BIO 102 EXAM #1 REVIEW

Viruses are categorized by

# of strands, envelope or not, & the purpose they serve (specific to ssRNA)

What are CAS proteins?

*C*RISPR *A*ssociated *P*rotein nuclease that chops up nucleic acids. -binds to RNA strand and unravels viral DNA strand to see if it is complementary, and chops up the DNA if it is.

List two differences and two similarities between ALL viruses.

*SIMILARITIES*: 1. all contain bacterial genome (RNA or DNA) 2. all have a protein coat-capsid *DIFFERENCES*: 1. vary in type of genome (RNA vs. DNA) 2. Size/Shape/Type of receptor it has to bind to 3. outer coating (envelope vs. no envelope)

Explain how viral genome can differ/vary.

*TYPE OF GENOME* 1. Can either consist of double or single stranded DNA (DNA virus) 2. Can either consist of double or single stranded RNA (RNA virus) *SIZE OF GENOME* between 3 and 2,000 genes in viruses genomes (smallest contain only a few, while largest contain hundreds of genes) *SHAPE OF GENOME* Can be linear or circular *ENDS COVALENTLY SEALED OR NOT*

Explain the purpose of glycoproteins.

-act as viral encoding (mRNA is translated to make these specific proteins) -bind to the receptors on other cells (ex. CD4) - LOCKING together w the next cell (specificity)

Describe the process of copying DNA in the lytic cycle. What happens if we don't copy DNA into each viral particle?

-copying DNA to make more of the genome, then follow the instructions of DNA: transcribe (DNA to RNA) then translate to make proteins that serve as components of the new viral particles made. - if we don't copy DNA into each new particle, they would be phage ghosts (no viral material inside)

Why do certain viruses need to be packaged with viral proteins as well as the viral genome?

-would not be a viable virion -original infection cannot be set up without these viral proteins - HAVE TO BE THERE

What are two ways that a virus can leave the cell? (do not need to get into the cycles, just explain the general process)

1. Bud off the cell, leaving cell alive (lysogenic) 2. bust out of the cell, killing the cell & allowing new viral particles to infect other cells. (lytic)

What are the basic rules every virus must follow when replicating?

1. Disassembly of the infectious viral particle - for genome to go into cell. 2. Replication of the viral genome - can happen simultaneously with #3, or in reverse order if a bunch of proteins are made before genome is copied. 3. Gets cell to synthesize viral proteins by the host cell's machinery 4. Reassembly of these components into new progeny virus particles - to get into new cells.

Describe the GENERAL life cycle of a bacteriophage. (SHOULD BE REVIEW)

1. Phage attaches to bacterial cell, injects DNA into cell - DNA acts as instructions for making more phages. 2. Viral DNA directs bacteria to make A LOT more viral components 3. Breakup of bacterial genome occurs - Total takeover using components of bacteria 4. After about 20 minutes, a protein is released that pokes/cuts out a hole/pore in cell, which allows 100-200 viruses to be released that can now infect other bacterial cells - CYCLE REPEATS!!

Name the basic difference between viruses and other parasites we know, such as bacteria, fungi, & eukaryotic parasites.

1. Viruses don't have their own machinery, they are the "ultimate hitchhikers", they take over the cell they infect & use all supplies the cell has to offer, while other parasites are the cells themselves & use their own machinery for DNA replication, transcription & translation.

Name the steps that CRISPR-CAS system goes through.

1. When viral DNA gets inserted, pieces of it get cleaved and get inserted into the genome. 2. Transcribe the CRISPR-locus, process it, and bind them to the CAS protein. 3. Surveying incoming DNA and looking for a complementary piece - chop up DNA if a match is made.

List three defenses bacteria has to protect its cells from viral infection (don't explain just list).

1. bacterial mutants 2. Foreign DNA can be identifies and cut up by cellular enzymes called restriction enzymes. 3. CRISPR CAS system

Answer the following questions about the Influenza virus: 1. Does it have an envelope? 2. Is it an RNA or DNA virus? 3. How does it get in the cell? 4. How does the genomic material get released?

