07.1 Structure of Bacteria and Archaea MS MI v2 *

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1 OpenStax-CNX module: m Structure of Bacteria and Archaea MS MI v2 * The BIS2A Team Based on Bis2A 10.1 Structure of Bacteria and Archaea by OpenStax Mitch Singer This work is produced by OpenStax-CNX and licensed under the Creative Commons Attribution License 4.0 By the end of this section, you will be able to: Abstract Describe the basic structure of a typical prokaryote Describe important dierences in structure between Archaea and Bacteria 1 Introduction In this module we will discuss the basic structural features of both bacteria and archaea. There are many structural, morphological and physiological similarities between bacteria and archaea. As discussed in Module 10.0, these microbes share many ecological niches and carry out similar biochemical and metabolic processes. Both lack a nucleus and organelles which are hallmarks of eukaryotes, so they are often grouped into a general category of prokaryotes. Figure 1 shows a basic evolutionary tree, starting with LUCA and branching into the three major domains. While both bacteria and archaea are classically grouped into the morphologically similar classication of prokaryotes, archaea are actually more closely related to eukaryotes. * Version 1.1: Jun 15, :42 pm

2 OpenStax-CNX module: m Figure 1: Bacteria and Archaea are both prokaryotes, but are dierent enough to be placed in separate domains. The trunk of the phylogenetic tree is a universal ancestor. The tree forms two branches. One branch leads to the domain bacteria, which includes the phyla proteobacteria, chlamydias, spirochetes, cyanobacteria, and Gram-positive bacteria. The other branch branches again, into the eukarya and archaea domains. Domain archaea includes the phyla euryarchaeotes, crenarchaeotes, nanoarchaeotes, and korarchaeotea. While bacteria and archaea are separate domains, morphologically they share a number of structural features. As a result, they face similar problems, such as the transport of nutrients into the cell, the removal of waste material from the cell, and the need to respond to rapid local environmental changes. In this section, we will focus on how their common cell structure allows them to thrive in various environments and simultaneously puts constraints on them. One of the biggest constraints is related to cell size. All cells have four common structures: (1) a plasma membrane, which functions as a barrier for the cell and separates the cell from its environment; (2) a cytoplasm, which is the jelly-like substance inside the cell that contains all of the soluble reactions; (3) nucleic acids, which serve as the genetic material for the cell; and (4) ribosomes, where protein synthesis takes place. Although bacteria and archaea come in a variety of shapes, the most common three shapes are as follows: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (Figure 2). Both bacteria and archaea are generally small compared to typical eukaryotes. For example, most bacteria tend to be on the order of 0.2 to 1.0 µm in diameter and 1-10 µm in length. However, there are exceptions. Epulopiscium shelsoni is a bacillus-shaped bacterium that is typically 80 micrometers (µm) in diameter and µm long. Thiomargarita namibiensis is a spherical bacterium between 100 and 750 µm in diameter, which is visible to the naked eye. For comparison, a typical human neutrophil is approximately 50 µm in diameter.

OpenStax-CNX module: m61910 3 Figure 2: Bacteria and archaea fall into three basic categories based on their shape, visualized here using scanning electron microscopy: (a) cocci, or spherical (a pair

3 OpenStax-CNX module: m Figure 2: Bacteria and archaea fall into three basic categories based on their shape, visualized here using scanning electron microscopy: (a) cocci, or spherical (a pair is shown); (b) bacilli, or rod-shaped; and (c) spirilli, or spiral-shaped. (credit a: modication of work by Janice Haney Carr, Dr. Richard Facklam, CDC; credit c: modication of work by Dr. David Cox; scale-bar data from Matt Russell) A thought question: One question that comes to mind is why are bacteria and archaea so small? What are the constraints that keep them microscopic? How could bacteria such as Epulopiscium shelsoni and Thiomargarita namibiensis overcome these constraints? Think of possible hypotheses that might explain this phenomena. 2 The Bacterial and Archaeal Cell: common structures Introduction to the basic cell stucture Bacteria and archaea (Figure 3) are unicellular organisms, which lack internal membrane-bound structures that are disconnected from the plasma membrane. Therefore, they do not have a nucleus, but instead their genetic material is located in an area of the cell called the nucleoid. The bacterial and archaeal chromosome is often a single covalently closed circular double stranded DNA molecule. However, some bacteria have linear chromosomes and some bacteria and archaea have more than one chromosome. Besides the nucleoid, the next common feature is the cytoplasm (or cytosol), which is the "aqueous" jelly-like region encompassing the internal portion of the cell. The cytoplasm is where the soluble (non-membrane) reactions occur, and which contains the ribosomes - the protein-rna complex where proteins are made. Both bacteria and archaea have a cell membrane, the phospholipid bi-layer that denes the boundary of the cell. In prokaryotes, the cytoplasmic membrane also contains all membrane-bound reactions, including the electron transport chain, ATP synthase, and photosynthesis. Finally, bacteria and archaea have cell walls, the rigid structural feature that gives denition to the cell shape.

OpenStax-CNX module: m61910 4 Figure 3: The features of a typical prokaryotic cell are shown.

