Final (cumulative) Flashcards
How many human cells do adult humans contain? How many bacteria do we each have?
10^13 human cells and 10^13 microbial cells living in/on the human body
How many symbiotic microbial species have been identified? How many species are there per person?
10,000 symbiotic microbial species have been identified, ~1,000 per person
What % of the human microbiota live in the GI tract? What mass is this?
95%, ~2 kg
What is a microhabitat? How are they characterized? Also provide some examples
The specific area where microbes grow (e.g. skin, GI tract, etc)
- They are not homogenous, they differ in pH, temp, [salt], etc.
What is a microbiota and what is an example?
Microbiota describes all the microbes in a microhabitat - e.g. the skin microbiota
What is a microbiome and what is an example?
A microbiome is the entire collection of microbiota in a particular system - e.g. the human microbiome
If we can’t culture the organisms in a microbiome of an individual, what is the microbiome also known as?
The collection of functional genes on an organism
True or false: the microbes among our major microbiota are all conserved
False; there is variation in microbes among our major microbiota
True or false: the bacteria in the GI tract are characterized by phyla since there’s so many species of bacteria in the GI tract
True
True or false: every given microbiota tend to have a dominant organism
True
What are two reasons for why we study the human microbiome?
The acquisition, composition and maintenance of microbiota is essential for:
1. Influences growth and development from birth to 3 years old
2. Influences health and immune response
What 3 things is research on the human microbiome focused on identifying?
- The species composition of microbiota
- The critical organisms that influence health, development and disease
- Therapies to prevent and treat health conditions caused by changes to our microbiota
The stomach to the colon becomes increasingly (aerobic/anaerobic)
- Explain what this is good for (2)
Anaerobic
1. Great for fermentation
2. Reduces growth of aerobic pathogens (organisms that use oxygen as a final electron accepter tend to be pathogens which we don’t want)
What 4 phyla are primarily found in the GI microbiota?
- Bacteroidetes (Gram-negative)
- Firmicutes (Gram-positive)
- Actinobacteria
- Proteobacteria
What type of culture system does the colon resemble?
A continuous culture system
How many cells/g of fecal matter do we shed everyday?
~10^11 (1/3 of the fecal mass)
Is there more bacteria in the stomach or in the large intestine? Explain why
More in the large intestine because not a lot of organisms can survive in the acidic environment of the stomach
What 2 bacterial phyla help digest complex plant materials like cellulose? What do humans uptake from this?
Bacteroidetes and Firmicutes help digest complex plant materials (especially high fiber foods)
- 10-15% of human nutrition (caloric uptake) comes from SCFA (short-chain fatty acids) generated by fermentation
What do GI bacteria produce for our health? Give 2 specific examples
Biosynthesis of essential compounds
- Vitamins (E. coli in guts makes vitamin B12)
- Amino acids
What do GI bacteria produce to control microbe number?
Bacteriocins and lantibiotics. Bacteriocins go and form pores in the cell membrane of other microbes, which increases their osmotic pressure and makes them explode
- This helps control microbe number
What do GI bacteria produce for the immune system?
Produces anti-inflammatory molecules to prevent chronic inflammation
True or false: there’s a correlation between irritable bowel syndrome (IBD) and an imbalance of microbes in infancy (e.g. do to antibiotics)
True
Describe the gut-brain axis
Nerves that connect the GI tract to the central nervous system (i.e. vagus nerve) form the gut-brain axis.
We normally think of the brain sending signals to influence GI tract function to tell us when we’re hungry/full, but GI microbiota generate neurotransmitter-like metabolic byproducts that send signals to the brain (this is one way that microbes influence our development)
Microbial neurochemicals have been found that mimic signals responsible for feelings of happiness, fear, anger, etc.
True or false: The GI microbiota of individuals diagnosed with depression are different from “happy” individuals
True
When does bacterial colonization begin in individuals?
