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Questions tagged [kinetics]

Kinetics is the study of rates of chemical or biochemical reactions, as well as the metabolic flux rates of biochemical intermediates within the body (e.g. glucose, amino acids, lipids, bile acids).

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What is the dependent variable of a relative fluorescence graph?

So it was asked what was the dependent variable of this experiment. I know that as students, we're wired to think that the y-axis is the dependent variable while the x-axis is the independent variable ...
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What is the concentration/molecules per cell of iodothyronine deiodinase in a cell?

I'm trying to parameterize an in silico model and need the approximate concentration (M), or molecules per cell, of iodothyronine deiodinase type II (D2) enzyme in a human cell, ideally a glial cell. ...
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How does hydration affect digestion?

My textbook( biochemistry by Satyanarayana, 4th edition pg.no:166) says: The polysaccharides get hydrated during heating which is essential for their efficient digestion. (I think there is a typo ,...
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Does the dissociation of serotonin receptors and their ligands really take hours?

If I understand the principle of neurotransmission correctly, then after binding to a receptor on the postsynaptic side, neurotransmitter molecules must be dissociated from the receptor and removed ...
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What are the on-rate and off-rate constants for 5-HT1 receptors binding 5-HT?

The class of 5-HT1 receptors binds serotonin (5-HT) reversibly (Wikipedia). I'm interested in the on-rate and off-rate constants $k_{\text{on}}$ and $k_{\text{off}}$ of this process. So my question ...
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In the Lineweaver-Burk Plot, why does the x-intercept = -1/Km?

Taking the reciprocal of both sides of the Michaelis-Menten equation yields the Lineweaver-Burk Equation: $ \dfrac{1}{V} = \dfrac{K_m}{V_{max}}\dfrac{1}{[S]}+ \dfrac{1}{V_{max}} $ Plotting a $ \...
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Derivation of Michaelis-Menten kinetics for discrete stochastic simulations

According to this article, [...] the propensity function for the conversion reaction S → P in the well-mixed discrete stochastic case can be written $a(S) = \frac{V_{max}\cdot S}{K_m + S/\Omega}$...
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Is this adaption of the Gillespie algorithm using Michaelis constants justifiable?

I would like to run a discrete simulation of a biological system as it can be done, e.g., using the Gillespie algorithm. However, the Gillespie algorithm requires you to know the reaction rate ...
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Kinases that are ATP-sensitive at physiological conditions?

Phosphorylation is an ATP-dependent process performed by kinases. At physiological conditions it is generally assumed that ATP concentration is high enough so that ATP is not a limiting factor. ...
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Concentration of a specific promoter in a cell?

I want to simulate transcription activation by a given transcription factor (TF) with known kinetics. The binding rate $k_{on}$ is given in $\mu M^{-1} s^{-1} $, describing a bimolecular reaction ...
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Convert flux value in nmol/min/mg protein to nmol/min/cell?

This is a question about unit conversion. I found an experimental measurement of the saturation uptake of glucose in yeast: $$V_\textrm{max} \approx 650 \textrm{nmol}/\textrm{min}/\textrm{mg protein}$...
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Is there a way to quantify in vivo cholesterol transport rates?

I have always had trouble grasping the physiology of lipoprotein cholesterol transport. The "standard" description found in the literature is that liver synthesizes cholesterol which is carried in "...
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Fastest G protein coupled reactions

As per few references, fastest G protein coupled reaction known is Drosophila melanogaster phototransduction which produces quantum bumps with average latency of 45 ms (and peak response around 200 ms)...
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Does pH affect Michaelis constant?

I have been trying to confirm the Km of a substrate (which is 34 +/- 4 mM). This value was obtained in 50 mM MOPS, pH 6.3. I conducted my kinetics assay in a buffer of pH 7 and obtained a Km value in ...
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Incremental denaturation of protein mixtures

When a protein solution is heated above the denaturation temperature, it seems that denaturation does not happen at the time the temperature is reached, but it takes some time. I assumed that ...
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Change in synthesis rate of a molecule changes equilibrium concentration

I was reading the topic of 'The concentration of the molecule can be adjusted quickly only if the lifetime of a molecule is short' from Molecular Biology of the Cell by Alberts. At the end of pg-837 (...
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Prenatal hyperkinetic dysfunction and its effect on endurace

Do people with an hyperkinetic dysfuntion have a better endurance? Are they fitter in cause of their Dopamine-overdose or any other reason? I have a case, where someone does not do any sports, but ...
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Enzyme kinetics [closed]

I can't understand how to study enzyme kinetics. Say I have a lipase and want to study the kinetics of this lipase using a fluorogenic substrate, how would I do this? From what I understand I would ...
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Why are enzyme-catalysed reactions slower at lower substrate concentration?

Suppose I'm using 200 nmoles of enzyme and 2 mmoles of substrate. The enzyme should be saturated but if I use 50 mmoles of substrate, the reaction will be faster. Why? I just can't get it! Even at ...
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Michaelis-Menten Kinetics: Does measuring apparent Km and Vmax take into account competing reactions?

I am learning about why it is important to measure Km and Vmax for each experimental setup because measuring the "apparent" Km and Vmax includes enzyme inhibitions of which one might not be aware. ...
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$S_{0.5}$ vs $K_m$ values in enzyme kinetics

What is the difference between $S_{0.5}$ values and $K_m$ values in enzyme kinetics?
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At what substrate concentration will an enzyme work at 40% of its maximum rate if its Km = 0.095M?

The question involves the Michaelis-Menten kinetics equation. Here is what I did: I took the Michaelis-Menten equation, replaced v with 0.4Vmax, canceled the Vmaxes (one on each side), and solved ...