BIOL 2320 J.L. Marshall, Ph.D.

HCC-Stafford Campus

Chapter 4- A Survey of Prokaryotic Cells and Microorganisms*

*Lecture notes are to be used as a study guide only and do not represent the comprehensive information you will need to know for
the exams.

4.1 Basic Characteristics of Cells and Life Forms

The basic unit of life is the cell. Both prokaryotic and eukaryotic cells are defined by a cell membrane. The
internal components are contained in the cytoplasm.

What is life?
The characteristics of life are: heredity, growth, development, metabolism, responsive to the environment,
and transport (figure 4.1).

4.2 Prokaryotic Profiles: The Bacteria and Archaea

Prokaryotic cells, Bacteria and Archaea, are the most ancient cells on Earth. Both are simple cells with basic
features common to all cells: cell membrane, cytoplasm, ribosomes, and one or two chromosomes.
Prokaryotic cells can have a cell wall, surface coatings, and appendages like flagella and pili.

The Structure of a Generalized Bacterial Cell

Typically, when the term prokaryotic cell is used, it is often referring to bacteria A “typical” bacteria cell is
shown in figure 4.2.

Cell Extensions and Surface Structures

Bacteria have appendages that extend from their outer surface. Some are used for motility and some are used
for attachment.

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Flagella – Bacterial Propellers

Flagella (singular = flagellum) in bacteria are hair-like, helical appendages, 10 - 20 m long and 0.02 m in
diameter, originate in the plasma membrane, and that are used for motility (swimming) (fig 4.2, fig. 4.3).
Bacteria that have flagella and can swim1 are motile; if they don’t have flagella and can’t swim are non-motile.
Flagella are composed of a protein called flagellin and are anchored in the plasma membrane & cell wall at a
structure called the basal body. They are much smaller than flagella or cilia in eukaryotic cells. Generally, ALL
spirilla, about half of the bacilli, and a small number of cocci have flagella.

Special staining techniques or electron microscopy (fig 4.4) allows one to see the arrangement of flagella.
These are used for taxonomic identification. Flagella vary both in number and arrangement according to two
general patterns: Polar, where the flagella are attached at one or both ends of the cell, and non-polar, where
flagella are distributed over the cell’s length.

Terms to describe flagella arrangement:

1. atrichous = without flagella

2. monotrichous = one flagellum located at a polar end (e.g. Pseudomonas aeruginosa)

3. lophotrichous = a cluster of flagella located at one end.

4. amphitrichous = single flagellum or cluster of flagella located at each polar end

5. peritrichous = flagella found laterally; non polar

6. periplasmic flagella or endoplasmic flagella are found in spirochetes. Their motion is rotating, similar
to a corkscrew. (fig. 4.7)

Movement can be coordinated to move in a particular direction. If nutrients are available in the environment,
the bacteria can move towards the nutrients or chemicals, for example (fig. 4.5, fig. 4.6):
taxis = movement.

chemo = chemicals; photo = light; aero = oxygen.

1Some bacteria can “swim” very fast. Thiospirillum moves at about 5.2 mm/minute – this is the equivalent of a 6 ft. tall human
swimming 1040 meters in 1 minute! Michael Phelps won the gold medal in 2008 for swimming 200 meters in 1 min 42 seconds. If he
could swim as fast as Thiospirillum, he would have only taken

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HCC-Stafford Campus

positive = towards; negative = away from.

So, movement toward a food source would be called positive chemotaxis; movement away from something
toxic, negative chemotaxis.

Bacteria movement is described as "run-and-tumble" since the flagella spin for a time (during which the
bacterium “runs”) and then stop for a time (during which the bacterium “tumbles” with the current).

Nonflagellar Appendages: Fimbriae and Pili

Fimbria are small (< 10nm), bristle-like fibers which sprout off the surface of bacterial cell walls (fig. 4.8).
Composed of protein and other macromolecules, they function in the bacteria’s ability to stick to surfaces and
to each other. “Velcro for bacteria”.

