Homologous chromosomes have the same ______, but have different ______.

Homologous chromosomes are pairs of chromosomes, one inherited from each parent, that share the same genes at the same loci. However, they may carry different versions of these genes, known as alleles. For example, one homologous chromosome may carry an allele for blue eyes, while its homologous counterpart may carry an allele for brown eyes. This distinction is crucial for genetic variation within a population.

The other options do not accurately describe the relationship of homologous chromosomes. Proteins and RNA relate more to expression levels and functions rather than directly to the structural similarities and differences between homologous chromosomes. Similarly, the terms chromosomes and traits do not align conceptually with the nature of homologous pairs. Nucleotides and bases refer to the building blocks of DNA but do not capture the functional aspect of gene expression and allele variation. Thus, the focus on genes and alleles in the correct answer captures the essence of genetic diversity and inheritance.