Viruses and Virions

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Questions and Answers

How does a virion facilitate infection?

  • By existing as an extracellular form that can transfer the viral genome to new hosts. (correct)
  • By directly replicating within a host cell without needing any host machinery.
  • By immediately integrating its genome into the host's chromosome upon entry.
  • By forming a symbiotic relationship with the host cell, enhancing its metabolic processes.

Why are proteins on the virion surface crucial for viral infection?

  • They are essential for the virion's attachment to the host cell. (correct)
  • They degrade the host cell's DNA, preventing it from interfering with viral replication.
  • They neutralize antibodies, disabling the host's immune response.
  • They protect the viral genome from UV radiation and other environmental stressors.

What is the primary role of the viral envelope?

  • To accelerate the metabolic rate of the infected host cell.
  • To provide structural rigidity and protect the viral genome.
  • To enhance the virion's ability to infect host cells. (correct)
  • To synthesize proteins required for viral replication.

How does the capsid contribute to viral survival?

<p>By providing a protective shell for the viral genome outside the host cell. (A)</p> Signup and view all the answers

Which type of virus is expected to have the highest mutation rate?

<p>Small RNA viruses (B)</p> Signup and view all the answers

Based on what criteria did David Baltimore classify viruses?

<p>Host they infect and genome structure (B)</p> Signup and view all the answers

What role does lysozyme-like enzymes play in bacteriophages?

<p>Aiding in both infection and release of the virus from the host cell. (C)</p> Signup and view all the answers

During which step of viral replication does the host cell machinery synthesize viral nucleic acid and protein?

<p>Synthesis (C)</p> Signup and view all the answers

What characterizes the eclipse phase of viral replication?

<p>The virus has attached to and entered the host cell, but infectious virions are undetectable. (D)</p> Signup and view all the answers

What determines the host specificity of a virus?

<p>The presence of specific receptors on the host cell surface that interact with viral surface proteins. (B)</p> Signup and view all the answers

How does a lytic viral infection differ from a lysogenic viral infection?

<p>Lytic infections destroy the host cell quickly, while lysogenic infections incorporate viral DNA into the host genome. (A)</p> Signup and view all the answers

What is the key outcome of lysogenic infection that can lead to new genetic properties in the host?

<p>Acquisition of new genetic information through transduction. (B)</p> Signup and view all the answers

How does a temperate phage behave in the lysogenic pathway?

<p>It integrates into the bacterial genome as a prophage without transcribing viral genes. (D)</p> Signup and view all the answers

What is the primary purpose of using a plaque assay in virology?

<p>To quantify the number of infectious virions in a fluid sample. (D)</p> Signup and view all the answers

How does viral replication in animal cells differ from that in bacteriophages?

<p>Animal viruses enter the host cell with the entire virion, while bacteriophages typically inject only their nucleic acid. (C)</p> Signup and view all the answers

What is a characteristic outcome unique to viral infection in animal cells?

<p>Transformation of normal cells into tumor cells. (C)</p> Signup and view all the answers

According to the RNA world hypothesis, what role might viruses have played in early molecular evolution?

<p>Viruses may be remnants of an ancient RNA-based world, contributing to early evolution. (D)</p> Signup and view all the answers

Which of the following statements is true about negative-strand RNA viruses?

<p>They must first be transcribed into complementary mRNA genomes. (C)</p> Signup and view all the answers

How does shingles differ from chickenpox with respect to transmissibility?

<p>Shingles is less contagious than chickenpox. (B)</p> Signup and view all the answers

What is a key factor that contributed to the emergence and spread of mpox (monkeypox) after smallpox eradication?

<p>The lack of smallpox immunity in populations that were no longer vaccinated against smallpox. (B)</p> Signup and view all the answers

What makes poliovirus unique compared to other animal viruses?

<p>It primarily targets human cells, specifically motor neurons, leading to paralysis. (D)</p> Signup and view all the answers

What is the function of hemagglutinin (HA) in the influenza virus?

<p>It allows the virus to bind to host cells. (C)</p> Signup and view all the answers

Why does the influenza vaccine need to be updated each year?

<p>The virus undergoes antigenic drift and antigenic shift, causing changes in its surface proteins. (B)</p> Signup and view all the answers

How does antigenic shift contribute to the emergence of pandemic influenza strains?

