General Biology I Unit 22 ReviewProkaryotes – Bacteria and Archaea

What Are Prokaryotes?

• Prokaryotes are single-celled organisms that lack a membrane-bound nucleus and other organelles
• Consist of two domains: Bacteria and Archaea, which diverged from a common ancestor billions of years ago
• Prokaryotic cells are typically much smaller than eukaryotic cells, ranging from 0.1 to 5 μm in diameter
• Possess a cell wall composed of peptidoglycan (bacteria) or pseudopeptidoglycan (archaea) that provides structure and protection
• Contain a single circular chromosome made of DNA located in the cytoplasm, not enclosed within a nuclear membrane
• Ribosomes in prokaryotes are smaller (70S) compared to those in eukaryotes (80S)
• Some prokaryotes have additional small, circular DNA molecules called plasmids that can be transferred between cells
• Prokaryotes are found in virtually every habitat on Earth, including extreme environments (hot springs, deep-sea vents, and highly acidic or alkaline environments)

Bacterial Cell Structure

• Bacterial cells have a cell envelope consisting of a plasma membrane, cell wall, and sometimes an outer membrane (in gram-negative bacteria)
• The plasma membrane is a phospholipid bilayer that serves as a selective barrier, controlling the passage of substances in and out of the cell
• The cell wall, composed of peptidoglycan, maintains cell shape and protects the cell from osmotic stress
  • Peptidoglycan is a polymer of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) sugars cross-linked by short peptide chains
• Gram-positive bacteria have a thick cell wall composed of many layers of peptidoglycan
• Gram-negative bacteria have a thin cell wall and an additional outer membrane containing lipopolysaccharides (LPS)
• Bacterial cells may possess surface structures such as flagella for motility, pili for attachment and DNA transfer, and capsules or slime layers for adherence and protection
• The cytoplasm contains ribosomes, storage granules, and the nucleoid region where the DNA is located

Archaeal Cell Structure

• Archaeal cells share some similarities with bacterial cells but also have unique features
• Like bacteria, archaea have a cell wall, but it is composed of pseudopeptidoglycan or other polymers (S-layer proteins) instead of peptidoglycan
  • Pseudopeptidoglycan contains different sugars and amino acids compared to bacterial peptidoglycan
• Archaeal plasma membranes are composed of unique lipids with ether linkages and branched hydrocarbon chains, making them more stable in extreme environments
• Some archaea, particularly methanogens, have a cell wall composed of pseudomurein, which is similar to peptidoglycan but contains different sugars
• Archaea lack an outer membrane, but some species have a surface layer (S-layer) of glycoproteins that provide structural support and protection
• Archaeal flagella, called archaella, are structurally distinct from bacterial flagella and are composed of different proteins
• The cytoplasm of archaeal cells contains ribosomes, storage granules, and the nucleoid region, similar to bacterial cells

Prokaryotic Genetics

• The prokaryotic genome consists of a single, circular chromosome made of double-stranded DNA
• The genome is located in the cytoplasm in a region called the nucleoid, which is not enclosed by a nuclear membrane
• Prokaryotic DNA is highly compact and supercoiled, associated with DNA-binding proteins called nucleoid-associated proteins (NAPs)
• Prokaryotes can also possess extrachromosomal DNA elements called plasmids, which are small, circular, self-replicating molecules
  • Plasmids often carry genes for antibiotic resistance, virulence factors, or metabolic capabilities
• Gene expression in prokaryotes is tightly regulated and involves transcription and translation occurring simultaneously in the cytoplasm
• Prokaryotes can undergo horizontal gene transfer (HGT) through three main mechanisms: transformation, transduction, and conjugation
  • Transformation involves the uptake and incorporation of naked DNA from the environment
  • Transduction occurs when bacterial viruses (bacteriophages) transfer DNA from one cell to another
  • Conjugation involves the direct transfer of DNA through cell-to-cell contact via a specialized structure called a pilus
• HGT allows prokaryotes to rapidly adapt to new environments and acquire new functions, such as antibiotic resistance or metabolic capabilities

