If the arrangement of the groups on the active site or the substrate was even slightly different, the bonding almost certainly wouldn't be as good - and in that sense, a different substrate wouldn't fit the active site on the enzyme. This process of the catalyst reacting with the substrate and eventually forming products is often summarised as:.
The formation of the complex is reversible - the substrate could obviously just break away again before it converted into products. The second stage is shown as one-way, but might be reversible in some cases. It would depend on the energetics of the reaction.
So why does attaching itself to an enzyme increase the rate at which the substrate converts into products? It isn't at all obvious why that should be - and most sources providing information at this introductory level just gloss over it or talk about it in vague general terms which is what I am going to be forced to do, because I can't find a simple example to talk about!
Catalysts in general and enzymes are no exception work by providing the reaction with a route with a lower activation energy. Attaching the substrate to the active site must allow electron movements which end up in bonds breaking much more easily than if the enzyme wasn't there. Strangely, it is much easier to see what might be happening in other cases where the situation is a bit more complicated. What we have said so far is a major over-simplification for most enzymes. Most enzymes aren't in fact just pure protein molecules.
Other non-protein bits and pieces are needed to make them work. These are known as cofactors. In the absence of the right cofactor, the enzyme doesn't work. For those of you who like collecting obscure words, the inactive protein molecule is known as an apoenzyme.
When the cofactor is in place so that it becomes an active enzyme, it is called a holoenzyme. There are two basically different sorts of cofactors. Some are bound tightly to the protein molecule so that they become a part of the enzyme - these are called prosthetic groups.
Some are entirely free of the enzyme and attach themselves to the active site alongside the substrate - these are called coenzymes. Prosthetic groups can be as simple as a single metal ion bound into the enzyme's structure, or may be a more complicated organic molecule which might also contain a metal ion.
The enzymes carbonic anhydrase and catalase are simple examples of the two types. The ideal gas law is easy to remember and apply in solving problems, as long as you get the proper values a. Carbonic anhydrase is an enzyme which catalyses the conversion of carbon dioxide into hydrogencarbonate ions or the reverse in the cell.
If you look this up elsewhere, you will find that biochemists tend to persist in calling hydrogencarbonate by its old name, bicarbonate! In fact, there are a whole family of carbonic anhydrases all based around different proteins, but all of them have a zinc ion bound up in the active site.
In this case, the mechanism is well understood and simple. We'll look at this in some detail, because it is a good illustration of how enzymes work.
The zinc ion is bound to the protein chain via three links to separate histidine residues in the chain - shown in pink in the picture of one version of carbonic anhydrase. The zinc is also attached to an -OH group - shown in the picture using red for the oxygen and white for the hydrogen. If you look at the model of the arrangement around the zinc ion in the picture above, you should at least be able to pick out the ring part of the three molecules.
The zinc ion is bound to these histidine rings via dative covalent co-ordinate covalent bonds from lone pairs on the nitrogen atoms.
Simplifying the structure around the zinc:. The arrangement of the four groups around the zinc is approximately tetrahedral. Notice that I have distorted the usual roughly tetrahedral arrangement of electron pairs around the oxygen - that's just to keep the diagram as clear as possible. So that's the structure around the zinc.
How does this catalyse the reaction between carbon dioxide and water? A carbon dioxide molecule is held by a nearby part of the active site so that one of the lone pairs on the oxygen is pointing straight at the carbon atom in the middle of the carbon dioxide molecule. Attaching it to the enzyme also increases the existing polarity of the carbon-oxygen bonds. If you have done any work on organic reaction mechanisms at all, then it is pretty obvious what is going to happen.
The lone pair forms a bond with the carbon atom and part of one of the carbon-oxygen bonds breaks and leaves the oxygen atom with a negative charge on it.
The next diagram shows this broken away and replaced with a water molecule from the cell solution. All that now needs to happen to get the catalyst back to where it started is for the water to lose a hydrogen ion. Our cells use these twenty amino acids to produce many different proteins. These can be grouped into a number of different types depending on their function. A few of these are outlined in the following table:. You can explore the world of proteins in 3-D in this clip and there are lots of cool free apps which will let you play with protein molecules such as Atomdroid on Android or Molecules for iOS.
Life consists of a series of complex chemical reactions. Later in this unit you will learn more about two such complex chemical reactions: respiration and photosynthesis. In order for most of the chemical reactions which take place in living things to occur they need a catalyst. Catalysts are molecules which affect the rate of a chemical reaction, normally by speeding them up , without being changed in the process.
Enzymes are the catalysts of life and are made of proteins. That's why this group of proteins has been chosen to explore in more depth in this topic.
DNA controls all of the chemical reactions which take place in a cell through which enzymes are produced and when. You're probably getting sick of hearing this by now, but the shape of enzymes like all proteins is crucial to their function. A key component of the shape of an enzyme is its active site.
Most enzymes can only catalyse a very small number of reactions, quite often just one, because the shape of the active site of an enzyme is complimentary to the specific substrate s it binds to in the reaction. Take the enzyme amylase for example. This is found in your saliva and catalyses the breakdown of the complex carbohydrate starch into much smaller maltose sugar molecules [try keeping a plain flavoured crisp in your mouth for a few minutes without swallowing and you might just be able to taste this sugar being produced by your salivary amylase].
The shape of the active site of an amylase enzyme molecule is specific to the shape of its substrate starch. Therefore, amylase can only catalyse this reaction.
This is why cells must produce many different enzyme molecules, from the DNA code, for all the different chemical reactions which are catalysed in cells. Notice by the way in the diagram that enzyme molecule remains unchanged as a result of the reaction - remember this is a key feature of a catalyst along with speeding up the reaction. As enzymes are chemical molecules they can be affected by the conditions that they're in. Remember the importance of shape to the function of proteins?
Well, if the conditions change it can change the shape of the enzyme. If the active site of the enzyme changes as a result of the change of conditions, then the enzyme will not be able to bind to its substrate which will prevent the enzyme from catalysing the reaction.
It is for this reason tha each enzyme has its own optimum conditions. The genes of most eukaryotes contain non-coding segments called introns that must be removed from the transcribed messenger RNA before that can reach a ribosome. This process, in which the RNA is cleaved at the start and end of each intron and then the protein-coding exon sequences are re-joined, is termed splicing and the protein—RNA complex that catalyses this reaction is the spliceosome.
It consists of five small RNA molecules, protein complexes and magnesium ions and again, the catalytic unit is formed from RNA and stabilised by the proteins and ions. The structure of the RNA component of the spliceosome is very similar to that of a much smaller ribozyme, the self-splicing group II intron that is found in the genomes of all organisms.
Tinkering with the structure and function of large and small ribozymes has already generated many new insights into molecular biology and molecular structures with novel chemistry and functions. They are certain to play an increasingly important part in the emerging discipline of synthetic biology. Viscous muddy pond edges may have been incubators for the rise of self-replicating RNAs on ancient Earth.
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Site powered by Webvision Cloud. Skip to main content Skip to navigation. Clare Sansom reports. Topics Biotechnology enzymes Life Structural biology. Related articles. Research Protein synthesis revolution on way as large peptides made in hours not days TZ Flow chemistry can now make peptide chains up to amino acids long in one go.
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