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Microbio > Test 2 - Viruses and Viral Reproduction, Prions, Bacterial Genetics > Flashcards

Test 2 - Viruses and Viral Reproduction, Prions, Bacterial Genetics Flashcards

1
Q

What are viruses?

A

Non-reproducing, non-metabolizing (non-living), “particles.”

-no cytoplasm/membranes etc

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2
Q

Virion

A

Floating free viruses (inactive - waiting to get into a host cell - becomes a virus when it is doing something inside a host cell)

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3
Q

Obligate intracellular parasites

A

Use resources of the host cell

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4
Q

Three designs of viruses

A
  1. Naked
  2. Enveloped
  3. Bacteriophages
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5
Q

Which viral designs infect eukaryotic host cells?

A
  1. Naked

2. Enveloped

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6
Q

Which viral designs infect prokaryotic host cells?

A
  1. Bacteriophages
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7
Q

Bacteriophages

A

Viruses that are small enough to get into bacteria

-have to get through the peptidoglycan layer, which is why they look different

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8
Q

Standard parts of all viruses

A
  • Genetic material

- Protein capsid (shell)

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9
Q

4 options of genetic material that viruses can have?

A
  • Single stranded DNA
  • Single stranded RNA
  • Double stranded DNA
  • Double stranded RNA
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10
Q

Which genetic material options are never the genome of living organisms

A
  • Single stranded DNA
  • Single stranded RNA
  • Double stranded RNA
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11
Q

Capsid (shell)

A
  • hard rigid coating that protects the genome

- composed of capsomere proteins

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12
Q

Individual subunits that compose the capsid?

A

Capsomeres

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13
Q

What is the capsid and the genome called?

A

Nucleocapsid

*enveloped viruses have nucleocapsid with another layer on the outside

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14
Q

What is the envelope in enveloped viruses made from?

A
  • 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.
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15
Q

Requirements of an enveloped virus?

A
  • 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

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16
Q

Glycoprotein spikes

A
  • 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
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17
Q

Why do naked virus’ not have glycoprotein spikes

A

Because the capsomere proteins are enough to act as the key for the virus to get into the cell

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18
Q

Stabilizing proteins

A
  • Tegument or matrix –glue to hold envelope closer to nucleocapsid
  • –last a little longer outside of the host body
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19
Q

unique viral enzymes

A
  • Reverse transcriptase
  • Protease
  • Integrase
  • RNA dependent RNA transcriptase
  • lysozyme
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20
Q

Reverse Transcriptase, which viral types have this enzyme?

A

Make DNA from RNA template

-retroviruses

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21
Q

Protease

A

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
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22
Q

Integrase

A

Joins viral genes to host genome (incorporation)
to make provirus
-w host forever until death!
ex: herpes

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23
Q

RNA dependent RNA transcriptase

A

Uses RNA template to construct new complementary RNA

  • necessary to make RNA from RNA
  • found in +sense RNA, -sense RNA, ds RNA
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24
Q

Lysozyme

A

Found only in bacteriophages

-Digests peptidoglycan in cell wall

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25
Q

Bacteriophage: complex capsid divided into:

A
  • Head
  • Tail
  • Tail fibers on base plate
  • Unique enzyme - lysozyme on base plate, which digests peptidoglycan
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26
Q

If a virus uses the lytic cycle then its called a ______ virus

A

Virulent; attacks and destroys

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27
Q

If a virus uses the lysogenic cycle then its called a _____

A

Temperate virus; mild, medium, not too extreme, will wait for a trigger to express genes

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28
Q

Steps of the Lytic Cycle

A
  1. Attachment/Adhesion
  2. Penetration/entry
  3. Synthesis
  4. Assembly
  5. Release (Lysis)*

*host cell explodes and dies

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29
Q

Lytic cycle

A

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

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30
Q

Lysogenic cycle

A

May be delayed (hours, weeks, years, decades)

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31
Q

Lytic cycle: Step 1 Attachment

phage, naked, enveloped

A
  • 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

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32
Q

Ligand proteins*

A
  • 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
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33
Q

