Test 2 - Viruses and Viral Reproduction, Prions, Bacterial Genetics Flashcards
What are viruses?
Non-reproducing, non-metabolizing (non-living), “particles.”
-no cytoplasm/membranes etc
Virion
Floating free viruses (inactive - waiting to get into a host cell - becomes a virus when it is doing something inside a host cell)
Obligate intracellular parasites
Use resources of the host cell
Three designs of viruses
- Naked
- Enveloped
- Bacteriophages
Which viral designs infect eukaryotic host cells?
- Naked
2. Enveloped
Which viral designs infect prokaryotic host cells?
- Bacteriophages
Bacteriophages
Viruses that are small enough to get into bacteria
-have to get through the peptidoglycan layer, which is why they look different
Standard parts of all viruses
- Genetic material
- Protein capsid (shell)
4 options of genetic material that viruses can have?
- Single stranded DNA
- Single stranded RNA
- Double stranded DNA
- Double stranded RNA
Which genetic material options are never the genome of living organisms
- Single stranded DNA
- Single stranded RNA
- Double stranded RNA
Capsid (shell)
- hard rigid coating that protects the genome
- composed of capsomere proteins
Individual subunits that compose the capsid?
Capsomeres
What is the capsid and the genome called?
Nucleocapsid
*enveloped viruses have nucleocapsid with another layer on the outside
What is the envelope in enveloped viruses made from?
- Phospholipid bilayer from their last host cell
- masks/covers capsid from host immune system
- -since the envelope came from host cell, body sees it as its own - not foreign.
Requirements of an enveloped virus?
- Has to stay warm and in an isotonic solution
- Will live better inside the human body whereas a naked would survive better outside the human body
Glycoprotein spikes
- called peplomeres
- -function as key to get into a host cell (necessary to do so)
- -naked virus doesn’t need this because capsomere functions as the key
Why do naked virus’ not have glycoprotein spikes
Because the capsomere proteins are enough to act as the key for the virus to get into the cell
Stabilizing proteins
- Tegument or matrix –glue to hold envelope closer to nucleocapsid
- –last a little longer outside of the host body
unique viral enzymes
- Reverse transcriptase
- Protease
- Integrase
- RNA dependent RNA transcriptase
- lysozyme
Reverse Transcriptase, which viral types have this enzyme?
Make DNA from RNA template
-retroviruses
Protease
Cuts viral multi-proteins
- ribosome makes proteins in a long chain then protease cuts them into individual proteins and puts them together while moving from one cell to another
- speeds up viral infection time
- –ex- someone who finishes getting ready in the car
Integrase
Joins viral genes to host genome (incorporation)
to make provirus
-w host forever until death!
ex: herpes
RNA dependent RNA transcriptase
Uses RNA template to construct new complementary RNA
- necessary to make RNA from RNA
- found in +sense RNA, -sense RNA, ds RNA
Lysozyme
Found only in bacteriophages
-Digests peptidoglycan in cell wall
Bacteriophage: complex capsid divided into:
- Head
- Tail
- Tail fibers on base plate
- Unique enzyme - lysozyme on base plate, which digests peptidoglycan
If a virus uses the lytic cycle then its called a ______ virus
Virulent; attacks and destroys
If a virus uses the lysogenic cycle then its called a _____
Temperate virus; mild, medium, not too extreme, will wait for a trigger to express genes
Steps of the Lytic Cycle
- Attachment/Adhesion
- Penetration/entry
- Synthesis
- Assembly
- Release (Lysis)*
*host cell explodes and dies
Lytic cycle
A cycle that causes immediate replication to make baby viruses that use up all host cell resources eventually ending in the host cell exploding/dying and releasing baby viruses
Lysogenic cycle
May be delayed (hours, weeks, years, decades)
Lytic cycle: Step 1 Attachment
phage, naked, enveloped
- Receptor proteins on host cell surface (specificity)
- Virus binds to receptor proteins (on the bacteria) by ligand proteins (on the virus)
phage: tail fibers
naked: capsomeres
enveloped: peplomers
Ligand proteins*
- Phage: tail fibers - capsomeres on the tip
- Naked: Capsomeres (physically and chemically binding)
- Enveloped - capsomeres can’t bind to host cell because of the envelope, so peplomeres function as ligand proteins
Drug targets (*)
Ligand proteins - Some antivirals prevent binding of ligand to receptor proteins (“attachment antagonists”)
Uncoating inhibitors - prevents uncoating of virus
Fusion Inhibitors - bacterial cell can’t fuse with cell membrane to release genome
