Microbio Chapter 13

abnormal/uncontrolled growth

mainly caused by mutations that result in inappropriate timing or level of expression of proto-oncogenes/repression of tumor supressor genes -caused by multiple changes at different sites of DNA

tumors

majority are not caused by viruses but by mutations in host genes that regulate cell growth

informal terms

-used for groups of animal viruses that are not taxonomically related but share critical characteristics like primary route of transmission (enteric or respiratory viruses) -zoonotic viruses cause diseases that are transmitted from animal to human -arbovirus (arthropod borne) spread by arthropods like mosquitoes, ticks, etc

hemagglutination

-certain viruses cause red blood cells to agglutinate (clump) -occurs when individual viral particles attach to surface molecules of multiple red blood cells simultaneously, connecting cells to form an aggregate

lysogenic conversion

-change in phenotype of a lysogen as a consequence of specific prophage it carries

transmissible spongiform encephalopathies

-characteristic sponge like appearance of the brain tissue gives rise to these -all prion diseases

chronic infections

-characterized by continuous production of low level of viral particles -person can transmit virus to others even in absence of symptoms

Acute infections

-characterized by sudden onset of symptoms of a relatively short duration -result in a burst of virions being released from infected host cells (virus-infected cells often die but host may survive) -influenze, mumps, etc -symptoms result from localized or widespread tissue damage following cell death and damage caused by immune response itself

oncogenic viruses

-ciruses that lead to cancer formation

cell culture/tissue culture

-commonly used to cultivate most animal viruses

complex viruses

-complicated structures (capsid, head with nucleic acid (can be icosahedral nucleocapsid), tail, base plate, tail spikes and tail fibers) -ex. phages

titer

-concentration of infectious phage particles in original phage suspension

viroids

-consist solely of a small ss RNA molecule that forms a closed ring -all known viroids infect only plants where they cause serious diseases -enter plants through wound sites rather than binding to specific receptors

normal vs infectious cellular prion protein

-differet shape of protein which influences its stability

ds DNA replication

-ds DNA virus DNA has 2 complementary strands (+ and -) (+/-) -(+/-) genomes can be transcribed to produce mRNA -mRNA = (+) strand -mRNA is translated to make proteins and ds DNA genome serves as a template for DNA replication

Generalized transduction

-due to packaging error during phage assembly -some phages degrade bacterial chromosome into many fragments during lytic infection (an short bacterial DNA fragments can be mistakenly packaged into phage head during assembly) -any gene of donor cell can be transferred this way

bacterial culture infected with temperate phage

-some particles enter lytic cycle and others lysogenize their host -random -metabolic state of host cell has influence: if bacterial cell is growing slowly because of nutrient limitation then lysogenic infection is more likely to occur

ss RNA virus

-some types have a (+) RNA strand genome meaning genome also serves as mRNA -some types have a (-) RNA strand genome, meaning the genome is the complement to mRNA

specialized vs generalized

-specialized: only bacterial genes adjacent to the integrated phage DNA can be transferred

-viridae

-suffix of the names of virus families (no pattern of names: sometimes name inficates appearance of virus and other times it is named for geographic area from which it was first isolated) (-virus = numerous genera in a family : species name may be name of disease the virus causes like poliovirus)

nucleocapsid

-the capsid and the nucleic acid it encloses

naming

-unlike bacteria, viruses are commonly referred to only by their species name or by informal name (not capitalized) -ex. rhabdovirus

repressor

prevents expression of gene required for excision: it is essential for maintaining lysogenic state

PrPSC

prion protein, scrapie -infectious prion proteins -less susceptible to degradation by proteases and being insoluble, leading to aggregation

Bacteriophage/phage

viruses that infect bacteria -kill bacteria so they limit bacterial populations in nature

antigenic shift

when a new subtype of a virus is formed by reassortment between different strains o a virus or between different viruses

reassortment

-can happen when 2 different strains of a segmented virus infect the same cell -during replication, new viral particles are made that have combinations of genome segments from the initial infecting strains -ex. strain 1: a-e, strain 2: A-E -all new viral particles being generated must have a total of 5 segments but can originate from either parent strain so new viruses can have different combinations (aBCDe)

oncogenes

-carried on some viruses -similar in DNA sequence to proto-oncogenes -can lead to tumor formation

