Prokaryotes: Bacteria & Archaea

Prokaryotes

Organisms that lack a membrane-bound nucleus and other membrane-bound organelles. They are typically single-celled and include bacteria and archaea, characterized by circular DNA in a nucleoid region.

Horizontal Gene Transfer

The non-sexual movement of genetic material between different species. This process, which includes transformation, transduction, and conjugation, significantly increases genetic diversity, often contributing to traits like antibiotic resistance.

Obligate Aerobes

Bacteria that absolutely require oxygen for cellular respiration to produce energy. They cannot survive or grow in an anaerobic (oxygen-free) environment.

Facultative Anaerobes

Bacteria that can metabolize and grow in the presence of oxygen, utilizing aerobic respiration. However, they are also capable of switching to anaerobic respiration or fermentation for energy production in the absence of oxygen.

Endospores

Remarkably tough, dormant, and non-reproductive structures produced by certain bacteria (e.g., Bacillus, Clostridium). They provide extreme resistance to harsh conditions such as heat, radiation, chemicals, and desiccation, enabling bacterial survival over long periods.

Koch’s Postulates

A set of four criteria developed by Robert Koch to establish a causative relationship between a specific microbe and a specific disease. These include: 1) the microorganism must be found in abundance in all diseased organisms but not in healthy ones, 2) it must be isolated from a diseased organism and grown in pure culture, 3) the cultured microorganism should cause disease when introduced into a healthy organism, and 4) the microorganism must be re-isolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Gram-positive

Bacteria characterized by a thick peptidoglycan cell wall that retains the crystal violet stain during the Gram staining procedure. They appear purple under a microscope due to the retention of the crystal violet-iodine complex, which is not easily washed out by alcohol.

Gram-negative

Bacteria that possess a thin peptidoglycan cell wall located between an inner and an outer membrane. During Gram staining, the crystal violet stain is washed out by alcohol, and these bacteria are then counterstained with safranin, appearing pink or red under a microscope. Their outer membrane contains lipopolysaccharides (LPS).

C. difficile Infection

A severe bacterial infection of the colon caused by Clostridioides difficile. It often occurs after antibiotic use, which disrupts normal gut flora, allowing C. difficile to proliferate and produce toxins leading to symptoms like severe diarrhea and potentially pseudomembranous colitis.

Symbiosis

A close and often long-term interaction between two different biological species. While often referring to mutualism where both species benefit (e.g., the Hawaiian bobtail squid and its bioluminescent bacterium Vibrio fischeri), it can also encompass commensalism (one benefits, other unaffected) and parasitism (one benefits, other harmed).

Autotrophs

Organisms capable of producing their own food from inorganic substances. This can occur through photosynthesis (photoautotrophs, e.g., plants, algae, cyanobacteria, using light energy) or chemosynthesis (chemoautotrophs, e.g., some bacteria and archaea, using chemical reactions).

Haploid Life Cycle

A life cycle in which the multicellular adult stage is haploid (n) and produces gametes through mitosis. The only diploid (2n) stage is the zygote, which undergoes meiosis immediately after formation to produce haploid spores that develop into the haploid adult. Commonly observed in many fungi and protists.

Diploid Life Cycle

A life cycle where the multicellular adult stage is diploid (2n) and produces haploid gametes (n) through meiosis. These gametes fuse during fertilization to form a diploid zygote, which then develops mitotically into a new diploid individual. This life cycle is characteristic of most animals.

Diversity of Bacteria

The vast genetic, metabolic, and ecological variety found within the domain Bacteria. Comprising over 50 different phyla, bacteria exhibit a wide range of adaptations, metabolic strategies (e.g., photoautotrophs, chemoheterotrophs), and roles in ecosystems (e.g., decomposers, pathogens, symbionts), thriving in almost every environment on Earth.

Pathogenic Bacteria

Bacteria that can cause disease in a host organism. They achieve this through various mechanisms, including producing toxins, invading host tissues, multiplying rapidly, or evading the host's immune response.

Archaea

A domain of single-celled organisms that are prokaryotes, distinct from bacteria and eukaryotes. They are known for living in extreme environments and having unique molecular characteristics, such as different cell wall and membrane compositions.

Peptidoglycan

A polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the bacterial cell wall. It is much thicker in Gram-positive bacteria than in Gram-negative bacteria.

Transformation (HGT)

A type of horizontal gene transfer where bacteria take up exogenous genetic material (naked DNA) from their surroundings, often DNA released by dead cells.

Mutualism

A symbiotic relationship between two different species where both organisms benefit from the interaction. An example is the relationship between the Hawaiian bobtail squid and Vibrio fischeri.

Obligate Anaerobes

Bacteria that are poisoned by oxygen and cannot grow or survive in its presence. They primarily rely on anaerobic respiration or fermentation for energy production.

