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Questions tagged [enzymes]

Enzymes are macromolecular biological catalysts that alter the rate of a reaction. Use this tag for question regarding enzyme kinetics, classification and action.

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Lack of control group in experiment?

I'm doing an experiment for Year 11 Biology to model how increasing the surface area of a potato affects the height of bubbles produced during a chemical reaction. It's supposed to show the ...
Katherine's user avatar
6 votes
2 answers
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What does ‘D’ in GADP (glyceraldehyde 3-phosphate) stand for?

Wikipedia says glyceraldehyde-3-phosphate can be abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, and many resources seem to use GADP as its abbreviation. I have no idea where ‘D’ came from. ...
chrononaute's user avatar
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Why FeMoco is not more widely adapted in industry

FeMoco has been a popular topic for case-study in computing chemistry. Unfortunately I don't think my understanding on the issue is complete because I still have some questions. If we already know ...
Minh Triet's user avatar
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Reason for differences in AChE aging/reactivation kinetics between neutral and charged organophosphorus inhibitors

According to the referenced papers, acetylcholinesterase that has been inhibited by an organophosphate possessing thiocholine as its leaving group is more susceptible to reactivation by oxime ...
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Enzymatic mechanism of Lipase

When lipase catalyses the hydrolysis of a triglyceride (oil/fat) which bond does it break and why? What about in the case of saponification (triglyceride + NaOH) in the presence of lipase? Is the same ...
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Why Michaelis Menten Assumption of equilibrium is necessary to integrate rate of ES production

I read in my textbook that the assumptions of equilibrium and of steady state used by Michaelis and Menten were simplifying assumptions intended to make the following equation one that can be ...
Zak's user avatar
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Effect of presence of competitive inhibitor on observed reaction constant

Suppose there is a solution of enzyme, its substrate, a competitive inhibitor, and a suicide inhibitor. The reaction rate constant for the reaction of the suicide inhibitor with the enzyme is known. ...
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Effect of competitive inhibitor on substrate inhibition

In an enzyme that undergoes substrate inhibition, how would the presence of a competitive inhibitor affect said substrate inhibition? Would the substrate concentration at which substrate inhibition ...
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How are enzyme inhibition constants assayed for "multi-inhibitors"?

Suppose there is a suicide inhibitor of an enzyme that reacts with the enzyme to form an inactive enzyme and another product. This "Another product", however, is capable of acting as a ...
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Why does Alcohol-Dehydrogenase prefer ethanol over methanol?

So I've had this experiment at university, where we tried using (yeast) ADH on different alcohols and measuring which one gets turned over the fastest. We also learned that ADH prefers shorter ...
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By what mechanism does amylase catalyze hydrolysis?

I've recently been learning bits and pieces of starch metabolism, and am wondering if anyone could explain exactly what is going on when alpha or beta amylase "cleaves" the 1-4 glycosidic ...
Matthew Finger's user avatar
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Why is AChE inhibited by triflates not susceptible to reactivation?

According to a report, certain esters of trifluoromethanesulfonic acid are capable of acting as irreversible inhibitors of acetylcholinesterase. Also, 3-PAM, while capable of reactivating AChE ...
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Are there natural enzymes that catalyze different reactions under different conditions?

Are there natural enzymes that catalyze different reactions under different conditions? For example an enzyme undergoes a conformational change under certain pH and starts catalysing a different ...
Euphorbium's user avatar
3 votes
2 answers
231 views

How is NADH or NADPH produced in industrial chemical synsthesis?

I am trying to find out how NADH or NADPH are produced in bulk. These molecules are very important biologically, however, they are also sold as chemical reagents and produced in large quantities. How ...
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Can lipases cleave fatty acids linked with amides instead of the usual esters?

The typical substrate for lipases are esters, such as triglycerides where fatty acids are linked to the glyerol through ester linkages. I'm interested in whether lipases (such as pancreatic lipase) ...
WaterMolecule's user avatar
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Constants in Enzyme Kinetics under the Rapid Equilibrium Assumptions

I am new to enzyme kinetics, and I am trying to write an rate equation for a rapid equilibrium random terreactant system. I have been consulting the books Enzyme Kinetics and Mechanism by Cook and ...
craziecaesium's user avatar
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2 answers
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Why does aldolase not act upon glucose-6-phosphate?

