Structure and Function of Prokaryotes (Chapters 2 and 4)
This section provides a description of the prokaryotic cell beginning with general features of
size, shape, and cellular organization. The 16S rRNA tree of life shows evolutionary differences
between Bacteria, Archaea, and Eukarya, and the commonality between mitochondria,
chloroplasts, and Bacteria. The chemistry and function of prokaryotic membranes are covered
including differences between cell walls of gram-positive bacteria, gram-negative bacteria, and
archaea. The mechanism of the Gram staining reaction is explained. The chapter concludes with
a discussion of important structures unique to bacteria: flagella, inclusion bodies, slime layers,
After completing these lectures and reading materials, you should be able to describe:
1) Two basic structural differences between eukaryotes and prokaryotes
2) Why prokaryotes are so successful in every environmental niche, whereas eukaryotes are
3) How rRNA is used to distinguish evolutionary relationships between all life and why the
mitochondrian and chloroplast are more similar to bacteria than to the eukaryotic cells in
which they are housed
4) The various sizes, shapes, and cellular arrangements exhibited by bacteria, and basic
meaning of pleomorphic and morphogenesis.
5) The three primary functions and chemistry of the cytoplasmic membrane plus the
function of each compound in the membrane (fatty acids, glycerol phosphate groups,
6) The basic differences between bacterial and archaeal membranes
7) The three different types of active transport and how all of them differ from passive
8) The composition of Gram-positive, Gram-negative, and archaeal cell walls and how these
differences contribute to:
a. the differential reaction to the Gram-staining procedure
b. different responses to environmental stress
c. different responses to penicillin and lysozyme
9) The appearance, composition, and function of various inclusion bodies
10)The production of the Gram positive bacterial endospore and how it enables spore-
forming bacteria to survive harsh environmental conditions
11) The various modes of prokaryotic locomotion.
12)The 3 parts of the bacterial flagellum, how it works energetically, how it is assembled in
13)The various arrangements of bacterial flagella and how these arrangements control
movement of the cell in one direction
14) How nutrient and light gradients alter prokaryotic movement
1 CHAPTER OUTLINE
I. Significance of Prokaryotes to Life on Earth
A. Bacteria cause the majority of diseases; no known archaeal pathogens
• Cholera Vibrio cholera
• Tuberculosis Mycobacterium tuberculosis
• Plague Yersinia pestis
• Pneumonia Streptococcus pneumonia, Klebsiella pneumonia
• 80% of all food borne infections are caused by bacteria
• antibiotic therapy is primarily used to combat bacterial infections
Yet, the vast majority of bacteria on Earth are not pathogenic at all! We spend enormous
amounts of energy studying pathogens because they most directly affect our lives.
B. Prokaryotes (Bacteria and Archaea) have much greater metabolic diversity than eukaryotes.
Environmental cycling of nutrients: all oxidative and reductive processes in nitrogen, sulfur, and
some metal cycles are carried out only by prokaryotes
C. Biotechnology: Bacteria and their viruses provide DNA and vectors for recombinant DNA
D. The small subunit rRNA gene sequence is THE quantitative measure of evolution and
relatedness (note that the size of this molecule is 16S in Bacteria and Archaea and 18S in
Eukarya. S = Svedberg units determined by centrifugal force). Review the structure and
function of the ribosome in Chapter 3 if you do not remember the details. Bacteria and archaea
do not evolve from the same branch point on the phylogenetic tree based on 16S rRNA gene
sequences. Bacteria are more related to mitochondria and chloroplasts than to archaea on this
E. Prokaryotes are the chemists on Earth, whereas eukaryotes are either physicists (plants) or
biologists (predators). Therefore, the majority of energy, both solar and geothermal, is utilized
and transformed by prokaryotes on this planet. As a consequence, they control every aspect of
life on Earth including nutrient cycles, climate, and the human body. This is the main reason that
the search for life on other planets is focused on prokaryotes.
II. Prokaryotic Morphology
A. Size, shape, and cellular organization
1. Prokaryotic cellular organization: prokaryotes are morphologically distinct from
eukaryotic cells and have fewer internal structures. Only a few are bounded by internal
membranes: nuclear region in Planctomycetales, and forespore in Gram positive bacteria.
2. Cytoplasmic contents:
a. Ribosomes: complex structures consisting of protein and RNA that are
2 responsible for the synthesis of cellular proteins (translation)
b. Nucleoid: a dense, irregularly shaped region in which the normally circular,
singular, chromosome of the prokaryote is found. Some prokaryotes have linear and/or
multiple chromosomes. In actively growing bacteria, the nucleoid has projections that
extend into the cytoplasmic matrix; these projections probably contain DNA being
actively transcribed by RNA polymerases.
c. Plasmids: small, closed circular DNA molecules that exist and replicate
independently of the bacterial chromosome. They are not required for bacterial growth
and reproduction, but may carry genes that give the bacterium a selective advantage (e.g.,
drug resistance, enhanced metabolic activities, etc.)
2. Prokaryotic cells vary in size although they are generally smaller than most eukaryotic
cells, with two known exceptions: Epulopiscium fisheloni, which grows as large as 80 by 600
μm, a littler smaller than “-“; and Thiomargarita namibiensis, which is the largest known
prokaryote at 400 μm wide. The large surface to volume ratio of prokaryotic cells allows for
rapid nutrient acquisition and cellular growth relative to eukaryotes. There are at least two
reasons for this – less space to fill (not as many macromolecules to create and generally small
genome size to maintain) and greater access to nutrients which are acquired by a variety of
uptake mechanisms through the cellular membrane.
