimper. I think my lab does not perceive me as the boss.
Just the guy who get the money for them to do stuff…
Q: Do we have to know the structures for all the things in glycolysis
Q: Q: DO wE need to know how to draw the structures for glycolysis for exams????
Yes. See Study List. Although I will never have you draw out the whole pathway,
knowing the 10 structures is incredibly useful for understanding the chemistry. In fact,
there is no other way to do so. If I do have you draw a structure, you will get the name,
and usually a molecue it will become, or a molecule that is used to make the thing you
have to draw. See the tests for many examples.
Q: Why did you lose weight? How?
Q: How much do you weigh?
I am in the process of losing weight with the goal of 130 (I am short…) and a BMI of less
than 20. Right now I weigh 136 and change, so about 5 lbs down from the starting
weight right before class started. It will help my running, but make my cage fighting
much less successful… It is also a nice demonstration (for the last lecture) that paying
attention to calories in and calories expended will give predictable results… I simply
closely monitor my calories ingested, and calories expended, and keep that total below
a weight-dependent calculated value for a certain amount of loss (roughly ½ a pound a
week). I use an App called LoseIt, available in both iPhone and Android environments.
Q: Is NAD different from NAD+ and FAD from FAD+?
NAD is often used for NAD+. They are the same thing. The important point is that this
verson of NAD+ (or NAD) is the oxidized form; it does not have an H- (hydride ion)
added to it, so it is technically positively charged. FAD is never written as FAD+
because its oxidized form is (as you can see from the slides books internet) is neutral.
The reduced form is FADH2, also neutral.
Q: Can you explain the part with the business end and the hydrogen transfer again
Q: What do you mean by the business end?
The basic idea is that although NAD+ is a complex molecule, there is a
very small part of it, the aromatic, charged pyridinium ring (drawn at the
top) that does all the chemistry. So I call this the business end. Just like
the business end of a sword is the point, sort of. This little ring is the part
that picks up a covalent H- (hydride) ion to become reduced, and gives
up when it transfers electrons to some other molecule.
that
Q: Whats the difference btw NAD+, NADH, NADH, and NADPH? Are they all related?
NAD+ is reduced to form NADH;
NADP+ is reduced to form NADPH.
NADP+ is a phosphorylated from of NAD+, and NADP/NADPH is used in very different
reactions than NAD/NADH, despite the high similarity between these two molecules.
Q: Your weekend name: Randall the Handle
Let me just put on my Wal Mart Livingroom Organ GangstaBeat® track here…
Q: Can you explain the coat hanger model again plasma. *prettyplease with sugar
We will talk about it more in class today, and it is delineated in detail in GG&K. It is
basically a cartoon of the flow of carbon from Glu to Fr1,6bP, which then splits into two
3 carbon molecules (hence the top of a triangle). Those two molecules are
interconvertable (the bottom of the triangle is that step) and G3P (the bottom right of the
triangle) is further converted into pyruvate step by step to give 2 ATP. This happens
twice, giving a gross profit of 4 ATP and a net profit of 2 ATP.
Q: trying to get fructose corn syrup removed from foods. What is your view and why?
There are some very interesting idea floating around about the effects of our massive
consumption of fructose, whether it is in the form of sucrose or HFCS. Everyone is in
fair agreement that it is not important whether we consume sucrose or HFCS. The
problem is that we consume a huge amount more 1:1 fru/glu (which is the rough ratio of
both sucrose or HFCS) compared to pure glucose (as plant starch) than we used to.
Also, it is clear that the metabolism of fructose is different from glucose. Some people
think this is very important, and other think it is less important. But I expect that the shift
from plant starch to massive consumption of sucrose-ratioed sugars will be a very
important driver of the obesity epidemic. But just how is not yet clear.
Q: Why is fructose better than glucose healthwise
It is almost certainly not. There are many people who believe that because fructose is
metabolized differently, and much more selectively by the liver, that it causes some
consequences. There are other people who think that fructose is no different from
glucose, but the massive amount of sugar currently being added to foods is a problem.
Q: Chargers or Broncos?
GooooooOOOOOOOO CHARGERS!
Q: Is hexokinase then a transferase
It is a kinase. It transfers phosphate from ATP to glucose, but people refer to it as a
kinase.
Q: Can you repeat why we need to create an oh on glucose to add a phosphte?
The transfer of PO4 to glucose requires nucleophilic attack by an OH, catalyzed by
hexokinase. The 1 carbon of glucose does not have an OH. It is a carbonyl (when in the
open chain form) and that is not a good nucleophile at all.
Q: Shouldn't electrons in water carried by OH instead off H?
They are. When an H- is removed from a molecule it is almost always removed from a
more electropositive atom like carbon that can support being a positive ion.
Q: Where is the H- come from?
You can look at H- being a hydrogen and its full sigma bond being pulled off of a
metabolite during oxidation. You can also look at it as being 2e and an H+ being taken
off a metabolite.
Q: Where does oxaloacetate come from?
We will get to that, bigtime. It is a Krebs cycle intermediate, and it has all kinds of
interesting features.
Wednesday 10-17 Lecture 6
Q: Enzymes dont change K, which is products over reactants, right? But don't allosteric
regulators control the amount of product that is made?
