BabcockHall

Is this a homework problem?

My first reaction to what you are proposing is that it is extremely ambitious for a high school project. Although docking programs can give some indication of affinity, I am not aware of programs that provide association rate constants.

Because of the chelate effect, oxalate is often better at binding metals than, say acetate, and this holds true for Mg(II). A reliable source for dissociation constants is Martell and Smith's multivolume compendium.

What are your thoughts? Once we know those, then we may be able to help you.

Do you have any acid-labile groups present?

I would put a minus sign on it, to indicate that it is hydroxide ion. And we can compare the pKa values of the conjugate acids of any two leaving groups to determine which base is stronger.

All else held equal, stronger bases make poorer leaving groups than weaker bases. Strong bases are less able to stabilize negative charge than weaker bases. Which is the stronger base?

@OP, Which is a better leaving group, hydroxide ion or water, and why?

@OP, If you have a sodium as a countering, what does that suggest about the rest of the reagent?

What I would do is look into which amino acids are catabolized into 4-carbon TCA intermediates such as fumarate, oxaloacetate, or succinyl CoA versus which ones are catabolized into pyruvate. For example, isoleucine is catabolized into acetyl CoA and propionyl CoA, and the latter compound can be converted into succinyl CoA in several steps.

"Most likely" is an odd choice of terms. Amino acids are classified as glucogenic (glycogenic), ketogenic, or both. Once anything is tranformed into pyruvate, I don't see what would prevent its further conversion. Therefore, I don't know what you mean by "...cannot be transformed from oxaloacetate to pyruvate." Can you explain? Can alanine be transformed into pyruvate? Once you have the answer to that, you will be on your way. BTW your title is a bit confusing. If there is a deficiency in this enzyme or in its allosteric activator, gluconeogenesis is likely to be impaired. I am not sure that I see the connection between that and the question of how the amino acids are glycogenic. Are you attempting to distinguish between those that are catabolized to pyruvate versus those that are catabolized to oxaloacetate?

@OP, Why not write out the light-dependent and light-independent reactions for us? Then we can discuss them.

The various isotopes produce can produce a kinetic isotope effect that is useful in understanding the mechanisms of reactions, including enzyme-catalyzed reactions. The various isotopes have different spectroscopic properties that are especially evident in nuclear magnetic resonance spectroscopy.

That might be the product. The starting material is a triacylglycerol.

Do you want to measure the amount of each via protein quantitation, or do you want to measure the rate at which an enzyme catalyzes a particular reaction (often called its activity)? You may need to fractionate your sample with standard protein purification techniques.

Do you mean benzene and toluene? What is the reason for your question?

“Anion gap = [Na+] – ([Cl-] + [HCO3-]) “The normal value is about 12 meq/liter (range 8 to 16). The anion gap estimates the unmeasured anions in the plasma and is normally composed of polyanionic plasma proteins such as albumin (1 g/dL of serum protein possesses negative charge equivalent to 1.7 to 2.4 meq/liter), phosphate, sulfate, lactate, and other organic anions. “The anion gap is particularly useful in evaluating metabolic acidosis. Elevated values indicate that the acidosis is due to ingestion or generation of a fixed acid, stronger than H2CO3, at rates that exceed the rate at which the anion can be excreted from the body. Examples are diabetic ketoacidosis, in which acetoacetic and b-hydroxybutyric acids are generated; lactic acidosis; and renal failure, in which the rate of generation of strong acids is normal but the anions the acids, e.g., phosphate and sulfate, cannot be normally excreted. Ingestion of methanol, which generates formic acid, ingestion of ethylene glycol, which yields oxalic acid, and salicylate intoxication all produce high anion gap acidosis.” p. 188 in Principles of Biochemistry: Mammalian Biochemistry, 7th ed., Smith E, Hill, RL, Lehman IR, Lefkowitz, RJ, Handler P, White A, McGraw-Hill, 1983 Thank you. I found the passage above to be helpful. I have not yet looked into the delta-delta gap. I have been examining the reactions I wrote out in the pdf (I have not yet figured out how to format them for this thread). If we take acetyl CoA as the starting material and imagine that only beta-hydroxybutyrate is formed, then no net protons are consumed or produced. If we instead imagine that only acetoacetate is formed, then one proton is produced. This is equivalent to four protons per palmitoyl CoA, the precursor to acetyl CoA. On the other hand, seven protons are produced in the beta-oxidation of one palmitoyl CoA to eight acetyl CoA molecules.

Do you recognize the starting material or the alcohol?

When the Krebs' cycle is too slow to consume all of the acetyl CoA from beta-oxidation, some of the acetyl CoA is used to make ketone bodies. When the three ketone bodies, acetone, acetoacetate, and beta-hydroxybutyrate are in abnormally high concentrations, this is ketosis. Type I (and occasionally Type II) diabetics suffer from diabetic ketoacidosis, in which the blood pH lowers (there are three grades of severity). What is unclear to me is the cause of the lowered pH. My working hypothesis is that the acid may be generated when the fatty acyl esters are oxidized to acetyl CoA (beta-oxidation), because each round should produce one proton. When I looked at the pathway to produce ketone bodies, I became convinced that the textbook presentations do not always write balanced equations for this pathway. The attached file is modified from one textbook: I added protons to reactions 2 and 4. Ketone_body_pathway_v1.pdf

I do not know the answer to your question, but I wonder whether or not you mean protein synthesis, as opposed to lipid synthesis.

Do you know what µM stands for? Do you know what molecular weight is?

A good place for you to start might be identifying the non-enzyme molecule that plays the key role.

I have been reading Cox and Nelson's Principles of Biochemistry, 6th ed., Chapter 19. I have some questions about the two regions of the thylakoid membrane. In one portion of the chapter, then refer to the stacks as grana and the non stacked regions as stromal lamellae. They seem to use appressed membranes synonymously with grana and nonappressed membranes synonymously with stromal lamellae. It also looks as if the phosphorylation of LHC-II-OH (light harvesting complex II) causes it to un-appress the membrane nearby, and when LHC-II-OPO32- is dephosphorylated, the surrounding membrane is appressed again. Is this correct? Are there any subtleties in the language I should know about?

This is a fairly complex question; therefore, a small amount of guidance is not entirely without justification. The answer to at least one of these questions depends upon whether the substrate is an ester or an amide.

@OP, what do you think is the bond order between carbon and oxygen in the two things labeled "CO" in your structure?