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Viruses & Bacteria and Archaea - Coggle Diagram
Viruses & Bacteria and Archaea
A virus consists of a nucleic acid surrounded by a protein coat
A virus is an infectious particle consisting of genes packaged in a protein coat
Viruses are much simpler in structure than even prokaryotic cells
Viruses can cause a wide variety of diseases
The Discovery of Viruses: Scientific Inquiry
Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration
In the late 1800s, researchers hypothesized that unusually small bacteria might be responsible
Later work suggested that the infectious agent did not share features with bacteria (such as the ability to grow on nutrient media)
In 1935, Wendell Stanley confirmed this latter hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)
Structure of Viruses
Viruses are not cells
A virus is a very small infectious particle consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope
The simple structure of viruses make them a useful biological system
Viral Genomes
Viral genomes may consist of either
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Viruses are classified as DNA viruses or RNA viruses
The genome is either a single linear or circular molecule of the nucleic acid
Viruses have between 3 and 2,000 genes in their genome
Capsids and Envelopes
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They cannot reproduce or carry out metabolism outside of a host cell
Viruses exist in a shady area between life-forms and chemicals, leading a kind of “borrowed life”
Viruses replicate only in host cells
Viruses are obligate intracellular parasites, which means they can replicate only within a host cell
Each virus has a host range, a limited number of host species that it can infect
Some viruses have broad host ranges, while others are able to infect only one species
For example, measles virus only infects humans
General Features of Viral Replicative Cycles
The viral genome enters the host cell in a variety of ways
Once a viral genome has entered a cell, the cell begins to manufacture viral proteins
The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules
Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses
Replicative Cycles of Phages
Phages are the best understood of all viruses
Phages have two alternative reproductive mechanisms: the lytic cycle and the lysogenic cycle
The Lytic Cycle
The lytic cycle is a phage replicative cycle that culminates in the death of the host cell
The lytic cycle produces new phages and lyses (breaks open) the host’s cell wall, releasing the progeny viruses
A phage that reproduces only by the lytic cycle is called a virulent phage
The Lysogenic Cycle
The lysogenic cycle replicates the phage genome without destroying the host
The viral DNA molecule is incorporated into the host cell’s chromosome
Phages that use both the lytic and lysogenic cycles are called temperate phages
A temperate phage called lambda (λ) is widely used in biological research
The integrated viral DNA is known as a prophage
Every time the host divides, it copies the phage DNA and passes the copies to daughter cells
An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode
Some prophages are expressed during lysogeny, and some cause the host bacteria to secrete toxins that are harmful to humans
Bacterial Defenses Against Phages
Bacteria have their own defenses against phages
Natural selection favors bacterial mutants with surface proteins that cannot be recognized as receptors by a particular type of phage
Foreign DNA can be identified as such and cut up by cellular enzymes called restriction enzymes
The bacterium’s own DNA is protected from the restriction enzymes by being methylated
Both bacteria and archaea can protect themselves from viral infection with the CRISPR-Cas system
It is based on sequences called clustered regularly interspaced short palindromic repeats (CRISPRs)
Each “spacer” sequence between the repeats corresponds to DNA from a phage that had infected the cell
Particular nuclease proteins interact with the CRISPR region; these are called CRISPR-associated (Cas) proteins
When a phage infects a bacterial cell that has the CRISPR-Cas system, the phage DNA is integrated between two repeat sequences
If the cell survives the infection, it can block any attempt of the same type of phage to reinfect it
The attempt of the phage to infect the cell triggers transcription of the CRISPR region
The resulting RNAs are cut into pieces and bound by Cas proteins
The Cas proteins use the phage-related RNA to target the invading phage DNA
The phage DNA is cut and destroyed
Natural selection favors phage mutants that can bind to altered cell surface receptors or that are resistant to enzymes