Allosteric regulators change the effectiveness of an enzyme as a catalyst. But it is still a
catalyst and as such it does not affect the equilibrium constant, that is, the extent to
which the reaction will proceed to completion. To put it in the way you asked the
question, allosteric regulators control the rate at which products are made (positive
allosteric regulators increase the rate, negative allosteric regulators decrease the rate),
but not the amount that is produced at equilibrium.
Q: Can you explain the step in glycolysis where NAD picks up the electrons
That is the glyceraldehyde-3-phosphate dehydrogenase reaction. Basically, the enzyme
catalyzes the oxidation of an aldehyde to a carboxylic acid, but does so while the G3P
molecule is covalently bound to a cysteine residue sulfer in the active site. Aldehydes
bound to thiols are (in analogy to hemiacetals) thiohemiacetals, and carboxylic acids
bound to thiols are (in analogy to esters) thioesters. So the NAD+ grabs an H- from the
thiohemiacetal to produce a thioester. Oxidation of an aldehyde into a carboxylic acid, in
disguise. Then a Pi groups displaces the carboxylic acid from its covalent linkage in the
active site, producing the product, 1,3 bis phosphoglycerate, which is more than capable
of spontanesously transferring its acid-linked Pi (or PO4, however you want to express
it) to ADP.
Q: You are going way too fast I don't even have time to text you man
If you raise your hand, I will stop and answer your question! That is the upside of raising
your hand. The downside is all that exposure. The upside of texting is the anonymity,
but the downside is exactly as you have stated it. I welcome both texting and raising of
hands…
Q: What's the relevance of lecturing on these steps. What's the take home on these
slides?
The take home is multiple. First, these are the CORE reactions of all living things.
Period. Second, they (and their reverse) are at the heart of glucose regulation (and
misregulation) in human health. Third, the demonstrate the chemical logic of a classic
metabolic pathway. Fourth, several principles that apply to all enzyme-catalyzed
metabolic pathways emerge from these reactions. Fifth, they are mega-bongo boss.
Q: How is it possible for all these reactions to happen without putting energy in to drive
it? Are they all spontaneous reactions ?
The critical feature is that
while not every reaction is
always spontaneous, the
entire pathway is
spontaneous, as are all
metabolic pathways. In
metabolism there is no free
lunch. It is helpful to look at
the slide “glycolysis free
energy landscape”
(included herein) that
clearly shows all the energy drops. You don’t need to be J. Willard Gibbs (the great
thermodynamics pioneer) to see that the net change in energy as you go from left to
right is a big drop, even though there a individual steps that are positive in that direction.
Think of a siphon. There is local uphill movement of water (or gasoline if you are
desperate or larcenous) but net downhill movement. That is a physically appropriate
analogy.
Q: Yo randawg, what are tautomers again?
Keto-enol is the ones we were talking about in the
formation of phosphenolpyruvate. See that:
phosphoENOLpyruvate. It is a phosphoryl ester
made with the enol from of the ketone that is
pyruvate. This is a molecule that will give up a lot of
free energy from hydrolysis of the phosphate. It is
useful sometimes to be back to your organic notes..
comes right back! Also, Wikipedia has a good
tautomers entry.
Q: Thank you for signing up for Cat Facts! Did you know that cats use their tails to
balance and have nearly 30 individual bones in them!
Feels like a forwarded text… but cats are metabolically very interesting since that eat a
massively protienacious diet; they have great sensitivity to too many carbs and fats, and
constitutively produce glucose by the glucose synthetic pathway we will discuss in a few
lecture. They are literally on the Atkins diet… the Catkins diet, I guess…
Q: Where can we find the link to the video you showed?
MOVIES section on the course website.
Q: Whatwasthecell that was chasing the little speck?
It is a leukocyte of the class known as neutrophils, who are nasty, brutish, and live about
a day. They are specialists at detecting, chasing and killing foreign invaders. A healthy
adult produces about 100 billion neutrophils PER DAY. They live fast, die young, and
leave a beautiful cytoskeleton…
Q: Can you explain where Galactose plays a role in respect to the overall Glycolosis
pathway?
I think you are asking how galactose is incorporated into glycolysis. It is connected to a
carrier called UDP by its 1-carbon, and then converted into glucose. This newly made
glucose-1-P is liberated from UDP and then “mutated” to Glu-6-P, a classic glycolytic
intermediate.
Q: What were the 3 ways that u said just before u stopped??
Just slip out the back Jack, make a new plan Sam, slip off the bus, Gus… just kidding.
The three ways we discussed were alternate metabolism to 3 carbon products that can
energy the pathway (fructose), modification to create glucose from a related hexose
(galactose) and liberation from the glycogen storage polymer.
Q: Is corn syrup good/bad for our metabolism ??
It is no different from natural cane sugar sucrose, which is one fructose connected to
one glucose in an easily hydrolysable bond. The problem appears to be that a variety of
processes and entities have made this 1:1 mix so readily abundant and pervasive that
our consumption of this mix is astronomically higher than say 50 or 100 years ago.
Whether the fructose itself is intrinsically “bad” or simply that the massive increase in
sugar consumption is “bad” is a topic of great importance and hot debate.
Q: Learning from randall the handle is like trying to take a sip of water from a fire hose.
Oh stop it! That is why I go to such lengths to provide study lists, old tests and problem
sets. The classroom is an incredibly important component of your learning the language
of metabolism and biochemistry. But I will try to stop more often for questions, and s p
e a k
more s l o w l y
Q: Is the pyruvate to ethanol pathway the one biofuels companies take advantage of for
algal biofuels?
