This page is an introduction to how proteins can work as enzymes - biological catalysts. You should realise that this is written to cover the needs of a number of UK-based chemistry syllabuses for 16 - 18 year olds. If you want detailed knowledge about enzymes for a biology or biochemistry course, you are probably in the wrong place! This is just an introduction.
|Enzymes as catalystsEnzymes are mainly globular proteins - protein molecules where the tertiary structure has given the molecule a generally rounded, ball shape (although perhaps a very squashed ball in some cases). The other type of proteins (fibrous proteins) have long thin structures and are found in tissues like muscle and hair. We aren't interested in those in this topic.|
These globular proteins can be amazingly active catalysts. You are probably familiar with the use of catalysts like manganese(IV) oxide in decomposing hydrogen peroxide to give oxygen and water. The enzyme catalase will also do this - but at a spectacular rate compared with inorganic catalysts.
One molecule of catalase can decompose almost a hundred thousand molecules of hydrogen peroxide every second. That's very impressive!
This is a model of catalase, showing the globular structure - a bit like a tangled mass of string:
|An important point about enzymes is that they are very specific about what they can catalyse. Even small changes in the reactant molecule can stop the enzyme from catalysing its reaction. The reason for this lies in the active site present in the enzyme . . .|
Active sites are cracks or hollows on the surface of the enzyme caused by the way the protein folds itself up into its tertiary structure. Molecules of just the right shape, and with just the right arrangement of attractive groups (see later) can fit into these active sites. Other molecules won't fit or won't have the right groups to bind to the surface of the active site.
The usual analogy for this is a key fitting into a lock. For the key to work properly it has to fit exactly into the lock.
You mustn't take this picture of the way a substrate fits into its enzyme too literally. What is just as important as the physical shape of the substrate are the bonds which it can form with the enzyme.
Enzymes are protein molecules - long chains of amino acid residues. Remember that sticking out all along those chains are the side groups of the amino acids - the "R" groups that we talked about on the page about protein structure.
Active sites, of course, have these "R" groups lining them as well - typically from about 3 to 12 in an active site. The next diagram shows an imaginary active site:
Groups like these help a substrate to attach to the active site - but only if the substrate molecule has an arrangement of groups in the right places to interact with those on the enzyme.
The diagram shows a possible set of interactions involving two ionic bonds and a hydrogen bond.
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 aholoenzyme.
|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 enzymescarbonic anhydrase and catalase are simple examples of the two types.
Zinc ions in carbonic anhydrase
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!)
|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.|
|The structure of the amino acid histidine is . . .|
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 . . .
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.
The next diagram shows this broken away and replaced with a water molecule from the cell solution.
. . . and the carbonic anhydrase enzyme can do this sequence of reactions about a million times a second. This is a wonderful piece of molecular machinery!
Let me repeat yet again: If you are doing a UK-based chemistry exam for 16 - 18 year olds, you are unlikely to need details of this reaction. I've talked it through in some detail to show that although enzymes are complicated molecules, all they do is some basic chemistry. It is just that this particular example is a lot easier to understand than most!
The haem (US: heme) group in catalase
Remember the model of catalase from further up the page . . .
The haem groups contain an iron(III) ion bound into a ring molecule - one of a number of related molecules called porphyrins. The iron is locked into the centre of the porphyrin molecule via dative covalent bonds from four nitrogen atoms in the ring structure.
There are various types of porphyrin, so there are various different haem groups. The one we are interested in is called haem B, and a model of the haem B group (with the iron(III) ion in grey at the centre) looks like this:
|The reaction that catalase carries out is the decomposition of hydrogen peroxide into water and oxygen.|
Essentially the reaction happens in two stages and involves the iron changing its oxidation state. An easy change of oxidation state is one of the main characteristics of transition metals. In the lab, iron commonly has two oxidation states (as well as zero in the metal itself), +2 and +3, and changes readily from one to the other.
In catalase, the change is from +3 to the far less common +4 and back again.
In the first stage there is a reaction between a hydrogen peroxide molecule and the active site to give:
The new arrangement around the iron then reacts with a second hydrogen peroxide to regenerate the original structure and produce oxygen and a second molecule of water.
And if you think about what has to happen to the hydrogen peroxide molecule in both reactions, it has to be more complicated than this suggests. Hydrogen peroxide is joined up as H-O-O-H, and yet both hydrogens end up attached to the same oxygen. That is quite a complicated thing to arrange in small steps in a mechanism, and involves hydrogen ions being transferred via amino acids residues in the active site.
So do you need to remember all this for chemistry purposes at this level? No - not unless your syllabus specifically asks you for it. It is basically just an illustration of the term "prosthetic group".
It also shows that even in a biochemical situation, transition metals behave in the same sort of way as they do in inorganic chemistry - they form complexes, and they change their oxidation state.
And if you want to follow this up to look in detail at what is happening, you will find the same sort of interactions around the active site that we looked at in the simpler case of carbonic anydrase. (But please don't waste time on this unless you have to - it is seriously complicated!)
Coenzymes are another form of cofactor. They are different from prosthetic groups in that they aren't permanently attached to the protein molecule. Instead, coenzymes attach themselves to the active site alongside the substrate, and the reaction involves both of them. Once they have reacted, they both leave the active site - both changed in some way.
A simple diagram showing a substrate and coenzyme together in the active site might look like this:
NAD+ as coenzyme with alcohol dehydrogenase
Alcohol dehydrogenase is an enzyme which starts the process by which alcohol (ethanol) in the blood is oxidised to harmless products. The name "dehydrogenase" suggests that it is oxidising the ethanol by removing hydrogens from it.
The reaction is actually between ethanol and the coenzyme NAD+ attached side-by-side to the active site of the protein molecule. NAD+ is a commonly used coenzyme in all sorts of redox reactions in the cell.
NAD+ stands for nicotinamide adenine dinucleotide. The plus sign which is a part of its name is because it carries a positive charge on a nitrogen atom in the structure.
The "nicotinamide" part of the structure comes from the vitamin variously called vitamin B3, niacin or nicotinic acid. Several important coenzymes are derived from vitamins.
Friday, November 9, 2012
PROTEINS AS ENZYMES
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