The relationship between phage and bacteria is in constant evolutionary flux
Replicative Cycles of Animal Viruses
There are two key variables used to classify viruses that infect animals:
An RNA or DNA genome, either single-stranded or double-stranded
The presence or absence of a membranous envelope
Whereas few bacteriophages have an envelope or an RNA genome, many animal viruses have both
Viral Envelopes
Many viruses that infect animals have a membranous envelope
Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell
The viral envelope is usually derived from the host cell’s plasma membrane as the viral capsids exit
Other viral membranes form from the host’s nuclear envelope and are then replaced by an envelope made from Golgi apparatus membrane
The herpesvirus is an example of this
Viral Genetic Material
The broadest variety of RNA genomes is found in viruses that infect animals
Retroviruses use reverse transcriptase to copy their RNA genome into DNA
HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome)
The viral DNA that is integrated into the host genome is called a provirus
Unlike a prophage, a provirus remains a permanent resident of the host cell
RNA polymerase transcribes the proviral DNA into RNA molecules
The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles released from the cell
Evolution of Viruses
Viruses do not fit our definition of living organisms
Since viruses can replicate only within cells, they probably evolved as bits of cellular nucleic acid
Candidates for the source of viral genomes include plasmids and transposons
Plasmids, transposons, and viruses are all mobile genetic elements
The largest virus identified about 20 years ago is the size of a small bacterium
Its genome encodes proteins involved in translation, DNA repair, protein folding, and polysaccharide synthesis
There is controversy about whether this virus evolved before or after cells
In the past decade several even larger viruses have been identified; how these evolved is an unresolved question
CONCEPT 19.3: Viruses and prions are formidable pathogens in animals and plants
Diseases caused by viral infections affect humans, agricultural crops, and livestock worldwide
Smaller, less complex entities called prions also cause disease and animals
Viral Diseases in Animals
Viruses may damage or kill cells by causing the release of hydrolytic enzymes from lysosomes
Some viruses cause infected cells to produce toxins that lead to disease symptoms
Others have molecular components such as envelope proteins that are toxic
A vaccine is a harmless derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen
Vaccines can prevent certain viral illnesses, such as smallpox, rubella, mumps, and others
Viral infections cannot be treated by antibiotics
Antiviral drugs can help to treat, not cure, viral infections by inhibiting synthesis of viral DNA and by interfering with viral assembly
A vaccine is a harmless derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen
Vaccines can prevent certain viral illnesses, such as smallpox, rubella, mumps, and others
Viral infections cannot be treated by antibiotics
Antiviral drugs can help to treat, not cure, viral infections by inhibiting synthesis of viral DNA and by interfering with viral assembly
Emerging Viral Diseases
Emerging viruses are those that suddenly become apparent
HIV, the AIDS virus, is a classic example
The Ebola virus is one of several emerging viruses that cause hemorrhagic fever, an often fatal illness
In 2014, a widespread outbreak (epidemic) of Ebola virus occurred
In 2017, 2018, and 2019, smaller outbreaks occurred in the Democratic Republic of the Congo
Other examples of emerging viruses include the chikungunya virus and the recently emerging Zika virus (2015)
One cause of rapidly emerging viral disease in humans is mutation of existing viruses into new ones that can spread more easily
A second cause is the spread of a viral disease from a small, isolated human population
A third cause is the spread of existing viruses from other animals
It is estimated that about three-quarters of new human diseases originate in this way
Flu epidemics are caused by type A influenza viruses; these infect a wide variety of animals including birds, pigs, horses, and humans
Strains of influenza A are given standardized names based on the viral surface proteins hemagglutinin (HA) and neuraminidase (NA)
As of 2017 18 types of HA, and 11 types of neuraminidase, have been identified
The H5N1 strain is quite deadly, because it is very different from influenza strains circulating among people for a long time
It is thus difficult for people to mount an effective immune response to this strain
