Lecture Four: Viruses & Prions

Question 1

Amino Acid

Answer 1

Molecules that combine to form proteins

There are 20 amino acids, each with different chemical properties.

Which amino acids are in a protein, and what order they are in determines everything about what that protein will do in a cell.

The mRNA and coding strand both encodes an amino acid sequence used to make a protein

Question 2

Coding Strand [DNA Transcription]

Answer 2

The coding strand (or informational strand) is the DNA strand whose base sequence is identical to the base sequence of the RNA transcript produced (although with thymine replaced by uracil).

Question 3

Animal Virus

Answer 3

A small infectious agent that is unable to replicate outside a living animal cell.

Animal viruses contain only one kind of nucleic acid, either DNA or RNA.

Replicate differently than a bacteriophage ( with an animal virus, entire capsid enters via endocytosis or membrane fusion)

Replication Steps:

1. Attachment/Absorption
2. Penetration
3. Uncoating
4. Biosynthesis
5. Maturation/Assembly
6. Release

Question 4

Bacteriophage

Answer 4

A virus that infects and replicates within bacteria and archaea

Replication steps:

1. Attachment/ absorption
2. Penetration
3. Biosynthesis
4. Maturation/assembly
5. Release

Question 5

DNA Polymerase

Answer 5

A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA.

“ase” = enzyme
“polymer” = what the enzyme makes, a polymer of nucleic acids
“DNA” = the specific polymer made by this enzyme

The virion contains an RNA-dependent DNA polymerase (reverse transcriptase)

Question 6

Endoplasmic reticulum

Answer 6

A network of membranous tubules within the cytoplasm of a eukaryotic cell, continuous with the nuclear membrane. It usually has ribosomes attached and is involved in protein and lipid synthesis

Subunits of this are rough endoplasmic reticulum, and smooth endoplasmic reticulum

ERGIC: Endoplasmic reticulum / Golgi intermediate compartment

Question 7

Enveloped virus

Answer 7

Virions that have an envelope which surrounds/covers the capsid:

Viral envelopes are phospholipid bilayers stolen from the host cell, either the nuclear envelope or the cell membrane

Embedded glycoproteins (spikes) are encoded in the viral genome (not stolen from the host)

Other envelope proteins & glycolipids, etc, are stolen from the host cell membrane

Envelopes in animal viruses have several purposes related to replication and transmission

Budding occurs in enveloped viruses

Question 8

Genome Types

Answer 8

A characteristic of a virus and a component of virions

These determine the steps a virus must take to replicate in host cells

RNA or DNA

One or two strands
dsDNA
ssDNA
dsRNA
ssRNA
+ sense ssRNA
- sense ssRNA

Retroviruses are weird RNA viruses

Question 9

dsDNA

Answer 9

Double stranded Deoxyribonucleic acid

They are antiparallel: the 5’ end on one is the 3’ end on the other. They are also complementary: every nucleotide on one strand base pairs correctly with a corresponding nucleotide on the other strand.

Question 10

dsRNA

[only need to know what the abbreviation means]

Answer 10

Double-stranded Ribonucleic Acid

Question 11

ssDNA

[only need to know what the abbreviation means]

Answer 11

Single-stranded Deoxyribonucleic acid

Question 12

ssRNA

Answer 12

single-strand RNA

Two types: + sense ssRNA
- sense ssRNA

Question 13

+ sense ssRNA

Answer 13

This is like mRNA and is directly translated by host ribosome; transcription is not needed

SARS-CoV-2 is an example of enveloped + sense ssRNA; causes COVID-19

Question 14

• sense ssRNA

Answer 14

This strand is complementary to mRNA; mRNA must be made based on this template.

Influenza is a enveloped, helical - sense ssRNA

Question 15

Golgi Apparatus

Answer 15

A stack of small flat sacs formed by membranes inside the cell’s cytoplasm

Prepares proteins and lipid (fat) molecules for use in other places inside and outside the cell

During viral maturation, ER proteins get sent to the membrane via the Golgi

ERGIC: Endoplasmic reticulum / Golgi intermediate compartment

Question 16

Host

Answer 16

The organism the virion attacks; can be bacteria or a human cell

Question 17

Host Range

Answer 17

A Characteristic of Virus

The spectrum of hosts the virus can infect

Bacteria (viruses that infect bacteria are called
bacteriophage)
Archaea
Fungi & protists
Plants
Animals

Some viruses can infect a broad spectrum of hosts
Rabies: all mammals

Some only able to infect specific species
Bacteriophage lambda: only some strains of E. coli

