Lectures 1-3 (Sept 26, Oct 1 and Oct 3) Is this system meant to substitute hand-raising? Nope. It is meant to augment hand raising for those who have questions but do not feel like voicing them in a 400 person class. I welcome and encourage questions from all sectors of the auditorium! Do we need to memorize structures of amino acids? You do NOT need to be able to draw them from the name or one letter code. You DO need to be able to look at a structure of one, and say what it is named, and what the one (or three) letter code is. But I PROMISE I will not play games like give you close-but-wrong structures to trick you. Not going to happen. Do we have to know the 3 letter abbreviations for the amino acids? Yes. It is like an English major asking if they need to know the alphabet. Really. So what is a double dagger? The "double dagger" that looks like this ‡ as a superscript‡ is a way of indicating free energy of activation, to distinguish it from free energy of a reaction. It is the "energy hump that controls rate, but not extent of an equilibrium as described in your chemistry classes. The equations you wrote in Microsoft Paint hurt my soul, please redo them. I actually used a stylus, long ago, but hand written has some soulful aspects, no? So was d=20? So then is 20kj equal to d in that slide No. d is any amount we want it to be. It is a variable that shows the general effect of lowering activation energy (ΔG‡ ) by the amount d, whatever it is. The beauty of equations is that they allow testing any value at all, by setting the variable to that value. So in class I said "OK, now we know how rate is affected by lowing activation energy by the amount d. Let's try one out. Let's choose 20kj/mole as a test value because this has a physical meaning, one hydrogen bond worth of stabilization, to see what happens.” Like that. Are we going to learn more about the protein folding problem? No. Not really. It is a great problem, and a deep one, but not one we are going to talk too much about in Metabolic, which presents its own set of great, deep problems. Out of curiosity- what happens if d>Aold? I am not sure that is possible. That would mean there is no barrier to the reaction and the substrate would have no stable existence. Could you explain again what you mean by there being an identical effect in both

directions? Well, if you lower the activation energy by d, the forward rate is accelerated by e to the d/RT and the reverse rate is accelerated by e to the d/RT as well. Identical multiplicative increases in forward and reverse rates. Catalysts are totally democratic… Where do you read ligand binding and enzyme catalysis? Slides or book? See class website for the PDF courses.ucsd.edu/rhampton/bibc102 L and B are units of molarity, right? They are in unit of concentration, correct. What is saturable Because there are a finite number of binding sites in a solution of a binding protein, or active sites in a solution of an enzyme, the number of bound liigands or enzyme reactions happening at a set time reaches a maxium. Anology: if there are 8 stations open at the DMV office, they they can only handle 8 customers at a time, so that is also a saturable system. What is metal ion catalysis Just like the name indicates, it is a type of enzyme catalysis in which a metal ion that is associated with the enzyme (usually tightly bound) is directly involved in the catalytic mechanism. You have seem many examples of metal-based catalysis in your O chem classes, and biology shows us many more. Whats the difference between V0 and R? Vo is the more technically accurate depiction of the enzyme catalyzed rate of reaction. It is technically the rate (or velocity) of the enzyme reaction at the initial time when the S concentration has not had any chance to diminish due to consumption by the enzyme reaction. What is the diff between kcat and km, and when do you use them? Km (often called the Michaelis constant) is the constant in the ratio S/(S + Km) that describes the fraction of maximal activity that a given concentration of S will produce for an enzyme that obeys Michaelis-Menton kinetics. The kcat is the maximum rate that a given enzyme can produce when operating at saturation. For a particular experiment, the velocity of an enzyme reaction Vo = [S/(S+Km)] x Vmax and Vmax = kcatEtot So put simply, Km pertains to the shape of the rate vs substrate concentration curve, and kcat pertains to the maximum rate of the enzyme Do you have efficient/productive study tips we could use for this weekend? Readings, problem sets, study list, terms list.

Did u say that when K=L its 100%? When L =,Kd, or S = Km, the binding/enzyme rate (depending on which equation you are looking at) is 50%. Don’t take my word for it: for the fraction S/(S + Km) let S = Km. What do you get…? Hi dr. Hampton, does Kd have a relationship to time? Will a higher Kd always take longer to saturate the substrate? What is the diff between non competitive inhibition and allosteric inhibition? Allosteric inhibition works through evolved binding sites on quarternary structured enzymes, and is a natural part of many regulated enzyme steps. Non competitive inhibition is one way that enzymologist describe the effects of enzyme inhibitors. It is much less useful to us then allosteric regulation which we will reference many times throughout this class, and your subsequent bio or biomedical careers. What's so great about making the graph linear? Often linearizing data allows for instant observation of things that are totally cryptic in the raw data. A beautiful example: two enzymes with the same Vmax but different Kms would have rate vs substrate data that looks very similar in raw data graphs but would clearly be two separate lines intersecting cleanly on the Y intercept in LB plot. Like that. Can you put your rap lyrics on the website? It's educational you know I will So is the chorismate mutase mechanism with Y and W as regulators comparable to a negative feedback loop? The Y branch, in which an abundance of a product prohibits its further production, is a negative feedback loop. The W branch, in which too much of the other branch activates the CM to promote alternate use of the chorismate to make Y, thus promoting balanced production of amino acids, is called “feed forward activation”. so tryptophan is added to chorismate or cm to activate? In studying the chorismate mutase (CM) reaction, you would have the enzyme CM present in a reaction mix with chorismate (the substrate) and be watching for formation rate of perphenate or the consumption of chorismate (either is fine). The observation is that if you also have W present, the rate of conversion of chorismate into perpenate by the CM enzyme is faster. Capiche? Is tryptophan what makes you sleep after you eat turkey? So people say. The trouble is, it is always associated with a massive turkey dinner, and who isn’t sleepy after TG dinner… what is S and E when you talked about cooperative binding?

If you are referring to ligand binding and enzyme catalysis, S is the substrate concentration, and E is the enzyme. What happens when the Hill coefficient is one? Then we have Michaelis-Menton kinetics. A rectangular hyperbola. Why does hemoglobin create a K value that is not constant. But myoglobin does. Hemoglobin evolved that way by acquiring a quarternary structure in which the binding of O2 has effects on the tetramer that affect the binding sites. Myoglobin is probably a bit more like that common ancestor molecule of hemoglobin and myoblobin, although that is a guess…. So for a non cooperative system the rate doesn't change? Sort of. The rate equation does not change. The rate is a function of substrate concentration, but that rate is described by constants that do not change. The Km and kcat extracted from the rate vs substrate concentration data at any substrate concentration would be the same. The constants are constant. A little subtler but I think you have the right idea. So anything with allosteric regulation is quaternary, so are most things that are quaternary regulated allosterically? The first is true. That essentially all (there are very very very rare exceptions) allosteric enzymes have 4o structure. But there are plenty of quaternary structured proteins that do not have allosteric properties. How do enzymes measure Ligand concentration? By binding. There is really no action at a distance in molecular biology… Is it hipster to say multimer instead of polymer? A multimer is another way of saying polymer. is O2 an allosteric activator for hemoglobin??? It is indeed. It is in the class of allosteric activators known a “homotypic” activators, meaning it increases the affinity for its own binding. A “heterotypic” activator would be something that increases the affinity for a distinct ligand. Does that mean myoglobin is not able to detect oxygen levels since k is constant? Myoglobin does not change its oxygen binding properties in response to oxygen. But it still binds it just fine. But with a constant Kd. Can u not edit out ur jokes on the podcast? Some I leave in, some I remove. There are jokes that work well in the context of the

classroom but may be misinterpreted or hurtful out of context. Does phosphorylation only activate enzymes? Phosphorylation can either activate or inhibit enzymes depending on the particular enzyme, and phosphorylation also has many many effects on proteins that are distinct from altering enzymes. Changes in cellular localization, association with other proteins, stability of that protein, and a host of other things have all been associated with this important covalent modification.

