Midterm 2 Flashcards
The Immune System… (3)
- Defends the body agaist infectious agents
- Mostly non-self reactive (but sometimes will)
- Is tightly regulated
Spleen
Important organ full of blooc, lots of lymphatic tissue.
Distributed lymphatic tissue ex
Gut. has more lymphatic tissue than the rest of the body put together because we get a lot of exposure to infection here and in the lungs
Innate vs Adaptive immune response
Innate - there is a problem
Adaptive - specific response to the actual infection. Targeted.
What is Complement?
C3a
C3b
- Cascade of serum proteins.
- C3a activated mast cells (C3aR)
- C3b activated macrophages (C3R)
LPS in immune response
The surface of bacteria has many polysaccharides.
LPS stimulate the immune response
Neuropeptides in the innate immune response
Pain is a neurological response of nerve stimulation via neuropeptides.
Neuropeptides activate the immune response.
CPG motifs
Runs of C and G in bacteria DNA that are unsual in humans.
Stimulus for inflammatory cells.
DAMPS
define
PAMPS?
- DAMPS = Damage associated molecular patterns
- Inflammatory cells respond to molecules associated with tissue damage
- eg. heat shock proteins
- LPS and CpG motifs are PAMPS
TLR
define
what do they do (3)
- Toll-like receptors
- Pattern recognition receptors
- Recognize patters associated with infection and inflammation; NOT specific antigen.
- Bind PAMPS (LPS and CpG) and DAMPS)
Mast Cell
- Found only in issue
- Look like basophils
- Highly involved in allergic response
- Also invovled in immunity and inflammation
Monocyte/Macrophage
- Monocytes are in blood
- Macrophages in tissue - specializations throughout body
- Phagocytic early responders to infection
- Eat bateria - though, not as well as neutrophils
- Involved in acute and chronic inflammation
Mast Cells in innate immunity
- Have TLR (bind PAMPS and DAMPS)
- Release histamine imediately and and prostaglandins over time (take longer to produce, last longer)
Histamine and prostaglandins
- Produced by Mast Cells
- Increase vascular permeability and vasodilation
Classic Characteristic of Acute Inflammation?
Vascular permeability and vasodilation
Vascular permeability allows fluid in - many soluble proteins
What does vascular permeability lead to?
- Leak in of soluble proteins inluding antibodies and complement
- If you have seen the bug before antibody will bind
- Complement will bind no matter what (more if it opsonized with a antibody)
Three ways to activate complement
- Classical (via antibody)
- Alternative => spontaneous cleavage of C3
- Lectins directly activate C (less important in this class)
Functions of Complement
4 functions
If you’ve seen the bug before
If you haven’t seen the bug before
- Target lysis (bacteria, virus)
- Target neutralization (prevent infectivity)
- Enhance phagocytosis
- Inflammation
- C3a is a factor that attracts immune cells to the location
- Complement binds directly & antibody will bind, activating killing pathways that include complement and phagocytosis
- Complement will bind directly, but antibody now can’t bind
Macrophage
what is it?
how is it activated?
Action?
- Early first responder in inflammation/infection
- Activated by CPG, DAMPS, PAMPS, Complement
- Takes in bacteria and kills by phagocytosis => activated macrophage to a heightened state (angry macrophage)
Macrophages can only take in 1 bacterium at a time? T/F
F. They can take in a number bacteria at once)
Phagocytic enhancers
Opsonization for phagocytosis
-
Antibody
- Macrophages hav fc receptors that bind to antibody on the bacteria
- Complement - macrophages have C3 receptors
bacterial phagocytosis (7 steps)
- Bacteria taken in
- Vesicle acidification
- Lysosome + phagosome => phagolysosome
- Lysosome contains digestive enzymes and nitrogen/oxygen intermediates etc
- Bacteria degraded
- Some material isn’t fully digested in residual body
- Garbage put out
NO
Nitric oxide
Reactive nitrogen intermediate
Very potent therefore requires IFNy to be used
Cytokines and chemokines
Cytokines are chemical messages from one sell to another
Chemokines are small molecules that are chemotatic - Chemotatic cytokines.
