Bio 1202 exam 3

what is a virus

an infectious particle consisting of genes packaged in a protein coat

-cannot reproduce or carry out reproduction outside of a host cell

how are viruses classified

(very small infectious particle consisting of nucleic acid enclosed in a protein coat, and in some cases, a membranous envelope

-viral genomes can either be double/single stranded DNA or double/single stranded DNA

-as either DNA viruses or RNA viruses

-the genome is either a single linear or circular molecule of the nucleic acid

-have about 3-2,000 genes in their genome

what is a capsid

-protein shell that surrounded the viral genome

-built from capsomeres (protein subunits)

-variety of structures that may be referred to as helical or icosahedral viruses

what is a viral envelope

-surrounds the capsids of influenza viruses and other viruses found in animals

-derived from membranes of host cells- often times from Golgi apparatus membrane

-contain a combination of viral and host cell molecules

-helps the viruses infect the host cell by binding to specific receptor molecules on the surface of the host cell

what are bacteriophages

aka phages

-they are viruses that infect bacteria

-their capsid head that holds their DNA is elongated

-protein tail piece that attaches the phage to the host cell and injects the phage DNA inside

what is a host range

-the limited number of host cells that each virus can infect

how do viruses hijack other cells in order to make copies

1)enter and uncoat their capsid

2)viral DNA replicates

3) transcribes and manufactures capsid proteins

4) self assembly of new viral particles that then exit from the cell

*uses host enzymes, ribosomes, tRNAs, amino acids, ATP, and other moleucules

what are the 2 alternative reproductive mechanisms for a phage

Lytic:

—(normal one) *results in death of the cell

—produces new phages and lyses the host’s cell wall, releasing the progeny viruses

—produces a virulent phage (a phage that only reproduces by the lytic cycle

—process: attaches, enters and uncoats, synthesis (replication), self assembly, release and causes death of the cell

Lysogenic:

—replicates the phage genome without destroying the cell

—the DNA is incorporated into the host cell’s chromosome

—produces temperate phages (phages that use both lytic and lysogenic cycles)

—process: the phage attaches, enters, integrates into the host genome, and replicates with the host cell during division.

what is a prophage and can you switch between the lytic and lysogenic cycle

-prophage: integrated viral DNA

-yes, environmental signals can trigger the switch between the two

why would viruses use one cycle over the other

-lytic is more fast and destructive so it’s used when conditions are optimal for rapid speed/immediate, mass production of progeny and leading to cell death

-lysogenic is more slow and can hide more easily, it replicates alongside the host genome and avoids destroying the cell, it’s used when resources are scarce or immune responses are high

how do restriction enzymes cut and do they cut the own bacteria DNA

-they cut double stranded DNA at specific nucleotide sequences

-bacteria’s own DNA is protected because it is methylated, preventing cuts

-results in either sticky ends (at the end) or blunt ends (in the middle)

what is a palindrome

-when its read the same way backwards and forwards

besides for restrictive enzymes, what is another way that bacteria/archaea can protect themselves from viral infections

-CRISPR cas system (clustered regularly interspaced short palindromic repeats)

-it is fast, inexpensive, and highly accurate

-1)a cell is transfected with an enzyme complex containing guide molecule, healthy dna copy, dna cutting enzyme 2)the synthetic guide molecule finds the target DNA 3)the enzyme cut the target DNA strand 4)the defective DNA strand is replaced with the healthy DNA copy

how can you classify viruses that infect animals

1) rna or dna genome, either single or double stranded

2) presence or absence of a membranous envelope

what is a provirus

-viral DNA that is integrated into the host genome

-permanent unlike prophages in the host cell

what is a retrovirus

-it is rna virus that uses reverse transcriptase (an enzyme) to convert its RNA into DNA within a host cell by using a RNA polymerase

-most viruses that infect animals have RNA genomes

*HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome)

what are some examples of animal viruses and which ones are important to US and worldwide

Double stranded DNA (dsDNA) - Poxvirus (has an envelope): small pox virus/ cowpox virus *problem worldwide

Single stranded DNA (ssDNA) - Parvovirus (no envelope): B19 parvovirus (mild rash) *problem worldwide

Double stranded RNA (dsRNA) - Reovirus (no envelope): Rotavirus (diarrhea)/ Colorado tick fever virus *problem worldwide

Single stranded RNA (ssRNA); serves as mRNA - Flavivirus (has an envelope): Zika virus (goes after fetus and results in an underdeveloped skull) *problem worldwide - emerging

ssRNA; serves as template for mRNA synthesis - Filovirus: Ebola virus (hemorrhagic fever-you bleed from everywhere) *problem mostly in west africa

why HIV unusual and what is its mutation rate

extremely high mutation rate, one mutation per 20,000-250 bases

unusual because of these stages:

1)HIV enters the cell

2)its a retrovirus so its information is stored on ssRNA instead of dsDNA found in most orgnaisms

3)HIV DNA enters the nucleus of the CD4 cell and inserts itself into their DNA then instructs the cell to make many copies of the original virus