Lecture 4 & 5 (Oct 8 and 10) When is the exact date of the midterm? The syllabus says two dates: Halloween and nov 5. Is entropy not a natural occurrence but requires energy to accomplish it? Disorder does not require energy correct? Gaining entropy is spontaneous. Thus a positive gain in entropy (ΔS is positive) will contribute to negative ΔG (by the amount -TΔS). Many important biochemical processes are primarily driven by changes in entropy, such as the hydrophobic effect. On the other hand, decreasing entropy (that is, putting a system into a configuration where where are fewer possible states) costs energy. Many uses of biochemical energy involve spending that energy to order systems, that is, to lower local entropy. I was reading your glucose article and my mind was blown upon finding out that glucose is the result of the OH group on one end of a linear molecule attacking the carbonyl C of an aldehyde on the other end. Hooray for learning new things! A new form of government: Anomerocracy! Do we need to know the individual steps in the chymotrypsin mechanism for the midterm and final? No electron pushing needed. But the catalytic cycle and the role of each of the 3 residues for sure. The first slide that you showed today (figure 1-29) looking at the arrows says that converting ATP to adp is is endergonic/ anabolic but you just said that delta G=negative 30.5 so isn't this rxn exergonic due to a negative delta G? On the slide with catabolism/anabolism diagram: the arrows say that converting ATP to ADP is endergonic/ anabolic.....does that mean ATP is consumed? Thi Anabolism involves building bigger biomolecules and structures from smaller parts ,and this often (almost always) takes energy. Classic example that you already know: the synthesis of proteins cost substantial biochemical energy. So often these reactions are driven by free-energy yielding reactions such at ATP hydrolysis. On the other hand, catabolism is the breaking down (usually oxidation) of big molecules to generate energy and parts for anabolism. One of the most important products of catabolism is… ATP, which is produced by oxidation of many fuels in the catabolic pathways. The confusion comes from the fact that many of the reactions of anabolism require energy and are indeed endergonic. The energy to drive those reactions to the right despite their need for free energy is provided by the hydrolysis of ATP. How was your birthday?? Most excellent. For an old guy. Ran 17 miles in the beautiful wine country of San Luis

Obispo central coast. The first 16 were great… Do we have to know the mechanism for how ATP turns into ADP or just the fact that it does/where it does for every mechanism? It is a hydrolysis reaction. I am not sure what you mean by the mechanism. How do you determine which is oxidized and reduced in the organic molecules that you showed us. In this class, does more c-o bonds equate to more oxidized? Usually the more oxidized versions will have more oxygen and less H, but one must look at transitions between molecules to know. A nice example is the conversion of ethanol (CH3-CH2OH) to acetaldehyde (CH3-CHO) which is a classic biochemical oxidation. What are the names if the processes to add and remove phosphorus I believe you mean phosphate (-PO4) the group that is often added or subtracted to other molecules. Addition of phosphate is called “phosphorylation” and almost always that phosphate is donated by an ATP molecule. The enzymes that catalyze this are called “kinases”. Enzymes that catalyze transfer of phosphate from ATP to proteins are called “protein kinases”. Removal of phosphate is called “dephosphorylation” and these reactions (which are examples of hydrolysis) are catalyzed by “phosphatases”. Enzymes that remove covalently bound phosphate groups from proteins are called “protein phosphatases” Do we need to memorize all these formulas? I thought you had in chem 6… anyway, you need to be able to work with them, but memorization is not necessary. I will say that knowing these few formulas makes it much easier to understand how ΔG’ and ΔE’ relate to each other, and to understand how concentrations of reactants and products affect the actual ΔG of a reaction in cellular conditions. Can u point to the transfer of deltaG in a phosphorylation mechanism? The ΔG is not really a specific reactant, but will determine which direction a reaction will go in spontaneously. Hello Professor Caliente! ;D I apologize ahead if you have discussed this already: do noncompetitive, competitive and allosteric inhibitors affect the enzyme isotherm the same way? As in the generic graph pictured given in the article. Also, Ibelieve allosteric is general term for noncompetitive? T or F? Competitive and non-competitive are terms very specifically used for small molecules (often drugs) that affect and enzyme often through interacting with the active site itself (competitive) or at other parts of the enzyme molecule (non or un competitive). Allosteric regulation is an evolved mode of regulation that involves multiple subunits and binding

sites of an enzyme that allow for (usually) natural molecules to control an enzymes action, and often to regulate that enzyme within the context of metabolism. The effects of each on the isotherms are distinct, and we will focus mostly on allosteric vs. michaelis –menton enzymes. So when using ATP as a coupling mechanism for a reaction it's not just the phos group that can attach but also the adenine and ribose group can become a good leaving group? That is correct. It depends on the particular enzyme reaction, but both Pi, and AMP, and sometimes other parts of the molecule can be added to directly involve the liberation of fee energy stored in ATP in driving a metabolic reaction. In class I showed you example of Pi being used (for glutamine synthetase) and AMP being used (in synthesis of palmitoyl-CoA) as leaving groups. Has anyone told you that you kinda sound like Seth Green? He is in my entourage After the NADH ring you showed on the board was reduced, it is still aromatic because the N also has a pair of electrons that contributes to aromacicity right? Because the carbon at the top positition loses its free pi electrons, one no longer has an aromatic ring, despite there being still 6 available. The technical term for the reduced ring is a “quinoid ring” and it is apparently not aromatic due to the localization of the pi electrons. What is moieity again? Moved too fast! (from googling this: “define moiety”) one of the portions into which something is divided : component, part <an ether molecule with a benzene moiety> 3 Sorry but What's that blue proton doing there again? The blue proton is simply provided from the pH buffered environment to ensure charge neutrality. if nadh is in reduced form and "reduced" means that it has gained electrons, why are there more hydrogen in its molecular structure? Well, often reductions are accomplished by addition of hydrides (H-) or by addition of hydrogen radicals (H.) as we will see. This can also be described as 2e plus an H+, the result is the same. Hey homie how's life Grand. I am a lucky and blessed to do this for a living.