However, it has not caused an epidemic because it is not transmitted from person-to-person
A deadly strain of H1N1, originally called the swine flu, was not actually transmitted to humans from pigs
Instead, the story was more complex, H1N1 was a unique combination of swine, avian, and human influenza genes
An epidemic of H1N1 occurred in 2009, reaching 207 countries, infecting over 600,000 people and killing almost 8,000
A global epidemic like this is called a pandemic
Influenza viruses have nine RNA segments in their genome, leading to many new genetic combinations
They also have a high rate of mutation
Normal seasonal flu viruses are not considered emerging viruses because variants of these viruses have been circulating among humans for a long time
However, these viruses still undergo mutation and reassortment
Variations thought to be most likely to occur each year are selected to generate vaccines
Changes in host behavior or the environment can increase the spread of viruses responsible for emerging diseases
New roads into a remote area may increase spread of viral diseases
The use of insecticides and mosquito nets may help prevent the spread
It is possible that global climate change may allow mosquitoes that carry viruses to expand their range
Viral Diseases in Plants
More than 2,000 types of viral diseases of plants are known and cause spots on leaves and fruits, stunted growth, and damaged flowers or roots
Most known plant viruses have an RNA genome
Many have a helical capsid, while others have an icosahedral capsid
Plant viruses spread disease by two major routes:
Horizontal transmission, entering through damaged cell walls
Vertical transmission, inheriting the virus from a parent
Prions are infectious proteins that appear to cause degenerative brain diseases in animals
Scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in humans are all caused by prions
Prions are incorrectly folded proteins, can be transmitted in food, act slowly, and are virtually indestructible
Prions are somehow able to convert a normal form of a protein into the misfolded version
Then several prions aggregate into a complex that can convert more proteins to prions, which join the chain
Prions might also be involved in diseases such as Alzheimer’s and Parkinson’s disease
There are many outstanding questions about these small infectious agents
Structural and functional adaptations contribute to prokaryotic success
Prokaryotes were the first organisms to inhabit Earth
Most are unicellular, but some species form colonies
Most prokaryotic cells are 0.5–5 µm, much smaller than the 10–100 µm of many eukaryotic cells
They have a variety of shapes including spheres (cocci), rods (bacilli), and spirals
Cell-Surface Structures
The cell wall maintains shape, protects the cell, and prevents it from bursting in a hypotonic environment
Most prokaryotes lose water and experience plasmolysis in hypertonic environments
Salt is used as a preservative because water loss slows reproduction of food-spoiling prokaryotes
Eukaryote cell walls are made of cellulose or chitin
Most bacterial cell walls instead contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides
Archaeal walls contain a variety of polysaccharides and proteins, but lack peptidoglycan
Scientists use the Gram stain to classify bacteria by cell wall composition
Gram-positive bacteria have simpler walls with a large amount of peptidoglycan
The walls of gram-negative bacteria have less peptidoglycan and are more complex with an outer membrane that contains lipopolysaccharides
Many prokaryotes have a sticky layer of polysaccharide or protein surrounding the cell wall
It is called a capsule if it is dense and well-defined, or a slime layer if it is not well organized
Both types enable adherence to the substrate or other individuals, prevent dehydration, and protect the cell from the host’s immune system
Some bacteria form metabolically inactive endospores when water or nutrients are lacking
The cell copies its chromosome and surrounds it with a multilayered structure
Endospores can withstand extreme conditions and remain viable for centuries
Some prokaryotes have hairlike appendages called fimbriae that allow them to stick to their substrate or other individuals in a colony
Pili (or sex pili) are longer than fimbriae and function to pull cells together enabling the exchange of DNA
Evolutionary Origins of Bacterial Flagella
Bacterial flagella are composed of 42 different kinds of proteins that form a motor, hook, and filament
Bacterial flagella likely originated as simpler structures that were modified stepwise over time
Only half of the flagellum’s proteins are essential
About half of those are modified versions of proteins with different functions