Ethanol that is produced by biological processes (rather than industrial processes) uses
fermentation as one of the strategies to convert feedstocks (such as corn-derived sugar)
into ethanol. It is one part of a fairly complex and emerging technology, and is probably
not how we will keep driving our cars in 100 years…but who knows?
Q: What were the other 2 cofactors (mentioned prior to TPP)?
By the time we got to TPP, we had also talked about NAD+ and its close relative
NADP+, and FAD
Q: I thought PO4 was the good leaving group, so how come the O stays on the middle
carbon in pyruvate
Well, the PO4 is transferred by attack by a correctly placed OH on the phosphate of
ADP that will receive the added PO4. If the OH of the terminal PO4 for ADP attacks,
then the “back end” O will become the OH of the enol form of pyruvate, which rapidly
become the more stable keto form. Think sn2 attack by the O on ADP to displace the
phosphoryl group from PEP.
Q: The slides say FPK-1. Is it really PFK-1?
Q: Is it FPK or PFK?
DAMN! You are absolutely right. I apologize.
Q: Today in section the T.A. said that the lecture problem sets are much easier and not
indicative of your midterm and final.
The problem sets are similar, but not identical to the test questions. Plus, some test
questions will be more challenging than others, but all will be straightforward. I hate
“tricky” questions. Hate them. With the rejoinder that life (but not any of my tests) is full
of tricky questions. Report back to me in 20 years if you find this to be false…
Q: Over all the reactions that we went over today, which ones do you want us to simply
understand or memorize
See the study list.
Monday 10-22 Lecture 7
Q: Where does the adp molecule that you use to react with 1,3bpg come from? Is it just
freely floating in solution?
The ADP generated in glycolysis is found in the cytosol. There is also (as we will learn)
ADP inside the mitochondrion that is converted into ATP, and can be transported out to
the cytosol as well.
Q: Are we allowed to text you questions while we are studying during times out of class?
And will you answer them?
Sure, and I will make all efforts. Email is a better medium for written answers because it
is faster to type with a keyboard.
Q: What about the magnesium ions do we need to know?
They are often employed in enzymes that process phoshphorylated compounds such as
ADP, ATP, etc. Those ions are critical but not something we will talk about much. You
will notice that never not once not ever have I mentioned magnesium on an example,
problem set or exam. But we would be dead without it.
Q: What is the electron pushing mechanism for the conversion of 6-phospho-gluconate
to d-ribose 5-phosphate
Not that you need to know this, but a basic group on the
enzyme pulls a proton off the 3OH, and at the same time
the –H is removed as a hydride, thus oxidizing the hexose
and creating the NADPH. Then the CO2 exits, and the
electrons from that bond move into aN enol form, with the
base from the first step donating back the H+. Finally, the
enol form resolves into the ketone with help from the first
basic residue and a second proton donating carboxyl
group. In this way what used to be the 3 carbon is (due to
the loss of the 1 carbon as CO2) is now the 2 carbon of
the newly made ribulose, with a carbonyl group (ketone).
See picture, but remember: YOU DO NOT NOT NOT
have to know this mechanism. But it is kind of beauteous.
Q: What's the importance of having cycles in metabolic pathways? What would be the
defect if only linear path exist?
That is a philosophical question, but it is true that cyclic pathways are catalytic, in the
sense that every OAA (one of the two starting molecules of the Krebs cycle) can support
a whole Krebs cycle, and is regenerated at the end of the cycle. So it can be viewed as
a higher level of stable catalytic processes due to the regenerative nature.
Q: RE: which is e1 e2 e3
E1, E2 and E3 are three separately described catalytic activities of the entire PDH
(pyruvate dehydrogenase) complex. Each “E” actually consists of multiple individual
proteins, and, and the three Es are each in multiple copies in a single PDH. The three
numbers refer to three separate reaction sets that occur, each using different cofactor.
They are called
E1- pyruvate dehydrogenase
E2- dihydrolipoyl tranacetylase
E3- dihydrolipoyl dehydrogenase
E1- Attack of the pyruvate by TPP, resulting in removal of CO2 from pyruvate, and
transfer of the acetyl group electrons to oxidized (-S-S-) dihydrolipoate, creating reduced
dihydrolipoate (-SH , -SH) with an acetyl group attached to one of the S atoms.
Q: Wow just how much do u run a year?
This summer I was running a bit more that 40 miles a week. Now, strangely, I am a bit
busier (which is a gift and a privilege) but still try to run 30 miles a week. I run between 1
and 3 marathons a year, and a bunch of ½ marathons, some 10Ks and one or two 5Ks.
I don’t like Mud or Zombie runs. Gimmicky.
Q: Out of curiosity, do these reactions produce some amounts of free radicals?
Not so much. The main source of free radicals, and it is very important, comes from
spillover and inefficiencies in the electron transport chain of the mitonchondrion, that we
will discuss in some detail.
Q: What was the electron transfer for the PDH catalytic cycle? Pyruvate tpp then...?
The electrons flow from pyruvate to oxidized lipoic acid (the oxidized form has a
disulfide bond and a ring structure; the reduced from has two sulfhydryl groups and an
open structure), and then from reduced lipoid acid to FAD, and then from FADH2 to
NAD to make the final reduced molecule NADH.
