MB351 Exam 3 Microbiology Study Guide: Diversity, Viruses & Biotechnology

What did Frederick Griffith's experiment demonstrate about heredity?

It showed that bacteria can transfer genetic information through the creation of S. pneumoniae strains.

What was the significance of the Avery-MacLeod-McCarty experiment?

It provided evidence that DNA contains genetic information.

Who built the first tree of life and what was used?

Carl Woese built the first tree of life using ribosomal RNA in 1976.

What does LUCA stand for and why is it important?

LUCA stands for 'last universal common ancestor' and is the hypothesized shared ancestor of the three domains of life.

What traits characterized the first life on Earth?

The first life forms, bacteria and archaea, appeared ~4 billion years ago and had anaerobic metabolism, not being photosynthetic.

What transition occurred with the emergence of phototrophs?

Phototrophs (cyanobacteria) and eukaryotes emerged with the transition to an oxygenated atmosphere.

What does the endosymbiotic theory propose?

It suggests that eukaryotes and eukaryotic organelles originated from the symbiosis of prokaryotes inside other prokaryotes.

What evidence supports the endosymbiotic theory regarding mitochondria and chloroplasts?

Both have circular genomes and 70s ribosomes, unlike the helical genomes and 80s ribosomes typical of eukaryotes.

What contributions did Schimper and Margulis make to endosymbiotic theory?

Schimper found that plastid division in plants is similar to binary fission; Margulis identified structures in eukarya from prokaryotic symbiosis.

Give a current example of endosymbiosis.

Filarial nematodes, like Brugia malayi, host Wolbachia spp., which is evolving into an organelle of the host.

Define culture-dependent genomics.

It involves sequencing a pure culture of microbes, but some cannot be isolated.

Define culture-independent genomics.

Metagenomics, which involves sequencing the DNA of complex microbial communities.

What is systematics?

The naming and classification of microorganisms, describing their traits and histories.

What is the difference between phylogeny and taxonomy?

Phylogeny refers to evolutionary relatedness, while taxonomy involves characterization, naming, and classification.

What is the binomial system of nomenclature?

A system where species are given descriptive genus and species names, e.g., Salmonella typhii.

What criteria must a microbial population meet to be considered a species?

They must be monophyletic, genomically coherent, phenotypically coherent, and clearly differentiated from other species.

What is a polyphasic approach in species definition?

It uses multiple combined methods to define a species.

What is multi-locus sequence analysis (MLSA)?

A method where multiple loci are examined and compared between species to create a phylogenetic tree.

What phenotypic traits can be used to identify an organism?

Traits such as morphology, motility, metabolism, physiology, and cell wall chemistry.

What are the criteria for formally validating a new prokaryote species?

Follow the International Code of Nomenclature, publish a detailed description, and deposit viable cultures in international collections.

What is the estimated total number of microbial species?

Predicted to be between 10^7 and 10^9 species.

What percentage of microbial species can be cultivated?

Only 1% of all microbial species can be cultivated.

How many microbial species are estimated to be in 1 gram of soil?

A single gram of soil contains approximately 20,000 species.

What limits our understanding of microbial diversity?

Factors include the inability to culture certain microbes and their presence in inaccessible environments.

What is microbial dark matter?

Microbial dark matter refers to uncultured microbes that remain unidentified due to limitations in current research methods.

What technologies are used to identify unculturable bacteria?

Genomic tools, fluorescent microscopy, and iChip technology.

What is the role of chemolithotrophs?

Chemolithotrophs can metabolize in environments that most organisms cannot, utilizing inorganic compounds as electron donors.

Name an electron donor used by phosphite oxidizers.

Phosphite.

What is the benefit of chemolithotrophy?

It allows organisms to metabolize in environments that are inhospitable to most other life forms.

What is the Calvin cycle?

A process in which CO2 is fixed with the enzyme RuBisCO to produce glyceraldehyde-3-phosphate.

Identify two examples of chemoautotrophs.

Acetogen (produces acetate) and methanogen (produces methane).

Define symbiosis.

Symbiosis is the relationship between normal microbiota and the host.