Proteins forming the rod, hook, and filament are all descended from a protein that formed a pilus-like tube
Flagella likely evolved as existing proteins were added to an ancestral secretory system
This is an example of exaptation, where structures adapted for one function take on new functions through descent with modification
Internal Organization and DNA
Prokaryotic cells lack complex compartmentalization
Some prokaryotes have specialized membranes that perform metabolic functions
These are usually infoldings of the cell membrane
Prokaryotes have less DNA and produce fewer proteins than the eukaryotes
Prokaryotes have one circular chromosome; eukaryotes have multiple linear chromosomes
Prokaryotes lack a nucleus; the chromosome is in the nucleoid, a region with no membrane
Prokaryotes may also have smaller rings of independently replicating DNA called plasmids
There are minor differences in DNA replication, transcription, and translation between eukaryotes and prokaryotes
These differences allow antibiotics to kill or inhibit bacterial cell growth without harming human cells
Reproduction
Prokaryotes reproduce quickly by binary fission and can divide every 1–3 hours under optimal conditions
There are three key features of prokaryote biology:
They are small
They reproduce by binary fission
They have short generation times
Rapid reproduction, mutation, and genetic recombination promote genetic diversity in prokaryotes
Three factors contribute to the high levels of genetic diversity observed in prokaryote populations:
Rapid reproduction
Mutation
Genetic recombination
Rapid Reproduction and Mutation
Cells produced by binary fission are generally identical, but differences can arise through mutation
Mutation rates are typically low, but mutations accumulate rapidly with short generation times and large populations
Rapid production of genetic diversity in prokaryote populations enables rapid adaptation by natural selection
Though structurally simpler than eukaryote cells, prokaryotes are highly evolved
Genetic Recombination
Genetic recombination, the combining of DNA from two sources, contributes to prokaryote diversity
DNA from different individuals can be combined by transformation, transduction, or conjugation
Movement of genes between individual prokaryotes of different species is called horizontal gene transfer
Transformation and Transduction
In transformation, prokaryotic cells incorporate foreign DNA taken up from their surroundings
For example, a nonpathogenic cell could take up a piece of DNA carrying an allele for pathogenicity and replace its own allele with the foreign allele
The resulting recombinant cell would be pathogenic
In transduction, phages (from “bacteriophages,” viruses that infect bacteria) carry prokaryotic genes from one host cell to another
Transduction is generally an unintended result of the phage replicative cycle
Conjugation and Plasmids
Conjugation is the process through which DNA is transferred between two prokaryotic cells
In bacteria, the DNA transfer is always one way: One cell donates the DNA and the other receives it
A piece of DNA called the F factor (F for fertility) is required for the production of pili
The F factor can exist either as a plasmid or a segment of DNA within the bacterial chromosome
The F Factor as a Plasmid
Cells containing the F plasmid (F+ cells) function as DNA donors
Cells lacking the F factor (F– cells) are recipients
An F+ cell can convert an F– cell to an F+ cell if it transfers an entire F plasmid to the F– cell
If only part of the F plasmid’s DNA is transferred, the recipient cell will be recombinant
R Plasmids and Antibiotic Resistance
Antibiotics kill most bacteria, but not those with R plasmids, plasmids that carry resistance genes
Some R plasmids carry genes for resistance to multiple antibiotics
R plasmids also have genes that encode the pili used to transfer DNA between cells, enabling the rapid spread of resistance
Diverse nutritional and metabolic adaptations have evolved in prokaryotes
Prokaryotes can be categorized by how they obtain energy and carbon:
Phototrophs obtain energy from light
Chemotrophs obtain energy from chemicals
Autotrophs require CO2 or related compounds as a carbon source
Heterotrophs require an organic nutrient to make other organic compounds
Energy and carbon sources are combined to give four major modes of nutrition:
Photoautotroph
Chemoautotroph
Photoheterotroph
Chemoheterotroph
The Role of Oxygen in Metabolism
Prokaryotic metabolism varies with respect to O2
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Nitrogen Metabolism
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Prokaryotes have radiated into a diverse set of lineages
