Prokaryotes Notes

Prokaryotes

• Include two domains: bacteria and archaea.
• Fully functioning cells.
• "Before a nucleus."
• Microscopic, ranging in size from $1$ to $10 \mu m$ in length and $0.7$ to $1.5 \mu m$ in width.
• Abundant in air, water, soil, and on most objects.
• Louis Pasteur showed that sterilized broth remains clear unless exposed to air.

Structure of Prokaryotes

• Lack a membrane-bounded nucleus; DNA is located in the nucleoid region.
• Have an outer cell wall.
• Some move via flagella.
• Lack membranous organelles.
• May possess accessory rings of DNA called plasmids.

Prokaryote Structure

• Key structures and their locations are essential to know.

Features of Prokaryotic Cells

• Key structures and their locations are essential to know.

Summary: Prokaryotes

1. Prokaryotes are classified into two domains: Bacteria and Archaea.
2. Prokaryotic cells are much smaller than eukaryotic cells.
3. Prokaryotes lack membrane-bound organelles.
4. DNA is located in a nucleoid region, and they sometimes have DNA arranged in circular plasmids.
5. Prokaryotic cells have three structures associated with their cell envelopes: cell membrane, cell wall, and glycocalyx.
6. Motile prokaryotes may move using a flagellum.

Characteristics Enabling Prokaryotes to Thrive

• Small size and rapid reproduction facilitate thriving in diverse environments.
• High genetic diversity through mutations.
• Rapid evolution of diverse adaptations.

Diverse Adaptations in Prokaryotes

• Most are unicellular, but some form colonies.
• Variety of cell shapes: spheres (cocci), rods (bacilli), and spirals.

Cell-Surface Structures

• Cell walls protect and maintain cell shape, preventing bursting.
• Bacterial cell walls contain peptidoglycan (modified sugars and polypeptides).
• Archaeal cell walls contain polysaccharides and proteins but lack peptidoglycan.
• Many have a sticky, protective outer layer called a capsule for adherence.

Bacterial Cell Walls

• Bacteria are categorized by cell wall composition via Gram stain response.
• Gram-positive bacteria have simpler walls with a thick peptidoglycan layer.
• Gram-negative bacteria have less peptidoglycan and an outer membrane with lipopolysaccharides.
• Lipopolysaccharides can be toxic (e.g., E. coli).

Cell-Surface Structures

• About half exhibit taxis, movement toward or away from a stimulus.
• Chemotaxis involves movement toward or away from a chemical stimulus.
• Some species can move up to $50x$ their body length per second
• Fimbriae are hairlike appendages for sticking to substrates or each other.
• Pili (sex pili) are longer appendages used for DNA transfer.

Cell-Surface Structures

• Some bacteria develop resistant cells called endospores when water or nutrients are lacking.
• Endospores are dormant and can survive extreme conditions for centuries.
• Examples: Clostridium botulinum (botulism), Clostridium tetani (tetanus), Bacillus anthracis (anthrax).

Motility

• Flagella are common motility structures that evolved independently in the three domains of life.
• Prokaryote and eukaryote flagella differ in structure, composition, and function.
• Bacterial and archaeal flagella are structurally similar but composed of unrelated proteins.
• Bacterial flagella consist of a motor, hook, and filament, with 42 different proteins.
• Bacterial flagella are examples of exaptation, where existing structures gain new functions.

Internal Organization and DNA

• Prokaryotes have less genomic DNA than eukaryotes.
• DNA is contained in a single circular chromosome, unlike multiple linear eukaryotic chromosomes.
• The chromosome is located in the nucleoid region without a membrane.
• Some bacteria have smaller DNA rings called plasmids carrying a few genes.

Summary: Prokaryotes

1. Three main characteristics that have enabled prokaryotes to thrive in diverse environments across the globe are: small size, rapid reproduction, and high genetic diversity.
2. Most prokaryotes are unicellular and occur in many shapes, the most common of which are cocci (spheres), bacilli (rods), and spirals.
3. Bacterial cell walls contain peptidoglycan (a network of sugars and proteins) and function to protect, maintain shape, and prevent bursting.
4. Superficial to the cell wall, many have a capsule, which is a sticky protective layer.
5. Biologists mainly categorize bacteria based on cell wall composition. Gram-positive bacteria have thick cell walls composed of peptidoglycan, whereas Gram-negative bacteria have cell walls with less peptidoglycan and an outer membrane with lipopolysaccharides (LPS).