<p>By causing major, abrupt changes through the exchange of genetic material between different strains. (C)</p> Signup and view all the answers

Which of the following is a similarity between coronaviruses and influenza viruses?

<p>Both are RNA viruses and are enveloped. (C)</p> Signup and view all the answers

What is a key difference in genomic structure between influenza viruses and coronaviruses?

<p>Influenza viruses have a segmented RNA genome, while coronaviruses have a single-stranded RNA genome. (A)</p> Signup and view all the answers

What is the primary target of PCR testing for SARS-CoV-2?

<p>Nucleocapsid (N gene) and spike proteins (S gene) (C)</p> Signup and view all the answers

How does the spike protein of coronavirus facilitate host cell entry?

<p>By binding to the ACE2 receptor on human cells. (D)</p> Signup and view all the answers

Which of the following correctly describes metabolic diversity?

<p>The different biochemical processes organisms use for energy and carbon fixation. (C)</p> Signup and view all the answers

What role do phototrophs play in ecosystems?

<p>They serve as the base of the food chain by converting light energy into chemical energy. (D)</p> Signup and view all the answers

What distinguishes oxygenic phototrophs from anoxygenic phototrophs?

<p>Oxygenic phototrophs produce oxygen as a byproduct of photosynthesis, while anoxygenic phototrophs do not. (B)</p> Signup and view all the answers

In what type of environment are anoxygenic phototrophs most likely to be found?

<p>Deep ocean environments with low oxygen levels (C)</p> Signup and view all the answers

What role do light-harvesting pigments play in phototrophs?

<p>Capturing light energy for photosynthesis. (B)</p> Signup and view all the answers

What is a significant ecological role of cyanobacteria in the environment?

<p>Producing oxygen in aquatic environments. (B)</p> Signup and view all the answers

How are anoxygenic phototrophs named, and what does this indicate about their environment?

<p>Based on their electron donor, highlighting their environmental preferences. (B)</p> Signup and view all the answers

How do cyanobacteria contribute to the carbon cycle?

<p>By fixing carbon dioxide into organic forms through photosynthesis. (B)</p> Signup and view all the answers

What is the role of microbes in the nitrogen cycle?

<p>Converting atmospheric nitrogen into ammonia, a form usable by plants. (B)</p> Signup and view all the answers

How do Rhizobium bacteria and legumes interact in nutrient cycling?

<p>Rhizobium bacteria fix nitrogen for legumes in return for carbohydrates produced by the plant. (C)</p> Signup and view all the answers

Which of the following is an example of the built environment?

<p>A city park with walking trails. (B)</p> Signup and view all the answers

What characteristics define good water quality?

<p>Balanced levels of turbidity, dissolved oxygen, temperature, pH, organic matter, and limited chemical contaminants. (C)</p> Signup and view all the answers

How can microorganisms affect water quality?

<p>By both helping in wastewater treatment and causing waterborne diseases. (A)</p> Signup and view all the answers

What is the primary goal of drinking water purification?

<p>Making water potable by removing pathogens and reducing chemicals and turbidity. (B)</p> Signup and view all the answers

Why is chlorination used in drinking water treatment?

<p>To disinfect by destroying a broad range of microbes. (C)</p> Signup and view all the answers

Flashcards

What are viruses?

Requires a host cell to replicate but contains a nucleic acid genome.

What is a virion?

The extracellular form of a virus that facilitates infection.

What is a naked virus?

Contains only the nucleocapsid.

What is an enveloped virus?

Consists of nucleocapsid plus an envelope of outer proteins & lipids. Proteins on the virion surface crucial for attachment

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What is a capsid?

Protein shell that encases the viral genome, protecting it when outside the host.

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What are capsomeres?

Individual protein units that comprise the capsid.

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Do RNA viruses have a higher mutation rate?

Small viral genomes have the highest mutation rate.

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How are viruses classified?

Classified by the host they infect and their genome structure.

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What is a bacteriophage?

Contains lysozyme-like enzymes for infection & release.

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What is attachment in viral replication?

Adsorption of the virion to the host cell.

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What is penetration in viral replication?

Entry or injection of viral nucleic acid into the host.

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What is synthesis in viral replication?

