Questions tagged [enzyme-kinetics]
Questions related to enzyme kinetics.
48 questions
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How can a Michaelis–Menten formalism be used when enzyme concentration isn't constant?
I understand that $V_\mathrm{max} = k_3[\ce{E}]_0$ in ordinary Michaelis–Menten (MM) kinetics. According to the lecture notes provided by my university (I don't believe they are available online), ...
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2
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Can glycerol slow down the kinetics of an inhibitor going to a binding pocket of a target enzyme?
I am currently doing enzymatic inhibition assays and in my current setup I observe that a commercial inhibitor is showing inhibition as expected. Still, the inhibition is not as strong as the ...
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2
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1
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Calculate IC50 from fluorescence kinetic
I have an assay in which a fluorescence signal is generated when the enzyme reaction progresses. The fluorescence signal increases until a maximum is reached. Than it keeps constant. The first 1 h ...
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120
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Derivation of general binding equation (macromolecule with multiple binding sites)
So the last days I'm stuck at trying to solve the an equation - but I just can't (see the screenshot below.
So the idea is that you have a receptor or enzyme with multiple binding sites for a Ligand (...
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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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2
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3
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290
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Approximate calculations of the product distribution under kinetic control
What is the product distribution when the energy difference between the transition states (∆TS = TS1 – TS2), is at 2 kcal/mol and when it is at 5 kcal/mol (assuming room temperature)?
I know that 1.4 ...
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348
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How does enzyme velocity decrease as reaction quotient approaches equilibrium constant?
I created a simulation which approximates molecule concentrations in a cell. One part of it are enzymes that can catalyze pre-defined reactions, e.g. $\ce{A <=> B}$.
I based the kinetics for ...
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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 ...
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0
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184
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Help understanding Isothermal titration calorimetry ITC
Trying to understand Isothermal titration calorimetry: ITC , from a public online forum (Off-topic question related to ITC binding studies) I got this question:
We performed an ITC binding study (...
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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 % ...
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Order in Enzyme Kinetics
In an interview for post-grad level, I was asked to explain the "order" of any generic enzymatic reaction involving competitive inhibition. I assumed that Michaelis-Menten Kinetics holds ...
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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 $\frac{v'...
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211
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Parabolic Arrhenius plot
I am currently doing a kinetic study on an enzyme catalysed reaction and plotting the Arrhenius graph ($\ln k$ vs $1/T$) I got a parabola. My idea is to take the derivative at each point, meaning ...
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Can you use Michaelis–Menten kinetics to model the ATP production rate for glycolysis and OXPHOS with glucose as a substrate?
I am an applied mathematician researching cell metabolism, but I have little experience in biochemistry. Currently, my PI and I are considering using Michaelis–Menten kinetics to study how varying ...
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Are good leaving groups good in both directions?
In biology, phosphate groups are often used, good leaving groups.
If I had an opposite case, where a phosphate group remains bound to an enzyme while the main substrate is removed (e.g. E-P04-S => ...
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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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why is $f_{ES}=\frac{[S]}{[S]+K_M}$
I'm working my way through the chapter on enzymes in "Biochemistry" with Stryer et. al, 9th edition. In the current paragraph it's claimed that the fraction of active sites bound to ...
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How to troubleshoot absorbance analysis when readings fluctuate
I am trying to measure creatinine in fluids by using an enzymatic (creatinine) test. I try to determine the concentration by the difference in absorbance before and after 5 minutes after a reagent is ...
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Why neglecting Bradford Solution Volume in the assay?
I would like to know why do we not need to take account of Bradford agent solution in dilution calculation?
For example, $\pu{2.5 \mu g mL-1}$ BSA will calculate from $\pu{0.4 \mu L}$ of $\pu{1 mg mL-...
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Calculate Michaelis-Menten constant of enzyme catalyzed reaction
I have:
$$\begin{array}{c|c}
\dfrac{v }{ [S]}/\pu{s^{-1}} & v \cdot 10^2/\pu{mol dm^-3 s^-1} \\ \hline
0.257\ & 5.15\\
0.895 & 4.48\\
2.00\ & 3.35\\
3.59\ & 1.8\\
4.82\ & 0....
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How to find the reaction rate in an enzyme reaction?
First time posting questions here, so let me know if I need to edit anything.
I need to decide $dC/dt$ and $dP/dt$ when the reaction is like this, where I only know we must have 2 substrates $S$ to ...
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Determine vmax and enzyme concentration (Michaelis–Menten)
I am given that the enzyme concentration is $\pu{15 nM}$ and the following data:
$$
\begin{array}{rl}
\hline
S/\pu{mM} & V/\pu{mM s^{-1}} \\
\hline
1 & 0.202 \\
2 & 0.368 \\
5 & 0....
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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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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.
$K_{M}$ ...
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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;
$$E + S \leftrightharpoons ES \...
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607
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Why a catalyst is not consumed in a reaction when all steps are reversible?