Drug targets (*)

A

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

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34
Q

Lytic cycle: Step 2 - Penetration/Entry - generally

A

-Genetic material enters cytoplasm

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35
Q

Lytic cycle: Step 2 - Penetration/Entry - Phage

A

Lysozyme and contraction of tail

-capsid remains outside -just need to find right host cell and protect genome, plugs hole made my lysozyme

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36
Q

Lytic cycle: Step 2 - Penetration/Entry - Naked

A
  1. 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)
  2. 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)
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37
Q

Uncoating

A

Removal of capsomeres in cytoplasm to allow genome to float freely, so it can take over

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38
Q

Lytic cycle: Step 2 - Penetration/Entry - Enveloped

A
  1. Endocytosis - Uncoating in cytoplasm (of host cell)
  2. Direct entry - Same process as naked
  3. Fusion of envelope and host cell membrane then uncut capsid
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39
Q

Lytic Cycle step 3 - Synthesis

A
  • 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!!

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40
Q

Template strand

A

Strand that is TRANSCRIBED to make mRNA

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41
Q

+sense strand RNA

A

Readable by human cells, starts with AUG

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42
Q

-sense strand RNA

A

Only in viruses, starts with complement to start codon TAC

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43
Q

Lytic Cycle step 4 - Assembly (maturation)

A
  • Viral parts put together
  • -capsomeres form capside
  • -Genetic material in capsid
  • -Enzymes in capsid
  • -Enveloped: peplomeres go to membrane
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44
Q

Lytic Cycle step 5 - Release (Lysis)

phages, naked, enveloped

A

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)
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45
Q

The Lysogenic cycle: Step 1: Attachment

A

Same as Lytic

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46
Q

The Lysogenic cycle: Step 2: Penetration

A

Same as Lytic

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47
Q

The Lysogenic cycle: Step 3: Incorporation

A

Viral genes join on host cell genes using the enzyme angers

-

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48
Q

The Lysogenic cycle: Step 3: Incorporation

A

Viral genes join on host cell genes using the enzyme integrase
-Once DNA is incorporated viral genes called PROVIRUS

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49
Q

The Lysogenic cycle: Step 3: Incorporation

A

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
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50
Q

Examples of known trigger which activate expression on viral genes:

A
  1. Examples of triggers - chemical, physical, emotional trauma
  2. Age (older) - shingles/chicken pox virus
  3. Hormones (menstrual, pregnancy, steroid use)
  4. Immune system weak (“cold sores”) –> immune system focused on fighting off cold, so a herpes outbreak happens
  5. UV radiation - “sun poising” (UV activation of herpes virus)
  6. 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.
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51
Q

The Lysogenic cycle: Step 3: Incorporation

A

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
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52
Q

The Lysogenic cycle: Step 4: Synthesis

A

Always starts with proviral DNA

-REVIEW LYSOGENIC SYNTHESIS STAGE WORKSHEET

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53
Q

The Lysogenic cycle: Step 5: Assembly

A

Same as Lytic

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54
Q

The Lysogenic cycle: Step 6: Release

A

Same as Lytic

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55
Q

Animal virus options

-Lytic cycle

A

Immediate replication with host cell death

56
Q

Animal virus options

-Lysogenic cycle

A
  • 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
57
Q

Cancer is a result of….

A

Uncontrolled cellular reproduction

-A proto-oncogene is converted to an oncogene by mutation

58
Q

How to turn on/off an oncogene

A
  • 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
59
Q

Known cancer-causing viruses

A
  • 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)

60
Q

Tumor suppressor genes

A
  • Loss of

- Normally on - inhibits mitosis in abnormal cells

61
Q

Apoptosis

A
  • Loss of
  • Normally - on cause abnormal cells to commit suicide
  • triggered when cells act abnormally
62
Q

Agiogenesis

A
  • 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
63
Q

Metastasis

A
  • 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
64
Q

Benign

A

Confined mass of abnormal cells, grow locally and cannot spread by invasion/metastasis

65
Q

Malignant

A

Spreading (by metastasis)

66
Q

What does Prion stand for

A

Proteinaceous infectious agents (only made of proteins)

67
Q

Mad cow disease actual name

A

Actual name: Bovine Spongiform encephalopathy

68
Q

Diagnosis of mad cow disease

A

Appearance of brain at autopsy

  • Plaques: fibrous masses of prion proteins that interfere with normal nerve cells
  • Brain becomes spongy (spaces)
69
Q

How do cows infect humans?

