Micro exam 5

What are some general characteristics of viruses

Minuscule, acellular, infectious agents having either DNA or RNA

cause infections of humans, animals, plants, and bacteria

Cannot carry out any metabolic pathway

cannot reproduce independently

have no cytoplasmic membrane, cytosol, organelles

has an extracellular (ex. virion) or intracellular state (ex. genome)

Neither grow nor respond to the environment

Extracellular state of viruses

called a virion

has a protein coat (capsid) surrounding nucleic acid

Some have envelopes

outermost layer (capsid or envelope) provides protection and recognition sites for host cells

Nucleocapsid

nucleic acid and capsid together

Envelope

nucleocapsid surrounded by envelope of host cell’s membrane

Intracellular state

capsid removed

virus exists as nucleic acid

Virulent (lytic) infection

replicates an destroys host

lysogenic infection

host cell genetically altered because viral genome becomes part of host genome

Single-stranded DNA or RNA of viruses may be plus sense ______ or minus sense _____

same as mRNA

complementary to mRNA

Genetic material of viruses

show more variety in nature of their genomes than do cells

primary way that scientists categorize and classify viruses

may be linear and segmented or single and circular

much smaller than genomes of cells

Most viruses infect only particular host cells why

due to affinity of viral surface proteins for complementary proteins on host cell surface

Host viruses may be so specific they only infect particular kind of cell in a particular host, what is an example of this

HIV

Generalists infect many kinds of cells or many different hosts, what is an example of this

West Nile Virus

All types of organisms are susceptible to what

Viruses

Bacterial viruses infect

bacteriophages (model systems for viral infections)

Archaeal viruses attack

Archaea

Animal viruses attack

animals (this is extensively studied)

plant viruses attack

plants

bacteriophage

a virus that infects and replicates within a bacteria

capsid

provides protection for viral nucleic acid

Capsids help the virus do what

attach to the host cell

Capsomeres are what

proteinaceous subunits that make up capsids

Capsomere

individual protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid making up the capsid

what are the three basic shapes of viruses

Helical, polyhedral, and complex

Helical shaped

capsomeres are bound together forming a circular tube around nucleic acid

rod shaped viruses have helical symmetry

Polyhedral shape

Spherical shape (a geodesic dome)

Icosahedron has 20 sides

complex shape

capsids can have many different shapes

Helical symmetry

rod-shaped viruses (ex. tobacco mosaic virus or TMV)

length of virus determined by length of nucleic acid

width of virus determined by size and packaging of capsomeres

Icosahedral symmetry

spherical viruses (ex. human papillomavirus)

most efficient arrangement of subunits in a closed shell

requires the fewest capsomeres

bacteriophages have what 2 parts

the head and tail

Viral envelope

acquired from host cell during viral replication or release (envelops is portion of membrane system of the host)

composed of phospholipid bilayer and proteins (some proteins are virally coded glycoproteins - spikes)

Envelope proteins and glycoproteins often play role in host recognition and for release after infection

Enveloped viruses are more fragile than naked viruses

viral classification is based on

type of nucleic acid

presence of an envelope

shape

size

viral genera have only been organized into what, why?

families

the relationship between viruses is not well understood by taxonomists

Viral replication is dependent on what

hosts’ organelles and enzymes to produce new virions

lytic replication

viral replication usually results in death and lysis of host cell

what are the 5 stages of the lytic replication cycle

attachment

entry (penetration)

synthesis

assembly

release

The most complex penetration mechanisms are found in what type of virus

tailed bacteriophages

Virions attach to cells via tail fibers that interact with what

polysaccharides on Escherichia coli LPS layer

Describe the attachment and entry of a bacteriophage

Virions attach to cell via tail fibers that interact with polysaccharides on the LPS layer of Escherichia coli

tail fibers retract, and tail pins contact the cell wall

T4 lysozyme forms small pore in peptidoglycan

tail sheath contracts, and viral DNA passes into the cytoplasm

capsid stays outside

Describe the assembly process of bacteriophages

Base → tail → sheath → DNA → Capsid → mature head → tail fibers → mature virion

Circular permutation

feature of many virus genomes where same genes are arranged in different orders

terminally redundant

some DNA sequences duplicated on both ends

T4 encodes what

primases, helicases, and 8-protein DNA replisome complex

Small DNA viruses use what for genome replication

host cell’s DNA polymeras

Complex DNA viruses use what for genome replication

their own polymerases (ex. T4)

T4 first replicates as a unit then forms what

concatemer (several genomic units recombined)

Virion synthesis takes how long

~ 30 minutes and ends in release

Early proteins

enzymes needed for DNA replication and transcription

Middle and late proteins

head and tail proteins and enzymes required to liberate mature phage particles

How does the genome get into the virion head

the genome is pumped into the head under pressure using ATP

What are the three stages of packaging the T4 genome into virion head

Proheads (bacteriophage head precursors) assembled

Packaging motor assembled at opening

Double-stranded linear genome pumped into prohead using ATP

Virulent mode

viruses lyse host cells after infection

Temperate mode

viruses replicate their genomes in tandem with host genome and without killing host

what are the two viral life cycles

virulent and temperate

virulent bacteriophages were the first viruses studied in detail what have we learned

Bacteriophages contain linear, dsDNA genomes that infect and kill their host

the study of these viruses established many fundamental principles of molecular biology and genetics

Examples include; T1, T2, T3, T4… T7

Temperate viruses

can undergo a lytic (short term) or lysogenic life cycle (long term)

