Biology 1151 Lecture 23 - Viruses & Prokaryotes
Viruses & Prokaryotes (Bacteria and Archaea)
Overview: A Borrowed Life
Viruses are the simplest biological systems.
A virus is an infectious particle consisting of genes packaged in a protein coat.
Viruses parasitize host cells to reproduce and carry out metabolic activities.
Most virologists consider viruses non-living, leading a "borrowed life."
A virus consists of a nucleic acid surrounded by a protein coat (capsid).
Viruses are not cells, but infectious particles with nucleic acid in a protein coat, sometimes with a membranous envelope.
The tiniest viruses are about 20 nm in diameter, smaller than a ribosome.
The viral genome can be:
Double-stranded DNA
Single-stranded DNA
Double-stranded RNA
Single-stranded RNA
Viruses are classified as "DNA virus" or "RNA virus" based on their nucleic acid type.
The viral genome is usually a single linear or circular molecule of nucleic acid.
The capsid is the protein shell enclosing the viral genome.
Capsids are built of many protein subunits called capsomeres.
The number of different proteins in a capsid is usually small.
The tobacco mosaic virus has a rod-shaped capsid with over 1,000 copies of a single protein in a helix.
Some viruses have accessory structures to help them infect hosts.
A membranous envelope surrounds the capsids of flu viruses (influenza viruses).
Viral envelopes are derived from the host cell membrane.
They contain host cell phospholipids and glycoproteins, as well as viral proteins and glycoproteins.
The most complex capsids are found in viruses infecting bacteria, called bacteriophages or phages.
"T-even" phages (T2, T4, T6) that infect Escherichia coli have:
Elongated icosahedral capsid heads enclosing DNA
A protein tailpiece that attaches to the host and injects DNA.
Viruses replicate only in host cells because they lack metabolic enzymes, ribosomes, and other protein-making equipment, making them obligate intracellular parasites.
An isolated virus is a packaged set of genes in transit between host cells.
Each virus type infects and parasitizes a limited range of host cells, known as its host range.
Host specificity depends on the evolution of recognition systems.
Viruses recognize host cells via a "lock and key" fit between viral surface proteins and specific receptor molecules on the host's surface.
Some viruses have a broad host range, infecting several species, while others infect only a single species.
West Nile and equine encephalitis viruses infect mosquitoes, birds, horses, and humans.
Measles virus infects only humans.
Most viruses of eukaryotes attack specific tissues.
Human cold viruses infect cells lining the upper respiratory tract.
The AIDS virus binds only to certain white blood cells.
Viral replicative cycles have characteristic general features.
A viral infection begins when the viral genome enters the host cell.
Genome entry mechanism varies with virus and host cell type.
"T-even" phages inject DNA into a bacterium.
Other viruses enter by endocytosis or fusion of the viral envelope with the host plasma membrane.
Once inside, the viral genome reprograms the host cell to copy viral nucleic acid and manufacture viral proteins.
The host provides nucleotides, enzymes, ribosomes, tRNAs, amino acids, ATP, and other components for viral protein production.
Many DNA viruses use the host cell's DNA polymerases to synthesize new genomes from viral DNA templates.
RNA viruses use virally encoded RNA polymerases that use RNA as a template.
Nucleic acid molecules and capsomeres self-assemble into viral particles.
The simplest viral replicative cycle ends with the exit of viruses from the infected host cell, which usually damages or destroys the host cell.
Cellular damage and death cause many symptoms of viral infection.
Phages: Lytic or Lysogenic Cycles
Phages are the best-understood viruses, some of which are complex.
Research on phages showed that some double-stranded DNA viruses can replicate via two mechanisms: the lytic cycle and the lysogenic cycle.
In the lytic cycle, the phage replicative cycle results in the death of the host.
In the last stage, the bacterium lyses (breaks open) and releases phages to infect others.
Each "regenerated" phage can infect a healthy cell.
Virulent phages replicate only by a lytic cycle.
Bacteria have defenses against phages.
Natural selection favors bacterial mutants with receptor sites no longer recognized by phages.
Bacteria produce restriction enzymes that cut up foreign DNA, including phage DNA.
Methylation of bacterial DNA prevents its destruction by restriction enzymes.
Natural selection favors phage mutants that bind to altered receptors or resist restriction enzymes.
In the lysogenic cycle, many phages coexist with host cells without destroying them, in a state called lysogeny.