1. yes! enveloped virus 2. RNA virus 3. gets in the cell by endocytosis - cant fuse w the plasma membrane since there are different pH outside our cells than inside the ends-some. 4. acidification of compartment --> protons get put into the compartment and this changes the shape of the proteins on the membrane of particle --> allows/mediates fusion of membrane of membrane of viral particle with membrane of endosome.

Flu epidemics are caused by type _______ influenza viruses. They infect a wide variety of animals: birds, pigs, horses, & humans

A

What is the lytic cycle?

A phage replicative cycle that makes lots of new virions that eventually results in the death of the host cell. - host cell did its job and gets killed - some phages only have this cycle (virulent phage) - phages attach, takes over bacteria and kills the cell, releasing phage progeny

Explain what a positive strand vs. a negative strand virus is in terms of ssRNA viruses.

A positive strand virus means the ssRNA is released into the cell, and can be immediately translated. A negative strand virus means the ssRNA is released into the cell, has to make a complementary copy of that genome, and translates that complementary copy - can not be immediately translated.

Which are more complicated: anti-virals or antibiotics?

ANTI-VIRALS!

Where does the lipid envelope that a virus might contain come from?

As the virus leaves, they bud off the cell and take either: 1. usually a piece of the plasma membrane 2. more complicated: get envelope through transit through other organelles in the cell (ex. ER and Golgi)

What is a common virus that infects E.coli cells?

Bacteriophage T4

Briefly describe what a bacteriophage is and it's structure.

Bacteriophages are the most abundant organisms in the biosphere - they are viruses that infect bacteria. They are made up of protein and genetic material (DNA) - head contains genetic material and is attached to tail sheath and tail fibers (both made out of protein) Tail fibers are proteins that land on the cell and are what mediate the attachment of the virus to the bacterial cell. - diff proteins based on what type of phage/bacterial cell (host range) -Once cell attaches to host cell, it injects their genetic material and can take over inside of the cell.

Give a brief summary of what the CRISPR-CAS system is.

Based on sequences called *C*lustered *R*egularly *I*nterspaced *S*hort *P*alindromic *R*epeats (CRISPR) -adapted immune system: bacteria basically has a "memory" of viruses that have infected their ancestors -can protect themselves from it.

Describe the disassembly of non-enveloped viruses.

Binding to receptors on the host cell triggers endocytosis, which puts the vision inside a compartment (endosome) -cannot give instructions when it is stuck inside that compartment -based on virus, they have different ways of getting out of that compartment 1. *Pore Formation*: poliovirus forms a pore in the endosome and releases its genome through that pore. 2. *Endosomal Membrane disruption*: adenovirus lyses the endosome, allowing the genome to bust out and get released in the cell.

Describe how the Influenza virus releases its viral genome.

Binds to receptor, and goes through endocytosis, where is it stuck in an endosome (compartment), so membrane surrounding viral particle fuses with the endosomal membrane to enter cell/cytosol.

Both influenza A & B have two prominent proteins on their outside surfaces. What are they and give a brief explanation why we need them.

Both of these proteins are essential to getting the viral particle inside the cell (Hemagglutinin) & getting viral particle to be able to bud away from the cell (neuraminidase) 1. *Hemagglutinin*: 18 subtypes known 2. *Neuraminidase*: 11 subtypes are known When talking about influenza: use H__N__ to be specific about what subtype of each protein (ex. H1N1).

How does the CRISPR-cas system know which incoming viral DNA strands to cut up?

CAS proteins unravel the double stranded viral DNA and see if any of the RNA (bound to the CAS proteins) from previous infections is a complementary strand. - if a match is made with the DNA and any of the CAS proteins, the protein will start cutting up the DNA strand, so there is no way for infection to take place - BLOCKED INFECTION (kind of like acquired immunity) - if a match is not made, the DNA will not get chopped up and the virus can infect the cell in this case.

Is the provirus doing anything in the cell?

Can sit silently, unless cell is actively going through the cell cycle, in which it will then transcribe to RNA/mRNA for both the new genome for the progeny AND to translate into new proteins.

Say the virus needs the host cell's ribosomes. How would we go about stopping bacterial propagation?

Certain drugs bind better to bacterial ribosomes than human ribosomes, so blocking bacterial ribosomes (using antibiotics) would work b/c bacterial ribosomes are made up from different RNA than human ribosomes (Diff proteins)

What is a nucleocapsid referring to?

