Questions tagged [enzymes]
Enzymes are globular proteins that catalyse a biochemical reaction, increasing the overall rate by reducing activation energy. Most chemical reactions in a cell need enzymes in order to occur at rates sufficient to sustain life.
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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 Difficult is Artificial ATP Synthesis?
One way of making ATP requires:
A membrane (would probably have to be a phospholipid bilayer)
A difference in H+ chemical potential across the membrane
ATP synthase anchored to the low-potential side ...
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Immunoaffinity chromatography: avoiding damage to the antibodies from proteases
What are the possible methods to prevent the digestion of antibodies (mainly Polyclonal) by proteases during affinity chromatography?
I read some papers about doing modifications to the anitbodies:
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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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What lysis buffer recipe is good for just breaking the cell membrane?
I am interested in the decellularization of plant leaves(more specifically maple) and thus need a lysis buffer. I want the buffer to only break the cell wall and cell membrane and I want to observe ...
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What enzyme could you use to delipidate lipidated serine?
I have a protein with a serine modified with an O-octanoyl group (ester linkage). What enzyme could I use to remove this group? Could I use a lipase, such as pancreatic lipase?
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Why is random protein selection not used more often in biotech to create proteins with desired enzymatic activity?
mRNA/cDNA display allows random libraries of up to ~ 10^13 proteins to be subject to selection for binding to arbitrary binders. In the listed studies, proteins selected for ATP binding also had ATP ...
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What keeps pyridoxamine phosphate inside the aminotransferase enzyme active site?
In the function of an aminotransferase enzyme after the first substrate (amino acid) has been deaminated there seem to be nothing binding the resulting pyridoxamine phosfate to the rest of the enzyme (...
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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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Is there a way to refine a low resolution Cryo-EM structure using high resolution partial crystal structures?
I'm working on running simulations of human topoisomerase IIa. These are best done by starting with high resolution structures to ensure the system is as accurate as possible. However, no crystals ...
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Is there a term to designate the property for an enzyme of catalyzing several reactions from the same substrate?
LacZ (beta-galacosidase) catalyzes the hydrolysis of lactose into either galactose and glucose or allolactose.
Is there a term to designate such property for a single enzyme of catalysing several ...
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Why aren't complex-stabilizing proteins like transcription factors considered catalysts/enzymes?
I'm not asking the question on a superficial level. Obviously, (most) transcription factors are not acting directly on a substrate to produce a chemical change. I pose the above question as more of a ...
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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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Is CRISPR mediated RNA editing less specific and less efficient than DNA editing?
According to this diagram, the high efficiency and the high specificity of CRISPR lies in its reversible binding with the target DNA. The Cas protein unzips the target DNA and have the gRNA to base ...
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Are there irreversible metabolic reactions that can happen in opposite ways depending on the cellular conditions?
Irreversible reactions are thermodynamically irreversible, not microscopically irreversible. "Irreversible" here means the reaction happens "out-of-equilibrium". It is a ...
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What is the function of dihydrofolate reductase in humans?
According to StatPearls, synthetic folic acid — as an artificial dietary supplement — needs to be converted into the active form tetrahydrofolate (THF) by dihydrofolate reductase.
In the cells, folic ...
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Nature of firefly Luciferase reaction mechanism?
The bioluminescence of the firefly luceferin (FL) is a two step process, with the first step requiring the enzymatic/catalytic ability of the luciferase to convert the FL into luciferyl adenylate.
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Why does pancreatin affect the pH of milk? [duplicate]
I just finished a lab for college and I was really intrigued by this. Since we're in a rush to finish the semester on time my professor didn't go into details much she just said something about fatty ...
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Does alternative splicing contribute to the diversity of enzymes?
I understand the role of alternative splicing in generating protein diversity, but for enzymes specifically, is alternative splicing responsible for the diversity of it? My professor told me something ...
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Influence of pH on rennet coagulation of milk [closed]
I was looking for the reason why rennin works most efficiently at pH 6.7 (closer to a neutral environment than acidic).
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Mechanism of the calcium-activated protein, Aequorin
In Aequorin, coelenterazine acts as the luciferin, producing light in the presence of calcium and oxygen.
It is unclear to me what part of the protein structure actually catalyses this reaction after ...
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is pepsin able to break down proteins into amino acids in human stomach? [closed]
I'm trying to find out if pepsin can break down proteins into amino acids after they are converted to peptides. Is pepsin able to separate amino acid monomers from the peptides?
can you please show me ...
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How does Clostridium perfringens cause target hemolysis?
