Chromosomal Structure

In the last section, we explored the “microanatomy” of DNA. Now let’s turn towards the bigger picture and explore more of the “macroanatomy”. To do this we will focus on eukaryotes since prokaryotic DNA lacks larger structural elements and instead exists in an uncondensed and uncontained form.


Eukaryotic DNA is magnitudes larger than prokaryotic DNA. If we left eukaryotic DNA to noodle about in its uncondensed helical form it would take up tons of space in the nucleus. Instead, the DNA is wrapped around proteins called histones and further condensed into nucleosomes.

Histones are able to bind to DNA due to containing lysine residues whose positive charges attract and bind to the negatively charged phosphates in the backbone of a DNA molecule. While this condenses eukaryotic DNA it also covers up the DNAs grooves preventing it from undergoing replication or transcription.

Heterochromatin and Euchromatin

When DNA is condensed it is called heterochromatin and since it is inaccessible it can’t be transcribed. This gives cells a convenient way of controlling which portions of DNA are expressed and which aren’t. As a result, different cells can carry out different functions depending on what parts of their DNA are being expressed.

In contrast, when DNA is uncondensed it is called euchromatin and is no longer tightly bound to a histone. Under these circumstances DNA’s grooves are accessible and the various enzymes of replication and transcription are able to actively replicate and express that DNA.

The transition between euchromatin and heterochromatin is controlled by altering the lysine (K) residues on histones. Most commonly the lysine residues on histones are acetylated or deacetylated. When lysine (K) is acetylated its positive charge is eliminated and the DNA backbone is no longer attracted to the histone causing it to fall off. At this point, DNA is converted from heterochromatin to euchromatin and can be actively replicated and transcribed.

To reverse this process and convert the DNA back into heterochromatin lysines are deacetylated resulting in the restoration of their positive charge. At this point, the DNA backbone becomes attracted to the histone and recondenses rendering it transcriptionally silent.


Nucleosomes can further condense into structures called chromosomes which contain most of the DNA in a cell. Chromosome structure can be a bit confusing because the same term is used for two similar but distinct entities. To keep the different entities straight we will distinguish between replicated chromosomes and unreplicated chromosomes.


Before jumping straight into the two different types I want to discuss two features common to both. The first feature is the telomere or repetitive sequences at the very end of the DNA strands. These repeated sequences are almost always in their heterochromatin form and act like little knots preventing the rest of the DNA from unraveling.


At the center of a chromosome is the centromere. The centromere helps hold the arms of a chromosome together and prevent it from unfolding into a less compact linear form. Again this region is comprised of heterochromatin and is transcriptionally silent.

Unreplicated Chromosomes

Unreplicated chromosomes consist of a single strand of dsDNA condensed into a stick-like shape. At the center of the stick there is the centromere and each branch off of that central point is called an arm. Capping each arm off is a telomere that prevents the strands from unraveling. This type of chromosome is present when a cell is quiescent (a fancy way of saying not replicating).

Replicated Chromosomes

Replicated chromosomes on the other hand have an X-like shape with a central centromere. The centromere holds two identical strands of dsDNA together giving this chromosome its characteristic shape. Again telomeres cap off the ends of the chromosome and prevent the strands from unraveling.

Why are there two identical copies of the same DNA though? When a cell plans to replicate it synthesizes a second copy of itself and tacks the two copies called chromatids together. Later down the line in either mitosis or meiosis, the two chromatids will be ripped apart and shared between two cells. This generates a new cell with exact same DNA as the previous one in order to keep everything organized the cell simply kept the identical strands of DNA together.

The Human Genome

Now that we’ve looked at the organization of eukaryotic DNA and chromosomes let’s explore a couple of important details about our own DNA. Human cells contain 2 pairs of 23 unique chromosomes for a total of 46 chromosomes within the nucleus of their cells.

Since we have two copies of each unique chromosome our cells are diploid (2n). Whereas many plant cells have four copies of each chromosome and are labeled tetraploid (4n). Of the two copies one came from our mother and the other came from our father. Therefore each parent contributed half of our total DNA.

Extranuclear DNA

In addition to nuclear DNA our cells also contain mitochondrial DNA (mDNA). Here the DNA exists in a large loop like it does in prokaryotes and is replicated independently. Collectively all of our DNA both in and out of the nucleus is referred to as the genome.