Q: Is the use of DNA fragments in important enzymes related to the endosymbiotic
theory?
You are incisive to notice that nearly all of the cofactors have ribonucleotide parts, as
though they might have been part of an RNA structure that bound to a ribozyme in the
days before proteins, when giant catalytic RNAs walked the earth, striking fear into the
hearts of metabolites…
Q: Your beard is for a costume... Are you, star trek style, mirror universe, evil Dr.
Hampton?
No, but I will be bald if all works out…
Q:In glycolysis when G3P--> 1,3 BPG, does it generate 2 NADH for every one
G3P or 1? (DHAP is converted to G3P, meaning 2 G3P are used in glycolysis)
Each G3P consumed in glycolysis generates 1NADH (look at the enzyme reaction.. this
will be clear). But each molecule of glucose results in this reaction happening twice.
One G3P is directly made, and the other is produced by TPI conversion of DHAP into
G3P (the horizontal line of the “coat hanger”).
Q: What are the important components that are regenerated in glycolysis?
Nothing is regenerated.. that is reserved for cyclic pathways. But ATP is replenished
from ADP, and IF glycolysis is to persist, NAD+ must be regenerated either by
conversion of pyruvate into ethanol, or by conversion of pyruvate into lactate.
Q: I'm really curious, why isn't the Wednesday Nov. 21st lecture in the regular room?
Because the voting indicates that a large majority of people are going the late night
Tuesday class, and so we will have like 20 or 30 people (or fewer) in that sprawling
lecture hall and that is not effective, useful or fun. So I got me a smaller room.
Q: What is the difference between deltaG', deltaGo, and deltaG?
ΔG’o is a free energy value for a reaction at a set of specified conditions (55M water,
25oC, pH7, and some others), and all products and reactants at 1M concentration. It
turns out that this particular free energy value will predict the equilibrium constant for the
reaction being so described, since ΔG’o = -RTlnKeq. So it is super useful because it
predicts that degree to which any reaction will proceed or go in reverse spontaneously.
The actual ΔG’ is the true ΔG’ for a group of reactants and products at their true cellular
concentrations, using ΔG’ = ΔG’o + RTln K (the product/reactant ratio you learned in
freshman chem.). Because of the “ ‘ “, the various other conditions like temp pressure,
water conc. etc are still standard. Finally ΔG is a very general term for the free energy
change for any process in any conditions. It is not used much in our work.
Q: Which carbons are the ones that stays with xitrate throughout the cycle instead of
going off as co2?
We will go over this in great detail. But the bottom line is that the new carbons are
spared through the first turn of the cycle.
Q: How is lipoic acid carrying electron from the decarboxylated pyruvate?
You have to think about –S—S– being oxidized, and the form with an open ring and two
–SH groups being reduced. You must be comfortable with this idea. It is carrying the
electrons in the –SH groups if you will.
Q: Why is oxaloacetate with 4C's not succinate-etc?
Perhaps you are asking why we don’t call oxaloacetate “alpha-keto succinate, which
would be a perfectly valid and very understandable term, or 2-keto succinate. But
oxaloacetate is historical.
Q: What does the alpha refer to in the nomenclature?
The carbon next to the carbolxylic acid end. The 2 carbon. alpha-keto glutarate has a
keton carbonyl at position 2, right next door to one of the carboxyl groups.
Q: Where do we stop for learning the kreb cycle mechs? Starting at succinate to
fumarate?
Q: Please stop rushing through everything last five mins. Please
The reason that I rushed through the Krebs stuff is that you ALSO have all that
information described in great detail in Glucose Glycolysis and Krebs. Still, I understand
the frustration and I will overlap that stuff a bit in the next lecture.
Q: Define dehydrogenase and isomerase
Dehydrogenases are enzymes (ase) that remove (de) hydrogen from a substrate in
order to oxidize it. Our most famous example is glyceraldehyde-3-phosphate
dehydrogenases that does exactly that, oxidizing the aldehyde G3P into a carboxylate
form. Isomerases are enzymes that catalyze the rearrangement of a substrate into a
different isomer. The number of atoms of product and substrate are the same. Mutases
do the same thing, and the names are used due to history.
Here are some of the acronyms suggested for OMSG.
Oh my secular god
Hampton: Old man, Spittin' Game (OMSG)
OMSG= oh my saggy glutes!
One Must Serve Guacamole
Oh my sticky gum
Oh My! Shaved Goats! Oxalate malonate...
OMSG...Ochem makes students groan?
Oh my sun god
OMSG: Oh Metabolics, Such Greatness
Orange Madness, Sanfrancisco Giants!!
Oh My Salty Gravy!
OChem Makes Students Grumble
Wednesday 10-24 Lecture 8
Q: Did u know that they only sell u half of the lecture notes? U have to buy it again or
they don't sell the other half
Yes. The cost is calculated by the page, so if I gave them the whole 18 lectures, the
cost would be almost double. No one is ripping anyone off.
Q: Can you go back to the midterm slide
Q: You said the midterm was next week but the slide says nov 5? Which is in two weeks
Midterm is on NOV 5 at 5pm-6:20pm. Due to big room shortages, we will ALL be in 108
Peterson.
TA review is also in 108 Peterson, on Sat Nov 3 from 2-5 PM.