What reactions would FADH2 power that NADH couldn't? It will be determined by the enzymes that choose to use this reducing agent rather then the NADH. You will see many examples of this, but there is no stark generality. Is there a relationship between formal charge and the redox of a biomolecule? Not really. One must be careful to consider the group being oxidized. For example, if there is an R group somewhere on a molecule that is charged but not involved in the oxidation or reduction reaction, this charge will not say anything about which form is present. A good example can be found in the NAD molecule. It has a negatively charged phosphate, and NADP has two, but these do not participate in the redox chemistry itself. The BETA glucose is more stable actually.... Your TA is wrong !!! Thanks! Being wrong is the normal territory for the working scientist. Being right is the working territory for the excellent student. Beta glucose is more stable. It has alternating alcohol/ch2oh group. Relieves steric problems -that enzymologist dude Thanks E dude… is phosphohexose isomerase also called phosphoglucose isomerase?? It is also called that. But don’t worry about it test-wise. I would never make you distinguish or commit points to one vs. the other. How is the weight loss experiment coming along? Dipped below 134 yesterday. Everything tastes incredibly delicious. NY Marathon is on Nov 3… why is the alpha glucose more stable than the beta glucose? It is actually the beta form that is slightly more stable, because that configuration has a bit less electrostatic and steric effects apparently. See enzyme dude answer above… Can you explain the coat hanger model again Because the aldolase reaction creates two products, (DHAP, and G3P) and the DHAP is converted into G3P which continues flowing down the pathway, glycolysis can be represented with a triangular “section” where the two products are made, and the bottom of the triangle is the conversion (by TPI) between the two three carbon products of aldolase. Convince yourself!! Does the process of glycolysis have to begin with glucose? Or can an input of intermediate molecules still partially travel through this cycle?

Intermediates can enter the pathway if they end up in the cell or are generated during other metabolic pathways. Do we have to know mechanisms? Only the few we discuss directly in class. Will you post the answers to the problem sets? They are in the link one down from the non-answered sets…. Check it out!

Lecture 6 & 7 (Oct 15 and 17) Do we need to memorize the structures of AAs? You need to be able to recognize them. That is very different from being able to draw them “cold”. For instance, if I showed you this amino acid, I would hope you would be able to say, “ that is lysine, or LYS, or K. But drawing it completely from memory is not necessary, almost never needed in even the most advance biomedical types, and does not help you understand lysine’s various uses in proteins and metabolism. Where does the extra phosphate for 1,3 BPG comes from? You mean the one that is a substrate of the GAPDH reaction? There is a relatively constant concentration of phosphate ions (PO4

2-) in cells. It is involved in all sorts of reactions, and this is one of them. Does glucose get broken down into both G3P and DHAP Exactly. The aldolase reaction has one substrate (fr 1,6 bP) and two products, DHAP and G3P. It is the “lysis” for which glyco-lysis is named. That one substrate-two products reactions is the “branch” in the “coat hanger” model of glycolysis as we draw it. Do we need to recognize each step that takes place in GAPDH? Yes. You have SH forming an adduct with the aldehyde carbon (analogous to the way anomeric rings form with OH and the aldehyde carbon in glucose), then you have NAD extracting H- from the adduct to convert it from aldehyde to carboxylic acid, then you have PO4

2- bumping the 3 carbon molecule off of its roost on SH to form the product. Voila. You look like mclovin from superbad Sigh. You are like the 10th person, from many walks of life, to tell me that. Loved that movie. McHampton. I made an on the cheap costume this year by taking advantage of the resemblance. Worked. In the isomerization of 3pg to 2pg, is Mg2+ a cofactor? Mg2+ is almost always involved in reactions that involved phosphorylated compounds to provide charge neutrality and binding energy. It is so common we don’t usually discuss its presence. Most of the time cofactors we talk about will do some fancier chemistry that involves bond making and breaking. What enzyme adds phosphate to fructose in the liver? It is called fructokinase

so when glycogen is used up, then fat starts burning in a workout? Glucose is the fuel of choice, and your statement is correct with the caveat that usually it is more that the ratios shift towards fat utilization and away from glucose. When a marathoner “hits the wall” late in their race, it is because their glycogen supplies are severely depleted and they are now running on mostly fat oxidation. That is called “bonking” when the glycogen is sufficiently low and it is not a pleasant feeling. if glycogen is stored in muscle, why is meat considered without carbohydrates? Nice! The composition is very low in carbs. [Meat] consists of roughly 75 percent water, 19 percent protein, 2.5 percent intramuscular fat, 1.2 percent carbohydrates and 2.3 percent other soluble non-protein substances. Your own skeletal muscle mass is probably about 30-40 percent of your weight, so lets say in the range of 20-30 kg, while your fully loaded muscle glycogen content is in the range of 300 grams. See? What enzymes remove phosphate groups? When they are specifically removing phosphate groups covalently bound to proteins, they are called phosphatases. Is glycolysis the primary entrance into the metabolic processes? Like airport security? I like that! Glycolysis is the primary way the carbohydrates like glucose, fructose, galactose, mannose, etc are metabolized, as well as smaller fragments. Fatty acids and proteins are metabolized by ending up as molecules that feed the Krebs cycle. Is lactic acid fermentation the only way to recycle NAD [or does the NAD from the electron transport chain get used as well?] When the ETC is working (and we have not covered this in class yet) NAD is also regenerated by fancy mechanisms that allow the electrons to be removed from the cytoplasmic NADH (just like in fermentation) but the be moved into the mitochondrion where they are used. This way provides a few more ATP to the whole mix. Do we need to know the structure of TPP? NO. You should be able to pick it out from a “lineup” of various cofactors, which is considerably easier than actually memorizing it. Is that CO2 from pyruvate lost via the six-member transition state decarboxylation mechanism? Shoot I don’t know. It is lost during the TPP catalyzed decarboxylation that results in a two carbon tetrahedral intermediate that is next transferred to lipoic acid. Is lactate the same as lactic acid? Yes. Technically, the lactate is the deprotonated form CH3-CO-CO2- and lactic acid is

neutral CH3-CO-CO2H, but people use these terms almost interchangeably. Especially trainers. Too cold to concentrate Im very enthusiastic to learn because there is AC today in the lecture hall Diversity is the spice of life! Do we have to know the reaction energies for glycolysis? NO Do we need to know the structure of each intermediate in glycolysis and the Krebs cycle Each metabolite. Yes. But if I have you draw one in a reaction, it will be as part of a reaction where either a substrate or a product from that reaction is provided. Look at the practice midterms, especially recent ones. Will we learn about gluconeogenesis We will indeed. Yo can I buy your Enzymes Rap song on iTunes? My cipher is from the heart, not the pocketbook, yo! Does regulation only count as allosteric if it takes place on a different subunit from the active site? Or does regulation on a different site of the same subunit also count as allosteric? Almost always, allosteric regulation involves multiple subunits that are bound together as quaternary structures. In the case where a substrate is causing its own allosteric effects (a sigmoidal rate-vs-substrate curve) the quanternary structure involves multiple subunits with the same active site. What does PFK-1 phosphorylate? Phosphfructokinase-1 phosphorylates fructose-6-phosphate (F6P). It is the third enzyme in glycolysis. It is beauty! How can we tell that PFK-1 is a quaternary protein structure? It's color coded which makes it look obvious but how is it separated into white and red? Those separations are done by researchers to allow easy discernment of separate polypeptide strands. This is not a structural biology class so there will be no challenges to pick out a quaternary from a non quaternary protein from molecular graphics. You said pfk-1 regulates atp or amp? ATP, AMP and ADP regulate PFK-1. ATP slows down its activity, and both AMP and ADP block ATPs ability to do this.