Summary: Prokaryotes

5. Taxis is the ability to move toward or away from a stimulus and includes chemotaxis, or movement toward or away from a chemical stimulus.
6. Endospores are dormant cells that can remain viable in inhospitable conditions for centuries. Examples of bacteria that form these include the bacteria that cause botulism, tetanus, and anthrax.
7. Bacterial flagella are the most common motility structure, but they likely evolved independently from those of eukaryotes and those found in archaea. This structure is made of three main parts: motor, hook, and filament.
8. Prokaryotes have less genomic DNA than eukaryotes. DNA is contained in a circular chromosome, whereas eukaryotic DNA is arranged in linear chromosomes.

Bacterial Metabolism

• Categorized based on oxygen requirements:
  • Obligate aerobes: unable to grow without free oxygen.
  • Obligate anaerobes: unable to grow in the presence of free oxygen (e.g., botulism, gas gangrene, tetanus).
  • Facultative anaerobes: able to grow with or without free oxygen.
  • Obligate = HAS TO
  • Facultative = can
  • Aerobic = oxygen
  • Anaerobic = an + aerobic = without oxygen

Nutritional and Metabolic Adaptations

• Energy and carbon sources are combined to give four major modes of nutrition:
  • Photoautotroph
  • Chemoautotroph
  • Photoheterotroph
  • Chemoheterotroph
  • Troph = nourishment/food
  • Auto = self
  • Hetero = other
  • Photo = light

Photoautotrophic Bacteria

• Use solar energy to reduce carbon dioxide to organic compounds.
• Photosynthetic.
• Anoxygenic (green sulfur and some purple bacteria in oxygen-poor conditions).
• Oxygenic.
  • Troph = nourishment/food
  • Auto = self
  • Hetero = other
  • Photo = light

Cyanobacteria

• Formerly called blue-green algae.
• Gram-negative bacteria that are photosynthetic.
• Believed to be responsible for introducing oxygen into the primitive atmosphere.
• Lack visible means of locomotion.
• Can live in extreme environments.
• Form lichens in association with fungi.
• Cyanobacterial blooms result from pollution in lakes and ponds.

Autotrophic Bacteria

• Bristle tube worms live in deep-sea vents, relying on chemosynthetic bacteria as food.

Chemoautotrophs

• Oxidize inorganic compounds to obtain energy.
• Use energy to reduce $CO_2$ to an organic compound.
• Chemosynthetic (chemical + create = make their own organic compounds).
• Live in deep-sea vents, e.g., 2.5 kilometers below sea level.

Heterotrophic Bacteria

• Most prokaryotes are chemoheterotrophs, taking in organic nutrients.
• Aerobic saprotrophs (sapro = decay) decompose large organic molecules to smaller molecules.
• Essential components of a healthy ecosystem.

Metabolic Cooperation

• Cooperation between different prokaryotic species occurs in surface-coating colonies called biofilms.
• Biofilms are common but can cause chronic infections, tooth decay, and contamination of medical devices.

Reproduction

• Three key features allow rapid reproduction in favorable environments:
  • Small cell size
  • Binary fission (division of one cell into two cells)
  • Short generation times

Adaptations of Prokaryotes

• Ongoing success results from physiological and metabolic diversification.
• Metabolic diversification was the first great wave of adaptive radiation.

Antibiotics

• Antibiotics can only be used on bacterial cells.
• Many target peptidoglycan and damage bacterial cell walls; others target protein synthesis.
• The outer membrane protects Gram-negative bacteria, increasing resistance.
• Bacterial resistance is increasing.
• Resistance genes can be transferred among bacteria via transformation, conjugation, or transduction.
• $90\%$ of Staphylococcus aureus are resistant to penicillin and increasingly to methicillin (MRSA).
• MRSA is common in hospitals.

Summary: Adaptations of Prokaryotes

1. Bacteria can be arranged into three categories based on their oxygen requirements: obligate aerobes, obligate anaerobes, and facultative anaerobes.
2. Bacteria can be arranged into four categories based on their energy and carbon sources: photoautotrophs, chemoautotrophs, photoheterotrophs, and chemoheterotrophs.
3. Most prokaryotes are chemoheterotrophs that take in organic nutrients.
4. Cyanobacteria were formerly called blue-green algae and are photosynthetic organisms believed to be responsible for releasing oxygen into the early Earth atmosphere.
5. Surface-coating colonies formed between different prokaryotic species are called biofilms.
6. Antibiotics can only be used against bacteria. Two main targets of antibiotics are peptidoglycan and protein synthesis.