Question 18

Hemagglutinin (HA)

Answer 18

An Influenza-specific structure

H spike

A spike protein serving as a receptor for cell surface sialic acids, aids in attachment

Vital in the Attachment phase of viral replication

Question 19

Matrix proteins

Answer 19

An Influenza-specific structure

In Biosynthesis: mRNA is translated into proteins
In the cytoplasm: proteins that will become nucleocapsid, matrix, RNA dependent RNA polymerases, and others, mostly for new virions.
In the ER: proteins that will be embedded in the membrane: spike proteins HA and NA, and a matrix protein

In Maturation/Assembly: New nucleocapsids are attached to a matrix protein that will help make sure the new virion has each of the 8 segments

Question 20

Neuraminidase (NA)

Answer 20

An Influenza-specific structure

N spike

A spike protein that degrades protective mucin; aid in attachment

facilitates release from sialic acids during viral release; aids in release

In attachment: digests mucus

In entry and uncoating: Causes the virus envelope to fuse with endosome membrane . . . nucleocapsids are free!

Question 21

Latency

Answer 21

Many viruses have different ways of “hiding” in host cells.

Incorporating the viral genome into the host genome is common
Retroviruses do this in humans, many bacteriophage do this
too

Other forms of latency exist
One example (from herpes viruses) is preventing the host
neuron apoptosis. If the neuron lives forever, so can the
virus particles!

Question 22

Naked Virus

Answer 22

Non-enveloped virus

Question 23

Nucleic Acid

Answer 23

Complex organic substance present in living cells, especially DNA or RNA, whose molecules consist of many nucleotides linked in a long chain.

Virus is a nucleic acid sequence

Found in and protected by virions

In uncoating: Nucleic acids are released into the cytoplasm

In biosynthesis: Direct the synthesis or proteins for capsid, enzymes, and spikes

Question 24

DNA replication (Polymerization Process)

[What enzyme does this; the template; the type of monomer; the product]

Answer 24

Definition: DNA replication is the process by which a molecule of DNA is duplicated; happens via base pairing, and constructing the opposite strand from 5’ to 3’

Enzymes: helicase, primase, DNA polymerase, and ligase

Template: each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand

Monomer: ??

Product: two DNA molecules consisting of one new and one old chain of nucleotides.

Question 25

Transcription (Polymerization Process) [What enzyme does this; the template; the type of monomer; the product]

Answer 25

Definition: The process of making mRNA from DNA; occurs in the nucleus Enzymes: RNA Polymerase Template: DNA Monomer: ?? Product: Single-stranded RNA molecule

Question 26

Translation (Polymerization Process) [What enzyme does this; the template; the type of monomer; the product]

Answer 26

Definition: The process of making a protein Enzymes: RNA-dependent RNA polymerase Template: RNA Monomer: ?? Product: Protein

Question 27

Prion

Answer 27

Misfolded proteins that can cause properly folded versions to also misfold. Cause TSE: Transmissible Spongiform Encephalopathy 6 - 10 year incubation period Symptoms: * Slow loss of alertness * Loss of coordination * Loss of weight * Delirium and death * “Spongy” regions of abnormal brain tissue

Question 28

PrP^C

Answer 28

prion protein (cellular version) and found in all neurons We don’t really know what PrPC does. We assume it stops working if it misfolds as PrPSC

Question 29

PrP^SC

Answer 29

prion protein (scrapie version) Infectious, misfolded, nonfunctional protein found in infected neurons the neurons that contain PrP^SC proteins die deadly, and is very resistant to heat and radiation (worse than endospores)

Question 30

Bovine Spongiform Encephalopathy (BSE)

Answer 30

Prion disease infecting cow aka Mad Cow Disease Caused by someone feeding leftover butchered sheep to cows Affected animals may display: changes in temperament (nervousness or aggression), abnormal posture, incoordination and difficulty in rising, decreased milk production, or loss of condition without noticeable loss of appetite

Question 31

Chronic Wasting Disease

Answer 31

Prion disease infecting deer and elk Similar to other animal TSE, but very communicable but method of spread is unknown Symptoms include The deer behave strangely, not hiding from humans / predators, and they eventually die within 2 years So far no human infections Deer shed huge amounts of PrP^SC into the environment Outbreak is quickly spreading in North America, with Idaho and Manitoba being the newest sites

Question 32

Creutzfeldt-Jakob disease

Answer 32

Prion disease infecting humans Can be spontaneous with median age of victim 68 years old Exposure to contaminated surgical instruments or infected organ In both cases genetic risk factors are known Symptoms include muscle twitching, progressive dementia Death between 1 and 5 years with roughly 500 cases in the US every year