For some pathogens, their ability to infect and colonize host tissues is due to their tenacious attachment via
fimbria. For example: Neisseria gonorrhoeae (agent of gonorrhea) and E. coli. Mutant forms of these
pathogens that lack fimbria are unable to cause infection, i.e. they are avirulent.

Pili are hollow, non-helical, filamentous appendages made of the protein pilin. They tend to be thinner,
shorter and more numerous than flagella (fig. 4.2). They are 0.02 m in diameter and 0.2 - 20 m in length.
They are found in Gram negative bacteria (enterics and pseudomonads) and one Gram positive bacterium
(Corynebacterium renale). While pili can serve as a way for the bacteria to adhere to surfaces, they are
primarily used to transfer genetic material between two bacteria of the same species.

A sex pilus functions in the transfer of DNA from one cell to another (sexual recombination) in a process
termed conjugation. (Figure 4.9) This will be discussed in detail in chapter 9.

The Bacterial Surface Coating, or Glycocalyx

The most external physical layer that surrounds a bacteria cell is referred to as the glycocalyx (fig. 4.10; fig.
4.11). The glycocalyx varies in thickness and chemical composition from species to species.

When the glycocalyx is very thin and loose it is called a slime layer; it functions to prevent desiccation.

A capsule is a specialized type of glycocalyx that is much thicker that a slime layer. Most capsules are
composed of polysaccharides and/or polypeptides, i.e. the glycocalyx is like a sticky, sugary coat. Capsules are
best seen in negative stains (fig 4.11).
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Note: Not all bacteria produce a capsule; this is useful for differentiating between species.

Quellung test is a serological test for typing pneumococcal capsules (Streptococcus pneumoniae). A specific
antibody combines with a specific capsular polysaccharide on different bacteria strains.

Functions of the capsule:

1. They provide protection against desiccation (drying out) by binding water molecules to the capsule.
2. Self defense: capsules block the attachment of bacteriophages (virus which infect bacteria).
3. They may be antiphagocytic, i.e. the capsule prevents white blood cells from “eating” the bacteria.
Streptococcus pneumoniae causes bacterial pneumonia, but only if the organism is encapsulated. This
makes Streptococcus pneumoniae virulent (able to cause disease). Unencapsulated cells are avirulent
(cannot causes disease and are quickly engulfed and destroyed by the body's phagocytic2 white blood cells,
macrophages and neutrophils).
4. They promote attachment to surfaces (i.e., substrate). Streptococcus mutans is an organism found in the
mouth and known to cause dental caries (cavities). It attaches to the surface of the teeth, producing
plaque.
5. If capsules are composed of compounds having an electrical charge, they may promote the stability of a
bacterial suspension. They prevent cells from aggregating or settling out because the similarly charged
surfaces tend to repel one another.

Medical significance of biofilms:

Biofilms are layers of several species of bacteria adhering to living or non-living surfaces. The clinical
significance is great when you consider that by due to their capsules, some bacterial colonize plastic catheters,
intrauterine devices, and pacemakers (figure 4.12). Read: 4.1- Making Connections, Biofilms – The Glue of Life.

4.3 The Cell Envelope: The Boundary Layer of Bacteria, The Cell Wall

The cell wall is a rigid structure that gives shape to the cell and protects the cell membrane. All bacteria
except mycoplasmas have a cell wall. Mycoplasmas are the exception to the rule. (Fig. 4.16, shows
pleomorphic Mycoplasma.) The primary function of the cell wall is to prevent the cell from expanding and
eventually bursting because of the uptake of water. The tendency is for bacteria to absorb water by osmosis
and to try to establish an equilibrium. This is because bacteria exist in a dilute environment (hypotonic
solutions) while the cytoplasm contains a concentrated solution of inorganic salts, sugars and amino acids.

2 phagocytosis – process by which one cell engulfs and “ingests” another.

