We left off last time examining the 3 domains of living things. Our goal today is to look at the differences among these Domains and to learn a little about prokaryotic morphology in the process.

Tables 1.3 and 22.1 in your book show some of the main differential characteristics of the 3 Domains. Note that the Bacteria and Archaea share certain characteristics - mainly because they both lack certain features of eukaryotic cells (e.g. nucleus, mitochondrion). But also note that Eucarya and Archaea share certain characteristics including:

1) similar RNA polymerases

2) immunity to many well known antibiotics that affect most Bacteria (including rifamycin, which binds to bacterial RNA polymerases, but not to those of Archaea and Eucarya),

3) similar methods of transcribing proteins (e.g. diphtheria exotoxin inhibits protein synthesis in Archaea and Eucarya but not in Bacteria).

The 16S/18S phylogenetic tree from last time also supports the idea that the Eucarya and Archaea are more closely related than the Eucarya and Bacteria. Note that the initial (deepest) branch of the tree leads to the Bacteria on one side and the Archaea and Eucarya on the other side.

As long as we have the tree up let's examine a few other ideas. First is the idea that the earth was hot when life evolved. This theory is supported by the fact that some of the deepest divergences in the Bacteria and Archaea are thermophilic organisms (therm = Gr. for heat; philo = Gr. for love) and that thermophiles exist in all of the major lineages of life (e.g., there are many thermophilic fungi).

Another neat idea that has been supported by 16S rRNA phylogenies is the endosymbiotic theory (put forth mostly by Lynn Margulis). This theory states that mitochondria and chloroplasts are the descendants of ancient bacteria that were incorporated into the cytoplasm of an ancestor of modern eukaryotic organisms (perhaps a relative of the modern Archaea). As it turns out these organelles have their own ribosomes and simple chromosomes. When the 16S rRNA of these organelles is sequenced and compared to all known sequences - the mitochondria end up being classified in the Proteobacteria (a big group within the Bacteria) and the chloroplasts end up in the Cyanobacteria (see figure 18.9, pg. 426). In other words, these organelles are actually bacteria that have been living quite happily as endosymbionts in eukaryotic organism for millions of years!

Structure of Bacteria and Archaea. Chapters 4 and 22.

Before we get on with looking at the major groups of microorganisms, I want to take a little time and talk about some structural aspects of microbes (this stuff is from the last part of Chapter 4 and parts of Ch. 22). I want to talk about this now because it will help us to understand the differences between Archaea and Bacteria (and between fungi and prokaryotes).

First let's talk about some structural similarities and differences.

You should already know the difference between prokaryotic and eukaryotic cells - if not review pgs. 10 -14.....Show Fig. 1.6 and 1.7.

Let's look a little more closely at some aspects of Bacterial and Archaeal cells.........

DNA. Bacteria and Archaea have their DNA (double stranded) contained in a single circular chromosome and they are haploid. Most Bacteria (and many Archaea) that have been examined, also have smaller circular DNA fragments called plasmids. Plasmids occur in some eucaryotes but are thought to be rare (more about plasmids when we discuss genetics).

Cell membranes. We already mentioned that the Archaea have unique plasma membranes (Table 1.3 and 22.1). Let's look at that a little more closely

Ether (Archaea) vs. Ester (Bacteria & Eucarya) linkages (Figure 4.36)

Crosslinked (Figure 22.2)

Cell Walls. All Bacteria that have cell walls have peptidoglycan in them. The thickness of the peptidoglycan layer is the main determinant of whether an organisms is gram + or gram -. Figure 4.42 shows a typical peptidoglycan from a Gram + bacterium (Staphylococcus aureus). Note the polysaccharide backbone consisting of alternating amino sugars (N-acetylglucosamine (NAG) and N-acetyl muramic acid (NAM)) linked by Beta 1-4 bonds (remember those from cellulose?). The Beta 1-4 bond can be broken by an enzyme called lysozyme which is present in your tears, saliva, blood, and other bodily fluids. These polysaccharide chains are held together by peptide cross links (thus the peptido in peptidoglycan). These peptides are rather odd in that they contain D-amino acids.

Antibiotics in the penicillin and cephalosporin groups inhibit the enzymes that are responsible for the formation of peptidoglycan. This is why these antibiotics do not affect members of the Archaea or Eucarya.

Fig. 4.44 shows a less confusing diagrammatic representation of the peptidoglycan layer.

Gram + and gram - bacteria......

Gram + cell walls... see figure 4.49 and overhead in class showing how teichoic acids (Fig. 4.47) help stabilize the peptidoglycan layer and connect it with the plasma membrane.

Gram - cell walls are quite different in that they have much less peptidoglycan and no teichoic acids. Plus they have an outer membrane. See Figure 4.49.

Figure 4.51......Note LPS which is antigenic and can function as an endotoxin in gram - pathogens such as Salmonella spp. andYersinia pestis (plague).

Also note the periplasmic space where many enzymes either float free and/or are attached to the cytoplasmic membrane.

Cell Walls of the Archaea.

Do not contain peptidoglycan or D-amino acids. Some of the methanogens have pseudopeptidoglycan (see Fig. 4.52). Note that it contains NAG. Other Archaea have protein or glycoprotein cell walls unlike any other cell walls known in the universe.

Fungal cell walls.

The main component of fungal cell walls is chitin which is a polymer consisting of N-acetylglucosamine (NAG) the monomer. Thus, NAG is present in all 3 Domains of life.

See Fig. 2-2 from Moore-Landecker (1996) for structure of a fungal cell wall.

Moore-Landecker, E. 1996. Fundamentals of the Fungi. Prentice Hall.

Many bacteria produce extracellular layers that serve different functions in different critters.

Capsules are slimy layers that are made of polysaccharides (monomers include NAG and glucose (in dextran) or polypeptides (monomers of D-glutamic acid in Bacillus sp.).

Capsules help bacteria attach to surfaces - e.g. Streptococcus mutans attaches to your teeth using a capsule. Capsules also function as a protective layer - as in S. pneumoniae which can avoid phagocytyosis in the blood only if it has a capsule. Figure 4.38 shows a negative stain of a Bacillus sp.

Sheaths are rigid tubes made of polysaccharides and polypeptides and are commonly found on some filamentous bacteria such as Thiothrix (Figure 21.30) and Sphaerotilus (see Fig. 4.39).

Slime Layers are usually polysaccharides that are produced by bacteria that exhibit gliding motility (move kind of like slugs; see Fig. 4.40).

S-layers or "protein jackets" are also found external to the cell wall on some members of the Bacteria. The function of these jackets is not known at this time.

Bacterial Appendages (pp. 100-104).

Fimbriae are appendages made of protein and are found on many types of bacteria. One type of Fimbria is the pilus (pl. = pili). We'll discuss the sex pilus in the genetics portion of the course (show Figure of mating E. coli). The main functions of fimbriae are attachment and transport.

Flagella (sing. = flagellum) are proteinaceous appendages that are used in bacterial propulsion. Compared to eukaryotic flagella (remember the 9 + 2 arrangement of microtubules) bacterial flagella are quite simple semi-rigid helices. The site of attachment of the flagellum to the cell wall is more complex, however. Describe rotary motor...........

This motor is under complex control in bacteria. Many bacteria exhibit chemotactic behavior in which they can move towards a source of food. Describe how this works........