Preventing phage attachment

-bacterium alters/covers a given receptor so the cell becomes resistant to a phage that required the receptor for attachment -can produce a protein to cover the phage receptor on cell wall; capsule or slime layer can also cover phage receptor

ss (-) RNA virus

- (-) RNA strand cannot be translated -must first be copies into a (+) strand before protein synthesis can occur (done by a replicase carried by the virus) -once (+) RNA strand has been produced, it can be translated to make viral proteins and is also used as a template for synthesizing new (-) RNA strands

quatal assay

-can be used to estimate a viral titer -titer of virus/endpoint = dilution at which 50% of the inoculated hosts are infected or killed (ID50 - infective dose or LD50 - lethal dose)

Temperate phages

-can either direct a lytic infection (productive infection) or lysogenic (incorporating their DNA into the host cell genome, where the infected cell is a lysogen;phage DNA exists within a cell without causing damage, so the phage DNA or prophage is replicated along with the host cell chromosome and when cell divides the prophage is passed onto cell's progeny)

Replication of Reverse-transcribing viruses

-RTV encode the enzyme reverse transceiptase; an RNA-dependent DNA polymerase (synthesizes DNA from an RNA template)

phage induction

-UV light (DNA damaging agent): SOS repair system activates a protease that destroys the repressor protein that maintains integration, so the prophage is excised from the chromosome and the cell eters the lytic cycle (productive infection) -lets phage escape from damaged host

Synthesis of phage proteins and genome

-after T4 DNA is injected into a host cell, some of genes on that DNA are transcribed and translated so the cell begins synthesizing T4 proteins (phage-encoded proteins are synthesized in a sequential manner during course of infection) -1st viral proteins produced = early proteins (impoerant for initial steps of phage multiplication) -early proteins include a nuclease that degrades the host cell's DNA and proteins that modify a subunit of the host cell's RNA polymerase so it no longer recognizes bacterial promoters (soon after infection, no host genes are expressed) aka phage takes over metabolism of bacterial cell for the synthesis of more phage particles -bacterial enzymes continue to function and allow biosynthesis and energy harvest to continue -late proteins synthesized toward end of infection cycle: structural proteins that make up the phage

Bacteria defense mechanisms

-altering receptor sites, restriction modification systems and CRISPR system

Attachment (adsorption)

-animal viruses have attachment proteins or spikes on their surfaces -receptors = glycoproteins on the host cell cytoplasmic membrane (more than 1 receptor is required for effective attachment) -because of specific receptors, particular virus may be able to infect only single or limited number of cell types

antigenic drift

-antigenic variation -occurs as mutations accumulate in genes encoding key viral surface proteins that are recognized by the immune system (a person whose immune response protected him/her against influenza virus one year may not be protected against the variant that circulates the next year)

generalized infection cycle of animal viruses

-attachment, genome entry, synthesis, assembly and release

CRISPR system

-bacterial cells that survive some phage infections retain small segments of phage DNA, incorporating them into their bacterial genome (spacer DNA = segments of phage DNA that are inserted into a chromosomal region called CRISPR) -clusters of regularly interspersed short palindromic repeats -space DNA provides historical record of past phage infections, allowing bacterial cell and progeny to recognize and block subsequent infections by same types of phages -functions by a type of RNA interference -CRISPR array is transcribed and cut into cRNAs which bind to protein Cas (when spacer RNA of Cas-crRNA complex base pairs with invading phage, that nucleic acid is targeted for destruction

Penetration and uncoating

-entire virion is taken into the cell (different from most phages where only nucleic acid enters and capsid stays outside of bacterium) -enveloped viruses enter host cell thru fusion with host membrane or endocytosis -fusion: lipid envelope of virion fuses with membrane after virion attaches to host cell receptor (nucleocapsid is released directly into cytoplasm) -endocytosis entrance: receptor-mediated endocytosis (cells bring certain extracellular material into the cell) -nonenveloped viruses cannot fuse to enter cells; virions enter only via endocytosis (nucleocapsid is released into the cytoplasm) -all viruses: nucleic acid separates from its protein coat before the start of replication (uncoating) -most DNA viruses multiply in nucleus

enveloped virus

-envelope = lipid bilayer outside of capsid -obtain bilayer from the host cell -in between nucleocapsid and envelope = matrix protein (only in enveloped viruses) -more susceptible to disinfectants because these chemicals damage the envelope and make the virus non-infectious

