Inhibition!

Hey guys hopefully THIS post is my last on enzymes before we are able to move on to glycolysis 🙂

The following graphs show the effect of substrate concentration, enzyme concentration, and different inhibitors acting upon the enzyme.

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Figure 1:  Effect of Substrate Concentration on Enzymatic activity

As seen in figure 1, the rate of reaction increases with substrate concentration as more substrate becomes available to be converted into products until it begins to level off at Vmax, where Vmax refers to the maximum velocity for the reaction to occur. This leveling off occurs when the substrate saturation occurs and all active sites of the enzymes are continuously being used to catalyze the reaction.

 ie09

Figure 2: Effect of Enzyme Concentration on Enzymatic Activity

Figure 2 displays the effect of enzyme concentration on the reaction rate. It can be seen that an increase in enzyme concentration increases the rate of reaction since there are more available active sites for the reaction to proceed resulting In an increase in reaction rate.

Competitive_inhibitor_graph

Figure 3: Effect of Competitive Inhibition on Enzyme Activity

Competitive inhibition, shown in figure 3, occurs when the inhibitor competes with the substrate for the active site, binding preventing the reaction to be catalyzed. Thus this causes a decrease in Vmax and a subsequent increase in km as the affinity for the substrate to bind to the active site decreases.

 Noncompetitive_inhibitor_graph

Figure 4: Effect of Non-Competitive inhibition on Enzyme Activity

Non-Competitive inhibition, figure 4, is as a result of the inhibitor binding to a site other than the active site on the enzyme, referred to as the allosteric site, changing the shape of the active site, preventing the reaction from proceeding. This therefore causes a reduction in Vmax. The affinity of the enzyme to bind to the substrate however remains the same, therefore km does not change.

Uncompetitive_inhibitor_graph

Figure 5: Effect of Un-Competitive inhibition on Enzyme Activity

Figure 5, displaying Un-competitive inhibtion shows a decrease in Vmax and a reduction in km. This is because inhibitors bind to the enzyme substrate complex preventing the final product from being formed, reducing the rate of reaction (and subsequent Vmax). Km decreases since the affinity for the substrate to bind to the complex increases since the inhibitor binds to the enzyme after it has binded to the substrate, it does not therefore reduce the ability of the substrate to bind to the active site.

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Enzyme Kinetics

Hey Guys! Thought i’d close off finally on a little enzyme kinetics !

 

FACTORS AFFECT THE RATES OF ENZYME-CATALYZED REACTIONS:

Temperature

Raising the temperature increases the rate of enzyme-catalyzed reactions by increasing the kinetic energy and the collision frequency of the reacting molecules. However an increase in temperature which causes an increase in heat energy can also increase the kinetic energy of the enzyme to a point that exceeds the energy barrier for disrupting the noncovalent intermolecular forces that maintain the enzyme’s three-dimensional structure. The polypeptide chain then begins to unfold, or denature, with an accompanying rapid loss of catalytic activity.
Hydrogen Ion Concentration or pH

For enzymes whose mechanism involves acid-base catalysis, the residues involved must be in the appropriate state of protonation for the reaction to proceed. The binding and recognition of substrate molecules with dissociable groups also typically involves the formation of salt bridges with the enzyme. Gain or loss of critical charged groups thus will adversely affect substrate bind- ing and thus will retard or abolish catalysis.
SUBSTRATE CONCENTRATION

For a typical enzyme, as substrate concentration is increased, vi increases until it reaches a maximum value Vmax . When further increases in substrate concentration do not further increase vi, the enzyme is said to be “saturated” with substrate. At any given instant, only substrate molecules that are combined with the enzyme as an ES complex can be transformed into product. 


THE MICHAELIS-MENTEN EFFECT OF SUBSTRATE CONCENTRATION

The Michaelis-Menten Equation shows the relationship between initial reaction velocity vi and substrate concentration [S].
The Michaelis constant, Km, is the substrate concentration at which vi is half the maximal velocity (Vmax/2).

