240 Midterm 2 content

Why have viruses been harder to deal with than bacteria?

because usually viruses dont behave like bacteria, so its difficult to classify and deal with them

What is a very common, early example of a virus in history?

Smallpox in egypt

What did Walter Reed do?

He found out that yellow fever virus was not caused by the water, but transmitted by mosquitos in 1901

What is the name of viruses that infect bacteria?

bacteriophages (plaque)

Who discovered bacteriophages (plaques)?

Felix D’Herelle

For Viruses, what is the size range, and the genome range?

size range - 10-100nm
genome range - few thousand to 200 000 nucleotides long

What is the structure of a Virus?

Could be single or doublestranded DNA and RNA, has a protein shell (capsid) aroudn genome, some viruses have the envelope (cell-derived membrane aroudn capsid)

what is the protein shell (capsid) made out of for viruses?

composed of many capsomere proteins

What is the difference between an enveloped virus and a naked virus

Enveloped virus - has a plasma membrane that surrounds the nucleocapsid
naked virus (unenveloped virus) - no plasma membrane

For Virsuses, the capsid + genome =

nucleocapsids

How is a virus capsid built, structure wise, 2 types

Some can be irregular, but the main types is helical (looks like bendy straw), and icosahedral (like a soccerball, but made up of many triangles on each face, each triangle side is a protein)

What are the 6 steps of replication for a virus?

1. Stick to a host cell

2. enter the cell

3. virus opens up and pours its genome in the cell

4. synthesis, replicate genome in the cell

5. create new viruses

6. new viruses leave the cell

What are the 3 cases of how viruses enter animal cells?

Basically viruses without an outer layer need the bubble route. Viruses with an outer layer can merge with a membrane, either at the cell surface (HIV) or inside the bubble (influenza).

1. Endocytosis of a non-enveloped virus (like rhinovirus) - It sticks to the cell, gets swallowed in an endosome bubble, then breaks out of the bubble and opens up to release its genome in the cell.

2. Membrane fusion of an enveloped virus (HIV) - It sticks to the cell and its outer layer merges directly with the cell membrane. No bubble is needed. The inside of the virus slips straight into the cell.

3. Endocytosis of an enveloped virus (Influenza) - It sticks to the cell and gets swallowed in a bubble. Then the bubble turns acidic, which makes the virus’s outer layer merge with the bubble’s wall, releasing its contents into the cell.

How do viruses enter plant cells? Plant cells are much more sturdy/harder to penetrate

Viruses looking for plant damage to insert into damage (insect damage, wind, humans, etc)

how do viruses take over bacteria?

tail fibers attach onto bacteria, viruses are almost like a screw, and screw through the cell wall of bacteria, then virus pushes its DNA through into the bacteria

What are the 3 hypothesis of where viruses come from

Coevolution hypothesis: Viruses originated at the same time as other microbes, and coevolved with them

Regressive hypothesis: viruses are previously alive organisms that have regressed over time to become host-dependent particles

Progressive hypothesis: viruses originated from genetic material, then gained the ability to replicate and be transmitted

What are the 4 steps to cultivating bacteriophage?

• 1 small amount of suceptible bacterial host cells are added to the phage sample

• the mixture is added to nutrient rich agar, and mixed

• the agar mixture is poured onto another nutrient agar base, and solidifies

• plaques will appear after incubation

is working/cultivating bacteriophage easy or harder than bacteria, and why?

harder, because bacteriophage is very small, and they need a specific host in order to work

What are the steps of viral purification (differential centrifugation)? 4 steps

• starts with a filtration to remove large cells and cellular debris

• begins first initial low speed centrifugation

• transfer supernatant (?) and centrifuge at medium speed, this is where pellets of whole and broken cells start of form

• transfer supernatant (?) and centrifuge at high speed (ultracentrifugation)

now the viruses have been turned to pellets, purified and concentrated

what is gradient centrifiguation? 3 steps

depends on different densities of viral components and particles

• the tube is filled with layers of decreasing conc of sucrose

• the virus is put on the top

• the mixture is centrifuged, and there should be a band of intact virus particles at one layer

What is the difference between gradient and differential centrifugation?

Differential centrifugation is a rough first step that makes pellets. Gradient centrifugation is a finer step that makes sharp bands.

Viral Quantification, how do you quantify them? 4 methods

This is not easy or straightforward, the methods are:

• direct count

• hemagglutination assay

• plaque assay

• endpoint assays

What is direct count for viruses, and what are 2 issues with it

an electron microscope is used to count the material, but this requires an expensive specialized microscope, and it doesnt differentiate between infectious and non-infections viral particles

What is the Viral quantification method hemagglutination, its pros and cons

Puts a bunch of viruses with red blood cells, so that the viruses should stick to the red blood cells, and see if they form a gel mat

• pros - its cheap, fast, and easy, no microscope needed

• some viruses wont stick, which means it doesnt differentiate viable/non-viable viruses, and doesnt show many virus’s there are

What is the Viral quantification method plaque assay? 2 steps, and what is it useful for?