Metabolism and Energy Production

• Prokaryotes exhibit a wide range of metabolic capabilities and can obtain energy from various sources
• Chemotrophs obtain energy from chemical compounds, while phototrophs use light energy to generate ATP
• Autotrophs can synthesize organic compounds from inorganic carbon sources (CO2), while heterotrophs rely on organic compounds for carbon and energy
• Prokaryotes can be classified based on their energy source and carbon source: photoautotrophs, photoheterotrophs, chemoautotrophs, and chemoheterotrophs
• Respiration in prokaryotes can be aerobic (using oxygen as the final electron acceptor) or anaerobic (using alternative electron acceptors like nitrate, sulfate, or ferric iron)
  • Aerobic respiration involves the electron transport chain and generates a proton gradient used for ATP synthesis
  • Anaerobic respiration yields less energy than aerobic respiration but allows prokaryotes to survive in oxygen-depleted environments
• Fermentation is an anaerobic process that generates ATP through substrate-level phosphorylation and produces various end products (lactic acid, ethanol, or hydrogen gas)
• Some prokaryotes, such as methanogens and sulfate reducers, have specialized metabolic pathways for obtaining energy from unique substrates
• Prokaryotes play crucial roles in biogeochemical cycles, such as the carbon, nitrogen, and sulfur cycles, by transforming and recycling essential elements

Reproduction and Growth

• Prokaryotes reproduce asexually through a process called binary fission, where a single cell divides into two identical daughter cells
• The cell cycle in prokaryotes consists of three main stages: the B period (before DNA replication), the C period (DNA replication), and the D period (after DNA replication and before cell division)
• DNA replication in prokaryotes begins at a single origin of replication (oriC) and proceeds bidirectionally until the entire chromosome is copied
• Cell division is initiated by the formation of a septum, a cell wall structure that grows inward and separates the two daughter cells
  • The septum formation is coordinated by the Z ring, a cytoskeletal structure composed of the protein FtsZ
• Prokaryotic growth is influenced by various environmental factors, such as temperature, pH, nutrient availability, and the presence of growth inhibitors
• Under optimal conditions, prokaryotes can exhibit exponential growth, characterized by a constant doubling time
  • The growth rate is determined by the generation time, which is the time required for a population to double in size
• Prokaryotes can enter a stationary phase when nutrients become limited or waste products accumulate, during which the growth rate slows down and the population size remains relatively constant
• Some prokaryotes can form endospores, dormant structures that are highly resistant to environmental stresses (heat, radiation, and chemicals) and can remain viable for extended periods

Ecological Roles and Importance

• Prokaryotes are ubiquitous in the environment and play critical roles in various ecosystems
• They are primary producers in many aquatic and terrestrial habitats, converting inorganic compounds into organic matter through photosynthesis or chemosynthesis
  • Cyanobacteria are important photosynthetic prokaryotes that contribute significantly to global oxygen production
• Prokaryotes are essential decomposers, breaking down dead organic matter and recycling nutrients back into the ecosystem
• Many prokaryotes engage in symbiotic relationships with other organisms, such as nitrogen-fixing bacteria (Rhizobia) that form nodules on the roots of legumes
• Prokaryotes are crucial in biogeochemical cycles, transforming and recycling elements like carbon, nitrogen, sulfur, and phosphorus
  • Nitrifying bacteria convert ammonia to nitrite and nitrate, while denitrifying bacteria reduce nitrate to nitrogen gas
  • Sulfur-oxidizing bacteria and sulfate-reducing bacteria play key roles in the sulfur cycle
• Prokaryotes are used in various biotechnological applications, such as the production of antibiotics, enzymes, and biofuels
• Some prokaryotes, particularly in the genus Streptomyces, are the source of numerous antibiotics used in medicine
• Prokaryotes are employed in bioremediation, using their metabolic capabilities to degrade pollutants and clean up contaminated sites

Prokaryotes in Human Health and Disease

• The human body harbors a diverse community of prokaryotes, collectively known as the microbiome
• Beneficial prokaryotes in the gut (gut microbiota) aid in digestion, nutrient absorption, and the development of the immune system
  • The gut microbiota helps prevent colonization by pathogenic microbes through competition for resources and production of antimicrobial compounds
• Some prokaryotes are opportunistic pathogens, causing infections in immunocompromised individuals or when they gain access to normally sterile sites
• Pathogenic prokaryotes employ various virulence factors, such as adhesins, toxins, and secretion systems, to colonize and damage host tissues
• Examples of bacterial pathogens include Streptococcus pneumoniae (pneumonia), Salmonella enterica (foodborne illness), and Mycobacterium tuberculosis (tuberculosis)
• Antibiotic resistance is a growing concern, as many bacterial pathogens have acquired resistance to multiple antibiotics through horizontal gene transfer and mutations
  • Misuse and overuse of antibiotics have contributed to the spread of antibiotic resistance, making infections more difficult to treat
• Probiotics, which are live microorganisms (mostly bacteria) consumed for their health benefits, are used to promote a healthy gut microbiome and prevent or treat certain conditions
• Research on the human microbiome has revealed its importance in maintaining health and its potential involvement in various diseases, such as inflammatory bowel disease, obesity, and even mental health disorders