viruses

virus

an infectious particle consisting of genes (nucleic acid) packaged in a protein coat; do not fit our definition of living organisms

1. nucleic acid (genes)

2. protein coat

3. membranous envelope (sometimes)

virus composition

1. are much simpler in structure than even prokaryotic cells

2. cannot reproduce or carry out metabolism outside of a host cell

3. exist in a shady area between life-forms and chemicals, leading a kind of “borrowed life”

characteristics of viruses

tobacco mosaic disease

stunts growth of tobacco plants and gives their leaves a mosaic coloration

unusually small bacteria might be responsible for tobacco mosaic disease

hypothesized by researchers in the late 1800s studying tobacco mosaic disease

the infectious agent did not share features with bacteria (such as the ability to grow on nutrient media)

suggested by later work on tobacco mosaic disease

Wendell Stanley (1935)

confirmed the hypothesis that the infectious agent of tobacco mosaic disease was not bacterial by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV)

1. double- or single-stranded DNA

2. double- or single-stranded RNA

what can make up viral genomes

1. DNA viruses

2. RNA viruses

two types of viruses

1. a single linear molecule of nucleic acid

2. a circular molecule of nucleic acid

virus genome types

between three and 2,000 genes

number of genes found in virus genomes

capsid

the protein shell that encloses the viral genome

capsomeres

protein subunits that make up capsids

1. helical

2. icosahedral viruses

types of viruses in relation to the structure of their capsids

viral envelopes

structures surrounding viral capsids that are derived from host cell molecules and contain a combination of viral and host cell molecules

1. influenza viruses

2. many other viruses found in animals

viruses that have viral envelopes

accessory structures

structures on viruses that help them infect hosts

bacteriophages (phages)

viruses that infect bacteria, are the best understood of all viruses

1. an elongated capsid head

2. a protein tail piece

structure of bacteriophages

elongated capsid head

encloses bacteriophage DNA

protein tail piece

structure that attaches the phage to the host and injects the phage DNA inside

obligate intracellular parasites

organisms that can replicate only within a host cell

host range

a limited number of host cells that a virus can infect

viral proteins are manufactured

what happens after a viral genome enters a host cell

1. enzymes

2. ribosomes

3. tRNAs

4. amino acids

5. ATP

6. other host molecules

structures and molecules that the virus makes use of in the host cell

spontaneously self-assemble into new viruses

what viral nucleic acid molecules and capsomeres do in host cells

1. the lytic cycle

2. the lysogenic cycle

two alternative reproductive mechanisms of phages

lytic cycle

a phage replicative cycle that culminates in the death of the host cell by lysing (breaking open) the host’s cell wall, releasing the progeny viruses

virulent phage

a phage that reproduces only by the lytic cycle

lysogenic cycle

a phage replicative cycle that replicates the phage genome without destroying the host by the viral DNA molecule being incorporated into the host cell’s chromosome

temperate phages

phages that use both the lytic and lysogenic cycles

prophage

the integrated viral DNA from a bacteriophage

environmental trigger

can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode

phage DNA is copied and the copies are passed to daughter cells

what happens to the phage DNA every time the host divides

restriction enzymes

cellular enzymes that recognize and cut up foreign DNA

methylation

causes the bacterium’s own DNA to be protected from restriction enzymes

surface proteins that cannot be recognized as receptors by a particular type of phage

proteins possessed by bacterial mutants favored by natural selection

CRISPR-Cas system

system based on sequences called CRISPRs, is used to protect both bacteria and archaea from viral infection

CRISPR-associated (Cas) proteins

nuclease proteins that interact with the CRISPR region and use the phage-related RNA to target the invading phage DNA

“spacer” sequence between the repeats

corresponds to DNA from a phage that had infected the cell

clustered regularly interspaced short palindromic repeats

what CRISPR stands for

phage DNA is integrated between two repeat sequences

what occurs when a phage infects a bacterial cell that has the CRISPR-Cas system

the cell can block any attempt of the same type of phage to reinfect it

what happens if a cell with the CRISPR-Cas system survives a viral infection

transcription of the CRISPR region

triggered by an attempt of a phage to infect a cell

the RNAs are cut into pieces and bound by Cas proteins

what happens to the resulting RNAs from CRISPR being transcribed

phage mutants that can bind to altered cell surface receptors or that are resistant to enzymes

phage mutants favored by natural selection favors

constant evolutionary flux

the relationship between phage and bacteria

1. an RNA or DNA genome, either single-stranded or double-stranded

2. the presence or absence of a membranous envelope

two key variables used to classify viruses that infect animals

1. envelope

2. RNA genome

structures that many animal viruses have both of, while few bacteriophages have them

viral glycoproteins

structures on a viral envelope that bind to specific receptor molecules on the surface of a host cell

