In this article we present work on chromosome structures for genetic algorithms (GAs) based on biological principles. Mainly, the influence of noncoding segments on GA behavior and performance is investigated. We compare representations with noncoding sequences at predefined, fixed locations with “junk” code induced by the use of promoter/terminator sequences (ptGAs) that define start and end of a coding sequence, respectively. AS one of the advantages of noncoding segments a few researchers have identified the reduction of the disruptive effects of crossover, and we solidify this argument by a formal analysis of crossover disruption probabilities for noncoding segments at fixed locations. The additional use of promoter/terminator sequences not only enables evolution of parameter values, but also allows for adaptation of number, size, and location of genes (problem parameters) on an artificial chromosome. Randomly generated chromosomes of fixed length carry different numbers of promoter/terminator sequences resulting in genes of varying size and location. Evolution of these ptGA chromosomes drives the number of parameters and their values to (sub)optimal solutions. Moreover, the formation of tightly linked building blocks is enhanced by self-organization of gene locations. We also introduce a new, nondisruptive crossover operator emerging from the ptGA gene structure with adaptive crossover rate, location, and number of crossover sites. For experimental comparisons of this genetic operator to conventional crossover in GAs, as well as properties of different ptGA chromosome structures, an artificial problem from the literature is utilized. Finally, the potential of ptGA is demonstrated on an NP-complete combinatorial optimization problem.