Enzyme

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Enzymes [1] act as specific catalysts. That is to say each enzyme accelerates one or more specific chemical reactions without affecting the final equilibrium concentrations of reactants and products, in addition the enzyme is never used up during the reaction it catalyses, and so is always available to catalyse more of the same reaction if needed. In thermodynamic language, enzymes reduce the activation energy of a reaction but do not affect the free energy change of the overall reaction. Many enzymes are so effective that they will catalyse intracellular reactions which are too slow to be observed at all under comparable conditions in the absence of enzyme catalysis. Enzymes are often highly specific, both for the molecules they will accept as substrates and for the precise chemical changes that they will catalyse, and the presence of active enzymes is essential to form most of the molecules in the cell.

Enzyme reactions can be either anabolic or catabolic in nature [2].  

Enzymes and substrates must first interact to form an enzyme-substrate complex before any reaction can occur. This happens through molecular motions where all of the molecules in a cell are constantly moving and colliding; however only a few collisions will result in a reaction. Enzymes will remain unchanged after catalysing the reaction.
The rate of encounter between the enzyme and the substrate is primarily dependant on the concentration on the substrate; meaning that, to increase the enzyme activity you must increase the substrate concentration.

Contents

The mechanism of Enzyme Action:

Enzymes increase the rate of reaction between 2 reactants in various possible ways:

Specificity

Enzymes are specific to the point of being able to distinguish between optical isomers.

The amino acids forming the active site mainly determine the specificity of the enzyme; a change in only a few amino acids in this region can result in a large change in the shape of the active site and this could then vastly change to affinity for the substrate or even change the substrate the enzyme is specific for.

The specificity of enzymes is exhibited in the ‘Lock and Key’ mechanism:


Lock and key.jpg


Taken from http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer&part=A1031 [4]

This illustrates the Lock and Key mechanisms and how the shape of the substrate is exactly complememtary to the shape of the active site. However the lock and key model doesn't fully explain enzymatic activity. The model indicates that the enzyme and substrate are unable to change shape.

A modification to the Lock and Key Model of enzymes is the Induced Fit Hypothesis, also known as the "Hand-shake Model" [5]. This hypothesis states that the structure of both the enzyme and substrate can change on binding. In essence the enzyme can wrap itself around the substrate molecule, untill the substrate is completley bound. This produces an enzyme-substrate complex, which places strain on a particular bond, therefore weakening said bond; to a point where it can interact with the enzyme amino acid groups, further non-organic groups or further bound substrates.

The change in the shape of the enzyme is known as a conformational change; the purpose of which is two fold:

  1. As mentioned above, the conformational change places strain on the desired bond, allowing for a more efficient reaction to take place,
  2. The new conformation brings amino acid groups essential to the enzyme reaction, which in the unbound conformation may distant from the active site, into the active site. These groups ensure the catalytic reaction will be optimal [6]. The most common groups to be brought into the Active Site of the Enzyme are those relating to Acid/Base chemistry - therefore promoting the reaction and ensuring optimal conditions [7].

Substrates and the Active Site

Whether an enzymatic reaction will occur is dependant on the substrate colliding and binding to the active site. Once a substrate binds onto the active site, it is held there by a variety of interactions. These interactions take place between charged residual groups of the amino acids in the conformed active site. Hydrogen Bonds and Ionic bonds generally occur - however they are very weak. These weak interactions are of the order of 3 - 12 kcal mol-1 (12.5 - 50.2 kJ mol-1[8] this is of the order of 1/10th the strength of an, on average, single covalent bond [9].

This ensures that enzyme-substrate formation is a reversible process.

Allostery

An allosteric enzyme couples the effector levels to enzyme activity; it couples signal to functionality. Allosteric enzymes have multiple binding sites (allosteric sites) and show cooperative binding [10].

Allosteric control of enzymes can be positive or negative and can have effects such as up regulate or down regulate activity.

Types of Allosteric control:

  1. Homotropic - The modulator is a substrate for the target enzyme aswell as the egulator e.g. Oxygen acting on Haemoglobin.
  2. Heterotropic - The modulator is the regulatory molecule but is not also the enzymes substrate.

Enzyme Types

There are many enzymes used in labs, each has it's own unique active site and so will catalyse a specific reaction. Restriction enzymes are one type of enzymes that are frequently used.