After glycolysis ends, what's the purpose of creating lactate, acetyl CoA, and lipoic acid? What's it related to? This is a question mashup. If fermentation is going on (and no oxidative processes are being used to get more energy out of the pyruvate) the formation of lactate in some cases or ethanol in others allows regeneration of the NAD needed for glycolysis, and production of a pyruvate product that can be excreted. IF the mitochondria is working, and the Krebs cycle is turning, then acetyl co a is produced to begin the process of further metabolizing the pyruvate for beaucoup energy. Is Glucokinase only found in the liver and hexokinase only found in regular cells? Yes Is fructose biphisphate and allosteric inhibitor or regulator? I believe what you mean is Fr2,6bP which is distinct from the glycolytic intermediate Fr 1,6bP. Fr2,6bP is an allosteric activator of PFK-1, and we will talk about this in more detail later, after the first midterm. Does phosphorylation of adp inhibit pfk1 activity Only in the sense that ATP is an inhibitor, and ADP is an activator, competing for the same site on the allosterically regulated PFK-1. Do we have to know all the enzymes involved? Yes Why is it always atp and not gtp or another ntp? That is a deep question, for which there is not a good answer, yet. But undoubtedly the early common organism evolved ATP as the primary source of hydrolytic free energy, and inventing new ways to use this old trick is much much easier than inventing new tricks. On the slow burn paper, you have the oxidation of glucose written as: C6H12O6 + 6O2----> 12CO2+ 6H2O Isn't it: C6H12O6 + 6O2----> 6CO2+ 6H2O Right? You are right. Sorry. My (super)bad. fpk or pfk? PFK PhosphoFructoKinase

Do we need to know the reactions on the first slide of lecture 6? No. For all those who don’t know what this slide is, it is a complex depiction of the ways various sugars are converted into glucose or other glycolytic intermediates. You do not have to know more than that this is a common way for sugars to be channeled into catabolism. However, I do want you to know the route for liver fructose’s catabolism: phosphorylation on the 1 carbon, cleavage into DHAP and glyceraldehye (without phosphate!) and then phosphorylation of the G to make G3P. Have you hit or do you still hit the bong? Before you were a good idea, maybe. Today, no mind altering substances except for those I produce by running, or crying in movies. Where does acetate get it's extra oxygen after CO2 is ejected? The acetyl group is really the acid portion of an ester, so generation of free acetate would require hydrolysis which adds an oxygen. But There is no extra oxygen. We go from CH3-CO-CO2 to CH3-CO, right? 32 ATP from one pyruvate? Or two from one glucose? OOPS! You are correct, from two pyruvates. I apologize. Will clarify in class. A tone compared to glycolysis. so the citric acid cycle is generating electrons by oxidizing carbons without oxygen? Yes Where did you go to grad school? University of Wisconsin Dept of Biochemistry. A wonderful place to learn the art of science. But cold cold cold. What ever happened to your weight loss experiment? As of today down to 132. Marathon in 13 days… What happened to the pyruvate attached to the TPP in the PDH cycle? It gets transferred to lipoic acid in the E2 subunit, and then that gets transferred to CoA-SH to make our desired product. Isn't NADPH the same stuff in photosynthesis? ‘Tis

Lectures 8 (Oct 22) How is it symmetrical? Aren't those two different groups on the Carbon Citrate is symmetrical even though there are different groups. The molecule can be divided by a mirror plane that reflecs one haif into the other. The carbon with the OH, the COO2, and the two CH2-COOH is not opically active. But it is “prochiral” meaning that there is sufficient structural information that the “left and right” CH2-COOH can be treated differently by an asymmetric pocket like an enzyme creates. why do we want the citrate to be asymmetric? It is not a matter of desire. The OH is moved to the “side” that is, the “older” CH2 to allows the subsequent reactions to occur. Why is keto favored over enol? That question came in and a few minutes later, this answer was texted by The E Dude, who is a fairly advanced chemistry student who is in our class. We likey! C doubly bonded to O is a much stronger bond then c=c so keto favored E dude See…? Why did the malate dehydrogenase reaction have a positive delta G? Often single reactions in a pathway do have positive ΔG’o, and thus Keq less than one. But so long as the metabolic pathway they are in is exergonic, no problem. A siphon has sections where water is running up hill. Like that. In the slides about the Krebs cycle I see 4 carbons on malate I thought there were 3 Malonate (or malonic acid) is OOC-CH2-COO (3 carbons OMSG), and is also called malonate. malate is the 4 carbon Krebs cycle molecule OOC-CH2-CHOH-COO, which to be name-gamish about it, could be called alpha OH succinate, but no one does call it that. Too bad. Doesn't the Krebs Cycle by itself only generate 2 ATP while the E/H chain generates the rest through chemiosmotic phosphorylation? Yes. Each turn of the Krebs cycle makes one GTP (which is equivalent to an ATP) so one glucose, two GTP from Krebs. But as you will see, the NADH, FADH are used to make a large amount of ATP. Isn't the inner membrane also referred to as the cristae? No. The invaginations (whirly protruberances) are called cristae. They allow much greater surface area and thus, more energy producing surface. On behalf of your sweaty metabolites, I thank you for your help

We’ve got powerful people on our SIDE yo!

