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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Can an adult without genetic lactase persistence still develop a tolerance for dairy foods?
While investigating the rise of adult lactose tolerance, I came across the news that China has been encouraging its citizens to drink more milk, even though most of the Asian population lacks the SNP (...
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How crowded is the bacterial cell?
I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity in vitro, I would argue that the substrate and enzyme concentrations resemble those in ...
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How fast does the rotor in ATP synthase spin?
I'm sure the exact frequency varies, but does anyone know roughly how many revolutions per minute / second the rotating center part makes?
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What inactivates pepsin in infants?
In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach.
Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
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Why do we have no enzyme to digest cellulose?
As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have an enzyme to digest cellulose?
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What effect has changing pH and salt concentration on protein complexes?
I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt ...
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Is the EC50 of an activating protein for an enzyme a good indicator for the binding affinity Kd?
We work with a membrane protein system where measuring the affinity between the enzyme and the upstream activating protein has been difficult, and when measured in detergent solution, it is almost 100 ...
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Origin of the biochemical term, Pi (inorganic phosphate)
I would like to know when the term Pi (inorganic phosphate) was introduced in the representation of biochemical reactions, how it was originally defined, and the justification given then for using it ...
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Grapefruits and CYP3A4
Grapefruit juice contains furanocoumarins, which irreversibly inhibit CYP3A4. For this reason, when one is taking certain medications it is necessary to not eat grapefruits because the inhibition of ...
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Examples of enzymes working in reverse?
I have always been taught that enzymes can catalyze both the forward and reverse reaction, and will increase the reaction rate in both directions. I understand that the thermodynamics of the reaction ...
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Why are restriction enzymes not frozen?
We all know restriction enzymes are proteins, but we never freeze them. They are instead provided in high glycerol containing solutions by companies and stored at -20C. Is there a reason why this is ...
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How is Taq polymerase produced?
I've seen Taq polymerase being marketed as either "native" or "recombinant". I understand that the recombinant version is produced by specially modified Escherichia coli strains that have the gene for ...
user132
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Why does cyanide inhibit CuZnSOD, but not MnSOD or FeSOD?
Different types of superoxide dismutase (SOD) contain different metal ions (Zn, Cu, Mn, Ni, or Fe), all of which allow them to catalyze one reaction, dismutation of superoxide anion, O2−. Cyanide can ...
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In which direction does ATP synthase rotate?
I heard about the rotation of ATP synthase in a biochemistry course. The professor said it will rotate counterclockwise. Is that true? If so, what mechanism defines its direction?
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How do the pharmacodynamics of the NSAIDs differ and are there "resistant" COX phenotypes?
I know that the non-steroidal anti-inflammatory drugs (e.g., aspirin, ibuprofen, naproxen) affect the enzymes cyclooxygenase (types I and II).
Is there any difference in the degree to which these ...
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Understanding association kinetics
I would like to understand the classic kinetic model of association / dissociation that tries to describe the concentration of a compound $[\ce{AB}]$.
Let's say we have a model:
$\ce{A + B} \...
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How does the enzyme ATP Synthase use a proton concentration gradient to make ATP?
I understand what the enzyme ATP synthase does, but I'm not exactly sure how it does it. I've heard that it uses rotary catalysis, but how exactly does this work? How is the energy from the H+ ion ...
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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 ...
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What is the correct model for enzyme-substrate complementarity?
This Wikibook shows both proposed models of enzyme-substrate complementarity, the Lock and Key model and the Induced Fit model. I've always been taught that the Induced Fit model is the proper one. ...
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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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What are the clotting factors' effect on avascular necrosis development?
Do clotting factors tpa and pai-1 lead to degenerative osteoarthritis in the same way that lupus anticoagulant and prothrombin might? Is one of these pathways particularly detrimental during formation ...
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What conditions are necessary for HPL (human pancreatic lipase) to activate?
What conditions are necessary for human pancreatic lipase to activate? Is there an optimal temperature or pH? How quickly does it take effect?
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How do bile salts affect lipase activity?
BACKGROUND: It is well known that bile salts are needed for emulsification of fats. It is then said that this increases the surface area for activity of pancreatic lipase, implying that bile salts ...
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Compare and contrast "Rubisco activity" and "assimilation rate" (is there a difference, and if so, what is it)?
I am confused about the variable "RuBisCO activity". How is it measured, and is it any different from the net assimilation rate?
Based on some background reading (e.g. Kling, 2008; Lambers et al 2011)...
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Are there enzymes for every given reaction?
This is a question that's been bugging me, and I haven't been able to find a definite answer anywhere.
We know there are thousands of enzymes (proteins, let's ignore catalytic RNA for now) that ...
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Origin of enzyme names
Sometimes I get confused about why this or that enzyme was named in this or that particular way.
1) TCA: Why was not isocitrate dehydrogenase named isocitrate decarboxylase?
