Prokaryotes

Prokaryotes vs. Eukaryotes

Prokaryotes

• Derivation of name:
  • Pro: before
  • Karyo: nucleus
  • Prokaryote: an organism that existed before the nucleus evolved
• Includes all bacteria.
• Characteristics:
  • No nucleus
  • No organelles (“little organs”) of any kind
  • Primary genetic material: one large piece of circular DNA
  • Secondary genetic material: many additional very small pieces of circular DNA called plasmids
  • Have cell walls
    • Prokaryotic cell walls are different from those of plants!
    • The cell wall is in addition to a cell membrane, which all cells have.

Eukaryotes

• Derivation of name:
  • Eu: good, true
  • Karyo: nucleus
  • Eukaryote: an organism with a true nucleus
• All organisms other than bacteria
• Characteristics:
  • Have a nucleus.
  • Have organelles.
  • Primary genetic material: linear DNA (not circular)
  • No secondary genetic material
  • 1000 × as much DNA as prokaryotes

Size

• Eukaryotes are 10 to 100 × bigger in size than prokaryotes
• Compare the eukaryotic cells (labelled “cells”) in the image with the much smaller bacteria cells (labelled “bacteria”).

Unknown source

Evolutionary Relationship between Prokaryotes and Eukaryotes

• The three domains reflect evolutionary relationships.
• Prokaryotes evolved first:
  • Domain Bacteria
  • Domain Archaea
• Eukaryotes followed:
  • Domain Eukarya

Figure 27.1, page 503, Campbell's Biology 5th Edition

Prokaryotes and Their Outer “Container”

• Cell membrane (plasma membrane)
  • Exists as it does in all living things.
• Cell wall
  • Unique to prokaryotes (in this specific, peptidoglycan form)
  • Made from peptidoglycan: a mixture of polysaccharides (sugars) and polypeptides (proteins)
  • Can differ among bacteria: Gram negative and Gram positive.
  • Is attacked by antibiotics like penicillin.
• Capsule
  • An additional sticky coat
  • Adds protection.
  • Helps bacteria stick to surfaces.

Unnumbered figure, page 505, Campbell's Biology 5th Edition

Prokaryote Movement

• Some prokaryotes can move, using flagella.
• Half of all prokaryotic species have this capability.
• In deciding which way to go, they show taxis.
  • Movement towards or away from a stimulus
  • Can be “positive” or “negative.”
  • Chemotaxis: movement towards or away from a chemical stimuli
  • Phototaxis: movement towards or away from a light stimuli
  • Magnetotaxis: movement towards or away from a magnetic stimuli

Cellular and Genomic Organization of Prokaryotes

• What they don't have:
  • No extensive internal membrane structures (e.g. organelles)
  • Thus, they don't have internal “compartments” like eukaryotes do.
• How is DNA organized?
  • Found in a region called the nucleoid, which is not a separate compartment like the nucleus is in eukaryotes.
  • The main piece of DNA is circular and located in the nucleoid region.
  • Additional smaller circular pieces of DNA called plasmids exist independently of the main DNA.
    • Carry only a few genes each.
    • Often have genes for antibiotic resistance or other special functions.
    • Can be transferred between bacteria during “sexual” encounters.

Prokaryote Reproduction

• They reproduce asexually, by binary fission.
  • One bacterium becomes two bacteria.
  • They produce two identical copies in the process; they are clones.
• They never have “sex,” exactly, but instead mix up their genetic material in three ways:
  • Transformation: bacteria simply absorb, across their cell membrane and cell wall, DNA that is floating around in the environment.
  • Conjugation: bacteria directly transfer DNA from one bacterium to another through structures called pilli.
  • Transduction: DNA is transferred from one bacterium to another by a virus.

Nutrition Basics

• All organisms need two things to live:
  • Energy
    • To do work
  • Carbon
    • Provides the chemical structure of all living things.
    • Carbon is like the “bricks” in a brick building: without it you would have no structure!
• So what is nutrition?
  • It is how organisms obtain these two resources.
  • There are four different ways for organisms to get energy and carbon…

Four Modes of Nutrition

Autotrophs (self-feeders): don't need other organisms for carbon

• Photoautotrophs
  • Use light as an energy source.
  • Use CO₂ as a carbon source.
  • Examples:
    • All photosynthetic prokaryotes (e.g. cyanobacteria, the most famous)
    • Plants (eukaryotes)
• Chemoautotrophs
  • Use inorganic chemicals as an energy source (H₂S, Fe²⁺).
  • Use CO₂ as a carbon source.
  • Example:
    • Some archaea living in hydrothermal vents do this since they have no light deep down in the ocean.