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Basic Types of Cell Envelopes

Within the eubacteria, there are two principle types of cell walls which can be differentiated by the Gram
stain3 (after Hans Christian Gram, the Danish physician who discovered it in 1884).

The terms “Gram positive” and “Gram negative” refer to the type of cell wall the bacteria have and what color
the bacteria stain when using the technique of Gram staining.

Gram positive bacteria stain purple

Gram negative bacteria stain red-pink

Almost all bacteria can be classified as either Gram positive or Gram negative. The staining is the result of the
specific architecture of their cell walls. *Fig. 4.15, compares Gram positive to Gram negative cells. Also see:
Fig. 4.13 and Table 4.1.

Structure of Cell Walls

Eubacteria have a cell wall composed of a polysaccharide made of two alternating sugars: N-
acetylglucosamine and N-acetylmuramic acid joined together by short peptides. The three-dimensional
framework formed by these molecules is called peptidoglycan (fig. 4.14).

The Gram Positive Cell Wall

The cells walls of Gram positive cells are 20 to 80 nm thick and are composed of dense layers of peptidoglycan
(fig. 4.15 & fig. 4.13a). Common to their composition are the acidic polysaccharides teichoic acid and
lipoteichoic acid. Also, there is only a thin periplasmic space between the cell wall and the cell’s plasma
membrane.

The Gram Negative Cell Wall

The cell wall of Gram negative bacteria contain a thin layer of peptidoglycan, about 8-11 nm thick (fig. 4.15, &
fig. 4.13b). The hallmark of a G- cell is there presence of an outer membrane (7 nm thick) surrounding the
peptidoglycan layer. It consists of lipoprotein, lipopolysaccharide (LPS), and phospholipid, making it similar
to the cell membrane.

3In order to see bacteria on a microscope slide, they must first be stained using dyes. There are dozens of different techniques and
dyes available that help in identifying different species of bacteria.
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Imbedded within the outer membrane are porin proteins which serve as channels for molecules to diffuse
through. Also, between the peptidoglycan and the inner cell membrane, there is a well developed periplasmic
space. The lipopolysaccharide has toxic properties. Referred to as endotoxin, LPS is responsible for
endotoxic shock, the result of a run-away immune response that can be fatal.

Nontypical Cell Walls

Mycobacterium and Corynebacterium have examples of non-typical cell walls which contain very-long-chain
fatty acids called mycolic acids; these contribute to their pathogenicity. Although these bacteria are G+, the
acid-fast stain is better suited for their study.

Mycoplasmas and Other Cell-Wall-Deficient Bacteria

Mycoplasmas naturally lack a cell wall, but they have sterols to maintain the cell structure. They vary in shape,
so they are typically described as pleomorphic. One of the most significant members of this genus is M.
pneumoniae, which can cause atypical pneumonia.

L-forms had a cell wall, but lost it due to mutation or continuous exposure to antibiotics.

Cell Membrane Structure

Cell membrane = plasma membrane = cytoplasmic membrane: is a thin (5-10 nm), pliable, lipid and protein
covering that defines a cell and controls the movement of molecules in and out of the cell (fig. 4.17).

Chemical analysis of the cytoplasmic membrane shows it to be 60-70% protein and 20-30% lipid, primarily
phospholipids. The membrane is composed of 2 layers of phospholipids arranged in a bilayer. Embedded
within the phospholipid bilayer are integral membrane proteins (some serving as channels; others as
receptors); proteins closely associated with the bilayer, but not embedded, are termed peripheral proteins.

