1
Q
Characteristics of viruses
A
- minuscule, acellular, infectious
- has either DNA or RNA (not both)
- cause infections on humans, animals, plants, and bacteria
- not considered living
- can infect any type of cell or organism
2
Q
Replication characteristics of viruses
A
- cannot reproduce independently
- neither grow nor respond to environment they just replicate quickly
- recruit host cells metabolic pathways to replicate
- DO NOT carry put their own metabolic pathways
3
Q
Why is a virus not considered living?
A
- they do not carry out their own metabolic pathways
4
Q
Virions
A
- complete virus particle
- a virus in its extracellular state is called a virion
5
Q
What are the must have components of a virion?
A
- nucleic acid (DNA or RNA)
- capsid
- enzymes (maybe)
6
Q
What characteristics do some virions have?
A
- envelope
- spike proteins
7
Q
What DNA or RNA can be in viruses?
A
- ssDNA
- dsDNA
- dsRNA
- ssRNA
8
Q
What are the two classifications of ssRNA?
A
- (-) sense RNA
- (+) sense RNA
9
Q
What are the components of a bacteriophage?
A
- nucleic acid
- capsid
- hollow rod covered in sheath plates
- base plate
- tails pins
- tail fibers
10
Q
Do bacteriophages have DNA or RNA?
A
they more commonly have DNA
11
Q
How do bacteriophages infect host cells?
A
They constrict and inject their DNA into the host cell by acting as a hypodermic needle. The host cell is then tricked into expressing viral genome.
12
Q
Hosts of viruses
A
- most can only infect a particular host cell
- can be cell or even strain specific
- this is due to affinity of viral surface proteins from complementary proteins on the host cell
13
Q
What is a generalist virus?
A
A virus that can infect many kinds of cells in many different hosts
- they can bind to host cells surface proteins that are found on many different cells
14
Q
How do host cells express viral genome?
A
The host cell is tricked into expressing viral genome. The viruses utilizes the host cells metabolic pathways and energy to synthesize its proteins.
- viral nucleic acid sequence serves as an instruction booklet for virus production
15
Q
What is unique about phage synthesis?
A
Phages do not need additional enzymes to be put together. This is because the parts of a phage assemble due to chemical chemistry.
- hydrophobic and hydrophilic regions
- positive and negative charges
16
Q
How many phages cause a cell to lyse?
A
about 200
17
Q
Capsid morphology
A
- a protein coat that covers nucleic acid of a virus
- can serves as a mean of attachment to host cells
- composed of capsomers
18
Q
What are capsomers?
A
they are proteinaceous subunits that make up the capsid of a virus
19
Q
Shapes of capsids
A
helical, polyhedral, complex (bullet shaped of rabies virus), hourglass
20
Q
Viral envelope
A
- acquired from host cell membrane during replication or release
- composed of phospholipid bilayer and proteins
- can have spike proteins
- proteins/glycoproteins on envelope play a role in host recognition
21
Q
budding process
A
- enveloped virus can bind with host because it has a phospholipid bilayer
- capsid enters the host cell
- capsid is degraded quickly because it is made of proteins so nucleic acid is released
- sense DNA can be directly translated
- viral proteins are made through translation
- viral proteins self-assemble
- as virus leaves cell, it pushes on host membrane and becomes enveloped
22
Q
Lytic replication
A
- has 5 stages
- phages are actively being produced
- host cell synthesizes viral proteins
- causes host cell to lyse when too many phages are produced
23
Q
What are the two types of viral replication?
A
lytic and lysogenic
24
Q
What are the 5 stages of lytic replication?
A
- attachment
- entry
- synthesis
- assembly
- release
25
What are the three ways viruses can enter host cells?
1. direct penetration (bacteriophages use)
2. membrane fusion
3. endocytosis
26
Lytic replication in bacteriophages
1. bacteriophages attach to host cell with their tail fibers
2. viral genome enters host cell via direct penetration (bacteriophage acts as a hypodermic needle)
3. phage DNA is translated, and viral proteins are synthesized
4. proteins self-assemble into bacteriophage configuration
5. newly assembled bacteriophages are release when cell lyses or through budding
27
What enzymes do bacteriophages code for to help release them?
- bacteriophages code for lysozyme enzymes that degrade NAG-NAM bonds to deteriorate the cell wall
- can also code for enzymes that degrade bacterial genome
28
Lysogenic replication
- modified replication cycle
- virus remains inactive
- host cells divide and replicate normally
- viral DNA is embedded into bacterial genome and is replicated
- viral DNA is passed on for generations
29
What is a virus that remains inactive called?
a prophage
30
What is lysogenic conversion?
Lysogenic conversion occurs when viral genome imbedded into the bacterial genome altars the phenotype of the bacteria.
31
How do viruses remain inactive as prophages?