Question 33

Variant Creutzfeldt-Jakob disease (vCJD)

Answer 33

Prion Disease infecting humans Most likely occurred when people hate BSE infected cows; also genetic risks Symptoms occur years later; main symptoms are rapidly progressive dementia, muscle twitching, and psychological changes Death is between months and years; faster than CJD Median age of victim is 28

Question 34

Fatal Familial Insomnia

Answer 34

Prion Disease Very rare, inherited prion disease in which neurons of the thalamus experience PrP^SC conversion at a high rate. Sleep is disrupted and can become impossible Symptoms include cognitive declines, autonomic dysfunctions Invariably fatal in ~1 year once symptoms appear. Occurs to older people: 40-60 yrs old

Question 35

Kuru

Answer 35

Prion disease infecting cannibal humans Common among the Fore people of Papua New Guinea; translates to “to shiver” Spread by eating human brains Symptoms include muscle twitching and loss of coordination, difficulty walking, involuntary movements, behavioral and mood changes, dementia, and difficulty eating Once ritual consumption of human brains became rare, Kuru disappeared.

Question 36

Scrapie

Answer 36

Prion disease infecting sheep Stanley Prusiner and his colleagues found abnormal proteins in spongiform tissue of sheep Symptoms include subtle changes in behavior or temperament, intense frequent rubbing against fixed objects to relieve itching, gait abnormalities such as incoordination, stumbling

Question 37

Protein

Answer 37

A chain of amino acids

Question 38

Ribosome

Answer 38

A particle consisting of RNA and associated proteins found in large numbers in the cytoplasm of living cells. They bind messenger RNA and transfer RNA to synthesize polypeptides and proteins.; the key to translation Virions do not have ribosomes Translates + sense ssRNA like it does mRNA

Question 39

RNA Polymerase

Answer 39

Use in the transcription of DNA to RNA

Question 40

RNA dependent RNA polymerase

Answer 40

An enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. One of the vProteins must be an RNA-dependent RNA polymerase since the host cell does not naturally have it Necessary for - vRNA ⇢ + vRNA - ssRNA viruses must have an RNA dependent RNA polymerase in the virion

Question 41

Attachment / Absorption

Answer 41

First step of viral replication in both animal cells and bacteriophages *In Bacteriophages*: Critical step. Most of the host defenses attempt to prevent this Requires a specific molecule to which the bacteriophage can attach (such as teichoic acid) *In Animal Cells*: Virus attaches to specific proteins and/or glycoproteins on host cell plasma membrane Spike proteins typically help viruses attach to host cells (HA and NA). Critical step hosts attempt to prevent. If attachment succeeds, the virus will probably kill or take over the cell. In our cells, the main defenses after this point involve shutting down the cell or killing it!

Question 42

Penetration

Answer 42

Second step of viral replication in both animal cells and bacteriophages *In Bacteriophages*: Bacterial wall is breached by phage enzymes Viral DNA or RNA is injected into cell *In Animal Cells*: virus enters via either: Receptor mediated endocytosis or Membrane fusion

Question 43

Uncoating

Answer 43

Third step of viral replication *in animal cells* Capsid and envelope (if present) are broken down to release nucleic acid into cytoplasm Host cell ingests virion in through endocytosis The endosome begins to acidify M2 proton channel allows the inside of the virion to acidify . . . this helps separate the nucleocapsids from the matrix Neuraminidase causes the virus envelope to fuse with endosome membrane . . . nucleocapsids are free!

Question 44

Biosynthesis

Answer 44

The third step of viral replication in *bacteriophages*; the fourth step of viral replication in *animal cells* This is the step where we see that viruses are nothing like cells. This is also the step where their genome type dictates what they must force the cell to do. The virus tries to make new virion parts, using host enzymes if possible. All virions contain the viral genome, which for some viruses is DNA, and for others, is RNA. *In Bacteriophages*: The cell begins to translate viral RNA (if a RNA virus) or transcribe viral DNA (if a DNA virus) The first proteins made regulate the host cell and alter transcription & translation. Virus takes over the protein production: the cell starts to make capsomeres and spike proteins. Host proteins are not made normally during this time. Some viruses induce degradation of host DNA Some viral proteins interfere with host gene transcription Some viral proteins repress host gene translation *In Animal Cells*: Proteins for capsid, enzymes, and spikes must be synthesized, as directed by the viral nucleic acid. Genome must be copied so that new virions can be made Biosynthesis is the step where genome type matters (DNA/RNA)

