Chap 21, 22 (viruses, bacteria, archea)

What part of the human body has the highest amount of prokaryotic diversity?

1. stomach

2. liver

3. kidney

4. skin

5. blood

1. stomach

What is the correct definition of a virus?

1. A group of microorganisms, including methanogens and certain halophiles and thermoacidophiles, that have RNA sequences, coenzymes, and a cell wall composition that are all different from all other organisms.

2. An ultramicroscopic (20-300 nanometers in diameter), metabolically inert, infectious agent that replicates only within the cells of living hosts, mainly bacteria, plants and animals: composed of an RNA or DNA core, a protein coat, and, in more complex types, a surrounding envelope

3. Any protozoan of the phylum Rhizopoda, able to change shape because of the movements of cell processes (pseudopodia)

4. Any cellular organism that has no nuclear membrane, no organelles in the cytoplasm except ribosomes, and has its genetic material in the form of single continuous strands forming coils or loops, characteristic of all organisms in the kingdom Monera

5. Ubiquitous one-celled organisms; spherical, spiral, or rod-shaped and appearing singly or in chains, comprising numerous and variously classified phyla

2. An ultramicroscopic (20-300 nanometers in diameter), metabolically inert, infectious agent that replicates only within the cells of living hosts, mainly bacteria, plants and animals: composed of an RNA or DNA core, a protein coat, and, in more complex types, a surrounding envelope

Which of the following is NOT an aspect of the lytic cycle of viral replication?

1. Phage DNA replicates and phage proteins are made.

2. The host cell lyses, releasing new phages

3. A phage infects a host cell with its DNA or RNA

4. Phage DNA integrates with the host DNA

5. New phage particles are assembled using the host’s cellular machinery

4. Phage DNA integrates with the host DNA

Which of the following is not an example of a virus?

1. Bacteriophage T4

2. strep throat

3. flu

4. common cold

5. HIV

2. strep throat

conjugation

transfer of DNA from one bacterium to another via cell-to-cell contact

transformation

the uptake of exogenous DNA from the surrounding enviornment

lytic cycle

a replicative cycle where an entity introduces its genome into a host cell and initiates replication by hijacking the host’s cellular machinery to make new copies of itself

transduction

virus-mediated transfer of DNA between bacteria

lysogenic cycle

a replicative cycle where an entity integrates its DA into the host cell’s genome, causing a latent infection

Can viruses persist without other organisms?

No, viruses are not alive, so they can’t persist without other organisms

What is the makeup of a virus?

RNA or DNA + a protein coat, sometimes a membranous envelope

Size of a virus

1 nm - 250 nm

Fossils of viruses in our dna

Viruses that effect egg and sperm could be passed down

What is the protein shell of a virus made of?

The protein shell, or capsid, is built from capsomeres (protein subunits)

What is the viral envelope of a virus?

It surrounds capsids of viruses found in animals, and takes the cell membrane of the host cell when lysed

What is a bacteriophage/phage?

A virus that infects bacteria

T/F: Viruses only replicate in host cells

True

Reproduction cycle of influenza virus

1. influenza virus attached to target epithelial cells

2. cell engulfs virus endocytosis

3. viral contents are released, viral rna enters nucleus, replicated by rna polymerase

4. viral mrna used to make viral proteins

5. new viral particles made, released into extracellular fliud

6. cell not killed in process; continues to make new viruses

Lytic cycle

1. phage infects cell

2. Phage dna circulaizes, separate from host dna

3. Phage dna replicates, phage proteins made, new phage particles assembles

4. Cell lyses (break)s and phages are released

Lysogenic cycle

1. Phage infects cell

2. Phage dna incorporates into host genome

3. Cells viides, prophage dna passed on to daughter cells

4. Stressful conditions → phage dna is excised from bacterial chromosome → lytic cycle entered

T/F: The lytic cycle includes the lysogenic cycle.

False

2 key variables of the viral replicative cycle

1. single-stranded rna or double-stranded dna genome

2. the presence/absence of a membranous envelope

   • glycoproteins stored in the er, transported by vesicles to the cell wall, envelopes new viruses

T/F: Retroviruses use reverse transcriptase to copy rna —> dna

True

What is HIV?

A retrovirus that causes AIDS

What is an emerging virus?

A virus that suddenly becomes apparant

What are examples of emerging viruses?

• Ebola viruses, cause hemorrhagic fever

• Chikungunya virus

• Zika virus

What are the three domains of life?

1. eukarya

2. archaea

3. bacteria

What differentiates prok and euk?

• prok are 0.5-5 microns, euk are 10-100 microns

• prok have no true nucleus or organelles, euk have nucleus and organelles

• prok dna located in nucleoid region, euk dna located in nucleus

• both cell wall, cell membrane, and ribosomes, euk has that + organelles

When did prok first start showing up?

~3.5 billion years ago

How manny microbial cells on the human body?

10 million

Whats the ratio between microbial to human genes in human bodies?

100-1

Where do human infants get their microbes from?

Mom’s in birth canal, breastmilk

Function of human microbiome?

• teaches human immune cells

• protection

What happens as an effect of overcleaning?

A lack of microbiomes —> immune system hindered against infections

What can combat overcleaning?

Pro/prebiotics

Bacilli prok?

• rod shaped

• solitary, some chains

• ex: pseudomonas aerugonsa

Cocci prok?

• spherical

• can be solitary, pairs, or clustrs

• ex: staphylococcus aerugonsa

Spirilla prok?

• spiral-shaped

• ex: treponema pallidum

Cell surface structures on bacterial cells?

Peptidoglycan; network of sugar polymers linked by polypeptides

Cell surface structures on archaeal cells?

Polysaccharides and proteins, lack peptidoglycan

What does a gram-positive stain mean:

Simpler walls, large amount of peptidoglycan

• peptidoglycan traps crystal violet which masks red safranin dye

What does a gram-negative stain mean?

toxic outer membrane, less peptidoglycan

• crystal violet easily rinsed away, revealing red safranin dye

Endospores?

Metabolically inactive, remains viable in harsh conditions

Fimbriae?

Velcro, allows them to stick to substrate or other individuals in colony

Pili?

Longer than fimbriae, exchanges dna in sexual reproduction

Motility?

Bacteria exhibits taxis:

• Chemotaxis: movement towards or away from mechanical stimulus

• Flagella for movement

T/F: The prok genome has less dna than the euk genome

True

How is the prok genome structured?

In circles, and located in the nucleoid region

What are plasmids?

Bacterial smaller rings of DNA

Bacterial reproduction?

Asexually by binary fission, short generation times

Bacterial diversity

Rapid reproduction, mutations, and genetic recombination

3 types of genetic recombination (combining dna from different sources)

1. Transformation: uptake of exogenous dna from surrounding environment

2. Transduction: virus-mediated transfer of dna between bacteria

3. Conjugation: transfer of dna from one bacterium to another

Photoautotroph nutritional modes

• energy source: light

• carbon source: CO2, HCO3-, or related compound

• types of orgs: photosynthetic proks (ex: cyanobacteria), plants, some protists (ex: algae)

Chemoautotroph nutritional modes

• energy source: inroganic chemicals (such as H2S, NH3, or FE2+)

• carbon source: CO2, HCO3-, or related compound

• types of organisms: certain prok (ex: Sulfolobus)

Photoheterotroph nutritional modes

• energy source: light

• carbon source: organic compounds

• types of orgs: some aquatic/salt-loving prok (ex: Rhodobacter, Chloroflexus)

Chemoheterotroph nutritional modes