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 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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plausible science for why an enzyme breaks down a substrate better at 4 degrees rather than 20 degrees [closed]
An enzyme was found to have an optimal temperature of 20 degrees. The same enzyme in sheep liver extract was found to have an optimal temperature of 4 degrees. What are some of the factors that 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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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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Betaine HCl stomach pH
It seems betaine HCL is often recommended for those suffering from "low stomach acid" -- which, as I understand, is having too high stomach pH for proper digestion (especially for proteolysis via ...
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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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Are Raf, MEK, and ERK MAP kinases?
I am trying to make sense of this diagram. Can Ras activate RAF or MAPKKK, or is RAF a MAPKKK, making MEK a MAPKK, and ERK a MAPK?
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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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What is meant by "catalytic amount of a hormone"?
This textbook says:
In the classic definition, hormones are secretory products of the ductless glands, which are released in catalytic amounts into the blood stream and transported to specific ...
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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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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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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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Can one use dialysis tubing several times?
I would like to know, if one can use dialysis tubes multiple times. Or is there a risk of plugging the pores? I use the tubes for dialysis of a solution that contains a precipitated enzyme (183 kDa) ...
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How can facultative anaerobes exist without catalase?
Catalase-negative bacteria may be anaerobes, or they may be facultative anaerobes that only ferment and do not respire using oxygen as a terminal electron acceptor
A facultative anaerobe is an ...
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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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How to derive rate of product formation for an allosterically inhibited enzyme?
I'm working through Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls, and in Chapter 3 there's an example of a simple allosterically inhibited enzyme with reaction scheme ...
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Is some of the energy of food lost during digestion?
I know that chemical energy of food is converted to heat energy to be used by the body in many metabolic reactions. Specifically, I know that the breaking down of bonds is what releases energy.
Does ...
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What is "enzymatic activity"? [closed]
I should be grateful if anyone would send me a link to an article or an encyclopedia/handbook contaning an explanation of the concept of enzymatic activity. Surprisingly, I did not manage to find ...
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How did our bodies decide on the right enzymes and where did we get them? [closed]
I have read that enzymes act as catalysts to reactions in our bodies and that they are extremely target-specific.
My question is how did our body know that a particular enzyme could act as a catalyst ...
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Why is a magnesium ion essential for ATP activity in enzymic reactions?
The Wikipedia entry on Magnesium in Biology includes the following:
ATP (adenosine triphosphate), the main source of energy in cells, must be bound to a magnesium ion in order to be biologically ...
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Why is glycerol kinase absent from adipocytes but present in the liver?
Why don't adipocytes have the enzyme, glycerol kinase? Wouldn’t it be more efficient for them to utilise glycerol present to synthesize triglycerides than to get it from the liver? So what is the ...
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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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How to dialyze large amounts of precipitated enzyme solution (ammonium sulfate)?
I am no biochemist, but I want to purify some liters of solution through dialysis. What I know are those dialysis tubes in glas vessels on stir plates for labs. But how is this done in industry for ...
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Allosteric regulation: why involve extra molecules
Why are molecules such as allolactose (for lac repressor) or 2,3-BPG (for haemoglobin) used for allosteric regulation rather than the actual molecules involved in biochemical pathways, such as lactose ...
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Secondary/ Acquired lactose intolerance
Acquired lactose intolerance may occur due to a sudden and high intake of milk-based diets. Lactase is an inducible enzyme.
So if lactase is an inducible enzyme then why increase intake of lactose is ...
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How does hydration affect digestion?
My textbook( biochemistry by Satyanarayana, 4th edition pg.no:166) says:
The polysaccharides get hydrated during heating which is essential for their efficient digestion.
(I think there is a typo ,...
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Enzyme kinetics types?
In lectures, we have discussed Michaelis Menten enzyme kinetics, but from lectures it was clear that this was not the only type of kinetics.
After looking into this, I have found enzymes that give a ...
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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 ...
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Do plants have cellulases?
I can't seem to find the answer to this. Not even Wikipedia could help- it mentioned bacteria and fungi that have cellulases but not plants. Using my own reasoning, I would think that
On the one ...
