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Enzymes and their local environment

In this video, we'll learn how different environments might affect an enzyme's function. Important environmental factors include pH and temperature. By Ross Firestone. Created by Ross Firestone.

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  • leaf green style avatar for user alexandra.m.p2
    At when the DNA polymerase bonds with the H+ ion instead of the Mg2+, is that a form of competitive inhibition? And does this always occur when the pH is changed? What would happen of the polymerases' pH was increased instead of decreased?
    (7 votes)
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    • piceratops sapling style avatar for user Woody Sorey
      Regarding your question of whether H+ will always bond to the aspartate residue of DNA polymerase, in the video's example the answer is essentially yes.

      Aspartate has a pKa of 3.9, which means that at pH 3.9 there is a 50% chance that at any given moment, any given aspartate will have that H bound to it. If you lower the pH by just a little bit then there will be just a little bit more H+ floating around, so then the aspartate will be protonated more often than not. If you drastically lower the pH (like the example in the video) you would massively increase the concentration of H+. Since there is so much H+ floating around, it is so overwhelmingly likely that the aspartate will be protonated at any given time that we can just assume that it is protonated.

      This is why DNA polymerase functions well at cellular pH; since there are relatively few H+ protons floating around, the aspartate in DNA polymerase is essentially always deprotonated, giving it a negative charge that will attract the Mg2+.
      (6 votes)
  • male robot hal style avatar for user Dakshina Sarma
    In the video at it says temperature changes disrupt the protein structure.Why does this happen and how?
    (4 votes)
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    • blobby green style avatar for user carlrrussell3
      The hydrogen bonds will start to break apart at higher temperature. The hydrogen bonds help give the protein or enzyme is folded shape. With this increase in temperature, the protein will unfold. This only leaves the primary structure intact.

      Note: Protein and Enzyme are used interchangeably here
      (2 votes)
  • piceratops seed style avatar for user rvchopko
    What exactly happens to enzymes when you increase temperature? What changes about their structure/activity?
    (2 votes)
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    • leaf green style avatar for user Ashley Arce
      In general, at high temperatures enzymes( which are proteins) denature. They start to loose their 3 dimensional structure as well as their 2ndry structure. The primary structure( amino acid chain) stays in tact however, heat is not strong enough to break those bonds between amino acids.
      (4 votes)
  • female robot grace style avatar for user Tyler
    , can a deviation from an enzyme's optimal pH also cause protein denaturation?
    (2 votes)
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  • mr pants teal style avatar for user Yverahderah
    I'm not sure if this is a mistake, but I think Ross' attribution of poor appetite and upset stomach to a fever's temperature increase is oversimplified, if not inaccurate altogether (normal fevers are 37.5degC to about 38.5degC, and I doubt our digestive enzymes are that sensitive to temperature). Since a fever is a symptom of an underlying illness, often an infection which involves our immune system fighting back, I think it is more likely that our immune response is triggering a series of physiological changes (hormones and such) that alter our appetite (e.g. leptin) and digestion.
    (3 votes)
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    • male robot johnny style avatar for user Dododeda
      Specifically speaking about stomach digestion, pepsin operates at a pH of 2 in the stomach, so I doubt that a fever (high temperature) would have that much of an effect on digestion in the stomach. I don't think the same can be said about enzymes operating in other parts of the digestive tract (i.e. small intestine). Most enzymes there operate at a higher pH (maybe 6 to 8, which corresponds to around neutral/normal pH levels). I think a rise in body temperature will affect that region of the body more than the stomach.
      (1 vote)
  • piceratops ultimate style avatar for user siddharthjhala.mask1
    hi
    i have a question at time ( - ) Ross Firestone said .
    that pepsin helps to convert protein into peptides , but my doubt is my textbook says that pepsin helps to convert protein into proteoses + peptones
    (1 vote)
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  • piceratops seedling style avatar for user Vlad Tee
    At when the DNA polymerase bonds with the H+ ion instead of the Mg2+, doesn't the H+ achieve the same effect as the Mg2+? Meaning the enzyme needs the phosphate group to stabilize and it did, why can't it work without the Mg2+ which i thought was just a cofactor?
    (2 votes)
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  • piceratops seedling style avatar for user Emilee Paige Demaray
    So your body temp rises and it increases the enzymes energy levels? That's what makes you sick?
    (0 votes)
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  • leaf red style avatar for user Chantel Fletcher
    At , Ross says that aspartate because protonated at a reduced pH. Why does this happen?
    (1 vote)
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  • blobby green style avatar for user ph menz
    Ok, so does the environment in which an enzyme generally function always determine the 'optimum' conditions in which catalysis occurs? We did an experiment investigating the time taken for Trypsin to hydrolyse the proteins in milk at different temperatures and even though it is an enzyme derived from pigs (that have a body temperature of 38.7°C - 40°C) it had the fastest reaction time at 50 degrees.
    Does this suggest that optimum temperature doesn't necessarily equate to the temperature at which the enzyme normally works? Could you please explain this, because im really confused!
    Thankyou!
    (1 vote)
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Video transcript

