prokaryotes, archaea, bacteria, viruses

Why is oxygen considered essential for most forms of life even though it is not classified as a nutrient?

Oxygen is essential because it serves as the final electron acceptor in the electron transport chain of cellular respiration. Its high electronegativity allows organisms to fully oxidize glucose and other organic molecules, releasing large amounts of energy in the form of ATP. Unlike nutrients, oxygen does not provide energy or carbon directly, but without it cells cannot generate ATP efficiently.

How many ATP molecules are produced in aerobic respiration compared to fermentation?

Aerobic respiration produces about 32 ATP per glucose molecule by completely oxidizing glucose with oxygen as the final electron acceptor. Fermentation, which occurs without oxygen and bypasses the electron transport chain, produces only 2 ATP per glucose. This large difference explains why aerobic organisms are more energy-efficient than anaerobic ones.

Why is oxygen toxic to some organisms?

Oxygen can be toxic because it produces reactive oxygen species (ROS), such as superoxide anions and hydrogen peroxide, during metabolism. These ROS damage proteins, lipids, and DNA. Organisms that lack protective enzymes like superoxide dismutase and catalase cannot detoxify ROS and therefore die in the presence of oxygen.

What enzymes allow aerobic organisms to survive exposure to oxygen?

Aerobic organisms typically produce enzymes such as superoxide dismutase, which converts harmful superoxide radicals into hydrogen peroxide, and catalase, which then breaks hydrogen peroxide down into water and oxygen. These enzymes neutralize reactive oxygen species and protect cellular structures from oxidative damage.

What are obligate aerobes and give an example.

Obligate aerobes are organisms that must have oxygen to survive and grow because they rely solely on aerobic respiration to generate ATP. They cannot use fermentation or anaerobic respiration. An example is Mycobacterium tuberculosis, the bacterium that causes tuberculosis in humans.

What are obligate anaerobes and give an example.

Obligate anaerobes are organisms that cannot survive in oxygen because they lack the enzymes to detoxify reactive oxygen species. They rely on anaerobic respiration or fermentation for ATP production. An example is Clostridium botulinum, the bacterium that produces the neurotoxin causing botulism.

What are facultative anaerobes and give an example.

Facultative anaerobes are organisms that can survive with or without oxygen. They prefer aerobic respiration when oxygen is available because it generates more ATP, but in its absence they can switch to fermentation or anaerobic respiration. A common example is Escherichia coli, which lives in the human intestine.

What are microaerophiles and give an example.

Microaerophiles are organisms that require oxygen but at levels lower than the concentration found in the atmosphere. They cannot survive in high oxygen environments because excess oxygen leads to toxic reactive oxygen species. An example is Helicobacter pylori, a bacterium that lives in the human stomach and is linked to ulcers.

How do prokaryotes carry out cellular respiration without mitochondria?

Prokaryotes perform respiration across their plasma membrane. The electron transport chain and ATP synthase are embedded in the plasma membrane, and in some cases, internal folds of the membrane such as mesosomes and lamellae increase the surface area available for energy production. This system allows them to generate ATP similar to eukaryotes but without organelles.

Where are photosynthetic pigments located in prokaryotes?

In prokaryotes, photosynthetic pigments like chlorophyll or bacteriochlorophyll are embedded in specialized thylakoid membranes or plasma membrane folds. Unlike eukaryotes, which use chloroplasts, prokaryotes rely on their cell membrane to carry out photosynthesis.

What is oxygenic photosynthesis and which organisms perform it?

Oxygenic photosynthesis is the process in which light energy is used to split water molecules, releasing oxygen as a byproduct, and generating ATP and NADPH for carbon fixation. It is carried out by plants, algae, and cyanobacteria.

What is anoxygenic photosynthesis and which organisms perform it?

Anoxygenic photosynthesis does not release oxygen because it uses electron donors other than water, such as hydrogen sulfide (H₂S) or ferrous iron (Fe²⁺). It is carried out by certain prokaryotes such as purple sulfur bacteria and green sulfur bacteria.