It is said that a catalyst speeds up the rate of a reaction but is not consumed (assuming no side reactions take place). Suppose we have the following reaction:
$$\ce{A + B <=> C} $$
catalysed ...
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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 ...
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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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Question on notation
Here, when they write $v/(\mathrm{mol\ s^{-1}\ (kg\ \text{protein})^{-1}})$ is $0.30$ for the first row first column, do they mean that the value is $0.30\ \mathrm{mol\ s^{-1}\ (kg\ \text{protein})^{-...
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How can subtilisin still function without its catalytic triad?
I read chapter 9 in the book Biochemistry (5th edition), by Berg, Tymoczko, and Stryer (provided in the NCBI site here). It describes the mechanism of action of the chymotrypsin enzyme. The catalysis ...
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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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3
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How can some enzymes work faster than the diffusion rates of the reactants allow?
Quoting Wikipedia: "Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible." Which are those enzymes and how can they be so fast?
One example is ...
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What is the fate of sulfur in cysteine when it participates in gluconeogenesis?
Amino acids can be broken down to yield pyruvate, which in turn can be used to construct glucose molecule in the process of gluconeogenesis. What happens to the sulfur atom in the amino acid cysteine ...
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Temperature dependence of reaction rates
Is it correct to say that "Increasing the temperature will always increase the rate of any chemical reaction"?
Many articles on the internet and textbooks say yes but what about biochemical reactions ...
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Michaelis menten constant motivation behind 1/2?
So the michaelis constant is defined as the substrate concentration at half maximal „reaction-speed“.
I was wondering why 1/2 ?
I guess for higher values you need more substrate, which could be a ...
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Hill equation with inhibition and activation
The Hill equation for an activating enzymatic interaction with cooperative multiplicity $n$ is
$$\frac{\mathrm d[\ce{P}]}{\mathrm dt} = V_\mathrm{max}\frac{[\ce{S}]^n}{K_\ce{S} + [\ce{S}]^n}\tag{1}$$
...
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Enzyme Kinetics - Given Km find substrate concentration at a certain velocity
From what I understand about the Michaelis Menten Model
Km defines the amount of substrate required to reach half-saturation.
1/2 Vmax corresponds to Km on the x axis
Generic formula is v = Kcat [...
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2
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Measuring a high Michaelis constant using fluorescence
We have the task of measuring kinetic parameters of an oxidase reaction that has a $K_M$ of about $2 \,\text{mM}$. For that, we want to use a fluorescence assay based on Amplex Red. The latter is a ...
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Inactivation of enzyme: Why inactivation constants do not follow the Arrhenius equation? [closed]
The Arrhenius equation may not account for the temperature effect on thermal inactivation rate constants. Why can the thermal inactivation kinetics not be expected to follow Arrhenius? The reason that ...
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High concentration of ferric ion catalyst decreases rate of decomposition of hydrogen peroxide in the Fenton reaction
I did a project on the Fenton reaction and rate of decomposition of $\ce{H2O2}$. I used colorimetry to measure the rate of decolourisation of methylene blue when I mixed $\pu{5e-6 mol}$ $\ce{FeCl3}$ ...
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Why enzyme-catalyzed reactions mostly go one way?
I listened to the lecture about enzymes. Professor downplayed the question in the subject. He said that enzymes are able to work both ways, but practically speaking reactions with overwhelming ...
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How to calculate the kinetic order of an enzymatic reaction?
This question is concerning the metabolism of ethanol by an alcohol dehydrogenase enzyme.
Usually people metabolize alcohol equivalent to "one beer per hour". One beer is said to contain 33cL. The ...
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Are enzymes with superior catalytic properties more sensitive to temperature changes?
I am wondering whether enzymes with superior catalytic properties are more or less temperature sensitive than average enzymes.
I know that enzymes lower the activation energy, Ea. So the more ...
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Enzyme Kinetics two enzymes in complex with one substrate
Given an enzyme reaction where two enzymes are required to form the complex, for example $\ce{2E +S-> E3S->2E +P}$, how would I calculate complex concentration assuming steady state ...
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Can you discriminate a monooxygenase from other enzymatic mechanisms by the requirement of NADPH?
I am working on a project about CYPs 450. It seems that most of them function as monooxygenases but there are other categories as well.
Assuming that the question makes sense, is it correct to say ...
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Lowest Michaelis constant Km
I want to find a lower limit of the Michaelis constant for some evaluations of Michaelis-Menten enzyme kinetics.
What is the lowest $K_m$ you ever encountered? Is there a theoretical limit?
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Michaelis-Menten rate law for enzyme which catalyzes two reactions: steady state?
Suppose an enzyme $\ce{E}$ can catalyze two reactions:
\begin{align}
\ce{S1 + E &<=> S1E -> P1 + E} \tag{R1} \\
\ce{S2 + E &<=> S2E -> P2 + E} \tag{R2}
\end{align}
I want ...
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Equations Used in Isothermal Titration Calorimetry
I have been attempting to understand and derive the formulas used for ITC which can be found here starting on page 310. I am particularly interested in the single set of identical sites. To first ...
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