I am studying microbiology as a part of my course and I was studying Clostridium perfringens.
While studying its hemolytic characteristics, I came to know that it causes target hemolysis (i.e. zone of ...
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What are the possible causes of Lactase persistence?
Lactase enzyme which is responsible for the digestion lactose (a disaccharide milk sugar) normally its production decreases when a young mammal is weaned but mostly Humens continue to produce this ...
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Can we compare the effectiveness of an inhibitor by checking how much they change Km and Vmax during a reaction?
While comparing two inhibitors, can we check how they alter the Km and Vmax of the reaction and then decide which inhibitor is more potent.
I tried explaining in this way:
While I think the answer ...
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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 can't humans digest dietary fiber when we can digest starch?
So, I can see that there's a couple of questions touching on this subject already, but none of them answer the aspect that I'm curious about:
Dietary fiber is a polymer composed of multiple starch ...
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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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Can enzymes be externally administered?
I was reading about Tay Sachs disease - it is essentially the deficiency of the enzyme hexosaminidase. Why can't the disease be treated by administering the enzyme (prepared artificially/extracted ...
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Why does ATP act as an allosteric inhibitor of glycogen synthase?
Why is ATP an allosteric inhibitor of glycogen synthase? Wouldn't high levels of ATP in the cell mean that the cell has sufficient energy, and in this case wouldn't excess glucose be stored as ...
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What determines the nucleotides incorporated into RNA by polynucleotide phosphorylase?
Polynucleotide phosphorylase, in addition to its role as an exonuclease, is also involved in the post-transcriptional addition of nucleotides to RNA in a template-independent manner:
“Polynucleotide ...
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What is the effect of an acidic solution on hydrolytic enzymes?
I'm working on a school research project and my research question is "What is the effect of increasing concentrations of Acid X on hydrolytic enzymes, measured through the loss of mass of leaf ...
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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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Is the kinase domain of a protein kinase the same as the catalytic domain?
I am learning about protein kinases and I have read that the protein kinase domain is a structurally conserved protein domain containing the catalytic function of protein kinases. I am wondering ...
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Can a constitutively active kinase be highly regulated?
I am studying the protein kinase GSK3 and I am learning about the regulation of its activity. Many journal papers that I have read have stated that GSK3 is unique because it is a constitutively active ...
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Do phagocytes need antibodies to be able to engulf pathogens (to function)?
I recently saw a question about monoclonal antibodies, that are specific to a certain virus, being split (into their constant and variable regions via an enzyme), and the question asked whether some ...
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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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How do enzymes not change the overall energy change of the reaction they're catalysing if they lower the activation energy?
Based on the Induced-Fit model of enzyme action, enzymes catalyse a reaction by lowering the activation energy of a single forward reaction over and over. But I read that enzymes don't change the ...
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Why are many skin depigmenting agents toxic to the body?
Coming from a developing country, I know many people who regularly use these creams to lighten their skin and some of them have developed liver and kidney problems as a result.
I know that many ...
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Do carboxylesterases, arylesterases and acylesterases count to the enzyme class of lipases? [duplicate]
I am currently examining the acyl transfer catalysis activity of several enzymes that I was told are all lipases. Through reading a couple of papers including these enzymes I found out that all of ...
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Basis of enzyme nomenclature — pyruvate dehydrogenase
In the formation of AcetylCoA from pyruvate, why is the enzyme called “pyruvate dehydrogenase (complex)” when it involves the decarboxylation of pyruvate or the replacement of a carbonyl group by ...
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Which enzymes use ATP?
It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well ...
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Are there ribozymes that cut double strands
the header already says:
Are there any ribozymes known that cut double strands?
A kind of ribozyme equivalent to the Ribonuclease III.
With cut, I mean that the backbone of both strands, forming the ...
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What is the "GTP activator protein" that activates GTP-cyclohydrolase-1?
From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011)
The metabolic profile ...
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ATP Synthase EC number
Why ATP synthase EC number is 7(Translocase)?
My textbook says it's a hydrolase but when i checked its EC number it was changed to 7.
And also ATPase(adensointriphosphatase) page that was previously ...
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Will Saliva make food go bad
My mom was telling me that if I put the unfinished bowl of milk and cereal back to the fridge, the saliva that has been stuck to the spoon gets passed to the milk. The saliva in milk will make milk go ...
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Alkaline Phosphatase and Ligase Protocol for Cloning
In the image the circular molecule is a restricted vector and the linear red molecule is a DNA insert.
I found this protocol in my lessons notes, but I don't understand how it is possible that ligase ...
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