Normal Microbiota (Gut Flora)

The community of microorganisms (bacteria, archaea, fungi, viruses) that naturally inhabit a specific environment in the body, such as the human gut, without causing disease. They play crucial roles in digestion, vitamin synthesis, and protection against pathogens.

Photoautotrophs

Organisms that use light as an energy source to synthesize organic compounds from inorganic materials like carbon dioxide. Examples include plants, algae, and cyanobacteria.

Archaea Cell Walls

Cell walls in Archaea lack peptidoglycan and often contain pseudopeptidoglycan (pseudomurein), s-layers (protein/glycoprotein layers), or other unique polysaccharides.

Plasmid

Small, circular, extrachromosomal DNA molecules found in bacteria that can replicate independently. Plasmids often carry non-essential genes that provide advantageous traits, such as antibiotic resistance or virulence factors.

Fimbriae (Pili)

Short, hair-like protein appendages on the surface of bacterial cells. They are primarily used for attachment to host cells, abiotic surfaces, and to other bacterial cells to form biofilms. A specialized pilus, the 'sex pilus', is involved in conjugation.

Flagella

Long, whip-like protein structures extending from the bacterial cell surface, responsible for bacterial motility. They rotate to propel the bacterium, allowing it to move towards or away from various chemical or physical stimuli (chemotaxis).

Capsule

An organized, outermost layer of some bacteria, typically composed of polysaccharides or polypeptides. The capsule provides protection against phagocytosis by host immune cells and aids in adhesion to surfaces.

Nucleoid

The irregular-shaped region within a prokaryotic cell cytoplasm where the genetic material (the bacterial chromosome, usually a single circular DNA molecule) is concentrated. Unlike a eukaryotic nucleus, it is not enclosed by a membrane.

Conjugation

A method of horizontal gene transfer where genetic material, typically a plasmid, is directly transferred from one bacterial cell to another through a temporary cytoplasmic bridge formed by a sex pilus.

Transduction

A type of horizontal gene transfer in bacteria where bacterial DNA is transferred from one bacterium to another by a bacteriophage (a virus that infects bacteria). This can involve generalized or specialized transduction.

Chemoheterotrophs

Organisms that obtain both their energy and carbon from breaking down organic compounds. This is the most common mode of nutrition for bacteria and archaea, as well as all animals, fungi, and many protists.

Fermentation

An anaerobic metabolic process that produces energy (ATP) by converting sugars to acids, gases, or alcohol in the absence of oxygen. It does not require an external electron acceptor and produces less ATP than cellular respiration.

Aerobic Respiration

A metabolic pathway that uses oxygen as the final electron acceptor in the electron transport chain to break down glucose and other organic molecules, generating a large amount of ATP (energy) for the cell.

Binary Fission

The primary method of asexual reproduction in prokaryotes (bacteria and archaea) and some eukaryotic organelles. A single parent cell divides into two genetically identical daughter cells after replicating its DNA.

Cocci

Spherical or oval-shaped bacteria. They can appear singly, in pairs (diplococci), in chains (streptococci), or in grape-like clusters (staphylococci).

Bacilli

Rod-shaped bacteria. They can exist singly, in pairs (diplobacilli), or in chains (streptobacilli).

Spirilla

Spiral-shaped bacteria, often characterized by a rigid, wavy form. Other spiral forms include vibrios (comma-shaped) and spirochetes (flexible, corkscrew-shaped).

Commensalism

A type of symbiotic relationship between two organisms where one organism benefits, and the other organism is neither significantly harmed nor significantly helped.

Parasitism

A symbiotic relationship where one organism, the parasite, derives benefits at the expense of the other organism, the host, which is typically harmed by the interaction.

Exotoxins

Toxic proteins secreted by certain bacteria (both Gram-positive and Gram-negative) that can act on specific target cells or tissues in the host. They are highly potent and often cause specific disease symptoms.

Endotoxins

Lipopolysaccharide (LPS) components of the outer membrane of Gram-negative bacteria. Endotoxins are released primarily when bacterial cells lyse, triggering a strong, generalized inflammatory response in the host that can lead to fever, shock, and DIC.

Virulence Factors

Molecules or traits produced by pathogens that enable them to establish infection, evade host defenses, cause damage to host cells/tissues, and ultimately lead to disease. Examples include toxins, adhesins, capsules, and enzymes.

Antibiotic Resistance

The ability of infectious microorganisms, particularly bacteria, to survive and grow in the presence of an antibiotic that would normally kill or inhibit them. This often arises from genetic mutations or the acquisition of resistance genes via horizontal gene transfer.

Broad-spectrum Antibiotics

Antibiotics that are effective against a wide range of bacteria, including both Gram-positive and Gram-negative species. While useful for treating unknown infections, they can disrupt normal microbiota more severely.

