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Prokaryotes I - Cellular and Genetic Organization

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Introduction and Goals

Prokaryotes are everywhere. They have been found at the deepest depths of the oceans and high above in the atmosphere. Based on sheer numbers and species diversity, they are the most successful group of life on the planet. A group of studies published in Summer 2012 showed that each human has their own “microbiome” with as many as a thousand different strains of bacteria. Prokaryotes are an essential component of Earth’s ecology, and many human diseases are caused by bacteria, so understanding their biology is important in many different fields.

This tutorial is the first in a three-part series discussing prokaryotes. By the end of this first tutorial you should have a basic understanding of:

  • The basic features of all prokaryotes
  • The diverse lifestyles of prokaryotes
  • Why prokaryotes can undergo rapid evolutionary change
  • The basic genetic organization of prokaryotes
  • How prokaryotes can acquire new genetic information through asexual reproduction

Performance objectives:

  • Summarize the major differences between prokaryotic and eukaryotic cells
  • Describe the two domains within prokaryotes, including their relationship to eukaryotes
  • Explain how prokaryotes reproduce and exchange genetic information
  • Discuss the evolutionary consequences of a short generation time

Basic Features

Figure 1. Colorized Image of a Bacterial Colony. (Click to enlarge)

A defining feature of prokaryotes is their lack of membrane-bound nuclei. This is not to say they lack subcellular specialization because some prokaryotes have very elaborate internal membranes. However, they generally have less subcellular specialization than eukaryotes (organisms with membrane-bound nuclei and organelles). Also, prokaryotes are usually much smaller than eukaryotic cells (1-5 microns compared to 10-100 microns). They are often described as single-celled organisms, but they can form colonies that show a remarkable level of complexity (as depicted in this colorized image of a bacterial colony shown in Fig. 1). The shape of individual cells is used to classify prokaryotes; they can be either spherical (coccus), rod-shaped (bacillus), or helical (spirillum).

This animation is a simple game to test your understanding of the basic features of a prokaryote. 




In the last few decades, several taxonomic schemes have been used to describe life; you were introduced to this concept in Tutorial Two. One of the simplest divides life into prokaryotes and eukaryotes; that is, those organisms without nuclei went into one group and those with nuclei went into another, respectively. Another commonly used scheme divides life into five kingdoms: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia. You may see one of these schemes in an older textbook or website. Keep in mind that classification schemes strive to show the evolutionary relationships between groups, and in recent years it has become apparent that the evolutionary relationships of prokaryotes are quite complex. One prokaryotic group, the Archaea, have some features that are more eukaryotic than prokaryotic. Although the Archaea lack a nucleus, their genetic organization is more like that of a eukaryote.


Figure 2.  The Three-Domain System of Classification. (Click to enlarge)

To reconcile new data, the taxonomic scheme of life has been revised. The most current scheme proposes that life be divided into three domains. In this scheme prokaryotic organisms can belong to the domain Archaea or the domain Bacteria, while those organisms that have a nucleus comprise the third domain, Eukarya (Figure 2). Organisms that belong to each of these three domains are sometimes referred to as the archaebacteria, eubacteria and eukaryotes, respectively. Figure 2 illustrates the relationship among the three domains. Keep in mind that the last universal common ancestor (LUCA) of life on earth most likely arose over 3.5 billion years ago. This organism probably had a fairly complex cell structure; this is discussed in a recent Science News Article. What is the evidence from this article that supports the presence of LUCA?

Archaea are sometimes referred to as extremophiles, and many species live in extreme environments (e.g., hot springs, salt ponds, Arctic ice, deep oil wells, acidic ponds that form near mines, and hydrothermal vents); however, these environments are not extreme to those archaea. In fact, many extremophiles die when moved to our environment. Life is relative.

The remaining prokaryotes are classified as bacteria. Some textbooks and articles still refer to all prokaryotes as bacteria, but there is an increasing tendency to make a distinction between archaebacteria and bacteria.



Figure 3.  Thermophilic (heat-loving) bacteria.  (Click to enlarge).  Limestone terraces, formed by precipitation from calcium-rich water flowing from a raised hotpool. Pink, green, and brown-colored archaebacteria occupy the thermal gradients in the flowing water (60-100°C).

Prokaryotes by the Numbers

In terms of metabolic impact and numbers, prokaryotes dominate the biosphere. They outnumber all eukaryotes combined. They live in a myriad of environments and a teaspoon of common dirt can harbor 100 million or more bacteria. Not only are bacteria plentiful in total numbers, but the species diversity may be quite high as well. Although recognizing distinct species of bacteria is a challenge for microbiologists modern approaches using DNA diversity analysis, suggest that new species of bacteria evolve quite rapidly. Recent studies suggest that in that same teaspoon of soil there could reside up to 1 million different species.  However, bacterial are very light and the debate about the total mass of prokaryotes on earth continues.