What are the three types of symbiotic relationships?

Mutualism, commensalism, and parasitism.

Give an example of mutualism.

Gut microbes and humans.

What is an example of commensalism?

Certain microbes on the skin and humans.

What characterizes parasitism?

One organism benefits at the expense of the host, potentially causing disease.

Where are microbes commonly found in the human body?

Respiratory tract, skin, mouth, gastrointestinal tract, and vagina.

What does a prokaryotic organism gain in a mutualistic relationship?

A stable environment, hydration, minerals, and protection from predators.

What does a eukaryotic organism gain from a prokaryotic partner?

Nutritional benefits from prokaryotic metabolic products.

What are transient microbiota?

Microbes that are only temporarily present on the body.

What are normal microbiota?

Microbes that permanently colonize the host without causing disease under normal conditions.

What are opportunistic pathogens?

Microbes that can cause disease when conditions allow, often when they leave their normal habitat.

What conditions can lead to opportunistic infections?

When normal microbes enter unusual body parts, when the immune system is suppressed, or due to microbial antagonism.

Describe the mutualistic relationship in the rumen microbiome.

Rumen microbes help ruminants digest indigestible compounds, producing fatty acids for food.

What is the role of leghemoglobin in soybean root nodules?

It acts as an oxygen buffer to facilitate nitrogen fixation by nitrogen-fixing bacteria.

What do bees gain from their microbiome?

Bacteria in the bee microbiome digest plant carbohydrates and provide protection against pathogens.

What type of relationship exists between Hawaiian bobtail squids and A. fischeri?

A mutualistic relationship where both organisms benefit.

What symbiotic relationship exists between Hawaiian bobtail squids and A. fischeri?

A mutualistic relationship where the squid provides nutrients and protection to A. fischeri, while A. fischeri provides bioluminescence for camouflage.

What is quorum sensing in relation to A. fischeri?

Quorum sensing is a process where the concentration of A. fischeri affects the production of bioluminescence based on population density.

What is the Lux operon?

The Lux operon is a set of genes in A. fischeri that is positively inducible and regulates bioluminescence based on the presence of an autoinducer.

What happens to the Lux operon when A. fischeri levels are high?

The autoinducer levels are high, activating the Lux operon, resulting in bioluminescence.

What occurs when A. fischeri levels are low?

Autoinducer levels are low, the Lux operon is off, and bioluminescence does not occur.

What is the effect of a mutation where the autoinducer is always bound to the Lux operon?

It leads to constant expression of the Lux operon, causing the squid to glow continuously, making it a target for predators.

What is the consequence of a mutation preventing the Lux activator from binding to DNA?

The Lux operon cannot be activated, leading to no bioluminescence and increased predation risk for the squid.

What is Wolbachia and its role in arthropods?

Wolbachia is a bacteria that influences sex determination in arthropods, such as pill-bugs.

Define a virus.

A virus is a genetic element that can only replicate within a living host cell and is not considered alive due to its inability to maintain metabolism independently.

What is the difference between a virus and a virion?

A virus refers to both extracellular and intracellular forms, while a virion is specifically the extracellular form of a virus.

Describe the viral genome.

The viral genome consists of nucleic acid, either DNA or RNA, and can be single-stranded or double-stranded.

What are capsids and capsomeres?

A capsid is a protein shell that protects the viral genetic material, while capsomeres are the protein subunits that make up the capsid.

What is the nucleocapsid?

The nucleocapsid is the combination of the virus's nucleic acid and the proteins surrounding it in enveloped viruses.

What are surface proteins in viruses?

Surface proteins, or spike proteins, are crucial for attaching to host cells and may include enzymes for infection and replication.

Are viral genomes complete?

No, viral genomes are not complete as they rely on host cells for most of the genetic information needed for reproduction.

What do viral genomes encode?

Viral genomes encode structural proteins, replication proteins not made by the host, proteins for gene regulation, and proteins for viral release.

What is the difference between naked and enveloped viruses?

Naked viruses lack a lipid envelope, while enveloped viruses have one. Enveloped viruses are generally more virulent.