Combination of nucleic acid (viral genome RNA or DNA) and capsid that encloses it.

Why do we replicate viral genome?

Complementary strands can be translated, as well as used for the viral genome of new progeny.

What are some popularly known RNA viruses?

Corona Virus, Influenza virus, HIV, polio virus, rabies virus.

Is the receptor for Corona Virus' sole purpose to be a receptor? If not, what is its other purpose?

Corona virus ACE2 receptor is not there to serve as a receptor, the virus has evolved to bind to that receptor shape. - its purpose is to serve as an enzyme that converts specific molecules to something else

Do viruses carry out their activity in the cytosol or nucleus?

DEPENDS ON THE VIRUS!! -sometimes viruses carry out all of their activity in the cytosol (don't have to go into nucleus) & sometimes they go to the nucleus depending on the virus.

Fill in the blank. Based on genome, viruses are classified as ________ viruses or __________ viruses

DNA; RNA

A lot of viruses that cause clinically important diseases are ______ stranded.

DOUBLE ex. parvovirus is single stranded and causes a mild rash, while Polyomavirus is double stranded and causes more serious issues such as tumors. Both are DNA viruses

The largest viruses usually contain what type of genome? A. Double stranded B. Single stranded

Double stranded

How does the lysogenic cycle allow cells to get infected if the progeny doesn't bust out of the cell like in the lytic cycle?

Every time the bacteria divides, each one duplicates with the DNA of the virus thats integrated into the bacterial genome (the prophage!)

Explain the production of glycoproteins (where are they made)?

For production of glycoproteins: finished off in the ER, get processed in the Golgi, and then inserted into the plasma membrane, to be outside of cell.

State the function of hemagglutinin.

Functions both as a receptor-binding protein and as a protein that mediates fusion with host cell. -binds to sialic acid on surface of host cell(very prominent molecule found in epithelial cell of respiratory tract - found on glycolipids & glycoproteins) - changes shape due to differences in pH --> mediates fusion so it is now able to fuse.

What are the proteins found on the envelope of the HIV particle? What are their purpose?

GLYCOPROTEINS : gp120 and gp41 -spikes found on outside of HIV molecule. 1. *gp120*: necessary for binding to CD4, primary receptor on helper T/macrophage cells. 2. *gp41*: responsible for fusion between envelope of particle and plasma membrane of target cell.

How can we block viral HIV infections using the pre-viral proteins it contains? In other words, how can we get this virus to leave our cells alone if they are using so many of our cell's components?

HAART: *H*ighly *A*ctive *A*nti *R*etroviral *T*herapy - goes after enzymes (viral proteins) that we don't have - these three HIV enzymes are targets for inhibitors since we dont have them - combination of 3+ inhibitors (doesn't have to be all 3 anti-enzymes) of reverse transcriptase, protease and integrate ; can mix and match (like inhibitory "cocktails") that block the activity of these enzymes. - used to block the replicative cycle of HIV ex. typical HAART treatment can consist of 2 anti-reverse transcriptase & an anti-protease.

Describe how HIV releases its viral genome.

HIV (AIDS virus): Once glycoproteins bind with receptors, membrane that surrounds the viral particle fuses with the plasma membrane. -Once it fuses, genome is released in the cell.

List the pre-viral proteins that HIV contains. Why does HIV need these?

HIV is packaged with these essential enzymes that are required for the initial steps of infection and genome replication - our cells do not have these enzymes so they have to be packaged in the HIV particle. 1. *Reverse Transcriptase*: turns RNA into DNA - HIV is a retrovirus, so first thing that has to be done once viral particle fuses with plasma membrane, is RNA will code for production of a double stranded DNA strand using this enzyme. 2. *Protease*: cuts protein (there is a long polyprotein and this enzyme cuts it into several HIV proteins from the same linear strand1) 3. *Integrase*: inserts double stranded DNA into chromosomal DNA of host cell - called provirus.

Explain the SPECIFIC glycoproteins HIV contains, and well as what they do.

HIV particles have. lipid envelope that has glycoproteins *gp120* and gp41*, that bind to CD4 and the coreceptors on cells of the immune system (macrophage or helper T cells)

Explain why it may be a problem for viruses to use their host's machinery (ex. their host cell's ribosomes).

