April 18, 2008
Differences between the molecular biology of Prokaryotes and Eukaryotes
So Molecular biology is still progressing pretty slowly, and today we
just focused on basics of molecular biology, but we did cover some of
the differences between prokaryote and eukaryote genetics.
The most obvious difference between the two is that prokaryotic DNA
is generally arranged into circular structures, while eukaryotic DNA
is arranged in linear strands. Furthermore, eukaryotic genomes
contain multiple chromosomes, while prokaryotic genomes only contain
one. This difference may be a result of the massive bloat that has
occurred in eukaryotic genomes. While eukaryotic genes tend to be
longer and more complex than prokaryotic genes, they are also only a
fraction of the total length of the nucleic acid strand. Prokaryotic
genomes are up to 90% coding sequences, while coding sequences in
eukaryotic organisms is often around 3%. Furthermore, eukaryotic
genes are peppered with introns, spans of non-coding sequences within
an operon, while prokaryotic genes are generally free of such nonsense
All of this means that eukaryotes tend to have much more DNA than
prokaryotes. One explanation of the difference in the morphology of
the DNA is simply that as the length of the nucleic acid sequence got
longer, it got too long to be effectively manipulated as a single long
loop. Breaking this loop might then become advantageous and be
selected for by evolutionary processes. This is merely a hypothesis
though (and not mine).
Whatever the reason for the morphological differences in the DNA of
prokaryotes and eukaryotes, this has led to substantial differences in
how DNA is manipulated in the different branches of the tree of life.
While the basic secondary structure (the double helix) remains the
same, there exist substantial differences in storage and replication
of the two forms of DNA. I will look first at storage.
While during most of the cellular cycle the DNA exists in a state of
relative disorder, enzymes such as gyrases and topoisomerases will
supercoil the DNA for efficent packing during cell division and in
order to control expression of parts of the genome. While
supercoiling exists in both eukaryotes and in prokaryotes, since
prokaryotes have circular genomes this results in different patterns
than does supercoiling in eukaryotes. In prokaryotes, domains of the
circular genome tend to be pinched off from the loop to form small
There are more significant changes in terms of the process or
replication. Because the prokaryotic genome is relatively small and
contained within one circular molecule, only one site of replication
initiation is needed. This point is known as ori. Replication
begins from this point and proceeeds in both directions around the
loop till it meets up with the replication fork traveling in the other
direction. A result of this form of replication is that the ori
sequence is regenerated first during replication providing a new site
for replication to begin, even as the original round of replication is
still proceeding. Thus during cell division, the chromosomes that are
segregated into the two halves of the dividing cell are still
replicating, and are often 70% completed. This is one factor that
contributes to the very quick division rates in prokaryotic
organisms–only the last 30% of the genome needs to be replicated
before it begins to divides once more.
Since the chromosome does not have ends, the entire genome can be
copied. Eukaryotic genomes are linear and because of the nature of
DNA polymerase, the enzyme that replicates DNA, the last few bases on
each chromosome are lost with each replication. This has led to the
development of telomeres: non-coding DNA on the ends of the
chromosomes that can be lost without harm to the organism. The loss
of the last few bases is caused by the enzyme “loosing hold” of the
DNA strand, and falling off. However, because the prokaryotic genome
is circular, this is not a problem, and the entire genome can be
This implies that DNA in prokaryotes is substantially less packed
during cell division than it is in eukaryotes. During most of the
cell cycle in eukaryotes, DNA is loosely in a mass in the nucleus.
However, during replication, the DNA is tightly packed into tiny X
like structures that we commonly see DNA as being represented as. In
this state, DNA is all but inaccessible. It is coiled so tight as to
keep the genetic material arranged so that it can neatly be segregated
into the two new daughter cells. However, as discussed above, many
functions are still taking place on the DNA of prokaryotes even while
it is dividing. Part of this surely a result of the difference in
size of the genomes of eukaryotes and prokaryotes. Part of it is
surely because eukaryotic DNA is stored within a nucleus, unlike
prokaryotic DNA. Part of this is surely because prokaryotic DNA does
not have loose ends (being circular) like eukaryotic DNA.
The final difference between eukaryotes and prokaryotes that I want to
discuss is the difference between the haploid/diploid status.
Eukaryotes often have life stages where they are either haploid or
diploid. Being diploid refers to having two copies of every
chromosome (one from each parent). Prokaryotes, because they only
have one chromosome, cannot be diploid. As such, the re-combinative
properties of sexual reproduction are unavailable to them. On the
other hand, the genes that they do have are expressed. Eukaryotes are
generally well described by classical mendelian genetics. Having two
copies of each gene (one on each copy of the chromosome) nicely
explains the recessive/dominant paradigm established by Mendel.
However, in a prokaryotic genome, there is generally only one copy of
each gene, and thus the dominant/recessive paradigm does not apply.
Each and every gene will be expressed, making prokaryotes a much
better vehicle for developing new genes: there is no interference
from dominant forms. Disadvantageous forms of a gene are much less
likely to persist in a community of prokaryotes, since a more
advantageous dominant form of the gene cannot “cover” for it. This is
but one reason why prokaryotes tend to have much greater rates of
change in their genomes than eukaryotes.
More next time!
The information for this post was attained from Brock’s Biology of
Microorganisms and the April 10th Microbiology Lecture by Dr. Popa.