Prokaryotes and the Origins of Metabolic Diversity

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Prokaryotes and the Origins of Metabolic Diversity

• Chapter 27 AP Biology

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Classification

• Traditional 5 Kingdom system placed all
  prokaryotes in Kingdom Monera
• More recently, two major branches of prokaryotic
  evolution have been identified
• Archaea
• Eubacteria

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Evidence for New Bacterial Classification

• Ribosomal RNA
• Completely sequenced genomes

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What are the Archaea?

• Term Archaea refers to antiquity of groups
  origin from earliest cells
• Most species inhabit extreme environments
• Hot springs
• Salt ponds
• Few or no modern organisms can exist in such
  conditions
• Conditions resemble those of early Earth

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What are the Eubacteria?

• Most bacteria are in this group
• Differ from archaea in many key ways
• Structural
• Physiological
• Biochemical

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Reclassifying Bacteria

• Two groups diverged so early in history of life
  that classification has been revised
• 6 Kingdom system
• 2 bacterial 4 traditional
• 3 Domain system
• Domain is higher than Kingdom
• Domain Archaea, Bacteria and Eukarya

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Relationships of the 3 Domains to Each Other

• Eukarya and Archaea share a common ancestor that
  lived more recently than the ancestor common to
  archaea and bacteria
• Evidence from molecular systematics supports this
  hypothesis
• Bottom line even though archaebacteria and
  eubacteria are both prokaryotic, archaebacteria
  are more recently(and thus more closely) related
  to Domain Eukarya

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Characteristics of Prokaryotes

• VERY diverse group

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Characteristics of Prokaryotes - Morphology

• Most are unicellular
• Some do tend to aggregate into 2 to several
  celled groups or even colonies MAY even see a
  simple type of multicellularity with division of
  labor in some!

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Characteristics of Prokaryotes - Morphology

• Cell shapes
• Very important in identification
• Spheres (cocci)
• Rods (bacilli)
• Helices (spirilla and spirochetes)

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Characteristics of Prokaryotes - Morphology

• Size
• Most between 1-5 micrometers
• Compare to 10-100 micrometers for most eukaryotic
  cells

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Characteristics of Prokaryotes Cell Surface

• Cell walls external to plasma membrane
• Maintains cell shape
• Protects cell
• Prevents bursting in hypotonic environment
• However, like all cells, prokaryotes can
  plasmolize when placed in a hypertonic
  environment
• Hence, salt on meat keeps it fresh

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Characteristics of Prokaryotes Cell Surface

• Cell walls in plants and bacteria are ANALOGOUS
  rather than HOMOLOGOUS

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Characteristics of Prokaryotes Cell Surface

• Material of cell wall in bacteria is
  Peptidoglycan
• Polymers of sugars crosslinked w/ short
  polypeptides
• Polypeptides vary from species to species

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Characteristics of Prokaryotes Cell Surface

• GRAM STAIN
• Useful tool in identifying bacteria
• Gram negative vs. Gram positive bacteria
• Gram negative bacteria do not take gram stain
• Gram negative are more complex with an additional
  outer membrane
• Gram negative more threatening than gram positive
  
• Tend to be more resistant to antibiotics
• Outer membrane impedes entry of antibiotics into
  the cell

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Gram Stain
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Characteristics of Prokaryotes Cell Surface

• Capsule
• Sticky substance secreted outside cell wall
• Enable bacteria to adhere to substrate
• Provides more protection
• Allow bacteria to stick to each other as colonies

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Characteristics of Prokaryotes Cell Surface

• Pili
• Surface appendages
• Help bacteria stick to each other and substrates

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Characteristics of Prokaryotes Motility

• ½ of species capable of movement
• Remember at the size of bacteria, even water
  would seem very thickmucous linings of lungs,
  even more so.
• 3 main methods of movement

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Characteristics of Prokaryotes Motility

• Flagella
• May be scattered or concentrated
• Prokaryotic and eukaryotic flagella are ANALOGOUS
  not HOMOLOGOUS
• Prokaryotic flagella are 1/10 the width of
  eukaryotic flagella
• Prokaryotic flagella are not covered with plasma
  membrane
• Not based on the same structure as eukaryotic
  flagella
• 92 structure vs crank
• No microtubules in prokaryotic flagellum

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Bacterial Flagella
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Characteristics of Prokaryotes Motility

• Movement of spiral bacteria
• Filaments spiral around the cell under the outer
  sheath of the cell wall
• Filaments slide past each other
• Cell moves like a cork screw
• Very effective in highly viscous environments

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Characteristics of Prokaryotes Motility

• Secretion of slimy chemicals
• Gliding motion using flagellar motors that lack
  actual flagellar filaments.