Wouldn't it have been at ...
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Can any enzyme be produced?
After reading about how recombinant insulin is produced, the following question occured to me. Does the current level of technology allow any enzyme to be produced in a similar way?
As I see, ...
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Why are diabetic people often overweight?
I was looking at diabetes the other day, and I noticed something strange. Lower amounts of lipase are a symptom of diabetes, as is overweightness. However, since lipase is the enzyme that breaks down ...
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How can I measure bacterial alkaline phosphatase activity?
I want to measure alkaline phosphatase activity using PNPP in my mutant bacteria strains, but all the protocols I found involve purification of the phosphatase (which I have no need of).
Does anyone ...
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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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Why is it often the case that an enzyme is favorable only towards one direction of a reaction and not both directions?
In class when we're studying enzymes like amylase or protease it only works well when you're using it to break down compounds like polysaccharides. I'm just curious but why is it not possible for ...
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What is the biological mechanism underlying caffeine intolerance? (CYP1A2 or other?)
As far as I can tell, caffeine metabolism occurs primarily via the CYP1A2 enzyme. I am curious as to whether mutations in the CYP1A2 gene are associated with caffeine intolerance. Some site that is ...
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For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex?
I'm trying to figure this out. I cannot find any publications that go into good detail about the chemistry of PBP inhibition by β-lactam antibiotics.
PBPs cross-link adjacent pentapeptides to form ...
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Enzymatic error rate
I am aware that each enzyme generate a certain amount of misproducts.
This is well documented, for example, for the DNA polymerase.
I am interested in enzyme involved in biochemical processes, so for ...
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How do DNA, enzymes, hormones etc. reach their proper cellular locations?
I was trying to understand DNA transcription from this chapter, and there seems to be no explanation on how exactly the proteins, enzymes and other molecules manage to find each other inside the cell. ...
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Renin - enzyme or hormone?
Wikipedia says :
The kidneys secrete a variety of hormones, including erythropoietin,
and the enzyme renin.
Can a substance be both an enzyme and a hormone ? Why is renin both an enzyme and a ...
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The effect on the efficacy and potency of a non-competetive antagonist binding to the active site of the receptor (dose-response curve)
According to the book "Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy" by Golan et al, non-competetive antagonists can bind to both the allosteric site and the active site.
I ...
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Is there a tool to find the action of an enzyme in a metabolic pathway?
Is there any tool to search the biochemical action of a particular enzyme in a metabolic pathway of an organism? In other words, how can I find if enzyme "E" is involved in the metabolic pathway for ...
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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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Why is aconitase classified as a lyase?
Aconitase in the TCA (tricarboxylic acid) cycle isomerizes citric acid to isocitric acid via cis-aconitic acid intermediate. Since overall it functions as an isomerase, why it does not belong to ...
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Why are enzyme-catalysed reactions slower at lower substrate concentration?
Suppose I'm using 200 nmoles of enzyme and 2 mmoles of substrate. The enzyme should be saturated but if I use 50 mmoles of substrate, the reaction will be faster. Why?
I just can't get it! Even at ...
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What are the units of enzyme activity?
I was looking at this graph of turnip peroxidase activity and I saw that they use units of 1/sec for enzyme activity. What does this unit intuitively represent and how is it calculated?
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Is there an enzyme for the transformation of the hydroxyl group?
I would like to know, is there any enzyme which does the transformation of hydroxyl group to any other functional group using the enzyme.
The substrate is aromatic hydroxyl group. Product should not ...
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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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When is the lactase in lactose-free milk active?
Recently we have started suspecting that one of our children has hypolactasia (lactose intolerance), and so accordingly I have had my first exposure to lactose-free dairy- and dairy-like products. In ...
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Why are plants unable to take up Phosphorus directly in their organic form like Phytic Acid?
I am researching acquisition strategies of phosphorus by decidious trees. I am reading a lot that plants take up nutrients as their inorganic form. In the case of P according to literature this is ...
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What is the meaning behind Kcat / Km?
I'm trying to understand enzyme kinetics, the formula for Km and Kcat make sense to me.
Km , the substrate concentration at which the reaction rate is half of Vmax
Kcat, used to describe the ...
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What happens when you tag a protease with its own degradation tag?
I've been learning about the ClipXP, ClipAP, and Lon proteases. They are proteases from the AAA+ family, which seek out proteins tagged with certain peptide sequences, unfold them, and chop them up.
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What happens to the enzymes produced by the digestive system?
Our digestive system produces a lot of enzymes and they help to catabolize the food, and after completing their work are they excreted out or as they are also made up of proteins are they catabolized ...
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Function of the alpha subunit in mitochondrial ATP-synthase?
Within the catalytic core of mitochondrial ATP-synthase there are two different types of subunits; $\alpha$ and $\beta$. From what I have read, the catalytic sites occur only in the $\beta$ subunit so ...
