4.5 Viruses and Prokaryotes Flashcards
Viruses
Obligate intracellular parasites that must have access to host’s cells to function
Only able to infect cells containing the correct receptors
non-cellular and lack the ability to metabolize and grow
Unknown whether they respond to external stimuli
Genetic code is heritable allowing for adaptation and evolution but completely dependent on their host for reproduction
Diverse group that infects all domains of living organisms
Adapt to their changing environments and evolve through natural selection
Virion
an individual viral particle
Origin of viruses
A single virus has been found in the fossil record from 30,000 year old permafrost in Siberia
Remnants of ancient viral genes are found in “junk” DNA of living species
Researchers generally agree that viruses don’t share a single common ancestor
Three hypotheses of virus evolution: regressive, progressive, and virus-first
Regressive hypothesis
AKA de-evolution hypothesis
Viruses were once free-living cells or intro cellular parasites that decreased complexity and eventually lost ability to reproduce on their own
Progressive hypothesis
AKA escapist hypothesis
Viruses arose from RNA or DNA, or from self-replicating mobile genetic material like transposons, that acquired the ability to leave their native host cell for another
virus-first hypothesis
Viruses existed as the first self-replicating entities, predating cells
Baltimore classification system
Developed in early 1970s by Nobel prize-winning virologist David Baltimore
Grouped based on how they produce the positive-strand mRNA from the genome needed to produce required proteins
Groups include dsDNA, ssDNA, dsRNA, (+)ssRNA, (-)ssRNA, ssRNA-RT, dRNA-RT
Retroviruses
Virus that contains reverse transcriptase that converts their RNA to DNA which can then be incorporated into the host genome
Group I virus
dsDNA: mRNA is transcribed from the dsDNA genome
Group II virus
ssDNA: ssDNA genome is converted to dsDNA before transcription
Group III virus
dsRNA: mRNA transcribed from the dsRNA genome
Group IV virus
(+)ssRNA or positive sense single straaquirednded RNA: genome acts as mRNA or several rounds of transcription produce mRNA
Group V virus
(-)ssRNA or negative sense single stranded RNA: genome transcribed to +mRNA to be used as mRNA
Group VI virus
ssRNA-RT: ssRNA converted to dsDNA by RT and then incorporated into host genome for transcription
Group VII virus
dsDNA-RT: dsDNA converted to ssRNA intermediate that acts as mRNA, ssRNA converted to dsDNA by RT for replication
Capsid
Shell made of protein subunits called capsomeres that package the contents of a virus
Envelope
Outer shell of some viruses, composed of phospholipids and associated proteins
Contain matrix proteins that increase stability of outer membrane, but don’t make them invulnerable to changes in temperature, pH, and certain chemicals
Helical capsids
Long cylinders
Icosahedral capsids
Multifaceted three-dimensional spheres formed from 20 equilateral triangles
Enveloped viruses
Can have an icosahedral or helical capsid
Possess a plasma membrane derived from their host surrounding the capsid
Complex viruses
Can have icosahedral and helical shapes with an outer cell wall or have the two shapes put together to form a head and tail
Bacteriophages
AKA phage
Viruses that infect bacteria
Many have an icosahedron head and helical tail
Viral glycoproteins
On the outer layer of many viruses
Attach to viral receptors on host cell, initiating key events early during the infection process
Permissive cell
Host cell that allows virus to attach and also use the cell to replicate
Effects of viral infection on cell
Viral replication cycle after the biochemistry, structure, and function of host cell frequently causing damage
May go through apoptosis to minimize amount of virions produced
Lytic cycle
- Attachment: capsid protein or envelope glycoprotein of virion binds to receptor on membrane of host cell
- Penetration: genetic material enters through endocytosis, fusion, or injection
- If capsid enters host cell an uncoding process occurs in which the capsid is degraded
- Low pH can promote uncoding - Replication of viral genetic material and capsids