Q: Do we have to know all the structures for these pathways?
Yes, according to the study lists. The basic pathways, glycolysis, pentose phosphate
(oxidative only), the Krebs cycle, glyoxylate cycle. In most cases on an exam, a
structure will be accompanied by a related one (write the products of the reaction that
cleaves fr1,6bP as depicted in the glycolytic pathway; something like that). Because the
different molecules in a pathway are connected by chemical principles, understanding
the chemistry at the level we talk about makes it much more straightforward to know the
structures. Use the previos tests as your guide, and the short lecture associated
problem set.
Q: u said that [the problem sets] are pretty representative of the difficulty of tests
problems. Which one is it
There was a confusing preamble in the original web page section about problem sets.
Thanks for pointing that out. I have fixed it. The Short Lecture Associated Problem sets
are good representatives of typical test questions in terms of answer length, depth of
knowledge, and material emphasis.
Q: Oops Made Stinky Gas (OMSG)
Ah ha! And I thought that was a weird ringtone.
Q: What do u mean by old and new site?
I believe I meant old and new acetate, because citrate (CO2--CH2-)2-C(OH)-CO2- has
two acetates (CO2-CH2-) attached to the same boldfaced, red carbon. One comes
from OAA, whose formula is CO2--CH2-C(O)- CO2-, and so has been attached to the
product before the reaction even occurred, and the other is transferred from CH3-COSCoA, and so is newly added to the molecule.
Q: What does d and l mean
d- and l- are biochemically commonly used terms for two mirror imgage, or
enantriomeric , versions of the same molecule. The way d and l are determined is fairly
complex and historical, but they refer to the same thing as the R and S designations that
you learned about in Ochem. The R and S way is more rational, and can be derived
simply by knowing the 3d structure of a molecule, so more rational.
Q: How does the enzyme tell which acetate is old and new*?
Q: How does the enzyme tell which acetate is old and new*?
Basically, although the two CO2-CH2- groups are identical chemically there is enough
special information in the aconitase molecule to distinguish them. One way to picture
this is if you think about it is to picture the citrate molecule (CO2--CH2-)2-C(OH)-CO2- in
3d space. Let the two acetate groups be in the plane of the paper facing down, with the
boldfaced, red C in the plane of the paper too. Now the CO2- will face out of the plane
of the paper one way, and the OH will face the other way. Thus, this molecule, just like
you are me, has a front and a back, and a left and right side. The technical term for
these two sides is “pro R” and “pro S”. Suppose the enzyme has a pocket that binds to
the CO2- and the OH in space, then the “left” and “right” identical acetates will always
be in the same position in the enzyme. Because citrate is also made by an enzyme, the
new one will always be on the same side of the arrangement, and the older one will
always be on the other side.
Q: I still don't understand how the identical isocitrates are differentiated, could you
explain it again?
The best way to view the question is how “identical acetate groups” are processed
differently. The answer lies in the enzyme providing enough 3d information to discern
the old and new, that is the “proR” from the “proS”. I will not be asking you about this
subtle beautiful feature of enzymes in any exam, but I would be happy to explain it to
you in more detail at office hours.
Q: Sorry one more time, wat does biotin do?
Biotin is in the business of carboxylation, that is making CO2 gas active for addition to
molecules. In a carboxylation reaction, a carboxyl group (basically CO2 if you think
about it) is added to a substrate. That carboxyl group derives from CO2, and biotin
functions to make this happen.
Q: Whats your view of diet soft drinks. Specifically aspartate. Since it cannot be
digested like cellulose due to its ext functional group .what are the harms
You are thinking of Aspartame, which is actually the dipeptide EF, with a methanolic
ester at the carboxyl terminus. It can be metabolized, basically being hydrolyzed into the
component amino acids, and methanol. Despite the ominous sound of methanol (which
in high amounts is indeed toxic) the amounts produced by the sweetener are
prrrreeeetty small. So it appears that the metabolism is pretty safe, except for
pheylketourics, who have an inborn error in phenylalanine catabolism and then it is not
a good think to ingest aspartame.
Q: Boss, are we going over what happens where in the cell?
We will!
Q: Can you explain again why fat can't go through the Krebs cycle
Fat CAN go through the Krebs cycle. It is (as we will learn) broken down into our new
old friend acetyl-CoA, and then it will be efficiently oxidized into CO2 and reducing
equivalents. What CAN NOT happen is acetate can not be converted into glucose
because for every acetate (2C) that is put into the Krebs cycle, two CO2 (total of 2C) are
produced and removed. So there can be no net production of late Krebs products by
turning the cycle. Do the problems that pertain to this in Lecture Problem Set 8. You will
see clearly what I am talking about.
Q: Do humans use the glyoxylate cycle
No, but the 3 or so pounds of bacteria that inhabit their gut does.
Q: Why does glyoxylate condense with acetyl coa?
There is an enzyme called malate synthase the catalyzes this reaction.
Q: what is glyoxysome again?
It is a specialized organelle in some cells that harbors the glyoxylate cycle enzymes and
converts carbon in acetyl-CoA into succinate. A carbon chain building machine!
Q: Your podcasts always cut off at the end
I am sorry. I am hoping that setting my watch exactly with the room clock should stop
this annoying occurrence.
Q: Are you still planning on finishing all of lectures 8, 9, and 10 in the next 2 lectures
before the midterm?