Host cell machinery synthesizes viral nucleic acid and protein, redirected by the virus.

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What is assembly in viral replication?

Capsids are assembled, and viral genomes are packaged into new virions.

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What is release in viral replication?

New virions are released from the cell

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What is the eclipse phase of viral infection?

The virus has attached to the host cell and entered, but the infectious virus cannot be detected. The genome is uncoated and transcription begins.

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What is the maturation phase of viral infection?

New viral components are assembled into virions in the host cell but have not been released.

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What is lytic viral infection?

Virus redirects the host's metabolism to support replication and assembly, destroying the host.

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What is lysogenic viral infection?

Virus infects but incorporates its genome into the host genome and waits.

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What does lysogenic infection lead to?

Leads to the acquisition of new genetic information through transduction.

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What is the lysogenic pathway?

A temperate phage integrates into the bacterial genome as prophage.

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What is a plaque assay used for?

Quantifies the number of infectious virions present per volume of fluid.

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How is animal virus infections different?

Enter the host cell entirely, replicates in the nucleus, and uses receptors for macromolecules.

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What is a virulent infection?

Host cell lysis due to replication.

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What is a latent infection?

Viral DNA is not replicated, and the host is unharmed.

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What is persistent infection?

Slow release of virions through a budding process; host cells may not be lysed.

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What is transformation?

Normal cells convert to tumor cells.

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What is the RNA world hypothesis?

Early life was based on self-replicating RNA molecules.

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What is the varicella-zoster virus (chickenpox)?

Highly contagious, causing latent infection that can lead to shingles.

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What is unique about poliovirus?

Poliovirus targets human cells and causes paralysis, transmitted usually orally.

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What do you know about the influenza virus?

Enveloped virus with segmented RNA, uses hemagglutinin (HA) and neuraminidase (NA).

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What is antigenic drift?

Small, gradual changes in the viruses surface proteins (HA & NA).

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What is antigenic shift?

Major, abrupt change when different strains infect the same host.

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Are coronavirus genomes segmented?

Influenza has a segmented RNA genome, while coronavirus has a single-stranded RNA genome.

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What types of diversities are interconnected?

Phylogenetic, metabolic, and functional diversity.

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What are phototrophs?

Organisms that obtain energy from light.

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How does Oxygenic photosynthesis work?

Produce oxygen as a byproduct, using water as an electron donor.

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Explain anoxygenic phototrophs.

Do not produce oxygen, using alternative electron donors like hydrogen sulfide.

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How do bacteria help plants?

Rhizobium bacteria fix nitrogen for legumes, decomposers recycle nutrients, cyanobacteria provide fixed nitrogen.

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What is the built environment?

The human-made space where people live, work, and recreate daily.

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What is bioremediation?

Microbial cleanup of pollutants because they resemble familiar compounds.

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Study Notes

Viruses and Virions

  • Viruses need a host cell and possess a nucleic acid genome for replication.
  • A virion is a virus's extracellular form facilitating infection.
  • Examples of viruses include Flu Virus, SARS-COV-2, and Zika Virus.

Naked vs. Enveloped Viruses

  • Naked viruses consist solely of a nucleocapsid and are common among bacterial viruses.
  • Enveloped viruses have a nucleocapsid plus an outer envelope made of proteins and lipids.
  • Virion surface proteins are essential for host cell attachment.
  • A viral envelope is required to infect host cells, and virus-specific envelope proteins are essential for host attachment and release post-replication.

Capsid and Capsomeres

  • The capsid is a protein shell enclosing the viral genome, providing protection outside the host.
  • Capsomeres are individual protein units constituting the capsid; most viruses have a single type that aids in self-assembly.

Viral Mutation Rates

  • Small viral genomes within RNA viruses exhibit the highest mutation rates, including dsDNA, ssDNA, RNA viruses, and viroids.
  • Mutation rates are slower for large viral genomes in higher eukaryotes and prokaryotes.

Viral Classification

  • Viruses are classified based on the host they infect and their genome structure.

Baltimore Classification System

  • David Baltimore established this system in 1975 for retroviruses and reverse transcriptase.
  • Classification is based on the host they infect and their genome structure.

Bacteriophages

  • Bacteriophages have lysozyme-like enzymes for infection and release.
  • They are enzymes inside virions since viruses lack metabolic processes.

