Viruses: Discovery and Structure

Viruses

• Viruses consist of little more than genes in a protein coat
• A virus comprises nucleic acid encased in a protein coat

Virus Discovery

• Ending theory of viruses came from experiments
• Viruses are replicating particles much smaller and simpler than bacteria

Virus Structure

• Viruses have nucleic acid enclosed in a protein coat or membranous envelope sometimes
• Viral genomes are either DNA or RNA depending on the nucleic acid
• Viral genomes can be double or single-stranded DNA or RNA
• Genomes are organized in a single linear or circular molecule, but some viruses have multiple nucleic acid molecules
• The capsid is the protein shell enclosing the viral genome and can be rod-shaped, polyhedral or more complex -Built from capsomeres
• Viral envelopes derived from the host cell membrane contain viral-encoded glycoproteins for virus-host interactions
• Some viruses contain a few viral enzyme molecules within their capsids

Bacteriophages

• Bacteriophages have a head containing DNA
• Bacteriophages have a tail sheath
• Bacteriophages have a tail fiber

Virus Replication

• Viruses can only replicate in host cells
• Viruses are obligate intracellular parasites, so they can only replicate within a host cell
• A particular virus can infect cells of only a limited number of host species
• There is a "lock and key" fit between viral surface proteins and specific receptor molecules on the outside of cells

Viral Replicative Cycles

• A virus enters a cell, releasing viral DNA and capsid proteins after being uncoated
• Host enzymes replicate the viral genome
• Host enzymes transcribe the viral genome into viral mRNA
• Host ribosomes make more capsid proteins
• New virus particles self-assemble and exit the cell

Lytic Cycle

• The lytic cycle results in the death of the host cell
• The lytic cycle occurs during the last stage of infections, where the bacterium breaks open, releasing phages
• Virulent phages replicate only by a lytic cycle

Lytic Cycle Steps

• T4 phage uses its tail fibers to attach to specific surface proteins on an E. coli cell, that act as receptors
• The tail sheath contracts, injecting phage DNA into the cell while leaving an empty capsid outside and the host cell DNA is hydrolyzed
• Phage DNA directs production of phage proteins using components within the cell
• Proteins self-assemble to form phage heads, tails, and tail fibers
• The phage genome is packaged inside the capsid, and the head forms
• Phage enzymes damage the bacterial cell wall, allowing fluid to enter, and the cell bursts, releasing 100-200 phage particles

Lysogenic Cycle

• Allows replication of the phage genome without destroying the host
• Temperate phages use both modes of replicating within a bacterium and have only one short tail fiber
• Viral proteins incorporate temperate phage DNA into a specific site on the E. coli chromosome by breaking and joining circular DNA molecules
• A prophage is viral DNA integrated into the bacterial chromosome
• Lysogeny allows viruses to propagate, without killing the host cells as prophages generate active phages that lyse their host cells

Bacterial Defenses Against Phages

• Natural selection favors bacterial mutants with surface proteins that phages no longer recognize as receptors
• Restriction enzymes identify viruses as foreign and cut them up
• CRISPR-Cas systems defend bacteria against phage infection

CRISPR-Cas System

• CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) have sequences forward and backward with "spacer DNA" in-between
• CAS (CRISPIR-associated) nucleases identify and cut phage DNA, defending the bacterium
• Phage infection triggers transcription of the CRISPR region of bacterial DNA which consists of DNA from previously infecting phages, separated by repeats
• The RNA transcript becomes short RNA strands complementary to the invading phage's DNA
• Each short RNA strand binds to a Cas protein, forming a complex
• Complementary RNA binds to DNA from the invading phage and the Cas protein cuts the phage DNA
• After being cut, the entire phage DNA molecule is degraded and can no longer be replicated

Animal Viruses

• Key variables in replication cycles are the nature of the viral genome and presence or absence of membranous envelop

Animal Virus Envelopes

• Glycoproteins on the outer surface of the envelope bind to specific receptor molecules on the host cell
• The viral envelope is usually derived from the host cell's plasma membrane