4)New virus particles are assembled and leave the cell to go infect other CD4 cells

what are the difference classes of HIV medication

1) Prevent HIV entry - Fusion and Entry inhibitors

2) Prevent RT replication - Non nucleoside reverse transcriptase inhibitors

3) Prevent HIV replication - nucleoside/nucleotide analogues

4) prevent HIV integration - Integrase inhibitors

5) prevent HIV assembly - protease inhibitors

what is a vaccine, how is it administered, are they 100% safe, and why might not someone get vaccinated for a viral disease

-harmless derivative of pathogenic microbes that stimulate the immune system to mount defenses against the harmful pathogen

-usually administered by injection, but can be orally or nasally

-they are not 100% safe

-someone might choose to use antiviral drugs to help treat viral infections by inhibiting synthesis of viral DNA and by interfering with viral assembly

what are the 4 disease patterns and examples of problematic viral diseases

epidemic: widespread occurrence of an infectious disease in a community at a particular time (flu like illness caused by the influenza virus H1N1 from Mexico and the US in 2009) H=hemagglutinin *N=Neuraminidase

pandemic: global epidemic (black death, 1918 spanish flu, and HIV/AIDS)

endemic: a disease that exist permanently in a particular region or population (malaria in Africa and chicken pox in the US)

sporadic: diseases that are seen only occasionally and usually without geographic concentration (tetanus, rabies, and typhoid fever)

vertical vs horizontal transmission

vertical: inheriting the virus from a parent through reproduction

horizontal: entering through damaged cell walls

what is a prion

-infectious proteins that appear to cause degenerative brain diseases in animals

—they are mis folded proteins that can be transmitted in food, act slowly, and are virtually indestructible

-they convert normal proteins into the misfolded version-several prions aggregate into a complex that can convert more proteins to prions- they have no genetic material unlike a virus

-involved in alzheimer’s, Parkinson’s, scrapie in sheep, mad cow disease, and Creutzfeldt Jakob disease

viral vs bacterial diseases

viral: caused by viruses (needs a host) and resolve with symptom management more widespread areas like a fever

bacterial: caused by bacteria and needs antibiotics and more localized areas

why are flu vaccine not 100% effective

-flu strains are constantly mutating

-you have to get the vaccine before you come in contact with the flu

plant vs animal viruses

plant: usually has RNA, lacks an envelope, and enter cells via wounds/vectors

animals: usually has DNA, has an envelope, and enter cells through endocytosis or membrane fusion

decomposers vs parasitic vs mutualistic

decomposers: break down and absorb nutrients from nonliving organic material- hyphae and mycellium body structures

parasitic: absorb nutrients from living hosts- haustoria (specialized hyphae) body structure (helps to extract nutrients from plants)

mutualistic: absorb nutrients from hosts and reciprocate with actions that benefit the host- arbuscular (help to exchange nutrients with plant hosts)

what is the structure of a fungus and how is it different from other multicellular organisms

-other multicellular organisms are mostly multicellular filaments and single cells (yeast)

-fungi structure increases their ability to absorb nutrient

-it forms networks of branched hyphae (have tubular cell walls strengthened with chitin) that combine to make mycelium-unlike other multicellular organisms, fungi do not have specialized tissues or organs, and their cell walls are made of chitin rather than cellulose.

-most of the time that hyphae is divided into cells by septa with pores allowing cell to cell movement of organelles

Septate hypha vs coenocytic hypha

septate: hypha that is divided into cells by septa, with pores allowing cell to cell movement of organelles

coenocytic hypha: hypha that lacks septa and has a continuous cytoplasmic mass with hundreds or thousands of nuclei

ectomycorrhizal vs arbuscular mycorrhizal vs mycorrhizae fungi and why is mycorrhizae fungi unusual

ectomycorrhizal fungi: froms sheaths of hyphae over a root and grows into the extracellular spaces of the root cortex

Arbuscular mycorrhizal fungi: extends arbuscules through the root cell wall and into tubes formed by invagination of the plasma membrane

mycorrhizae: mutually beneficial relationships between fungi and plant roots; they deliver phosphate ions and minerals to plants; most vascular plants have mycorrhizae; colonizes soils by the dispersal of haploid cells called spores

what do fungi use for sexual signaling to communicate their mating type

pheromones

plasmogamy vs karyogamy

*both are forms of reproduction

plasmogamy: fusion of cytoplasm; union of cytoplasm from two parent mycelia

karyogamy: fusion of the nuclei; produces diploid cells that is short lived and undergoes meiosis to produce haploid spores

*the paired processes of karyogamy and meiosis produces genetic variation

what mode do fungi use to reproduce and which is better

-both sexually and asexually

sexually by karyogamy and plasmogamy and meiosis

asexually by spores, budding (yeast reproduction by simple cell division), or fragmentation of hyphae

