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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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'...
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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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Interaction of trifluoroacetates with acetylcholinesterase

There exists a substance called TMTFA, or 3-(N,N,N-Trimethylammonio)-2,2,2-trifluoroacetophenone. It is known for being able to inhibit acetylcholinesterase at femtomolar concentrations. The TMTFA-...
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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 ...
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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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Thyroid peroxidase - can atomic iodine serve as iodinating agent?

McMurry's Organic Chemistry (7th Ed.) states, that Tyrosine is iodinated by mechanism of electrophilic aromatic substitution and the iodinating agent is $\ce{I+}$ or $\ce{HIO}$ formed by thyroid ...
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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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How much glucose oxidase is usually deposited on a glucometer strip?

The concentration of serum glucose is on average roughly around 5 mmol/L and let's say a typical blood droplet applied to a glucometer is 1μL. We are therefore depositing 5 nmol of glucose on the test ...
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Why does the Michaelis-Menten constant decrease in the presence of non-competitive inhibitor?

Non-competitive inhibitors don't bind to the active sites of enzymes. However, in the presence of non-competitive inhibitors, the Michaelis-Menten constant is found to decrease. Why is this so?
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What are the specific disadvantages of using a bio-catalyst (called Lipolase) in the synthesis of the drug pregabalin?

I am studying the synthesis of a drug pregabalin, for which both chemical and bio-catalysts are used. Using a biocatalyst is way better than chemical route, as explained here. In fact, The invention ...
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Enzyme Assay - pectinase

I am working on Enzyme Assay.I assayed the enzyme in different buffers from $pH\ 1-12.5$ However,the enzyme has good activities starting from $pH\ 1-10.5$ Is that possible to have enzyme activity in ...
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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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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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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 ...
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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 ...
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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 ...
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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.&...
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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 ...
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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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Reaction rate constants for the inhibition of cholinesterases by various carbamates

Darvesh et al. [1] have conducted a study on the anticholinesterase activity of various carbamates derived from phenothiazine. The authors measured the inhibition rate constants of rivastigmine for ...
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Does cellulase catalyze the hydrolysis (or break down) of soluble starch?

I’m attempting to perform an Iodometric redox titration to evaluate the vitamin c concentration in a particular solution. These solution have dissolved within them up to 2% cellulase enzyme. In an ...
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Do enzymes that digest ᴅ-glucose react with ʟ-glucose?

ᴅ-Glucose is common in nature and ʟ-glucose is synthesized in the lab. I know that humans can't use ʟ-glucose in their aerobic pathways because it doesn't match the active site of the enzyme, but why ...
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Solving for Concentration Using pseudo-First Order Kinetics

The following graphs represent a pseudo-first order bi-molecular reversible reaction with the formula $\ce{A + B <=> C}$: The reaction product has an extinction coefficient of $\pu{50000 M-1 cm-...
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Why are carbamates capable of inhibiting acetylcholinesterase?

Certain carbamate compounds, such as the insecticide carbaryl or the Edgewood carbamates such as EA-3990, can inhibit the enzyme acetylcholinesterase. Unlike organophosphorus compounds, however, they ...
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Calculate optimal surroundings for given reaction mechanism to lower activation energy?

Let's take a reaction that's fairly well understood, which in this case means that the reaction mechanism is known, maybe something like this from here: If we know the reaction mechanism, we also ...
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Differentiating random and ordered sequential mechanisms in enzyme kinetics

Can random and ordered sequential mechanisms be descern by Lineweaver-Burk plot? Why or why not? Because for orederd sequential mechanism I got different LB plot depending on which substrate is held ...
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Calculate the flow rate in the steady state of a dynamic equilibrium

I have the following situation: I am interested of the reactions rate of an enzymatic reaction, depending of the substrate concentration. The thing is, that I don't add the substrate directly to the ...
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Have Mossbauer spectroscopy on 67Zn ever been used to study Zinc containing enzymes?

Have Mossbauer spectroscopy with 67Zn as absorber and 67Ga as emitter ever been used to study zinc containing enzymes? The perfect answer will contain link to article/book where example of 67Zn usage ...
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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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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 ...
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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 ...
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Does HI-6 form a covalent adduct with acetylcholinesterase?

According to sources provided below, the oxime HI-6, or Asoxime Dichloride, as it is also called, besides being a reactivator of acetylcholinesterase that has been inhibited by organophosphorus ...
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Hydrolysis of phosphoryl-oximes

When acetylcholinesterase that has been inhibited by an organophosphorus compound is reactivated by an oxime, a phosphoryl-oxime is formed, which is then somehow hydrolyzed in the blood. One study ...
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Collagen digestion

As far as I know, pepsin is used very often in collagen solutions extraction. Since it only cleaves the telopeptides and leaves the triple helix chains of the collagen intact. I was wondering if there ...
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Given the pH optimum of Angiotensin 1, how do I determine its charge?

I'm given the following information I'm then asked to determine the charge of the substrate Angiotensin 1 at the pH-optimum. I have found the pH-optimum to be 6.9. How do I go about answering this ...
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How to determine the speed of GLUT1 transporter using Michaelis-Menten kinetics?

I am reviewing a passage in my Lehninger Biochemistry Textbook (6th Edition), and the following passage has me very confused. How can one sentence from this passage claim that when [S]out = Kt, the ...
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Glycogen Hydrolase

Can glycogen hydrolase cleave both glycogen and starch bonds? My intuition says yes because they are both a 1-4(6) glycosidic linkages but I bet I am missing something.
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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’...
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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 ...
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Is there a software that can predict the shape of a custom protein, given its amino acid sequence?

I know that the internet is full of enzyme and protein simulators which can show active site and 3D structure (like bioblender), but the problem with these programs is that they use predefined ...
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Word for a specific enzymatic process?

Foreword: I am developing a variable-processing program for my Computer Science research project. One particular part of the program mimics the behavior of biological enzymes, except instead of ...
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