So today, we're going to talk about the effects of the environment on enzymes and how a changing environment can affect an enzyme's ability to catalyze a reaction. But first, let's review the idea that enzymes make reactions go faster. And looking at a reaction coordinate diagram, you'd notice that enzymes speed things up by lowering a reaction's activation energy. Now, it's important to recognize that enzymes work best in specific environments. And when I say environment, I can be really referring to many different aspects of an enzyme's surroundings. But right now, we're really only going to be focusing on pH and temperature values. So let's take another look at this by imagining that we have this person over here. And he's hungry, so he's eating some food. Now, there are a bunch of different digestive enzymes in this guy's body that are going to help him break down all the food he's eating into tiny usable parts. So first the food will be in his mouth. And one of the enzymes found inside a human's mouth is called alpha amylase, which is responsible for breaking down complex carbohydrates like starches into small simple carbohydrates like individual sugars. And alpha amylase is able to work well in your mouth since it functions best at a pH of around 7, which is about the same pH as a human's mouth. Now moving along, the food that our guy ate is going to go all the way down to his stomach, where a whole different group of enzymes will start breaking down the food. Now, one enzyme that humans have in their stomachs is called pepsin, which breaks down big proteins into smaller peptides. Now, pepsin will be most active at a pH of around 2, which is also the pH of your stomach, which is so low because of all the stomach acid that you'd find there. Now in terms of temperature, both of these enzymes typically work at a temperature of around 37 degrees, which is the same as body temperature. But you can see that these two different enzymes are functioning at different environmental conditions. So what would happen if we took an enzyme and moved it into a different environment? Well, let's first look at the effects of changing the pH of an enzyme's environment and jump right in with an example. So remember that DNA is a very negatively charged molecule because of all the negatively charged phosphate groups that you'd find on DNA. And in order for the enzyme DNA polymerase to help out with DNA replication, it binds a magnesium ion cofactor, which it uses to stabilize all the negative charge on DNA. Now under normal pH conditions, the DNA polymerase hold onto that magnesium ion through an electrostatic interaction between magnesium and one of its aspartate residues, which would be deprotonated and thus negatively charged at neutral pH values. Now, if we were to take DNA polymerase and put it into an environment with a reduced pH, then that aspartate residue will become protonated since the pH has dropped so much. And in its protonated form, aspartate no longer has a negative charge and can't hold on to that magnesium ion anymore. And overall, this means that DNA polymerase won't be able to do its job properly in a low pH environment. And keeping this enzyme at an appropriate pH is essential to its normal function. So now, let's take a look at the effects of temperature changes on enzyme function. So remember that proteins need to fold into their secondary, tertiary, and possibly quaternary structures in order to be in their functional form. And significant changes to a protein's temperature can disrupt a protein's folded geometry and cause it to lose its functionality. If we have our same person from before, who was really hungry and really wants to eat, but now this person get sick with a fever, his temperature will rise. And a bunch of the digestive enzymes in his body will get all jumbled up and won't be properly folded anymore. And this is why you might have a hard time eating and digesting food when you have a fever. And this can sometimes lead you to throwing up anything you'll eat since all of the digestive enzymes in your body won't work anymore because of the increase in your body's temperature. And the food you eat will just sit there, sit there in your body and make you feel sick. So what did we learn? Well, first we learned that enzymes generally function only under very specific environmental conditions. And different enzymes will often function ideally in different environments from other enzymes. And next, we learned that changes to an enzyme's environment, like changes to the surrounding pH or temperature, can lead to a loss of enzyme functionality.