TNF, IL-1, IL-8
Cytokines and chemokines secreted Macrophages that are Neutrophil growth factors, make more CAMs and increase the whole cal.
CAMs and step process they are involved in
- Cell adhesion molecules
- Only present at site of inflammation because of chemokines secreted by macrophages
- Selectin on neutrophil binds to Sialyl-Lewisx
- Neutrophil rolling, sheds selectin
- Integrin on Neutrophil binds E selectin
- Adhesion, Neutrophil in.
Neutrophil
- Most common white blood cell
- Important early responder in bacterial infection
- Highly phagocytic in tissue
- Once they get into tissue they have a phenotypic change - live longer
Netosis
Large strands of DNA released into local environment by exploding neutrophils
Associated cellular proteins are sticky and they get all over bacteria
How do dendritic cells become active?
- Cellular garbage put out by macrophages and neutrophils
- Takes in garbage by phagocytosis and takes it to lymph node for presentation
Uptake vs movement in dendritic cells?
High uptake = slow movement
low uptake = high direct movement
Class 2 MHC
structure
In dendritic cells
- Alpha side and beta side
- Peptide fits into beta pleated sheet “like a hotdog in a bun”
- In a vesicle that merges with phagolysosome and minds broken down x2 peptide. Goes to surface to present to T cell area in lymph node.
T cells
process in adaptive immunity (up to producing effector cells)
- Leaders of the immune response
- Very specific. Random gene arrangement => diversity
- Many T cells speak to 1 dendritic cell at once
- T cell receptor and CD4 recognize peptide
- DC sends IL-12 (cytokine) to T cell and B7 on DC binds to CD28 on T cell = co-stimulation
- Co-stimulation leads to transcription of IL-2 and IL-2R
- IL-2 stimulates IL-2R, causing T cells to clone
- Some clones are memory cells, others are effector cells
T cell variety jobs
Memory
Helper - go to B cell area
Killer - make IFNy and that stimulates macrophages to be more angry
Activation of B cells - Process
- Helper T cells go to B cell area
- Dendritic cell spans T cell and B cell area, secreting some bacteria pieces
- B cells have IgG and IgM on surface that recognize antigens and bring it in by receptor mediated endocytosis
- B cell is now active
- B cell breaks down antigen and presents on Class 2 MHC
- When T cell clone finds a B cell with the same antigen it sends IL-4 and co-stimulation
- IL-4 = B cell growth factor; stimulates B cell cloning
- Some B cells become memory cells, most become plasma cells that produce antibodies
Plasma cells
- what they do
- structure
- Different stimulations
Clones B cells programmed to make antibodies
Lots of ER bc they are making lots of soluble protein
- IL-4 Stimulation -> IgE
- Naturally produce IgA
- IFNy stimulation => IgG
*
Basic antibody structure
- 2 identicle havy chains and light chains
- Fab region on the light chains and Fc region on the heavy chains
- Fab regions are highly diverse
- Fc region defines the class of the antibody
- Fc or Fab can bind first
- Fc binds to complement leading to MAC attack (lysis of pathogen)
Fc variations
IgG
IgM
IgA
IgE
IgD
Monomer antibodies
IgG, IgE, IgD
Dimer Antibodies
linkage
IgA
linked at Fc
Pentamer Antibodies
IgM
J Chain a little up from Fc tips so antibodies can pivot and show Fc region
What do antibodies do?
the big thing
the 4 things
They help other things kill
- Opsonization for phagocytosis
- Fix complement
- Block attachment
- Neutralize toxins
Opsonization for Phagocytosis
- Bacteria get coated w antibody
- Fc regions on antibody find Fc gamma receptors on macrophages and neutrophils
- Macrophages and neutrophils will take up bacteria regardless, but the candy coating opsonizes them
Antibody function: Fix Complement
- Antibodies on bacteria surfae need to be special distance apart so the 2 can bind complement
- 2+ Clq fragments need to be bound by antibodies for complement cascade to incur
- Complement binding (on own or with antibody) causes formation of membrane attack complex - MAC Attack
- Makes pore in membrane and the cell will die
Antibody function: Block attachment
- Many viruses invade by brinding to receptors on cells
- If antibodies are bound to the virus, the virus can’t bind to cell receptor
- Also works with some bacteria + extracellular protozoa
Antibody Function: neutralize toxins
- Antibody binds to toxins and created immune complexes of toxin
- Prevents toxin from acting bc now it can’t bind
- Toxin can then be taken out of circulation to the liver
IgG
- how much of Ig pool?
