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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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Enzyme catalysis

Enzymes increase the rate of a reaction. They cannot affect the rate constant thus the rate of both the backwards and forwards reaction is increased. This means the same enzyme catalyses the forwards ...
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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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Function of coenzymes: do they act as substrate shuttles?

My biochemistry textbook, "Harper's Illustrated Biochemistry", states: Coenzymes serve as recyclable shuttles that transport many substrates from one point within the cell to another. The ...
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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 ...
2 votes
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Can humans metabolize D-malate?

Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements. So what happens when we consume D-malate? ...
2 votes
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Competitive inhibition - Similarity between substrate and inhibitor

I have this question - Q. Competitive inhibitor which binds to the enzyme (a) has structural similarity with the product (b) is chemically similar to the substrate (c) has physical structure similar ...
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What is the enzyme production rate of a single E. Coli bacterium?

Suppose an E.Coli bacterium intakes a plasmid which encodes for an enzyme, if the promoter strength is known, is is possible to predict the rate at which the enzyme is produced? Is there an equation ...
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Bi-phenyl degradation pathway in lignin

I am studying lignin - and really like the bi-phenyl degradation pathway of DDVA by SYK-6, as shown below But I can't find any literature on whether this pathway transfers from the dimer to the ...
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Reason for sorbitol synthesis in human body

Sorbitol has been proved to be a major contributor to development of complications due to chronic diabetes. It forms in retina, lens, kidneys, peripheral nerves, ovaries and seminal vesicles by the ...
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Covalent modification of Pyruvate Kinase in RBCs

Human body has 4 isozymes of PK and I am particularly interested in the RBC isozyme. It is capable of being covalently modified through phosphorylation catalysed by Protein Kinase A which is in turn ...
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2 answers
123 views

Efficiency of molecular motors vs. human-made motors

On the wikipedia page for "Molecular motor", it says "In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors." without any ...
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Is there a DNase that works at low temperature, and is it also commerically available?

In preparation for FACS, I need to keep mammalian neurons on ice (in PBS-- / BSA), but as they still die while waiting ~30 minutes, they release their DNA into the solution. This leads to cell clumps. ...
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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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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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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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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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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 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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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 ...
2 votes
1 answer
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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 ...
2 votes
2 answers
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Enzyme inhibitors against common cold viruses

Would some inhibitors of viral enzymes work against common cold viruses? Are there any studies? What could a treatment look like? A lot of common cold viruses are rhino viruses which are picorna ...
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Will amylase inhibitors affect the colorigenic reaction between starch and iodine?

I'm doing an experiment for my IB bio EE involving colorimetry. I'm not experienced at all with colorimetry, so I'm having some trouble planning it. The experiment is on enzyme kinetics, and I'm ...
2 votes
1 answer
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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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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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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 exactly is casein digested?

I mean it seems first step is rennin or pepsin digestion in stomach - then what happens with remaining peptides? I am interested in the whole process from casein to amino acids. Is there brush border ...
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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 ...
3 votes
1 answer
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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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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 ...
6 votes
1 answer
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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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Why does the pH decrease, when adding pancreatin to different types of milk (cow milk, soy milk etc.)?

I'm experimentally observing how pancreatin affects the pH in different types of milk. Why does the milk's pH decrease when I add an enzyme solution to different types of milk (e.g., cow milk, soy ...
3 votes
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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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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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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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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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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 ...
3 votes
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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 ...
4 votes
1 answer
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How do organophosphates affect kidney function?

Many organophosphates, besides inhibiting acetylcholinesterase, can also permanently inhibit the enzyme neuropathy target esterase, leading to nerve damage. NTE also happens to be found in the kidneys,...
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Definition of Cofactor, Coenzyme and Prosthetic Group

This question arises from a student multiple choice question regarding whether certain inorganic ions present in certain enzymes (Cl− in catalyse and Zn2+ in carbonic anhydrase) could be classified as ...
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How does aminoacyl-tRNA synthetase recognize different tRNAs?

There are about 20 aminoacyl-tRNA synthetases, one for each amino acid. Each aminoacyl-tRNA synthetase has a binding site that recognizes a specific amino acid, and other binding areas that recognize ...
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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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