I was recently asked to explain why (fructose-bisphosphate) aldolase does not act on glucose 6-phosphate in glycolysis and waits until the formation of fructose 1,6-bisphosphate. I did not know much ...
AvadaMouse's user avatar
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How does one derive a KD from an equilibrium titration experiment? I am definitely making a mistake somewhere

Any help would be greatly appreciated. Thank you in advance. If I have an antibody A and a target B, and experimentally titrate the antibody against a single concentration of B, and then measure the % ...
Justin's user avatar
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How does coenzyme A produce proton from pyruvate ions?

Coenzyme A (CoA) is a complex molecule consisting of mercaptamine, β-alanine, pantoic acid, diphosphate, pentose, phosphate and adenine moieties: Which part of it actually plays role in the formation ...
Awe Kumar Jha's user avatar
1 vote
1 answer
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pH for optimal kinetic for enzyme reaction

If I am given the following enzyme reaction: where K$_{EH,1}$=K$_1$ = $10^{-4}$ and K$_{EH,2}$=K$_2$ = $10^{-8.2}$. Iwant to calculate at which pH I have the optimal kinetics by calculating $\frac{v'...
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How does creatine increase DHT levels?

I'm interested in learning how creatine increases DHT levels in the context of 5α-reductase inhibitors (5ARIs). A study (doi: 10.1016/j.urology.2013.02.045) found that 5ARI-induced DHT deficiency ...
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Using 3 layer ONIOM(M06-2X:PM7:UFF) over 2 layer ONIOM(M06-2X:AMBER) or 2 layer ONIOM(M06-2X:OPLS) to study enzymatic aldehyde reduction

I'm trying to model the reaction mechanism of an enzymatic steroid reduction. Experimental research proposes a large variety of intermediates, which I believe would each require separate ...
Runa's user avatar
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Parabolic Arrhenius plot

I am currently doing a kinetic study on an enzyme catalysed reaction and plotting the Arrhenius graph ($\ln k$ vs $1/T$) and I got a parabola. My idea is to take the derivative at each point, meaning ...
Tymothée Waldner's user avatar
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Can I degrade PLA into something usable?

I have a lot of 3D printer waste and don't have a recycling machine for it. As a side project, I was wondering if there is any way to degrade/compost/recycle it meaningfully. I have my Uni's chemistry ...
Genesis Of Gaming's user avatar
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1 answer
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Phosphate transfer in hexokinase

In glycolysis, hexokinase transfers a phosphate group from ATP to glucose. This is an example of the coupling of an exergonic reaction with an endergonic reaction, such that the endergonic reaction is ...
Abdelrahman Mohamed 's user avatar
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1 answer
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Why does Phenylalanine to Tyrosine release H2O?

So I was reviewing Tyrosine and Phenylalanine metabolism (according to this video) and maybe I'm missing something but in the first step, 1: Oxygen atom reacts with Phenylalanine to make up Tyrosine, ...
Hareka's user avatar
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Why doesn’t the amount of ligand needed to reach a fraction-bound value of 0.5 increase as the starting protein concentration increases?

In a Kd binding curve of fraction-bound on the y-axis and ligand concentration on the x-axis, it’s known that the Kd is equal to the ligand concentration [L] needed for [PL]/[Ptotal] =0.5. However, I’...
biryaniboi's user avatar
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Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry showing both reactant ligands?

I am desperately searching for an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactose synthase -- we have ...
Gunther Schadow's user avatar
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What is an enzymatic reaction for which a detailed tertiary structure showing all ligands is available on the PDB?

This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate ...
Gunther Schadow's user avatar
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How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center?

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose ...
Gunther Schadow's user avatar
7 votes
0 answers
309 views

Is a hydrocarbon bio-battery feasible?

Hydrocarbons have some of the highest energy densities and specific energies of any chemical fuel. Unfortunately, our primary use of them is in thermal engines, whose efficiency is limited by Carnot'...
Lawnmower Man's user avatar
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1 answer
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What happens to an enzyme after it breaks down a starch molecule?

I am a master distiller at a distillery and I am about to make some whiskey. First adding corn, cooking it and releasing it's starches. After that, will add in some malt, packed with enzymes to break ...
Matt's user avatar
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11 votes
4 answers
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What is an example of chemical reaction that can be assisted by both an inorganic catalyst and an enzyme?

I have been researching chemical reactions of inorganic catalysts and enzymes and cannot find a chemical process where an inorganic compound can be replaced by an enzyme (or vice versa) and have the ...
Puzzler's user avatar
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2 votes
0 answers
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How to find the reaction rate in an enzyme reaction?