If we want to stop a viral infection, we would not be able to make a drug that blocks the virus' ability to translate a piece of mRNA because... THEY USE OUR RIBOSOMES!! Blocking those ribosomes would be blocking our own protein translating.

Why does changing just a few amino acids make a difference in the subtype of Neuraminidase and Hemagglutinin?

It changes the primary structure, therefore making a HUGE change in function/shape. - immune system will no longer be able to recognize and defend against it.

State the function of neuraminidase regarding sialic acid. Explain why sialic acid residues form.

It cleaves sialic acid residues on both host cell and viral particle - enables virus to leave the host. - since sialic acid found on membrane of host cell, the new viral particles would have sialic acid on them since they steal the membrane of the host. - the viral particle needs to detach and go infect more cells, so Neuraminidase cuts the sialic acid to release newly made viral particles.

Does HIV only infect one type of cell?

NO! Target cell is based on coreceptor - either helper T cell or macrophage.

Do ALL viruses make their host cell make more and more of itself all the time?

NO! not all viruses do this at all times.

Are glycoproteins and receptors the only proteins that are found on the membrane?

NO!! -Membrane can have proteins that were the target cell's normal proteins. - when it buds off the host cell, doesn't have to only be virally encoded proteins on the membrane, but also cellular proteins that ended up being embedded in the membrane. - happen to be in membrane that gets pulled off.

Can it only be protein receptors that a virus has to attach to? Does this matter?

NO!! Doesn't have to be proteins (receptors), can be glycolipid or sugar found on outside of cell - Doesn't matter --> just remember it has to be **very specific**

Do viruses just infect bacteria?

NO!! Viruses infect not just bacteria, but humans, animals, plants ---> every type of living organisms!!

Do capsomeres (protein subunits), have to be made up of the same protein to make up a capsid?

NO!!! Proteins subunits *DO NOT* have to be same type of protein. - proteins that make up capsids could be multiple subunits of the same type of protein OR more than one protein put together.

In the inside of a viral particle, is genomic material (DNA/RNA) the only thing found inside?

NO!!! Replication of the viral genome & synthesis of the viral proteins by the host cell translation machinery may require *pre-made viral proteins* that get packaged along the viral particle. -these are proteins of viral origin- coded for by viral instructions (viral mRNA) - the cell made them for the virus.

Are receptors sole purpose to be receptors for these viruses?

NO!!! These receptors recognized by these viruses are not on the bacterial surface to serve as the receptors for viruses - they have other functions. - the viruses have evolved to bind to these shapes, so they become the viral receptors. - work as the receptors, but that is not their sole purpose.

If a bacteriophage has a change in proteins (ex. in tail fibers), does the host range still say the same?

NO!!! change in proteins ---> change in host range These proteins are what is attaching to the cell, if they change, they can't infect the same type of cells.

Are viruses just a naked piece of nucleic acid the virus packages?

NO!!! Contain a protein coat (capsid), envelope, proteins on outside membrane, etc.

Can viruses be extracellular (stay on the outside of cells)?

NO!!!! Always intra-cellular, must go inside cells to infect.

Are viruses only enclosed in a capsid?

NOPE!!! In some viruses, the protein coat (capsid) if further enclosed by a lipid envelope. (ex. HIV and influenza) - often, a few viral proteins are packaged in a particle as well.

Explain how bacteria uses bacterial mutants to protect its cells from viral infection.

Natural selection favors bacterial mutants w/ surface proteins that cannot be recognized as receptors by a particular type of phage. - defense: mutation away from its own recognition - any change the host bacterial cell makes to the shapes of the receptors can alter whether or not the phages recognize the receptors -favored to survive!!! viruses cannot attach. - the virus can only get in if the receptor is a certain shape.

Can a single virus infect all types of cells?

No!!! It is quite limited in the amount of cells it can affect. This is known as the *host range*.

is there a name for phages that use ONLY the lysogenic cycle?

No, because phages either only use lytic cycles (virulent phage) or both lytic and lysogenic cycles (temperate phage).

Do other parasites (bacteria, fungi, & eukaryotic parasites) get energy from other sources? What about viruses?