Bacterial Virus Replication Cycle

  • A permissive cell supports the virus's full replication cycle.
  • Attachment: The virion adsorbs to the host cell.
  • Penetration: Viral nucleic acid enters or is injected into the host.
  • Synthesis: The host cell synthesizes viral nucleic acid and protein, redirected by the virus.
  • Assembly: Capsids are assembled, and viral genomes are packaged into new virions.
  • Release: New virions are released from the cell.

Latent Period of Viral Infection

  • This is the phase between viral entry and new viral particle release.
  • Critical replication steps are undergoing, so infectious virions are undetectable outside the cell.
  • Eclipse Phase: The virus attaches to the host and enters, but infectious virus is undetectable because the viral genome is uncoated, and viral mRNA transcription and protein synthesis begin; viral genome replication produces new genetic material for assembly.
  • Maturation Phase: New viral components are assembled into virions inside the host, preparing for release via lysis or budding.
  • The period ends when assembled virions release into the extracellular environment; it lasts minutes to hours in bacteriophage infections but hours to days in animal viruses.

Viral Attachment and Host Specificity

  • Viruses use surface proteins to attach to their host.
  • These proteins interact with receptors (proteins, carbohydrates, glycoproteins, lipids, or macromolecules) on the host cell surface.
  • Receptors perform normal functions for the cell.

Lytic vs. Lysogenic Viral Infection

  • Lytic Infection: The virus redirects the host's metabolism to support replication, destroying the host (e.g., Bacteriophage T4, Influenza, and SARS). ssDNA and RNA bacterial viruses only conduct lytic life cycles.
  • Lysogenic Infection: The virus incorporates into the host's genome, waiting for optimal conditions before entering the lytic phase (e.g., HIV, Phage B, and Phage CTX).
  • Lytic infections are fast and destructive, while lysogenic infections are dormant and allow long-term survival.
  • Lysogenic viruses can switch to lytic, leading to active infection and host destruction, with some viruses having both phases.

Acquisition of New Genetic Information

  • During lysogenic infection, bacteriophages can transfer genetic material between bacteria through transduction, leading to the acquisition of new genetic information.
  • Temperate phages integrate into the bacterial genome as a prophage during the lysogenic pathway.
  • The virus genes are not transcribed, and the viral genome is passed onto daughter cells, giving the host new properties and creating lysogen hosts.
  • Bacteriophage lambda integrates into the host chromosome, where a repressor protein keeps it incorporated.
  • If the repressor is inactivated, the phage enters the lytic stage, causing cell stress and DNA damage.
  • A lytic lifestyle is favored when host cells are plentiful, whereas lysogeny is favored when host cell numbers are low.

Plaque Assay

  • It quantifies viral suspension by determining the number of infectious virions per fluid volume, measured in titer units.
  • Used for bacteriophages and animal viruses that cause visible cell damage, to isolate genetically identical populations, compare wild-type vs. mutant viruses, and monitor viral replication and vaccine development.

Animal vs. Bacteriophage Infections

  • Animal Viruses: The entire virion enters the host cell, replicates in the nucleus of eukaryotic cells, and uses host cell receptors for macromolecules in intercellular communication
  • Both: the infection, type of host replication, capsids, and classification by genome structure
  • Bacteriophages: Most have head-and-tail structures with dsDNA genomes and overlapping genes.

Outcomes of Viral Infection in Animal Cells

  • Virulent infection results in host cell lysis due to replication.
  • Latent infection involves viral DNA without replication, leaving the host unharmed.
  • Persistent infection involves slow virion release through budding, potentially without host cell lysis.
  • Transformation converts normal cells to tumor cells.

Origin of Viruses and RNA World Hypothesis

  • Origin of viruses remains uncertain, with 3 main hypotheses: regressive, progressive and virus-first
  • The RNA world hypothesis suggests early life was based on self-replicating RNA molecules.
  • RNA viruses may be remnants of this RNA-based world, indicating viruses played a role in early molecular evolution.

Archaeal Viruses

  • Negative-strand RNA viruses have complementary mRNA genomes.
  • Example: Rabies virus and Influenza virus.