The viral genome codes for a protein that suppresses prophage genes
- viral proteins are not synthesized
32
Lysogenic replication process
1. phage attaches to host cell with tail fibers
2. viral DNA enters the cell through direct penetration
3. phage DNA is imbedded into bacterial DNA
4. host cell replicates normally w/ viral DNA also being passed to new generations
5. prophage DNA can be excised from bacterial DNA through induction
6. synthesis of prophage proteins can occur
7. prophages self-assemble
8. prophages made cause cell to lyse and release them
33
How does lysogenic replication result in more prophages being made?
This is possible because as host cells replicate the amount of host cells doubles. Viral genome only has to be injected into one cell and can be replicated into many other cells. All hosts cells can then produce phages when induction occurs.
34
What is induction?
Induction is the step in lysogenic replication that excises phage DNA from the bacterial DNA, which allows synthesis of phage proteins.
35
How can a lysogenic phage become lytic?
- if host cell is in a stressful environment
- usually a 2nd infection
- cell will go from lysogenic to lytic to actively produce phages
36
Lysogenic enzymes
- lysogenic phages do not produce enzymes that chew up bacterial DNA
37
restriction/modification system
- use of restriction enzymes to fight off phages
- innate immunity response of bacteria
- restriction enzymes are added to plasmids and placed in bacteria cells
38
How does a restriction enzyme work?
1. it is added to a plasmid sequence
2. plasmid is put into bacteria cell
3. restriction enzymes sequence is expressed
4. restriction enzymes are made to recognize palindromic sequences
5. restriction enzymes cuts palindromic sequences on viral genes
39
How do bacteria cells protect their DNA from restriction enzymes?
Bacteria methylate their DNA so it cannot be recognized by restriction enzymes
40
Phages evolve
phages have evolved over time, and some can also methylate their DNA to prevent restriction enzymes from chewing it up
41
How is the restriction enzyme gene sequence added to a plasmid?
1. plasmid is cut and left open to place sequence
2. restriction enzyme sequence is placed in cut plasmid
3. ligase is used to bind DNA to DNA to secure restriction enzyme sequence in plasmid
42
Restriction/modification system...How does it get into the bacteria cell?
- restriction enzymes are made to recognize palindromic sequences
- a restriction enzyme sequence is put into a plasmid and the plasmid is put into a bacteria cell
43
Restriction enzyme function in bacteria
- expressed in bacteria cell
- restriction enzyme recognizes palindromic sequences in nucleic acid and will chew it up
- bacteria DNA is methylated and prevents enzyme from chewing it up
- viral phage DNA is not methylated and is chewed up by enzyme
- BUT over time phages have adapted and began to methylate their DNA to limit the function of restriction enzymes
- this is INNATE IMMUNITY of bacteria cells to fight off phages
44
CRISPR/ cas system
- clustered regulatory interspaced short palindromic repeats / CRISPR associated protein (cas gene)
- cas genes are present in bacterial genome which codes for cas 9 enzymes
- if a bacteria cell survives a phage attack it can utilize CRISPR system to
- repeat sequences
- spacer sequences: small bits of viral DNA
45
CRISPR / cas system
- spacer sequences are placed in between repeat sequences
- repeat sequences form repeat sequence loops (already in DNA)
- cas 9 enzyme recognizes loops and can bind to chew up viral DNA even if it is methylated
- ADAPTIVE IMMUNITY of bacteria cells
- cas gene can be passed in to next generation of cells
46
CRISPR in humans
- if a disease sequence is placed in between repeat sequences it can be chewed up
- this can knock out bad genes but creates wholes in our genome
- can be used to make designer babies but this is illegal
47
CRISPR in embryos (Dr in China)
- a doctor in China cut out the gene for CCR5 from parents chromosomes and implanted them into an embryo
- embryo lacked gene for CCR5
- prevents HIV because it needs to bind to CCR5 in order to enter a cell
48
CRISPR to fight cancer
- cytotoxic T cells have PD1
- out cells and cancer cells can express PDL1
- BUT we don't want cancer cells to express PDL1 because when it binds to PD1 on cytotoxic T cells it prevents the release of cytotoxins to kill cancer cell
- SO, cytotoxic T cells that lack PD1 protein have been made so when they attach to cancer cells that have PDL1, they are not inhibited and release cytotoxins to kill cancer cells
- if this is done, each individuals OWN cytotoxin T cells need to be used on them
- these cells fought cancer longer
49
Angiogenesis
cancer cells stimulate angiogenesis to have a constant blood supply to the cell
- although angiogenesis is used in the womb, it becomes foreign as we age
50
Suicide system
- a promotor is placed near LlaIR protein in bacteria genome
- this promotor is ONLY activated when a phage binds to the bacteria
- used in cheese process because phages are present and kill bacteria before it can do its job