- Exact mechanism varies from group to group - Assembly: packaging viral genome into new capsids
- Enveloped viruses obtain an outer membrane from host as well
- Can be passive and occur spontaneously or active (requiring enzymes) - Release: method depends on virus and can occur through lysis or exocytosis
Latency
A lag between when the virus infects the host, and when it replicates and affects the host
Lysogenic cycle
Viral DNA becomes integrated with host genome
Only seen in bacteriophages
- Phage attaches to the cell surface of bacterium
- Viral DNA enters the bacterial cell
- Virus DNA integrates into bacterial DNA
- Integrated prophase replicates when bacterial DNA replicates
Prophage
Bacteriophage genome that has been incorporated into a bacterial genome
Lysogen
Bacterial host whose DNA has integrated bacteriophage DNA
May cause lysogenic conversion
Induction
Shifting from lysogenic to lytic cycle
Can be triggered by environmental factors
Phage DNA removed from host DNA and enters lytic cycle
Lysogenic conversion
Bacteria infected by phage that exhibit new phenotype
Prion
Proteinaceous infectious particles that contain no genetic code
Extremely hardy and don’t break down in the intestinal tract
Disease caused by irregular variant of a normal protein produced by the host
Cause the brain to form lesions and spread by eating nervous tissue of an infected individual
Replicate by entering a cell binding to the normal version of the protein, and converting it into the infectious variant, forming a new prion, making replication exponential
Bovine cattle encephalopathy
“mad cow” disease
Spongiform encephalopathy caused by a prion
Creutzfeldt-Jakob disease
Humans can develop it by eating beef infected with BSE
Viroids
Small, circular ssRNA particles that aren’t housed in a capsid nor produce proteins
Sole function is to reproduce RNA sequence using host cellular machinery
Viroid diseases infecting agricultural crops cause losses costing millions of dollars every year
Hepatitis D
Has viroid properties since it can only replicate in the presence of the hepatitis B virus
Microbial mats
Consist mostly of bacteria, although archaea are sometimes present
The individual prokaryotes in a microbial mat carry out different metabolic functions
Can be found in damp areas
Analysis of 16S ribosomal DNA
Has provided insight into some evolutionary relationships between different groups of bacteria
Woese’s 11 groups of bacteria
- gram-positive
- chlamydiae, green nonsulfur, – actinobacteria
- planctomycetes
- spirochaetes
- fusobacteria
- Cyanobacteria
- thermophilic sulfate reducers
- acidobacteria
- proteobacteria
Bacterial taxonomy
Bergey’s Manual of systematic bacteriology
ICBM and LPSN taxonomy
Does not fit into traditional Linnaean taxon comic system, but when used authorities recognize over 1000 phyla
Archaea clades
korarchaeota, euryarchaeota, crenarchaeota, nanoarchaeota
Korarchaeota
Primitive archaeans only found in hot springs and deep sea vents
Euryarchaeota
Includes methanogens and halobacteria
Crenarchaeota
Includes many thermopiles and sulfur-dependent extremophiles
Nanoarchaeota
Obligate symbionts of a crenarchaean
Diplobacilli
(diplococci) pairs of cells
Streptobacilli
(streptococci) chains of cells
Staphylococci
Clusters of cells
Archaean plasma membrane
Phospholipid composed of phytanyl sidechains instead of fatty acids seen in bacteria
Sometimes monolayer instead of bilayer
Gelatinous capsule
Additional layer surrounding the cell wall that serves as camouflage from a host’s immune system and to aid in attachment to surfaces
Nucleoid region
Condensed genetic material of a prokaryote
Invaginations
(or infoldings) in the plasma membrane of a prokaryotic cell that function in photosynthesis or respiration
Peptidoglycan
A polymer consisting of polysaccharide chains cross linked with peptides
Penicillin
Antibiotic that inhibits peptidoglycan cross-linking
Effective defense against gram-positive bacteria
Binary fission
Primary form of reproduction by prokaryotes
Results in formation of two identical daughter cells
DNA replicated, cell enlarges and produces material for a new cell wall, septum forms through equatorial region of the cell, cell pinches inward to form two separate cells