Enveloped RNA Virus Replication

• Glycoproteins on the viral envelope bind to specific receptor molecules on the host cell, allowing cellular uptake
• Cellular enzymes trigger digestion of the capsid and viral genome
• The viral genome acts as a template for complementary RNA strands, that are synthesized by viral RNA polymerase
• Using the complementary RNA strands as templates, new copies of viral genome RNA are produced
• Complementary RNA strands function as mRNA and are translated into capsid proteins in the cytosol and glycoproteins for the viral envelope in the ER and Golgi apparatus
• Vesicles transport envelope glycoproteins to the plasma membrane
• A capsid assembles around each viral genome molecule
• Each new virus buds from the cell, its envelope studded with viral glycoproteins derived from the host cell membrane

Viral Genetic Material

• RNA can be viral genetic material
• Class IV genomes can directly serve as mRNA and be translated into viral protein immediately after infection
• Class V genomes act as a template for mRNA and pack viral enzymes within the capsid
• Retroviruses contain two identical molecules of single-stranded RNA and two molecules of reverse transcriptase
• Reverse transcriptase transcribes an RNA template into DNA, an RNA to DNA information flow
  • HIV (human immunodeficiency virus) causes AIDS (acquired immunodeficiency syndrome)
• A provirus is integrated viral DNA formed when a retrovirus, like HIV, inserts its converted DNA into the host cell's genome

Virus Evolution

• Plasmids are small circular DNA molecules replicated independently and transferred between cells, found in bacteria and unicellular eukaryotes like yeast
• Transposons are DNA segments that can move within a cell's genome

Viruses, Prions, and Disease

• Viruses and prions are formidable pathogens in animals and plants, where viruses can damage or kill a cell by causing lysosomes to release of hydrolytic enzymes
• Vaccines are harmless derivatives of pathogens, stimulating the immune system to mount defenses against the harmful pathogen

Emerging Viruses

• Epidemics such as Ebola and Zika emerge through mutation of existing viruses, dissemination of a viral disease from a small, isolated human population or spread of existing viruses from other animals

Viral Diseases in Plants

• Horizontal transmission occurs when a plant is infected from an external source of the virus
• Vertical transmission occurs when a plant inherits a viral infection from a parent

Prions

• Prions are misfolded forms of a protein normally present in brain cells and act slowly with long incubation periods
• Prions are virtually indestructible and not deactivated by heating to normal cooking temperatures

Prokaryotes

• Structural and functional adaptations contribute to their success
• Prokaryotes are spherical, rod-shaped, or spiral

Prokaryote Cell Structures

• Bacterial cell walls contain peptidoglycan
  • Peptidoglycan is a polymer of modified sugars cross-linked by short polypeptides
• Archaeal cell walls contain polysaccharides and proteins, but lack peptidoglycan
• Gram staining categorizes bacterial species by cell wall composition
  • Gram-positive bacteria have simple walls composed of a thick layer of peptidoglycan
  • Gram-negative bacteria have less peptidoglycan and have an outer membrane of lipopolysaccharides
• The capsule is a sticky layer of polysaccharide or protein that enables prokaryotes to adhere to substrates or other individuals in a colony
  • Capsules also protect against dehydration and the host's immune system in pathogenic prokaryotes
• Endospores are dormant, tough, non-reproductive structures produced by certain bacteria like Bacillus and Clostridium, to survive harsh conditions
• Fimbriae are short, bristle-like protein appendages facilitating adhesion and colonization
• Pili, or sex pili, are longer than fimbriae and allow prokaryotes to exchange DNA
  • Pili are hairlike appendages used for adhesion or movement

Prokaryote Genetic Diversity

• Rapid reproduction, mutation, and genetic recombination promote genetic diversity

Transformation

• Alteration of a bacteria's genotype and phenotype by the uptake of naked, foreign DNA from the surrounding environment
• Receptors on the surface of bacteria recognize DNA from closely-related species
• Under the right conditions, cells can be stimulated to take up small pieces of DNA

Transduction

• Phages or viruses can carry small pieces of host DNA from one species to another
  • This is an example of horizontal gene transfer

Conjugation

• Conjugation results in bacterial "sex"
• Conjugation is the direct transfer of genetic material between two temporarily joined bacterial cells via a mating bridge
• Conjugation requires a special piece of DNA called the F factor
  • F factor is the ability to form pili and donate DNA during conjugation -The transfer can happen via F plasmid
  • The transfer can happen via R plasmid
• Episomes can replicate as part of the host chromosome or independently

