Enzymes 2

Posted on February 22, 2014 by biochem1362blog under Reflection 4

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Welcome back folks, we did enzymes part 1, now it’s on to part 2.

YAYYYYYYYYYYYYYYYY!!!!!!!!!!!!!!!!!!!!!!!

To start off let’s continue with the features of enzymes. The catalytic power of enzymes was dealt with in part 1, so we will now focus on the specificity of Enzymes.

Try not to bite your tongue saying SPECIFICITY!!!!!

SPECIFICITY OF ENZYMES

A certain enzyme, is one that is very selective, we can also say that they are “picky” or “stush”. They are very selective on what substance they react with and also in the reaction they catalyse.

The substances that the enzymes work on are what we call SUBSTRATES.

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Also, in a reaction where an enzyme is present, or, an enzyme catalysed reaction, there are NO by products, or waste products and all reactions tend to yield a great percentage of product.

The products that are formed from an enzyme catalysed reaction are also “stush enzymes”.

In the chemical reaction involving enzymes, the substrate, has to stick or bind to the enzyme by a process called MOLECULAR RECOGNITION.

All this is saying is that the substrate compliments or suits the enzyme perfectly, it’s like a match made in heaven. Like peanut butter and jam, like ice-cream and cake, like biology and chemistry. This way, they form a mutual relationship, they both benefit from each other.

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The substrate binds to a specific area on the enzyme called THE ACTIVE SITE.

So, let’s talk about this active site!!!!!!!!!!!!!!!!!!!!!!

The active site is a pocket or cleft that is made to recognize certain substrates and thus, catalyse chemical transformation.

It is formed in the 3D structure by the group of a variety of Amino Acid residues. These Amino Acid residues are either adjacent or not in the primary formation.

At the ACTIVE SITE, the substrate associates or mingles with the active site via hydrophobic, electrostatic, hydrogen and Vanderwaal’s interactions. These are the same forces that cause the structure of protein to be stable and they are all weak forces of attraction.

The active site of enzymes can also, provide catalytic groups. These groups are the “R” groups of Amino Acids residues and they give certain interactions and allow chemistry which stabilizes the transition state form for the chemical reaction to occur.

When a substrate binds together with an enzyme at the active site by the weak forces we discussed above, a complex is formed. This complex is called THE ENZYME SUBSTRATE COMPLEX.

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There are different Hypotheses models to explain how enzymes are catalytic and specific.

The two major ones are:

THE FISCHER’S LOCK AND KEY HYPOTHESIS
THE KOSHLAND’S INDUCED FIT HYPOTHESIS.

Let’s talk about Fischer’s hypothesis first; it implies the lock and key method.

Look at the figure below!!!

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In the diagram, we can clearly see that the key is analogous to the substrate, while the lock is the enzyme. The key fits into the lock perfectly. In the same way, the substrate fits into the enzyme perfectly forming the enzyme substrate complex. There shape coincides so the complex is formed. If however, another substrate was to try to fit into the active site of this enzyme, the complex would not be formed since the substrate doesn’t match the enzyme’s active site.

In the same way, my car keys can only start my car, if I were to try to start someone else’s car with my keys nothing would happen because they DO NOT MATCH.

The product that is formed, is different from that of the substrate in terms of shape, thus, it is unable to fit into the active site and is released for another substrate of the same shape to bind to the active site once again.

THE INDUCED FIT HYPOTHESIS!!!!!!!!!!!!!!

This hypothesis is self explanatory. The fit of the substrate to the active site is induced. Initially, it does not have a perfect fit; however, as the substrate is brought towards the active site or is on its way to the active site, it induces its shape into the enzyme. The active site now becomes an exact fit when the substrate is in the active site of the enzyme.

The products formed, also have a different shape so they are set free for more substrates to enter.

The diagram below shows the Induced Fit hypothesis:

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THE FACTORS AFFECTING REACTION RATE OR REACTION VELOCITY.

There are a number of factors that can affect the rate of reaction velocity, involving enzymes that is. They include:

Ø Substrate concentration
Ø Enzyme concentration
Ø Temperature
Ø pH

SUBSTRATE CONCENTRATION

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In the graph above, the main focus is on the blue line known as Michaelis Menden curve. At first, as substrate concentration increases, reaction rate increases steadily. This is because; there are more collisions between substrates and the active site, more effective collisions. The point at which the line plateau or levels off, is the point where saturation level has been reached.

That is, the amount of substrate level is continuously increasing but there are no more active sites available so they have to wait on the next available active site. The reaction is still in process; however, the rate is not increasing. In this illustration, the only variable is the substrate concentration. Temperature, enzyme concentration and pH are kept constant.

