Questions tagged [enzyme-kinetics]
Enzyme kinetics is the study of the rates of enzyme-catalysed reactions
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Increasing enzyme concentration does not increase product formation
I am cutting DNA strand 40 nt long with enzyme with single cleavage site in DNA. At the lowest concentration of enzyme I use, 50% of the substrate is cleaved, however, increasing enzyme concentration ...
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Relationship between Km and IC50 in cellular uptake assay
I'm going to describe the scenario in general terms at first so as to try and get to the theoretical content of the problem, but I'll post a link to the paper which got me thinking about it at the ...
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Different enzymes catalyzing the same reaction but in opposite directions
Nelson, D. L., & Cox, M. M. (2017). Principles of Biochemistry 7e. W. H. Freeman. 13.3: Phosphoryl Group Transfers and ATP: Inorganic Polyphosphate Is a Potential Phosphoryl Group Donor.
(This ...
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Why does an Enzyme-Substrate Complex have slightly less energy than the substrate alone?
In some books the graph of the change in free energy during an enzyme-catalysed reaction is depicted as shown below, where S = substrate, E = enzyme, P = product, and T* represents the transition ...
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How to theoretically calculate amount of product in first-order reaction?
I was wondering if it was possible to calculate the amount of product theoretically produced from in vivo (human) values to determine if that's the only enzyme causing the increase in amount of ...
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Meaning of "offsetting the adverse kinetics from the altered glutamate decarboxylase binding capacity" in a paper
From the review titled "Pyridoxine-Dependent Epilepsy and Antiquitin Deficiency Resulting in Neonatal-Onset Refractory Seizures":
It is suggested that sudden, severe cerebral suppression ...
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How to predict enzyme activity computationally
if I have an enzyme and its corresponding substrate, are there computational methods that I can use to predict its enzymatic activities? I understand that we can determine its activity using various ...
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How does one derive a KD from an equilibrium titration experiment?
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 % of B that is bound after the solutions reach equilibrium, I ...
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Difference between IC50 and Michaelis-Menten constant
I am new to biology, and getting to know the term IC50, I found that there is a connection between IC50 and Michaelis-Menten constant by the Cheng-Prusoff equation
$K_{i}=\frac{\mathrm{IC}_{50}}{1+\...
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effect of pH, temperature and enzyme concentration on Km
I understand that enzyme concentration does'nt affect Km since the Micaelis Menten equation is based on the steady state approximation wich requires high levels of substrate compared to enzyme (that's ...
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What other sites do non-competitive inhibitors bind to apart from allosteric sites?
I learned competitive inhibition and non-competitive inhibition.
My teacher told me that we should say that non-competitive inhibitors bind to somewhere on the enzyme apart from active sites.
I ...
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Why such strange enzyme kinetics?
I measured some enzyme kinetics in a practical course using a substrate-based FRET assay. Unfortunately some of my plots show weird effects. There was always a decrease in signal after 35 minutes. But ...
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What is the dynamic range under initial conditions?
could someone help me to understand the following sentence better?
It's from the book "A Practical Guide to Assay Development and High-Throughput Screening in Drug Discovery".
And it's about ...
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Turnover number of the enzyme catalase
My textbook says that catalase is the fasting acting known mammalian enzyme and it can act on 40 million molecules of hydrogen peroxide per second.
Does that mean that is acting on that number of ...
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Enzyme inhibitor leads to higher turnover rate?
I'm currently working on a project where I have to deal with enzyme inhibition.
The purified enzyme shows a good substrate turnover. When I try to inhibit it with different inhibitors described in ...
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Does Invertase catalyse the hydrolysis of other sugars other than sucrose?
I recently did a lab where we tested out the substrate specificity of Invertase on different types of sugars such as sugar alcohols and disaccharides, measured by the absorbance of red using a ...
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Meaning of some unit of measurement of kinase activity
I need help knowing what $cpm \times 10^3$ means in Figure 4(C) of this paper (https://www.sciencedirect.com/science/article/pii/S0022202X15323149#f0010). It appears to be a unit of kinase activity.
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Low-tech or low-cost technique for quantitative estimation in enzymology
If an accurate measurement of enzymologic quantities is needed, then following established methods in the field is necessary.
However, it is sometime of great usefulness to ballpark a value before ...
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Is there an enzyme that functions without being associated with a complex?
I'm looking for an enzyme that does not function as part of a complex in its active state. Preferably it also is not part of a kinase or other kind of activating cascade as well though I would ...
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kcat in uncompetitive enzyme inhibition
Why doesn't $k_\text{cat}$ change in uncompetitive inhibition, given the fact that uncompetitive inhibition lowers the enzyme–substrate complex efficiency (which is the reason for lowering of $V_\text{...
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Finding total concentration of enzymes
Sorry if my question is very basic for biology majors because I am not. I am trying to build a mathematical model of a particular pathway using systems of differential equations and in order to reduce ...
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What are " temporal kinetics"?
I am new to Biology and I am reading some papers about kinase proteins. I know what kinases do in the body. However, I found it hard to understand what are "kinetics". I googled this term ...
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Why doesn't enzyme reaction rate rise linearly with substrate concentration?
This is the graph of the Michaelis-Menten equation which describes the relationship between reaction rate and substrate concentration:
I don't understand why it is hyperbolic. Intuitively, I would ...
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Does it make sense to express membrane transporters as concentration?
Let's assume a situation where a molecule, S, is transported out of the cell by membrane transporter T. For simplicity we do not consider any other synthesis or production processes. Furthermore, we ...