No recombination or exchange of genetic material
Transformation
Fragments of DNA are taken in from environment and incorporated into genome
DNA fragments released to environment by ruptured or dead cells
Transduction
During a bacteriophage’s switch from lysogenic stage to lytic cycle, imprecise excision of viral DNA from host genome may cause one or more bacterial genes to be packaged into the capsid
Genetic material is then transferred from one cell to another when infected by the same virus
Conjugation (bacteria)
Duplication and transfer of a plasmid from a donor cell to a recipient cell
A donor cell extends a long, hollow pilus to a recipient cell forming a conjugation bridge
Donor cell replicates a plasmid by threading one of the DNA strands through the conjugation bridge while the recipient cell adds the complementary strand to form its own copy of the plasmid
Plasmid can later be reintegrated with bacterial genome at the nucleoid region
Nitrogen fixation
Nitrogen in air is converted to ammonia and nitrates
Atmospheric nitrogen gas cannot be used by most living things
Ammonia can be used to build amino acids
Nitrates in the soil can be used by plants
Symbiotic roles of prokaryotes
- mutualism
- commensalism
- parasitism
Mutualism
Prokaryotes live in GI tract of many animals
In humans they help produce certain vitamins such as b-12 and vitamin k and digest some proteins and carbohydrates
In many animals that eat grass and woody plants, such as cattle and termites, bacteria that live in the gut digest cellulose for them, allowing them to receive nutrients
Commensalism
Symbiosis in which one species benefits and the other is unharmed
Bacteria inhabiting skin consume and metabolize their host’s sweat but cause no harm
Parasitism of prokaryotes
Pathogenic prokaryotes are considered parasites
Harm host by infecting them
Uses of genetically engineered bacteria
Production of pharmaceutical agents, antibiotic, enzymes, vitamins
Use of bacillus thuringiensis
Used in biological control to produce natural toxins that target pest insects such as mosquitoes, black flies, and agricultural pests.
Bioremediation
Bacteria are used to degrade or remove pollutants from the air, water, and soil
Pathogens
Infectious microorganisms responsible for causing illness
Robert Koch
German physician and early supporter of the germ theory of disease
Koch’s postulates
Link specific microorganism to a disease
- The microorganism can be found in high abundance in symptomatic individuals. The microorganism isn’t present in healthy individuals.
- The microorganism can be isolated from a symptomatic individual and grown in a laboratory culture.
- Inoculating a healthy individual with the cultured microorganism produces the disease
- The microorganism in the inoculated, diseased individual can be retrieved and identified as the same microorganism from the original diseased host
Have been significant revised within the field of modern microbiology:
Seemingly heathy individuals can be asymptomatic carriers
Pathogens little viruses and prions can’t be cultured
Complex disease associations can’t be linked by a simple set of methodological principles
Horizontal transmission
Spread of an infection from one person to another usually due to contact with bodily fluids
Outbreak
Disease occurs suddenly and in high numbers within an area
Epidemic
Disease outbreak spreads to a greater number of people over a larger area
Pandemic
Declared if original outbreak rapidly spreads to multiple countries, continents, or entire globe
Oncogenic viruses
Have the capacity to cause cancer
HPV → cervical cancer
Long-term hepatitis B → liver cancer
Vaccine mechanism
Expose healthy individuals to small amounts of inactivated viruses specific proteins or subunits of a virus, or live, attenuated viruses
Help develop immunity by imitating infection so immune system can produce T cells and antibodies to fight that infectious agent
Attenuated virus
Weakened virus
Influenza
Causes fever, sore throats runny nose, coughing, and exhaustion
Symptoms begin two days after exposure and can continue for 1-2 weeks