The human fetus is sterile, colonization begins during and immediately following birth via contact with skin and feeding (as soon as a baby is born, bacteria of vaginal microbiota starts colonizing the fetus)
What is the early composition and development of microbiota heavily influenced by? And what is “abnormal” development due to C-section correlated with?
Early composition and development of microbiota is heavily influenced by birth conditions, and “abnormal” development is correlated with development of future disease conditions (allergies, IBD, diabetes, obesity)
How does breast milk select for “normal” microbiota?
Breast milk contains sugars the infant can’t digest that select for “normal microbiota” (vs bottle-feeding or formula)
What age do microbiota stabilize by?
~3 years old
True or false: microbiota is different between vaginal birth and C-section but both stabilize by 3 years old
True
What is the hygiene hypothesis?
Exposure to microbe-associated molecular patterns (MAMPs) early in life is crucial to neonatal gut maturation and immune system development
What are microbe-associated molecular patterns (MAMPs)
Heavily repeated cell surface sugars, proteins, lipids that are unique to specific microbes, but are generally present in a lot of microbes
What can insufficient exposure to MAMPs result in?
Reduced colonization resistance and susceptibility to immune-mediated disease (increased risk of infection, asthma, allergies, diabetes, obesity, IBD, anxiety)
True or false: GI microbiota differ significantly among people
True
What does GI microbiota differences between individuals depend on?
Distance between individuals
Short-term changes are ______ in healthy people with stable and resilient microbiota
Short-lived
What 3 SCFAs does microbial fermentation produce in the GI tract?
Butyrate, propionate, acetate
Microbial fermentation produces SCFAs, which are important for… (4)
Important signalling molecules that
1. suppress inflammation
2. strengthen tight junctions between epithelial cells to prevent pathogens from moving between cells
3. promote beta-oxidation (consumes O2 in gut which suffocates aerobic pathways”)
4. Reduce fatty acid and cholesterol production
What is microbial dysbiosis?
A change in the composition of the microbiota
Inadequate development of “normal” GI microbiota may allow pathogenic species to…
Access the gut epithelium
What is the mechanism for IBD?
Inadequate development of “normal” GI microbiota may allow pathogenic species access to the gut epithelium, Immune system responds via inflammation, immune system learns to view normal microbiota as “foreign”, gut becomes more aerobic, leads to IBD
True or false: GI dysbiosis may result in inflammation that leads to neurodegenerative diseases like Parkinson’s and Alzheimer’s
True
Explain why farmers used antibiotics to promote animal growth
Obese animals have GI microbiota distinct from lean animals (they tend to have less diverse GI microbiota, aka fewer species)
Animals with a high fat/low fiber diet have ____-like microbiota
Obese
Animals with a low fat/high fiber diet have ____-like microbiota
Lean-like
Describe the fecal transplants in mice and what the results showed
Germ-free (GF) mice have ~40% less body fat than wildtype mice. Following fecal transplant from obese human, GF mice gain ~60% more body fat wth no dietary changes. When the fecal transplant was done from a lean human to a mouse, the mouse didn’t gain mass
GI microbiota of obese animals consist of (high/low) methanogen counts
- Explain why
High
- Methanogens remove H2, which favours increased fermentation rates (which increases the amount of SCFAs available to the host)
- More acetate = cholesterol and lipid synthesis in the liver
GI microbiota of lean animals consist of (high/low) methanogen counts
Low
- Greater H2 concentrations inhibit fermentation
- Less SCFA available to host
What happens to the GI microbiota during and after antibiotic treatment?
Antibiotics taken orally will affect normal GI microbiota and the disruption can allow colonization/growth of (antibiotic resistant) pathogens, but this usually returns back to normal after treatment
What is an example of an antibiotic resistant pathogen that likes to colonize the guts during antibiotic treatment? What are some of the symptoms?
Mild C. difficile infection results in diarrhea, abdominal pain and fever. Severe cases result in septic shock (and death) after entering the blood.