References for Images:

https://biochem1362blog.wordpress.com/wp-content/uploads/2014/02/terminator21013.jpg

http://bltshop.deviantart.com/art/Enzyme-Substrate-173836053

http://cheezburger.com/6579483392

http://roadshowhaberleri.com/wp-content/gallery/most-mobile/enzyme-active-site-substrate-and-product

https://biochem1362blog.wordpress.com/wp-content/uploads/2014/02/494a8e8421b688f627e00d62c7fd6522.jpg

http://emptyemptyme93.blogspot.com/2010/08/lock-and-key-paradox.html?zx=ae0a35ad410040b5

http://csls-text.c.u-tokyo.ac.jp/active/07_03.html

Enzymes 1

Posted on February 22, 2014 by biochem1362blog under Reflection 4

ENZYMES PART 1

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Enzymes are biological catalysts. In simpler terms, they are very little structures that perform a very important job in the body; they speed up the chemical reactions that take place in different areas of our body by providing a different pathway with lower activation energy. This activation energy is simply the amount of energy needed to start a chemical reaction. They are essential for life since they speed up a number of reactions that we all need to survive. I know what you are thinking………………………………………………………………….

Well take a lot at the diagram below!!!!

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In this diagram the red curve indicates the activation energy needed to convert reactants to products. If we were to compare the red curve with the green curve, it is clear to see that the activation energy of the green curve is a lot lower than that of the red curve, therefore, less activation energy needed to convert reactants to products. Note also that the amount of reactants and products remains the same. SO, although the enzyme speeds up how fast reactants are converted to products it does not change the amount of reactants or products and remains itself unchanged.

IMPORTANCE OF ENZYMES!!!!!!!!!!!!!!!!!

In cellular respiration, sucrose (table sugar) and oxygen are converted to carbon dioxide, water and of course energy by the following reaction;

C12H22O11 + 12O2————à 12CO2 + 11H2O + ENERGY

This reaction occurs in seconds in the cells of the body, however, table sugar is able to stay on the shelf or on the table for years and years. The mere fact that in the body, a reaction like this can occur in seconds compared to years outside the body highlights the many talents and importance of enzymes. Some of you may be thinking about stocking up on lots of sugary stuff to get energy from looking at this reaction but it also has a down side to it, so be very careful.

Most enzymes are proteins!!!!!!!!!!!

In this sense, they are called biomolecules.

Some RNA molecules pretend to be enzymes.

Yes it’s true some RNA (Ribo Nucleic Acid) molecules can act as enzymes. We can also call them RNA catalysts, or biologically, RIBOZYMES and although they are not enzymes they are qualified for their acting role in a number of ways:

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They are substrate specific( which we will discuss in more detail later on)
They speed up the reaction rate
They come out from the reaction just as they went in, they don’t change their structures.

There are also ABZYMES, which are antibodies that have features similar to catalysts. *Antibodies are a special kind of protein that is found in fluids of the body, they are also blood travellers.

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TRANSITION STATE.

The transition state in a reaction is the point at which the substrate is no longer a substrate, that is, it is on its way to becoming a product but it is still not fully converted to a product. Let’s use an analogy to break things down a little.

The popular TV series TEEN WOLF!!

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In the show, a teenage boy named Scott discovers that he is half human: half wolf and it certain instances, he undergoes a change from human to wolf. The point at which Scott’s nails get long and sharp, his body becomes covered with hair, his back arches and his teeth become long and sharp and deadly, that extreme point of pain where all these events are occurring is his transition state. He is not yet a full wolf but he is no longer a human teenage boy.

TRANSITION STATE

Let’s apply this to chemical reactions now, the transition state is the point where the reactants or should we say atoms are at its highest level of organization in the middle of the structure of reactants and that of the products. So, as soon as some bonds in a reaction are being broken, some are also being formed.

Enzymes have three features that make them unique:

They have catalytic power
They are specific (Specificity)
They are regulators

For now, we’ll focus on the catalytic power of enzymes.

A lot of enzyme catalyzed reactions are very effective, an enzyme can make a reaction occur over ONE MILLION times faster than if the reaction had no enzymes present.

WOWWWWWWWWWWWWWWWWWWWW!!!!!!!!!!

SO HOW THEN DO WE NAME ENZYMES???????????????

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The nomenclature for enzymes can sometimes be easy. Some enzymes are named based on the substrate they work on.

For example: Lipase is the enzyme that hydrolyses lipids and sucrose is the enzyme that hydrolyses sucrose.

Simple enough right??????

It can get even simpler, anything ending with the suffix “ase” are most likely enzymes in biochemistry.

What about trypsin and pepsin?? They are also enzymes but their name doesn’t provide us with any clues that they are enzymes.

To make things more complicated, some enzymes have more than one name, for example: Glyceraldehyde-3- phosphate, Triose phosphate and 3-phosphoglyceraldehyde refers to the same enzyme.

So how are we supposed to deal with a situation like that?????????

Thankfully, a brilliant group of people from the International Union of Biochemistry and Molecular Biology, or IUBMB, came up with a system of naming. In this system the enzymes are put into 6 main classes.

Each class has subclasses and each subclass has sub-subclasses.

The classes, subclasses and sub- subclasses, as well as single participants are given a specific number, in this way, a chain of up to 4 numbers relate to a certain enzyme or the Enzyme Commission number (EC).

The six main classes are illustrated below:

Class	What it catalyses
1. Oxidoreductases	redox reactions
2. Transferases	transfer of molecules
3. Hydrolases	cleaving of bonds by adding water
4. Lysases	reactions where a double bond is formed by removing a group or adding a group a double bond
5. Isomerases	reactions where intramolecular arrangements are present
6. Ligases/Synthesases	reactions that join 2 molecules to each other