Reaction joining

The first reaction, the addition of formaldehyde to the amino compound, is catalyzed by either acids or bases. Hence, it takes place over the entire pH range. The second reaction joins the amino units with methylene links and is catalyzed only by acids. The rates of these reactions have been studied over a broad range of pH (28). The results are presented in Figure 1. 

There are many potential molecules and possible routes to the synthesis of biomolecules that might form the basis of a primitive metabolism but thus far we have not addressed the question of information propagation or Darwinian evolution. Information storage must be contained within a sequence, such as words in a sentence or the base sequences within the genetic code, and that requires a polymerisation reaction, which is preferably autocatalytic to reproduce the information accurately. Peptides and nucleotides have this property, although the condensation reaction joining them together needs to be activated. 

A condensation reaction joins two molecules and splits out a small molecule. The small molecule is usually water. The formation of a peptide bond is an example of a condensation reaction. The conditions necessary for a condensation reaction vary with the functional groups involved. In most cases, a catalyst will be present. The two most common catalysts are acids and enzymes. Two alcohols will condense to form an ether. A carboxylic acid condenses with an alcohol to form an ester. A carboxylic acid condenses with an amine to form an amide. 

Conversely, ester condensation reactions join acyl groups from CoA derivatives to Schiff bases derived from glycine or serine. Succinyl-CoA is the acyl donor... 

A second kind of polymerization process occurs when molecules with two functional groups react. We ve seen, for example, that a carboxylic acid reacts with an amine to yield an amide (Section 23.14). If a molecule with two carboxylic acid groups reacts with a molecule having two amino groups, an initial reaction joins the two molecules together, and further reactions then link more and more... 

Law Five (ab)c = a(bc) (associative law of multiplication). The two rules are adopted to eliminate ambiguous cases. Rule 1 complex elements must be broken down into their fundamental counterparts and then reacted and rule 2 a reaction in a series of reactions joins the new polymer to the next element on the right. Thus we have Equations 28, 29, 30, 31, and 32. Finally, in conformity with Law Five, we have Equations 33 and 34. The chemical structures associated with Equations 28, 29, and 30 are shown in Figure 2. 

Two different approaches are commonly used for the synthesis of alkynes. In the first, an appropriate electrophile undergoes nucleophilic attack by an acetylide ion. The electrophile may be an unhindered primary alkyl halide (undergoes Sn2), or it may be a carbonyl compound (undergoes addition to give an alcohol). Either reaction joins two fragments and gives a product with a lengthened carbon skeleton. This approach is used in many laboratory syntheses of alkynes. 

The main difference is that no discrete enol or enolate is actually formed. Instead CO2 is lost from the malonate as the acylation occurs. This is an improvement from Nature s point of view—it is much easier to lose a proton from a carboxylic acid than from a CH2 group. This reaction joins two C2 units together and the whole process can be repeated as many times as necessary. 

Amino acids can be polymerized to form chains through condensation reactions, joining together by so-called peptide bonds, and they are often referred to as the building blocks of peptides and proteins. 

Terpenes are formed by coupling double-bond isomers of the same momoner, isopentenyl pyrophosphate (IPP), with loss of a pyrophosphate ion (15, 16). Three such coupling reactions join four IPPs, each with hve carbon atoms, to make geranylgeranyl-pyrophosphate, the C2o-precursor of diterpenes such as taxol (Fig. 3). Linear terpene precursors, which differ only in the number of IPP units joined, can be assembled by a few polyprenyl synthase enzymes, as the monomers are identical and the only variable is how many monomers to link together. In subsequent steps, these linear polyenes undergo cation-induced cyclizations to create the starting frameworks for terpenes and their derivatives. 

The next step then would be nucleophilic reaction of the carbanion with the electrophilic carbon of the thiocarbonyl group. This reaction joins carbons 1 and 3, as was predicted from the numbering scheme. 

Cleavage and isomerization. Fructose 1,6-bisphosphate is cleaved in step 4 into two, three-carbon monophosphates, one an aldose and one a ketose. The bond between carbons 3 and 4 of fructose 1,6-bisphosphate breaks, and a C-0 group is formed. Mechanistically, the cleavage is the reverse of an aldol reaction (Section 23.2) and is carried out by an aldolase enzyme. (A forward aldoI reaction joins two aldehydes or ketones to give a /1-hydroxy carbonyl compound a retro aldol reaction cleaves a -hydroxy carbonyl compound into two aldehydes or ketones.)... 

Somewhat arbitrarily we may divide all reactions into the two categories of building reactions and facilitating reactions. A building reaction joins two hitherto unattached carbon atoms or completes a heterocyclic ring not used as a protection for some functionality or introduces-functionality at a previously unfunctionalized site. All other reactions are facilitating reactions. 

Economy of reactions Joining monomers to make macromolecules is economical if the monomers can be joined by the same chemistry. If the monomers contained different functional groups, synthesis of each polymer would require a different kind of catalyst for each monomer added to the chain. Clearly, it is more economical to use a generic catalyst to put together each of the many monomers required for synthesis. 

This new complex has the same reactivity as the catalyst we started with, so it will quickly find another alkene to undergo [2 + 2] cycloaddition with. There is now one in the same molecule, so a fast intramolecular reaction joins up the five-membered ring and produces a second metallacyclobutane. As before, there are two alternative ways for this metallacyclobutane to break down, and the productive one gives a third carbene complex and the cyclic product. 

FIGURE 25.16 Step-by-step growth of a polypeptide chain with mRNA acting as a template. Transfer RNAs carry amino acid residues to the site of mRNA that is in contact with a ribosome. Codon-anticodon pairing occurs between mRNA and RNA at the ribosomal surface. An enzymatic reaction joins the amino acid residues through an amide linkage. After the first amide bond is formed, the ribosome moves to the next codon on mRNA. A new tRNA arrives, pairs, and transfers its amino acid residue to the growing peptide chain, and so on. 

The In-Fusion assembly reaction joins any two pieces of DNA that have an overlap of 15 bp at their ends by using unique properties of the 3 -5 exonuclease activity of poxvirus DNA polymerase (6), whereas the isothermal assembly reaction is a single-reaction method for assembling multiple DNA molecules that have a greater overlap of -20-200 bp at their ends and is performed by the concerted action of a 5 exonuclease (T5 exonuclease), a DNA polymerase (Phusion polymerase), and a DNA ligase (Taq DNAligase)... 

Coupling reactions join two carbon-containing groups together. 

---