Nucleotide analogues - fake nucleotide drugs to replace nucleotides in DNA (road block)
- cant finish synthesis phase
- viral enzymes responsible for speeding up replication are sloppy (our cells catch the wrong nucleotides)
Protease inhibitors - cam stop assembly phase, w/o protease individual capsomeres can’t form a capsid
Lytic cycle: Step 2 - Penetration/Entry - generally
-Genetic material enters cytoplasm
Lytic cycle: Step 2 - Penetration/Entry - Phage
Lysozyme and contraction of tail
-capsid remains outside -just need to find right host cell and protect genome, plugs hole made my lysozyme
Lytic cycle: Step 2 - Penetration/Entry - Naked
- Endocytosis
- “trojan horse method” - the virus stick to the outside, the host cell realizes there is a protein stuck to the outside, and engulfs the virus voluntarily, cell digests and releases the genome (phagocytosis) - Direct Entry - Attaches, uses capsomeres to make a pore to release genome into cytoplasm, no need to do uncaring (capsid remains stuck to the outside of the host cell)
Uncoating
Removal of capsomeres in cytoplasm to allow genome to float freely, so it can take over
Lytic cycle: Step 2 - Penetration/Entry - Enveloped
- Endocytosis - Uncoating in cytoplasm (of host cell)
- Direct entry - Same process as naked
- Fusion of envelope and host cell membrane then uncut capsid
Lytic Cycle step 3 - Synthesis
- Host genome shuts down
- Genome of virus detects all cell activities:
- -produces viral parts
- –1. Genome copies
- –2. Optional enzymes
- –3. Peplomers and matrix, if enveloped
**BE ABLE TO REDRAW ALL ON THE LYTIC CYCLE HANDOUT!!
Template strand
Strand that is TRANSCRIBED to make mRNA
+sense strand RNA
Readable by human cells, starts with AUG
-sense strand RNA
Only in viruses, starts with complement to start codon TAC
Lytic Cycle step 4 - Assembly (maturation)
- Viral parts put together
- -capsomeres form capside
- -Genetic material in capsid
- -Enzymes in capsid
- -Enveloped: peplomeres go to membrane
Lytic Cycle step 5 - Release (Lysis)
phages, naked, enveloped
Cell ruptures to release virus particles
- Phages: host cell explodes (lysozyme digests cell wall peptidoglycan - water enters cell and it explodes)
- Naked: Host cell explodes - an enzyme changes permeability of cell membrane to water, cell takes on water and explodes
- Enveloped: viruses must bud out of membrane to gain envelope and peplomers from:
- -Host cell membrane
- -Other membranes (nuclear membrane, golgi apparatus, ER)
The Lysogenic cycle: Step 1: Attachment
Same as Lytic
The Lysogenic cycle: Step 2: Penetration
Same as Lytic
The Lysogenic cycle: Step 3: Incorporation
Viral genes join on host cell genes using the enzyme angers
-
The Lysogenic cycle: Step 3: Incorporation
Viral genes join on host cell genes using the enzyme integrase
-Once DNA is incorporated viral genes called PROVIRUS
The Lysogenic cycle: Step 3: Incorporation
Viral genes join on host cell genes using the enzyme integrase
- Once DNA is incorporated viral genes called PROVIRUS
- Once incorporation occurs most of the time the inserted genes are silent/unexpressed until an activation occurs (trigger) to express the viral genes
Examples of known trigger which activate expression on viral genes:
- Examples of triggers - chemical, physical, emotional trauma
- Age (older) - shingles/chicken pox virus
- Hormones (menstrual, pregnancy, steroid use)
- Immune system weak (“cold sores”) –> immune system focused on fighting off cold, so a herpes outbreak happens
- UV radiation - “sun poising” (UV activation of herpes virus)
- AA arginine - ratio w/ AA lysine (increased arginine compared to lysine more likely to get an outbreak, increased lysine compared to arginine - less likely to have an outbreak.
The Lysogenic cycle: Step 3: Incorporation
Viral genes join on host cell genes using the enzyme integrase
- Once DNA is incorporated viral genes called PROVIRUS
- Once incorporation occurs most of the time the inserted genes are silent/unexpressed until an activation occurs (trigger) to express the viral genes
The Lysogenic cycle: Step 4: Synthesis
Always starts with proviral DNA
-REVIEW LYSOGENIC SYNTHESIS STAGE WORKSHEET
The Lysogenic cycle: Step 5: Assembly
Same as Lytic
The Lysogenic cycle: Step 6: Release
Same as Lytic
Animal virus options
-Lytic cycle
Immediate replication with host cell death
Animal virus options
-Lysogenic cycle
- Dormant/latent infection - triggered later
- Persistant - continuous release (at a much slower time) - host cell lives. Ex; genital/oral herpes. Releasing viruses at all times for the rest of an infected individuals life.