Infection of an E. coli cell by phage l (lambda) begins when the phage binds to the cell surface and injects its DNA.
What happens next depends on the replicative mode: lytic or lysogenic cycle.
During a lytic cycle, viral genes turn the host cell into a λ-producing factory; the cell lyses and releases viral products.
During a lysogenic cycle, the λ DNA molecule integrates into a specific site on the E. coli chromosome, creating a segment within the bacterial DNA known as a prophage.
Viral proteins break both circular DNA molecules and join them together
As the host divides, it copies the prophage DNA and passes copies to daughter cells.
The viruses thus propagate without killing the host cells on which they depend.
A single infected cell gives rise to a large population of bacteria carrying the virus in prophage form.
Prokaryotes: Archaea & Bacteria - Masters of Adaptation
Parts of Utah’s Great Salt Lake have a salt concentration of 32%, nearly 10 times saltier than seawater.
The lake’s distinctive pink color is caused by red photosynthetic pigments produced by trillions of Halobacteria, a single-celled archaean.
This archaean is among the most salt-tolerant organisms on Earth.
Many other prokaryotes are adapted to extremely harsh conditions.
Deinococcus radiodurans can survive a radiation dose of 3 million rads, (3000 times what is fatal to a human).
can grow at a pH of 0.03, acidic enough to dissolve metal.
Some prokaryotes live in rocks 3.2 kilometers below the Earth’s surface!
Many are also very well adapted to ‘normal’ habitats, in which most other species are found.
Prokaryotes still dominate the biosphere.
More prokaryotes inhabit a handful of fertile soil or the mouth or skin of a human than the total number of people who have ever lived!
Structural and Functional Adaptations of Prokaryotic Cells
Generalized Structure of Prokaryotic Cells:
No membrane bound nucleus, only a nucleoid region containing a single looped chromosome
Cell wall present, but of different composition/structure than eukaryotic cell walls
No membrane bound organelles
Numerous appendages such as fimbriae and pili allow anchoring and attachment
Most prokaryotes that are motile have one or more flagella, though they are different in size, structure and function (are analogous) to the eukaryotic flagellum.
Prokaryotes are very small.
Prokaryotes were the first organisms to live on Earth.
Most prokaryotes are unicellular, although some species aggregate in colonies.
Most prokaryotes have diameters in the range of , compared to for most eukaryotic cells.
The most common shapes among prokaryotes are spheres (cocci), rods (bacilli), and spirals.
Nearly all prokaryotes have a cell wall & capsule external to the plasma membrane.
In nearly all prokaryotes, a cell wall maintains the shape of the cell, protects the cell, and prevents it from bursting in a hypotonic environment.
Many prokaryotes secrete another sticky protective layer of polysaccharide or protein.
This layer is called a capsule if it is dense and well defined or a slime layer if it is poorly organized.
Capsules and slime layers allow cells to adhere to a substrate or other individuals in a colony.
Some capsules and slime layers protect against dehydration, and some increase resistance to host defenses.
Populations of prokaryotes grow and adapt rapidly because:
They are small.
They reproduce by binary fission.
They have short generation times. A single cell in favorable conditions produces a large colony of offspring very quickly.
Prokaryotes reproduce asexually via binary fission, synthesizing DNA almost continuously.
Short generation times and large populations enhance mutation rates in prokaryotes.
Mutations are the major source of genetic variation in prokaryotes.
With generation times of minutes/hours, prokaryote populations adapt rapidly to environmental changes as natural selection favors mutations that confer greater fitness.
As a consequence, prokaryotes are important model organisms for scientists who study evolution in the laboratory.
Prokaryotes are highly evolved.
For more than 3.5 billion years, prokaryotic populations have responded successfully to many different types of environmental challenges. A great diversity of nutritional and metabolic adaptations have evolved in prokaryotes.
Nutritional and Metabolic Adaptations
Organisms can be categorized by their nutrition based on:
How they obtain energy.
Their source of carbon (needed to build organic molecules).
Nutritional diversity is greater among prokaryotes than among all eukaryotes.
Energy source and carbon source combine to group prokaryotes according to four major modes of nutrition:
Photoautotrophs: Photosynthetic organisms that harness light energy to drive the synthesis of organic compounds from .
Cyanobacteria are photoautotrophic prokaryotes.
Plants and algae are photoautotrophic eukaryotes.
Chemoautotrophs: Need only an inorganic molecule like as a carbon source but obtain energy by oxidizing inorganic substances.