 

Michaelis Menten

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! 🙂

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

Hey guys 🙂

I know its been a while since I’ve posted anything ( a week to be exact ) but ive been quite the busy bee! So that being said I decided to give a major post on the basics for amino acids 🙂

So let’s start off with the basic stuff.

question

and Last but NOT least:

question

What are amino acids?

Let’s start with a basic structure :

Reference: http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html

So there we have it folks! the basic structure of an amino acid, containing an amino group, a carboxyl group, and a variable R group also known as the “side chain.” Later on we will see that the interactions between the varying side chains, as well as the amino group play an important role in forming different types of bonds for various structures.

Two amino acids, come together, through condensation, to form a peptide bond.

Peptide bond

Reference: https://courses.worldcampus.psu.edu/welcome/biol011/lesson02_09.html

Later on in this blog, we will refer back to peptide linkages, and polypeptide chains, so make sure you understand the basics!!

Moving on we ask;What are amino acids used for?

Well to begin with, there are two different types of amino acids, Essential, and non essential amino acids. Naturally I am sure you will be able to guess the difference between two.

Essential amino acids :

These amino acids ust be obtained from the diet, since they cannot be synthesised on their own. There are roughly ten essential amino acids.

Non-Essential amino acids:

The body is able to synthesize these amino acids. Usually the body uses already exsisting carbon skeletons, and convert them to the respective amino acids. One example of this is the conversion of alanine to pyruvic acid.

Here’s a general picture of whats happening for the curious ones:

c01f010

Reference: https://kubon-sagner.e-bookshelf.de/products/reading-epub/product-id/595941/title/Essential%2BBiochemistry%2Bfor%2BMedicine.html?autr=%22Mitchell+Fry%22

Finally we move on to some chemical reactions involved with amino acids! 😀

Here’s a look at general peptide chain:

peptide1

Reference:http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html

From these peptide bonds, polypeptide chains can be formed,which can cause further structures to be created, as the polypeptide chain begins to fold. The polypeptide chain folds as a  result of different interactions between the different amino acids and the formation of hydrogen bonds, sometimes various sulphide bonds The different degrees of folding in the structure, classifies it as either primary,secondary or tertiary.

Primary and Secondary structures.

Reference: http://www.mhhe.com/biosci/ap/ap_prep/chemH5.html

Let’s Pause for a cause here and get some definitions under our belt.

Here’s a useful website I found describing everything in a pretty concise understandable manner.

http://www.mhhe.com/biosci/ap/ap_prep/chemH5.html

They give a concise definition of amino acids stating that they are a  “Class of organic acids that comprise the building blocks for proteins.”

They also explain hydrogen bonding in an easy, understandable way stating that hydrogen bonds are, ”  A weak attraction between a slightly positive hydrogen atom on one molecule and a slightly negative oxygen or nitrogen atom on another molecule, or between such atoms on different parts of the same molecule; responsible for the cohesion of water and the coiling of protein and DNA molecules, for example.”

Understanding hydrogen bonds is important seeing as they form the basis for primary, and therefore secondary and tertiary structures.

So now that we’ve taken a moment to understand, let’s dive straight into these amazing structures 😀

Primary structures:

  •  These are a linear sequence of amino acids joined by peptide bonds
  • The nucleotide bases in the gene encoding the protein determines this sequence.

Secondary structures:

  • Regular folding of regions in polypeptide chains are observed.
  • Two examples of secondary protein structures can be seen in the alpha helix and beta pleated sheet.

Tertiary Structures:

  • These are usually globular
  • For soluble globular proteins, they are usually folded in away that the hydrophobic links are buried within the structure, while the hydrophilic chains are on the outside.

protein-structure

Reference : http://www.umass.edu/molvis/workshop/prot1234.htm

So there you have it folks! 🙂 the basics of amino acids.

Hope you had a fun time learning 😀

Next time we’ll go into detail about the secondary structures of proteins, that is, alpha helices and beta pleated sheets.

Until next time

Au Revoir