Questions tagged [enzyme-kinetics]

Enzyme kinetics is the study of the rates of enzyme-catalysed reactions

Filter by
Sorted by
Tagged with
2 votes
0 answers
60 views

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+\...
user avatar
0 votes
1 answer
50 views

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 ...
user avatar
  • 131
3 votes
1 answer
97 views

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 ...
user avatar
  • 131
1 vote
1 answer
72 views

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 ...
user avatar
0 votes
1 answer
34 views

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 ...
user avatar
1 vote
1 answer
114 views

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 ...
user avatar
  • 153
0 votes
1 answer
116 views

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 ...
user avatar
0 votes
0 answers
19 views

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 ...
user avatar
  • 1
1 vote
1 answer
66 views

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.
user avatar
1 vote
1 answer
19 views

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 ...
user avatar
  • 1,105
-1 votes
1 answer
61 views

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 ...
user avatar
3 votes
1 answer
295 views

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{...
user avatar
3 votes
2 answers
59 views

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 ...
user avatar
0 votes
1 answer
179 views

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 ...
user avatar
  • 111
1 vote
1 answer
540 views

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 ...
user avatar
  • 723
2 votes
0 answers
45 views

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 ...
user avatar
-1 votes
1 answer
92 views

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 ...
user avatar
  • 7
1 vote
1 answer
83 views

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 $...
user avatar
2 votes
1 answer
82 views

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 ...
user avatar
  • 23
1 vote
1 answer
84 views

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 ...
user avatar
2 votes
0 answers
56 views

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 ...
user avatar
  • 328
-3 votes
1 answer
1k views

Why is the Km of an enzyme half of Vmax? [closed]

Why is the Km of an enzyme half of Vmax?
user avatar
-2 votes
1 answer
2k views

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 ...
user avatar
  • 201
0 votes
1 answer
76 views

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. ...
user avatar
  • 9
-2 votes
1 answer
162 views

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 ...
user avatar
  • 19
5 votes
1 answer
640 views

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 ...
user avatar
  • 51
2 votes
0 answers
606 views

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 ...
user avatar
  • 21
0 votes
1 answer
89 views

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 ...
user avatar
  • 1
1 vote
0 answers
19 views

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^{...
user avatar
  • 183
1 vote
1 answer
170 views

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?
user avatar
  • 55
2 votes
0 answers
18 views

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. ...
user avatar
2 votes
1 answer
56 views

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 ...
user avatar
1 vote
1 answer
2k views

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 ...
user avatar
2 votes
0 answers
36 views

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?
user avatar
  • 149
1 vote
2 answers
205 views

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, ...
user avatar
1 vote
0 answers
372 views

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 / ...
user avatar
  • 1,337
1 vote
2 answers
360 views

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 ...
user avatar
4 votes
2 answers
469 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 ...
user avatar
  • 8,754
2 votes
1 answer
817 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 ...
user avatar
1 vote
0 answers
31 views

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 ...
user avatar
9 votes
1 answer
2k views

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 ...
user avatar
  • 4,716
2 votes
0 answers
682 views

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 ...
user avatar
  • 121
2 votes
2 answers
459 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 ...
user avatar
  • 91
6 votes
1 answer
4k views

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?
user avatar
4 votes
2 answers
3k views

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 ...
user avatar
  • 328
5 votes
1 answer
260 views

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 ...
user avatar
4 votes
1 answer
180 views

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 ,...
user avatar
  • 4,716
2 votes
1 answer
365 views

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 ...
user avatar
  • 2,921
2 votes
1 answer
71 views

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 ...
user avatar
1 vote
2 answers
2k views

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 ...
user avatar
  • 2,340