Varicella-Zoster Virus (VZV)

  • Chickenpox is highly contagious and spreads through direct contact, droplet transmission, and airborne transmission. It establishes latent infection in root ganglia and can lead to shingles through stress, menstruation, or UV light exposure.
  • Shingles is less contagious, occurs only in those previously exposed to chickenpox, and affects nerve bundles, causing sensory issues.

Smallpox and Monkeypox (Mpox)

  • In 2024, the WHO states mpox is a public health emergency of international concern and declared smallpox eradicated in 1980.
  • Global smallpox eradication used widespread vaccination, which cross-protected against orthopoxviruses like mpox
  • As smallpox vaccination ended, mpox emerged and spread because there was a lack of immunity and continued presence of mpox.

Differences between Chickenpox and Shingles

  • Chickenpox is highly contagious, spreads easily, and establishes latent infection possibly leading to shingles.
  • Shingles is less contagious, occurs only after chickenpox, and affects nerve bundles.

Poliovirus

  • Poliovirus uniquely targets human cells, causing irreversible paralysis, is part of the enterovirus family. It is transmitted via the fecal-oral route and specifically infects motor neurons.

Influenza Virus

  • Virion Characteristics: It has a negative-sense single-stranded RNA genome, enveloped with hemagglutinin (HA) for host cell binding, and neuraminidase (NA) for virion release, plus a segmented genome that's the core of frequent genetic reassortment.
  • Highly contagious, infecting the respiratory tract and causing seasonal epidemics with fever, cough, sore throat, and body aches due to constant mutations.
  • The influenza virus vaccine is based on predicted viral strains, but antigenic drift (gradual change) and shift (abrupt change) alter the virus enough to evade the immune system.
  • Vaccine effectiveness can be reduced by genetic changes that mismatch circulating strains.
  • Antigenic drift causes small changes in HA and NA surface proteins, resulting in seasonal variations and partial unrecognizability and Antigenic shift involves a major change when different strains infect the same host and exchange material, which can lead to new strains.

Coronavirus and Influenza Viruses

  • Similarities: Both are RNA viruses, enveloped, and transmitted via aerosols causing respiratory diseases.
  • Both have spike proteins, but with different binding mechanisms (ACE2 receptor in coronavirus, hemagglutinin in influenza).
  • Differences: Influenza has a segmented RNA genome, whereas coronavirus has a single-stranded RNA genome and they replicate in different parts of the cell; coronaviruses replicate in the cytoplasm, while influenza viruses replicate in the nucleus.
  • COVID-19 has a more severe pathogenesis than influenza.

COVID-19 and Influenza

  • Viruses share virion characteristics, with both being enveloped RNA viruses, but influenza is segmented while coronavirus is non-segmented.
  • Influenza infects the upper respiratory tract, causing seasonal epidemics, while COVID-19 leads to systemic effects with more severe disease. COVID-19 cases have been significantly higher, especially in global pandemics.
  • Protection: Various platforms exist for COVID-19 vaccines (mRNA, viral vector), while the flu vaccine is inactivated or subunit-based.

Coronavirus Testing

  • The N gene (nucleocapsid protein) and S gene (spike protein) are targeted in PCR tests for SARS-CoV-2 detection.

Coronavirus Attachment

  • The coronavirus spike protein (S protein) binds to the ACE2 receptor, with ACE2 receptor expression influencing susceptibility and disease severity.

Diversity Types

  • Phylogenetic diversity refers to evolutionary relationships between organisms.
  • Metabolic diversity pertains to biochemical processes for energy and carbon fixation.
  • Functional diversity is the variety of functions in ecosystems.
  • These diversities are connected, with phylogenetic relationships affecting metabolic and functional abilities.

Phototrophs Defined

  • Phototrophs get energy from light as the base of the food chain.

Phototroph Importance

  • As the base of the food chain, phototrophs use light, produce food through photosynthesis, and provide energy. They also are essential in producing oxygen and fixing carbon which is a key element to maintaining functioning ecosystems.

Oxygenic vs. Anoxygenic Phototrophs

  • Oxygenic phototrophs produce oxygen using water as an electron donor, including plants, algae, and cyanobacteria.
  • Examples of anoxygenic species includes purple and green sulfur, and heliobacteria. As they use something other than water they do not produce water as a result.
  • Both types use light for photosynthesis and pigments such as chlorophyll, but differ in specific pigments, function, and electron donors.

