Week 5-Lecture 24

Key Concepts

• Prokaryotes: Bacteria and Archaea, lacking a nuclear envelope and membrane-enclosed organelles.
• Bacteria: Single-celled organisms with peptidoglycan in their cell walls, diverse shapes (cocci, bacilli, spiral), and reproduction via binary fission.
• Gram Staining: A technique to classify bacteria based on cell wall composition (Gram-positive with thick peptidoglycan layer, Gram-negative with thin peptidoglycan and outer membrane).
• Antibiotics: Substances targeting bacterial cell wall synthesis, membrane function, translation, metabolism, transcription, or DNA replication.
• Viruses: Small infectious particles with genetic material (DNA or RNA) and a protein coat (capsid), obligate intracellular parasites.
• Bacteriophages: Viruses that infect bacteria.
• Retroviruses: RNA viruses using reverse transcriptase to copy their RNA genome into DNA.
• Genetic Reassortment: The mixing of genetic material from different viral strains, leading to new viral variants.

Prokaryotes: Bacteria vs. Archaea vs. Eukarya

• Nuclear Envelope: Absent in Bacteria and Archaea, present in Eukarya.
• Membrane-Enclosed Organelles: Absent in Bacteria and Archaea, present in Eukarya.
• Cell Wall (Peptidoglycan): Present only in Bacteria.
• Membrane Lipids: Branched hydrocarbons in Archaea, unbranched in Bacteria and Eukarya.
• Highlights commonalities between Bacteria and Archaea, and unique features of each group.

Bacteria: Diversity, Structure, and Function

• Diversity: Found on various surfaces, including the human body. Examples: E. coli, Streptococcus.
• Shapes: Spherical (cocci), rod-shaped (bacilli), and spiral.
• Size: Typically 0.5 to 5 microns, smaller than eukaryotic cells (10-100 microns).
• Nutrition: Some are photosynthetic (make their own food), others are scavengers (feed on surrounding environment), and some are pathogens (attack other organisms).
• Movement: Motile bacteria use flagella for propulsion. Exhibit taxis (movement towards or away from stimuli, e.g., chemotaxis).
• Reproduction: Primarily through binary fission (asexual reproduction).
• Internal Organization: Lack complex architecture of eukaryotes. Circular DNA genome located in the nucleoid region. Plasmids (small, circular, extra-chromosomal DNA) may be present.
• Genetic Diversity: Arises from rapid reproduction, mutation, and genetic recombination.

Genetic Diversity in Bacteria

• Bacteria are used to study molecular genetics due to their simple structure.
• Bacterial chromosomes are circular DNA molecules with few associated proteins.
• Plasmids replicate independently of the bacterial chromosome.
• Rapid reproduction allows new mutations to quickly increase genetic diversity.
• Genetic diversity also arises from recombination of DNA from different bacterial cells.

Bacterial Cell Surface Structures and Gram Staining

• Cell Wall: Contains peptidoglycan (sugar polymers cross-linked by polypeptides). Eukaryotic cell walls are made of cellulose or chitin.
• Gram Staining: Classifies bacteria based on cell wall composition.
  • Gram-positive: Thick peptidoglycan layer, retains crystal violet stain (purple/violet color).
  • Gram-negative: Thin peptidoglycan layer and outer membrane, crystal violet stain washes off, counterstained with safranin (pink/red color).
• Lab Demonstration of Gram Staining:
  1. Sterilize nichrome loop and cool.
  2. Take a loop full of culture and make a smear on the slide.
  3. Air dry the smear.
  4. Heat fix the smear.
  5. Add crystal violet for one minute, then wash off.
  6. Add Gram's iodine, then wash off.
  7. Add de-colorizer (acetone alcohol), then wash off.
  8. Add safranin for two minutes, then wash off.
  9. Air dry the smear.
  10. Add emulsion oil and observe under the oil lens of the microscope.
• Gram staining provides initial information for clinicians to classify bacterial infections.