Retrovirus

-ex. HIV -have a (+) strand RNA genome and carry reverse transcriptase within the virion -after entering the host cell, reverse transcriptase uses RNA genome as a template to make one strand of DNA -complement to that DNA strand is synthesized to make ds DNA which integrates into the host cell chromosome -once integrated, viral DNA may remain in a latent state or may be transcribed into RNA which is translated to synthesize viral proteins needed for production of new virions

lytic / virulant phages

-exit host at the end of the infection cycle by lysing the cell -ex. T4 (ds DNA phage; during its infection cycle the phage takes over a bacterial cell: 5 step process : attachment, genome entry, synthesis, assembly, and release)

M13

-filamentous phage -initiates infection by attaching to a protein on the F pilus -single stranded DNA genome that enters the cytoplasm of the bacterial cell where host cell DNA polymerase syntehsizes complementary strand (double stranded DNA = replicative form (RF)... one strand of RF is used as a template to make mRNA and copies of phage's single stranded genome)

2. Genome entry

-following attachment, bacteriophage injects its genome into the cell -ex. T4 degrades a small portion of the bacterial cell wall using an enzyme located in the tip of its tail (lysozyme degrades peptidoglycan); tail contracts so the phage particles "squat" on surface of cell; phage DNA is injected through the host's cell wall and membrane along with into interior of cell while the capsid remains on the outside of the cell; virus separates nucleic acid from its protein coat before replication

ss (+) RNA replication

-genome functions as mRNA -viral RNA can immediately bind to host cell ribosomes and be translated to make proteins (one of them is viral replicase) -replicase is needed to make additional (+) RNA strand copies but it can only do this by first using the (+) RNA strand as a template to make multiple complementary (-) RNA strands and these (-) RNA strands act as templates to produce (+) RNA strands -newly synthesized (+) RNA strands can be translated to make more viral proteins or they can be packages into new virions being formed

animal cells

-grown in liquid medium -used as host cells for virus culture -can divide repeatedly with proper nutrients -divide slower than bacteria -cell types making up solid tissues grow as monolayer (single sheet of cells adhering to bottom of the flask) -white blood cells grow as single cells in suspension

ds RNA virus

-has a genome that consists of both a (+) RNA strand and a (-) RNA strand (uncommon) -must carry own replicase because the host cell machinery is unable to translate ds RNA -replicase immediately uses (-) RNA strand of the ds RNA molecule as a template to make (+) strand RNA; which is translated to make more replicase an infection cycle is continuous

Viral diseases of plants

-individual cells or specialized organs of the plant may die and tumors may appear -infected plants become stunted in their growth -when plant viruses infect a cell they do not attach to specific receptors (enter through wound sites in the cell wall)

antiviral medication

-interferes with activities of enzymes required for viral replication -slows progression of viral infection

Assembly and Maturation

-involves bringing together newly formed viral nucleic acid with capsid proteins and packaging them to form the nucleocapsid -spontaneous self-assembly that occurs when there is an appropriate amount of viral nucleic acid and capsid proteins in the host cell -viral capsomeres assemble to form capsids into which the genome is packaged -modificationn of newly synthesized viral proteins -nonenveloped viruses mature fully in host cell cytoplasm -some maturation steps for enveloped viruses occur as virion leaves the host cell (virus deposits protein into host cytoplasmic membrane and assembled nucleocapsid binds to these regions of membrane before exiting host cell

International Committee on Viral Taxonomy

-keeps database of recognized viruses -key characteristics: genome structure (type of nucleic acid and strandedness) and hosts they infect (bacteria, archaea, animals, plants) and viral shape and disease symptoms

5. Release

-late in infection, phage-encoded lysozyme is produced: enzyme digests host cell wall from within, causing the cell to lyse and therefore release the phage -burst size (number of phage particles released) -phage partiles infect any susceptible cells in environment and process of phage replication is repeated: entire process from entry of nucleic acid to exit of phage takes about 30 min

ss DNA replication

-like ds but a complement to the ss DNA molecule must be synthesized to generate a double stranded (+/-) DNA molecule -genes can be expressed to produce the encoded proteins -newly synthesized DNA strand which is complementary to ss DNA genome also acts as a template for producing more ss DNA genome copies

Lysogen

-morphologically identical to an uninfected cell -immune to superinfection (infection by same type of phage) because the repressor that maintains the prophage also binds to operator on incoming phage DNA -immune to lysogenic conversion