- Tumor formation (cancer)-oncogene activation, making multiple host cells rather than multiple baby viruses
Cancer is a result of….
Uncontrolled cellular reproduction
-A proto-oncogene is converted to an oncogene by mutation
How to turn on/off an oncogene
- At least 2 mutations to change the status of the gene from proto to oncogene
- some inserted viruses seem to activate proto-oncogenes, or act as oncogenes
Known cancer-causing viruses
- Human papilloma virus (genital warts and cervical cancer)
- Hepatitis B and C viruses = liver cancer
- Human herpes virus 4 = Burkitt’s lymphoma (coinfection with malaria)
- Human herpes virus 8 = Kaposi’s sarcoma (confection with HIV-1)
*Need two oncogenes to cause cancer (4 mutations - 2 mutations = 1 oncogene)
Tumor suppressor genes
- Loss of
- Normally on - inhibits mitosis in abnormal cells
Apoptosis
- Loss of
- Normally - on cause abnormal cells to commit suicide
- triggered when cells act abnormally
Agiogenesis
- Normally off - growth of new blood vessels into a mall of new cells
- Only needed during fetal development, if turned on during adult body will feed mass of cells and allow tumor to get larger
Metastasis
- Normally off - separation and spread of cells
- Essential during fetal development. If turned on in adult body can cause breast cancer cell to detach and spread to a different part of the body
Benign
Confined mass of abnormal cells, grow locally and cannot spread by invasion/metastasis
Malignant
Spreading (by metastasis)
What does Prion stand for
Proteinaceous infectious agents (only made of proteins)
Mad cow disease actual name
Actual name: Bovine Spongiform encephalopathy
Diagnosis of mad cow disease
Appearance of brain at autopsy
- Plaques: fibrous masses of prion proteins that interfere with normal nerve cells
- Brain becomes spongy (spaces)
How do cows infect humans?
- Mad cow disease may have come from sheep with a brain disorder called scrapie
- Infected sheep and cows were rendered into feed for cattle, passing the disease from one animal to another
- Disorder strikes primarily the brain and the rest of the CNS
- Humans eat infected meat
*Unusual - BC COWS DONT EAT MEAT
Molecular Nature of disease
- normally occurring proteins (c-PrP)
- -alpha helix (flexible)
- In disease, converted to deformed version of some proteins (p-PrP)
- -Beta sheet (flat,stiff)
Flat prion protein flattens all proteins that the cell makes which causes symptoms
Scrapie
Disease of sheep
-Symptoms: scrape their bodies raw by rubbing against fences, post etc. Gradual loss of strength, inability to stand, erratic behavior
Kuru
-1st human prion disease studied
-Stanley Pruisher - noble prize for medicine
-Fore tribe in New Guinea
Symptoms: “trembling disease” - gradual loss of motor control and death
Transmitted by: Cannibalism
–ritual eating of relative’s remains
–Brains eaten by women and children (most infectious part) - highest rate of disease
-Skin and muscle eaten by men
Creutzfeldt-Jakob Disease
- Typical disease - hereditary disease normally in 50-75 year old individuals
- Slow onset (1 year) and death from degenerative brain function loss
Variant creutzfeldt-Jakob
Seen in England
- 1980’s 166 deaths in England, 25 in France
- Disease humans get from eating meat with mad cow disease
- Same symptoms as typical disease
- Happens in younger people
- No genetic component
- Link to BSE infected cows and head injuries
Chronic Wasting Disease
- found in: mule deer, elk (now some white tail deer)
- body begins to digest own tissues for energy/nutrients, loss of muscle, and eventually death
- Humans have same symptoms deer do:
- –loss of muscle tissue, thin emaciated
- Squirrel populations - may also be susceptible to this disease
In all organisms _____ introduce random variation
Mutations
Recombination
New combinations of genes in population
In Eukaryotes what does sex accomplish?