Other parasites provide their own sources of metabolic energy, while viruses use the materials of the cells they infect.

If a phage is going through the lysogenic cycle, does that mean it can't go through the lytic cycle as well? What about vice versa?

Phage can go through lysogenic to make a whole bunch of cells with viral piece, then go through lytic to kill the cell after its done its "job". - to initiate lytic, this can happen using high UV radiation or chemicals Phage cannot go through lytic then lysogenic, b/c the host cell dies after lytic!

What are some popularly known DNA viruses?

Pox virus, herpes virus, adeno virus, parvovirus

What is propagation?

Producing offspring or multiplying/spreading

Once HIV'S genome goes into the cells, its genome (RNA) goes through __________ _____________, meaning the ssRNA ----> __________.

REVERSE TRANSCRIPTION ; DNA strand.

Describe the disassembly of enveloped viruses.

Requires *FUSION OF ENVELOPE WITH ANY MEMBRANE* of cell. (can be plasma membrane or endosomal membrane) -once envelope fuses, genome is able to get released.

Where does the double stranded DNA that gets inserted into the chromosomal DNA come of host cells of HIV come from?

Reverse transcriptase creates a complementary DNA copy of RNA (HYBRID), which then will be separated to make complementary DOUBLE STRANDED DNA. - this double stranded DNA will then get inserted into the chromosomal DNA.

What makes one subtype of neuraminidase and hemagglutinin different from another?

SHAPE!! - the amino acids that make up these 2 proteins make the shape vary between each subtype. - between two subtypes, there doesnt need to be a lot of different amino acids - changing just a few amino acids ---> greatly changes shape of a protein!1

Describe what the CRISPR locus is.

Short viral DNA sequences (cleaved off from when DNA was inserted form virus) from previous viruses are integrated into the CRISPR locus - viral DNA gets put in between these repeat sequences of the bacterial genome.

Corona virus is a ______ stranded _____ virus.

Single; RNA

True or False: BOTH influenza A and influenza B have Hemagglutinin (HA) and Neuraminidase (NA) on their surface.

TRUE!

Explain how we can use the antivirals, such as "Tamiflu", to target Neuraminidase. Wouldn't targeting neuraminidase affect us in a bad way?

Tamiflu acts as Neuraminidase's target, sialic acid, and gums up the activity of Neuraminidase, making it so that the activity is blocked. - this makes it so that host cells are stuck to sialic acid, and can't bud away to infect other cells. This gives us a way to block viral infection since we dont have neuraminidase, so it doesn't affect us if we block the activity.

Give a brief explanation about HIV and its host range.

The glycoproteins on HIV (gp120/gp41) only bind to CD4 and other receptors on cells of the immune system, such as macrophage and helper T cells. -Only when HIV binds to these receptors, can it bind and fuse into plasma membrane.

How can we reiterate our lock and key example in terms of viruses?

The receptor that a virus attaches to be has to be a very specific shape and size in order for the virus to attach and bind to it. THIS IS SPECIFICITY !!! -it finds something to attach to, and binds to it.

Explain how the Corona virus vaccine interacts with the spike glycoproteins of the virus.

The vaccine targets these spike glycoproteins and tries to get our immune system to recognize these proteins, bind to them, and not allow those proteins to bind to our receptors on H2. -does not recognize entire particle- it recognizes glycoproteins and binds them with defensive proteins to prevent them from binding with the receptor.

Explain how bacteria uses restriction enzymes to protect its cells from viral infection.

These cellular enzymes called restriction enzymes recognize DNA sequences that are not supposed to be there (viral DNA) and cut it out. -viral intruders inject DNA, bacteria says "not today!!!" and chops them out.

How do restriction enzymes know to not cut their own cellular DNA?

They don't cut their own DNA because those DNA are protected from the restriction enzymes by being methylated. -put CH3 groups on certain bases that basically "TAG" the DNA as self-known, and any DNA that don't have these methylated tags are cut out.

What do viruses carry with them?

Very little beyond genetic instruction/material - some type of nucleic acid - might carry with them some enzymes - mainly nucleic acids that have been packaged in proteins.

Where do glycoproteins that stud the lipid envelope come from?

