Importance of Natural Resources

Enzymes: Nature’s Factory Workers

Professor Dave here, let’s learn about enzymes. We now know that proteins
are polymers of amino acids, and since there are 20 amino acids in the body, and
each protein has hundreds of amino acids, there are a mind-boggling number of
possibilities for primary protein structure. This is how proteins can be so
diverse and serve so many functions in the body. One type of protein is called
an enzyme. An enzyme is a protein that serves some catalytic function in the
body. Remember that a catalyst is something that lowers the activation
energy of a reaction, and enzymes catalyze biochemical reactions. These are
critical molecules for living organisms because nature can’t do chemistry like
we do chemistry in the lab. In the lab we can throw anything we want into a flask and heat it up, cool it, down use strong acids and bases,
or any number of strange exotic compounds. But inside your body, nature has to do chemistry at body
temperature and neutral pH, only with the materials at hand and using only the
reactions it has stumbled upon by blind chance over the past few billion years.
Thus the enzyme evolved. An enzyme takes a chemical reaction that would be nearly
impossible inside the body and makes it up to a trillion times more favorable,
such that it is feasible to occur on a normal biological time scale. So how do
they work? Well every enzyme has a specific substrate, and the enzyme
recognizes its substrate with extremely high specificity, so it’s kind of like a
lock and key, where a specific molecule is the key that activates the enzyme’s
function. There is a specific area on the enzyme that the substrate will bind to
which is called the active site. The substrate will bind to the active site
because it has just the right shape and composition to do so, meaning it is the right size but it also has functional groups that make favorable electrostatic
interactions with certain key residues in the active site of the enzyme, whether
those are van der Waals interactions, hydrogen bonds, or any other interaction
of this type. The substrate might fit into the active site as is or it might
cause an induced fit, where the enzyme changes shape slightly once the
substrate is inside. But either way, once the substrate is inside the active site
and binding has occurred, a number of things might happen. One possibility is that the enzyme
causes the substrate to bend in a particular way, which it will do in order
to make certain interactions with the enzyme, and when in this bent
configuration some of the bonds become weaker and easier to break. This is one
way the enzyme qualifies as a catalyst. The molecule would have a hard time
breaking apart on its own but in the conformation induced by the enzyme, the
activation barrier associated with the reaction is much smaller, so many enzymes
have the task of breaking down large molecules like the ones we eat to form
the tiny components that we can use to build our own biomaterial. Once the
enzyme catalyzes the reaction, the reaction proceeds, the altered substrate
leaves, and the enzyme can then go and catalyze another reaction. Enzymatic
activity is always stereospecific, meaning that if a substrate can exist as
two mirror images, only one of those forms will fit into the active site of the
enzyme. Most enzymes have names that end in “ase” so you’ll know an enzyme when you
hear one. The rest of the name usually has to do with what the enzyme operates
on. For example, the enzyme lactase breaks down lactose, the sugar found in milk,
into two smaller sugars. We will learn about these types of molecules next. It
is a deficiency in lactase that causes lactose intolerance in some people,
because without enough of this enzyme it is very difficult to digest lactose, as
nothing is present to break it down once ingested. But breaking down molecules into pieces
isn’t the only thing that enzymes can do. Let’s look at the categories. We already
mentioned enzymes that break down molecules, and those could be a hydrolase,
which catalyzes the hydrolysis of a chemical bond, which effectively
separates a molecule into two pieces, or a lyase, which also cleaves covalent
bonds, but by means other than hydrolysis. An enzyme with the opposite function, a
ligase, is an enzyme that joins two molecules together. A transferase is an
enzyme that transfers a functional group from one molecule to another, an
isomerase catalyzes a spatial rearrangement of the substrate, and an
oxidoreductase is an enzyme that transfers electrons from one molecule to
another. Sometimes when an enzyme operates on its substrate, they will
temporarily become covalently linked. This can happen if a residue in the
active site has a nucleophilic group like the hydroxyl group on serine, which
can react with an electron-deficient atom in the substrate, kind of like an
SN2 reaction. Sometimes an enzyme simply does acid-base catalysis, meaning it
either donates a proton or accepts a proton from some functional group on the
substrate to make it more reactive. An example of this is when a residue in the
active site is acidic, like lysine, which if protonated at the amino group, can
donate this additional proton. Sometimes in order to function, an enzyme requires
certain cofactors or coenzymes. This is some other thing that must also bind to
the enzyme before it can operate on the substrate. Cofactors are things like
metal ions, where as coenzymes are actual organic molecules like vitamins. That’s why we need to get all our
vitamins, so that our enzymes can function properly. So you can see that
there is a great variety of enzymatic activity, and all of it is biologically
crucial. Certain enzymes break large molecules down into the small components
we need for other enzymes to then build up all the biomolecules in our bodies,
which is constantly happening in every cell in our bodies. We will come
back to enzymes later but for now let’s move on to some other biomolecules. Thanks for watching, guys. Subscribe to my channel for more tutorials, and as always, feel free to email me:

