Chapter 27 – Prokaryotes and the Origins of Metabolic Diversity
Lecture Notes
The World of Prokaryotes:
I. The biomass of prokaryotes outweighs eukaryotes by 10 fold!
a. Prokaryotes are found wherever there is life, and also in habitats where it is too hot, cold, acidic, salty
for eukaryotes to live (ex. Hot springs, salt marshes)
II. Most prokaryotes are beneficial or benign – only some are harmful:
a. Harmful – bubonic plague (Black Death), tuberculosis, cholera, STD’s
b. Helpful – bacteria in our intestines that provide vitamins, bacteria in our mouth that prevent harmful
fungi from growing, decomposers, bacteria that keep the Carbon cycle going
i. One of the most important roles of bacteria is to act as decomposers…if we did not have these,
eukaryotic life would cease
III. Many prokaryotes live in symbiotic relationships with other organisms
IV. We know 5,000 species of prokaryotes but scientists estimate that there are 400,000 – 4 million species on
Earth
V. They are divided into two main groups:
a. Archaea earliest cells; inhabit extreme environments
b. Bacteria  differ from Archea in structural, biochemical, and physiological ways
VI. In the 5 kingdom system, prokaryotes were in the Kingdom Monera, but in the new 3 Domain system,
prokaryotes take up 2 of the domains (Bacteria and Archaea)
The Structure, Function, and Reproduction of Prokaryotes:
I.
Most prokaryotes are unicellular, but some do live in pairs or colonies
a. Cell shape – a very common way to classify them; 3 main shapes:
i. Cocci – spheres
ii. Bacilli – rods
iii. Spirilla/Spirochetes – spherical
II.
Nearly all prokaryotes have a cell wall  this helps in hypoosmotic environments (no bursting!)…but
it cannot help in hyperosmotic environments (drying out!)
a. Function: maintains shape; physical protection; prevents cells from bursting in hypotonic environments
b. Made up of peptidoglycan; VERY different from eukaryotic cell walls (different biochemistry)
c. Gram Stain  can identify/classify bacteria
i. Gram positive = simpler cell wall; more peptidoglycan; usually less harmful
ii. Gram negative = more complex cell wall; less peptidoglycan but contains lipopolysaccharides
– which can be toxic; usually more harmful (b/c of toxins and can also be resistant to
antibiotics- penicillin doesn’t always work against them)
d. Capsule  sticky layer outside the cell wall that helps them attach to stuff; also helps resist the host
cells defenses
e. Pili  structures on the outside of the cell that also help with attachment
III.
Many prokaryotes are motile (can move)
a. Common mechanisms:
i. Flagella – different in structure than eukaryote flagella, may have one or many; this propels
bacteria!
ii. Spirochetes – use rotating filaments and these organisms move like a corkscrew
iii. Filamentous chains with slimy threads – glide along these slimy chains
b. About half move randomly, and about half are capable of directional movement (move with a purpose)
i. Taxis  move toward or away from a stimulus
1. Ex. Chemotaxis – move toward food/oxygen or away from toxic substances
IV.
Cellular and Genomic organization of Prokaryotes is different from that of eukaryotes
a. Prokaryotes:
i. Lack a true nucleus and do not have much compartmentalization
ii. Have smaller/simpler genomes
1. 1/1000th the amount of eukaryotes
2. One circular chromosome
a. Found in nucleoid region, double stranded DNA
b. Sometimes called a genophore
3. May also have plasmids (these carry only a few genes)
a. Can carry genes for resistance, metabolism of unusual nutrients
b. These replicate independently of the chromosome and may be shared from one
prokaryote to the next (during conjugation)
iii. Prokaryote ribosomes are smaller than eukaryotes and differ in content
V.
Prokaryotes grow and adapt rapidly
a. Binary fission = asexual reproduction (they do NOT have mitosis or meiosis!)
b. Ways to transfer genes – “sexual” reproduction
i. Transformation – uptake of foreign genes from environment
ii. Conjugation – direct transfer of genes from one prokaryote to another (sex pili)
iii. Transduction – viruses transfer genes between prokaryotes
c. Most common source of genetic variation in prokaryotes = MUTATION
i. VERY short generation times, so mutations that are favorable to the prokaryotes are passed on
very quickly
1. Generation times typically 1-3 hours, but can be as short as 20 minutes
2. Because they replicate so quickly, growth is stopped usually because they run out of
nutrients or colonies poisons themselves with toxins from accumulating metabolic
wastes
d. Endospores  structures that bacteria can form to withstand harsh conditions
i. Can remain dormant for centuries or more
ii. Even boiling water cannot kill endospores – typically have to use an autoclave (pressure
cooker) to kill the endospores; this is an issue when canning fruits or vegetables
iii. If they are placed in a more hospitable environment, they will rehydrate and become active
(divide) again
e. Many microorganisms release antibiotics which are chemicals that inhibit the growth of other
organisms
i. They do this because they are competing for space and nutrients
ii. Humans have found some of these and now use them against pathogenic bacteria
Nutritional and Metabolic Diversity:
I.