- if a phage binds, LlaIR is expressed, and bacteria cell will die
- if no phage binds, bacteria have the green light to continue its work
51
Replication of animal viruses
- do not have tail fibers or pins
- have different attachment proteins
- spike proteins on envelope or capsid
- can be RNA or DNA viruses
52
3 forms of penetration into host
1. direct penetration
2. fusion
3. endocytosis
- most animal viruses utilize fusion
53
RNA in animal viruses
- can have -ssRNA
- can have +ssRNA
54
+ssRNA
- can be translated directly
- has AUG start codon
- codes for parts of viruses to assemble more
- is still transcribed into a -ssRNA to make more +ssRNA so new viruses can be made
- -ssRNA serves as template to make more +ssRNA
55
-ssRNA
- cannot be translated directly
- has UAC codon instead of start codon
- need RNA dependent RNA polymerase to male +ssRNA
- enzyme is very error prone
56
Retroviruses
- convert RNA into DNA
- use reverse transcriptase
- very error prone
57
Enveloped vs Naked animal viruses
- envelope is a phospholipid bilayer
- enveloped viruses cause persistent infections
- envelope can be from our membrane
- when viruses undergo budding they can take a piece of our membrane and also pick up proteins on membrane
- naked viruses are released by exocytosis or lysis
58
how do animal viruses exit host cells
- enveloped viruses use budding
- naked viruses are released through lysis or exocytosis
59
What are the two phases of animal viruses?
1. lytic
2. latent (same as lysogenic)
60
Animal viruses: lytic replication
- same as bacterial viruses
- host cell is actively making viruses
- causes lysis of cell
61
Animal viruses: latent replication
- same as lysogenic replication of bacteria viruses
- viral DNA is embedded into out DNA
- cells reproduce and pass on viral DNA for generations
- can go from latent to lytic if cell undergoes stress
62
What kind of stress can cause a latent phase viruses to become lytic?
- usually a 2nd infection
- if a bacterial infection also attacks same cell
- lack of nutrients
63
What are three ways that viruses are cultured in lab?
1. in mature organisms
- bacteria. plants, animals
2. in embryonated chicken eggs
3. in cell tissue culture
64
Embryonated chicken egg virus culture
- possible because embryo is free of microbes and also contains a nourishing yolk sac
- allows for skipping of step one of viral replication (attachment) because it can be directly injected into egg
- inexpensive compared to tissue culture
- can be used to make vaccines
- separation of viruses from egg proteins is very difficult
65
Vaccine process in chicken embryo
1. viruses is injected
2. virus replicates
3. virus is extracted from egg (with traces of egg proteins as well)
4. viruses are purified
5. viruses are radiated
- kills virus to prevent replication
6. virus is made into vaccine and injected into humans
7. dead virus triggers MHC1 and MHC2 to create memory B cells with antibodies but virus CANNOT replicated to cause an actual infection
8. if virus ever infects body, memory B cells are already made to fight it off
66
Cell tissue culture
- used to make vaccines for people that are allergic to poultry/eggs
- more expensive
- cultured in actual cells of tissue
67
Are viruses alive?
- some say no because they lack characteristics of life
- some say yes because they utilize sophisticated methods to invade and control host cells & can use host cells to replicate
- people that say yes say "they are the least complex living entities"
68
Viroid
- biological in origin but NOT alive
- small, circular pieces of RNA
- lack capsid
- do NOT code for proteins just trigger rolling circle over and over
- infectious and pathogenic to plants
69
How do voroids infect plants?
- trick plants into making even more copies of them
- plant growth is affected because production of their own RNA is affected
- cannot code for their proteins efficiently enough because they are making more viroid RNA then their own
70
Prions
- Cellular PrP protein: alpha helical prions (good prions)
- Prion PrP protein: beta prions (bad prions)
71
Cellular PrP protein
- "good prions"
- alpha helical shape
- made by all mammals
72
Prion PrP protein
- "bad prions"
- beta sheet structure
- VERY hard to denature
- can convert cellular PrP into Prion PrP
- makes good into bad and then makes more bad
73
What specifically makes Prion PrP proteins apparent?
- they have aa 129 as methionine
- changes shape of normal prions into beta sheet structure
- causes PrP to fold into prion PrP
74
What do Prion PrP proteins cause?
- causes mad cow
- bad version (prion PrP) can come in contact with cellular PrP and convert it into Prion PrP
- creates neurological issues that cause cow to act abnormal
75
How can Prion PrP be spread in cattle?
- can be spread in cattle feed
- infects all cattle
- will need to be put down
76
Damage caused by Prion PrP
- cause neurological degeneration and loss of brain matter
- large vacuoles begin to form in brain
77
How can Prion PrP be destroyed?
- can only be destroyed by incineration or autoclaving in NaOH
microbiology
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