Restriction endonucleases are used naturally in a wide range of prokaryotes as a self-defence mechanism against foreign DNA molecules.  The prokaryotes own DNA is methylated so it will not be cut by the enzyme.They recognise a specific 4-8 base pair palindromic sequence and by carrying out a hydrolysis reaction cut at that specific point. They may cut to form a blunt end or a sticky end. A blunt end is when the enzyme cut the DNA symmetrically. Asymmetrical cleavage leaves sticky end, these are unpaired bases. These sticky end can anneal to complementary bases on another strand [11].

Kinetics

Kinetic parameters:

Two important enzyme parameters in a simple enzyme catalysed reaction are the Michaelis-Menten constant (Km) and the maximum reaction velocity (Vmax)

The michaelis-menten equation:


V = Vmax [S]/Km [S]


To obtain Vmax and Km the enzyme activity must be recorded and then plotted on a double reciprocal plot, a Lineweaver-Burk plot, and the Michaelis Menten equation is then rearranged to look like this: 1/V = (Km/Vmax)(1/S)+1/Vmax [12].

350px-Lineweaver-Burke plot svg.png

Taken from www.search.com/reference/Lineweaver-Burk_plot [13]
A Lineweaver-Burk plot showing all the necessary parameters.

Inhibition

Enzymes can be inhibited by denaturing which is when a protein is changed in structure to form a randomly coiled peptide which exhibits none of its usual functions. Denaturing can result from extreme temperatures and pHs, as these alter the bonding in the molecule.

Inhibition can also be initiated by the binding of specific molecules called inhibitors. These can be split into categories:

  1. Irreversible Inhibitors are molecules that permanently bind to the enzyme's active site or specific side chain, commonly to the serine (CH2OH) or cysteine (CH2SH) by covalent bonds. Thsi inactivates the enzyme so the substrate cannt bind.
  2. Competitive Inhibitors are competing molecules that will have a very similar structure to that of the natural substrate and thus will be complementary to the enzyme active site. Vmax stays the same, but Km increases This type of inhibition can be overcome by an increase in substrate concentration.
  3. Non-competitive inhibitors bind to a region on the enzyme other than the active site, causing changes to enzyme shape resulting in disruption of the active site. This decreases the turnover number of the enzyme rather than preventing substrate binding- Vmax decreases but Km stays the same. This cannot be overcome with an increase in substrate concentration.
  4. Uncompetitive inhibitors only bind to an enzyme-substrate complex; so both Km and Vmax decreaae as it takes longer for the substrate to leave the active site. This also cannot be overcome by an increase in substrate concentration.
    We are able to distinguish the types of inhibition occurring by looking at the graph of enzyme activity [14].

Inhibitor graph.jpg
Taken from http://ibhow.files.wordpress.com/2010/06/7-6-4.jpg?w=399&h=275 [15]

Competative Inhibitors show the same Vmax value however we see an increased Km value and non-competitive inhibitors show a decreased Vmax but the same Km.

Targets for drug action

We are able to exploit these mechanisms of inhibition to engineer drugs with therapeutic effects.
By targeting an enzyme in drug therapy we have the ability to change whole metabolic reactions that are catalysed by that particular enzyme. We can investigate possible new drugs by exploring drug-reaction interactions and drug-pathway interactions [16]
Some examples of Drug Inhibitors:

References

  1. Molecular Biology of the Cell 5th ed (2007) Alberts et.al. 159-169
  2. Nigel P. O. Green (1989). Biological Science. 2nd ed. Cambridge: Cambridge University Press. p.167.
  3. Molecular Biology of the Cell 5th ed (2007) Alberts et.al. 159-169
  4. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer
  5. http://www.portlandpress.com/pp/books/online/glick/searchresdet.cfm?Term=induced-fit%20theory%20%28rack%20model%29
  6. The World of the Cell, 3rd Edition, (1996) Becker et.al. p146, p147
  7. The World of the Cell, 3rd Edition, (1996) Becker et.al. p146
  8. Royal Society of Chemistry [RSC]fckLRfckLRhttp://www.rsc.org/ebooks/archive/free/SP9780851869209/SP9780851869209-FP015.pdf
  9. The World of the Cell, 3rd Edition, (1996) Becker et.al. p146
  10. J.Mol.Biol. (2004) 336, 263-273
  11. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman
  12. Molecular Biology of the Cell 5th ed (2007) Alberts et.al. 159-169
  13. http://www.search.com/reference/Lineweaver-Burk_plot
  14. Biochemistry 6th (2006) Stryer et.al. pg51
  15. http://ibhow.files.wordpress.com/2010/06/7-6-4.jpg?w=399&h=275
  16. BMC Bioinformatics 2010, 11:501
  17. Biochemistry 6th (2006) Stryer et al.
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