What pigments are used in oxygenic photosynthesis versus anoxygenic photosynthesis?

Oxygenic photosynthesis uses chlorophyll a as the main pigment, while anoxygenic photosynthesis uses bacteriochlorophylls, which absorb different wavelengths of light suited to low-light environments such as deep water or sediments.

What are the four categories of organisms based on energy and carbon sources?

Photoautotrophs: Use light for energy and CO₂ for carbon (plants, cyanobacteria). Chemoautotrophs: Use inorganic chemicals for energy and CO₂ for carbon (nitrifying bacteria). Photoheterotrophs: Use light for energy but organic compounds for carbon (purple non-sulfur bacteria). Chemoheterotrophs: Use organic molecules for both energy and carbon (animals, fungi, many bacteria).

Who discovered Archaea as a separate domain and how?

Carl Woese discovered Archaea in the 1970s by sequencing ribosomal RNA. He found that they were genetically distinct from both Bacteria and Eukarya, leading to the three-domain classification of life.

In what types of environments are Archaea commonly found?

Archaea often live in extreme environments such as hot springs (thermophiles), salt lakes (halophiles), acidic pools (acidophiles), and anaerobic habitats like swamps and animal guts (methanogens).

What are methanogens and why are they important?

Methanogens are a unique group of Archaea that are strict anaerobes and produce methane gas by reducing CO₂ with H₂. They are important in the carbon cycle and are found in wetlands, sewage treatment plants, and the digestive tracts of animals such as cows.

What is the hallmark of bacterial cell walls?

Bacterial cell walls contain peptidoglycan, a polymer of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) cross-linked by peptides. This structure provides rigidity and protection.

Do Archaea have peptidoglycan in their cell walls?

No, Archaea never contain peptidoglycan. Instead, they may have pseudopeptidoglycan, S-layers made of protein, polysaccharide-based walls, or sometimes no wall at all.

How do archaeal membranes differ from bacterial membranes?

Archaeal membranes are made of branched hydrocarbon chains attached to glycerol by ether linkages, which are chemically more stable. Bacterial membranes are made of fatty acids attached to glycerol by ester linkages.

What size are prokaryotic ribosomes and what are they made of?

Prokaryotic ribosomes are 70S in size, composed of a large 50S subunit and a small 30S subunit. They are the site of protein synthesis and are targeted by many antibiotics that block bacterial translation.

What is the nucleoid in a prokaryotic cell?

The nucleoid is the region inside a prokaryotic cell where the single circular chromosome is located. It is not surrounded by a membrane and often contains associated proteins that help organize and compact the DNA.

What are fimbriae and what is their function?

Fimbriae are short, hair-like protein filaments that extend from the bacterial surface. They are used for attachment to surfaces, tissues, or other cells, which is important in colonization and infection.

What is a capsule and why is it important in pathogenic bacteria?

A capsule is a sticky outer layer made of polysaccharides or proteins that surrounds some bacteria. It helps bacteria evade the immune system, prevents desiccation, and allows attachment to host tissues. Capsules make some bacteria more virulent.

How do bacterial flagella differ from eukaryotic flagella?

Bacterial flagella are made of flagellin and move by rotating like a propeller, powered by a proton motive force. Eukaryotic flagella are made of microtubules in a 9+2 arrangement and move with a whip-like motion using ATP.

Why do Gram-positive bacteria stain purple?

Gram-positive bacteria have a thick peptidoglycan layer that traps the crystal violet dye during Gram staining, so they appear purple under a microscope.

Why do Gram-negative bacteria stain pink?

Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane containing lipopolysaccharides. During Gram staining, the violet dye is washed out and replaced by the pink counterstain safranin.

What is endotoxin and where is it found?