Functions of cell membrane:

1. The membrane is semipermeable, selectively permeable, or differentially permeable. Permeable means

that molecules can cross the membrane. Impermeable means that they cannot cross the membrane.
Except for water and some lipid-soluble molecules (e.g. alcohol), few compounds can pass through the cell
membrane by simple or passive diffusion.
2. The cell membrane is involved in secretion, releasing molecules to the external environment.
3. In bacteria the cell membrane is involved metabolic activities.
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4.4 Bacterial Internal Structure

Contents of the Cell Cytoplasm

The gelatinous solution internal to the cell’s plasma membrane is referred to as the cytoplasm and is
approximately 70-80% water; within which is a complex solution of proteins, lipids, nucleic acid, salts, sugars,
amino acids, and other small molecules. Everything else that constitutes the living cell is also found within the
cytoplasm:

Intracellular Structures

Bacterial Chromosomes and Plasmids: The Sources of Genetic Information

The chromosome consists of a single, or double, circular molecule of DNA containing ~4000 genes. The
chromosome in the bacterial cell aggregated in a structure called a nucleoid. It is folded into a tight mass
viewable only with an electron microscope (fig. 4.18). Many bacteria also carry additional genetic information
contained on a plasmid. Plasmids replicate separately from the chromosome, and often contain genes that are
beneficial to the bacterium. Plasmids have been used extensively in genetic engineering.

There is no nuclear membrane surrounding the chromosomes of prokaryotic cells similar to the one found in
eukaryotic cells.

Ribosomes: Sites of Protein Synthesis

Ribosomes: A protein – RNA structure where protein synthesis is carried out. (Figure 4.19). The mRNA will
dock to the complete structure of the ribosome, in bacteria the size is 70S, and the genetic information in the
mRNA is converted to protein (a string of amino acids).

Inclusion bodies, deposits; granules Inclusion bodies, deposits; granules

These structures form from reserve nutrients which bacteria store up during periods of nutrient abundance.
Since bacteria have no adipose tissue or other cellular structures, these substances exist as dense, almost
crystalline deposits in the cytoplasm.

Examples:

• volutin granules = metachromatic granules, composed of polyphosphate.

• poly --hydroxybuterate (PHB) granules are found in aerobic bacteria under high carbon, low nitrogen
conditions (fig. 4.20).

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The Bacterial Cytoskeleton

Cytoskeleton has been identified in certain bacteria. Many rod shaped and spiral shaped bacteria have
cytoskeleton. One cytoskeletal protein that has been identified is actin (Fig. 4.21)

What Exactly Is A Spore?

Bacterial Endospores: An Extremely Resistant Life Form

Certain species of bacteria produce spores. The spore is a metabolically dormant form which can undergo
germination and form a new vegetative cell under the proper conditions. The spore is formed within the
vegetative cell when the cell is growing under less than optimal nutritional or environmental conditions.
Endospores form within the vegetative cells of Gram+ Bacillus (fig. 4.22), Clostridium, and Sporosarcina.

Endospore Formation and Resistance

Sporogenesis is the name given to the process of spore production (fig. 4.22). Spores are highly resistant to
desiccation, staining, disinfection, chemical and radiation exposure, heating, and freezing. Spores can be
virtually immortal - for example, viable spores have been isolated from a 250 million year old salt crystal.

Medically relevant examples of spore forming bacteria include:

Bacillus anthracis – the agent of anthrax

Clostridium botulinum, C. tetani, and C. perfringens – the agents of botulism, tetanus,

and gas gangrene, respectively

The Germination of Endospores

Spores can go through germination when they encounter favorable environments. It fully reverts to a vegetative cell.

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4.5 Bacterial Shapes, Arrangements, and Sizes

Bacterial morphology = shape and size of bacteria.

1. Shape
The shape of a bacterium is determined by its rigid cell wall.

Basic shapes characteristic to bacteria (fig. 4.23; fig. 4.24):

1. spherical = coccus (pl. cocci)

2. rod = bacillus (pl. bacilli)

3. curved rods = vibrio (pl. vibrios)

4. spiral rods = spirillum (pl. spirilla).

(rigid helix shape; most are harmless saprobes)

helical rods = spirochete (pl. spirochetes)

(flexible helix, motile; some of the most dangerous - e.g. syphilis)

See also Table 4.2.