Viral particle directed the cell (b/c they need them) to translate mRNA into these viral proteins and inner them into the plasma membrane. - when the particle buds off, they take a coat of lipid envelope (from the plasma membrane) that has those viral proteins in them that are necessary to infect another cell.

Is integrating viral DNA into bacterial chromosome (prophage) silent or does it make cell even more toxic than if it wasn't integrated?

Virulent piece of prophage is mostly silent (surprising most genes), but sometimes it can make produce some extra genes and makes bacteria A LOT MORE TOXIC. - ex. E.coli 0157.H7 is more toxic than regular E.coli b/c it produces toxins/viral genes due to instruction from viral prophage.

If we can't block the virus' machinery since it is also ours, how can we block viral infections? In other words, how do anti-virals work?

We have to pick something (usually an enzyme) that viruses have, that humans don't have in common (an equivalent copy of), and block that - antiviral drugs/vaccines do this - blocking enzyme function will stop the virus from propagating, but still allows us to keep living?

What is the difference between prophage and provirus?

When BACTERIOPHAGE is a temperate phages phage integrates itself into bacterial chromosome/DNA, and that combination is called prophage. When viral DNA gets inserted into OUR chromosome, we call it a provirus.

Explain the usage of ribosomes for both bacteria and viruses when they get inside human beings (to be specific.... do they each use their own or the cells they're in?).

When bacteria gets inside human beings, they don't use human being's ribosomes; they use their own ribosomes on which they translate their RNA Viruses would use the host cell's ribosomes *REMEMBER: VIRUSES ARE USING THE HOST CELL'S MACHINERY*

If viruses such as Corona Virus, Filovirus, and HIV all have a genome of single stranded RNA, why are they put into different categories?

When each virus releases their genome (the ssRNA) into the cells they infect, that ssRNA may deal with/serve as different things. *Corona virus*: positive ssRNA virus - ssRNA serves directly as mRNA - translated as it - when ssRNA is released, the instructions for the protein that they want the cell to make is contained in that genome. *Filovirus*: negative strand ssRNA virus - ssRNA serves as a template for mRNA synthesis. - once genome goes in, makes the cell make a complementary copy of that genome; copy then serves as mRNA & gets translated into proteins that virus needs. *HIV*: ssRNA serves as template for DNA synthesis - reverse transcription. - when genome goes in, forces cell to use its nucleotides to make a double stranded complementary DNA copy following instructions of ssRNA.

What is prophage referring to?

When viral (phage) DNA integrates with the genome of bacteria.

Why do viral particles need so many subtypes of Neuraminidase and Hemagglutinin? Why not just have 1?

When we are infected with the flu and survive, the immune system has seen and recognized the shape of these proteins (NA and Hemagglutinin) and have formed defensive proteins against them. - if we are infected w/ that same strain, we will not get sick again b/c our defensive proteins (like antibodies), will bind to it and prevent infection. - changing just a few amino acids makes it so our antibodies can't recognize the proteins anymore, so that is why we still get sick - influenza changes shapes/subtypes!

What is a host range?

a # of host cells it can infect, which is based on the shape of the receptor it attaches to on a particular cell.

What is the lysogenic cycle?

a viral replication cycle that replicates the phage genome without destroying the host.

Fill in the blank. Lipid envelopes are often studded with ________.

glycoproteins.

What is a capsid?

protein coat/shell that encloses the viral genome

What are capsids built from? Explain briefly.

protein subunits called capsomeres -capsomeres come together to form the capsid that surrounds the nucleic acids.

Fill in the blank: Viruses vary greatly in __________ and _____________.

size; shape

Fill in the blank: Viruses are ________ ______ _____________ particles.

stripped down infectious

Phages that use *BOTH* the lytic and lysogenic cycles are called ____________ _____________.

temperate phages.

How can the bacteria possibly defend itself by sticking the viral DNA in its genome (CRISPR locus)?

the CRISPR locus is transcribed into an RNA strand. That RNA is then processed (each phage DNA processed individually and cut apart from one another) and bound to Cas proteins, which will then find a complementary match.

Fill in the blank: ALL aspects of viral propagation depend on ________________________________________.

the host cell's machinery.

A phage that reproduces *ONLY* by the lytic cycle is called a ___________ ____________.

virulent phage.