an envelope made from golgi apparatus membrane

replaces the viral membranes formed from the host’s nuclear envelope

the host’s nuclear envelope

place where other viral membranes are formed in the host cell

viruses that infect animals

have the broadest variety of RNA genomes of all viruses

retroviruses

viruses that use reverse transcriptase to copy their RNA genome into DNA

HIV (human immunodeficiency virus)

the retrovirus that causes AIDS (acquired immunodeficiency syndrome)

provirus

the viral DNA that is integrated into the host genome

RNA polymerase

transcribes the proviral DNA into RNA molecules

unlike a prophage, a provirus remains a permanent resident of the host cell

difference between a prophage and a provirus

1. mRNA for synthesis of viral proteins

2. genomes for new virus particles released from the cell

functions of the proviral RNA molecules

bits of cellular nucleic acid

thing that viruses likely evolved as given that they can replicate only within cells

1. plasmids

2. transposons

candidates for the source of viral genomes

1. plasmids

2. transposons

3. viruses

types of mobile genetic elements

the size of a small bacterium

size of the largest virus known to exist

proteins involved in translation DNA repair, protein folding, and polysaccharide synthesis

what the viral genome encodes

whether viruses evolved before or after cells

controversy surrounding viruses and cells

1. cause the release of hydrolytic enzymes from lysosomes

2. cause infected cells to produce toxins that lead to disease symptoms

3. have molecular components such as envelope proteins that are toxic

ways that viruses may damage or kill cells

vaccine

a harmless derivative of pathogenic microbes that stimulate the immune system to mount defenses against the harmful pathogen, and thus can prevent certain viral illnesses

antibiotics

CANNOT treat viral infections

antiviral drugs

drugs used for viral infections that can help to treat, not cure, viral infections

they inhibit synthesis of viral DNA and interfere with viral assembly

way in which antiviral drugs can treat viral infections

emerging viruses

viruses that suddenly become apparent

ebola virus

one of several emerging viruses that cause hemorrhagic fever, an often fatal illness

1. chikungunya virus

2. zika virus

3. ebola virus

examples of emerging viruses

influenza virus named H1N1

the virus that appeared in Mexico and the United States and caused a pandemic in 2009

epidemic

a general outbreak

pandemic

global epidemic

1. RNA viruses have an unusually high rate of mutation

2. the disease can be disseminated from a small, isolated human population and can eventually spread around the world

3. about three-quarters of new human diseases originate by spreading to humans from animals

three processes that contribute to the emergence of new viral diseases

type A influenza viruses

influenza viruses that infect a wide variety of animals including birds, pigs, horses, and humans; are the cause of flu epidemics

1. hemagglutinin (HA)

2. neuraminidase (NA)

the viral surface proteins that standardized names of strains of influenza A are based on

1. changes in host behavior

2. changes in the environment

3. new roads into a remote area

4. global climate change

can increase the spread of viruses responsible for emerging diseases

may allow mosquitoes that carry viruses to expand their range

way in which climate change can increase the spread of viruses

the use of insecticides and mosquito nets

may help prevent the spread of emerging viruses

more than 2,000 types

number of viral diseases of plants that are known

1. spots on leaves and fruits

2. stunted growth

3. damaged flowers or roots

symptoms that are caused by viral diseases of plants

1. typically have an RNA genome

2. a helical capsid or icosahedral capsid

characteristics of most plant viruses

1. horizontal transmission, entering through damaged cell walls

2. vertical transmission, inheriting the virus from a parent

two major routes that plant viruses spread disease:

horizontal transmission

viruses entering through damaged cell walls

vertical transmission

inheriting the virus from a parent

prions

infectious, incorrectly folded proteins that appear to cause degenerative brain diseases in animals and also infect plants; they act slowly, and are virtually indestructible

1. scrapie in sheep

2. mad cow disease

3. creutzfeldt-jakob disease in humans

examples of diseases caused by prions

transmitted through food

how prions can be transmitted

1. are somehow able to convert a normal form of the protein into the misfolded version

2. several prions aggregate into a complex that can convert more proteins to prions

mechanism by which prions cause disease

1. alzheimer’s

2. parkinson’s disease

diseases that prions may be involved in

1. the phage attaches to a host cell and injects its DNA

2. the phage is either virulent or temperate

3. destruction of host DNA

4. production of new phages

5. lysis of host cell causes release
   of progeny phages

steps of the lytic cycle

1. the phage attaches to a host cell and injects its DNA

2. the phage is temperate only

3. the genome integrates into a bacterial chromosome as a prophage

4. the prophage is replicated and passed on to daughter cells OR can be induced to leave the chromosome and initiate a lytic cycle

steps of the lysogenic cycle