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What is allosteric regulation?
I've found multiple definitions for allosteric regulation and struggling to understand which one is correct. My text book says:
'Another way of regulating enzyme activity is through allosteric ...
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Enzymes extracted from diferent tissue, may have diferent $K_m$ values under the same conditions?
My laboratory team has been used succinate dehydrogenase (1.3.5.1) from Gallus gallus domesticus breast (the most meated part of the chicken, where you will obtain nuggets) to determine $K_{m}$ and $...
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Do there exist enzymes that can take up multiple cofactors to do different reactions?
I was thinking about enzyme catalysis, and it seems like enzymes can only catalyse one kind of forward/reverse reaction (please correct me if I am wrong). Does there exist an enzyme that can catalyse ...
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How could pharmaceutical metabolizing bacteria be used to synthesize them?
Lets say I have a pharmaceutical "P". It can be broken down by enzymes of one strain of bacteria into two molecules one of which can be further metabolized enzymatically by a different strain of ...
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Which enzyme is Nick Lane referring to?
In Life Ascending the author, Nick Lane, refers to an enzyme in his introduction:
'' It concerns an enzyme (a protein that catalyses a chemical reaction) that is so central to life that it is found ...
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How to calculate the turnover number?
I understand that Kcat (turnover number) = Vmax/total enzyme concentration.
However the formula I have been given is Kcat = specific activity/molecular mass of enzyme.
What is the relationship ...
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Struggling to make sense of Km [closed]
So I have two substrates for one enzyme and I measured the product formation-> michaelis menten kinetics. The Vmax for both substrates is the same, the Km however is higher on substrate number 2. ...
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Michaelis Menten kinetics - Plotting to find V-max and Km [closed]
In dealing with the question above I know that if we plot 1/v against 1/[isocitrate] we can get V-max = 1/intercept and Km = slope/intercept.
However when I express the two rows of values in ...
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Michaelis-Menten equation; how to find the constants from enzyme activity experimental results?
I was wondering what the constants in the Michaelis-Menten equation actually mean in experimental data of enzymes. How do I process the data to find Km and Kcat?
I did an experiment on catalase and ...
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How to convert between Kunitz units and Enzymatic units?
I've googled around and there has been the common answer of 1.5 U = 1 Kunitz Unit, but none of those answers have come from a reputable source, so I am really doubtful. :(
The enzyme I use comes in ...
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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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Determining the Value of Inhibition constant
I am trying to understand how the inhibition constant is calculated for competitive inhibition.
$\frac{K^{app}}{V^{app}} = \frac{1+I/K_i}{V/K_m}$.
But often in secondary plots, $\frac{K^{app}}{V^{...
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The threshold of Ki
Is there any threshold (Ki) between strong and week small molecule inhibitors?
When I see the (Ki) values in any published work, how can I decide if this good or bad inhibitor?
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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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What does enzymatic equilibrium in % represent?
I am studying an enzyme which can catalyse a chemical reaction in both directions. The paper I am looking at is mentioning a thermodynamic equilibrium of 1% in the synthase direction.
What does that ...
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Can lysozyme also lyse gram-negative bacteria and if yes, how fast?
Lysozyme attacks peptidoglycan, which are found in Gram-positive bacteria. I know someone who uses lysozyme to lyse Escherichia coli, which is Gram-negative. How is that possible? Can lysozyme lyse ...
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Measuring Enzyme Kinetic constants
Is it possible to experimentally determine $k_1$ and $k_{-1}$ of the Michaelis Menten model:
$\ce{E + S <-->[k_1][k_{-1}] ES ->[k_{cat}] E + P}$,
or their ratio?
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How can ionized amino acid form be important for the catalytic activity?
I can imagine that protonated amino acid form, particularly at the active site, is important for the catalytic activity so hydrogen bonds can be created between the substrate and the enzyme. However, ...
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Specific activity vs turnover number of enzymes in BRENDA
From my understanding, the specific activity (A, units: umol/min/mg protein) can be derived from the turnover number (k, units: 1/seg) and the molar mass of an enzyme (MW, units: g/mol):
A = k / MW / ...
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What are the structural factors affect enzyme's Km?
Is there any rules (should not be exact), to estimate the kinetic changes in an enzyme if I did any mutation on it?
If I cannot estimate the new kinetic values, is it possible at least to clarify or ...
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Enzyme kinetics at the chemical level
I am stumped by two questions:
Why do we take only the initial 10%(or may be 9.99999....%) of S conversion as the rate of the enzyme reaction. why not more than 10%?
Why doesn't the velocity keep on ...
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Gibbs free energy and entropy in enzyme catalysis
In enzyme catalysis, the formation of the enzyme-substrate complex causes a reduction in the entropy of the system. If entropy reduces, the gibbs free energy will become less negative. How then is ...
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Assay for Glycosyltransferase
I want to do an assay to see, if an ordered enzyme is active or not. It's a glucosyltransferase from S. mutans which hydrolyses sucrose into fructose and glucose. It then connects the glucose-monomers ...
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Understanding Enzyme saturation curve
From the above picture it can be seen that, in the region "B" the activity of enzyme is not proportional to the substrate concentration.
Why don't we achieve enzyme saturation linearly? Why do we go ...
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Kinetics of allosteric regulation [duplicate]
I have found a diagram similar to the following one in my biology textbook. The diagram describes allosteric regulation.
However, I do not quite understand why the maximum reaction rate $V_{max}$ is ...
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