Genes and Chromosomes

Objective: Define gene and allele without assuming every gene encodes a protein.

A gene is a DNA region whose sequence contributes to a functional product, often an RNA and sometimes a protein through an RNA intermediate. Genes include or interact with regulatory sequences that affect where and when products are made; boundaries can vary with transcript structure and context. A locus is a position on a chromosome, and alleles are sequence variants at a locus. In a diploid organism, homologs may carry different alleles. Genotype describes genetic variants, while phenotype is an observable feature influenced by genotype, environment, and development. One gene can affect more than one feature, and many traits involve multiple genes.

Objective: Relate DNA packaging to access and distinguish chromosome scales.

Eukaryotic nuclear DNA is associated with proteins, including histones, to form chromatin. Nucleosomes organize DNA around histone cores, and additional levels of folding help package long molecules. Chromatin structure influences access by transcription, replication, and repair machinery, although condensed versus open is not a simple universal on/off switch. Chromosomes become especially condensed and visible during cell division. Prokaryotic chromosomes are also organized but do not generally use the same nuclear chromatin arrangement. A DNA sequence, a gene, a chromosome, and a genome refer to different scales.

Objective: Use the DNA-to-RNA-to-protein model with important exceptions.

For many protein-coding genes, DNA is transcribed into RNA, and messenger RNA is translated into a polypeptide that folds and may be modified. This is a useful information-flow model, not a rule that every gene makes a protein or that information can never move from RNA to DNA; reverse transcription occurs in some biological systems. Gene expression varies by cell type, signals, and developmental stage. DNA sequence comparisons can reveal variants, RNA measurements indicate transcript abundance under sampled conditions, and protein measurements address products more directly. A change in mRNA level need not yield a proportional change in protein amount or trait.