5. pleomorphic rods are those that show individual variation in shape. Examples: Mycoplasma
pneumoniae (fig. 4.24).

2. Arrangement

Bacteria divide by binary fission. One cell makes a copy of its DNA, then a new cell wall and cell membrane
form and two new cells are formed. While some bacteria cells separate after fission, some do not; they
continue to adhere to one another, leading to group arrangements (fig. 4.25):

1. pairs (diplo-), such as diplococcus or diplobacillus.

2. chains (strepto-), such as streptococcus or streptobacillus.

3. clusters: tetrad (4)

4. grape-like clusters (staphylo-), such as staphylococcus .

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5. palisade arrangement - the cells are lined side-by-side like matchsticks or a picket fence and
occasionally occur at angles to one another. (e.g. Corynebacterium diphtheriae, Fig. 4.24).

3. Size
Bacteria exhibit a wide range of sizes.

Shape/Type of Bacteria Range of Diameter Range of length

cocci 0.5 to 3.0 μm
bacilli 0.2 to 2.0 μm 0.5 to 20 μm
vibrio and spirilla 0.2 to 2.0 μm 0.5 to 100 μm
spirochetes 0.1 to 3.0 μm 0.5 to 250 μm
Note: these are only ranges; different species (and strains within a species) might vary considerably.

4.6 Classification Systems of Prokaryotic Domains: Archaea and Bacteria

Classification systems are useful in identifying unknown organisms and organizing them based on evolutionary
relationships. There are a wide variety of different testing methods used to identify and classify bacteria, in
particular.

Bacterial Taxonomy: A Work in Progress

One method that has been used to classify bacteria is Bergey’s Manual od Systematic Bacteriology, which is
based on a phenotypic, or phrenetic, method of classification. Phylogenetic (evolutionary) relationships are
also crucial in classification. See table 4.3.

A Diagnostic Scheme for Medical Use

Table 4.4 is representative of how medicine organizes infectious bacteria. Criteria used in medicine is oxygen
usage, Gram stain results, and biochemical tests.

Species and Subspecies in Bacteria

Bacteria species are organized using different criteria than used for animals. Bacteria are defined into a
species based on their rRNA. Microbes can be further divided into strains and types.

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4.7 Survey of Prokaryotic Groups with Unusual Characteristics

A survey of medically important and ecologically important groups.

Free-Living Nonpathogenic Bacteria

Photosynthetic Bacteria

Bacteria that are dependent on sunlight.

Cyanobacteria: Microbial Marvels

Cyanobacteria are among the most dominant microbes on Earth. They are Gram-negative photosynthetic
bacteria. They produce oxygen as a result of their photosynthesis. Cyanobacteria share evolutionary
relationships with chloroplasts. Cyanobacteria also play an important role in the nitrogen cycle (figure 4.28).

Green and Purple Sulfur Bacteria

They are photosynthetic, having bacteriochlorophyll, and not giving off oxygen as a result of their
photosynthesis. They live in sulfur springs, lakes and swamps (figure 4.29).

Gliding, Fruiting Bacteria

They are gram-negative and live in water and soil. They can glide over moist surfaces. One of the most studied
and complex gliding bacteria is Myxococcus (figure 4.30).

Unusual Forms of Medically Significant Bacteria

Chlamydias and rickettsias are unusual in that these are bacteria that live inside host cells. They are referred
to as obligate intracellular parasites.

Rickettsias

They are very tiny Gram-negative bacteria. They alternate between hosts, insects and humans. They causes
diseases like Rocky Mountain Spotted Fever (figure 4.31).

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Chlamydias

Chlamydia trachomatis is a sexually transmitted disease that can also cause blindness.

Archaea: The Other Prokaryotes*

*We will not go through this section, but it is still a good source of information about this group. Refer to table
4.5 to see an overview of the three (3) major Domains.

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