Prokaryote Metabolism

• Metabolic adaptations have evolved in prokaryotes

Oxygen's Role in Metabolism

• Obligate aerobes require oxygen to survive and cannot grow without it, relying on aerobic respiration
• Obligate anaerobes cannot survive or grow in the presence of oxygen and lack the necessary enzymes to detoxify oxygen
• Anaerobic respiration uses alternative electron acceptors in the absence of oxygen
• Facultative anaerobes can survive and grow in both the presence and absence of oxygen

Nitrogen Metabolism

• Nitrogen fixation is the conversion of atmospheric nitrogen gas (N2) into usable forms like ammonia (NH3), by bacteria

Metabolic Cooperation

• Metabolic cooperation enables use of environmental resources individual cells could not use on their own
• Heterocysts are specialized, thick-walled cells that carry out nitrogen fixation in cyanobacteria
• Biofilms are communities of microorganisms encased in a self-produced matrix that adheres to a surface

Prokaryote Diversity

• Prokaryotes have radiated into a diverse set of lineages

Bacteria

• Bacteria are a diverse group
• Some bacteria include proteobacteria, chlamydias, spirochetes, cyanobacteria, and gram-positive bacteria

Archaea

• Archaea can live in extreme conditions
• Includes extremophiles and methanogens
• Extremophiles are “lovers” of extreme conditions, like extreme halophiles (highly saline environments) and thermophiles (hot environments)
• Methanogens release methane as a byproduct

Prokaryotes in the Biosphere

• Prokaryotes play crucial roles in the biosphere, including chemical recycling by decomposers
• Prokaryotes engage in ecological interactions

Symbiosis

• Ecological relationship of two species living in close contact
  • A host is the larger organism
  • A symbiont is the smaller organism
  • Mutualism benefits both species
  • Commensalism benefits one species and does not harm the other
  • Parasitism benefits one species while harming the other. Pathogens are parasites that cause disease

Prokaryotes and Humans

• Prokaryotes can have beneficial and harmful impacts
  • Mutualistic bacteria benefit the human body
  • Pathogenic bacteria can cause disease
  • Exotoxins are proteins secreted by bacteria and other organisms
  • Endotoxins are lipopolysaccharide components of the outer membrane of gram-negative bacteria

Prokaryotic Technology

• Prokaryotes are used in research
• They are used in bioremediation to remove pollutants

The Immune System

• Pathogens are disease-causing agents such as bacteria, fungi, and viruses
• The immune system enables an animal to avoid or limit infections

Immunity

• Innate immunity is the body's first line of defense against pathogens, acting quickly and generally
  • It recognizes traits shared by broad ranges of pathogens and utilizes a small set of receptors for a rapid response
  • The barriers are skin, mucous membranes and secretions
  • Internal Defense consists of phagocytic cells, natural killer cells, antimicrobial proteins and inflammatory response
• Adaptive immunity is a specialized immune response which allows the body to remember and mount a faster, more effective response upon subsequent encounters
  • Humoral responses use antibodies to defend against infection in body fluids
  • Cell-mediated responses use cytotoxic cells to defend against infection in body cells

Immunity Response

• Recognition and response rely on traits common to groups of pathogens in innate immunity

Invertebrate Immunity

• Lysozyme is an enzyme that breaks down bacterial cell walls
• "Identity tags" mediate pathogen recognition stimulate an innate immune response
• Phagocytosis involves hemocytes, or major immune cells, surrounding, engulfing, and destroying pathogens through toxic compounds and lysosomal enzymes

Vertebrate Immunity

• Barrier defenses include mucous membranes and skin, with lysozyme used as a method to destroy pathogens
• Cellular innate defenses use Toll-like receptors (TLR)
  • Toll-like receptors are mammalian recognition proteins like the Toll protein of insects to produce signals that initiate responses tuned to the invading microorganism