- structure
- what it’s good at
- other goo things
- 70-75% of total Ig pool
- Monomer
- Fixes complement well
- Opsonization for phagosytosis
- Blocks attachment well
- Good at neutralizing toxins
- Passes through placenta - early protection
IgM
- 10% of total Ig pool
- Pentamer
- Great at fixing complement bc the fc regions are the righ distance for complement
- Not good at opsonization bc the 5 fc regions won’t fit into fc receptor
- Good for neutralizing toxins
- good at blocking attachment
- Appears early in infection, wanes quickly
IgA
- 15% of total Ig pool
- Dimer
- In secretions (tears etc)
- Protects mucous membranes in lungs and gut
- Good a blocking attachment
- Can’t fix complement (bc to available fc receptors)
- Can’t opsonize for phagocytosis (bc fc regions aren’t available)
- Okay at neutralizing toxins
IgE
- Low levels in circulation
- Monomer
- Binds to Fc on mast cells
- Part of allergic rxn
- Not good at anything
*
IgD
- Surface Ig
- Monomer
- Unknown function
agammaglobulinemia (ivlg)
You get no antibodies
Monoclonal antibodies
(3)
produced in lab for experiments, diagnosis and treatment
Almost always IgG bc it has the longest lifespan
Some cancer are result of expansion of B cells and diagnosis by finding monoclonal antibodies in circulation
Immunity to intracellular infection
- Baceria is inside cell so antibodies can’t be used
- cell mediated immunity
Imune response to extracellular infection
Innate and antibody
Extracellular bacterial infection when you haven’t seen the bug before
- Antibody won’t bind
- Complement will bind directly and kill due to clotting factors breaking down C3
- Neutrophils and macrophages wil phagocytose and kill whether or not they have seen it before us
- Dendritic cells will take up bits for presentation at the lymph node
Extracellular bacterial infection when you have seen the bug before
- Antibodies will bind and opsonize for phagocytosis
- Complement will bind directly and lyse, but will also be opsonized
- Neutrophils phagocytose and kill
- DCs still take up bits for presentation
Post strep glomerulonephritis
- Strep brings about antibodies
- Immune complexes of antibody and antigen form
- Complexes get deposited in kidney glomerulus and clogs it
- Macrophages and neutrophils recognize the candy coated thing and try to eat it but it can’t eat the whole glomerulus => frustrated phagocytosis
- Complement gets activated
- Destruction of kidney tissue
Post strep rheumatic fever
- IgG responds to strep antigen
- Strep antigen looks like an antigen on heart cells
- Antibody tricked into thinking heart cells are foreign
- Heart valves and myocardium damaged
Tuberculosis
- Lives in phagosome and prevents lysosome fusion
- Resists killing. IFNy from T cells helps but IFN production is also shut down
- No effective antibody response - only response is from effector T cells
- Effector T cells create a granuloma (tubercule) of macrophages and T cells to starve it out
- T effector cells produce IGNy to stimulate Macrophages ot creat TNF and IL-1
- You get a tubercule with macrophages on inside and T effector cells producing IFNy to keep it up
Tuberculosis and HIV
HIV => low T cell levels => can’t continue tuburcule => tuberculosis wins
Listeria
- Gets into phagosome, shuts down lysosome fusion and gets out
- Motile so it can infect other cells
- Presented on class 1 MHC to outside, so now listeria antigen is on cell surface
- Cytotoxic T cell sees this and kills the cell
Treetop disease
description
How is the mechanisms advantageous for the virus?
- Catipillar feeds on contaminated foliage
- Enhanced locomotor behaviour
- Virus climbs to top of tree and liquifies
- Enhances spread of the virus
How does treetop disease virus cause the climbing phenotypes?
Virus disrupts hormones so catipillar climbs as it would during moulting
Are viruses always harmful?