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Characteristics of Prokaryotes Motility

• DIRECTION of motion
• In a uniform environment prokaryotes wander
  randomly
• In a non-uniform environment bacteria exhibit
  TAXIS
• Movement towards or away from a stimulus
• Chemical stimuli (food, oxygen, toxin) -
  Chemotaxis
• Light - phototaxis
• Many different receptor molecules on the cell
  surface can detect substances

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Characteristics of Prokaryotes -Internal Membrane
Organization

• Lack compartmentalization
• Do possess some specialized membranes that
  perform metabolic functions
• Invaginations of plasma membrane

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Characteristics of Prokaryotes -Genome

• Much less DNA than in eukaryote
• 1/1000
• No nucleus instead a nucleoid region
• Snarl of fibers that is the bacterial chromosome
• One circular DNA molecule in form of a ring
• Very little protein

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Characteristics of Prokaryotes -Genome

• Plasmids
• Smaller rings of DNA
• A few genes only
• All essential genes are in the main chromosome
  can live without plasmids
• Confer antibiotic resistance and some other
  special characteristics
• Replicate independent of main c-some
• Easily transferred between partners - conjugation

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Characteristics of Prokaryotes -Genome

• Replication and translation
• Basically similar to eukaryote
• Some differences
• Bacterial ribosome slightly smaller
• Bacterial ribosome differs in protein and RNA
  content

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Characteristics of Prokaryotes Growth,
Reproduction and Gene Exchange

• NO MITOSIS OR MEIOSIS
• ONLY ASEXUAL REPRODUCTION
• Binary fission
• DNA made almost continuously
• Single bacterium gt colony via repeated divisions
• NO growth in cell size growth only in numbers
• Conditions determine rate of growth

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Characteristics of Prokaryotes Growth,
Reproduction and Gene Exchange

• Endospores
• Resistant cells
• DNA of bacterium becomes encased in a durable
  wall
• DNA can survive almost anything
• Right Anthrax Endospore

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Characteristics of Prokaryotes Growth,
Reproduction and Gene Exchange

• Rates of growth
• Most bacteria have generation time of 1-3 hours
  (some can double 20 min)
• Bacterial growth in nature is usually limited by
  some nutrient or other factor

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Characteristics of Prokaryotes Growth,
Reproduction and Gene Exchange

• Genetic Recombination CAN occur in prokaryotes,
  but NOT by meiosis or syngamy (fertilization)
• Transformation genes taken up from the
  surrounding environment
• Conjugation genes are transferred directly from
  one prokaryote to another
• Transduction genes are transferred between
  prokaryotes by viruses

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Characteristics of Prokaryotes Growth,
Reproduction and Gene Exchange

• All methods of genetic recombination in
  prokaryotes are ONE WAY
• NOT MUTUAL contributions of TWO parents in sexual
  reproduction

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Characteristics of Prokaryotes Growth,
Reproduction and Gene Exchange

• MUTATION IS THE MAJOR SOURCE OF VARIATION IN
  PROKARYOTES
• Generation time is QUICK
• A favorable mutation can be RAPIDLY passed to a
  LARGE number of offspring
• Adaptation to environmental change is RAPID

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Nutrition and Metabolism

• All major types of nutrition and metabolism that
  exist evolved first in prokaryotes
• Nutrition how an organism the two things it
  needs in order to make its organic compounds
• Energy
• Carbon

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Nutrition and Metabolism

• Photoautotrophs
• Use light energy to make organic compounds from
  carbon dioxide
• Cyanobacteria
• No chloroplasts, but do have membranes with light
  harvesting pigments

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Nutrition and Metabolism

• Chemoautotrophs
• Need carbon dioxide as carbon source like
  photoautotrophs do
• DONT need light as energy source
• Instead of light, they obtain energy by oxidizing
  INORGANIC substances like
• Hydroten sulfide
• ammonia
• Unique to prokaryotes (often archaebacteria)

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Nutrition and Metabolism

• Photoheterotrophs
• Can use light to make ATP
• Need to get carbon in organic form
• Must consume glucose, for example.
• Again, unique to only certain prokaryotes

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Nutrition and Metabolism

• Chemoheterotrophs
• Must consume organic compounds for energy
• Must consume organic compounds for carbon source
• MOST prokaryotes are this
• SAPROBES decomposers that absorb nutrients from
  dead organic matter
• PARASITES absorb nutrients from body fluids of
  living host
• MUCH variety some can even break down petroleum

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Nutrition and Metabolism

• Chemoheterotrophs are important in the cycling of
  nitrogen through ecosystems
• NITROGEN FIXATION
• Conversion of inert atmospheric nitrogen into
  ammonia
• Makes atmospheric nitrogen available to organisms
  for incorporation into organic compounds
  (proteins, for example)

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Nutrition and Metabolism

• Bacteria and Oxygen
• Obligate aerobes
• use oxygen for cell respiration
• CANNOT grow without oxygen
• Facultative aerobes
• Will use oxygen if present, but can also grow by
  fermentation
• Obligate anaerobes
• Cannot use oxygen are are poisoned by it
• Probably first bacteria

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Evolution of the Different Modes of Nutrition and
Metabolism

• Early Earth environments were always changing
• WHY?
• New life forms CAUSED environment to change
• Life forms that evolved did so in response to
  changes brought on by predecessors.