B 3. Prokaryotes come in a variety of shapes including spheres (cocci), rods (bacilli), ovals
(coccobacilli), curved rods (vibrios), rigid helices (spirilla), flexible helices (spirochetes),
filaments, and stalked (appendaged) or budded. Cocci are found alone, in clusters (staphylo),
pairs (diplo), chains (strepto), and tetrads (sarcina). The names of prokaryotes often come from
their morphology (e.g. Streptococcus, Staphylococcus, Methylosarcina, etc.)
4. Some bacteria lack a single, characteristic form, and are called pleiomorphic (as
opposed to monomorphic). They undergo morphogenesis (change in form) as the culture ages.
III. Prokaryotic Cell Membranes
A. General functions:
1. It retains the cytoplasm and separates the cell from its environment by serving as a
selective permeable barrier, allowing some molecules to pass into or out of the cell while
preventing passage of other molecules.
2. It contains proteins involved in transport (nutrient acquisition and waste removal) and
other substances that enable bacterial detection of and response to chemicals in the environment.
3. It is the location of a variety of crucial metabolic processes including respiration (e.g.
proton motive force) and photosynthesis
3 B. Structure (review macromolecules in Chapter 3 if unfamiliar to you)
1. The plasma membrane of most bacteria consists of a phospholipid bilayer with
hydrophilic surfaces (interact with water) on both surfaces and a hydrophobic interior (insoluble
2. The carboxylic acid group of fatty acids is linked through an ester bond in bacterial
cell membranes to form glycerol phosphate lipids.
3. Archaeal cell membranes are linked by ether bonds, which are more chemically stable
than ester bonds. These structures are important to many thermophilic (heat-loving organisms)
species of archaea. The hydrophobic region of Archaea lipids are linkages of isoprene units
instead of fatty acids found in Bacteria and Eukarya.
4. In some cases, ether linkages occur at both ends of the isoprenoid chain (biphytanyl).
This results in a lipid monolayer, which is even more stable than a lipid bilayer. Archaea have
both monolayer and bilayer membranes, while Bacteria have only the lipid bilayer.
5. Hopanoids are flat sterol-like compounds that impart greater rigidity to the
membrane. They are found in Bacteria (but not in Archaea) in contrast to sterol and cholesterol
found in Eukarya.
6. Proteins associated with the membrane may either be peripheral (loosely associated
and easily removed) or integral (embedded within the membrane and not easily removed).
7. Glycolipids, oligosaccharides, and integral proteins may also play a role as receptor
molecules to detect and respond to chemicals in their surrounding.
8. The membrane is highly organized, asymmetric, flexible, and dynamic
C. Transport functions
1. Passive diffusion (osmosis) does not require energy, is simple passage of a
molecule from an area of higher concentration to one of lower concentration. Membranes
are most permeable to water. Facilitated diffusion is also passive, but requires binding of the
molecule to a transport protein (e.g. permease). The protein undergoes a change in conformation
to let the molecule diffuse through the membrane.
2. Active transport requires energy to bring chemicals into the cell against its
concentration gradient; i.e. the molecule can move from an area of lower concentration (outside
the cell) to one of higher concentration (inside the cell).
Three types of active transport:
a. Simple transport. Energy is driven by the PMF (proton motive force) across the membrane.
There are three types. Uniporter moves a single substance from outside to inside. Antiporter
"exchanges" one substance with like properties for another (e.g. Na out and H in). Symporter
4 involves and anion and cation (e.g. H and HSO in a4 the same time).
b. Group translocation. e.g. the phosphotransferase system (PTS). Phosphoenol pyruvate
(PEP), an intermediate in glucose metabolism (from glycolysis), is hydrolyzed to pyruvate. The
resulting energy output and subsequent high-energy phosphate group are transferred through a
cascading series of enzymes and finally to glucose, which itself is phosphorylated and
transported into the cell. Further metabolism of glucose via glycolysis liberates more PEP,
which enables more glucose to be translocated. In group translocation, the energy for transport
is provided before the transport occurs (transfer of high-energy phosphate from PEP to carrier
c. ABC (ATP binding cassette) transporters. The periplasm is the space between the cell wall
and the cell membrane. Periplasmic binding proteins are highly specific and bind substrate at
low concentrations. They transfer the substrate to a protein transport channel, which is linked to
an ATPase on the inner side of the membrane. ATP is hydrolyzed following transport, so the
energy is provided after transport occurs.
IV. The Prokaryotic Cell Wall
A. The cell wall is a rigid structure that results in the characteristic shapes of the various
prokaryotes and protects them from osmotic lysis.
B. Peptidoglycan (sometimes referred to as Murein):
1. Gram-positive bacteria have cell walls that consist of a thick layer of a peptidoglycan
with very little space between the cell membrane and cell wall.
2. Gram-negative bacteria have a very thin layer of peptidogycan within a large
periplasmic space between the cell membrane and the outer membrane. The outer membrane
of Gram negative bacteria is so called as it has membrane lipid components.
3. Peptidoglycan is the physiological basis for the gram stain (discovered by Christian
Gram in 1884): The peptidoglycan acts as a barrier for crystal violet-iodine complex. The
peptidoglycan polymer dehydrates and shrinks when the