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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Are there any alternatives to the Epicentre product Plasmid Safe?

I need to remove any traces of linear DNA (both single and double stranded) from a ligation reaction while keeping circular DNA intact. Up to now, I have used Epicentre's Plasmid Safe to do the job. I ...
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Are there any enzymes without aromatic amino acids?

I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just ...
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Does alpha-amylase from different species have different *optimal* conditions?

Do the optimal conditions for the enzyme isoforms differ between species? Specifically, do the optimal pH and temperature for alpha-amylase differ for that enzyme produced by B. lichiniformis and A. ...
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Adenosine metabolism

Are adenosine or its catabolites increased in inflamed airways? How can I assess this? I am trying to use inhibitors for adenosine deaminase, xanthine oxidase, and purine nucleoside phosphorylase, but ...
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Are there any enzymes synthesised by humans that specifically catalyse the hydrolysis of non-cyclic Imides?

Imides or dicarbonyl amides are an interesting class of compounds that includes the pharmaceuticals thalidomide, aniracetam and a few other drugs. These compounds, however, are cyclic and I'm ...
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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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42 views

Why do some enzymes have giant structures around the active site?

As a part of my inorganic chem. course (it's a required course at my college), we have a module called Introduction to Bioinorganic Chemistry. There, the prof. showed examples of enzymes like ...
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What changes do ants make to the soil they use for building ant hills

I live in South India ,and among the many species of ants in and around our house, some of them except the weaver ants build the typical small ant hills in the garden. I have examined the coarse sand ...
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50 views

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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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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Why does M1 RNA together with C5 protein in 100mM Mg(II) fail to cleave tRNA?

Sidney Altman discovered that RNA moeity of RNAse P (M1 RNA) alone is able to perform enzymatic cleavage of ptRNA, which won him the Nobel Prize of Chemistry in 1989. However, when I read the Nobel ...
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Molecular Docking Enzyme Inhibitor Biosensor?

I had some task to study Molecular Docking relations with Biosensor and I am really new with this discipline (beginner). I am docking C60 with Glucose Oxidase and my question is: what would happen if ...
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473 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 ...
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What is the protocol for extracting Protease Onion?

I am Investigating the protease concentration in certain fruits and vegetables. I am unable to find the protocols for the extraction from onions. I want to purify my protein using the ammonium ...
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103 views

Degradation of PMSF in protein extract while dialysing - safe for feeding to animals?

I would like to use the protease inhibitor PMSF in enzyme isolation. The obtained enzyme diamine oxidase (or better the protein extract) is tested oral on dogs. According to Wikipedia, PMSF has a ...
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Would canines that consume the stomach of ruminant prey animals benefit from any of the bacteria and enzymes present in the rumen?

This question is inspired by the growth in popularity of raw diets for pet dogs. Green tripe is a common addition to these diets, with many claims of probiotic benefits. Here's an example from a ...
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217 views

Modulating the level of acetyl CoA

Describe what might happen if there were no mechanisms for modulating the level of acetyl CoA. I am not sure what is meant by "modulating the level of acetyl CoA", or what mechanisms contribute to ...
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570 views

Proteases in the blood

I’m reading on hormones and the book talks about how peptide or amine hormones are easily broken down by proteases present in the blood plasma. This has led me to question the interactions between ...
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364 views

What's the purpose of Cdk activity having more than one method of becoming inactive?

Cdk becomes partially active once its bound to cyclin and then gets phosphorylated and fully active once a Cdk-activating kinase (CAK) phosphorylates the partially active Cdk. This fully activated Cdk ...
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234 views

Cereal Alpha and Beta Amylase temperature range and reaction rate

This question is motivated by a practical application in bread making. While it is well known which are the optimal (highest reaction rate) temperatures for both alpha and beta amylase, I am not able ...
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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 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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Does Topiramate work by supplanting Pyridoxal phosphate in enzymes?

I have seen it said that the precise mechanism of action of migraine medicine Topiramate is not known. But I certainly see a resemblance between that molecule and PLP (Pyridoxal phosphate, the ...
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Lower optimum temperature of plant Catalase

Most resources give an optimum temperature of 35° C for Catalase. after performing the AP Catalase enzyme lab in school, using blended potatoes, our results gave a greater reaction rate at a room ...
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Can Mung Bean Nuclease only digest a ssDNA 5' overhang?

Can Mung Bean Nuclease only digest a ssDNA 5' overhang, if the double-stranded region of DNA (20bp) is A-T rich at the ends? Does this enzyme degrade 5' overhang (5bp or 30 bp) with 100% efficiency?
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Is there any current knowledge of how DNA polymerase is “motivated” to perform error corrections during transcription?

I was trying to understand the process of how polymerase performs error corrections on DNA. Every paper on this topic mentions what happens during the process, but there's no mention of how it happens....
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Cellulase Sample Digestion Protocol?