Yes, and I promise that you will not be tested on anything I have not discussed in
lecture.
Q: This is starting to get a little overwhelming... is there something on the website that
breaks all of this down piece by piece?
Well, the problem sets and the study lists help. The way perhaps to break it down is to
remember the function of each pathway, to keep in mind the “useful” products. Also, by
considering individual pathways and their reactions, you can consider the reactions in
smaller circumstances. Once you know the individual pathways, you can start seeing
how one feeds or competes with another, how they are interconnected.
Q: So if you split at isocitrate, one pathway is for atp and the other pathway is stored as
fat?
That sounds about right. The glyoxylate cycle employs acetate to make bigger
molecules such as glucose; and the first enzyme of the pathway the defines it as
different from Krebs is splitting of isocitrate by isocitrate lysase. The other way of
processing isocitrate is in the Krebs cycle, where it gets oxidized in part of a multi step
oxidation that makes, eventually, ATP.
Monday 10-29 Lecture 9
Q: On the problem sets there is a question about the Kreb's cycle. What does the
"turns" mean? How can you have one cycle and 500 turns? Pleaseeeeeee explain
A “turn” is when the reactions around the cycle each occur once, taking us back to OAA,
the substrate of the first reaction and also the product of the last reaction. This problem,
and the related one of the glycoxylate cycle, are there to show the cyclical nature of the
process. A SINGLE OAA molecule, and thus a single Krebs cycle, can support the
oxidation of thousands of acetyl groups fed into this set of reactions. Each time a cycle
occurs, one acetyl group enters, two CO2 come out, A GDP is converted into a GTP,
and FADH2 is generated, and we end up with a regenerated OAA, which can start the
process again.
Q: What time is the review session on saturday?
Q: When is doth review session good sir?
OOPS sorry. TA Review: 2-5 PM in 108 Peterson Sat Nov 3
Randy Extra OH: 3-5 PM
Q: What lectures does the midterm cover
Q: Does the midterm cover up to todays lecture?
1-10. Lectures 1-10.
Q: Is the midterm curved?
The final grade is decided from the distribution of numerical scores. So yes. And it is
very generous, because this is a difficult class.
Q: Can you explain, structurally, oxalate, malate, succinate, because they all have 4
carbons in the krebs cycle
I believe you mean oxaloacetate, (not oxalate), malate, and succinate. They all do have
4 carbons. Succinate is the simplest, CO2-CH2-CH2-CO2 then CO2-CH=CH-CO2
(fumarate; from hydrogen loss), then malate CO2-CHOH-CH2-CO2 (from water
addition) then oxaloacetate (from oxidation) CO2-CO-CH2-CO2. One way to view it is
the gradual conversion through oxidation, water addition, then oxidation, from the simple
highly reduced middle two carbons of succinate (-CH2-CH2-) to the more oxidized
middle two carbons of OAA (-CO-CH2-)
Q: What's ims
Q: what does IMS stand for on the mitochondria drawing?
IMS = inter membrane space, between the outer membrane and the inner membrane
Q: We didn't finish lecture 8. Should we disregard whatever we didn't cover in class?
We now have.
Q: Is pyruvate dehydrogenase complex the same as PDH cycle?
The cycle of reactions that the PDH undergoes is sometimes described that way,
because all the participating cofactors are restored to their original states. The complex
is the set of actual enzymes (with their attached cofactors and fancy 3d arrangements)
that allow this cycle of reactions to convert pyruvate + CoASH + NAD+ into AcCoA,
CO2, and NADH.
Q: What is the function of the cofactors electron acceptors?
To pick up electrons and the donate them to the next acceptor along the ETC (electron
transport chain)
Q: Where are the flavo proteins used? Location and what reactions
A number of the complexes employ flavonoid cofactors such as FAD in the course of
there reactions. These include PDH, complex I and complex II. Note that complex I and
PDH, the flavonoids work “under the radar” meaning they are not release as their
reduced forms, but rather are involved in transfer of electrons, like in PDH where FAD is
converted into FADH2, then then that is restored to FAD as the electrons are passed to
NAD, all inside the enzyme.
Q: Why is there four complexes do inner membrane carriers if we only have 3 listed?
I think you mean that complex II (succinate dehydrogenase) is depicted as being next to
the membrane. It is still a strongly membrane associated protein.
Q: What was the point of showing us the lipid bilayer again
To indicate that the interaction and placement of the complexes intimately involves the
bilayer. Purification of these complexes requires solubilization using detergents that
replace the membrane molecules in a manner that allows solubility without loss of
complex structure. Very difficult.
Q: What's the relation b\t quinomes and cytochromes ?
The most significant one, and the one we focus on, is the transfer of electrons from
reduced ubiquinone (QH2) skittering around in the membrane, and cytochrome c,
converting it from its oxidized form Fe+3, to its reduced form Fe+2. This is accomplished
by Complex III, called, not surprisingly, ubiquinone:cytochrome c oxidoreductase. The
net occurrence is QH2 transfers electrons to 2 cyt c, converting each to the reduced
form (Fe2+), but the actual enzymology uses a complex cycle called “the Q cycle” that
.
involves transient production of half reduced QH , and then fully reduced QH2 in the
course of this process. The net reaction is QH2 + 2 cytcox –> Q + 2cytcred
Q: Can u please explain the relative light absorption graph again?