No. Many are beneficial. Only something result in disease (different than infection).
Study of viruses has potential to (2)
- Aid disease prevention
- Help our understanding of the fundamentals of host biology
Where are viruses?
Everywhere. Air, food, surfaces, genomes
How many herpes viruses infect most people?
- Lifelong infection
How do viruses become part of the human genome?
They must infect germ cells
Integrated ancient viruses (2 examples)
- Koala retrovirus, cause of koala AIDS is currently becoming endogenized
- Virus on chromosome 7 essential for placenta development
- Syncytin is a captured viral gene essential for the semipermeable layer
Know: Viruses co-evolve with their host through an exchange of genetic information
Ancient ________ and __________ infections in egyptian mummies
poliovirus and small pox
Define virus
3 further defining factors
submicroscopic, obligate intracellular parisite
- produced from preformed parts
- Do not grow or undergo division themselves
- lack genetic information for generation of metabolic energy and protein synthesis.
Are viruses alive? 1 theory
Alive while inside and when outside they are just complex assemblages of metabolically inert chemicals
Electron microscopy
(review diagram)
- pure populations of viruses or cells infected with viruses can be visualized
- ultrathin sample embedded on copper grid
- Chamber has a vacuum
- Electrons pass through sample and are detected with digit camera/phosphor screen
- Staining with heavy atoms necessary to diffract electrons and see structures
Virus Particle
molecular structures that package viral genomes in infected cells and transmit them to new host cells
Virion
define
must (5)
these explain:
A complete, infections virus particle (many defective particles are made)
- Correctly assembled
- Escape the cell for which they are made
- Withstand the EC environment
- Attach to and enter a host cell
- Releast the viral genome (into host cell)
Explains why there is such diversity in viruses
bacteriophage t4 (musts for virus)
herpes simplex virus type 1 (action)
- Bacteriophage = virus that infects bacteria. Bacteria are all thoughout our body. Has to infect, replicate, withstand EC env
- Herpes infects oral epithelial cells => cold sores. Travels through neurons to tri. ganglia => achieves latency
Capsid
traits - structure (3)
Job (3)
why are the jobs important? (1)
- Rigid, symmetrical container for viral genomes
- metastable
- Protein subunits are multipily redundant - many copies called capsomers
- Participate in infection
- Protect genome from
- physical damage (mechanical forces)
- Chem damage (IV radiation)
- Enzymatic damage (cell nucleases)
- Damage to 1 or more capsomer may make virus dysfunctional or innoculous
4 virus morphologies (2 most common)
- helical **
- icosahedral **
- enveloped
- complex
Helical capsids
features
what kind of genome do they usually hold?
how do these bind to viral genome?
What governs length and diameter?
- look like straws, simplest
- not human
- Single type of capsomer stacked around central axis to form a helical structure
- Hollow centre of helix contains viral genome (usually ssRNA)
- Electrostatic interactions. RNA -ve backbone, G, A, Hist +ve
- Amount of RNA
Icosahedral Capsids
shape
why do so many viruses take this shape?
- 20 faces
- animal and plant viruses, many enteric (gut) viruses
- Strength - resistance to shear forces
- Tight packaging of genome (sm SA for lg vol)
- Genetic economy - can be built from a few repeating subunits
How do we decontaminate surfaces with icosahedral capsids
Bleach. Will damage capsids.
Enveloped Viruses
- Host derived lipid envelopes protect viruses and contain both viral and host glycoproteins
- viral glycoproteins are made by host
- Space in between the membrane the capsid is the tegument
Glycoproteins
- Important for enveloped viruses that contain host and viral glycoproteins
- Viral glycoproteins are made by host
- Many host integral membrane proteins are glycosylated
- N-Glyc - sugar added to N on asparagine
- O-Glyc - sugar added to serine/threonine
Influenza Envelope
Has host glycoproteins incorporated into its envelope
HA, a lectin that binds sialic acid receptor to get into cell
NA, enzyme that cleaves sialic acid allowing progeny viruses to be released from the host cell
Can integration of host proteins confer an advantage to the virus?
Yes. Better invasion
How does glycosylation of virus proteins affect immune regulation
Hides viral proteins because host membrane proteins are commonly glycosylated.