Genetic Diversity in Prokaryotes

• Prokaryotes have considerable genetic variation.
• Three factors contribute to this genetic diversity:
  • Rapid reproduction
  • Mutation
  • Genetic recombination

Reproduction in Prokaryotes

• Prokaryotes reproduce asexually by binary fission.
• Generation time can be as short as 12 minutes.
• Mutations are generated rapidly and passed on to offspring more quickly than in eukaryotes.
• Prokaryotes are haploid (n).
• Some bacteria form resistant endospores under unfavorable conditions.

Genetic Recombination

• Genetic recombination combines DNA from two sources, contributing to diversity.
• Prokaryotic DNA from different individuals can be brought together by transformation, transduction, and conjugation.
• Movement of genes among individuals from different species is called horizontal gene transfer.

Genetic Recombination

1. Conjugation

• Conjugation pilus forms between two cells.
• Donor cell passes DNA to recipient cell through the pilus.
• Occurs in a one way direction.

1. Transformation

• Occurs when cell picks up free pieces of DNA from other prokaryotes.
• Becomes incorporated into genome.

1. Transduction

• Occurs when bacteriophages carry portions of bacterial DNA from one cell to another.
• Serve as vectors.

Summary: Prokaryote Reproduction

1. Prokaryotes reproduce asexually by means of binary fission. As such, their cells can be described as haploid.
2. Genetic diversity is maintained through genetic recombination, which is defined as the combining of DNA from two sources.
3. Prokaryotic DNA from different individuals can be brought together by transformation, transduction, and conjugation.
4. The movement of genes among individuals of different species is called horizontal gene transfer.

Prokaryotic Diversity

• Prokaryotes have radiated extensively due to diverse structural and metabolic adaptations.
• They inhabit every environment known to support life.
• Dramatic revision of prokaryote phylogeny has resulted from molecular research.
• Molecular analysis led to the split of prokaryotes into Bacteria and Archaea.
• New advances in molecular systematics have enabled the analysis of over 1,700 entire prokaryote genomes.

Bacteria

• Include the majority of prokaryotes familiar to most people.
• Every major mode of nutrition and metabolism is represented.
• Wide diversity of nutritional modes can be found even within small taxonomic groups.
• There are about 16,000 known species.
• The number of undiscovered bacteria species is estimated to be in the range of $700,000$–$1.4$ million.

A Comparison of the Three Domains of Life

*Response to antibiotics

Bacterial Diseases in Humans

• Sexually transmitted diseases: Syphilis, gonorrhea, chlamydia
• Respiratory diseases: Strep throat, scarlet fever, tuberculosis, pneumonia, Legionnaires’ disease, whooping cough, inhalation anthrax
• Skin diseases: Erysipelas, boils, carbuncles, impetigo, acne, infections of surgical or accidental wounds and burns, leprosy (Hansen disease)
• Digestive tract diseases: Gastroenteritis, food poisoning, dysentery, cholera, peptic ulcers, dental caries
• Nervous system diseases: Botulism, tetanus, leprosy, spinal meningitis
• Systemic diseases: Plague, typhoid fever, diphtheria
• Other diseases: Tularemia, Lyme disease

Bacteria – Some major groups

Chlamydias

• Gram-negative parasites that can only live within animal host cells.
• Chlamydia trachomatis causes blindness and non-gonococcal urethritis.
• Koala populations are suffering from chlamydia.

Bacteria – Some major groups

Spirochetes

• Helical gram-negative heterotrophs.
• Move in a spiral pattern by rotating internal, flagellum-like filaments.
• Many species are free-living, but some are parasitic.
• Treponema pallidum causes syphilis, and Borrelia burgdorferi causes Lyme disease.

Bacteria – Some major groups

Cyanobacteria

• Gram-negative photoautotrophs that generate $O_2$ through plant-like photosynthesis.
• Plant chloroplasts likely evolved from cyanobacteria by endosymbiosis.
• Abundant in freshwater and marine phytoplankton.