Inorganic substances include hydrogen sulfide (), ammonia (), and ferrous ions (), among others.
This nutritional mode is unique to prokaryotes.
Photoheterotrophs: Use light to generate ATP but obtain their carbon in organic form from other organisms.
This mode of nutrition is limited and restricted to a few marine and halophilic prokaryotes.
Chemoheterotrophs: Must consume organic molecules for both energy and carbon.
This nutritional mode is found widely in prokaryotes, protists, fungi, animals, and even some parasitic plants. Humans are chemoheterotrophs.
Prokaryotic metabolism also varies with respect to oxygen.
Obligate aerobes: Require for cellular respiration.
Facultative anaerobes: Use if it is present but can also grow by fermentation in an anaerobic environment.
Obligate anaerobes: Are poisoned by and use either fermentation or anaerobic respiration, in which inorganic molecules other than accept electrons from electron transport chains.
Electron acceptors include nitrate ions () and sulfate ions ().
Nitrogen-fixing prokaryotes (cyanobacteria and some archaean methanogens) convert to , converting atmospheric nitrogen to a form that they (and eventually other organisms) can incorporate into organic molecules.
Prokaryotes can metabolize nitrogen in a wide variety of compounds, while eukaryotes are limited in the forms of nitrogen they can use.
Nitrogen-fixing cyanobacteria are the most self-sufficient of all organisms, requiring only light energy, , , water, and some minerals to grow.
Molecular Systematics and Prokaryotic Phylogeny
Until the late 20th century, prokaryotic taxonomy was based on criteria such as shape, motility, nutritional mode, and response to Gram staining.
These criteria may be valuable in culturing and identifying pathogenic bacteria, but they may not reflect evolutionary relationships.
Applying molecular systematics to the study of prokaryotic phylogeny has been very fruitful.
Microbiologists began comparing sequences of prokaryotic genes in the 1970s.
Carl Woese and his colleagues used small-subunit ribosomal RNA as a marker for evolutionary relationships.
They concluded that many prokaryotes once classified as bacteria are actually more closely related to eukaryotes and that they belong in a domain of their own—Archaea.
More recently molecular systematists have analyzed larger amounts of genetic data, including hundreds of entire genomes.
They found that a few traditional taxonomic groups, such as cyanobacteria, are monophyletic.
Other groups, such as gram-negative bacteria, are scattered throughout several lineages.
One important lesson that has already emerged from studies of prokaryotic phylogeny is that the genetic diversity of prokaryotes is immense.
Another important lesson is the significance of horizontal gene transfer in the evolution of prokaryotes.
Over hundreds of millions of years, prokaryotes have acquired genes from distantly related species, and they continue to do so today.
As a result, significant portions of the genomes of many prokaryotes are actually mosaics of genes imported from other species.
Horizontal gene transfer can make it difficult to determine the root of the tree of life.
Still, it is clear that for billions of years, prokaryotes have evolved in two separate lineages: bacteria and archaea.
Domain Archaea
Exhibits a great amount of diversity in extreme environments and in the oceans.
The first prokaryotes to be classified in domain Archaea are species that can live in environments so extreme that few other organisms can survive there.
Such organisms are known as extremophiles or “lovers” of extreme environments.
Extremophiles include extreme thermophiles and extreme halophiles.
Extreme halophiles live in salty places like the Great Salt Lake and the Dead Sea.
Extreme thermophiles thrive in hot environments.
The archaean Sulfolobus oxidizes sulfur in sulfur springs in Yellowstone N. P.
One extreme thermophile near deep-sea hydrothermal vents is informally known as “strain 121,” since it can double its cell numbers even at .
Other Archaea do not live in extreme environments.
Methanogens obtain energy by using to oxidize , producing methane as a waste product.
Methanogens are among the strictest anaerobes and are poisoned by .
Although some methanogens live in extreme environments, other species live in swamps/marshes where other microbes have consumed all the oxygen.
"Marsh gas" is actually methane produced by archaea.
Other methanogens live in the anaerobic guts of animals, playing an essential role in their nutrition.
Methanogens are important decomposers in sewage treatment facilities.
Domain Bacteria
Include the vast majority of familiar prokaryotes.
Bacteria range from the pathogenic species that cause strep throat and tuberculosis to the beneficial species that make Swiss cheese and yogurt.
Gram-negative bacteria
Among pathogenic bacteria, gram-negative species are generally more deadly than gram-positive species.