Sugar decorations block antibody binding sites.
complex virus - bacteriophage t4
structure
genome
- ocosahedral head containing dsDNA
- helical tail (empty)
- Hexagonal base plate
- Protuding protein tail fibres
Binding of bacteriophage t4 to e coli process
- long tails fibres recognize membrane protein OmpC or LPS of E. coli - REVERSIBLE
- 3+ long tail fibres bound => conformational change in baseplate; short tail fibres extend, bind IRREVERSIBLY to core region of host LPS
- Contraction of tail sheat + penetration of outer membrane
- T4 lysozyme degrates gram peptidoglycan layer
- Inner membrane degraded
- Phage DNA delivered to cytoplasm
Viral infection of Eukaryotic cells
-
Attachment
- REVERSIBLE electrostatic interactions
- IRREVERSIBLE tight interactions with receptors
-
Penetration (pH dependend) by either
- (enveloped) membrane fusion at the cell surface
- receptor mediated endocytosis
- specificity of these interactions defines the host range of the virus
Bacteriophage capsid morphology
complex
genome type of tobacco mosaic virus
ssRNA
What type of genome can icosahedral capsids hold?
any kind
How does influenza virus enter the cell?
Receptor mediated endocytosis with sialic acid receptor
Sialic acid is ubiquitous on cell surfaces. What does this mean for influenza virus tropism?
By binding sialic acid, the virus is able to gain entry to a number of cell types
HIV mechanism of entering the cell
- Initial attachment of HIV envelop gylcoprotein to cell surface glycoaminoglycans - REVERSIBLE
- Stable binding to protein receptor, CD4 - IRREVERSIBLE
- Binding co-receptor - IRREVERISBLE
- Conformational change causes exposure of fusion peptide (hydrophobic)
- Fusion. Viral and cell membranes mix
- Viral genome deliviered into host
Ebola virus cell entry
- Host cell takes in Ebola by macropinocytosis
- Stable binding to intracellular receptor
- Membrane fusion + RNA release
Why do delilivered viral genomes travel to the nucleus?
exceptions?
That’s where the polymerases are - so virus can replicate using host machinery or integrate its genome into the host
It would need its own mRNA, own polymerases
Lytic Replication
Fast growing viruses
Latency
Lysogeny
When viruses establish a dormant state in a host cell\
Called lysogeny in temperate phages
How do latent infections maintain long term persistence in their hosts?
The virus isn’t replicating so it is relatively invisible to the immune system. Isn’t producing any proteins to be recognized as antigens.
What consequences does latency have for immune surveillance?
A passive mechanism for integrating genome into host
allows virus to pick an optimal time to replicate
How is latency achieved?
Integration into host genome (retroviruses)
long term retention of viral episome - the virus can allow the genome to be associated with the host chormosome - can divide into daughter cells
episome
a type of latency where the viral genome latches onto host chromosome and can be divided into daughter cells as such.
How is latency advantageous?
- Carriage of the viral genome through many cycles of cell division (using host polymerases + nucleotides) => energetically favourable
- Evasion of immune surveillance
- few to no protens made (only ones made promote cell cycle, antigen presentation, and undermine antiviral response)
Bacteriophage Infection
lytic?
Course
lytic infection
- Penetration => viral DNA delivered to cytoplasm
- Host gene expression arrested => host DNA/RNA degredation
- Viral enzyme synth (~5 mins)
- Viral DNA replication (~10 mins)
- Formation of new viral particles (~12)
- Lysis of host and release of viral particles (~30)
Bacteria: Defense against viruses
explain
real life uses
Restriction endonuclease
- Cuts DNA at restriction sites in foreign DNA
- Makes 2 incisions on sugar phosphate backbone
- Diff bacteria make diff restriction enzymes
- Host DNA protected bc it is heavily methylated
- useful for gene cloning and forensics (distinct digestion pattern for diff human DNA samples)
- Can lead to recombinant DNA
Central Dogma
how to viruses change it?
