Eukaryotic Genome Structure Tutorial on Comparative Genomics part I NSF DBI-1515704

What is a eukaryote? Eukaryotes are organisms that are not bacteria or archaea. They can be single celled, like protozoa (including the organism that causes malaria), or multicellular, like animals and plants. Eukaryotic cells tend to have multiple intracellular compartments called organelles that are separated by membranes. An image of a eukaryotic cell is shown to the right (By Zaldua I., Equisoain J.J., Zabalza A., Gonzalez E.M., Marzo A., Public University of Navarre - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/ind ex.php?curid=46386894).

What do chromosomes look like? Eukaryotic chromosomes (sister chromatids) are bundled pieces of DNA that are wrapped by histones into nucleosome structures that fold into chromosomes. The underlying A, C, G, T are the base pairs seen in the double helix at right. This image is taken from https://pmgbiology.com/tag/centromere/.

What are genes and what do they look like? The following link contains images on the structure of a gene. Genes are stretches of DNA sequence embedded in chromosomes, like the one shown on the previous slide. Different bits of DNA sequence have different functional roles. Some bits play a role in binding the molecules that regulate gene “expression”, called transcription factors. Others encode the segments of a gene that are expressed. These segments are called exons and are discontinuous, separated by segments that do not encode the functional part of a gene, called introns.

What is the underlying chemistry? DNA is not just a string of letters. It is an organic chemical, a polymer made up of monomer units that come in four types (A, C, G, T). It forms a double helix where A and T bind each other and C and G bind each other. This occurs through a set of regular hydrogen bond donor and acceptor combinations. Here is what it looks like, taken from http://www.bioinfo.org.cn/book/biochemistry/chapt27/bio2.htm. It has two distinct grooves: a major groove and a minor groove, with different chemical groups in each groove as indicated that allow for transcription factors to bind specifically to different bases. The image on the right shows the grooves in the structure of the double helix itself. This is taken from http://www.biology.arizona.edu/biochemistry/activities/DNA/03t.html.

How do the different bases function differently? There are different chemical groups on the different bases in the different grooves. These enable different proteins that regulate the “expression” of the genes to find the genes they are supposed to be regulating.