-sexually is better for genetic diversity

-asexually is better for speed

what is fungi related to and where is it in terms of evolution

-most closely related to animals and are from the opisthokonts clade

-related to unicellular protists called nucleariids; multicellularity arose seperately in animals and fungi

what are the five phyla of fungi

1) chytrids (100 species)- has flagellated spores called zoospores

—examples: deadly amphibian pathogen, potato wart

2) zygomycetes (1000 species)- hyphae are coenocytic, asexual sporangia produces haploid cells, produces zygosporangia sexually, can survive unfavorable conditions; ex: black bread mold (rhizopus stolonifer)

—examples: molds, parasites, and commensal symbionts

3) glomeromycetes (160 species) - once considered zygomycetes, form arbuscular mycorrhizae

—example: rhizophagus irregularis, glomus mosseae, gigaspora

4) ascomycetes (65,000 species) - largest fungi group; produce sexual spores in sacklike asci contained in fruiting bodies called ascocarps; aka sac fungi aka cup fungi vary in size and complexity; more than 25% form symbiotic associations with green algae or cyanobacteria called lichens; reproduce asexually by enormous numbers of asexual spores called conidia

—example: sac fungi

5) basidiomycetes (35,000 species) - clublike structure called a basidium, a transient diploid stage in the life cycle; aka club fungi; decomposers of wood; longlived dikaryotic mycelium; produces fruiting bodies called basidiocarps sexually; numerous basidia in a basidiocarp are sources of sexual spores called basidiospores

—example: mushrooms, puffballs, shelf fungi, birds nest fungi

what are endophytes

fungi that live inside leaves or other plant parts

-most are ascomycetes

-they make toxins to help defend the host plant; others help the plant tolerate heat, drought, or heavy metals

what is a lichen, what are the different types, and what is their role ecologically

-symbiotic association between a photosynthetic microorganism and a fungus

—the photosynthetic component is green algae or cyanobacteria which occupies an inner layer below the lichen surfacee

—the fungal component is often times an ascomycete

-important pioneers on new rock and soil surfaces and also are given scientific names; initiate soil formation; help fix atmospheric nitrogen to fertilize ecosystems; provides food and shelter for wildlife

DIFFERENT TYPES:

1) fruticose (shrublike0

2) foliose (leaflike)

3)crustose (encrusting)

what is ergotism

toxic condition caused by eating grain (typically rye) that is contaminated with Claviceps purpurea fungi

-symptoms include nervous spasms, burning sensations, hallucinations, and temporary insanity

-salem witch trials of 1692

-ergots contain lysergic acid, the compound in LSD that produces hallucinogenic effects.

what is the general term for a fungal infection in animals

mycosis

examples of fungal diseases

ringworm and athlete’s foot

systematic mycoses: spreads through the body

—coccidioidomycosis produces tuberculosis like symptoms

some mycoses are opportunistic

—candida albicans, which causes yeast infections

what role does fungi play in medicine

-fungi can be used to produce antibiotics for bacterial infections, like penicillian

-fungi will also lead to applications in biotechnology

—yeast gene homologs for Parkinsons and Huntingtons diseases

—yeast insulin like growth factors for diabetes

what are key characteristics of animals

-they are heterotrophs that ingest their own food

-they are multicellular ekaryotes

-cells are supported by collagen (structural proteins) not cell walls

-nervous and muscle tissue are unique

-reproduce sexually mostly in the diploid stage, they did undergo cleavage (rapid cell division) which leads to the formation of a multicellular hollow blastula which then undergoes gastrulation which forms a gastrula with different layers of embryonic tissues

-one larval stage *larva=before jevenile; sexually immature and morphologically distinct from the adult

-share a unique family of developmental genes ( Hox genes which are a subset of homeobox genes)

what do Hox genes do

-they regulate the development of body form and can produce a wide range of animal morphology

how many species are described and is that an accurate amount

1.9 million species are described

-not accurate

-estimated to be far more (10-50 million)

when did the most common ancestor live and what was it

lived about 770 MYA

may have resembled modern choanoflagellates

what are the five eras and a significant event for each one

Neoproterozic Era

• includes the Ediacaran biota

• evidence of animal embryos and of predation found

Paleozoic Era

• Cambrian explosing marks the earliest fossil appearance of many major groups of living animals

• those fossils are of bilaterians; organisms with the bilaterally symmetric form, complete digestive tract, and one way digestive systems

*decline of edicaran and cambrian explosion is bc of 1)new predator prey rls 2)rise in atmospheric oxygen 3)evolution of Hox gene complex and addition of new microRNAs

Mesozoic Era

• coral reefs and the first mammals emerged

• dinosaurs were the dominant terrestrial vertebrates

• flowing plants and insect diversified

Cenozoic Era

• followed mass extinctions of both terrestrial and marine animals

• mammals increased in size and exploited vacated ecological niches

• global climate cooled

what is a body plan

a set of morphological and developmental traits

bilateral vs radial symmetry

bilateral: two symmetrical halves; dorsal (top) and ventral (bottom) sides, right and left side, anterior (front) and posterior (back) ends; typically have sensory equipment like a brain and a central nervous system; ONE line of symmetry

radial: symmetrical around an axis; top and bottom but no front and back or left and right; often are sessile or planktonic (drifting or weakly swimming); can have MULTIPLE lines of symmetry