Prokaryotes can be grouped into 4 groups based on nutrition
a. Nutrition refers to how an organism gets two things from the environment: ENERGY and a CARBON
SOURCE
b. Table 27.1  KNOW the 4 major groups
Table 27.1 Major Nutritional Modes
Mode of Nutrition
Energy Source
Carbon Source
Types of Organisms
AUTOTROPHS:
Light
CO2
Cyanobacteria,
Photoautotrophs
plants, certain protists
(algae)
Inorganic Chemicals
CO2
Certain prokaryotes
Chemoautotrophs
HETEROTROPHS
Light
Organic Compounds
Certain prokaryotes
Photoheterotrophs
Organic Compounds
Organic Compounds
Most prokaryotes and
Chemoheterotrophs
protists; fungi;
animals; some
parasitic plants
***Photoheterotrophs = use light energy to make ATP but don’t release oxygen
II.
Nutritional Diversity Among Chemoheterotrophs
a. Most prokaryotes are chemoheterotrophs; this includes:
i. Saprobes  decomposers that feed on dead organic matter
ii. Parasites  absorb nutrients from live hosts
b. There is such diversity in chemoheterotrophs that almost any organic molecule can serve as food for at
least some species
i. Ex. Petroleum = some bacteria can metabolize this and are used to clean up oil spills
III.
Nitrogen Metabolism
a. Nitrogen metabolism is another area of nutritional diversity in prokaryotes
b. Nitrogen is an essential component in proteins and nucleic acids
c. Prokaryotes are the only ones that perform key steps in the nitrogen cycle:
i. Some convert ammonia to nitrite
ii. Others convert nitrite or nitrate into nitrogen gas
iii. Others can use nitrogen gas directly as their source of nitrogen
1. Nitrogen Fixation  process of converting nitrogen gas into ammonia
a. The nitrogen fixing bacteria are currently the MOST IMPORTANT
ecologically
IV.
Metabolic Relationships to Oxygen
a. Obligate aerobes  need oxygen and cannot grow without it
b. Facultative anaerobes  will use oxygen if it is present, but can also do fermentation without it
c. Obligate anaerobes  poisoned by oxygen
V.
Photosynthesis evolved early in Prokaryotic life
a. Because the environment of the early Earth was changing so rapidly, nutritional modes and metabolic
processes changed very rapidly
b. Because energy metabolism of even the simplest photoautotrophs is relatively complex, it seems
reasonable to assume that the FIRST prokaryotes were heterotrophs and lived off the “primordial soup”
i. Glycolysis evolved early = this is evidenced by the fact that glycolysis is present in almost
every group of modern organisms
ii. As organisms began using up the earth’s resources, natural selection would have selected for
organisms that could harness light to make their own molecules… photosynthesis
c. Other evidence of Photosynthesis evolving early:
i. Photosynthetic groups are scattered among most branches of prokaryotic phylogeny = common
ancestor
ii. Age of cyanobacteria = these release oxygen and based on the geologic evidence for
accumulation of oxygen beginning 2.7 billion years ago, this suggests these organisms were
already prevalent (and they do photosynthesis)
d. Some modern prokaryotes have simpler modes of photosynthesis with only one photosystem; one
theory is that cyanobacteria first evolved with these simpler structures
e. Cyanobacteria changed the Earth in a major way  changed it from a reducing atmosphere to an
oxidizing one = they caused the “Oxygen Revolution”
i. Most obvious adaptation due to this changing environment was the evolution of cellular
respiration
IMPORTANT TO KNOW:
**Most Important TYPE of Prokaryote: NITROGEN FIXERS
**Most Important Ecological ROLE of Prokaryotes: DECOMPOSERS
**Prokaryotes have glycolysis enzymes, genes, cell walls, photosystems I and II  all of these things came
before eukaryotic cells!!
A Survey of Prokaryotic Diversity:
I.
It was hard to classify prokaryotes before molecular systematics (DNA) because they are so small
a. Before DNA, they were classified based on nutritional mode and gram positive vs. gram negative
II.
Researchers started to examine the SSU-rRNA (rRNA from the small subunit of ribosomes because even
the earliest prokaryotes have ribosomes), they were able to classify the prokaryotes based on similarities or
differences in the nucleic acid sequences
III.