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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 ...
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why can proteolysis only occur once on a enzyme?
My texbook says that proteolysis can occur once in the lifetime of the enzyme? I know that proteases must cleave the zymogen at more or more specific locations, but why can't the process take place ...
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Presence of Aromatase enzyme in males : Result of Natural Selection
Males have increased chances of getting cardiovascular diseases than females ; one of the reasons might be less level of oestrogen ( which decreases deposition of low density lipoprotein LDL in blood ...
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Is the occurrence of a particular enzyme in a given subcellular location a random phenomenon? [closed]
Enzymes occur in different subcellular locations. Some are specific to a given subcellular location, whereas others are heterogeneously distributed. What evolutionary decisions influence the occurence ...
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Nomenclature of enzymes involved in synthesis of glutamine
I am considering nitrogen fixation and in my lecture notes, there is the statement
The glutamine synthetase- glutamate synthase system requires use of an ATP molecule as well as reducing power. ...
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The effect of 3D structure and solubility of the binding site of enzyme on its affinity Km and maximum activity Vmax? [closed]
Could some one provide me with some resources or papers where I can read more about the following:
1- How can the 3D structure of an enzyme affect its Km and Vmax? (some papers, books or articles ...
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Why half of the protein is saturated when [L] =Kd
let's suppose the following reaction:
At equilibrium we can calculate the Kd (Dissociation constant) using the following formula:
Kd = [P][L] / [PL] or kd / ka
We can then use the Hill equation to ...
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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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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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What organisms are Chloroperoxidase enzymes found in?
Are they found in humans? I'm wondering because they display a structural similarity to glucose-6-phosphatase, which is an important enzyme in gluconeogenesis.
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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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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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The effect of pH on catalase
Why does catalase still produce oxygen when mixed with 1 mL of 0.1M NaOH (pH 13), but not when mixed with 1 mL of 0.1M HCl (pH 1)? Catalase's ideal from what ive researched is 7. In other words, since ...
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Rate-determining steps in enzyme catalysed reactions
According to my chemistry book, there are 3 simplified steps within an enzyme catalysed reaction:
S + E → ES
ES → EP
EP → E + P
Where S is substrate, E is enzyme, ES is enzyme substrate complex, EP ...
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In the Lineweaver-Burk Plot, why does the x-intercept = -1/Km?
Taking the reciprocal of both sides of the Michaelis-Menten equation yields the Lineweaver-Burk Equation:
$ \dfrac{1}{V} = \dfrac{K_m}{V_{max}}\dfrac{1}{[S]}+ \dfrac{1}{V_{max}} $
Plotting a $ \...
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Does protein kinase A accelerate glycolysis or slow it down?
In liver cells, the activity of PFK-1 is regulated by the PFK-2/FBP-2 complex, whose activity is in turn controlled by glucagon and insulin.
Glucagon activates protein kinase A. Then protein kinase ...
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How does changing the shape of ATP synthase specifically prevent the enzyme from working any longer?
I am currently stuck on working out how to answer this question:
"A random mutation causes the enzyme ATP synthase to change shape so that it can no longer function. Describe the impact this would ...
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Does DNA helicase or topoisomerase actually "unwind" DNA?
I am reading through my textbook (Genetics, Brooker 4th edition) and the summary it gives seems imprecise for the functionality of helicase and topoisomerase.
The following is an exerpt:
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Understanding of the saturation function in the Monod-Wyman-Changeux Model
I am reading Mathematical Physiology, Sneyd. I am a undergraduate mathematician interested in pursuing the field, so forgive me if my terminology is off. In this example, the writer considers a ...
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Enzyme inhibitors, reversible or irreversible? [closed]
So far, I know about competitive, non-competitive inhibitors and allosteric inhibitor. Which ones are reversible and which ones are irreversible?
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Enzyme Inhibition by alpha-2 macroglobulin
Alpha-2 macroglobulin is a plasma protein which acts as an anti-protease. It does so by a "bait mechanism" - the protease cleaves the bait domain, following which a conformational change causes ...
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