protein for proteins

[ramanan]

is peptide bond formation a spontaneous process or enzyme requiring one.

virtually in translation it is spontaneous one. but, is there a case where the enzymes can be employed for peptide bond formation?can anybody give the name of the enzyme?

[Xavier]

This is a far more insightful question than it first appeared to me. At first I thought, its enzyme mediated, of course; for example... ..hmmmm!

But peptides are generally made in ganglia within cells and, whilst the formation is enzyme mediated, it is the translated DNA code that specifies the peptide sequence.

Indeed an enzyme that non-specifically joined peptide strands together would be a liability anywhere in a body as proteins are so ubiquitous and so essential.

 

In order to make a sufficiently specific enzyme, the nature of at least the last half dozen amino acids of each peptide being brought together would have to be examined by the enzyme, making it a complex beast (equivalent to an antibody, which uses a massively redundent system of trial and error to match up with its targets)

 

I'm sure that somewhere out there such an enzyme exists, though. I can't think of an example. Am I missing something obvious?

[muad'dib]

A peptide bond is a covalent bond between two amino acids as a result of a dehydration reaction.

 

When the carboxyl group of an amino acid is adjacent to the carboxyl group of another an enzyme can catalyze a dehydration reaction (loss of a water molecule) and join the two amino acids together. This happens in ribosomes during translation. A ribosome is made up of two subunits consisting of ribosomal RNA (rRNA) and proteins. Since enzymes are proteins I guess it could be said that in this case the ribosome is the enzyme, but it does take an enzyme for the bond to be made.

 

I'm sure under certain conditions (like high temperatures) the dehydration reaction joining the two amino acids will occur without the enzyme, but it wouldn't be spontaneous.

 

The joining of two amino acids is an endergonic reaction meaning that energy is absorbed or taken out of the surroundings. This type of reaction is nonspontaneous. That is why without an enzyme it would take something like heat to form peptide bond.

[ramanan]

i understand that inside the body the conditions are well suited so that things just get being done. but why i asked this qstn is for in vitro practices. for example if we figr out the enzyme that makes peptide bond formation it could really worth a lot for protien engineering.when watson and his colleagues were figuring out the process of translation their first thought was the enzyme mediated reaction. now we can able to picturise everything. we know it happens in the ribosomes.the research now also proves like there need tobe no enzymes to catalyse the reaction. rna too can do that(ribozymes).until we have more answers we should not jump in to conclusion.if i come across any such i will inform.xpectin the same from u guys

[Radical Edward]

peptide bonds can form spontaneously. The main purpose of enzymes is to lower the energy at which a particular reaction can occur (look up Gibbs Free Energy) and hence make it more likely to happen.

[Skye]

By the way, in vitro synthesis of peptides has been around for quite some time using fairly simple organic synthesis techniques (Merrifield solid-phase synthesis). However, it doesn't match the rate at which bacteria or yeast will produce a protain, so it isn't used a great deal.

[muad'dib]

Peptide bond formation cannont be spontaneous becuase it is a dehydration reaction in which energy is taken out of the surroundings. Joining monomers together (in this case amino acids) to form a polymer (a polypeptide in this case) is an endergonic, or exothermic reaction; a cell expends energy to do this.

 

In order for a reaction to be spontaneous the change in Gibb's free energy is negative meaning the energy of the system decreases. That's not the case with peptide bond formation, in which the energy of the system increases; or in other words the free energy of the products is higher than the free energy of the reactants.

 

The purpose of enzymes is to lower the activation energy of a reaction (the energy that is required to start the reaction). There are some reactions that are spontaneous but would take so long to occur that there is no appreciable change after years. In cases like these enzymes make the reaction occur much faster. There are cases though where without enzymes no change whatsoever would occur because the reaction itself is nonspontaneous.

[Proton Head]

An enzyme does in no way affect the spontaneity or the balance of a chemical reaction. It just speeds the reaction up (by lowering the activation energy).

 

As noted by the previous poster an enzyme cannot make a nonspontaneous reaction (such as peptide bond formation) occur without expending energy.

 

Peptide bond formation in the cells is catalysed by the rRNA-protein complex known as ribosome. But for the bonds to be formed energy in the form of ATP has to be provided.

Right now I can't remember whether the ribosomial enzyme which actually catalyzes the bond formation is a protein or an rRNA.

 

But the important thing to remember here is that if a reaction doesn't occur spontaneously, adding an enzyme will not help one bit.

However if a reaction indeed does happen spontaneously, adding an enzyme can speed it up a great deal.

[Guest swankyman]

Hi

 

Under certain conditions a protease (protein cleaving enzyme) can be perswaded to form peptide bonds instead of hydrolyse them. A classic example is to take pepsin or trypsin and use it in the presence of acetonitrile ( a hydrophobic solvent). Cant remember whether this requires high amino acid concentration to drive the reaction (Sorry)

 

there are also enzymes that are not part of the translation macherinery that generate peptide bonds such as those involved in the formation of macrocycle molecules in bacteria (i think macrocycles are mostly antibiotics)

 

 

rich