A
  1. Mad cow disease may have come from sheep with a brain disorder called scrapie
  2. Infected sheep and cows were rendered into feed for cattle, passing the disease from one animal to another
  3. Disorder strikes primarily the brain and the rest of the CNS
  4. Humans eat infected meat

*Unusual - BC COWS DONT EAT MEAT

70
Q

Molecular Nature of disease

A
  • 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

71
Q

Scrapie

A

Disease of sheep
-Symptoms: scrape their bodies raw by rubbing against fences, post etc. Gradual loss of strength, inability to stand, erratic behavior

72
Q

Kuru

A

-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

73
Q

Creutzfeldt-Jakob Disease

A
  • Typical disease - hereditary disease normally in 50-75 year old individuals
  • Slow onset (1 year) and death from degenerative brain function loss
74
Q

Variant creutzfeldt-Jakob

A

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
75
Q

Chronic Wasting Disease

A
  • 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
76
Q

In all organisms _____ introduce random variation

A

Mutations

77
Q

Recombination

A

New combinations of genes in population

78
Q

In Eukaryotes what does sex accomplish?

A

Reproduction and recombination

Sex = *vertical gene transfer

79
Q

Ways that sex introduces variability (recombination)

A
  • Random assortment of chromosomes during meiosis
  • Random gamete fusion
  • Random mate choice (who you choose to combine genes with is relatively random)
80
Q

Recombination - Bacteria

A

Reproduction (binary fission) = vertical gene transfer

**DOES NOT allow for genetic variability (binary fission = cloning)

81
Q

Horizontal gene transfer

A

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)

82
Q

3 Processes to accomplish horizontal gene transfer

A
  • Transformation
  • Conjugation
  • Transduction
83
Q

What helps bacteria maximize genetic variation

Underlying “givens” in terms of how bacterial genomes are different from out own

A
  1. new DNA will always replace the existing homologous DNA segment (any new fragment is assumed to be better - even if it really isn’t)
  2. 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
84
Q

What happens to the old fragment of DNA that is replaced?

A

Recycled and monomers are used later

result: new genes in an old cell

85
Q

Transformation

-Discovery: griffith experiment

A
  • 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!)
86
Q

Discovery: griffith experiment donor cell, and recipient cell

A

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)

87
Q

Bacterial conjugation

A

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

88
Q

F plasmid genes

A
  • Synthesis of pili
  • Surface exclusion
  • Stabilization of mating pairs
  • DNA transfer (getting f plasmid across)
  • regulation
89
Q

Hfr conjugation

A

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
90
Q

Generalized transduction

A

“General”
Involved with lytic life cycle viruses
-Mistake in assembly
–random fragments of host 1 DNA injected into host 2

91
Q

Specialized Transduction

A

“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

92
Q

What was the scientific result of Frederick Griffith’s experiments with Streptococcus pneumoniae?

A

He showed that the DNA from strain S cells could transform strain R cells.

93
Q

Bacteriophages are important for which of the following processes?

translation
transcription
transduction
transformation

A

Transduction

94
Q

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.
A

Involves a virus

95
Q

Frederick Griffith discovered

DNA.
transformation.
the lac operon.
transposons.
conjugation.
A

Transformation

96
Q

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.
A

Contain an F plasmid

97
Q

Transfer of random pieces of DNA mediated by phage is known as:

  • transformation of competent cells.
  • specialized transduction.
  • transposition.
  • conjugation.
  • generalized transduction.
A

Generalized transduction

98
Q

How does an F+ cell differ from an Hfr cell?

A

Hfr strains have the F plasmid integrated into the chromosome.

99
Q

Why does conjugation between an Hfr strain and an F- strain not result in two Hfr strains?