Individuals are contagious about 2-7 days after infection
Typically caused by influenza A virus which occurs naturally in wild birds and several other animal species
Influenza A subtyped based on glycoproteins on surface of viral envelope
HIV-1
Enveloped (+)ssRNA retrovirus
Primarily attacks CD4+ helper T-cells, macrophages, and other immune cells
Causes AIDS leading to the eventual failure of the immune system
Arose through zoonosis when it crossed the species barrier from chimpanzees to humans in West Africa during the early 1900s
Ebola
Virus causes fever , sore throat, muscle pain, headaches, rash, and hemorrhage, both internal and external bleeding
Transmitted through contact with bodily fluids
Symptoms develop within a few days or weeks of infection
Mortality of about 50% but can be as high as 90%
Death occurs about onset of symptoms
Enveloped (-)ssRNA viruses with a long filamentous shape
Infects monocytes, macrophages, liver cells, fibroblasts, and endothelial cells
Replication of virus triggers inflammatory response and can lead to sepsis
COVID-19
SARS-CoV-2 or severe acute respiratory syndrome coronavirus 2 is an enveloped (+)ssRNA virus in the coronavirus family
Infects cells in the respiratory tract by exploiting their ACE2 (angiotensin-converting enzyme) cell surface receptors to gain entry
Bats have been identified as an animal reservoir though scientist are still evaluating the possibility of an intermediate mammalian host in the zoonotic jump to humans
Symptoms include fever, dry cough, shortness of breath, and fatigue
Hypothetical archaean pathogens
Of prokaryotes, only bacteria are known to cause disease, though it is speculated that the high similarity between archaean and eukaryotic proteins could mean that symptoms of hypothetical archaean pathogens might present similar to autoimmune disease
Biofilms
Thin films of bacteria that stick to surfaces
Tuberculosis (structure and treatment)
Caused by Mycobacterium tuberculosis
Weakly gram-positive aerobic bacillus with an outer membrane
Difficult to treat due to outer structure and existence of drug-resistant strains
Invade air sacs in the lungs and consumed by alveolar macrophages, where they reproduce
Other immune cells that aid the macrophages form inflammatory granulomas
In granulomas, can evade destruction by cytotoxic T lymphocytes or entering dormant state
These granolas, characterized by necrosis in their centers, are called tubercles
Tuberculosis (stats, symptoms)
1% infection rate per year
Estimated that about 1/3 of world’s population is infected, though mostly dormant
Most cases in Africa and South East Asia
90% of cases produce latent, asymptomatic disease
Symptoms include fever, weight loss, and fatigue
Symptoms of pulmonary TB include chest pain productive cough, and in up to 20% of cases extra-pulmonary spread of disease
Tuberculosis disease process
- Mycobacteria enter the air sacs in the lungs
- Mycobacteria are consumed by alveolar macrophages
- Immune cells surround the infected macrophages
- The immune response forms a granuloma
- Mycobacteria reproduce within the granuloma and are released
- Mycobacteria disperse to continue the infection cycle
Foodborne illness
Symptoms include nausea, vomiting, diarrhea, cramps, and fever
Severe complications or death can occur it bacteria enters blood stream
Common culprits include viruses such as norovirus and hepatitis A and bacteria such as salmonella, escherichia coli, campylobacter, and listeria
Can be avoided by washing hands, practicing safe food handling, storing refrigerated foods below 40°F keeping raw foods separated from other foods, cooking meats to their recommended temperatures, and avoiding raw or unpasteurized dairy products
MRSA
Methicillin-resistant Staphylococcus aureus
Gram-positive non-spore forming coccus that grows in clusters or chains
Staphylococcus aureus typically found on the skin and upper respiratory tract but causes disease if able to enter other tissues
Symptoms include red pustular bumps, fever, or deeper abscesses that reach into the soft tissue under the skin
Life-threatening if untreated and can cause necrotizing fasciitis or toxic shock syndrome
