Prokaryotes: Single-Celled Organisms

What is a Prokaryote?

Cell Type
All living cells are of two types that differ radically in their structure. Most Eukaryotic cells are quite a bit larger than prokaryotic cells. They also have a considerably more complex interior, as you can see from these diagrams. During this topic and the ones that follow, you will learn about the structure and function of both cell types in detail.

All life on earth is believed to have arisen from an early form of life that appeared more than 3.5 billion years ago. These original ancestors evolved into the three main lines of organisms that we see today. Two of the lines, called Domains, are the Archaea and the Bacteria. Both groups have prokaryotic cells, and the members of the two domains are very similar in appearance. The bacteria are distinguished from the archaea based on biochemical differences, such as the composition of cell walls. The branching of the two domains on the diagram indicates the evolution of subgroups of related organisms from each line. We will look at some of these subgroups as the course progresses.

Domain Eukarya
The central line on this diagram represents the emergence of a third domain called Eukarya. These Eukaryotic organisms comprise the forms of life that are most familiar to us, including plants and animals. However, the prokaryotic organisms are far more abundant. In fact, the collective mass of organisms in Domains archaea and bacteria is more than 10X that of all eukaryotes on earth.

Multi-Celled Organisms
These organisms are cyanobacteria. They consist of spherical cells that attach to one another forming very long filaments. The filaments are viewed by light microscopy on the left and at higher power via scanning electron microscopy on the right.

Bacteria are extremely abundant and live almost everywhere, although they are much too small to be seen by the naked eye. This image shows bacteria from the human mouth. They are viewed using the highest magnification of a light microscope.

These organisms are from the Domain Archaea. It should be obvious that they are all prokaryotes. However, it is impossible to distinguish them from bacteria based on appearance. In fact, until recently the Archaea were named archaebacteria.

Volcanic Springs
Most extreme thermophiles are archaeans. All archeans have lipids with a unique structure that makes them more resistant to heat and acidity than the lipids of organisms in domains bacteria and eukarya. The archean thermophiles thrive in very hot environments. For example, Sulfolobus can survive in water that is nearly boiling. It is common in the sulfur-rich waters of volcanic springs where the temperature can reach 90°C. The sediment of this volcanic pool in New Zealand is colored orange by the presence of Sulfolobus.

Methanogens are archeans that obtain energy by using carbon dioxide to oxidize hydrogen. This releases methane as a waste product (hence the name methanogen). Since these prokaryotes are poisoned by oxygen, they must live in extremely anaerobic environments. One such place is the swamp or marsh where other organisms have consumed all of the oxygen in the water. The so-called swamp gas is the methane emitted by large numbers of swamp-dwelling methanogens.

Animals and Methanogens
Methanogens are also found in the anaerobic gut of animals, especially herbivores. The methane that these prokaryotes produce is belched or exhaled by many animals, such as sheep. The somewhat tongue-in-cheek news article from which the picture came claims that one-fifth of the world’s methane emissions came from farm animals. You can read the whole article by clicking on the “News” icon. The title is “Baaaaardon me! Sheep can’t stop burping.

Extreme Conditions
If you have watched the TV show CSI, you know that analysis of DNA samples is of great importance to crime labs. But did you know that this process requires an enzyme from an extreme thermophile?

The so-called PCR method of processing DNA is only possible because of an enzyme extracted from these bacteria. They live in hot springs at temperatures above 170° F and have an unusual enzyme that can function at such high temperatures.

Prokaryotes that live in extreme environments are sometimes called extremophiles and most of them, unlike T. aquaticus, are in Domain Archaea. Recently, these archeans have become of great interest to chemical and biotechnology companies who hope to find species with new enzymes that can function under a variety conditions, including extremes of temperature, pH, pressure, and salt concentration. Such enzymes could find wide usage in a spectrum of industrial processes. Here in the last image, we see a kind of new age “prospecting” with the “minors” searching a hot spring for archeans.

Prokaryotic Cells: What Structures Are Present in All Cells?