Fast Growth, Reproduction and High Rates of Evolution

In some cases, prokaryotes can divide in as little as 20 minutes (although much slower rates are also observed). Generally, prokaryotes have three factors that enable them to grow and reproduce rapidly. First, prokaryotes have a small genome (genetic material). Second, prokaryotes have simple morphologies (structural features). Third, prokaryotes reproduce via binary fission(cell division in which a prokaryotic chromosome replicates and the mother cell pinches in half to form two new daughter cells) as shown in Figure 4.

Figure 4. Bacterial Cell Division - Binary Fission. (Click to enlarge). The elongated bacteria is undergoing binary fission.

Binary fission is simply cell division in which two identical offspring each receive a copy of the original, single, parental chromosome. Therefore, Binary fission is a type of asexual reproduction (reproduction that does not require the union of two reproductive cells, and that produces offspring genetically identical to the parent cell). A population of rapidly growing prokaryotes can synthesize their DNA almost continuously, which aids in their fast generation times. Even as a cell is physically separating, its DNA can be replicating for the next round of cell division, as seen in the animation on binary fission below.


This simple animation shows binary fission in a prokaryote.

These three factors (small genome, simple morphology, and binary fission) allow for a short generation time when compared to eukaryotic cells. This short generation time means that evolutionary changes occur relatively quickly when compared to longer-lived species.


Genetic Organization of Prokaryotes Aids Fast Generation Times

Compared to eukaryotes, prokaryotes usually have much smaller genomes. On average, a eukaryotic cell has 1000 times more DNA than a prokaryote. This means that less DNA must be replicated (copied) with each cell division in prokaryotes.

The DNA in prokaryotes is concentrated in the nucleoid. The prokaryotic chromosome is typically a double-stranded DNA molecule that is arranged in a single large ring. What shape are eukaryotic chromosomes?

Prokaryotes often have smaller rings of extrachromosomal DNA termed plasmids (these are also found in a few eukaryotes). Most plasmids consist of only a few genes. Plasmids are not required for survival in most environments because the prokaryotic chromosome programs all of the cell's essential functions. However, plasmids may contain genes that provide resistance to antibiotics, metabolism of unusual nutrients, plasmids that confer virulence, and other special functions. Plasmids replicate independently of the main chromosome, and many can be readily transferred between prokaryotic cells.




Asexual Reproduction and the Transfer of Genetic Information Between Prokaryotes

Prokaryotes do not alternate between the haploid and diploid states, so meiosis and fertilization are not components of their life cycles. Rather, binary fission is the main method of reproduction in prokaryotes. This form of asexual reproduction means that the genetic variation created by meiosis and random fertilization (you will learn more about this in Tutorial #11) does not occur in prokaryotes. Nonetheless, genetic variation does occur in prokaryotes, and mutations are one source of variation in the population. Genetic variation within a population can be beneficial because it provides the raw materials for a population to adapt to a changing environment. Greater diversity in the gene pool increases the likelihood that at least some of the organisms in a population will have the right genetic combination to survive if environmental conditions change.

Three mechanisms by which prokaryotes transfer genes between individuals (transformation, conjugation, and transduction) will be discussed next.



One way that genetic material can be moved between bacteria is transformation. Transformation occurs when prokaryotes acquire genes from their surrounding environment. This DNA might have been left behind by other bacteria (from the same or different species) when they died. The foreign DNA is directly taken up by the cell and expressed. If the DNA contains a beneficial gene (e.g., one encoding for antibiotic resistance), then the individuals harboring that gene will have a selective advantage over their non-transformed counterparts. As long as individuals with this gene reproduce more successfully, compared to those lacking the gene, they will be more fit and the gene will increase in frequency (i.e., microevolution, via natural selection, will occur).

Other examples include transformation of nonpathogenic bacteria into pathogenic (harmful) strains. When harmless Streptococcus pneumoniae bacteria are placed in a medium containing dead cells of the pathogenic strain, they can take up the DNA from the dead pathogenic cells. If the formerly harmless bacteria pick up the gene for pathogenicity, they will become pathogenic themselves. It is important to point out that pathogenicity may not confer a long-term increase in fitness; if the host dies, the microsymbiont has lost its' "home". As such, it is often said that the "smartest" pathogens are those that cause the lowest mortality.



Genetic material can also move between bacteria by conjugation. The mechanism of conjugation requires that two living prokaryotic cells physically join with one another. Typically DNA transfer only goes one way, with the "male" using an appendage called a pilus (plural, pili). In order to produce pili, prokaryotes must have a plasmid termed the F factor(fertility factor plasmid). When a cell has the F factor plasmid, it is said to be F+. This F+ condition is heritable. If an F+ cell divides, both of the resulting cells will be F+. This condition is also "contagious." After an F+ cell conjugates with a "female" cell that does not contain the F factor, the "female" cell obtains the F factor plasmid and becomes F+ ("male").