Microbiome

The ecological community of microorganisms (bacteria, archaea, fungi, viruses) coexisting within a specific environment, such as the human gut, skin, or a soil sample, along with their collective genomes (metagenome).

Biofilm

A complex aggregation of microorganisms from one or more species, typically embedded in a self-produced extracellular polymeric substance (EPS) matrix and adhering to a surface. Biofilms provide protection and are often associated with chronic infections.

Host specificity

The range of host organisms that a particular pathogen can infect. This is determined by the pathogen's ability to bind to host cells, acquire nutrients, and overcome host defenses.

Antiseptics

Chemical agents applied to living tissues (e.g., skin) to reduce the number of microorganisms and prevent infection by inhibiting their growth or killing them.

Disinfectants

Chemical agents applied to inanimate objects or surfaces to kill or inactivate microorganisms, thus preventing the spread of infection.

Sterilization

A process, either physical or chemical, that completely destroys or removes all forms of microbial life, including spores, from an object or surface.

Pasteurization

A heating process applied to food and liquids (such as milk) to kill pathogenic microorganisms and reduce the total number of spoilage organisms, thereby extending shelf life without significantly altering flavor or nutritional value.

Opportunistic Pathogens

Microorganisms that normally do not cause disease in a healthy host but can become pathogenic under certain circumstances, such as a weakened immune system, disruption of normal microbiota, or entry into a normally sterile body site.

Vertical Gene Transfer

The transmission of genetic material from a parent organism to its offspring, typically through reproduction.

Quorum Sensing

A system of communication used by bacteria to coordinate gene expression and behavior (e.g., biofilm formation, virulence) in response to changes in their population density.

Aerotolerant Anaerobes

Bacteria that can grow and survive in the presence of oxygen, but do not use it for metabolism. They rely solely on anaerobic processes like fermentation.

MRSA

Methicillin-resistant Staphylococcus aureus, a type of staph bacteria that has become resistant to many antibiotics, including methicillin, amoxicillin, and penicillin, posing a significant public health threat.

Extremophiles

Organisms, primarily Archaea and some bacteria, that thrive in physically or geochemically extreme conditions that are detrimental to most life forms on Earth (e.g., very high/low temperatures, high salinity).

Protists

A diverse group of eukaryotic microorganisms that are not plants, animals, or fungi. They are mostly unicellular, often found in aquatic environments, and exhibit a wide range of nutritional and reproductive strategies.

Mitochondria

Membrane-bound organelles found in most eukaryotic cells, responsible for generating the majority of a cell's supply of adenosine triphosphate (ATP), used as a source of chemical energy, through cellular respiration. Often referred to as the 'powerhouses' of the cell.

Alternation of Generations

A life cycle that alternates between a multicellular haploid (gametophyte) stage and a multicellular diploid (sporophyte) stage. This life cycle is characteristic of plants and some algae.

Prokaryotic Cell Size Comparison

Prokaryotic cells are much smaller than eukaryotic cells, typically 1-10 \mu m long and 0.7-1.5 \mu m wide.

Oldest Recorded Life

Prokaryotic fossils, dating back to approximately 3.5 billion years ago.

HGT in E. coli Significance

Approximately 17\% of E. coli genes are estimated to have originated from other bacteria through horizontal gene transfer.

Cytoplasm

The gel-like substance that fills the prokaryotic cell, containing the genetic material and other structures.

Gram-positive Antibiotic

Penicillin is commonly effective against Gram-positive bacteria due to their thick peptidoglycan wall.

Gram-negative Antibiotic

Cephalosporins are a type of antibiotic commonly used to treat Gram-negative bacteria, considering their outer membrane.

Endospore-Related Diseases

Three severe diseases caused by bacteria that form endospores are Anthrax, Tetanus, and Botulism.

Botox Origin

The therapeutic agent Botox is derived from botulinum toxin, produced by endospore-forming bacteria.

Bacterial Ecological Contributions

Beyond being pathogens, bacteria play vital ecological roles such as nitrogen fixation and decomposition.

Bacterial Industrial Contributions

Two significant products derived from bacterial metabolism with industrial importance are ethanol and antibiotics.

E. coli O157:H7

A strain of E. coli particularly known for causing severe outbreaks of foodborne illness.

WHO Critical Antibiotic Resistance

According to the WHO, Acinetobacter, Pseudomonas, and Enterobacteriaceae are critical priorities for new antibiotics due to carbapenem resistance.

Koch's Postulates Founder & Year

Robert Koch established Koch's Postulates in 1884.

Archaea Membrane Adaptation

A unique feature of Archaeal membranes, ether bonds between lipids, allows them to withstand extreme temperatures.

Archaea-Eukarya DNA Packaging

Archaea use histone proteins to organize their DNA, a feature shared with Eukarya but not Bacteria.