First time posting questions here, so let me know if I need to edit anything. I need to decide $dC/dt$ and $dP/dt$ when the reaction is like this, where I only know we must have 2 substrates $S$ to ...
Yuki.F's user avatar
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5 votes
2 answers
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Why does allosteric binding produce a sigmoidal curve?

Allosteric binding is where the enzyme can be regulated through having ligands bind onto somewhere that is not the active site. This will then induce a conformational change on the active site, hence ...
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7 votes
3 answers
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Why use Km in catalytic efficiency?

The catalytic efficiency of an enzyme is given by $k_{cat}/k_M$ where $k_{cat}$ is the turnover number, or the number of molecules that can be produced per second per active site of an enzyme. $K_{M}$ ...
John Hon's user avatar
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1 vote
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Do phosphoryl thiocholines, their uncharged analogs, and other organophosphates, interact differently with Acetylcholinesterase?

As asked in the title, would the various salts -such as hydrochloride or methyl iodide- of V-Agents interact any differently with acetylcholinesterase compared to the neutral compound? For instance, ...
user73910's user avatar
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3 votes
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Is Km the concentration needed to keep the enzyme running at max speed?

$K_m$ is the Michaelis constant, which is the concentration of substrate needed to achieve a rate of $\frac{V_{max}}{2}$. $V_{max}$ is the maximum number of molecules that can be reacted per second. ...
John Hon's user avatar
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5 votes
1 answer
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How do enzymes affect a reaction's equilibrium?

I am not sure to understand something I read in a educational journal (1) Introduction Lets consider the following reversible enzyme-catalysed reversible reaction; $$E + S \leftrightharpoons ES \...
user68044's user avatar
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3 votes
1 answer
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Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
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3 votes
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Differences in AChE inhibition kinetics between VX and VR

According to the referenced paper, VR has an AChE inhibition reaction rate constant almost 4 times that of VX. Interestingly, its reaction rate constant for aging of the enzyme is less than that of VX,...
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2 votes
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132 views

How can DI water inhibit peroxidase activity?

I'm troubleshooting an IHC staining issue, and according to Thermo-Fischer's website, "Deionized water can sometimes contain peroxidase inhibitors that can significantly impair enzyme activity.&...
Sophia Miranda's user avatar
2 votes
0 answers
37 views

Why is Chlormephos highly toxic despite requiring metabolic activation?

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/kg. For ...
user73910's user avatar
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6 votes
1 answer
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Does the mechanism of AChE inhibition by Isoparathion depend on chirality?

It is known that the inhibition of acetylcholinesterase by isomalathion can proceed either with diethyl succinate as the leaving group or thiomethyl, depending on the specific stereoisomer of ...
user73910's user avatar
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-1 votes
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Could shear force from blending denature alpha amylase / glucoamylase enzymes?

I am trying to break down the starches in a certain variety of oats in the most efficient way possible. I have to break the whole oats down after cooking, so they are finer particles for the amylases ...
Amphibio's user avatar
4 votes
1 answer
167 views

Why are isomers of parathion less active acetylcholinesterase inhibitors than paraoxon?

Parathion itself has been found to be a very weak inhibitor of acetylcholinesterase. It normally requires metabolic activation and the conversion into paraoxon in the body to actually start exhibiting ...
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What is the chemical reaction behind ginger milk curd?

Pouring hot milk into ginger juice solidifies the milk. All I know is that ginger juice contains Zingibain that could break down milk proteins into smaller polypeptides. I'm confused as though why is ...
Christopher Boo's user avatar
2 votes
0 answers
33 views

How do structural differences between neostigmine and TL-599 contribute to differences in toxicity?

Stevens and Beutel studied the activity of several carbamate anticholinesterases. Among other things, they found that the (4-trimethylammonio)phenyl dimethylcarbamate iodide (The para-analog of ...
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5 votes
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Why are S-thiocarbamates less toxic than carbamates?

According to Haley and Rhodes, neostigmine bromide (alternatively known as Prostigmine) has an LD50 in mice of around 0.165 mg/kg by IV injection. Pubchem claims that this is also the LD50 for ...
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4 votes
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Can bis-quaternary aromatic compounds act directly on acetylcholine receptors?

The book Cholinesterases and Anticholinesterase Agents gives examples of bis-quaternary aromatic compounds that are capable of inhibiting acetylcholinesterase. Page 400 gives examples of some such ...
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