What are two ways that antibiotic-resistant pathogenic infections (due to initial antibiotic treatment) within the GI tract are treated?
- Surgical removal of the colon
- Fecal transplant, where microbiota from “a healthy” individual is transferred to a patient suffering GI dysbiosis
Describe how fecal transplants work
The microbiota from a “healthy” individual is transferred to a patient suffering from GI dysbiosis. The normal species will hopefully competitively displace the pathogenic organisms.
- Fecal transplants can be done via colonoscopy, enema, or “poop pill”
- Success treating post-antibiotic C. difficile infections has established this as an active area of research
What is a probiotic? Provide some examples of probiotics
Ingestion of live, “beneficial” bacteria
- e.g. ingestion of some Bacillus species can prevent colonization of pathogenic S. aureus strains
- e.g. BIfidobacterium, Lactobacillus via yogurt, fermented foods, baby formula
What is a prebiotic?
Ingestion of nutrients that promote growth of “beneficial” bacteria
What is a synbiotic?
A mix of Pre- and Pro- biotics
True or false: there are oral, respiratory, urogenital and skin microbiota which all have unique, stable communities of specific microorganisms, and all of them suffer from various dysbioses
True
What is the mycobiome?
Eukaryotic yeast species in and/or on us, e.g. fungal symbiotes
What is the virome?
Resident plant, animal and microbial viruses (includes the phage living inside the gut)
What is the eukaryome?
All the other eukaryote organisms that live on us (other than fungi), like protozoa, helminths, etc. common in animal GI tracts
What are translocase systems in general and what are the two universal translocases in all prokaryotic cells?
Translocase systems moderate the transport of proteins (that must either be embedded in the membrane or released on the outside of the cell) using ATP, GTP or PMF to power the movement process
Two universal translocases:
- Sec - general secretion system
- Tat: Twin-arginine translocase
What 2 things is the Sec translocase system responsible for in general?
- It facilitates the co-translation of membrane-associated proteins into the cytoplasmic membrane (uses GTP to power translocation).
- It transports unfolded extracellular proteins out of the cytosol
What is the Tat translocase responsible for?
Transports folded extracellular proteins out of the cytosol (e.g. proteins that have cofactors folded into them). RR (twin arginine on leader peptide)-mediated, which recognizes the Tat translocase and uses PMF to power translocation out of the cell (Tat is the most energetically demanding pathway)
Describe the Sec translocase pathway for membrane-bound proteins
A signal recognition particle (SRP) binds to the signal sequence of a protein and the protein (and ribosome still bound) migrate to a membrane-bound secretion system (Sec translocase), before being embedded into the membrane as it is being translocated
Describe the Sec translocase pathway for secreted proteins
SecA chaperone binds a signal sequence on the protein and the protein is transported to the membrane-bound secretion system (Sec translocase) before being secreted out of the cytoplasm
What are the two-step translocases in general and what are the examples of them?
Two-step translocases move proteins out of the cell one membrane at a time in G- bacteria
Type II and V
What are the one-step translocases in general and what are the examples of them?
Move proteins across both membranes in G- bacteria in one step. Some can move proteins across both membranes and into a recipient cell in one step (so moving proteins across 3 membranes) which is great for moving toxins across cells
Type I, III, IV, and VI
Describe type II secretion systems and an example of something that is secreted using this system
Two-step translocase
Sec or Tat move proteins across the inner membrane and then a second translocase moves folded proteins across the outer membrane.