DNA dependent DNA polymerase uses dsDNA as template to make more dsDNA
RNA polymerase uses dsDNS as template to make + sense RNA
Ribosomes translate +RNA into amino acid chain
Viruses can to reverse transcription
What sort of information is encoded in the viral genome?
- replication of viral genome
- assembly of packaging genome into viral particles
- Regulation and timing of replication cycle
- Modulation of host defenses
- Spread to other cells + hosts
What kind of information isn’t encoded in viral genomes
info for.. (3)
- complete protein synthesis
- proteins incocled in energy production or biosynthesis
- Centromeres, telomeres
+ssRNA virus translation location
how do they replicate their genome
generate
- Directly translated in the cytoplasm by hot ribosomes because they resemble mRNA
- viral RNA-dependent RNA polymerase
- polyproteins that get cleaved by viral or host proteases into viral proteins
Why to proteases make good drug targets?
If they don’t work the polyproteins can’t be cleaved into viral proteins
For the virus, are there any disadvantages to relying on host proteases?
The cell would have control over the genome
Why would the genes for RNA dep RNA polymerase be transcribed at the 3’ end
There will be multiple rounds of protein synthesis. If it is at the 3’ end it is at the perfect position to lay down another strand right away
Antiviral defense for Eukaryotes?
Immune system is triggered by Pattern Recognition Receptors that recognize foreign molecular patterns such as dsRNA and 5’-triphosphate RNA
How do viruses replicate their genomes? (2)
- Confrom to host machinery (use host ribosomes)
- Alter host machinery for own use
All roads of virus genomes lead to….
mRNA
Poliovirus
- method of spread
symptoms
structure
entry
- water bourne - mostly fecal-oral spread
- 95% infections asymptomatic, 5% lead to flu-like symptoms
- 1% goes to CNS, replicates in motor neurons and leads to paralysis
- Icosahedron - can survive gut acidity
- Enters cells my receptor mediated endocytosis, +ssRNA
- Normal function of receptor is epithelial cell-cell contact
Poliovirus vaccines
- Salk - Inactivated polio vaccine
- formalin killed
- injection
- Sabin - oral polio vaccine
- Attentuated by temp of growth
- Gives mucosal immunity
Polio genome replication
- +ssRNA => dsRNS replicative intermediate => +ssRNA progeny genomes
- co-translational - polyprotein cleavage and processing at same time
Viral genome processing sequence
catalyzed by?
intial genome -> replicative intermediate -> progeny genome
RNA-dependent RNA polymerase
Hep C intial genome
+ssRNA
Flu initial genome
-ssRNA
Ribavirin
- Phosphorylated and activated in cells
- Incorporated into viral RNA during genome replication
- Base analog for A and G - can pair with U or C
- Causes potentially lethal hypermutation
Herpes Simplex Virus
genome
capsid
How does it express its genes?
How does it express its genes?
Where does this happen in the cell?
- dsDNA virus
- Enveloped icosahedron
- Host RNA polymerase
- Viral DNA-dep DNA polymerase
- Nucleus, bc it depends on host RNA polymerase
Acyclovir
- Herpes treatment
- Relies on specific enymatic activity
- Herpes phosphorylates drug 3000 times better than host
- Acyclovir triphosphate incorporates into viral DNA terminating chain
- Inhibits herpes DNA polymerase
- Looks like G
- Host cell hurt too - oh well
HIV entry and mechanism inside
- Virus engages primary receptor and co-receptor => infection intialized
- Fusion => virion contents dumped
- RNA is virus reverse transcribed into dsDNA
How to retroviruses express their genes and replicate their genomes?
Reverse transcription
dsDNA from reverese transcription is longer than the RNA that went in
Zidovudine
why doesn’t it block host polymerase?
= AZT
- An analog of T
- Phosphorylated and incorporated into growing viral dsDNA
- Chain terminator
- It does, just has way higher affinity for HIV reverse transcriptase
Viral evolution with reverse transcriptase
- Reverse transcriptase is error prone
- 1 mistake every 10 000 so one mistake every genome
- Produces viral quasispecies
- Quick evolution
- Why vaccines don’t work
Ebola route of transmission
body liquids exchange
4 symptoms of acute inflammation and their causes (look these up)
- Redness
- swelling
- pain
- heat
