Questions tagged [enzyme-kinetics]
Enzyme kinetics are the studies of the biophysical properties of enzymes and their substrates.
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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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Computing equilibrium constants of unsymmetrical reactions
I'm looking for the equilibrium constants of unsymmetrical biochemical reactions from the database, Thermodynamics of enzyme-catalyzed reactions.
For instance, enzyme 4.1.2.13 catalyzes the ...
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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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Relationship between enzyme kinetics and similar phenotype
Question: Can the same phenotype or trait observed from $AA$ and $Aa$ be explained by enzyme kinetics (of protein)?
It is understood that a gene locus includes a long series of nucleotides of DNA on ...
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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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How does one calculate [Et] (total enzyme concentration) in enzyme kinetics using Vmax?
I'm trying to work out a question where I have to calculate the Kcat of an enzyme-catalysed reaction. I've read that Kcat= Vmax/[Et]. I have worked out Vmax using a Lineweaver-Burk plot, which is 8.3 ...
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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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Non-Competitive Inhibition vs Allosteric Inhibition
The Vmax of a reaction is lowered in presence of a non-competitive inhibitor (compared to the control - without a inhibitor)
However, (Vmax of the reaction stays the same in presence of an allosteric ...
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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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What is differential enzyme inhibition?
My textbook says that differential enzyme inhibition is useful for clinical applications, such as acid phosphatase. But I don't understand why, or how their differential activity can be measured.
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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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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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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 from 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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Enzymes faster than diffusion rates [closed]
Quoting Wikipedia: "Some enzymes operate with kinetics which are faster than diffusion rates, which would seem to be impossible." Which are those enzymes?
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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 ...
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Ways to monitor enzyme kinetics with very fast time resolution?
I'm interested in any way to do time-resolved study of enzyme kinetics. I am studying some physical variables that may affect kinetics, but I want to study how quickly they take effect, and how long ...
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Glucose Oxidase, Condition to be Active?
I most recently was reading/watching information on honeys antibatical and antimicrobial properties. The enzyme Glucose Oxidase came up often as a main antimicrobial, yet it is inactive in honey. ...
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Enzyme kinetics: recommended literature to grasp the concepts better
I have had a few biochemistry courses, but I still feel confused and a bit scared each time they try to explain and apply enzyme kinetics or even chemometrics in different situation during class. On ...
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Enzyme kinetics: Effect of immobilization on kinetic parameters
What is the typical effect of enzyme immobilization on the kinetic parameters of an enzyme's activity?
Can one assume that they'd stay approximately the same or is there a gross change? Any way to ...
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Reason Non linear Lineweaver–Burk plot [closed]
V vs S plot looks like hyperbolic but 1/V vs 1/S plot is not linear at all. Looks like some kind of exponential growth. What can be the reason?
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Does the Michaelis-Menten equation take in account the non-enzyme formation of products?
I only recently learned about the Michaelis-Menten equation, since I am not studying biology or anything related. Let's write the equation as
$$\frac{d[P]}{dt} = V_{max} \cdot \frac{[S]}{K + [S]}$$
If ...
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Why is competitive inhibition reversible?
My Biochemistry book mentions that 'competitive inhibition' is a reversible form of inhibition. But given that the inhibitor is blocking the active site and prevents an enzyme-substrate complex to be ...
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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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Do we actually know the molecular dynamics of any enzyme?
That is right, is there a limitation, say Heisenberg's uncertainty principle or something that limits our understanding of machinery of enzymes at atomic level? Can we know how do they actually work?
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