unit 8 (acellular pathogens) Flashcards
characteristics of viruses
infectious acellular pathogens, obligate intracellular parasites w/ host and cell type specificity, DNA or RNA genome, genome surrounded by protein capsid
types of host cells that viruses can infect
every type of host cell (plants, animals, fungi, protists, bacteria, archaea)
host range definition
the host cells that viruses can infect, viruses are only able to infect the cells of one or a few species of an organism
host range determined by
certain specific surface receptors on host cells that viruses can attach to
virus transmission modes
direct and indirect contact, mechanical and biological vectors
size range of viruses
20-900 nm
genetic material of viruses
either DNA or RNA, never both
capsid definition
protein coat that surrounds the viral genome and enzymes needed to direct the synthesis of new virions
capsomere definition
protein subunits that make up a capsid, made of one or more different types of capsomere proteins that interlock to form the closely packed capsid
naked viruses (nonenveloped viruses) definition
viruses formed only with nucleic acid and capsid
enveloped virus definition
viruses formed w/ a nucleic acid packed capsid surrounded by a lipid layer
viral envelope definition
small portion of phospholipid membrane obtained as the virion buds from the host cell.
spikes definition
protein structures that extend outward and away from the capsid on some naked and enveloped viruses
spike function
allow the virus to attach and enter a cell
spike protein examples
influenza virus spikes hemagglutinin (H) and neuraminidase (N)
capsid shape types
helical, polyhedral, or complex
helical capsid
capsid is cylindrical or rod shaped, with the genome fitting just inside the length of the capsid
polyhedral capsids
consist of nucleic acid surrounded by a many sided capsid in the form of an icosahedron
icosahedral capsid
3D, 20 sided structure that resembles a soccer ball
complex capsid
have features of both polyhedral and helical viruses
what does the International committee on taxonomy of viruses (ICTV) do?
develops, refines, and maintains a universal taxonomy of viruses
viruses are classified into
families and genera\
viruses are classified based on
viral genetics, morphology, chemistry, and mechanism of multiplication
viral family names end in
-viridae
viral genus names end in
-virus
lytic animal virus infection stages
attachment, entry and uncoating, transcription, replication of viral DNA and proteins, assembly, and release
animal viruses enter the host cell by
endocytosis or membrane fusion
endocytosis definition
engulfment by host cell
membrane fusion definition
fusion of viral envelope w/ host membrane
tissue tropism definition
most viruses only infect certain types of cells within tissues
attachment (lytic animal virus)
virus become attached to target cell by binding to specific host cell receptors w/ viral glycoproteins (spike proteins)
entry and uncoating (lytic animal virus)
the host cell engulfs the virus by endocytosis, the viral capsid and envelope are digested as it enters the cell, uncoating the viral enzymes and genetic material
transcription (lytic animal virus)
viral DNA enters host cell nucleus, where it is transcribed by viral RNA polymerase to create mRNA
replication of viral DNA and proteins (lytic animal virus)
transcription of viral DNA by RNA polymerase creates mRNA which is read by a ribosome to synthesize viral proteins. viral DNA is replicated.
assembly (lytic animal virus)
new phage particles are assemble using viral proteins and DNA that were replicated
release (lytic animal virus)
new viral particles that were made are released into extracellular fluid, allowing them to infect new cells. The host cell is not killed by this and continues to produce new virions
types of nature of viral genome in viruses
dsDNA, ssDNA, ssRNA, dsRNA
three types of RNA genome
dsRNA, +ssRNA, -ssRNA
if a virus contains +ssRNA genome
it acts as cellular mRNA and can be translated directly to make viral proteins
if a virus contains -ssRNA genome
host ribosomes cannot translate it until the -ssRNA is replicated into +ssRNA by viral RNA-dependent RNA polymerase
retrovirus definition
+ssRNA viruses that carry reverse transcriptase
retrovirus replication cycle stages
attachment, entry and uncoating, synthesis of dsDNA by reverse transcriptase, integration, synthesis of viral RNAs, synthesis of viral proteins, assembly and maturation, release, replicating cells w/ latent virus
provirus definition
integrated viral genome in host genome that can remain in the host for a long time (latency) and does not excise from the host genome
retrovirus example
HIV
attachment (HIV retrovirus)
HIV fuses to host cell surface. HIV binds to the CD4 receptors on helper T cells, which allows the secondary binding of chemokine coreceptor to the viral envelope
entry and uncoating (HIV retrovirus)
HIV and host membrane fuse and viral genetic material enters the cell while the envelope is left at the surface. HIV’s matrix and capsid protein are digested as it enters the cell, releasing viral enzymes and viral RNA
synthesis of dsDNA by reverse transcriptase (HIV retrovirus)
reverse transcriptase uses host nucleotides to convert viral RNA to DNA. the single stranded DNA is reverse transcribed again to create dsDNA
integration (HIV retrovirus)
integrase, an enzyme that entered the cell w/ the virus, carries the dsDNA into the nucleus through a nuclear pore. integrase then nicks the host chromosome, allowing the HIV DNA to insert itself into the host chromosome.
