Enzymes : Interactions

Hey!

We’re back on to a side note about the different types of interactions in enzymes :). So let’s get started shall we

Interactions between side chains can either stabilize or destabilize the structure of an enzyme. Since side chains can either be negative or positive in charges which can either repel each other, when they are alike, or attract each other when they are opposite in charge. This can either prevent, or allow the specific structure of an enzyme.

Examples of amino acids, which can prevent the formation of a particular helix structure include: 

  • Glutamate
  • Lyseine
  • Argeine

Large bulky side chains next to each other can result in steric hinderance, or interference preventing the formation of the helical structure. Steric hindrance, also known as steric interference has to do with the fitting together properly of the structures.

Normally, positive charges of amino acids are most times found three or four residues away from the negative charge, forming anion pair which can stabilize a helical structure.

Finally in helical structures, the four amino acids at the end of the helic do not fully hydrogen bond. The net macro dipole moment goes from negative to positive. That is, the carbonyll part of the group, to the amino or nitrogen part of the amino acid molecule.

And for a final Note: Helicies often prefer to interact in an antiparrallel manner, so that their macro dipoles interact favorably.

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Enzymes Part ii

Hey guys! Time for another update on enzymes ! 😀

The following is the follow up video used to derive the wonderful knowledge I am about to present on you 😉

So Let’s start off shall we!

From time to time, you may hear us refer to an enzyme’s activity as being specific. Well what is this specificity? Specificity of an enzyme refers to the selective qualities of an enzyme where molecular recognition occurs. But what is this molecular recognition? Molecular recognition is based on the structural complementary shapes between the enzyme and its substrate. THIS is the basis of specificity.

Moving on to another important term when dealing with enzymes are their functionality is the active site. This “site” as referred to is generally a pocket or cleft, specialized to recognize specific substrates and catalyze chemical transformation. It is usually formed by a 3D strucutre by a collection of different amino acid residues which may or may not be adjacent in the primary sequence.

Let’s pause here. Make SURE  you remember what is meant by primary sequence and amino acids. This is VERY important in understanding enzymes, their structure and their ability to function.

Continuing,

The interactions between the active site and the substrate occur via the same forces that stabilize the protein structure. That is, Hydrophobic interactions, electrostatic interactions and hydrogen and vanderwaals forces.

Do you remember the definitions of these interactions?

If not :

  • Hydrophobic interactions refers to interactions between water and non-polar molecules

Hydrophobic Interactions

  • Electrostatic interactions refers to when opposite charges, usually from the R groups, are attracted to each other forming a bond, allowing stabilization of the structure

Electrostatic Interactions

  • Hydrogen bonding involves bonds being formed between hydrogen and electronegative atoms.
  • Vanderwaals bonding are induced by electrical interactions between between two or more atoms or molecules which are very close to each other.

Now that we have been reminded about the different ways that an enzyme can be stabilized, we can finally conclude that an active site provides specific interactions that stabilize the formation of the transition state for the chemical reaction. Catalytic groups provide this facility since they contain the R groups which are the main component in the chemical aspect of this biochemical phenomenon.

 

In my next post, We shall be taking a more detailed look into the interactions of R groups of the amino acids and how they help stabilize the structure further.

 

Enzymes

Hey guys ! It’s me again 🙂 giving yet another posts on enzymes. Whooo hooo!!

Okay so before we get started I thought i’d make reference to the very informative videos that I have obtained all my information which I am about to summarize for you 🙂

Video Link : 

So let’s start shall we!

Summarizing, as we’ve learnt before, enzymes are biological catalyst which can speed up the rate of a chemical reaction by providing an alternative pathway for the reaction to occur at a lower activation energy.

Let’s pause for a cause here :

What do we mean by activation energy?

Well activation energy refers to the minimum amount of energy for a reaction to occur.

Okay. We can continue 🙂

As seen in the video, some RNA molecules or ribozymes can act as enzymes since they are substrate specific, enhance reaction rates, and emerge from the reaction unchanged.

Again. Let’s pause.

What are some features of these biological catalysts? ( ….. you might ask.)

  1. They have catalytic power, meaning the ability to speed up a reaction while the molecule itself remains unchanged.
  2. They can be regulated or controlled in some way

Also something fascinating noted in the video was that some antibodies, which prior to this I thought dealt strictly with the body’s immune system, have catalytic properties. These special antibodies are referred to as abzymes. This got me thinking about how so many different small little things work together to make our magnificent bodies function properly, as these factors work together. Truly remarkable if you ask me!