- Proteins attach to a secretion pore and are pushed out of the cell by ATP-mediated pseudopilin extension (pilus)
Example: common for AB toxins
Describe type V secretion systems and an example of something that is secreted using this system
Two-step translocase
Sec moves autotransporter proteins across the inner membrane
The transporter domain of the autotransporter forms a pore in the outer membrane for the passenger domain to exit the cell
(autoproteolysis separates the two domains in the periplasm)
Example: Exoenzymes (IgA protease)
Describe type I secretion systems and examples of things that are secreted using this system
One-step translocase
ABC transporters that move proteins across both bilayers in one step. An inner membrane ABC transporter delivers proteins to a periplasmic membrane fusion protein via ATP hydrolysis, which pushes the protein out an outer membrane pore
Common for secretion of bacteriocins, biofilm mediators (LapA), RTX toxins
Describe type III secretion systems and examples of things that are secreted using this system
One-step translocase
“Injectisomes”: Transports proteins directly from the cytosol of the bacterial cell into the cytosol of a recipient cell (prokaryote or eukaryote)
- Upon contact with a recipient cell, the tip fuses with the host cell membrane and proteins are transported using PMF
Found in both pathogens and symbionts (potentially found in Rhizobia)
Examples: used to transport cytotoxins or Nod factors
Describe type IV secretion systems and examples of things that are secreted using this system
One-step translocase
Transports proteins/DNA directly from the cytosol of the bacterial cell into the cytosol of a recipient cell (prokaryote or eukaryote)
- ATP-mediated
Examples: Responsible for conjugation in prokaryotes and is used to transfer F plasmids and tumour-inducing plasmids; also transfers proteins into other cells or into the extracellular space (pertussis toxin)
Describe type VI secretion systems and examples of things that are secreted using this system
One-step translocase
Transports proteins directly from the cytosol of the bacterial cell into the cytosol of a recipient prokaryotic or eukaryotic cell via an ATP-mediated T4 phage-like injection system (like injectisome, just uses ATP instead of PMF)
- When close to a target, contractile sheath proteins undergo a conformational change that extends a spike out of the donor cell and into the recipient, delivering the exoproteins
Example: primarily used in microbial warfare (used by bacteria that want to kill other bacteria)
What are 2 ways in which signals can act on a cell?
- Signals can act directly as effector molecules (e.g. inducers bind to transcription factors and turn transcription on)
- Signals can act indirectly by binding to cell surface receptors
What is the first component of a two-component regulatory system?
The sensor kinase
- The transmembrane (receptor) histidine kinase autophosphorylates (using ATP) when bound to a signal and transfers the phosphoryl group to a response regulator
What is the second component of a two-component regulatory system?
Usually, a transcription factor that is active when phosphorylated
What is the third (?) component of a two-component regulatory system
A phosphatase that removes the phosphate from the transcription factor to inactivate the signal.
Define quorom sensing
Density-dependent mechanism for cellular communication to induce a population or a community response
What 5 things does quorum sensing regulate?
Biofilm formation, sporulation, competence (taking up DNA), bioluminescence and production of virulence factors
What is the name of signalling molecules involved in quorum sensing? What 2 classes do they fall into?
Autoinducers (peptide or non-peptide) that accumulate as population densities increase
What does it mean when quorum is reached?
A high enough concentration of a signal is reached and coordinated gene regulation occurs
What are G- autoinducers? Explain how they regulate gene expression and what expression results in
Acyl homoserine lactones (AHLs)
AHLs diffuse out of the cell into the surrounding environment if cell concentrations are low.
When cell densities are high, the AHL concentrations increase both outside and then inside the cells (build up)
- The built up AHLs are more likely to bind transcription factors, specifically activators (some bind a sensor kinase that regulate transcription factors) that bind to the chromosome and upregulate the synthesis of AHL synthase
- (some down-regulate gene expression)
AHL acts as a co-…
Activator
What are G+ autoinducers? Explain how they regulate gene expression and what expression results in
G+ bacteria (and archaea) that regulate gene expression by quorum sensing produce species-specific oligopeptide autoinducers (AIPs)
- Pre-AIPs are transported out of the cells (ABC transporters) into the surrounding environment
- When cell densities are high, the AIP concentration increases outside the cells
- The AIPs bind sensor kinases (2CRS)
- Results in coordinated up-regulation of quorum-specific genes (some down-regulation gene expression)
Describe the overall structure of the autoinducers. What do autoinducers vary in (depending on the species)?