Is there an effective way to use cellulase(s) and/or lignase(s) to remove unwanted plant debris from a sample? I'm working with a series of fresh water grab samples for environmental assessment. The ...
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Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
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Looking for a good and complete Enzimology exercises book

I mean, I want to practice with challenging exercises and I want to know the theory behind them. So, I started reading: Organic Chemistry: Yurkanis, P. Enzyme kinetics: Bisswanger, H. Biotechnology ...
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What are the marker enzymes for Nucleus, Ribosomes and cell membrane?

Are there any marker enzymes present for ribosomes, nucleus and cell membrane. For mitochondria there are many, for lysosome it's cathepsin. I read about the marker enzymes of most of the other ...
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135 views

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 ...
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60 views

Cooperative Enzyme Question

I'm currently studying for the MCATs. After doing some biochemistry practice questions, I came upon a question that I believe may be incorrectly posed. I was wondering if I'm correct in saying this or ...
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which enzyme phosphorylates sodium potassium pump?

I know that Na+/k+ pump possess atp-ase function; so the pump will hydrolyze ATP into ADP + Pi. And I see in a figure that the pump is phosphorylated but couldn't really find which protein catalyzes ...
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Do we know how dangerous six-eyed sand spiders are?

The Sicariidae family contains the well-known and dangerous Loxosceles spp. (fiddle-backs, violin spiders). The family's other two genera, Sicarius and Hexophthalma (six-eyed sand spiders) have ...
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How can we quantify the effect of pancreatin (biological enzyme) on the clarification of milk powder

Alright so I'm trying to quantify the rate at which casein (protein constituent of milk powder) is converted into a product (I am unaware of) by pancreatin (a biological enzyme that speeds up the ...
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Question about vitamin b6 product and cycling

Can the b6-product of a vitamin b6 reaction such as transaminase be recycled back to active vitamin b6 in man, and if so by means of what reaction?
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What does “operationally soluble” mean, re. Tax10 enzyme?

I am trying to work out whether the enzyme Tax10 is soluble or insoluble. I need to know if some buffers won't work with Tax10. I am trying to confirm Tax10 activity, having confirmed protein ...
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What options exist to quantitatively detect enzyme activity in non-model insect tissue?

Evolution/genomics person here: what are the options to measure the activity or presence of broad categories of enzymes--like peroxidases or catalases--active in a specific tissue (in a non-model ...
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What are the enzymes with the lowest concentrations in a cell?

Or are there any enzymes which are only translated one time per cell?
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Is osteoid an uncalcified substance?

I recently learned about Osteoid (the substance secreted by osteoblasts during intramembranous ossification), and I read that it was an "unmineralized organic component of bone." Now, does this mean ...
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355 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 / ...
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What are the chemical characteristics of cofactors that functionally differentiate them from the side chains of amino acids?

Cofactors are essential for the function of many enzymes, such as NAD+ in the glycolytic pathway - I was wondering how the chemical properties of these cofactors allow them to fulfil their function ...
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Can methionine peptidase liberate selenomethionine?

Can methionine peptidase liberate selenomethionine from proteins? I'd be happy to know if any can that are active in humans, but am also especially curious about METAP2.
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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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What enzymes I shall use for preparing single cell suspension from cardiac tissue for flow cytometry?

Can anyone suggest which enzymes I shall use for preparing single cell suspension from cardiac tissue. I will be looking at both cell surface and intracellular antigens involving cardiomyocytes and ...
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Energy cost of chewing vs production of enzymes

Consider a hypothetical case that you ingest a piece of starch. Which is more costly energetically 1) chewing + reduced amount of enzymes production needed or 2) sole production of all the enzymes for ...
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Can a ribozyme be present on two different RNA molecules?

Suppose we have a ribozyme that consists of an 'enzyme' strand and a 'substrate' strand. (e.g. hammerhead ribozyme) Is it possible to have the enzyme strand of the ribozyme on one RNA molecule and ...
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What is the oxidation state of iron at the photosynthetic reaction center?

Is the iron at the reaction centre in the $3^+$ or $2^+$ oxidation state? For instance, 1AIG is $2^+$ or, perhaps it will depend upon charge separation state? I checked the PDB: some are $3^+$ ...
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Where occurs diamine oxidase in kidneys - in cells or in extracellular space?

I would be interested in where the enzyme diamine oxidase in kidneys of human/animals mainly occurs? In cells or in extracellular space? A literature reference if available would be great. Thanks!
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Calculation of NADPH molecules number needed to reduce a substrate in enzymatic reaction

I am inquiring if it is just simply possible - as it seems to be - to calculate the number of NADPH molecules needed by an enzyme (let say for example Dihydrofolate Reductase DHFR) to reduce the ...