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Enzyme time!
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So far, you know that a lot of chemical reactions are happening in your body.
But all of these reactions are slow.
Even a simple reaction will take a lot of time!
Because we all know that reactions occurs when two molecules "crash" in the correct order and all those other right conditions.
What makes all these reactions go fast in a second?
The answer is right here in this article everybody.
They are Enzymes. Our body's well - known catalyst!
Now, an enzyme is a type of catalyst. A catalyst is a substance which makes reactions go faster. In order for enzymes to do it's job, it needs something to react with. That is the Substrate.
The Active site is the part that enzymes bind with the substrates.
And the others are all called Allosteric sites. We will talk about them later.
Here's a good thing to know - Most enzymes are proteins. So they are made out of amino acids. However, some proteins are made out of RNA molecules which are called Ribozymes. So not every enzymes are not proteins.
Say, can it be possible to mark how enzymes work in a graph?
The answer is Yes. We can show that with the Reaction coordinate diagram!
This is the Reaction Coordinate Diagram. And it shows how much energy we need/use to complete a reaction.
The X coordinate shows us the process of the reaction and the Y coordinate shows the amount of energy that we need for the reaction to occur.
As you know A is the reactant and B is the product.
For the reaction to be spontaneous, A has a higher energy level then B does.
It might be nice if the reactions just go to A to B straight,
but that's not the case in most reactions.
Instead, they need to overcome an "Energy barrier" to be a different molecule. The highest point of the energy barrier is called the Transition state. (‡)
The transition state is where the most amount of energy is used and when the molecule is the most unstable.
The Free energy of activation, or activation energy (ΔG‡ or EA) is the energy barrier from A --> B. And it's shown as the difference between A and the transition state.
Lastly, the Standard free energy change (ΔG˚ or ERXN) is the net change in energy levels between A and B. And it's the energy that is released once the reaction is over. And Enzymes lower the reaction's activation energy to speed up the reaction.
There are two ways to represent how enzymes bind and react to substrates.
One is called the Lock/Key model and the other one is the induced fit model.
The Lock and Key model was introduced by Emil Fischer. It shows that the enzyme and the substrate binds together perfectly like puzzle pieces.
The Induced fit model was shown by Daniel Koshland.
And It is a modification of the Lock and key model.
The induced fit model shows that the substrate and enzyme does not quite fit perfectly. So the amino acid (side chains) of the active site changes it's position depending on the substrate while not giving any harm to the enzyme itself. After the reaction is done, the active site returns into it's normal position.
The induced fit model is used more often because it shows better how the enzyme and substrate binds.
Sometimes, an Inhibitor can bind to the enzyme and change the active site.
If that happens, the original substrate cannot bind to the enzyme.
So the substrate competes with the Inhibitor for their own purposes.
We call this Competitive Inhibition.
In competitive inhibition, just like the name says, the substrate and the inhibitor "race" each other to go to the active site.
And whoever goes to the active site first gets the enzyme.
So if the substrate got in first, the reaction will occur and the inhibitor cannot bind to the enzyme and vice versa.
But the inhibitor doesn't always go to the active site.
It can go to the allosteric site as well too!
Note: The Allosteric site includes every place of the enzyme except for the active site.
When in a competitive inhibition but the inhibitor goes to the allosteric site, we call this the Allosteric competitive inhibition.
In allosteric competitive inhibition, the same thing happens just like the competitive inhibition, but the inhibitor goes to the allosteric site instead of the active site.
However, For Non competitive inhibition, the substrate and the inhibitor doesn't necessarily compete each other.
Instead, the substrate can bind the enzyme until the inhibitor sticks to the enzyme's allosteric site. (Active site if there's no substrate)
In other words, Both of them can bind, but if that's the case, nothing happens.
Sometimes, enzymes are named for their functions.
An example is DNA Polymerase, which is named because it is a polymer that works on DNA. The suffix "~ase" is tagged along with enzyme names.
If you're familiar with Amino acids, you will know that we can classify amino acids like aromatic, aliphatic groups.
Just like that, we can also classify enzymes as well!
Number 1: Transferase.
Transferases transfer specific functional groups from one molecule to another.
A + BX --> AX + B
Where A and B are the molecules and X is a functional group.
A good example of a transferase is an enzyme called Peptidyl transferase.
What this enzyme does is to link amino acids that is derived from the TRNA in translation to a growing polypeptide chain. And it also makes sure that they don't jumble up as well.
For short, Ala - Gly - His + TRNA - Ser --> Ala - Gly - His - Ser + TRNA
Notice how the Serine residue moved from one molecule to another.
Number 2: Ligase.
Ligases Joins two molecules together into one.
A + B --> AB
Speaking of Ligases, doesn't it gives you the feeling of our old friend?
That's right! It's DNA Ligase!
As we all know, DNA Ligase Fills up the Okazaki Fragments of the lagging strand at DNA replication. In other words, DNA Ligase joins the two strands of DNA to a single strand.
Number 3: Oxidoreductase.
Long name, but if we look closely, the name has the word "Oxido" and "Reduct". By that, we can figure out that this enzyme uses Oxidation and Reduction!
And that's true. They do use OR to catalyze reactions.
As you may know, Oxidation is when a molecule loses electrons and Reduction is when a molecule gains electrons.
A + B: --> A: + B
NOTE: ":" is a pair of electrons.
An example of a oxidoreductase is something called Lactate Dehydrogenase.
Which it was a pain to learn about because it was in cellular respiration.