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Evolution of the Different Modes of Nutrition and
Metabolism

• Origin of Glycolysis
• 1st prokaryotes chemoheterotrophs
• Absorbed organic compounds floating around
• ATP probably among those compounds
• Universal role of ATP as energy currency suggests
  that prokaryotes fixated on this early.
• As bacteria used up ATP, natural selection would
  favor those cells possessing enzymes that could
  regenerate ATP from ADP by using energy obtained
  from OTHER nutrients that were plentiful in the
  area.
• Thus, perhaps a step by step evolution of
  glycolysis
• Glycolysis is common to all modern organisms
  thus probably ancient.
• Also fits that glycolysis does not require oxygen
  which would not have been present in early Earth
  atmosphere.

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Evolution of the Different Modes of Nutrition and
Metabolism

• Electron Transport and Chemiosmosis
• Chemiosmosis is common to ALL 3 DOMAINS so it
  probably also arose fairly early.
• Original function of proton pumps was probably to
  deal with expulsion of hydrogen ions that
  resulted from wastes of fermentation process

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Evolution of the Different Modes of Nutrition and
Metabolism

• Origin of PHOTOSYNTHESIS
• What if fermenting prokaryotes used up nutrients
  faster than they were replaced?
• Any organism that could make its OWN organic
  compounds would have a BIG advantage.
• Earliest prokaryotes probably used pigments to
  absorb harmful UV rays
• Later, these pigments became tied to systems that
  drive ATP synthesis (like light reactions of
  photosyn.)
• Earliest photosynthetic prokaryotes probably like
  green sulfur bacteria and purple sulfur bacteria
  today.
• Split hydrogen sulfide instead of water to get
  electrons
• Produce NO oxygen.

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Evolution of the Different Modes of Nutrition and
Metabolism

• The Oxygen Revolution
• Eventually, some photosynthetic eubacteria had
  the metabolic machinery to use water instead of
  hydrogen sulfide
• CYANOBACTERIA (blue green algae)
• Changed the world by releasing oxygen as a waste
  product into the atmosphere.
• These are the same guys that built stromatolites
• Around 2.5 billion years ago
• Evidence of oxygen is rust in rocks.
• New oxygen rich atmosphere would have meant DEATH
  for many prokaryote species
• SOME of these still live in anaerobic
  environments
• others evolved antioxidant mechanisms so they
  would not be broken down by oxygen

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PHYLOGENETIC CLASSIFICATION OF PROKARYOTES

• Ribosomal RNA analysis
• Shows EARLY SPLIT between the two bacterial
  domains
• Archaebacteria appear to have at least as much in
  common with eukarya as with eubacteria (maybe
  more)

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DOMAIN ARCHAEA

• Inhabit extreme environments Extremophiles
• Methanogens
• Extreme Halophiles
• Extreme Thermophiles

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DOMAIN ARCHAEA

• Methanogens
• Hydrogen gas used to reduce CO2 to methane
• Anaerobic
• Swamps, marshes
• Decomposers for sewage treatment
• Inhabit gut of some animals (cattle)

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DOMAIN ARCHAEA

• Extreme Halophiles
• Live in saline places
• Great Salt Lake Dead Sea
• Some require salt, some just tolerate

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DOMAIN ARCHAEA

• Extreme Thermophiles
• Hot environments
• Hot sulfur springs in Yellowstone Natl Park
• Deep Sea Vents
• May be most closely related to Eukaryotes
• Get energy by oxydizing sulfur

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DOMAIN BACTERIA

• Most prokaryotes
• Proteobacteria
• Gram-positive bacteria
• Cyanobacteria
• Spirochetes
• Chlamydias

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Ecological Impact of Prokaryotes

• Chemical Cycles
• Decomposers
• Autotrophic prokaryotes fix carbon for use by
  other organisms
• Nitrogen fixing bacteria

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Ecological Impact of Prokaryotes

• Symbiotic Bacteria
• Legumes and nitrogen fixing bacteria
• Nodules
• Bacteria provide usable nitrogen
• Plants supply sugar and other nutrients
• Metabolic byproducts of E. coli benefit humans

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Ecological Impact of Prokaryotes

• Bacteria and Disease
• Usually cause illness by producing toxins
• Exotoxins secreted
• Endotoxins part of outer membrane
• salmonella
• Can become opportunistic if immune system is weak
  and just grow more.

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Ecological Impact of Prokaryotes

• Used in Industry
• E. coli white rat
• Decomposers of unwanted compounds
• Cultured to produce antibiotics
• Food industry
• Recombinant DNA technology
• Produce human insulin, growth hormone