Question 45

Maturation / Assembly

Answer 45

Fourth step of viral replication in bacteriophages and fifth step of viral replication in animal cells *In Bacteriophages:* Assembly of capsomeres into capsids around DNA core *In Animal Cells:* Capsid is assembled around the genome & any internal enzymes (if there are any) If enveloped, spike proteins are inserted into host cell membrane or nuclear membrane into the part of the membrane that will become the envelope! Envelope wraps around capsid

Question 46

Release (lysis)

Answer 46

Fifth step of viral replication in bacteriophages and sixth step of viral replication in animal cells *In Bacteriophages:* Other viral proteins cause host cell lysis Host cell bursts, releasing the virions and killing the host cell about 50 - 200 new phages produced *In Animal Cells:* Release: one of these: Lysis Occurs with non-enveloped viruses Host cell bursts releasing viruses, can result in tissue death Budding Occurs with enveloped viruses Exocytosis-like exit from the host cell; host cell remains viable (but is a virion-producing zombie

Question 47

Tissue Tropism

Answer 47

A Characteristic of Virus Aka Viral Tropism Tissue tropism is the spectrum of cells/tissues the virus can infect Mostly for animal viruses Often not known, but the key is that viruses tend to specialize in using certain pathways to enter host cells For example, SARS-CoV-2 virions must attach to the enzyme ACE-2 and/or receptor TMPRSS2 as part of cell entry The cells that display ACE-2 help explain the various forms of COVID-19 Many influenza viruses must attach to specific sialic acids Typically you hear this as in “SARS-CoV-2 has a tropism for respiratory epithelia”

Question 48

Transmissible spongiform encephalopathy

Answer 48

Diseases caused by prions aka Prion Diseases

Question 49

Virion

Answer 49

the complete, infective form of a virus that moves between host cells, with a core of RNA or DNA and a capsid. “Virus Particles” Their only job is to enter a new host cell and safely deliver the nucleic acids; this is the only thing they can do. They encode proteins that will be synthesized by the host cell: Structural proteins that will become part of new virions In some cases, nucleic acid synthesizing proteins (RNA polymerases, DNA polymerases, reverse transcriptase) These are often necessary for making nucleic acid copies for new virions Enzymes that steal host components (such as 5’ caps) for use in viral replication Regulatory proteins that change the cell’s behavior Virions are non-motile, don’t communicate with other virions, do not secrete toxins or anything else, are immune to antibiotics and antivirals (antiviral medications attack other stages of the virus cycle).

Question 50

Capsid [what molecule(s) make up the structure]

Answer 50

A virion structure Protective **protein** shell around the core Often repeating geometric shapes Sometimes an envelope encases the capsid

Question 51

Capsomere [what molecule(s) make up the structure]

Answer 51

A virion structure **Proteins** which make up the capsid Capsid shapes reflect the shapes of capsomeres

Question 52

Envelope [what molecule(s) make up the structure]

Answer 52

A virion structure Only present in some viruses **phospholipid bilayers** stolen from the host cell, either the nuclear envelope or the cell membrane Embedded **glycoproteins** (spikes) are encoded in the viral genome (not stolen from the host) Other envelope proteins & glycolipids, etc, are stolen from the host cell membrane Envelopes in animal viruses have several purposes related to replication and transmission. Envelopes of bacteriophage have unknown functions and sources Envelopes trick our immune systems Host cell membrane identifies itself with glycoproteins; the virion steals this! Envelopes allow easy fusion with new host cell membrane: this provides a route of entry Envelope help the virion avoid drying out (this keeps them active in the air, for example) Envelopes affect our disinfection choices Solvents such as alcohol do not affect naked viruses! Anything that can disrupt a lipid membrane can inactivate enveloped virions! Only budding, and NOT lysis, occurs with enveloped viruses

Question 53

Genome [what molecule(s) make up the structure]

Answer 53

A virion structure **RNA or DNA** genome found in the capsid

Question 54

Spike Proteins [what molecule(s) make up the structure]

Answer 54

A Virion structure Can have several functions, but most have one that attaches to the outside of the host cell. Hemagglutinin (HA) and Neuraminidase (NA) are spike proteins

Question 55

Virus

Answer 55

The nucleic acid sequence that encodes information to reprogram a host cell to make “virus particles” or “virions.” A virus is information. Effects of viruses: Cell damage (cytopathy) and cell death Immune responses such as interferon production (in animals) or CRISPR/CAS activation (in bacteria) Mutations (if the virus alters the host genome) do not all share a common or universal ancestor They do not have a place in this universal phylogeny