What role does the microbiome play in a bee's health?

The bacteria in a bee's microbiome digest plant carbohydrates and provide protection against pathogens.

What are naked viruses?

Naked viruses have no layers aside from the capsid.

What are enveloped viruses?

Enveloped viruses have an outer layer made of a phospholipid bilayer and viral proteins.

Which type of virus is generally more virulent?

Naked viruses are generally more virulent than enveloped viruses.

What is the size range of viruses?

Viruses range in size from 20-200 nm.

Can viruses be seen with a light microscope?

No, viruses are too small to be seen with light microscopy; an electron microscope is required.

How do viruses attach to host cells?

Viruses attach through noncovalent interactions between the capsid or envelope proteins and host surface carbohydrates.

What is tissue tropism?

Tissue tropism refers to a virus's ability to infect specific types of tissues.

Describe the lytic cycle.

The lytic cycle involves the virus taking over the host cell's machinery, replicating, and causing cell lysis.

Describe the lysogenic cycle.

The lysogenic cycle involves the virus integrating into the host cell's DNA and remaining hidden until activated.

What is latency in viruses?

Latency is the ability of a virus to remain dormant during its life cycle.

How does latency help viruses infect more individuals?

Latency allows viruses to survive while new susceptible hosts enter the population.

What types of viruses are considered lysogenic?

Bacteriophages are considered lysogenic.

What types of viruses are considered latent?

Animal viruses, such as herpes zoster, are considered latent.

What kind of transduction occurs in the lytic cycle?

Generalized transduction occurs in the lytic cycle.

What kind of transduction occurs in the lysogenic cycle?

Specialized transduction occurs in the lysogenic cycle.

Describe latency in the Varicella zoster virus.

The Varicella zoster virus causes chickenpox and remains latent in host neurons, reactivating as shingles.

What is the Baltimore classification of viruses?

The Baltimore classification categorizes viruses based on their genome type, such as dsDNA, ssDNA, dsRNA, and ssRNA.

What is a positive sense (+) ssRNA virus?

+ ssRNA viruses have a genome that can be translated immediately into proteins.

What is a negative sense (-) ssRNA virus?

- ssRNA viruses cannot be translated immediately and require conversion to + ssRNA.

What are retroviruses?

Retroviruses use reverse transcriptase to convert their ssRNA genome into DNA.

Where do retroviruses fit in the central dogma of genetics?

Retroviruses introduce a new arrow from RNA to DNA in the central dogma.

What are some hosts of viruses?

Hosts include bacteria, archaea, animals, plants, protozoans, fungi, and other viruses.

What are the five main steps of viral replication?

1) Attachment, 2) Penetration, 3) Macromolecular synthesis, 4) Assembly, 5) Release.

DELETE What is a mnemonic for the five steps of viral replication?

An example mnemonic is 'All People Must Avoid Rabies' (APMAR).

What are the five steps of viral replication?

Attachment, Penetration, Macromolecular synthesis, Assembly, Release

What mnemonic can help remember the steps of viral replication?

All People Must Avoid Rabies (APMAR)

What occurs during the attachment step of viral replication?

The virion binds to the host cell using surface proteins that interact with specific structures on the host cell.

What is penetration in viral replication?

The viral nucleic acid enters the host cell where it will be expressed and replicated.

What is latency/lysogeny in the context of viral replication?

A state where viruses can delay replication and remain dormant within the host genome.

What happens during macromolecular synthesis in viral replication?

The viral nucleic acid is replicated, and viral proteins are synthesized based on the viral genome.

What occurs during the assembly step of viral replication?

Nucleocapsids are assembled from viral nucleic acid and capsid proteins.

What is the release step in viral replication?

The host cell releases complete virions, and if the virus is enveloped, it acquires the envelope at this stage.

What type of genome does the T4 bacteriophage have?

The T4 bacteriophage has a dsDNA genome.

What does the T4 bacteriophage infect?

The T4 bacteriophage infects E. coli.

What is burst time in viral replication?

The duration from attachment to release during a single replication cycle.