Lysogeny

state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome

lysogen

host cell that harbors temperate virus

lysogeny is maintained by phage-encoded

repressor proteins

What are the general steps in a lytic pathway starting with a temperate virus

temperate virus attaches to the host cell

injects the viral DNA

Lytic events are initiated

Phage components are synthesized and virions are assembled

lysis of the host cell and release of new phage virions

What is the general pathway of temperate virus through a lysogenic pathway

Temperate virus attaches to host cell

Injects viral DNA

Viral DNA is integrated into host DNA

(cell becomes a prophage)

Viral DNA is replicated with host DNA at cell division

(an induction step can result in these cells switching over to a lytic pathway where host cell is lysed)

Bacteriophage lambda infects what

E. coli

Bacteriophage lambda structure

linear, dsDNA virus with head and tail

complementary, single-stranded “cohesive” regions have 12 nucleotides long at the 5’ terminus of each strand

When bacteriophage lambda penetrate what happens in the host cell

DNA ends base pair, forming the cos site, and DNA ligates and forms double-stranded circle

when lambda enters the lytic pathway what happens

lambda synthesizes long, linear concatemers of DNA by rolling circle replication

genome-sized lengths cut at cos sites; genomes packaged into phage heads

When lambda is lysogenic its DNA integrates into E. coli chromosome where

at the lambda attachment site

what does the lambda use to attach at the attachment site

lambda integrase

what induces the lytic pathway of bacteriophage lambda

cell stress

How is the lysogenic DNA added to the host cell DNA

a site-specific endonuclease creates staggered ends of phage and host DNA

Lambda genome integrates and gaps are closed by DNA ligase

What are the key elements of regulation

two repressor proteins:

cl protein (lambda repressor) and cro repressor

when do repressors accumulate

after infection

cl protein (the lambda repressor)

causes repression of lambda lytic events

cro repressor

controls activation of lytic events

what controls the infection outcome

first repressor

When cro is not repressed and lambda low which event happens

cell lysis

when cro is repressed and lambda high which cycle does it go through

lysogeny

animal virus infection

major tenets (capsid and DNA/RNA genome, infection and takeover of host, assembly, and release) are universal

classified by genomes

most human viral diseases are caused by RNA viruses

What are the two key differences between animal virus infections

Entire virion enters the animal cell

or

Eukaryotic cells contain a nucleus, the site of replication for many animal viruses

Unlike prokaryotes, how does a virion enter the animal cell

the entire virion enters the cell, not just the genome

ssRNA are

large

dsDNA are

HUGE

overview of viral infection of animal cells

bind specific host cell receptors, typically used for cell-cell contact or immune function

different tissues and organs express different cell surface proteins (often viruses only infect certain tissues)

Entry usually occurs by fusion with cytoplasmic membrane or endocytosis

what are 3 general steps of virion entry via cell recognition and membrane fusion/endocytosis

Rotavirus virion is bound to cell surface proteins/receptors

virion is engulfed by host cell membrane

compartmentalization

Viral DNA-genomes replicate where

in the nucleus

Viral RNA genomes replicate where

most viral RNA is replicated or converted to DNA within nucleocapsid (not in the nucleus, just in the cytoplasm)

where does uncoating or shedding of the capsid occur

at the cytoplasmic membrane or cytoplasm

what are examples of positive-sense ssRNA virus

polio and coronavirus

what are examples of negative-sense ssRNA virus

rabies and flu

Double-stranded RNA virus examples

rotavirus

What is the process of protein synthesis and genome replication in animal RNA viruses with a positive-sense ssRNA virus

Receptors on cytoplasmic membrane of host recognize the +ssRNA virus

+ssRNA is used in translation of viral proteins; genome acts as mRNA

transcription by viral RNA polymerase using a -ssRNA complementary strand as a template

Transcription occurs to copy +ssRNA

Assembly of proteins and genome

what is the process of protein synthesis and genome replication in animal RNA viruses with a negative-sense RNA virus

Receptors on cytoplasmic membrane of host cell recognizes -ssRNA virus

-ssRNA virus is inserted into the host cell

Transcription by RNA-dependent RNA transcriptase

Complementary +ssRNA to act as a template and mRNA

+ssRNA can be translated into viral proteins

+ssRNA can be further transcribed into copies of -ssRNA

Copies of -ssRNA and viral proteins can be assembled for dispersal

what is the process of protein synthesis and genome replication in animal RNA viruses with a double-stranded RNA virus

receptors on cytoplasmic membrane of host recognise dsRNA virus

dsRNA in inserted into the cell

Unwinding of dsRNA yields -ssRNA and +ssRNA

-ssRNA is transcribed by viral RNA polymerase to make complementary RNA strands

+ssRNA acts as template and as mRNA

Translation of viral proteins from +ssRNA

Viral proteins and viral genome (dsRNA) are assembled into new viruses

Most DNA viruses assemble in the

nucleusmost

Most RNA viruses develop where

solely in the cytoplasm (anywhere outside the nucleus)

The number of viruses produced depends on what

on the type of virus and size and initial health of the host cell

Enveloped viruses can cause what

persistent infections (doesn’t kill the host cell immediately) via budding

Naked viruses are released by what

exocytosis or lysis

What is the process of budding

Viral capsid is drawn to the plasma membra

Budding of the virus occurs, encapsuling the virus

cytoplasmic membrane of host envelopes the virion

Virulent infection

lysis of host cell, most common (especially naked cells)

Latent infection

viral DNA exists in host genome and virions are not produced; host cell is unharmed unless/until virulence is triggered

Persistent infections

release of virions from host cell by slow-budding does not result in cell lysis (infected cell remains alive and continues to produce virus)