4 OpenStax-CNX module: m Figure 3: The features of a typical prokaryotic cell are shown. 3 Constraints on the bacterial and archaeal cell One common, almost universal feature of bacteria and archaea is that they are small, microscopic to be be exact. Even the two examples given as exceptions, Epulopiscium shelsoni and Thiomargarita namibiensis, still face the basic constraints all bacteria and archaea face; they simply found unique strategies around the problem. So what is the largest constraint when it comes to dealing with the size of bacteria and archaea? Think about what the cell must do to survive. Basic common cellular functions So what do cells have to do to survive? They need to transform energy into a usable form. This involves making ATP, maintaining an energized membrane, and maintaining NAD + /NADH 2 ratios. Cells also need to be able to synthesize the appropriate macromolecules (proteins, lipids, polysaccharides, etc.) and other cellular structural components. To do this, they need to be able to either make the monomers, or get them from the environment. Therefore, cells need a way to bring in nutrients from the environment, move compounds around inside the cell, and get rid of waste products that accumulate internally. So how do they do this? What is the mechanism by which these processes occur in bacteria and archaea? The answer is diusion. And using diusion to move compounds around leads to major constraints. Why? Diusion and its importance to bacteria and archaea Movement by diusion is passive and proceeds down the concentration gradient. For compounds to move from the outside to the inside of the cell, the compound must be able to cross the phospholipid bilayer. Then, as long as the concentration is lower inside, the compound will want to move into the cell. Nutrients that enter the cell tend to be broken down into useable pieces. As a result, the internal concentration of these nutrients is low. This is one of the mechanisms bacteria and archaea use to aid in the transport of metabolites; by keeping the internal pool of metabolites low, the desired compounds will continue to enter the cell by passive transport.

5 OpenStax-CNX module: m Diusion is also used to get rid of waste materials, such as CO 2. As waste products accumulate, their concentration rises compared to the outside environment and the waste product can leave the cell. Movement within the cell works the same way, compounds will move down their concentration gradient, away from where they are synthesized to places where their concentration is low and therefore may be needed. Remember that the process is random, blind to destination. The ability of two dierent compounds to interact, therefore, becomes a meeting of chance. In small conned spaces, random interactions or collisions can occur more frequently than in large spaces. The ability of a compound to diuse is dependent upon the viscosity of the solvent. For example, it is a lot easier for you to move around in air than in water (think about moving around underwater in a pool). If you put a drop of food coloring into a glass of water, it quickly diuses until the entire glass has changed color. Now what do you think would happen if you put that same drop of food coloring into a glass of corn syrup (very viscous and sticky)? It will take a lot longer for the glass of corn syrup to change color. As you will soon read, the cytoplasm is very viscous. It contains many proteins, metabolites, small molecules, etc. and has the viscosity more like corn syrup than water. So diusion in cells is slower and more limited than you might have expected. So, if cells rely on diusion to move compounds around, what do you think happens as the internal volume of the cell gets bigger? Do you see the problem? So how do cells get bigger? So for cells that rely on diusion, like bacteria and archaea, size does matter. Then how do you suppose Epulopiscium shelsoni and Thiomargarita namibiensis got so big? Take a look at these links and see what these bacteria look like morphologically and structurally. Epulopiscium shelsoni link 1 1 and Epulopiscium shelsoni link 2 2 and Thiomargarita namibiensis link 1 3. Based on what we have just discussed, in order for cells to get bigger, that is, for their volume to increase, intracellular transport must somehow become independent of diusion. One of the great evolutionary leaps was the ability of cells (eukaryotic cells) to transport compounds and material intracellularly independent of diusion. These mechanisms will be discussed in Modules 10.2 and Compartmentalization also provided a way to localize processes to smaller organelles, which overcame another problem caused by the large size. Compartmentalization and the complex intracellular transport systems have allowed eukaryotic cells to become very large in comparison to the diusion-limited bacterial and archael cells. Glossary Denition 3: capsule external structure that enables a prokaryote to attach to surfaces and protects it from dehydration Denition 3: conjugation process by which prokaryotes move DNA from one individual to another using a pilus Denition 3: Gram negative bacterium whose cell wall contains little peptidoglycan but has an outer membrane Denition 3: Gram positive bacterium that contains mainly peptidoglycan in its cell walls Denition 3: peptidoglycan material composed of polysaccharide chains cross-linked to unusual peptides Denition 3: pilus surface appendage of some prokaryotes used for attachment to surfaces including other prokaryotes

6 OpenStax-CNX module: m Denition 3: pseudopeptidoglycan component of archaea cell walls that is similar to peptidoglycan in morphology but contains dierent sugars Denition 3: S-layer surface-layer protein present on the outside of cell walls of archaea and bacteria Denition 3: teichoic acid polymer associated with the cell wall of Gram-positive bacteria Denition 3: transduction process by which a bacteriophage moves DNA from one prokaryote to another Denition 3: transformation process by which a prokaryote takes in DNA found in its environment that is shed by other prokaryotes

Connexions module: m Prokaryotic Cells. OpenStax College. Abstract. By the end of this section, you will be able to:

Connexions module: m Prokaryotic Cells. OpenStax College. Abstract. By the end of this section, you will be able to: Connexions module: m44406 1 Prokaryotic Cells OpenStax College This work is produced by The Connexions Project and licensed under the Creative Commons Attribution License 3.0 By the end of this section,