Lectures 9 (Thurs Oct 24) Reminder to take off that study list thing about glucose regulating the glycogen thing Ah yes. Just a note: I removed a few items from the Lecture 6 study list. You only have to know how fructose enters the glycolytic pathway. You do not need to know how mannose or galactose does so. You do not need to know how glucose allosterically regulates glycogen phosphorylase. You do not need to know the composition of the two disaccharides mentioned. The current study list is up to date. Do you know if your lecture slides for lectures 11-20 are available to purchase yet? I am working on them. So not yet. Sorry Since oxaloacetate is regenerated in the [Krebs] cycle, would it be considered an enzyme? Enzymes are ONLY catalytic macromolecules, and 99.9 percent of those are proteins, made up of folded, genetically encoded polypeptide chains. Just because a small metabolite is regenerated does not make it any of those things. But it is true that enzymes are regenerated into their original form. Can we get candy on Halloween to charge up our metabolism? That sounds like a very good idea. R- Arginine A- Alanine N- Asaparagine D- Asparatate Y- Tyrosine Sweet! (serine, tryptophan, glutamate, glutamate, threonine) U can request ur boss to remove the table in the middle If only…. Succinate also inhibit succinate dehydrogenase?? No. There are cases of negative cooperativity where high concentrations of a substrate will cause an enzyme to process that substrate more slowly, but that is through fancy allosteric effects. Do we need to know all of the gly oxylate cycle? It is just two reactions that are new to the cycle and a few that are bypassed. Isocitrate instead of undergoing isocitrate dehydrogenase, then alpha ketoglutarate dehydrogenase, then succinylCoA synthetase, then succinate dehyrogogenase, then fumarase to get to L-malate, the simple, streamlined GC takes isocitrate, cleaves it to succinate and glyoxylate, then adds AcCoA to the glycoxylate to make L-malate. Voila, an end run around all that CO2 release. Two AcCoA go in, one succinate comes out. A

carbon skelton building machine‼ What does glyoxylate produce. Just bigger carbons like Malays? The glyoxylate cycle produces succinate, from two acetates. No CO2, so acetate can be used to build big things, like plant stems and such. Glucose and such. promotion of outstanding architecture, planning and urban design throughout the San Diego region. - Sent from HeyWire - Free Texting This is that “Orchids and Onions” reference in that nice phone call we got. The Galbraith Hall got an “Orchid” award. I guess not for their cooling system…. I've heard of the name game! Randy randy bobandy. Bonanafonany. Feeefifofanny. RANDY! As you can tell form the link below, it would be feee fi momandy, Randy, but good on you. Here a Youtube of the stellar Shirley Ellis performance, complete with 60s dancing. I’m embarrassed to say I listened to this on my transistor radio I would bring to school… http://www.youtube.com/watch?v=5MJLi5_dyn0 Why would you do glyoxylate cycle instead of Krebs cycle if they require the same starting molecules Well the Krebs cycle allows you to extract energy from acetyl groups, but not use them for anabolism because every time you put to acetyl carbons into the cycle, two CO2s are lost… no bulk production of anything. Conversely the GC allows you to use those acetyl group carbons to build bigger molecules. How do we reproduce mitochondria. Has their genetic sequence been integrated into our DNA? Mitochondrial reproduction is totally under the control of the cell, which makes sense because it is 100% a eukaryotic organelle now and can not live by itself. The eukaryotic genome is full of genes that encode mitochondrial proteins and their sequences represent their bacterial ancestor sequences. The actual mechanics of mitochondrial expansion and growth are still mysterious and represent an important frontier in cell biology. Oxalix acids have 2C. But oxyloacetate has 4. Whats up with that? Oxaloacetate looks like an oxalic acid group bound to an acetate, so it makes a lot of sense. The formula is CO2-CO-CH2-CO2 the first two carbons are an “oxalyl” group and the next two are an acetyl group. Not as weird when you look at it that way. What vitamins/ Supplements do you suggest The tasty ones. I take Vit C despite it making no discernable difference in the frequency or severity of my colds, and I take Vit B12 because a top neuroscientist I know says this is a must, and I take Q10 because they gummi tablets have this delicious peach flavor.

Mmmmm Learned in my lab about cytochrome p450s, which are promiscuous binders of drugs/other ligands. Are those the same as the cytochromes we're talking about here? They are the same in that they have a heme group-bound iron, and they use that iron to perform acts of electron transfer. But they are a whole separate class of enzymes that like you say have an amazingly broad substrate range that allows them to initiate the detoxification of many compounds that body may never have seen before. Some people think these unique enzymes were an important part of humans increased ability to forage and gather edible plants without too grave consequences. Can you show us a video of the mitochondria light thing That’s a great idea. I need to look into that. I have drawn a cartoon of the process in The Electron Transport Chain and Oxidative Phosphorylation, my new reading for Metabolites. Which pathways are we responsible for on the midterm? The ones listed in the study lists. Glycolyisis, oxidative Pentose phosphate, Krebs, Glyoxylate, ETC, OxPhoe Is there a review session for the midterm? Indeed there is. 108 Peterson, 1-4 pm. TAs only. Podcast for your convenience. I will have extended office hours on Wed from 2:30 – 5:30 Can you explain how the E'o values are indicative of the a chain being present in the half reaction table? Well, table 19-2 in the slides shows the collection of half reactions with the E’o values in order from most likely to give up an electron (NADH) to most likely to take up an electron (O2 to H2O). The order that allows the largest number of exergonic transfers, thus releasing the energy in small multiple steps, are in the same order as the complexes 1-4. Which implies that they pass the electrons in that order. And they do. any mechanisms that we should know in particular in electron transport chain? Just the ideas I present in class and the new reading to that level of detail. There are really no mechanisms per se. are FAD and FMN synonymous? They function the same way, and we encounter FAD more often in this course. Both types of cofactors are found in the ETC complexes, buried in those complex systems. Is there a good way to remember or "intuitionize" the step in which phosphoenolpyruvate is created? The enol is a very dry concept, and water is removed from 2PG to make PEP. When someone is at a PEP ralley, cheering, they sweat a lot, losing water.

Lecture 10 (Tuesday October 29) I am sad to say that those questions were lost from my Text+ account (that is the iOS app I use to do this texting). If they re-appear I will post them.

Lecture 11 (Tuesday November 5; Midterm was 10/31) When can I get the grade for the midterm?? The midterms will be delivered to the class next week. Is the space between the outer membrane space also the cytosol? I don’t know what that means. The space between the outer membrane and the inner membrane is called the Inter Membrane Space (IMS) and it has a similar composition of small molecules (like metabolites (ATP, glucose, etc) but the molecular weight cutoff for simply diffusion is about 5000 mw (metabolites are typically in the 100-1000 range) so the protein composition is quite different, and brought about by import mechansms. In the malate-aspartate shuttle, do they only flow in one direction (like malate always in, alpha-kg always out) or do they both go in both directions? That direction is (electrons flowing in on the back of malate) is the usual way during sugar catabolism because Does malate-asp shuttle involve complex II? No. The glycerol-3-P shuttle does load the electrons onto Q, using an enzyme that is like (but not) complex II. Doesn't the alpha keto become NH3+ not NH2? Yes. Sorry. The alpha NH2 in an amino acid is indeed protonated at pH 7. Why do the conversion of pyruvate to lactate when we can use the malate aspartate shuffle and conserve the high energy molecule pyruvate? If pyruvate consumption is efficient, then the NADH will be restored to NAH+ by the shuttles we talked about, giving more energy and continued glycolysis. In many cases, the glycolytic pathway will proceed in situations where the pyruvate buildup outstrips (due to desperate need, sudden action, poor oxygenation) its consumption by the PDH-ETC. In those cases, LDH converts the pyruvate to lactate, restoring the NAD+ by a fermentation route. In intense short term exercise (like say a 50 yard maximal sprint), the glycolytic pathway is the primary sources of ATP production (fast, high power) and lactate buildup (also called oxygen debt) is a clear and common consequence of this imbalance between high power glycolytic ATP generation and slower but more efficient oxidative metabolism. Why does entering the ETC earlier mean more electrons? Electrons fed into complex one cause proton pumping at complex I, III, and IV while electrons fed into the ETC at QH2 (or complex II for that matter) only cause proton pumping to occur from complex III and IV. Less proton pumping, less stored gradient energy, less ATP production.

