Which proteins are enzymes

The next diagram shows an imaginary active site:. Remember that these "R" groups contain the sort of features which are responsible for the tertiary structure in proteins.

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 ones with the "H"s in them are groups capable of hydrogen bonding. It is possible that one or more of the unused "R" groups in the active site could also be helping with van der Waals attractions between them and the substrate. 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. Robert Penchovsky of Sofia University in Bulgaria is using a similar approach to design ribozymes that detect and respond to the presence of specific small molecules.

An aptamer is a short nucleic acid sequence or a small protein that binds to a given molecular target. Most aptamers are synthetic, and allosteric ribozymes — ones that are active only with a ligand bound outside the catalytic domain — can be designed by fusing an RNA aptamer containing the binding site with, for example, a catalytic hammerhead ribozyme. Hammerhead ribozymes are fairly small, tractable molecules that can be synthesised relatively easily.

There are other biologically important ribozymes, however, that are right at the other end of the macromolecular spectrum. They had established that the ribosome is a ribozyme. It is interesting that this, too, can be compared to a Boolean logic gate, in this case a NAND gate with G represented by 1 and A by 0.

It is not even possible to imagine scientists creating a ribozyme that is structurally and functionally as complex as the ribosome any time soon. But researchers are already tinkering with natural ribosomes to subtly alter their properties. Initially, this was limited by their inability to control which out of a pool of large and small ribosomal subunits available would form active complexes.

The ribosome is not the only large molecular machine that has been shown to be a ribozyme. 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.

Andy Extance discovers why the compound best known as a fertiliser is a surprising candidate to power enormous container ships. The Royal Society of Chemistry aims to use Cop26 as a springboard to a more sustainable future. Aa Aa Aa. Protein Function. How Diverse Are Proteins? Actin filaments red and microtubules green are two different kinds of proteins that provide structure to cells. Courtesy of Dr. Takeshi Matsuzawa and Dr. Akio Abe. Figure 3: Enzymes and activation energy. Enzymes lower the activation energy necessary to transform a reactant into a product.

Figure 4: Examples of the action of transmembrane proteins. Transporters carry a molecule such as glucose from one side of the plasma membrane to the other. Figure 5: The fluid-mosaic model of the cell membrane. Like a mosaic, the cell membrane is a complex structure made up of many different parts, such as proteins, phospholipids, and cholesterol. Proteins serve a variety of functions within cells.

Some are involved in structural support and movement, others in enzymatic activity, and still others in interaction with the outside world. Indeed, the functions of individual proteins are as varied as their unique amino acid sequences and complex three-dimensional physical structures. Cell Biology for Seminars, Unit 2. Topic rooms within Cell Biology Close. No topic rooms are there. Or Browse Visually. Student Voices. Creature Cast. Simply Science. Green Screen.

Green Science. Bio 2. The Success Code. Why Science Matters. The Beyond. Plant ChemCast. Postcards from the Universe. Brain Metrics. Mind Read.