Replication of RNA virus

-most = ss and replicate in the cytoplasm -replication requires a virally encoded RNA polymerase (replicase), which is an RNA-dependent RNA polymerase (whereas RNA polymerase is a DNA-dependent RNA polymerase)

Release of enveloped viruses

-most enveloped viruses are released by budding (process where virus acquires its envelope) -Before budding, virally encoded protein spikes insert into certain regions of host cell's membrane and matrix protein accumulates on inside surface -assembled nucleocapsids are extruded from cell at these regions and are covered with a layer of matrix protein and lipid envelope -some enveloped viruses obtain their envelope from membrane of an organelle by budding into the organelle and are transported in vesibles to the outside of the cell

lambda phage

-most studied temperate phage -linear chromosome but 2 ends have complementary single-stranded overhands that join togethe inside host cell to form circular molecule, which can direct lytic infection or integrate into E coli chromosome (lysogeny) -integration: uses phage-encoded enzyme (integrase) that inserts phage DNA into host cell chromosome at certain site and integrated phage DNA (prophage) replicated along with host chromosome before cell division (prophage can be integrated forever or can be excised from host chromosome by phage-encoded enzyme: lytic infection begins)

productive infections

-new viral particles that are formed from viral infections

4. Assembly (Maturation)

-once multiple copies of the phage genome and structural components of phage are produced, they assemble to produce new phage particles -phage head is formed and DNA is packed into it; tail is attached and tail spikes added -self-assemble and certain phage proteins serve as scaffolds to help protein components associate

plaque assay

-one of most precise methods for determining the concentration of animal viruses in a sample

release of transducing particle from phage-infected hose

-particle binds to another bacterial cell and injects its DNA... bacterial DNA may then integrade into the recipient cell by homologous recombination

generalized transducing particles

-phage heads that contain only bacterial genes in place of phage genes -cannot direct a phage replication cycle

1. Attachment

-phage particles collide with host cells by chance -on contact, phage attaches by means of protein on tail to receptor on host cell surface/pilus -ex. in case of T4, receptors are on the bacterial cell wall and they normally perform important functions for the cell but the phages used them and exploit the molecule for their own use (if a cell lacks the receptor used by that phage then the cell is resistance to infection by that certain phage)

PrPC

-prion protein, cellular -normal cellular form -easily destroyed by host cell proteases -normal turnover processes destroy older molecules as new ones are synthesized

restriction-modification systems

-protect bacteria from phage infection by quickly degrading incoming foreign DNA through restriction enzymes and modification enzymes

capsid

-protects nucleic acid from enzymes and toxic chemicals in the environment -protein coat carries enzymes required by the virus for infection of host cells -simple in chemical structure (because viral genomes are small and can encode only limited number of proteins) -composed of identical protein subunits (capsomeres) arranged in precise manner

modification enzyme

-protects the host cell's own DNA from action of restriction enzyme (adds methyl groups to nucleobases recognized by restriction enzyme and restriction enzymes cannot degrade methylated DNA so it only degrades incoming phage DNA but not host DNA) -may methylate incoing phage DNA before restriction enzyme has actedf, meaning phage DNA will not be degraded and it will replicate and lyse the host cell

Spikes

-protein structure on animal viruses that allows virion to atach to specific receptor sites on host cells -sticks out from lipid bilayer of enveloped viruses or capsid of non-enveloped viruses

restriction enzyme

-recognizes specific short nucleotide sequences in foreign DNA (like phage DNA) and cuts the DNA molecule at these sequences

Release of non enveloped viruses

-released when the host cell dies -many viruses trigger apoptosis (programmed cell death) prior to release of viral particles -virions release from dead cells can invade any healthy cells in the area

obtain animal cells

-remove tissue from animal and process it to get individual cells and cells can then be grown in a flask with a liquid nutrient medium (form primary culture) but normal cells can divide only a limited number of times so primary cultures must be regularly made -tumor cells often used in cell culture (multiply indefinitely in vitro: result in established cell line)

Replicase mistakes

-replicase lacks proofreading ability and makes more mistakes than DNA polymerases -generate mutations dueing replications which lead to antigenic variation (allow some RNA viruses to adapt to selective pressures)