Next, in the lecture, a Transition State was mentioned. This referred to the highest energy arrangement of atoms that is intermediate in structure between the structure of the reactant and the structure of products.

Noting that :

Changes

structure of substrate ————–> structure of product

 

So now we ask, how do we name these enzymes?

  • based on their substrate : like lipase and sucrose
  • based on a description of the action/reaction performed : Example pyruvate carboxlase
  • And sometimes, well sometimes we just find outta timin’ enzymes, like trypsin pepsin and catalase

Another way to classify enzymes is by the EC number, where there are six main categories that we should know:

  1. Oxidoreductoses —> Catalyzes oxidation reduction reactions
  2. Transferases —> Catalyzes transfer of C, N, or P containing groups
  3. Hydroloses —> Catalyzes cleavage of bonds by addition of water
  4. Lyases —> Catalyze cleavage of C-C, C-S and certain C-N bonds.
  5. Isomerases —> Catalyzes racemization of optical or geometrical isomers
  6. Ligases —> Catalyzes formation of bonds between carbon and O, S, N coupled to hydrolysis of high energy phosphates.

SO. To be honest. memorizing these categories are gonna be quite a challenge for me. But through practice I think, like everything else we should be able to get the hang of it !:) now that we’ve gotten that FUN part ( extreme sarcasm here) out of the way, we can finally move on to Cofactors!

Cofactors refer to a non protein component which allows an enzyme to function properly.

Cofactors can either be inorganic or organic.

Inorganic cofactors can usually refer to metal ions, examples being Zinc 2+, or Mg 2+

Organic factors however, can lead to something known as “co enzymes” which are frequently derived from vitamins where transparent association can lead to “co substrates” where as permanently associated vitamins can lead to what we know as a “prosthetic group.”

Which leaves me to conclude about inorganic catalyst.

These kids never get 100% of the product and cannot be regulated. Examples where inorganic catalysts are used include the haber process, and the contact processes within the industry .

Alright folks! That’s it for this post! I know there’s plenty more to write about here. Hopefully by the next two days i’ll be able to catch up. Also a new quiz will be coming up soon! so make sure you’re on top of your game! 🙂

Enzymes! :)

References:

See J. E. and E. T. Bell, Proteins and Enzymes (1988).

The Columbia Encyclopedia, s.v. “enzyme,” accessed March 16, 2013, http://www.credoreference.com/entry/columency/enzyme

Hey guys!

So previously we had covered amino acids and their linkages, that is polypeptides bonds and the structures that are formed along with them. This Week we’ve moved on to a somewhat more exciting topic. ENZYMES!

Now this is a HUGE topic, but to help us along i came across a little article that could help us.

According to “Credo Reference” an enzyme, also known as a biological catalyst, accelerates the rate of a reaction without being permanently chemically changed. Enzymes achieve this phenomenon by providing a different reaction pathway for the reaction to occur, thus lowering the activation energy required for the reaction to take place.

Factors which affect the rate at which the enzyme work include specific temperature ranges, pH ranges. The efficiency of a particular enzyme can also be measured usually by a turnover rate, measuring the number of molecules of compound opon which the enzyme works per molecule of enzyme per second. A useful example given in the article was of Carbonic anhydrase which has a turnover rate of 106  for removal of carbon dioxide from the blood binding it to water. Thus this rate means that one molecule of the enzyme can cause a million molecules of carbon dioxide to react in one second.

Also briefly mentioned in the helpful post, is the occurence of denaturation, where a denatured enzyme refers to an enzyme which has been altered in its chemcial and physical structure, so much so that it can no longer serve its purpose. Once an enzyme loses its shape, it can no longer catalyze its reactions since enzymes are selective for the molecules upon which they act, known as substrate molecules. Most enzymes will react with a small group consisting of closely related chemical compounds, demonstrating absolute specificity, thus having one substrate molecule, appropriate for the reaction.

An interesting fact, about enzymes is that some require non protein molecules, not excluding coenzyme molecules. These nonprotein components which are tightly bound to the protein are also referred to as prosthetic groups.

The active site is known as the region on the enzyme where the catalytic event takes place. Prosthetic groups, as mentioned above are usually located there. The side-chain groups of amino acid residues make up the enzyme molecule also participating in the catalytic event.

Another example given is in the enzyme trysin which brings together a histidine residue from one section of the mlecule with glycine and serine residues from another. Conclusively the side chains of these residues in this particular geometric arrangement produce the active site which accounts for the enzyme’s reactivity.