Reproduction and recombination
Sex = *vertical gene transfer
Ways that sex introduces variability (recombination)
- Random assortment of chromosomes during meiosis
- Random gamete fusion
- Random mate choice (who you choose to combine genes with is relatively random)
Recombination - Bacteria
Reproduction (binary fission) = vertical gene transfer
**DOES NOT allow for genetic variability (binary fission = cloning)
Horizontal gene transfer
Existing cells can absorb pieces of DNA from other bacterial cells (a process bacteria have, but humans don’t)
-Bacteria had to introduce this because their vertical gene transfer gave them no recombination (variability)
3 Processes to accomplish horizontal gene transfer
- Transformation
- Conjugation
- Transduction
What helps bacteria maximize genetic variation
Underlying “givens” in terms of how bacterial genomes are different from out own
- new DNA will always replace the existing homologous DNA segment (any new fragment is assumed to be better - even if it really isn’t)
- Plasmids move freely into both the genome and other plasmids. Provides an easy way to transport genes into another cell
- recombination more likely with abnormal excision of plasmid genes
What happens to the old fragment of DNA that is replaced?
Recycled and monomers are used later
result: new genes in an old cell
Transformation
-Discovery: griffith experiment
- studying pneumocci with capsules
- if you inject bacteria with capsules into a mouse the mouse will die
- killing bacteria but leaving capsules wouldn’t make mouse sick
- injecting mouse w/o capsule bacteria results in the mouse staying alive
- injecting capsuleless bacteria and dead bacteria with capsules killed mouse - researchers found live capsule less bacteria AND bacteria with capsules (which they did not inject!)
Discovery: griffith experiment donor cell, and recipient cell
Cell that is dead is donor cell, genome is fragmented and floating around. a recipient cell (of the same species, which is necessary to get a genome piece, not necessary to get a plasmid) is nearby. Recipient takes in gradient and recycles homologous DNA (i.e fragments a, b taken in, a,b that cell already has are sent out)
Bacterial conjugation
Donor cell must be: F+
Recipient cell must be:F-
may be same species, F+ cell makes sex pili, copy of F plasmid is sent along pili to F- cell
-O or origin is where it starts
Recipient becomes F+ (plasmid carrying donor)
If an F plasmid joins R or T plasmid, it is more beneficial to recipient
F plasmid genes
- Synthesis of pili
- Surface exclusion
- Stabilization of mating pairs
- DNA transfer (getting f plasmid across)
- regulation
Hfr conjugation
Genes transferred are more likely to be useful “high frequency combination”
Before conjugation:
Donor cell:
-f plasmid incorporates into genome
-cell is now F+ and Hfr donor
During conjugation:
-Entire circle begins to transfer
Results of Hfr
- Recipient gains: partial F plasmid transferred (soon recycles)
- selected genome genes from donor
- DOES NOT become a donor
Generalized transduction
“General”
Involved with lytic life cycle viruses
-Mistake in assembly
–random fragments of host 1 DNA injected into host 2
Specialized Transduction
“Specific”
Involved with lysogenic life cycle viruses
-mistake made during synthesis stage
-specific genes on host 1 genome flanking insertion point of viral genes injected into host 2 genome
What was the scientific result of Frederick Griffith’s experiments with Streptococcus pneumoniae?
He showed that the DNA from strain S cells could transform strain R cells.
Bacteriophages are important for which of the following processes?
translation
transcription
transduction
transformation
Transduction
The horizontal transfer process known as transduction
- involves a mutagen.
- requires a pilus.
- requires a cell to be “competent.”
- involves a virus.
- requires a plasmid.
Involves a virus
Frederick Griffith discovered
DNA. transformation. the lac operon. transposons. conjugation.
Transformation
In conjugation, F+ cells
- contain an F plasmid.
- serve as recipient cells.
- contain “jumping genes.”
- can transfer DNA only to other F+ cells.
- do not have conjugation pili.
Contain an F plasmid
Transfer of random pieces of DNA mediated by phage is known as:
- transformation of competent cells.
- specialized transduction.
- transposition.
- conjugation.
- generalized transduction.
Generalized transduction
How does an F+ cell differ from an Hfr cell?
Hfr strains have the F plasmid integrated into the chromosome.
Why does conjugation between an Hfr strain and an F- strain not result in two Hfr strains?
Conjugation is typically disrupted before the fertility factor can be transferred.
Which of the following is a characteristic of an F+ cell?
Ability to synthesize sex pili, presence of a fertility factor, and ability to mate with an F- cell.
What benefit does the F- strain receive from mating with an Hfr strain?
It acquires new, potentially beneficial genes from the Hfr strain.
Which genome types carry out the Lytic life cycle?