How does nadh translate to ATP? NADH electrons move through complexes I, III, and IV which uses the free energy from the collection of redox reactions to generate a proton gradient that drives ATP synthesis. Perhaps you want to know exactly how MUCH ATP? The ideal case states that one NADH will yield something like 2.5 ATP, while each QH2 will yield just 1.5, but these numbers are highly variable in actual tissues and real life. Can you explain the answer for the second clicker question again about the malate-aspartate shuttle? The important function of the MA shuttle as we described it is to remove electrons from NADH in the cytosol (thus restoring NAD+ for further glycolysis) and move them into the matrix where there are added to NAD+ in there for entry into the ETC. A win-win. The electrons literally ride in on malate, which is produced in the cytosol from oxaloacetate, and restored to oxaloacetate in the matrix by reducing NAD+. If NADH can't move across the mitochondrial membrane, how do you generate/synthesize new NADH molecules in the matrix? Great question! It turns out that NAD synthesis is an active field or research (surprisingly enough) and the latest model for human cells (Nikiforov et al. JBC 286:21767 (2011); figure from that paper) is that an NAD precursor (called NMN, is synthesized in the cytosol, by one of two pathways. NMN is transported into the mito, where it is converted into NAD+ by addition of AMP. Wild! And trapped! You said the end result of the maleate asp shuttle is to move NADH from cytosol to matrix when you were talking about cognates. So both shuttles are about electrons- NADH can't move across the membrane? Correct. Both shuttles serve the purpose as written to move NADH electrons from the cytosol (thus restoring NAD+; needed for continued glycolysis) to the matrix. In one case, the electrons end up on QH2, in the other case, the electrons end up on NADH in the matrix. Does electron shuttling always carry electrons into the matrix for catabolic reactions? During oxidative metabolism, the electrons flow into the matrix to free up NAD in the cytosol. Those individual transports can be used for other purposes in other circumstances. Are UPCs regulated They have a complex tissue-specific and interesting biology that is a current subject of active research. I want mine upregulated to feel warmer and to burn more calories‼

Learning anabolism is such a pain in the adispose tissue! You will never be the same!

Lecture 12 (Thursday November 7) "Citrate" is an ingredient in Gatorade. Will the citrate I'm drinking post-run be used in Krebs Cycle metabolism? Can it make the Krebs go without glucose? After all, the acetyl groups from glucose are used to make citrate... It can be used in catabolism by entering the mitochondrion, or used in anabolism for lipid synthesis (we will learn about this soon). I think the amount of citrate in the Gaid is more for the taste, but I could be wrong. Or as a counterion for electrolytes, but citrate can and will be metabolized. You sound like you have a cold again It is going away. It is a miracle that I didn’t get really sick running NYC 26.2. Can you briefly explain the importance of brown adipose tissue? Brown adipose tissue is particularly important in converting abuntant lipid energy in adipose into metabolic heat. It is sort of like an electric blanket but one that uses metabolism rather than current. There are probably many functions of the UCPs that allow BAT to work like it does. In what kind of tissues is fr 26bp made? The most important one we talk about is liver, where the bifunctional enzyme PFK2/FBP2 programs both synthesis (PFK2) and breakdown (FBP2). But this fructose variant is made in nearly every tissue and has broad roles in controls carbohydrate use and metabolism both in many mammalian tissues and in many non mammalian organisms. Not prokaryotes (bacteria) however. If glucagon causes phosphorylation of regulatory enzymes, does insulin cause dephosphorylation? Yes. The mechanisms of glucagon and insulin are usually directly antagonistic, especially at the level we study them. Does gluconeogenesis happen in the cytosol? Yes for nearly all of the reactions, but pyruvate conversion into OAA happens in the mitochondrion, and then either OAA is further converted into PEP in the matrix (when NADH is abundant in the cytosol) or the OAA is carried out of the mitochondrion by conversion to malate transport and then recoverstion to OAA (the backward reaction to that used in MA shuttle). The reactions up to G6P occur in the cytosol. How does FBPase2 detach a phosphate off of F26bP? It catalyzes the hydrolysis of the phosphate-carbon bond. Some soulless fiends took many many pieces of candy leaving the last third of the class with none. What happened to sharing is caring? We can only hope that candy will sweeten their dispositions. Robert Lustig at UCSF

would say they are doing you a favor. What's pathology Abnormality and/or misfunction associated with or causative of disease. Dic-tion-ary my friend. 01/02:My heart is currently beating so fast due to coffee and I'm just curious...since the malate-aspartate shuttles take place in cardiac tissues, when coffee To my understanding, the main effects coffee causes are CNS-based, including quickening of the heart. And deliciousness. What is the difference between Fr 1,6 P and Fr 2,6 P??? Fr16bP is a main glycolytic and gluconeogenic intermediate. Fr26bP is a regulator of gluconeogenesis and glycolysis that serves as a “signal of glucose abundance” due to the way it affects the key enzymes PFK1 and FBP1. What is NTP? It was on a few of the utp slides. That is just a generic term for “nucleotide tri phosphate” like GTP ATP, etc. Sometimes enzymes that use on will use others as well and this is how that genrality is expressed. What happens if you are hypo glycemic then? Hypo glycemia is the situation when you blood sugar drops below the ideal amount. In mild cases one will feel not great or very hungry…in severe cases it can be life threatening. Ironically one the places it is most common to observe hypoglycemia in everyday life is when diabetics who are diligently monitoring their blood glucose and self-administering insulin (which is still necessary until someone invents a “mechanical pancreas”) will overshoot the amount of insulin needed and have a severe hypoglycemic episode. So Udp leaves and takes the oxygen of the 1 carbon with it? I would probably look at it as the O on the phosphate of UDP is replaced by the O on the glycogen non-reducing end. The actual details of which atom go where must be resolved by mechanistic enzymology. But yeah, like that. How do the enzymes know to cut it at the very end if the glycogen chain and not in the middle or somewhere else? The active site, which uses some pretty fancy acid base chemistry to weaken the α1-4 bond and allow phosphate to be a nucleophile, is able to only accommodate an END of the chain. In fact it can only accommodate an end with more than 4 glucose subunits in before a branch… hence the need for debranching enzyme… So glycogen releases glucose? Glycogen is a substrate (a big one) of glycogen phosphorylase. This enzyme catalyses the release (by addition of phosphate) of glucose-1P.

