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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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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Natural status of flavors produced via fermentation but using GM organisms [migrated]

If a flavor ingredient (e.g. vanillin) was produced via a natural fermentation process, starting from a natural substrate (e.g. sugar) I know that it can be labelled as "natural" (at least ...
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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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Structure and reactions of the cofactors of oxidoreductases such as ferredoxin

I have seen the word flavoprotein being used in place of ferredoxin in few places and vice-versa. I have not found any source that mentions them both together and explains the relation between them. ...
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Calvin cycle- combining three “turns”

In the common Calvin cycle diagram, it is commonly stated that "three cycles are combined to show the production of 1 molecule of G3P". How does the G3P molecule escape from this cycle in ...
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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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Why can't C1r cleave C4 proteins?

I am researching the complement system, and have ran into something I'm not really sure about. In the past, the C1r2s2 complex was thought to be an 8-like structure tucked inside C1q's collagenous ...
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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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Why is this oxoglutarate dehydrogenase and not oxoglutarate decarboxylase?

I was looking at the oxoglutarate dehydrogenase complex and saw the reaction mechanism for its E1-TPP mechanism, which results in the formation of a stabilized carbanion intermediate. The mechanism ...
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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.
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What does it mean for an enzyme to be “constitutively partially active”?

I am reading a paper* about the link between the enzyme GSK3 and autism, and I have come across the following statement: Unlike many kinases that require a signal to be activated, GSK3 is ...
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AMPK, PAN-AMPK, western blot

What does it mean by adding PAN before the AMPK. I am trying to do a western blot assay on AMPK and I am confused by PAN-AMPK, AMPK. does it mean pancreases? Is pan-ampk the total ampk?
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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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What is “KK1 enzyme”?

In the book "The Kaizen Way" by Robert Maurer, I've read the following: When we’re sitting, our muscles go into a form of hibernation, causing our bodies to shut down the enzyme (called KK1)...
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What is the function of human Trypsin Inhibitor if trypsin is secreted in the inactive form of Trypsinogen? [closed]

I was reading about pancreatic digestive enzymes in a Textbook of Medical Physiology and I came across Trypsin Inhibitor. The text stated that: It is important that the proteolytic enzymes of the ...
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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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How can cane sugar sucrose be different from beet sugar in regard to carbon-13 content?

According to an article in SCIENZA IN CUCINA, by Dario Bressanini, le Scienze Blog content of $^{13}C$ differs in sucrose in beet sugar compared to cane sugar. What is this due to? Are there any ...
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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 ...
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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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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 ...
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What is the best way to find which domains in a list of InterPro IDs are catalytic?

What is the best way to find which domains in a list of InterPro IDs are catalytic? (In this case, we are looking at human enzymes and their domains' InterPro IDs.) Thanks in advance! Setz
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How to produce and isolate an enzyme?

I have recently learned that one of the best ways to isolate a protein in industry is via Chromatography. What are other ways enzymes are isolated in industry? Are there other ways?
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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 ...
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132 views

Activated carrier molecules and their relationship to enzymes

I am reading Molecular Biology of the Cell, and one thing I don't quite get is the difference between an enzyme and an activated carrier molecule. I understand that enzymes lower the activation energy ...
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Regarding the role of enzymes

Textbooks commonly state that the role of enzymes is to speed up a chemical rxn by lowering its activation energy. However, I'm unsure what enzymes like helicase, DNA/RNA polymerase, and restriction ...
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Can plants break down cellulose for energy?

I know humans and other animals start using their own proteins as food when starving. This made me wonder if a plant that is deprived of sunlight, after using up its sugar reserves and other carbs, ...
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Histone Deacetylase Inhibition

So I am trying to brush up on my knowledge of HATs and HDACs. I am reading the just the 1st paragraph of the background of this study I remember learning that HATs turn things on on, and HDACs turn ...
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Are there any small peptides with protease activity?

I'm looking for a very small protease to base an engineered protein on. I did a search for "peptides with protease activity" but all the results seem to be as peptides to be used as protease ...
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Why would Aspergillus Oryzae produce lactase when no lactose is present?

Studies [1] have shown that lactase is produced by A. oryzae when grown on wheat bran and spent beer grains. Why would A. oryzae produce lactase when these substrates have no lactose? In [1], it's ...
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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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What is the definition of a polybasic cleavage site?

I keep coming across the term "polybasic cleavage site" which is implicated in increasing the virulence of many viruses, but I'm struggling to find a definition. Is it just a sequence of amino acids ...
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How is the protease inhibited by lopinavir different in SARS-CoV-2 compared to SARS-CoV?

The protease inhibitor lopinavir, originally developed as a cure against AIDS and HIV, has been shown efficient against SARS Coronavirus SARS-CoV. Dayer M R, Taleb-Gassabi S, Dayer M S. Lopinavir; ...
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72 views

How is honey not toxic to our epithelial cells?

Being a supersaturated solution of sugar, honey pulls the water out of cells it comes in contact with via osmosis - killing the cells. It also contains the inactive enzyme glucose oxidase, which when ...
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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 ...
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Regulation of the TCA cycle and glycolysis by adenine nucleotides

Why is the tricarboxylic acid cycle regulated by the ADP/ATP ratio as stated in the following quote : Isocitrate dehydrogenase is allosterically stimulated by ADP, which enhances the enzyme's ...
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Glucose 6-phosphate dehydrogenase: reaction mechanism

I have searched the internet for the reaction mechanism of G6PD but couldn't find it, so I am asking whether anyone here knows its mechanism and whether they could recommend some sources that give ...
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Photolysis in the Light Reactions of Photosynthesis [duplicate]

I'm a bit confused concerning photolysis. During the light reactions, photons are used to excite the chlorophyll molecules so they are passed to the primary electron acceptor. The electrons initially ...
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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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How is plasmin formed from plasminogen?

In Ganong's Review of medical physiology it is mentioned that plasminogen is converted to active plasmin when tissue type plaminogen activator hydrolyses the bond between Arg560 and Valine 561. Can ...
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886 views

How can we digest lactose even though it has Beta glycosidic linkages?

I have Read that we cannot digest cellulose because we do not have enzymes to digest Beta glycosidic linkages in Cellulose Then how is it that we have an enzyme called Lactase to digest the Beta ...
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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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What happens if an enzyme stops working in the body?

For example, if the enzymes in the digestive system stop working will the digestion still occur as enzymes are only catalysts for the reactions. Thank You
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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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Cheap enzyme assay for a high school lab

At the moment, I'm designing an experiment for a high school lab with no financial resources. I need to assess the impact of a variety of factors on a specific enzyme's reaction with its respective ...

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