synthesis of viral RNAs (HIV retrovirus)
new viral RNA is synthesized when RNA polymerase transcribes the section of the chromosome that contains the viral DNA
synthesis of viral proteins (HIV retrovirus)
new viral RNA is used as genomic RNA and to make viral proteins. the mRNA of viral DNA is translated by ribosome and the viral proteins are created
assembly and maturation (HIV retrovirus)
the viral proteins get taken to the cell’s surface where they get embedded into the cell membrane, forming new immature HIV virus
release (HIV retrovirus)
once a new immature HIV virus forms, it buds off, taking the host cell’s membrane and using it as an envelope. Mature virions form when proteases break down the polyproteins chains in the virion
replicating cells with latent virus (HIV retrovirus)
latent virus is replicated when host cells divide, creating another infected cell with the potential to create new virions and infect other cells
persistent infection definition
occurs when a virus is not completely cleared from the system of the host but stays in certain tissues or organs of the infected person
effects of persistent viruses
virus may remain silent or undergo productive infection without seriously harming or killing the host
mechanisms of persistent infection
involve regulation of viral or host gene expressions or the alteration of host immune response
primary categories of persistent infections
latent infection and chronic infection
examples of latent viruses
herpes simplex virus, varicella-zoster virus, Epstein-Barr virus
examples of chronic viruses
hepatitis C and HIV
latent virus definition
viruses that are capable at remaining hidden or dormant inside a cell
chronic infection definition
disease w/ symptoms that are recurrent or persistent over a long time
mechanisms by which HIV maintains chronic persistence
prevention of viral antigens of the surface of infected cells, altering immune cells themselves, restricting expression of viral genes, and rapidly changing viral antigens through mutation
viral growth curve stages
inoculation, eclipse, burst, burst size
inoculum stage
inoculum of virus causes infection, binding to cells
eclipse stage
viruses bind and penetrate the cells, no virions detected in the medium
burst stage
virions are released and lysed from the host cell at the same time
burst size stage
number of virions released per bacterium
one-step multiplication curve for bacteriophage
host cells lyse, releasing many viral particles into the medium, which leads to a very steep rise in viral titer
Viral titer definition
number of virions per unit volume
viroids consist of
a short strand of circular RNA capable of self-replication
viroid replication
take control of host machinery to replicate their RNA genome
do viroids have capsids?
viroids do not have a protein coat to protect their genetic information
viroid diseases examples
agriculture diseases: potato tuber spindle disease
virusoid definition
subviral particles, best described as non-self replicating ssRNAs
virusoid replication
like viroids, but require the cell be infected w/ a specific “helper” virus.
helper virus function for virusoid
helper virus enters host cell and released virusoids which replicates its RNA independently from the helper virus
helper virus example
subterranean clover mottle virus
prion definition
misfolded rogue form of a normal protein found in the cell that can stimulate other endogenous normal proteins to become misfolded, forming plaques
prion formation caused by
genetic mutation or occurs spontaneously
plaques
large aggregates of prions
disease caused by prions
transmissible spongiform encephalopathy
TSE transmission
eating contaminated meat, heredity, by contact w/ contaminated tissue
viral virulence factors examples
adhesions, antigenic variation
viral adhesion examples
spike protein hemagglutinin, glycoprotein gp120
hemagglutinin functioning
allows influenza virus to bind to sialic acid on the membrane of host respiratory and intestinal cells
gp120 functioning
allows HIV to attach to helper T cell through interaction w/ CD4 receptor and chemokine coreceptor
types of antigenic variation
antigenic drift, antigenic shift
antigenic drift definition
result of point mutations causing slight changes in the spike proteins hemagglutinin and neuraminidase
antigenic shift definition
major change in spike proteins due to gene reassortment, which typically occurs when two different flu viruses infect the same host cell
antigenic variation results in
continual emergence of new strains that the immune system will not recognize
cellular components that help us identify an organism
sequence of a DNA molecule when compared to known sequences housed in a database, comparing protein signatures
molecular analysis of DNA methods
nucleic acid probing, agarose gel electrophoresis, restriction fragment length polymorphism (RFLP) analysis, southern blots and modifications, and microarray analysis
nucleic acid probing tests for/how
identifies the presences of a certain DNA sequence using artificially constructed DNA probes that complementary bind to the certain DNA sequence
what do agarose gel electrophoresis tests do
physically separate DNA fragments of different sizes and compared to known size fragments of DNA ladder, which can identify the individual or species to which the DNA belongs
how do agarose gel electrophoresis test work
DNA samples w/ colored dye are put into wells. negative electrode is placed near the DNA, positive electrode opposite DNA. DNA has a negative charge and will be drawn to the positive electrode, smaller DNA molecules will travel through the gel faster. DNA ladder that has known size of fragments is used to determine the sizes of other samples
what do restriction fragment length polymorphism tests do?
allows for the visualization by agarose gel electrophoresis of distinct variants of a DNA sequence caused by differences in restriction sites
southern blot
allows researchers to find a particular DNA sequence within an sample
northern blot
allows researchers to detect a particular mRNA sequence expressed in a sample
microarray technology
a nucleic acid hybridization technique that allows for the examination of many thousands of genes at once to find differences in genes or gene expression patterns between two samples
polyacrylamide gel electrophoresis (PAGE)
separates proteins based on their charges and/or their size using process similar to agarose gel electrophoresis
primers function
DNA replication requires the use of DNA primers for the initiation of replication in PCR
polymerase chain reaction (PCR) function
allows for rapid amplification of specific DNA sequence
PCR steps
denaturation, annealing, and extension
denaturation (PCR step)
dsDNA containing the target sequence is denatured at 95 degrees
annealing (PCR step)
temp is lowered to 50 degrees to allow DNA primers complementary to the ends of the target sequence to anneal to the template strands, with one primer annealing to each strand
extension (PCR step)
temp is raised to 72 degrees, optimal temp for DNA polymerase, allowing for the addition of nucleotides to the primer using the single-stranded target as template
PCR cycles yield
double the number of dsDNA target strands, cycle is run 25-40 times
reverse transcriptase PCR function
used to detect mRNA expression
real-time PCR function
quantifies a particular sequence in the original sample
next generation sequencing function
allow for rapid and inexpensive sequencing of the genomes of many organims,