Carbon ring with a nitrogen carbon chain coming off one side, with an R group
Vary in:
1. Length of the acyl chain (4-18 carbon)
2. R group (-OH, =O, -H)
What are 3 bacterial species that can produce light via bioluminescence?
Vibrio, Aliivibrio, and Photobacterium
Bioluminescent bacteria can colonize the _____, resulting in a _____ relationship
The light organs of marine creatures such as squid and flashlight fish, mutually beneficial relationship
Describe the mutually beneficial relationship between bioluminescent bacteria and marine creatures
Bacteria provide light for defense and predation, bacteria receive nutrients from the host (some of which are required for the bioluminescent reaction)
Describe how E. scolopes (bobtail squid) become colonized with A. fischeri (bioluminescent bacteria)
E. scolopes are sterile at birth, but are colonized by A. fischeri within hours (ubiquitous in the ocean water). Ciliated ducts trap bacteria in mucous layer, and the squid produces antimicrobials/NO (nitrous oxide) to eliminate other species. Chemotactic sugars lure A. fishceri inside as well.
What does the presence of A. fischeri stimulate within the light organ?
Presence of A. fischeri stimulates maturation of the light organ.
Once colonized, what happens to A. fischeri?
A. fischeri lose their flagella and grow exponentially
What happens to A. fischeri at high concentrations (aka when the bacteria reach quorum)?
A. fischeri is bioluminescent and protects the squid by providing counter-illumination at night when squid is hunting (protects squid from predators).
- Basically, at night, the bobtail squid uses the blue-green light to mask itself (and shadow) from predators
What do squid colonized by A. fischeri do every morning?
The squid burrows into the sand and vents ~90% of the A. fischeri and the process begins again (throughout the day, the bacteria starts re-colonizing the squid for night)
What chemical reaction within A. fischeri allows for bioluminesence?
A.fischeri uses RCHO + FMNH2 as a 2-component luciferin. At night, the bobtail squid directs O2 into the light organ.
Luciferase produces light in the presence of a luciferin and oxygen:
RCHO + FMNH2 + O2 -> RCOOH + FMN + light (reaction catalyzed by luciferase)
What helps regulate the light intensity of the bioluminescence within the A. fischeri?
Augmentation of its ink sac and an “iris” helps regulate the light intensity
A. fischeri expresses ___ at basal levels, which is an _____ that produces _____
LuxI, AHL synthase, Al-1-type AHL autoinducer (3OC6-HSL)
What is the AHL autoinducer in A. fishceri and what happens to it at high concentrations? Explain the downstream effects as well
It normally diffuses throughout the squid light organ. At high concentrations, 3OC6-HSL binds LuxR. LuxR is an activator protein (transcription factor) which binds to activator binding sites and induces the Lux operon.
What is LuxI responsible for on the Lux operon?
AHL synthase, so more 3OC6-HSL is synthesized, which binds to LuxR that further induces the Lux operon (positive feedback loop)
What are LuxC, LuxD and LuxE responsible for on the Lux operon?
Lux C, LuxD and LuxE produce a multicomponent fatty acid reductase which synthesizes RCHO (a long-chain fatty aldehyde) which forms part of the 2-component luciferin
What are LuxA and LuxB responsible for on the Lux operon?
LuxA and LuxB produce a heterodimeric enzyme (functional luciferase)
What is LuxG responsible for on the Lux operon?
LuxG produces an FMN reductase (FMNH2, a reduced electron carrier part of the 2-component luciferin
Where is S. aureus found on humans and what was it once thought to be? What is it’s usual function?
S. aureus is ubiquitous on skin and nasal passages and once thought to be commensal (usually prevents bad pathogens from sticking to it)
Describe how S. aureus can cause humans harm
S. aureus is now known as an opportunistic pathogen if it can bypass the innate immune defense (e.g. by entering the blood stream through a cut)
- Produces a variety of virulence factors that lead to an impressive variety of infections (pyogenic, aka pus-forming infections)
What is a regulon and how does it relate to S. aureus?
