4.1 Genomes, Chromosomes and Homologues

The genome is the whole genetic information of an organism. Nearly every nucleated cell in a multicellular organism contains a complete genome even though differentiated cells express different gene subsets. Genomics examines sequence, gene location, coding and regulatory regions, and non-coding DNA. Comparative genomics aligns sequences between organisms to infer ancestry, find conserved functional regions and propose functions for unfamiliar sequences.

Genome size is the number of base pairs in one complete set. It is not proportional to complexity or gene number: some plants and lungfish have much more DNA than humans because genome size includes repeats and other non-coding sequences. Chromosome number is species-characteristic but is also not a complexity scale.

A typical prokaryote has one main circular DNA molecule concentrated in a nucleoid, not enclosed by a nuclear membrane. Many have smaller independently replicating plasmids that may carry useful genes such as antibiotic-resistance determinants. In the IB comparison, prokaryotic DNA is described as not associated with histones; eukaryotic nuclear DNA is linear, divided among chromosome types, associated with histones and normally enclosed in a double-membrane nucleus.

During interphase, each eukaryotic chromosome is long, thin chromatin. Before division, replicated chromatin condenses. A replicated chromosome contains two genetically identical sister chromatids joined at a centromere. Homologous chromosomes are different: one came from each parent, and the pair carries the same genes at corresponding loci but may carry different alleles.

A diploid nucleus contains two homologues of each chromosome type; a haploid nucleus contains one. Human somatic nuclei normally contain 46 chromosomes in 23 pairs, whereas gametes contain 23. Replication doubles DNA quantity but does not change ploidy: a replicated diploid cell remains diploid because it still has two homologous sets.

Homologues separate in meiosis I and sister chromatids separate later. Each gamete receives one chromosome from every pair and one allele at each locus. Fertilization combines two haploid sets to restore diploidy. Confusing chromosome, chromatid and homologue makes inheritance diagrams impossible to interpret reliably.

Plasmids illustrate why a genome must be defined carefully. The main bacterial chromosome contains genes needed for ordinary survival and reproduction, while plasmids often carry accessory functions that matter in particular environments. Horizontal transfer can move a plasmid between cells, spreading an allele without parent-to-offspring reproduction. That process is genetically important but is distinct from the Mendelian inheritance modeled later in this chapter.