Iron-containing heme groups buried in the various proteins of the complexes 1,2, 3 and
4 have light absorption properties that change when oxidized or reduced. Literally the
colors change between the two states. Using a spectrophotometer, this change can be
measured, and so one can tell WITHOUT PURIFYING or even breaking the mitos open,
whether a particular cytochrome (with it iron-containing heme group) is in the oxidized or
reduced state.
Q: So ubiquinone and cytochrome have same functions? What are the differences?
Both have the capacity to pick up electrons and then pass them on. This cycling
between oxidized (fewer e) and reduced (more e) is the commonality of all electron
carriers that participate in the ETC. They are some of the “T”s of the ETC.
Q: So what's the point of the iron sulfur clusters
They are one of the ways that Fe ions involved in the inner workings of the electron
transport chain complexes transact movement from the start to the end. Electrons tht
start at NADH or succinate are transferred many times along the way to O2, and some
of those transfer points are the Fe ions in Fe-S clusters.
Q: Are these just all protein enzymes in the mitochondria?
The enzymes are best thought of as four separate redox complexs, called complex I, II,
III, and IV. The heme, flavonoids, and iron-sulfer clusters are features of those redox
proteins that allow them to do their electron transport thing.
Q: Omg what's going on
It is really all about the four complexes, the path the electrons take from NADH to O2,
the protons that are pushed out to the IMS, and the way that ATP is made from that
proton gradient. That is what is going on when you boil it down to a sweet sticky syrup.
Q: Will there be a reading for these past lectures? They help.
I am working on it. But the book actually has very good descriptions of these processes.
Q: What is "not c" under cytochrome mean?
Cytochrome c is a free small soluble protein, and that is a major exception to the usual
observation that cytochrome proteins are embedded in tightly membrane-associated
complexes. So not cytochrome c.
Q: What was the point of the half cell you drew on the board
That half cell reaction, Fe+3 + e- –> Fe2+ , and its reverse, is the main way that iron is
employed in the ECT. Fe+3 picks up e from some donor and then transfers it to the next
acceptor along the path. Electron on, electron off…
Q: You look like William Bonaparte Esquire
I don’t know who that is… but Napoleon was diminutive… perhaps that is your
reference.
Q: What's the difference between "integral membrane" and "membrane bound" proteins
Sorry, that was a little esoteric, but very useful. Integral membrane proteins actually
have segments on both sides of the membrane and are essentially part of the
membrane. The only way to get them out for purification is to use detergents that take
the place of the bilayer molecules in a manner that allows them to be soluble. Very
tricky biochemistry. This is why Efram Racker and his posse were such wizards, along
with many of the other people doing biochemical approaches to study the ETC.
Q: How are we making oxygen
We are not making O2, but rather are consuming it in the final depositing of electrons
from the ETC to make H2O. The O2 comes from photosynthetic organisms that are the
ENTIRE reason we have oxygen on Earth. At one time we did not….
O2 is a substrate of Complex IV, as is reduced cytochrome C.
Q: When the iron gets oxidized where does the electron go
On to the next acceptor in the collection of “stepping stones” that form the complex path
through the four complexes and finally to H2O.
Q: Does NADH dumping electrons on to Q and succinate dumping electrons on to Q
happen simultaneously?
Complex I, which catalyzes the transfer of electrons from NADH onto Q, and Complex II
which catalyze the transfer of electrons from succinate onto Q, are two separate
enzymes that both use Q molecules as substrates. There is sufficient Q in the inner
membrane of the mitochondrion to allow both reactions to occur simultanseously, but
each enzyme will work on a separate molecule of Q. They don’t work together on the
same Q molecule. It would be like two types of hexokinase in a solution with glucose.
Each would be working on glucose molecules simultaneously, but separate molecules.
Or separate bank tellers woring on the same group of customers. They are all working
at the same time on separate customers.
Wednesday 10-31 Lecture 10
Q: Will the review be podcast?
Workin’ on it! Make sure the TAs wear the mic, since it is recorded through that.
Q: Why doesn't complex 2 pump out protons ? What does it do?
Complex II simply (although at the molecular level it is anything but simple) moves
electrons from succinate (OMSG: -O2C-CH2-CH2-CO2-) to QH2. That is very important
in its own right because the more QH2 provided, the more proton pumping action you
get from the subsequent transfers through complex III and IV.
Q: What's the relation b\t quinomes and cytochromes ?
Ubiquinone (or Q as we usually call it) is a quinone-based electron carrier that is present
on the surface of the mitochondrial inner membrane. It is a molecule that carries
electrons from its production as a complex I and II product to complex three where it
those electrons are used to reduce cytC, which is one of the many cytochromes that lurk
in the ETC. The actual transfer of electrons through these complexes involves many
electron transfers between carriers, hidden in the complexes, and some of these are
cytochromes that have the classic heme-bound iron prosthetic group. However the most
important cytochrome for our purposes is the simple single subunit cytochrome c, which
is reduced by complex III and then oxidized by complex IV.
Q: Where is cytochrome oxidase in the etc?
It is complex IV. The water-maker!
Q: Where does the energy to Pump protons from complex 1, 3,4 come from?
The complex set of redox reactions that start with NADH or succinate giving up their
electrons and end with oxygen becoming water are all exergonic, and the energy
produced by the passage of electrons gradually from molecules that like to get oxidized
(like NADH) all the way down to those that love to get reduced (like O2) provides the
free energy to push protons up a gradient, thus storing energy.