Heterotrophs (other-feeders): need other organisms for carbon

• Photoheterotrophs
  • Use light as an energy source.
  • Use organic molecules as a carbon source.
  • These are rare.
• Chemoheterotrophs
  • Use organic molecules as an energy source (e.g. sugar).
  • Use organic molecules as a carbon source (e.g. proteins, sugars, fats, nucleic acids, etc.)
  • The most common form of nutrition on Earth: used in most prokaryotes, protists, fungi, and animals.

Summary of Nutritional Modes

• The two most common modes of nutrition:
  • Photoautotrophs: use sunlight for energy, CO₂ in the atmosphere as a carbon source.
  • Chemoheterotrophs: “eat” other organisms for energy and carbon.

Notes on Prokaryotic Chemoheterotrophs

• The most common nutritional mode in prokaryotes.
• The chemoheterotrophic lifestyle among prokaryotes includes two categories:
  • Saprobes (decomposers)
    • Get their nutrition (energy and carbon) from dead organisms.
    • Prokaryotes are the greatest biodegraders on the planet! If something is not biodegradable then bacteria generally can't break it down.
  • Parasites
    • Get their (energy and carbon) from living organisms.

Prokaryotes and the Nitrogen Problem

• The problem:
  • All living organisms need nitrogen, since it is found in proteins and nucleic acids.
  • The majority of the nitrogen on the planet is in the atmosphere (N₂) and is unusable by living organisms.
• The solution:
  • Some prokaryotes can convert unusable N₂ into a usable form like NH₃.
  • This is called nitrogen fixation.
• An example: the symbiotic relationship between prokaryotes and the group of plants called legumes (peas, beans, alfalfa, etc.).
  • Bacteria live in nodules on the legume roots and fix nitrogen, thus providing a benefit to the plant.
  • The plant, in turn provides sugar and other organic nutrients to the bacteria.
  • This is a specific kind of symbiotic relationship called mutualism.

Oxygen: One Bacteria's “Food” is another Bacteria's “Poison”

• For some organisms, oxygen is required for life: they are obligate aerobes (“obliged to use oxygen”)
  • Obligate is from “oblige”—to be bound or compelled.
  • Aerobe: air/oxygen
• For other organisms, oxygen will poison them: they are obligate anaerobes (“obliged to not use oxygen”)
  • An: no, not
  • Example from the domain Archaea: methanogens
    • Convert CO₂ to CH₄ (methane).
    • Found in the gastrointestinal tract of animals.
    • Found in swamps, marshes, and sewer treatment facilities.
• For yet other organisms, either condition is fine: they are facultative anaerobe (“not required to not use oxygen”)
  • Facultative: not required or compulsory; optional

Oxygen Revolution

• No oxygen existed on planet Earth after its creation (4.5 billion years ago).
• Life emerged around 3.8 billion years ago in an anaerobic environment.
• Therefore, the original prokaryotes were obligate anaerobes!
• Cyanobacteria evolve between 3.4 and 2.5 billion years ago.
  • Able to photosynthesize
  • Produce oxygen as a byproduct of photosynthesis.
  • Oxygen buildup oxidizes iron in the oceans forming iron oxide (i.e. “rust”).
    • Evidence: banded iron formations appear in marine sediments (ancient “rust”).
• Results of the oxygen revolution:
  • Once all the iron in the oceans and on land was oxidized…
    • Oxygen concentration increased in the oceans.
    • Oxygen concentration increased in the atmosphere.
  • As a result, obligate anaerobic bacteria become marginalized:
    • They have nowhere to run, and nowhere to hide.
    • Well, not exactly; they simply have to search for places without oxygen.
  • Obligate aerobic bacteria evolve.
  • Cyanobacteria is responsible for the creation of oxygen-rich atmosphere, although other organisms now help contribute.

From Princeton's Geo 206: History of the Earth course