Recent systematics evidence points to 4 major groups of gram-negative bacteria
Proteobacteria – diverse clade grouped into 5 subgroups, each named by a greek letter (alpha, beta, gamma, delta, and epsilon)
Chlamydias – parasitic and only survive within animal cells; one species causes the most common STD in the U.S.
Spirochetes – includes several notorious pathogens including Treponema pallidum that causes syphilis and Borrelia burgdorferi that causes Lyme disease.
Cyanobacteria – these photoautotrophs are the only prokaryotes with plant-like, oxygen-generating photosynthesis.
Prokaryotes' Roles in the Biosphere
If humans were to disappear from the planet, life on Earth would go on for most other species.
Prokaryotes are so important to the biosphere that if they were to disappear, the prospects for many other species surviving would be dim.
Life depends on the recycling of chemical elements between the biological and chemical components of ecosystems, and prokaryotes play an important role in this process.
Chemoheterotrophic prokaryotes function as decomposers, breaking down dead organisms as well as waste products and unlocking supplies of carbon, nitrogen, and other essential elements.
Prokaryotes play a central role in many ecological interactions.
An ecological relationship between organisms that are in direct contact is called symbiosis.
If one of the symbiotic organisms is larger than the other, it is called the host, and the smaller is known as the symbiont.
In parasitism, one symbiotic organism, the parasite, benefits at the expense of the host.
The parasite eats the cell contents, tissues, or body fluids of the host. Unlike predators, parasites do not kill the host, at least not immediately.
Parasites that cause disease are called pathogens. Many pathogens are prokaryotic.
In mutualism, both symbiotic organisms benefit.
Prokaryotes and Humans
Prokaryotes have both beneficial and harmful impacts on humans.
Pathogenic prokaryotes represent only a small fraction of prokaryotic species.
Humans depend on mutualistic prokaryotes.
Your intestines are home to an estimated 500 to 1,000 species of bacteria; their cells outnumber all human cells in the body by as much as ten times.
Different bacterial species living in different portions of the intestines vary in their ability to process different foods.
In 2003, scientists published the first complete genome of one of these gut mutualists, Bacteroides thetaiotaomicron.
The genome includes a large array of genes involved in synthesizing carbohydrates, vitamins, and other nutrients needed by humans.
Signals from the bacterium activate human genes that build the network of intestinal blood vessels necessary to absorb nutrient molecules.
Other signals induce human cells to produce antimicrobial compounds to which B. thetaiotaomicron is not susceptible.
This action may reduce the population sizes of other, competing species, thus potentially benefiting both B. thetaiotaomicron and its human host.
Humans have learned to exploit the diverse metabolic capabilities of prokaryotes.
Humans have long used bacteria to make cheese and yogurt.
Bacteria can be used to make durable, biodegradable natural plastics.
Prokaryotes are harnessed in bioremediation, the use of organisms to remove pollutants from air, water, and soil.
Anaerobic bacteria decompose organic matter in sewage into material that can be used as landfill or fertilizer.
Other bioremediation applications include cleaning up oil spills and precipitating radioactive material from groundwater.
Through genetic engineering, humans can now modify prokaryotes to produce vitamins, antibiotics, hormones, and many other products.
Prokaryotes cause about half of human diseases.
Approximately 2 million people a year die of the lung disease tuberculosis, caused by the bacillus Mycobacterium tuberculosis.
Another 2 million die from diarrhea caused by other prokaryotes.
Pathogens cause illness by producing poisons called exotoxins and endotoxins.
Exotoxins are proteins secreted by certain bacteria and other organisms.
Exotoxins can produce disease even if the bacteria that manufacture them are not present.
An exotoxin produced by Vibrio cholerae causes cholera, a serious disease characterized by severe diarrhea.
Clostridium botulinum, which grows anaerobically in improperly canned foods, produces an exotoxin that causes botulism.
Endotoxins are lipopolysaccharide components of the outer membrane of some gram-negative bacteria.
In contrast to exotoxins, endotoxins are released only when the bacteria die and their cell walls break down.
Endotoxin-producing bacteria include Salmonella typhi, which causes typhoid fever, and other Salmonella species, which cause food poisoning.
Pathogenic prokaryotes pose a potential threat as weapons of bioterrorism.
In 2001, endospores of Bacillus anthracis, the bacterium that causes anthrax, were sent through the mail. 18 people developed inhalation anthrax and 5 died.
The threat of bioterrorism has stimulated intense research on pathogenic prokaryotes.