Prokaryotes date back to 3.5 billion years ago
They now inhabit every environment known to support life
Advances in genomics are just beginning to reveal the extent of prokaryotic diversity
An Overview of Prokaryotic Diversity
Genetic analysis conducted in the 1970s led to the division of prokaryotes into Bacteria and Archaea
Analysis of over 1,700 genomes indicates a few of the traditional groups are monophyletic, but others are scattered throughout several lineages
An Overview of Prokaryotic Diversity
In the past, the polymerase chain reaction (PCR) was used to analyze individual prokaryote genes
Today, metagenomics is used to obtain entire prokaryotic genomes from environmental samples
Though only 16,000 prokaryote species have been named, a handful of soil can contain 10,000 species
Horizontal gene transfer has played a key role in the evolution of prokaryotes
Significant portions of the genomes of prokaryotes are mosaics of genes imported from other species
For example, in a study of 329 bacterial genomes, an average of 75% of the genes in each genome had been horizontally transferred at some point
Bacteria
Bacteria include the vast majority of prokaryotic species familiar to most people
Every major mode of nutrition and metabolism is represented among bacteria
Exploring bacterial diversity
There are about 16,000 known species of bacteria
The actual number is estimated to be 700,000–1.4 million species
Proteobacteria
Gram-negative bacteria including photoautotrophs, chemoautotrophs, and heterotrophs
For example, the sulfur bacterium Thiomargarita namibiensis, is an autotroph that obtains energy by oxidizing H2S and producing sulfur as a waste product
Heterotrophic proteobacteria include several pathogens
Neisseria gonorrhoeae causes gonorrhea
Vibrio cholerae causes cholera
Helicobacter pylori causes stomach ulcers
Chlamydias
All species parasitize animal cells and have gram-negative walls lacking peptidoglycan
For example, Chlamydia trachomatis causes nongonococcal urethritis, the most common sexually transmitted disease in the United States
Spirochetes
These bacteria are helical gram-negative heterotrophs that spiral through the environment by rotating internal filaments
Many are free-living, but others are pathogens
For example, Treponema pallidum, causes syphilis, and Borrelia burgdorferi, causes Lyme disease
Cyanobacteria
These bacteria are gram-negative photoautotrophs
Plant chloroplasts likely evolved from cyanobacteria by the process of endosymbiosis
Solitary and filamentous cyanobacteria are abundant components of freshwater and marine phytoplankton
Gram-Positive Bacteria
Gram-positive bacteria are a diverse group
Actinomycetes are colony forming bacteria including pathogens and soil decomposers
Soil-dwelling species of Streptomyces are cultured as a source of antibiotics, including tetracycline
Other subgroups include pathogens such as Staphylococcus aureus; Bacillus anthracis, the cause of anthrax; and Clostridium botulinum, the cause of botulism
Methanogens are obligate anaerobes that produce methane as a by-product of their metabolism
They are found in diverse environments
Under kilometers of ice in Greenland
In swamps and marshes
In the guts of cattle, termites, and other herbivores
Euryarchaeota is the clade that includes many of the extreme halophiles, most methanogens, and some extreme thermophiles
Most of the extreme thermophiles belong to another clade
TACK is a supergroup composed of the remaining, closely-related clades of archaea
The group is named for its component clades
Thaumarchaeota
Aigarchaeota
Crenarchaeota—includes most extreme thermophiles
Korarchaeota
Prokaryotes play crucial roles in the biosphereIf prokaryotes were to disappear, the prospects for any other life surviving on Earth would be dim
Prokaryotes play a major role in the recycling of chemical elements between the living and nonliving components of the environment
For example, some chemoheterotrophic prokaryotes are decomposers, they break down dead organisms and wastes and release carbon and other elements
Prokaryotes can convert some molecules to forms that are taken up by other organisms
Autotrophic prokaryotes use CO2 to produce sugars and O2 that are consumed by other organisms
Nitrogen-fixing bacteria transform atmospheric nitrogen into forms available to other organisms
Some prokaryotes can increase the availability of soil nutrients that plants require for growth
In mutualism, both symbiotic organisms benefit
In commensalism, one organism benefits while neither harming nor helping the other
In parasitism, an organism called a parasite harms but does not usually kill its host
Parasites that cause disease are called pathogens