Researchers are identifying a great diversity of Archaea in extreme environments in the ocean
a. SEE TABLE 27.2
i. This shows that Archaea have just as much in common with eukaryotes as they do with bacteria
b. Many Archaea live in extreme environments:
i. Methanogens  produce methane as a waste; are poisoned by oxygen (anaerobic); live in
swamps and marshes and in our digestive systems; important decomposers in sewage treatment
1. On a global scale, methanogens produce enough methane to play a major role in the
greenhouse effect
ii. Extreme halophiles  salt-lovers; live in places like the Great Salt Lake and the Dead Sea
iii. Extreme thermophiles  thrive in hot environments; 60°-80° C
c. Two major groups of Archaea: (SEE FIGURE 27.13)
i. Euryarchaeota
ii. Crenarchaeota
**Prokaryotes are put into these two groups based on the differences in a SSU-rRNA
IV.
Most known prokaryotes are bacteria
a. Every major mode of nutrition and metabolism is represented
b. Bacteria are divided into 5 main groups:
i. Proteobacteria  large and diverse group of bacteria (has 5 sub-groups); gram-negative
ii. Chlamydias  parasites; walls lack peptidoglycan; one species is the most common cause of
blindness, another causes the most common STD in the US
iii. Spirochetes  helical; move in a corkscrew-like motion; some are free-living but some are
pathogens; can cause syphilis and Lyme disease
iv. Gram-Positive Bacteria  includes all the gram positive bacteria and also some of the closely
related gram negative species; the diversity of this group rivals the Proteobacteria group; can
cause tuberculosis, leprosy, botulism, “walking pneumonia”, but is also important in breaking
down organic substances in soil
v. Cyanobacteria  photoautotrophs; only bacteria with plant-like, oxygenic photosynthesis; can
be solitary or colonial; abundant wherever there is water – so they are an important food source;
some species can do nitrogen fixing
The Ecological Impact of Prokaryotes:
I.
Main Role of prokaryotes: decomposing organic matter
II.
Prokaryotes are indispensable links in the recycling of chemical elements in ecosystems
a. Life depends on the recycling of chemical elements
i. Decomposers recycle carbon and nitrogen…if we did not have decomposers, these elements
would get locked in dead organisms and waste products
ii. Autotrophic prokaryotes make organic compounds from carbon dioxide which helps food
chains
iii. Prokaryotes are the only organisms to metabolize inorganic molecules elements like iron, sulfur,
nitrogen and hydrogen
1. Cyanobacteria do nitrogen fixation which stocks the soil and water with nitrogenous
compounds that other organisms can use to make proteins
b. ALL LIFE ON EARTH DEPENDS ON PROKARYOTES AND THEIR METABOLIC
DIVERSITY  they represent every mode of nutrition/metabolism (even oil!)
III.
Many prokaryotes are symbiotic
a. Prokaryotes usually interact in groups (although some are singular)
b. Symbiosis  ecological relationships between organisms that are in direct contact
c. Many use hosts
d. Three major categories:
i. Mutualism  both the prokaryote and host benefit
ii. Commensalism  prokaryote benefit with no effect on the host
iii. Parasitism parasite benefits at the host’s expense
IV.
Pathogenic prokaryotes cause many human diseases
a. Pathogenic bacteria cause about half of all human disease
b. Opportunistic Bacteria  bacteria that is always present, but waits until the immune system of the
host is low and then causes disease
i. Ex. The bacteria that causes pneumonia is usually present in the throats of healthy people but
actually causes the disease when the hosts defenses are down
c. Robert Koch  German physician; identified the bacteria responsible for anthrax and tuberculosis
i. Koch’s Postulates = a set of 4 criteria for determining whether a specific pathogen is the cause
of a disease
d. How do pathogenic prokaryotes produce the symptoms of disease?
i. Disrupt the health of the host by invading tissues
ii. More common = produce toxins that can cause illness
1. Exotoxins = proteins secreted by prokaryotes
2. Endotoxins = components of outer-membranes of certain gram-negative bacteria
e. Since the discovery of “germs” in the 19th century, improved sanitation has significantly reduced infant
mortality and extended life expectancy; antibiotics have also helped
f. More than half of our antibiotics come from soil bacteria (which the bacteria produce to try to fight off
encroachment from other microbes)
g. Antibiotic-resistant strains of pathogenic bacteria are serious health threats today and are made worse
by the widespread and overuse of excessive antibiotics
V.
Humans use prokaryotes in research and technology
a. E.coli is the “white rat” of research labs and is the best understood of all organisms
b. Bioremediation  use of organisms to remove pollutants from water, air, and soil
i. Treats sewage and cleans up oil spills
c. Humans also use prokaryotes as metabolic “factories”:
i. Chemical industry = makes acetone, butanol, and more
ii. Pharmaceutical companies = vitamins and antibiotics
iii. Food industry = makes cheese
Other Important things to Note:
- Prokaryotes have survived for billions of years longer than humans
- If all bacteria on Earth disappeared, recycling of nutrients would decrease drastically!