Click on the following to view an animation of an F-plasmid transfer.


Genetic material can also be moved between bacteria by transduction. In this event, the exchange of DNA between prokaryotes is made possible by phages(viruses that infect bacteria). Phages reproduce by injecting their genetic material inside the bacterial cell, then multiplying, and eventually bursting from the cell. In transduction, the phage DNA inserts somewhat benignly into the bacterial host chromosome. Here it can lay dormant for many generations. However, under certain conditions, the phage DNA removes (excises) itself from the bacterial chromosome (usually carrying pieces of the chromosome with it), then replicates and forms new phages that burst out of the cell. These phages can reinfect other bacteria and thereby transfer not only their own DNA, but pieces of the former host DNA into the newly infected bacterium.

 Figure 5. Overview of Transduction. (Click to enlarge)


Genetic Variation and Evolution

The short generation time associated with binary fission was pointed out earlier in this tutorial. We also know that mutations add new and different alleles to populations. These two factors (short generation times and mutations), combined with the processes of conjugation and transduction, help prokaryotic populations achieve vast genetic variation (without the alternation of haploid/diploid states seen in many eukaryotes). Generation times are minutes to hours, and can result in a beneficial mutation being heavily favored and passed on to a great number of offspring in a very short period of time. Once again, a short generation span enables prokaryotic populations to adapt very rapidly to environmental change. This adaptive evolution is as important now to prokaryotes as it was when prokaryotic life began to diversify a few billion years ago.



This tutorial introduced you to the prokaryotes. They are a very diverse group of organisms that are commonly referred to as bacteria; however, they are really comprised of two different domains. One domain, the Archaea, usually grow in the most extreme environments. Their ability to occupy extreme habitats is mirrored by their flexibility in utilizing resources; some species can use metals as an energy source, whereas others can live on oil or hydrogen sulfide. The other prokaryotic domain, the Bacteria, is much more abundant. Although diverse, members of both domains share some common features. Prokaryotes lack membrane-bound nuclei, they are generally single-celled or colonial, and they are very small. The genetic organization of prokaryotes and binary fission as a means for replication aids in their fast generation times, which contributes to relatively quick evolutionary changes. We will continue our discussion of prokaryotes in the next tutorial by exploring their metabolism, structure and function.




After reading this tutorial, you should have a working knowledge of the following terms:

  • Archaea
  • bacillus (pl. bacilli)
  • Bacteria
  • binary fission
  • chemoautotroph
  • chemoheterotroph
  • coccus (pl. cocci)
  • conjugation
  • Eukarya
  • eukaryote
  • extremophile
  • F factor
  • nucleoid
  • pathogenic
  • phage
  • photoautotroph
  • photoheterotroph
  • pilus (pl. pili)
  • plasmid
  • prokaryote
  • specialized transduction
  • spirillum (pl. spirilla)
  • transduction
  • transformation

Case Study for Prokaryotes I

In the case study for Tutorial #1, you were introduced to the Evolution Canyons in Israel (review the case study from Tutorial #1 if you do not recall the information). Researchers are interested in a variety of organisms’ responses to the extreme environmental differences between the south-facing (“African”) and north-facing (“European”) slopes of the Evolution Canyons.

One team of researchers is looking at evolutionary responses in a common soil bacterium Bacillus subtilis in the Evolutionary Canyons. B. subtilis is a good choice of organism for this research because it is a common model organism that has been used to study prokaryote genetics and the process of DNA replication in prokaryotes in laboratory settings and thus a great deal is already known about the organisms’ genetics. B. subtilis is also a good model organism because these bacteria are easily transformed in the lab.

Some of the team’s research findings include that the B. subtilis that live on the south-facing slopes are more efficient at producing biological molecules (“biosynthesis”) than those that live on the north-facing slope (Nevo, 2009).

  • Based on the genus name (Bacillus), what shape is this bacterium? Is it a member of domain Archaea or domain Bacteria?
  • What is a model organism (you will need to look this up in an outside source)?
  • What does it mean that B. subtilis is easily transformed in the lab?
  • Develop a plausible hypothesis for why bacteria living on the south-facing slopes have more efficient biosynthesis than those living on the north-facing slopes.


Nevo, E. (2009) Evolution in action across life in "Evolution Canyon" Israel. Trends in Evolutionary Biology; 1:e3 doi:10.4081/eb.2009.e3


Now that you have read this tutorial and worked through the case study, go to ANGEL and complete the tutorial quiz  to test your understanding (the due dates for the tutorial quizzes are posted on ANGEL).  Questions?  Either send your instructor a message through ANGEL or attend a weekly review session (the times and places are posted on ANGEL).