Antibiotic Targets and Bacterial Diseases

• Many antibiotics target peptidoglycan, damaging the bacterial cell wall.
• Gram-negative bacteria are more likely to be antibiotic-resistant.
• Capsules (polysaccharide or protein layer) cover many prokaryotes.
• Antibiotic Targets:
  • Inhibition of cell wall synthesis (penicillin, cephalosporin, vancomycin).
  • Disruption of cell membrane function (polymyxin).
  • Inhibition of translation (tetracycline, erythromycin, streptomycin, chloramphenicol).
  • Inhibition of metabolism (sulfanilamide).
  • Inhibition of transcription (rifamycin).
  • Inhibition of DNA replication (quinolones).
• Bacterial Diseases: Many bacteria are human pathogens (e.g., Bacillus anthracis causing anthrax).

Beneficial Roles of Bacteria

• Recycling of chemical elements in ecosystems.
• Chemoheterotrophic prokaryotes act as decomposers.
• Increase availability of nitrogen, phosphorus, and potassium for plant growth.
• Form biotic relationships with larger organisms.
• Applications:
  • Gene cloning using E. coli.
  • Production of transgenic plants using Agrobacterium tumefaciens.
  • Production of natural plastics, antibiotics, vitamins, and ethanol.
  • Bioremediation (e.g., using bacteria to metabolize oils).
  • Synthesis and storage of polyhydroxyalkenoate for biodegradable plastics.
  • Development of fertilizer sprays to stimulate bacteria growth.
  • Production of ethanol fuel from renewable plant products.

Viruses: Structure and Reproduction

• Much smaller and simpler than eukaryotes and bacteria.
• Infectious particles with genetic material (DNA or RNA) and a protein coat (capsid).
• Obligate intracellular parasites (reproduce only inside a host cell).
• Infect bacteria, archaea, and eukaryotes.
• Lack their own energy metabolism.
• Some large DNA viruses (e.g., vaccinia virus, pandora virus, Mimi virus) are studied for evolutionary insights.
• Consist of nucleic acid surrounded by a protein coat (capsid).
• Capsid is a protein shell enclosing the viral genome.
• Some viruses have envelopes (membranous coverings derived from host cell membranes).
• Bacteriophages have complex capsid structures (e.g., bacteriophage T4 with icosahedral head and tail apparatus).
• E. coli and its viruses are used as a model system for research.

RNA Viruses and Viral Diseases

• Retroviruses: Use reverse transcriptase to copy their RNA genome into DNA (e.g., HIV).
• Polio: Caused by polio virus, invades the nervous system, causing paralysis. Still endemic in Afghanistan, Nigeria, and Pakistan.
• SARS: Caused by a coronavirus, characterized by glycoprotein spikes (corona).
• Plant Viral Diseases: Common symptoms include spots on leaves and fruit, stunted growth, and damaged flowers or roots.
• Swine Flu (H1N1): Respiratory disease of pigs caused by type A influenza virus. Symptoms include fever, chills, cough, sore throat, body ache, headache, fatigue. Spreads through coughs, sneezes, and touching infected surfaces.
• Influenza A Viruses: Classified based on antigenicity of hemagglutinin (HA) and neuraminidase (NA) surface glycoproteins (16 HA subtypes, 9 NA subtypes). HA proteins are important for cellular receptor binding and fusion of viral and endosomal membranes. NA proteins help the virus release from infected cells.

Evolution of H1N1

• Swine origin influenza A (H1N1) viruses resulted from reassortment of avian, human, or swine viruses.
• Triple reassortment viruses with Eurasian Avian-like swine viruses.
• Genetic reassortment can lead to new types of viruses.
• Studying viruses is helpful for understanding evolutionary aspects.

Challenges Posed by Viruses

• Risk of generating novel viruses through reassortment.
• Resistance against drugs or inhibitors.
• Challenges in scaling up mass production of vaccines.

Conclusion

The lecture provided an overview of bacteria and viruses, highlighting their diversity, structure, reproduction, and impact on health and the environment. Bacteria are classified using Gram staining and can be targeted by antibiotics. Viruses, being obligate intracellular parasites, pose unique challenges due to their ability to mutate and reassort, leading to the emergence of new strains. Studying viruses is crucial for understanding evolutionary processes and developing effective control strategies.