Questions tagged [enzyme-kinetics]
Enzyme kinetics are the studies of the biophysical properties of enzymes and their substrates.
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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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When do enzymes catalyze reaction of both direction and when do they not? [duplicate]
I've read that enzymes can catalyse both forward and backward reaction so they don't change eqm position etc.
However protein kinase catalyses phosphorylation, while phosphatase catalyses ...
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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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402 views
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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1answer
692 views
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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2answers
336 views
Is the affinity of an enzyme or transporter for its substrate or solute influenced by the amino acids at the binding site?
The affinity of an enzyme or a protein transporter indicates the strenght of the binding of substrate/solute. An enzyme with higher affinity binds its substrate more strongly than a counterpart with a ...
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Enzyme kinetics; what happens at the peak of the Gibbs energy graph?
At the very peak, the energy is in a state of activation energy. Here, is the substrate just attaching to the enzyme, or is is substrate already breaking?
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Identifying type of inhibitor from $K_m$ and $V_{max}$
Apparently it is possible to identify whether an inhibitor is competitive or non-competitive from graphs of substrate concentration (x axis) and rate of reaction (y axis).
There needs to be a line ...
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How to derive rate of product formation for an allosterically inhibited enzyme?
I'm working through Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls, and in Chapter 3 there's an example of a simple allosterically inhibited enzyme with reaction scheme ...
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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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Enzyme kinetics types?
In lectures, we have discussed Michaelis Menten enzyme kinetics, but from lectures it was clear that this was not the only type of kinetics.
After looking into this, I have found enzymes that give a ...
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The effect of 3D structure and solubility of the binding site of enzyme on its affinity Km and maximum activity Vmax? [closed]
Could some one provide me with some resources or papers where I can read more about the following:
1- How can the 3D structure of an enzyme affect its Km and Vmax? (some papers, books or articles ...
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Why half of the protein is saturated when [L] =Kd
let's suppose the following reaction:
At equilibrium we can calculate the Kd (Dissociation constant) using the following formula:
Kd = [P][L] / [PL] or kd / ka
We can then use the Hill equation to ...
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What is the meaning behind Kcat / Km?
I'm trying to understand enzyme kinetics, the formula for Km and Kcat make sense to me.
Km , the substrate concentration at which the reaction rate is half of Vmax
Kcat, used to describe the ...
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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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Enzyme with long tube leading to active site?
Are there any enzymes that force one or more of their substrates to travel a relatively long distance through a small opening/tube through the enzyme and to the active site? (not a transport protein)
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Understanding of the saturation function in the Monod-Wyman-Changeux Model
I am reading Mathematical Physiology, Sneyd. I am a undergraduate mathematician interested in pursuing the field, so forgive me if my terminology is off. In this example, the writer considers a ...
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How can some enzymes work faster than the diffusion rates of the molecules it catalyzes allow? [closed]
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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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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Why does uncompetitive inhibition decrease the Michaelis constant?
I can't seem to find a good resource online that clearly outlines the difference between an uncompetitive, noncompetitive, and mixed inhibitor (I understand competitive inhibitor though).
More ...