Lactate Dehydrogenase (LDH) helps the oxidation/reduction when Pyruvate and NADH reacts to make Lactic acid and NAD+ in Lactic acid fermentation.
Pyruvate + NADH --> Lactic acid + NAD+
Click to Learn about Cellular respiration/Lactic acid fermentation.
Click to Learn about LDH in Wikipedia.
Number 4: Isomerase.
Isomerases helps to convert a molecule to one of it's Isomers.
A --> B
An enzyme called Phosphoglucose Isomerase catalyzes the reaction of glucose 6 phosphate to one of it's isomer, fructose 6 phosphate.
Glucose 6 - P --> Fructose 6 - P
Number 5: Hydrolase.
Hydrolases Uses water(H2O) to cleave a molecule into two other molecules.
A + H20 --> B + C
You might know what hydrolysis is if you learned about Amino acids.
Hydrolysis is the reaction where we use H2O to cleave peptide bonds of a polypeptide chain. And in hydrolysis, there is an enzyme called Serine Hydrolase. (Or Serine Protease)
This enzyme uses the nucleophilic amino acid Serine at the active site to catalyze hydrolysis.
Pro - Cys + H2O --> Pro + Cys
Number 6: Lyase.
Lyases are a bit special. These guys don't use hydrolysis nor oxidation to catalyze a reaction. Instead, what they do is to break bonds of a single molecule and then form a double bond or a ring structure to make it stable.
This type of reaction needs one molecule for the forward reaction, but two for the opposite reaction.
A --> B + C
For an example of lyase, there's an enzyme called Argininosuccinate lyase.
And it catalyzes the formation of the amino acid Arginine and the dicarboxylic acid Fumarate from the molecule Argininosuccinate.
There, ASL breaks N - C bond and makes a new double bond between the "Broken" molecules to make it stable.
Argininosuccinate --> Arginine + Fumarate
And.... That's the 6 types of enzymes shown today!
Sometimes, enzymes cannot do it's work all by itself alone.
They need some "Helpers" to do their job properly.
These "Helpers" are non protein molecules. We call them Cofactors.
We can go further into Cofactors and we can see that there are three different types of Cofactors that work differently.
The first are Co - enzymes. They are Organic(C based) cofactors that are loosely bound to enzymes. Co - enzymes carries molecules or electrons.
We can see that in the lactic acid fermentation process, lactate dehydrogenase uses NADH as a coenzyme.
Another type of a coenzyme is Coenzyme A. (CoA) Which carries acyl groups instead of electrons.
The next are Prosthetic groups, and these can be organic or inorganic.
Unlike Coenzymes, which are loosely bound, Prosthetic groups are either tightly bound or even covalently bonded to the enzyme.
Do you know about Hemoglobin? It's a tetramer protein that carries oxygen around our body. In hemoglobin, there is a molecule called heme.
Heme is a prosthetic group that consists a Fe2+ (Ferrous) ion in the center of an organic heterocyclic ring called a porphyrin. Which is made by four pyrrolic groups connected by Methine bridges. (=CH-)
The last ones are Metal Ions. And they are inorganic.
These Metal ions are Iron, Magnesium, copper, etc.
One more thing to say - Have you ever heard about Apoenzymes and Holoenzymes? Apoenzymes are enzymes that needs a Cofactor but doesn't have one. Apoenzymes are inactive - So it doesn't do anything unless the cofactor is bound to the enzyme.
Holoenzymes on the other hand, are Apoenzymes that has a Cofactor on it's side. To make it short, Apoenzyme + Cofactor = Holoenzyme.
When environmental factors, like PH or temperature changes too much that the protein can't stand, they undergo denaturation. And we've already seen how proteins undergo denaturation in amino acids.
Enzymes work the same way as well too.
For example, in DNA replication, DNA polymerase has to "Deal" with the negatively charged phosphate groups on DNA.
To stabilize the charges, DNA polymerase binds to the cofactor Mg2+ ion with one of it's aspartate residues. Which is deprotonated at normal PH conditions.
At normal PH, the negatively charged Aspartate residue will attract the positively charged Mg2+ ion through electrostatic interactions.
By using that Mg2+ ion, the DNA polymerase can stabilize the charge and can do it's job properly.
However if the PH is changed to low PH, the aspartate residue will be protonated and become into aspartic acid.
If that happens, the aspartic acid can't hold to the Mg2+ ion, and it can't function it's job. Note that H+ is not a cofactor. And a lot of H+ makes it a very acidic environment. Which is bad in this situation.
The other one is Temperature.
You may know what happens to proteins when they are in a very high temperature. They vibrate violently, breaking all the bonds that consist secondary, tertiary and quaternary structures.
Just like that, enzymes denature in temperature changes as well too.
That's it for now in about enzymes and it's functions.
In the next time, things will be a bit easy to understand If you learn some basic stuff about Kinetics! The next is all about Enzyme Kinetics you know!
~Credits Section~
All Images by Khan academy, Wikipedia, and Wikibooks.
I do not own any of these sites.
If you want to see where the images came from or learn more, go to
Wikipedia: https://en.wikipedia.org/wiki/Main_Page
Khan academy - MCAT: https://www.khanacademy.org/test-prep/mcat
Khan academy - Biology: https://www.khanacademy.org/science/biology
Wikibooks: https://en.wikibooks.org/wiki/Main_Page
2016. 2/15
By Haein Kim <해인이가 초5>
출처: http://ilovehaein.tistory.com/23?category=614534 [ilovehaein]