A

Conjugation is typically disrupted before the fertility factor can be transferred.

100
Q

Which of the following is a characteristic of an F+ cell?

A

Ability to synthesize sex pili, presence of a fertility factor, and ability to mate with an F- cell.

101
Q

What benefit does the F- strain receive from mating with an Hfr strain?

A

It acquires new, potentially beneficial genes from the Hfr strain.

102
Q

Which genome types carry out the Lytic life cycle?

A
  • ds DNA
  • ss RNA + sense
  • ss RNA -sense
  • ss DNA
  • ds RNA
103
Q

Which genome types carry out the Lysogenic life cycle

A 
retroviruses (ss RNA + sense) in animal host
ds DNA (eukaryotic host or phage)
104
Q

Which genomes can use either lytic or lysogenic life cycles?

A

ss RNA + sense, and dsDNA

105
Q

Ligand proteins

A
  • Some antivirals prevent binding of ligand to receptor proteins (“attachment antagonists”)
106
Q

Uncoating inhibitors

A
  • prevents uncoating of virus
107
Q

Fusion Inhibitors

A
  • bacterial cell can’t fuse with cell membrane to release genome
108
Q

Nucleotide analogues

A
  • 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)
109
Q

Protease inhibitors

A
  • can stop assembly phase, w/o protease individual capsomeres can’t form a capsid
110
Q

WHEN lysozyme is used, the genetic material must be:

A

dsDNA

111
Q

At which stage(s) of the viral life cycle is this lysozyme used?

A

Penetration and Release

112
Q

If a virus has the enzyme RNA dependent RNA transcriptase, then it may be a virus which is:

A

+sense RNA
-sense RNA
or ds RNA

113
Q

What molecule is made EACH time RNA dependent RNA transcriptase is used?

A

RNA

114
Q

If a virus has matrix/tegument proteins, then it must be:

A

An enveloped virus

115
Q

Where are matrix/tegument proteins found?

A

These molecules would be found between the envelope and nucleocapsid in the final assembled virus.

116
Q

The function of matrix/tegument proteins

A

Stabilize the envelope

117
Q

A virus with tegument/matrix proteins is more likely to survive where than other viruses?

A

Survive OUTSIDE the human body

118
Q

A virus with these tegument/matrix proteins must also make ____ proteins, which are NEVER found in viruses which LACK matrix/tegument proteins.

A

Peplomer

119
Q

If a virus uses the enzyme reverse transcriptase, then it must be:

A

A retrovirus

120
Q

A virus using reverse transcriptase would use it BETWEEN the ______ stage and the ______ stage of the life cycle.

A

penetration and incorporation

121
Q

RNA ss + sense genome, lytic cycle would make what directly from the genome?

A

RNA ss - sense strand

122
Q

DNA template strand genome would make what directly from the genome?

A

DNA ss non template strand

RNA ss + sense strand

123
Q

RNA ss - sense genome, lytic cycle would make what directly from the genome?

A

RNA ss + sense strand

A strand that starts with AUG…

124
Q

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

A

Release by budding

125
Q

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

A

Release by cell lysis

126
Q

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

A

Complete the penetration stage by endocysosis

127
Q

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

A

RNA ss – sense strands

128
Q

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

A

D

129
Q

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

A

130
Q

Abnormal prion proteins are called ____ ; and have key sections that are shaped______

A

pPrP; flat/beta shets.

131
Q

Vertical gene transfer is ________ while horizontal gene transfer is __________.

A

Binary fission; transformation, conjugation, or transduction

132
Q

The donor cell in transformation must be while the donor cell in bacterial conjugation must be ____.

A

dead; F+

133
Q

The recipient cell in transformation ________, while the recipient cell in bacterial conjugation _________.

A

Gets random DNA; gets plasmid DNA only

134
Q

Burkitt’s lymphoma

A
  • cancer of the jaw

- coinfection between human herpes virus 4 and malaria

135
Q

Kapsi’s sarcoma

A

connection between human herpes virus 8 and HIV-1

Microbio (7 decks)

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