• The virus is diluted and placed on target cells

• The plaques are counted to determine the plaque-forming unit (PFU) titer number

its useful for phages and plant viruses

What is the Viral quantification method Endpoint Assay? and the 2 types

An endpoint assay quantifies a virus by infecting cells and finding the diultion where half show infection/damage.
Type 1 - tissue culture infectious dose 50 (TCID), tests how much virus needed to see 50% cytopathic effect (CPE, visual dmg/change to host cell)
Type 2 - lethal dose 50 (LD50) - at what concentration do you see 50% of the test animal subjects die

How can a virus be named? list like 3 ways

extremely varied:

• simple letter/number combinations

• organisms they infect

• location of discovery of virus

• appearance of virus

• the disease it causes

How do the internation committee on taxonomy of viruses (ICTV) classify viruses? name like 5

ICTV classifies viruses based on order, family, subfamily, genus and species, morphology, genome structure, biolofical features, disease caused, envelope, and genomes

what is the baltimore classification system for classifying viruses?

its based around the mRNA production methods, it seperates the viruses into seven different classes, and developed by david baltimore (nobel laureate)

What is the first step of virus identification?

Electron microscopy, you look at it through a pricey specialized microscope, and see what it looks like

What is nucleic acid analysis for virus identification?

identifies viruses by genome sequence, and its used to study the virus’s evolution patterns

What are viroids? list 5 features

they consist only of naked RNA, very small (400 nucleotides), high internal complementarity, resistant to ribonucleases, only causes diseases in plants

What are prions? list 2 features about it

proteinaceous infectious particles, made out of just proteins, the replication method is still unclear

What happens in the lytic cycle for Viruses? 3 steps

The virus enters the bacteria, makes copies of itself, and bursts (lyses) the cell to get out.

What happens in the lysogenic cycle?

The phage inserts its DNA into the bacterium’s DNA and becomes a prophage. It gets copied along with the host’s DNA every time the cell divides, without killing the cell.

What is a prophage?

Phage DNA that has been inserted into the host cell’s genome and is “sleeping” there, sit there without killing the host cell

what makes a prophage switch from the lysogenic cycle to the lytic cell?

stress on the host cell

What is a temperate phage?

A phage that can do both cycles: it can be lytic, or it can hide as a prophage (lysogeny).

What is a Virulent phage?

A phage that is always lytic. It never hides in the host’s DNA.

How do you read this, and explain what shield and button well means

going left to right, the virus is diluted more and more, with red blood cells in each one, and seeing how much dilution, will still stick to the red blood cells

Sheild well - virus is there, virus links the red blood cells together into a shield
Button well - not enough virus, red blood cells clump together at the bottom

What is the difference between phylogenetic diversity and metabolic diversity fill in later

fill in later

What are the two kinds of cell metabolism fill in later

fill in later

What are the nutritional requirements for macronutrients?

C, N, P, S, O, H

What are the nutritional requirements for micronutrients?

required by most cells in trace amounts, includes Fe, Cu, Na, Mg, Mn, and others

Why do you need energy for cells

for oxidation, and providing electrons for ETC (fill in later)

Where does energy come from?

photosynthetic, organic or inorganic, OR chemical energy/chemo (organic or inorganic)

difference between litho and organo

either fill in later

What are all the combinations for the fundamentals of nutrition? energy - electrons - carbon source - eater

difference between hetero and auto troph

they

What is the energy source for chemoorganotrophs?

they get energy from oxidation of organic compounds

What is the energy source for chemolithotrophs

they are only foudn in prokaryotes, and get energ from oxidation from inorganic compounds

What is the energy source for phototrophs

they get energy from light captured by pigments, and they may by oxygenic or anoxygenic

what is carbon a major requirement for all organisms?

they need carbom for energy storage/manipulation, and structural purposes

How are autotrophs a primary producer of carbon

they fix C directly from CO2

for nutrient concentration what controls the growth rate?

the amount of nutrients available, and whatever nutrient there is the least of limits growth (like if everyone needs water, but theres only 2 drops of it, we are limited by the 2 drops)

What is the difference in the use of oxygn for obligate aerobes and microaerophiles

obligate aerobes require O2, microaerophiles grow best in low levels of O2

what is the main difference between aerotolerant anaerobes and obligate anaerobes and faculative anaerobes

aerotolerant arent harmed by O2, but dont use it, obligate cannot grow if there is O2, faculative can grow without O2, but grow better with O2