Metabolic pathways, such as the conversion of glucose into energy (ATP) through glycolysis, often involve a large number of enzymes and intermediate stages. It is difficult to imagine how such complex systems could have readily evolved. For biosynthetic pathways that produce basic building blocks of life, i.e. sugars, amino acids, nucleotides, etc., it is likely that these molecules were naturally found in the primordial soup and organisms would just harvest them from the environment. As things became more competitive and resources became scarce, those organisms that could produce some of their own building blocks from other components in the soup had an advantage. Thus, any newly evolved enzymes would confer great selective advantages. Then, as the the other contents would become scarce, then the organism that uses another compound to generate that compound would have the advantage. That is to say, take the following hypothetical sequence of events:

the organism is surrounded by an abundance of A, and uses it directly

	    A  A A   AAA  A A
	A AA A	=)AA
		A  A    A

as time passes, A becomes scarce in soup because organisms continue to consume it...

		=(  A

then, a certain lucky organism learns to harvest B through some enzyme that makes A. 

		B + enzyme 1 -> A

		B  B BB  B B
	BBBB	=)    B  BBB A

soon, the same thing happens as with A, where levels of B begin to be depleted.
		B  =(  

so now some organism finds a way to make B from C, giving it a metabolic pathway:

		C + enzyme 2 -> B 
		B + enzyme 1 -> A 

	C  C C C  =) C C CCC
	   C C  CC  CC  C  C CC

and so forth.

In 1945, N.H. Horowitz suggested that a system of this type could have evolved through gene duplication events. The protein that interacts with A gets duplicated, then the new enzyme could retain binding to A, but also evolve to interact with B. Another gene duplication event would allow a protein that binds to B, but also can interact with C. Thus, the enzymes for a pathway evolve in reverse to the order in which they act.

There is usually very little sequence homology between enzymes in the same pathway, although proteins in the same pathway often have similar fold, because structure is more conserved.

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