If glucagon activates glycogen phosphorylase to make more g1p, how does that glucose leave the cell and enter the blood stream? We will talk more about this later. Glu-1P is converted to Glu-6P for either use in glycolysis or release by dephosphorylation by an enzyme called glucose-6-phosphatase. G6P------ > Glu + Pi Isn't a too high blood glucose level diabetes? Chronic high blood sugar is a symptom of diabetes These enzyme names are killing me slowly.. They are challenging, but they wont kill you. You are a college student and thus all smart and stuff! What happens to glucose when you have enough glycogen stored up? It is used to make things, and especially FAT. We will get to this. Why does lactic acid build up in muscles during workouts? Is this transportation to the liver passive through the bloodstream? Or are there pathways that help the lactic acid get out of muscles and into the liver? If the demand for muscle action (cheetah! lion! opening in the offensive line!) outstrips the ability to further metabolize pyruvate made during sudden activity, the lactic acid will spill into the blood stream, indeed by transporters that allow diffusion of lactate into the blood stream. Then the Cori cycle.

Lecture 13 (Tuesday November 12) How can we check to see if we r receiving the clicker points? You can log onto Ted, and I need to keep updating the database. What's the standard deviation for the midterm? Also will there be a curve? Mean 71.6, SD 18, curve for sure. When and where can we pick up our midterms? Thursday in class, or at a site to be posted on the website How does unsaturated fat get converted to Ac-CoA? In the course of β-oxidation, the double bond will be manipulated to allow the process to continue. Where did the ".5" come from in the number of ATPs in Table 17-1? Thanks! A variety of direct studies on mitochondria and the complexes have arrived at a consensus of optimal conversion at 2.5 ATP per NADH entering the ETC from complex I, and 1.5 ATP per FADH2 produced at Complex II, (or other enzymes that produce QH2 as well). But this is an idealized case, and mitochondria are subject to a variety of challenges and conditions that can remove the from this ideal amount. What happens to acetyl coA production when the fatty acid has an odd number of Carbons? It cranks along until a propionyl-CoA is produced, and then then carboxylation to methylmalonyl-Coa, stereoinversion, and then cobalamin (B12) dependent switching of the Methyl group and a hydrogen radical to get our old friend succinyl-CoA. If lipids are stores of energy that can be used when no food is available, wouldn't we still go into comatose and all that when our glucose level drops or do our lipid stores come to the rescue? That is exactly right. We would use our protein stores and our glycerol molecules liberated from glycerides to make the needed glucose. But it is a collaborative effort. The more fatty acid energy that can be used, the more glucose is spared for the brain. The glucose levels will be protected to the best our our ability, and that includes using fatty acid oxidation, ketone body formation, and gluconeogenesis . Do you take any supplement at all when you work out or run a marathon? Cuz I am currently taking L-Carnitine I only take craploads of vitamin C with the hope it will limit my colds. It doesn’t seem to make a difference. Apparently L-carnitine does not have a lot of documented effect. But it can’t hurt you and there is probably a lot of individual variation. So if it helps, do it!

U should buy maggie a smart phone She does not want one. Refused one! Where do triglyceride come from and where do fatty acids come from? We consume dietary fats such as di and tri glycerides, and then break them down into glycerol and fatty acids, which we assemble into new glycerides, and package them into chylomicrons for delivery to tissues. We also synthesize fatty acids as well. How are fatty acids stored?? They are stored as glycerides in cellular bodies called lipid droplets, and in fat storing and measuring tissues called adipose tissue. Also in which order does the body metabolize? Is it glucose first, then fatty acids? Which one is utilized first It depends a lot on energy needs. In rest, we tend to conserve glucose, using abundant fatty acid stores to generate. But when exercise or effort is demanded by our brains (Fight! Flight!) the we preferentially use glucose and when we run out of those stores, we then use fatty acids. Since you pretty much isomerase a cis double bond of an unsaturated fa to trans. Why is trans fa bad? That particular isomerization briefly occurs during the β-oxidation of unsaturated fatty acids. But the problem with trans fatty acids comes from the bulk consumption of them and effects on lipoprotein metabolism, and blood vessel dynamics. You make me wanna study metabolics in the wee hours of the night. That is Rock/Awesome

Lecture 14 (Thursday November 14) Have you heard of the Study Buddy pills? If so, what is your opinion of them? They appear to be a concoction of herbal “stimulants” like Ginko and caffeine. Don’t know much about them. Prob not so different from coffee… What does PI stand for in the context of labs? PI stands for principle investigator, the head of the lab, and the person who is responsible for appropriate acquisition, management and spending of grant funds. Pleeeeaseee curve generously I Will! I thought you said last class that carnitine was the RDS for fatty acids, did I mishear you? Carnitine-mediated carrying of fatty acids into the mitochondrion is indeed the RDS for beta oxidation. Fatty acid synthesis is a distinct set of enzymes and processes, with the same chemistry occurring on the opposite direction. The RDS for fatty acid synthesis is carboxylation of acetyl-CoA by acetyl CoA carboxylase (ACC). Would malonyl CoA have a CH2 instead of a CH3 for the 2nd carbon? Yes-it is a methylene group. Do we have to memorize the enzymes of lipid anabolism/catabolism? No. You need to know the reactions of each pathway and the rate limiting enzymes for both processes. If glucagon activates glycogen phosphorylase to make more g1p, how does that glucose leave the cell and enter the blood stream? G1P is converted into G6P by a mutase, and this is dephosphorylated by Glu6 phosphatase in those tissues (liver) that have it. When would a system what to convert malate into pyruvate????? When a cell is in the midst of lipid anabolism, the generation of pyruvate is one pathway we talked about where NADPH is formed, (citrate → AcCoA and OAA OAA + NADH→ Mal + NADP → pyr + NADPH + CO2 The pyruvate is then moved into the mito used to make OAA for further AcCoA production from citrate. So the answer is when anabolism is high, and there is abundant glucose or other nutrients and abundant energy, and hormonal signals that say “build! Store!”. See fig 21-10 from Lehninger 5th ed or slides or to the right…

I thought acetaminophen is not included as an NSAID? You are correct. The pharmacology of acetaminiphen (Tylenol) is anti fever, but not very effectively anti inflammatory. Interestingly, the exact molecular target is not yet clear. It does inhibit the COX enzyme, but not very well. What does the attachment of head groups do chemically? It makes the phospholipids amphipathic, and thus able to participate in building the life-giving and essential lipid bilayers. They also serve a number of specific functions depending on the head group, the most interesting perhaps being generation of intracellular signals through enzyme-mediated cleavage. What is the difference between acetyl CoA and acyl CoA Acetyl CoA is a CoA with an attached ACETYL group (so CH3-CO-SCoA) while an acyl CoA is CoA with an acyl group attached. This can be any number of fatty acid or more exotic carboxylic acids (including acetate itself) but the usual use of this term is a fatty acid attached to CoA. Notice that Acetyl-CoA is one specific example of an acyl CoA.