Pathogenic Molecules

• TLR proteins bind to fragments of molecules characteristic of a set of pathogens
• TLR3 for double-stranded RNA
• TLR4 for lipopolysaccharides
• TLR5 for flagellin
• Main phagocytic cells are neutrophils and macrophages
• Neutrophils are white blood cells crucial for innate immunity that are first responders to infection and inflammation
• Macrophages are large phagocytic cells that engulf and digest pathogens, also playing a role in antigen presentation and inflammation
• Dendritic cells populate tissues that contact the environment and stimulate adaptive immunity
• Eosinophils defend against multicellular invaders, like parasitic worms, and discharge destructive enzymes
• Natural killer cells circulate through the body and detect the abnormal array of surface proteins of virus-infected and cancerous cells and are a type of lymphocyte
• Interferons interfere with viral infections to induce nearby uninfected cells to produce substances inhibiting viral replication
• Complement system enhances the body's ability to destroy pathogens and clear damaged cells
• Inflammatory response is the set of events triggered by signaling molecules released upon injury or infection
• Activated macrophages release cytokines that recruit neutrophils to the site of injury
• Mast cells, immune cells in connective tissue release signaling molecules like histamine in sites of damage
  • Histamine causes blood vessels to dilate and become more permeable

Pathogen Evasion

• Pathogens can evade innate immunity through invading host cells

Adaptive Immunity

• Adaptive immunity has receptors for pathogen-specific recognition -T and B cells are adaptive immune cells
• Some T cell migrate to the thymus
• B cells remain in the bone marrow
• Antigens elicit B or T cell response -Antigen receptors bind to a part of molecule from a pathogen
• Epitopes are the small, accessible portion of an antigen, that bind to an antigen receptor
• B cell antigen receptor includes the use of heavy and light chains linked together by disulfide bridges
• Each chain has a constant C region with similar amino acid sequences
• A transmembrane region anchors the receptor in the cell's plasma membrane
• Each chain possesses a variable region
• Amino acid sequence varies extensively
• B cell activation occurs through B cell linkage to an antigen receptor
• B cell activation leads formation of cells to of secrete a soluble form of the receptor, known as antibodies or immunoglobulin
• T cell antigen recognition relies on alpha and beta chains linked by disulfide bridges and constant/variable regions
• T cells link to presented antigens on surface of host cells
  • Major histocompatibility complex (MHC) molecules is present. -Host cell cleaves pathogen antigens, that get presented to the MHC molecule
  • T cell binds to the MHC
  • Antigen causes the presentation of an antigen fragment in an exposed groove of the MHC protein
• B and T cell development includes self-tolerance
• Some immature lymphocytes produce receptors for epitopes on the organism's own molecules
• Antigen receptors are tested for self-reactivity and destroyed if found to be self-reacting
• The remaining antigen receptors are nonfunctional, if reactive, and are only those that react to foreign molecules

Immune Cell Proliferation

• Proliferation of B and T Cells occurs through a math between an antigen receptor and an epitope, that activates the lymphocyte, causing multiple cell divisions
• Effector are cells that take effect and produces an immediate immune response to kill the antigen
• Memory cells enable effector production if there is another encounter
• Clonal selection selects and rapidly multiplies immune cells to fight a pathogen

Immunological Memory

• Long-term protection from a prior infection occurs
• Primary immune response is body's initial reaction from a foreign antigen, leading to production of effector cells
• Secondary immune response has greater magnitude
• Adaptive immunity defends against infection of body fluids and cells
• Humoral immune response occurs through production/circulation of antibodies in body's fluids
• Cell-mediated immunity response occurs through activation of immune cells or lymphocytes, primarily lymphocytes to defend against intracellular pathogens and cancer cells

Helper and Cytotoxic T Cells

• Helper T cells activate immune responses through enabling binding to foreign molecules to the antigen receptor of the helper T cell
• The antigen is displayed on an antigen-presenting cell and engulfs the pathogen
• The antigen is degraded and displays antigen fragments on class II MHC molecules on the cell surface
• A T cell binds via an antigen receptor and accessory protein called CD4
• B cells use cell to cell contact through class II MHC to present an antigen fragment to a helper T cell
• Cytotoxic T cells utilize toxic proteins in cells infected by pathogens before pathogens fully mature
• Neutralization and Opsonization are processes where antibodies prevent infection

Immunization

• Use of antigen to generate an adaptive immune and memory cell formation

Active and Passive Immunity

• Active defenses occur from when a pathogen infection or immunization prompts and immune response
• Passive defenses occur through receiving pre-formed antibodies rather than producing them