Final answer:
To determine if an organism is prokaryotic or eukaryotic, scientists would look for the presence of a membrane-bound nucleus and organelles through microscopic examination and molecular tests like ribosomal RNA sequencing. This helps classify the organism within the three-domain system consisting of Bacteria, Archaea, and Eukarya.
Step-by-step explanation:
To determine if an unusual organism found deep in the crust of the Earth is prokaryotic or eukaryotic, scientists would typically conduct a microscopic examination to look for cell features such as a membrane-bound nucleus and other organelles. Eukaryotic cells characteristically have these structures, while prokaryotic cells do not.
In addition to microscopic analysis, molecular tests such as sequencing ribosomal RNA (rRNA) genes can provide conclusive evidence.
This is because the phylogenetic tree of life, which includes the domains Bacteria, Archaea, and Eukarya, is based on differences in the structure of cell membranes and in rRNA. Ribosomal RNA sequencing helped differentiate these groups significantly due to the work of Carl Woese and researchers who proposed the three-domain system.
If the organism in question has a simpler structure, lacks a membrane-bound nucleus, and potentially resides in extreme environments similar to extremophiles in the domains of Bacteria and Archaea, it is likely prokaryotic.
Conversely, if it has a more complex cell structure with a defined nucleus and organelles, it would be classified as eukaryotic and be part of the Eukarya domain.