Reader Comments

  1. At 1:19 the video shows 98°C for body temperature. I mean °C or Kelvin is the way to go but it would be 98°F or in the proper metric system 36.67°C.

  2. im a high school student in north africa , and we have enzymes , proteins and such things as the subjects of the final exam , i wonder what grade americans study this , and gret video by the way , you have saved a life

  3. I'm a Brazilian student of Biological science, and I am trying to learn english. So, your videos help me a lot, cause I hear of a contents that I like at the same time that I try to understand your leanguage.

  4. Hey Proff Dave, I love your videos ! quick question 5:54 is Lysine acidic or basic ? I got kind of confused

  5. I always read my assignment (16-40 pages) and then I come here to understand what I just read. Thanks to your videos I'm an A+ Student 😀 Thank you! <3

  6. Not sure if I was listening carefully, but can an enzyme split an atom and create nuclear fission?
    Something like oxidoreductase or acid base catalysis

  7. Apart from some mistakes it´s well explained. Ligases and Lyases both cleave and combine molecules, for an enzyme always catalyses the reaction foward as well as rewind. The difference is that a Ligase needs energy for example from ATP and the Lyase doesn´t. Furthermore there was a mistake about the Coenzymes and Cofactors. Cofactor is the generic term for Coenzymes and Prosthestic groups. Coenzymes are molecules the bond only for the short moment of reaction while prosthetic groups are bond covalently to the enzyme. It has nothing to do with the type of molecule or ion. The ion you´ve described for example is a prosthetic group.

  8. At 6:14, the coordinate-covalent bonds between the ligands and the e- acceptor metal ion are polarized with a large negative dipole on the sulfurs and nitrogens and a large positive dipole on the metal, correct? This seems logical since the e- donor atoms have a greater electronegativity than the metal atom (say the metal in the picture is magnesium or zinc, for instance).

  9. Hey, I just found this channel. Was looking for something to remember everything I've learned and fill it with more stuff.
    This is just the fourth video I've watched yet but your channel seems nice.
    You also have a funny face and I like the way you speak in the videos, it makes me want to watch more.
    I don't know what I'm talking about, but thank you for this. Bye.

  10. Thanks it was really helpful. I understood it very well could you please explain the enzyme kinetics related to the Michaelis-Menten constant

  11. Thank you so much for your efforts to make up this video, I am a student from Egypt and you are really helping me with your videos in studying , keep going Mr Dave ??

  12. When i receive the salary i will earn from the job i will get from the exams i will pass, i promise you i will support you on patreon!

  13. Wait… how did living cells do chemistry before the enzyme evolved? Never mind, that's not why I'm watching this video.

  14. Professor Dave…. Thank you so much for sharing your outstanding illustrations on different facets of Biochemistry

  15. You really think this just "evolved? Moving one atom to another place? evolved? So it was just moving atoms around arbitrarily in the beginning till it found something that worked? (so some function developed to start experimenting with displacement and placement of atoms?) how did it know when it came across something usable? how did it remember what it did and not keep going on and on and on?

  16. Some notes i took

    Substrates have just the right shape and composition (meaning it has functional groups that have favorable electrostatic interactions (such as van der waals, hydrogen bonding, etc) with certain key residues in the active site of the enzyme) to bind to the active site of a certain enzyme. although the shape of the enzyme can change a little for induced fit binding.
    enzymes are always stereospecific meaning if there are mirror images of the same molecule, only one of them can fit into the active site.
    most enzymes have names that end in -ase
    cofactors are inorganic, like metal ions
    coenzymes are organic molecules, like vitamins

  17. I have to correct you at 4:15. It is not a deficiency in lactase that makes people lactose intolerant, because this is the normal state of an adult. We are not designed to consume milk as adults, lactose tolerance is the exception.

  18. hello i was a former revserve officer in my country i starting to study in colege man your the best proffesor thank you . i can learn from you

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