The Plasma Membrane
Cells could not exist without a structure to separate the cell interior from the surrounding environment. The plasma membrane is an amazing structure that forms the edge of the living cell and provides a selectively permeable barrier through which water, nutrients, and other essential molecules can enter while waste products are expelled. Like all biological membranes, it is a thin film of lipid and protein only 8 nm thick. It would take a stack of 8,000 plasma membranes to equal the thickness of paper.

Membrane Fluidity
The plasma membrane should not be thought of as a static structure. Indeed the phospholipids are in constant motion. They rarely flip-flop from one side of the membrane to the other, but do move laterally at a surprisingly rapid rate. It has been calculated that a phospholipid molecule can move 2 microns (the length of an average-sized bacterium) in 1 second. If the fatty acid tails of the lipids are unsaturated, they tend to kink which increases the fluidity of the membrane. As temperature is lowered, fluidity decreases (think of bacon grease hardening in the pan). A larger number of unsaturated fatty acids allows the membrane to remain fluid at lower temperatures. This is crucial, since a “hard” plasma membrane cannot function properly. In a typical cell, the lipid portion of the membrane has a consistency similar to salad oil.

Selectively Permeable Membrane
The plasma membrane is selectively permeable. It lets some substances through the membrane and not others. The hydrophobic interior of the bilayer is one reason membranes are selectively permeable. Hydrophobic molecules, those that are soluble in lipids, can easily pass through the membrane. In addition, small molecules like O2 can pass between phospholipids of the membrane.
On the other hand, large hydrophilic molecules like glucose and ions such as Sodium ions and Hydrogen ions, cannot pass through the membrane unaided.

Diffusion is the tendency for particles of any kind to spread out from where they are more concentrated to where they are less concentrated. This process can also be described as molecules moving down the concentration gradient.
Diffusion across a biological membrane is called passive transport, since the cell expends no energy to move the molecules. Oxygen and Carbon Dioxide molecules move into and out of cells by passive transport.

Proteins in the Lipid Bilayer
Many plasma membrane proteins span the membrane and protrude into the aqueous regions on either side. These parts of the protein are hydrophilic. The parts of the protein within the lipid layer are more hydrophobic and usually coiled into a helical structure. Some of these proteins serve as channels through the lipid layer, allowing hydrophilic molecules to enter the cell by diffusion. Remember that diffusing molecules always move down their concentration gradients. If a substance present outside of the cell is continuously being consumed within the cell, it will always be less concentrated in the cytosol and net movement will be into the cell as shown by arrow A. If the concentration of the molecule is the same on both sides of the membrane, diffusion will occur randomly in both directions with no net change as shown in B.

Proteins Also Function as Enzymes
Proteins within the membrane are often enzymes. Those with their active enzymatic site within the cytosol catalyze reactions within the cell, whereas proteins with an active site on the outside of the membrane can act on molecules within the environment. Some surface proteins are equipped with carbohydrate chains that may bear the enzymatic sites.
Proteins that span the membrane can act as signal transducers. This means that they have a binding site for a potential signaling molecule at the membrane surface and an active site on the inside of the membrane that catalyzes a specific reaction within the cell.

What is a Genome?
What is a genome? It is not a gnome, but as the name implies, it does consists of genes.
Each segment of DNA that specifies a specific protein (or polypeptide chain) constitutes a gene. A genome is the total genetic material within a cell. It is different for each species and can be defined as the sum of all the specific genes within the cells of that species or as all of the specific DNA sequences. The DNA that comprises genes is packaged into structures called chromosomes.

The Cell's Control Center
DNA controls cell structure and function by coding for all of the proteins within the cell. The code for the polypeptide chains of proteins is specified by specific regions on the DNA called genes. The nucleic acid, RNA, copies this genetic information. This diagram shows the DNA strands of a chromosome separating to allow the copying process from one DNA strand to begin. The light blue structure represents an enzyme required in the process. When copying is complete, the resulting RNA strand is released and carries the DNA’s instructions into the cytosol where protein synthesis occurs.