Q: In the weak acid uncouplers picture, on the low H+ side, does AH only go in one
direction to H+ + A-?
Perhaps a better way to look at it is that when there is more H+ on one side of the
membrane, there will be a higher concentration of AH (simple mass action like you
learned in Chem 6whatever) and those more abundant AH will be able to cross the
membrane and break down the gradient. It is a very un-fancy mechanism.
Q: Is that candy for the class?
Yes, but one of you sci-rats stole my blue crystals. DUDE, that was m’prop!
Q: If the outer membrane is very permeable, why don't the Hs flow out of the
mitochondria?
It does seem paradoxical. The answer lies in the fact that the inner membrane is highly
convoluted allowing proton gradient to exist fairly unperturbed, and also in the fact that
the gradient in normal circumstances does not sit around for long: it is tightly coupled to
ATP synthase, and each little increase in the gradient drives the next turns of the ATP
synthase. Sort of like two gears locked together. But if one waits long enough…
Q: Atp synthethas reversible? I read somewhere if you put atp in it rotates the opposite
direction and gives out Pi
That is true. The brilliant experiment showing the actual ATP dependent motion of the
gamma rotor (the camshaft in our lecture) depends on this reversibility.
Q: Can I have some of your blue meth?
Yu need to ask the sci-rats who grabbed the whole bag.
Q: Can u explain product exit?
When an enzyme converts a substrate into a product, sometimes that energetically
unfavorable step is the removal of the product from the energetically stabilizing
environment of the active site back out into the cruel world of aqueous solution. This is
the case with ATP synthase. In the active site, ADP and Pi readily interconvert to ATP; it
is a very special environment where this reaction is quiet fast and favorable. But back
out in water, the ATP gains a lot of free energy, so that is where the reaction needs
energy: pushing the product out of the active site. Proton motive force to the rescue.
Q: Does the arm rotating in the middle blow your mind? How insane is that? A
mechanical device we use in our world exists at the molecular level. Crazy
It is amazing, and appears to be a conserved theme in conversion of gradients into
motion. This gradient-to-rotation conversion must have arisen after gradients could be
formed, that is after membranes and containment became possible, although it is
possible I suppose to imagine exploiting a concentration gradient along a surface.
Maybe….
Q: RE: so the stater holds what end?
The epsilon subunit/side arm/stator provides inertia to the
F1 trimer so that the gamma subunit can rotate within
while the trimer (those three sets of alpha-beta subunits)
stays motionless. Like holding windup toy while you wind
it. If you didn’t hold the windup toy, the whole toy would
spin. Your non-winding hand (the one holding the toy) is a
stator.
Q: Can you post that mini movie online please? That was cool!!!
Did. It is there. Kind of small, but there.
Q: Does lecture 10 have to be on the midterm?
It is the funnest stuff so far. Embrace it. Also, it is actually fairly descriptive. Much less
memorization than the earlier stuff. The more complex metabolic features will be saved
for 11.
Q: Which part is F1 and which part is F0 ( f not) on an ATP synthase?
F1 includes all those soluble parts, like the (ab)3 trimer and the gamma “camshaft” and
the epsilon stator. The membrane embedded (and proton channel providing) Fo is the
integram membrane part.
Q: Whats the difference between the red n black line
The black line is the consumption of oxygen (showing the flow of electrons through the
ETC; you could also use succinate consumption or water production, but O2
consumption is very easy to measure in real time) and the red line is ATP production.
The fact that a number of perturbations, like adding CN- ions, or removing ADP cause
BOTH curves to change in the same manner is the coupling we are talking about. The
surprise came in realized that the coupling is through this H+ gradient.
Q: Was that last video slowed down or sped up?
That movie was in real time. You can see all the Brownian wobble that is due to the
constant bombardment of the molecules being observed with water molecules, like a
statistical hale storm. In your book, where the movie is shown as separate panels, the
time between each is 33 ms.
Q: How are enzymes 1-4 in the ETC coupled with ATP synthase ? Is it because of the
gradient made by the enzymes are "phunneling" the protons in to ATP synthase?
That’s sort of it. The enzyme action that moves the electrons from their starting places
(NADH or succinate) to O2 causes a proton gradient. This gradient is then “phunneled”
through ATP synthase to provide the energy of ATP production.
Q: Does the rotation of ATP synthase produce any heat due to friction between it and
the membrane?
Heat is really a macroscopic quantity that comes from the local molecules gaining
kinetic energy. Frictive heat is something seen in bulk materials and does not have a lot
of analogous features to these molecular events.
Q: why is the N in asparagine not charged but the N in other molecules like proline, with
the same number of bonds is charged?
The N’s in N termini found in all the amino acids, or the N at the end of the R group in
lysine are normally charged in physiological conditions (pH = 7) because they are amine
nitrogens, bound directly to a carbon with H’s or other carbons. This is in contrast to
“amide” nitrogens that are bound to a carbonyl carbon, that is bound to a carbon with a
double bonded oxygen. Amide nitrogens, due to the properties of a carbonyl group, and
much much more stable than amine nitrogens and are much less basic. So they tend to
be neutral in solution. Amine nitrogens and amide nitrogens look very similar but they
are very different.