- ds DNA
- ss RNA + sense
- ss RNA -sense
- ss DNA
- ds RNA
Which genome types carry out the Lysogenic life cycle
retroviruses (ss RNA + sense) in animal host ds DNA (eukaryotic host or phage)
Which genomes can use either lytic or lysogenic life cycles?
ss RNA + sense, and dsDNA
Ligand proteins
- Some antivirals prevent binding of ligand to receptor proteins (“attachment antagonists”)
Uncoating inhibitors
- prevents uncoating of virus
Fusion Inhibitors
- bacterial cell can’t fuse with cell membrane to release genome
Nucleotide analogues
- fake nucleotide drugs to replace nucleotides in DNA (road block)
- cant finish synthesis phase
- viral enzymes responsible for speeding up replication are sloppy (our cells catch the wrong nucleotides)
Protease inhibitors
- can stop assembly phase, w/o protease individual capsomeres can’t form a capsid
WHEN lysozyme is used, the genetic material must be:
dsDNA
At which stage(s) of the viral life cycle is this lysozyme used?
Penetration and Release
If a virus has the enzyme RNA dependent RNA transcriptase, then it may be a virus which is:
+sense RNA
-sense RNA
or ds RNA
What molecule is made EACH time RNA dependent RNA transcriptase is used?
RNA
If a virus has matrix/tegument proteins, then it must be:
An enveloped virus
Where are matrix/tegument proteins found?
These molecules would be found between the envelope and nucleocapsid in the final assembled virus.
The function of matrix/tegument proteins
Stabilize the envelope
A virus with tegument/matrix proteins is more likely to survive where than other viruses?
Survive OUTSIDE the human body
A virus with these tegument/matrix proteins must also make ____ proteins, which are NEVER found in viruses which LACK matrix/tegument proteins.
Peplomer
If a virus uses the enzyme reverse transcriptase, then it must be:
A retrovirus
A virus using reverse transcriptase would use it BETWEEN the ______ stage and the ______ stage of the life cycle.
penetration and incorporation
RNA ss + sense genome, lytic cycle would make what directly from the genome?
RNA ss - sense strand
DNA template strand genome would make what directly from the genome?
DNA ss non template strand
RNA ss + sense strand
RNA ss - sense genome, lytic cycle would make what directly from the genome?
RNA ss + sense strand
A strand that starts with AUG…
What would NEVER occur in RNA, ss + sense, lytic, naked viruses
Release by cell lysis
b. Release by budding
c. Penetration by direct entry
d. Penetration by endocytosis
e. All of the above could be found in this viral type
Release by budding
What would NEVER occur in DNA, ss, template strand, enveloped virus
Release by cell lysis
b. Release by budding
c. Penetration by direct entry
d. Penetration by endocytosis
e. All of the above could be found in this viral type
Release by cell lysis
A bacteriophage would never:
Use the lytic life cycle
b. Use the lysogenic life cycle
c. Be released by cell lysis
d. Complete the penetration stage by endocysosis
e. All of the above could be found in this viral type
Complete the penetration stage by endocysosis
RNA, ss + sense, lysogenic, enveloped virus would never, at any point in its life cycle, make:
Proviral DNA
b. Peplomers
c. RNA ss – sense strands
d. RNA ss + sense strands
e. All of the above would be created in this viral type
RNA ss – sense strands
DNA, ds, lysogenic, naked virus which penetrates by direct entry would not EVER:
Produce RNA ss + sense strands at any point
b. Use integrase
c. Release by lysis
d. Uncoat within the host cell
e. Produce DNA non-template strands
D
Uncoating would be found in all of the following situations EXCEPT:
Phage penetration of host cell
b. Endocytosis of a naked virus
c. Endocytosis of an enveloped virus
d. Fusion of an enveloped virus
e. Uncoating could happen in ALL of these instances
A
Abnormal prion proteins are called ____ ; and have key sections that are shaped______
pPrP; flat/beta shets.
Vertical gene transfer is ________ while horizontal gene transfer is __________.
Binary fission; transformation, conjugation, or transduction
The donor cell in transformation must be while the donor cell in bacterial conjugation must be ____.
dead; F+
The recipient cell in transformation ________, while the recipient cell in bacterial conjugation _________.
Gets random DNA; gets plasmid DNA only
Burkitt’s lymphoma
- cancer of the jaw
- coinfection between human herpes virus 4 and malaria
Kapsi’s sarcoma
connection between human herpes virus 8 and HIV-1