Prokaryotic Chromosome
The DNA within a prokaryote is barely visible, even in an electron micrograph. Most of the DNA It is contained within a single coiled chromosome. If a bacterial cell is ruptured to extrude the chromosome, its great length becomes apparent. All of the thin, thread-like loops in this electron micrograph are part of a single chromosome.

Circular Chromosome
The chromosome of prokaryotes is circular. The two coiled strands of DNA that make up the chromosome are illustrated in the diagram on the left. The adjacent electron micrograph is a small chromosome from a bacterial cell. At this magnification, the 2-strands of DNA and coiling of the chromosome are too small to see.

Nucleoid Region
The coiled circular chromosome of prokaryotes is packed within the nucleoid region of the cell. Proteins are bound to the DNA to cause some regions to coil even more tightly. Thus the chromosome actually contains a small amount of protein in addition to DNA. Packing a large chromosome into a small space is accomplished both by coiling and by folding the chromosome into loops.

In addition to the large, circular chromosome, many bacteria also have one or more tiny rings of DNA called plasmids. These structures have only a few genes and control functions such as resistance to antibiotics and metabolism of nutrients that are seldom encountered.

The Proteome
The proteins within a cell determine that cell's structure and its functions. Thus, each type of cell has a different set of proteins. The total of all proteins within a cell at a given time constitutes the proteome of that cell. The types of proteins that can be present within a cell are determined by the genes (remember that the total of all of the genes within a cell is called the genome). However, the specific proteins present at a given time, and the amount of each protein is determined in part by the amount of specific RNA that codes for each protein. As the diagram indicates, the amount of a specific protein is controlled by the rate at which its RNA is made, the rate at which the protein is synthesized, and the rate at which the protein is degraded within the cell.

Prokaryotic Cells: What Are Some Additional Features of These Cells?

Cell Wall
Almost all prokaryotic cells are surrounded by a cell wall that lies external to the plasma membrane. The cell wall helps maintain cell shape and gives some physical protection from the outside environment. The cell wall of prokaryotes contains a network of sugar polymers that are cross-linked by short polypeptides. This makes them completely different from the cell walls of eukaryotic cells which are composed of cellulose or chitin.
Cells in Domain Bacteria differ from those in Domain Archaea by having cell walls made of the specific polymer peptidoglycan. The chemical structure of a monomer of petidoglycan is shown here. You can see two modified sugar molecules, colored blue and pink, linked to a short peptide group of four amino acids. These monomers are linked together in long chains to form the structure of bacterial cell walls.

The Gram Stain
Gram staining is a very old technique used to distinguish between the two major groups of bacteria. A physician (named Dr. Gram) developed this procedure in 1884 and biologists are still using it today! The stain works because the violet component is retained by the thick cell wall of gram-positive bacteria causing them to appear dark violet or blue under the microscope. The thin cell wall of Gram-negative bacteria allows the violet stain to rinse out, leaving an underlying pink or orange color. Gram staining is often a first step in identifying bacterial species. It is important to know this for medical reasons, since negative bacteria are usually more resistant to antibiotics. Among disease-causing bacterial, gram-negative strains generally cause more serious health problems than gram positive ones.

Many prokaryotes have an additional structure called a capsule that surrounds the cell wall. The capsule is made of protein or polysaccharides and is sticky. It enhances the ability of cells to stick together or adhere to a substrate. In disease-causing bacteria, the capsule may also provide protection from the host’s immune system.
In the light microscopic view on the left, bacteria have been negatively stained and the capsule is visible as a clear area surrounding each bacterium. The image on the right is an electron micrograph that has been colored to show the capsule in green. The bacterial cell is a Streptococcus attached to a human tonsil cell by the sticky capsule. This is the bacteria that causes strep throat.

Pili and Fimbriae
Some bacteria have hair-like appendages called pili or fimbriae that protrude from the capsule and enhance ability to attach to a surface. The second image in this sequence shows the bacteria responsible for gonorrhea. The pili are clearly visible in the light microscope view on the left. The electron microscope on the right shows the bacteria attached to a mucus membrane of the human reproductive tract.