Lecture 15 (Tuesday, Thurs November 19, 21) What are the core reactions again? Glycolysis, Krebs, ETC, Pentose phosphate (oxidative only), Gluconeogenesis In clinic why is it important to know your triglyceride levels? Triglycerides are one way of gauging the burden of blood lipids that could potentially be unhealthy. Cholesterol is another lipid frequently measured. Over-high lipids (hyperlipidemia) correlates with a number of syndromes including high blood pressure, poor glucose clearance, and atherosclerosis. Is an isoprene the same thing as a terpene? Is isoprene the same as a monoterpene? A terpene is one type of isoprenoid, made from the five carbon building blocks we learned about. There are thousands of natural isoprene-derived molecules, (isoprenoids) and terpenes are one large subset. “Terpenes (/ˈtɜrpiːn/ tur-peen) are a large and diverse class of organic compounds, produced by a variety of plants, particularly conifers,[1] though also by some insects such as termites or swallowtail butterflies, which emit terpenes…Terpenes are derived biosynthetically from units of isoprene, which has the molecular formula C5H8. The basic molecular formulae of terpenes are multiples of that, (C5H8)n where n is the number of linked isoprene units. This is called the isoprene rule or the C5 rule. The isoprene units may be linked together "head to tail" to form linear chains or they may be arranged to form rings. One can consider the isoprene unit as one of nature's common building blocks.” Are you going to post/write any more pieces for this class? Unfortunately no. But the indicated readings in Lehninger (available in the biomed library or the bookstore) can be used to gain more information on a subject in the lectures. The reading lists include readings for the 4th, 5th, and current 6th editions. They are not required, but if they help by all means read them‼! Why is one of the squalene isoprene units not head to tail? Do isoprene units have to be connected head to tail? No. This is one of the flexibility points in the synthesis of natures isprenoids. Sometimes head to tail, sometimes not. Fancy. Do we have to memorize this melavonate pathway? You need to know the reactions that give mevalonate, (up to the reduction of HMG-CoA) and the general descriptions of the steps of sterol synthesis. If you have to draw a structure, you will have a guide structure to help you, or one that the “name game” can

help you realize. Like HMG-CoA…. What is the difference between NADH and NADPH again? NADH is usually the product of oxidation reactions that produce this reduced molecule during anabolism, and NADPH is the most common source of reducing equivalents for anabolism. Like fatty acid synthesis, and sterol synthesis. What is so bad about nitrogen that it needs to be safely stored? Free ammonia is very reactive. Damages tissue, it is also quite basic by comparison to other molecles. Do we need to know the amount of Carbons for each type of fatty acid? Carbon number associated with each name is not required. But those names will be useful to you someday. Is the shuttling of NH4+ why people use beta-alanine as a workout supplement? β-alanine is a naturally occurring amino acid that is NOT used in protein synthesis. It forms a dipeptide with histidine called carnosine, that apparently has some beneficial effects. I don’t know much about it. We are not covering this in class. But there is a whole whole whole lot of metabolism going on… Are the grades going to have plus and minuses? Yes Do You like Julian pies? MMMMMMMMMMMMM! They are awesolicious Wait, so we don't need to know the urea cycle right? You need to know about the urea cycle as indicated by the study list and the problem sets. When talking about the signal for increased urea production, you said the only function of fruc 2,6 BP is to regulate what? Fr2,6bP appears to function only as an allosteric regulator. It controls glucose consumption (glycolysis) and glucose production (gluconeogenesis). I mentioned it because like N-acetylglutamate, it functions solely as an allosteric regulator. Which is the bacteria and whic is the plant cell in the symbotic example you gave The rhizobium bacteria are symbiotic bacteria that occupy special cellular compartments in the root of legumes (the plants) and trade good protection and nourishment for their ability to produce fix nitrogen, producing NH3 from N2

So when nitrogen is removed from amino acid during catabolism it's first placed on what? Tis was the last clicker question today I didn't catch what the answer was In the liver, many amino acid NH3 groups end up being added to αKG to make glutamate. The glutamate is oxidatively deaminated to produce free ammonia (NH3) and αKG again. A little cycle that funnels nitrogen from various amino acids. What is the rate limiting step in the urea pathway? CPS I or carbamoyl phosphate synthetase one, that produces carbamoyl phosphate for use in the urea cycle. CPS I is found in the mitochondrion

2ATP + HCO3- + NH4

+ --> 2ADP + Carbamoyl phosphate + P Do we have to memorize the neurotransmitters from amino acids? No, but it is interesting to know about them.

Lecture 17 (Tuese November 24) Just to clarify: 70% participation in iclickers gives us 25 points, which is 10% extra credit since the course total is 250? The total course points are 275. 250 on exams and 25 clickers. I think we are saying the same thing numerically though. Is there a revised version of the terms / study list? The versions uploaded still say that we need to know photosynthesis stuff The study list is now revised as promised What is MCO STAND FOR? Multicellular organism How's hif produced It is a transcription factor that is made all the time, and that time it lingers in the cell is controlled by oxygen. When O2 is high, it is degraded rapidly and this keeps its levels low. When O2 is low, it is degraded slowly and so it builds up. You don’t need to know this but it is a very beautiful sensing mechanism. Is the only difference between isocitrate and alpha-OH glutarate just the position of the OH that changes? A: I drew isocitrate wrong! It has 6 carbons and the wild type IDH rxn is an oxidative decatboxylation. I will tell the whole class. To the left is isocitrate (6 carbons, as it should have). Normal IDH removes that middle CO2, reduces NAD, and creates αKG. Then the mutant IDH we talked about in class reduces the αKG (with NADPH) to make α2OH-glutarate. Sorry!! What is IAP? It is a cellular protein that controls the rate of cell death. There are many such proteins in different families. It is called “inhibitor of apoptosis” and you will hear more about such proteins in cell biology and signaling classes. When you hav a mono unsaturated fatty acid and you transform the cis to the trans double bond in lecture u said after we get the trans it can go right on to oxidation but how what does the double bond do? Does it jump right Into the Enoyl structure and skip the acytl coA dehydrogenase step? During β-oxidation of a cis double bonded FA, normal B oxidation proceeds until there is a fatty acyl co A with a 3,4 cis double bond. At this point an isomerase turns that into a 2,3 trans double bond (which looks just like the product produced during acyl CoA dehydrogenase. Then the beta oxidation continues with addition of H2O, etc. The acyl-

coA dehydrogenase step is skipped. Does annamox live in the roots of legumes? It is free living, and does some radical chemistry involving hydrazine. Does ribose 5 phosphate for making nucleotide come from pentose phosphate pathway or are there other pathways? The PP pathway as we discussed it is the main route of production of ribose 5P from glucose.