Habitats of Phototrophs

  • Oxygenic phototrophs thrive in sunlight-rich zones like oceans, land, and lakes ecosystems, where water and sunlight are abudnant.
  • Anoxygenic phototrophs thrive in environments where oxygen is scarce; or completely absent such as muddy environments, deep water and sulfur-rich seas.

Light-Harvesting Pigments

  • These critical compounds capture light energy of photosynthesis and convert it to chemical energy. Their diversification of pigments allows for absorption of a range of light wavelengths boosting maximum energy capture.
  • Pigments enable the diversity among species and contribute to a wide range of ecosystems.

Cyanobacteria's Environmental Role

  • Cyanobacteria are key primary producers in various ecosystems, supporting oxygen production and contributing to the global food chain. They also are the key oxygenic phototrophs and play a pivotal role especially in the nitrogen cycle.

Naming System of Anoxygenic Phototrophs

  • These organisms are named by the electron donor used through photosynthesis, such as in sulfur bacteria.
  • This system also highlights preferences in environments with low percentages of Oxygen.

Microbes in Carbon and Nitrogen Cycles

  • COâ‚‚ is converted through bacteria into organic matter through photosynthesis and this organic matter is consumed.
  • Bacteria convert N2 into NH3 which plants use and convert into nitrate which then becomes nitrogen gas through microbes.

Synergistic Microbe Relationships

  • Different bacterium and organisms cycle nutrients within symbiotic practices; decomposers breakdown organic components and transfer back nutrients, and can work as bacteria which transfers nitrogen.

What constitutes 'the built environment'

  • Where humans perform all activities and work. This often includes the transportation system, the parks and also homes/buildings in these areas.

Water Quality

  • Water quality is the condition of the water; chemical, biological and how suitable it is for a particular task. Some key indicators of water quality include turbidity, presence of solids and saturation of nutrients.

Sources of Contaminants

  • Examples of human-related contaminants include nitrates, animal waste, heavy metals, household waste and fertilizer. Some natural ones include salt, radon and heavy metals.

Positives/Negatives of Microbes to Water Quality

  • They assist with bioremediation and wastewater treatments, however can also form as a waterborne pathogen.

The Goals of Potable Water

  • Drinkable water must not have any pathogens, tastes or odors, and a low level of solids.

Waterborne Pathogens

  • An pathogen, originating in a water source, that is causing disease or illness.

Treatment Steps for Potable Water

  • Disinfection is a process using chlorine which removes pathogens through disinfection.
  • Coagulation is the act of adding ferric chloride or saline in order to facilitate in removing solids during said procedures.
  • Flocculation is then mixing the concoction, to improve agglomeration which helps remove more contaminents.
  • Water then experiences filtration and sedimentation to remove any additional particles before leaving the facility; all to create potable water from previously unclean water!

Chlorine and Ozone

  • Chlorine destroys pathogens, while controlling the color and odor. It helps increase efficiency but it has a transportation safety hazard in addition to being non-effective when concerning cryptosporidium. Another solution therefore is ozone where nearly all waterborne pathogens are eliminated but an extremely expensive and unstable procedure.

Indicators of Water Quality

  • The presence, absence or abundance of such quality indicators indicates the potential lack or existance of a certain disease. They determine if more treatment needs to occur.

Key Features of Good Indicators

  • Must be heavily present where pathogens exist.

Coliform's Importance

  • These organisms, when tested, represent strong fecal contamination as these intestinal carriers are often excreted in large quantities.

The Remediation Effect

  • A microbe is able to help clean up toxins in the current environment. All since they resemble familiar material to the organism.

Bacteria Degrading Plastics

  • They can remove plastics by creating enzymes, turning polymers into useable molecules.

Pseudmonas Syringae

  • Bad since it produces a protein on the outside which forms ice and causes frost damage at roughly -1 C but also helpful since animals often exploit that damage.

Microbial Genetics

  • Tree of life used an old version to track genetic material, as opposed to the rRNA sequencing technique.
  • Candidate phyla radiation members - or CPR - are bacterium without all known genetic features, which can often make then the minority percentage in tree of life sequencing.

Building Novel Machines

  • Biotech benefits from designing machines to have specific functions.

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