One may ask the question: How can these enzymes be identified and classified? Well, through crystalization of the amino acid sequence, and X-ray crystallography.

The informative post also mentions enzyme deficiency, where a number of metabolic diseases are known to be caused by deficiencies or malfunctions of the enzyme. An example of this is in albinism, caused by the enzyme responsible for the production of cellular pigments.

 

Tertiary Structure

Hello again!!

This is just a short closing post on tertiary and Quaternary structured proteins, just some general notes to fill in any blank spaces we might have been missing out.

In case we forgot, a tertiary structure of a protein basically refers to amino acids that are far apart in the linear sequence, as well as residues that are adjacent to each other.

Water soluble globular proteins.

In proteins such as myoglobin,while folding of chains occur spontaneously, the energy required to bury the non polar amino acids in the hydrophobic interior away from the surrounding hydrophilic aqueous medium is the driving force behind the folding of the polypeptide chain.

One may ask, How is this folding maintained, i.e. the confrontational 3D biologically active (native) conformation.

  • Hydrophobic interactions
  • electrostatic forces
  • hydrogen bonding
  • covalent disulphide bonds (if present)

Amphipathic

  • An amphiphathic molecule is one with two different affinities. i.e: Hydrophobic and hydrophilic. ( where hydrophobic is not water loving, and hydrophilic is water loving.)

A final note on Electrostatic Forces:

Electrostatic Forces refers to ionic groups of opposite charges which are attracted to each other. Like ammonium groups of Lys for example. They can also be referred to as an ion pair or a salt bridge.

 

 

Finally My last note is on Denaturation:

There are several ways in which a protein can be denatured.

  • Heat : An abrupt change, which occurs over a narrow temperature range. It is referred to as a co-ooperative process as Hydrogen bonds are continuously quickly broken.
  • UV : Causes Hydrogen bonds to once again be disrupted
  • Organic Solvents : Causes a change in hydration of ionic groups resulting in a change in the di elective constant.
  • Strong Acids/Bases through salt formation causing disruption of Hydrogen bonds
  • Chemicals : Such as Chaotrops which disrupts hydrophobic interactions. Detergents is another example of chemicals which can cause denaturation of proteins.

Amino Acids Part 2

So I promised that this time we’d take a closer look at secondary structures, that is alpha helices and beta pleated sheets.

The Alpha Helix

Image

Here are some basic pointers about this secondary protein structure:

  1. The o from the CO bond is hydrogen bonded to the H on the NH2 group of the 4th amino acid.
  2. Hydrogen bonds run parallel to the axis of the helix.
  3. There are 3.6 amino acids per turn of the helix, which are 0.54nm long
  4. Each aa residue is 0.15nm of the axis of the helix.
  5. Any side chains, are found on the outside of the helix.
  6. The abundance of hydrogen bonding gives the structure of the helix its stability.

If we take a closer look at this marvelous naturally occurring structure, we will see that certain amino acids are less often found in alpha helices than in others.

For examples:

Proline:

      The N atom in proline is a part of a rigid ring within the amino acid itself.This causes a destabilizing kink in the helix since rotation about the N-C bond is not possible.

Having trouble imagining what I’m referring to? Here’s a diagram to remind you about the structure of proline.

Image

 

 

 

The type of bonding exhibited in proline also prevents it from forming the correct pattern of H bonds due to the lack of H on the NH2 group. Because of these bonding factors, Proline is more suitable for, and mostly found at the end of an alpha helix where it alters the direction of the polypeptide chain, terminating the helix.

Another example of an amino acid which can destabilize an alpha helix is Glyceine since the R group, is the small, that is H, which allows high conformational flexibility.

 

Structure of Glyceine

 Image

 

 

Beta Pleated Sheet

Image

 

 

REFERENCES:

“Chubblyemonscience.” Last modified 2012. Accessed March 9, 2013. http://chubbylemonscience.blogspot.com/2012/11/secondary-structure-of-proteins-alpha.html.

Accessed March 9, 2013. http://commons.wikimedia.org/wiki/File:L-proline-2D-skeletal.png.

Accessed March 9, 2013. http://commons.wikimedia.org/wiki/File:Glycine-2D-flat.png.

Kaiser, Gary,Dr. “Doctor Kaiser Microbology.” Last modified 2005. Accessed March 9, 2013. http://webcache.googleusercontent.com/search?q=cache:http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit3/viruses/beta.html.