Bacteria – Some major groups

Gram-Positive Bacteria

• Diverse group.
• Actinomycetes are colony-forming bacteria composed mostly of soil decomposers and some pathogens.
• Streptomyces are soil-dwelling bacteria cultured as a source of antibiotics.
• Other subgroups include pathogens such as Bacillus anthracis, which causes anthrax.

Archaea

• Formerly considered bacteria.
• Many live in harsh conditions (extremophiles).
• Now thought to be more closely related to Eukarya than to Bacteria.
• Carl Woese and George Fox discovered that the base sequence of their rRNA differs from bacteria.
• Other differences:
  • Do not have peptidoglycan in their cell walls like bacteria.
  • Biochemically more like Eukarya than Bacteria.

Halophilic Archaea

• Salty lakes
• Halophiles
• Require high salt concentrations for growth

Thermoacidophilic Archaea

• Hot sulfur springs
• Thermoacidophiles
• Reduce sulfides and survive best at temperatures above $80°C$
• Plasma membranes contain unusual lipids that confer tolerance of high temperatures.

Methanogens

• Anaerobic marshes
• Methanogens
• Produce methane from hydrogen gas and carbon dioxide

Summary: Prokaryote Diversity

1. Some examples of bacterial diseases in humans include: Syphilis, Tuberculosis, Gonorrhoea and Food Poisoning. (Answers may vary, but you should know at least 4 diseases!)
2. Spirochetes are helical bacteria that move in a spiral pattern.
3. Archaea were once considered bacteria and are generally considered to be extremophiles (lover of harsh conditions). They are now thought to be more closely related to Eukarya than to Bacteria.
4. Archaea may be described as halophilic, thermoacidophilic, and methanogens, based on the environment they live in.

Prokaryotes Play Crucial Roles in the Biosphere

• Essential to the survival of many other species.
• Play a major role in chemical recycling between living and nonliving components of ecosystems.
• Some chemoheterotrophic prokaryotes are decomposers that break down dead organic materials and release mineral nutrients.
• Life as we know it would cease without decomposers.
• Prokaryotes can convert some molecules into forms that can be taken up by other organisms.
• Some produce sugars through photosynthesis.
• Others fix atmospheric nitrogen ($N_2$) into forms available to plants.
• Some can increase or decrease the availability of nutrients that plants require for growth.

Species Interactions

• May be free-living or symbiotic (two different species live together intimately).

Mutualism

• Both species benefit from the association.
• Mutualistic bacteria live in human intestines and release vitamins K and $B_{12}$, which help produce blood components.

Commensalism

• One population modifies the environment so that a second population benefits.
• Obligate anaerobes live in our intestine because bacterium E. coli uses up oxygen.

Parasitism

• Parasite benefits at the host's expense; disease-causing bacteria are called pathogens.
• Many form endospores.

Mutualistic Bacteria

• Human intestines are home to about $500$–$1,000$ species of bacteria.
• Many are mutualists that break down indigestible food in our intestines.

Pathogenic Bacteria

• All known pathogenic prokaryotes are bacteria.
• Cause about half of all human diseases.
• For example, more than 1 million people per year die from a lung disease caused by Mycobacterium tuberculosis.

Pathogenic Bacteria

• Usually cause disease by producing poisons classified as exotoxins or endotoxins.

Exotoxins

• Proteins that are secreted and can cause disease even if the bacteria are no longer present.
• For example, Clostridium botulinum secretes an exotoxin in improperly canned food.

Endotoxins

• Released only when bacteria die and their cell walls break down.
• For example, members of the genus Salmonella produce endotoxins that cause food poisoning.

Antibiotic Resistance

• Bacterial resistance to antibiotics has evolved rapidly since their introduction in the 1940s.
• Discovery of new antibiotics has not kept pace with the rate of resistance evolution.
• For every antibiotic in use, at least one bacteria species has evolved resistance.
• This is a form of directional selection.

Summary: Prokaryote Interactions

1. Relationships between species can be described as mutualism, commensalism, and parasitism.
2. Mutualistic and commensal relationships between humans and bacteria include: Human intestines are home to about 500–1,000 species of bacteria, which are mutualists that break down indigestible food in our intestines
3. Parasitic bacteria include pathogenic bacteria, which produce toxins that can be classified as either exotoxins or endotoxins.