DNA virus

-replicate in nucleus of host cell and use host cell machinery for DNA synthesis and gene expression -viruses encode own DNA plymerase which allows them to replicate even if host cell is not actively replicating its own chromosome

Replication

-replication stratgery = divided into DNA viruses, RNA viruses and reverse trascribing viruses

Specialized transduction

-results from excision mistake made by a temperate phage during transition from lysogenic to lytic cycle -phage DNA is usually excised from bacterial chromosome but sometimes a short piece of bacterial DNA on each side of phage DNA is taken and a piece of phage DNA remains in bacterial chromosome -excised DNA (contains bacterial and phage gees) replicates and becomes incorporated into phage heads during assembly (defective phage particles because don't carry entire set of phage genes) -phage particles are released when host cells lyse -when defective phage injects DNA into another bacterial cell, both phage and bacterial DNA enter, meaning bacterial genes may integrate into recipient's genome via homologous recombination

Size of viruses

-small -100 to 1000 times smaller than the cells they infect

Plaque assays

-used to quantitate phage particles in samples like sewage, seawater and soil -double layer of agar is inoculated with a bacterial host and phage-containing specimen and poured over agar dish -bacteria in soft agar multiply rapidly = dense lawn of bacterial growth -many phage particles lyse bacteria and release progeny phage that diffuse and infect neighboring bacteria

latent infections

-viral genome remains silent within a host cell yet can reactivate to cause a productive infection (replicate independently of host genome)

Virion

-viral particle -consists of nucleic acid surrounded by a protein coat (capsid)

cytopathic effect

-virus propagated in cell culture often causes distinct morphological alternations in infected cells -host cells may change shape, detach from surface or lyse

nucleic acid in viruses

-viruses have only a single type of nucleic acid: either RNA or DNA but never both (can classify virus as RNA or DNA virus with linear, circular, double stranded or single stranded genome)

attachment

-viruses have protein components allowing virion to attach/adsorb specific receptor sites on host cells (phages have tail fiberts and animal viruses have spikes)

non-enveloped / naked virus

-viruses that do not have an envelope -nearly all phages

Viral genome

-when in a host cell, cell hijack the cell's replication machinery and induce cell to make more viral particles

tumor

abnormal growth of tissue resulting from a malfunction in normally highly regulated process

helical viruses

appear cylindrical; capsomeres are arranged in helic similar to a spiral staircase -can be short and rigid or long and filamentous (capsid and nucleic acid)

icosahedral viruses

appear spherical when viewed with electron microscope but surface is 20 flat triangles arranged in soccer ball manner (capsid and nucleic acid)

persistant infections

can continue with or without symptoms for years/life of the host, sometimes without any symptoms -chronic and latent

Plaques

circular zones of clearing that form in lawn due to cell lysis by phage -each one represents a PFU initiate by a single phage particle infecting a cell

prions

composed solely of protein -agents that have been linked to man slow, always fatal human diseases -prion proteins accumulate in neural tissue -neurons die and brain function deteriorates as the tissues develop characteristic holes -lack any nucleic acid -unusually resistant to heat and chemical treatments that are commonly used to inactivate infectious agents -violate central dogma of replication that requires nucleic acid act as a template for replication of macromolecules -not made up of nucleic acid

benign

do not metastasize (spread) or invade nearby normal tissue

Viruses

genetic information (DNA or RNA) contained within protective protein coat -incapable of metabolism, replication or motility -outside of cell they are inert but inside cell they direct activities that have a profound effect on that cell (they are obligate intracellular parasites) -they are infectious agents but they are not organisms -some infect prokaryotic cells and others infect eukaryotic cells -bacteria ad eukaryotic cells can be growth in pure culture but viruses require live organisms as hosts

cancerous/malignant

have potential to metastasize

HPV

human papillomavirus -several HPV-encoded proteins interfere with the function of an important tumor suppressor gene product

regulate growth and cell division

involve genes that stimulate cell growth (proto-oncogenes) and ones that inhibit cell growth (tumor suppressor genes)

Synthesis of Viral Proteins

requires expression of viral genes and synthesis of multiple copies of viral genome -viral proteins are sometimes synthesized as a polyprotein that is cleaved by viral proteases into individual proteins

provirus

silent viral genome -cannot be eliminated from body (disease can recur even after extended period without symptoms) -ex. shingles from acute infection of chicken pox is a virus reactivating

inclusion body

site of viral replication -position depends on the type of virus