Endotoxin is the lipid A component of lipopolysaccharides (LPS) in the outer membrane of Gram-negative bacteria. When these bacteria die, lipid A is released and can trigger strong immune reactions, fever, and septic shock.

What disease does Bacillus anthracis cause and what makes it dangerous?

Bacillus anthracis causes anthrax and is dangerous because it produces tough endospores that can survive extreme environmental conditions, allowing it to persist in soil and infect hosts long after release.

Why is Mycobacterium tuberculosis difficult to stain and treat?

Mycobacterium tuberculosis has a thick, waxy outer layer made of mycolic acids. This prevents most stains from penetrating, making it acid-fast, and also makes it resistant to many antibiotics and immune defenses.

What bacterium causes Lyme disease and how is it transmitted?

Lyme disease is caused by Borrelia burgdorferi, a spirochete bacterium, and is transmitted to humans through the bite of infected deer ticks.

How do Rhizobium bacteria benefit legume plants?

Rhizobium bacteria live in root nodules of legumes, where they fix atmospheric nitrogen into ammonia. The plant can then use the ammonia to make proteins, while the bacteria receive carbohydrates from the plant.

What is leghemoglobin and why is it important in nitrogen fixation?

Leghemoglobin is a plant-produced protein in root nodules that binds oxygen tightly. It reduces oxygen levels to protect the nitrogenase enzyme, which is inactivated by oxygen, allowing nitrogen fixation to occur.

How do Anabaena cyanobacteria separate nitrogen fixation from photosynthesis?

Anabaena forms specialized cells called heterocysts that provide an oxygen-free environment for nitrogen fixation. Other cells continue photosynthesis, and the two cell types exchange nutrients through connections.

What role do methanogens play in ecosystems?

Methanogens convert CO₂ and H₂ into methane in anaerobic environments such as wetlands, sewage treatment plants, and animal digestive systems. They contribute to nutrient cycles but also release methane, a potent greenhouse gas.

What are the three main types of symbiosis and examples of each?

Mutualism: both partners benefit (Rhizobium and legumes). Commensalism: one benefits and the other is unaffected (harmless gut bacteria). Parasitism: one benefits at the expense of the other (Borrelia burgdorferi causing Lyme disease).

What are exotoxins and give an example.

Exotoxins are proteins secreted by bacteria that are highly potent and often specific in their action. For example, botulinum toxin blocks nerve signals and causes paralysis.

What are endotoxins and give an example.

Endotoxins are toxic molecules that are part of the outer membrane of Gram-negative bacteria. The lipid A portion of lipopolysaccharide is released when the bacteria die, triggering fever and shock.

Why are viruses called obligate intracellular parasites?

Viruses cannot replicate on their own. They lack ribosomes and metabolic enzymes, so they must enter a host cell and use its machinery to replicate their genome and produce viral proteins.

What determines the host range of a virus?

A virus’s host range is determined by the specific interaction between viral surface proteins and receptor molecules on host cells. This explains why some viruses infect only one species or one type of cell.

What is a capsid and what are common viral shapes?

A capsid is a protein shell made of capsomeres that protects viral nucleic acids. Viral capsids can be helical (rod-shaped), icosahedral (20-sided), or complex (bacteriophages with heads and tails).

How do retroviruses like HIV replicate?

Retroviruses contain RNA genomes and an enzyme called reverse transcriptase. They convert their RNA into DNA, which integrates into the host cell genome as a provirus, allowing long-term infection and new virus production.

How does influenza evolve into new strains?

Influenza evolves through antigenic drift, which is the gradual accumulation of small mutations in viral surface proteins, and antigenic shift, which is the reassortment of its segmented RNA genome when two strains infect the same cell. Antigenic shift produces entirely new viral strains that can cause pandemics.

What are bacteriophages and how do they infect bacteria?

Bacteriophages are viruses that infect bacteria. They have an icosahedral head that holds DNA, a helical tail, and tail fibers that attach to the bacterial surface. They inject DNA into the host through the tail, initiating infection