A regulon is a bunch of different operons under the control of a single promoter
- S. aureus contains an inducible set of regulons controlled by quorum sensing
What is AgrD responsible for in the S. aureus regulon?
AgrD, which is initially inactive after translation, synthesizes an autoinducing peptide (AIP)
What is AgrB responsible for in the S. aureus regulation?
AgrB is a cell membrane transporter, which transports the pre-AIP (which then becomes active outside of the cell)
What happens when AIP excreted by S. aureus is found in high concentrations?
At high concentrations, the AIP binds AgrC (AgrC is a histidine kinase)
What happens when AgrC gets activated in the S. aureus pathway?
AgrC phosphorylates AgrA (AgrA is a response regulator)
What happens when AgrA gets phosphorylated in the S. aureus pathway?
AgrA-P binds at activator binding sites within multiple regulons (upregulates the production of multiple virulence factors)
Why don’t S. aureus act pathogenic on our skin?
On our skin and nasal passages, the concentration of S. aureus is too dilute to trigger the system because we’re constantly shedding and washing ourselves (whereas in the bloodstream, it’s easier for S. aureus to multiply exponentially)
Describe the interplay between microbial warfare by GI microbiota and S. aureus
Certain bacillus species competing with S. aureus can secrete fengycin, a compound that can bind AgrC (histidine kinase) and prevent the phosphorylation/activation of AgrA. This prevents the transcription of virulence genes required for colonization of S. aureus, so it allows for the bacillus species to outcompete S. aureus
What was the miasma theory of infection? What replaced it?
The theory that bad smells cause infection
- The discovery of microbes led to the germ theory of disease which replaced the miasma theory
What 3 things was Robert Koch responsible for regarding the germ theory of disease?
- First to link specific bacteria to specific diseases
- Studied anthrax and tuberculosis (called “consumption” back then)
- Formulated postulates for determining the microbial cause of infection
What where Koch’s 4 postulates?
- The specific organism must be associated with the disease (should never be in organisms without the disease)
- The specific organism should be isolated in a pure culture
- The pure isolate should produce disease through injection into a model like a mouse
- The organism should be re-isolated from the diseased model (to verify that it’s the same disease)
What are 3 issues with Koch’s postulates?
- Many pathogens are found in asymptomatic carriers (and sometimes disease is due to toxins produced by the bacteria, rather than the bacteria itself)
- Many pathogens are unculturable
- Many pathogens lack a suitable animal model
What do modern versions of Koch’s postulates use?
Genomic-based approaches (why grow things in the lab when we can just sequence them directly?)
What were stomach ulcers originally thought to be the result of?
The overproduction of stomach acids due to eating spicy or being stressed
What did Marshall and Warren discover about stomach ulcers? What issues did they have and how did they resolve them?
They discovered/isolated H. pylori from tissue biopsies
- Couldn’t find an appropriate animal model (the organisms did not develop ulcers when H. pylori was put in the model organisms) so no one believed microbes could survive in the stomach
- So Marshall chugged a sample of H.pylori and developed gastritis :D Now all of Koch’s postulates were satisfied (because H. pylori was also re-isolated from Marshall’s stomach biopsy
True or false: H. pylori is found in a lot of us, but it’s usually benign because they live within the mucous layer and don’t penetrate our stomach lining
True
What does H. pylori look like and how does it cause ulcers/gastritis (gastric inflammation)?
Uses helical shape and polar flagella to penetrate thick mucous lining stomach epithelium
- Also produces toxins (VacA) to damage epithelial cells to gain nutrients from mucous or the skin (VacA penetrates stomach cells)
True or false: Gastritis due to H. pylori can be resolved with antibiotics
True
True or false: H. pylori infection can lead to gastric cancer in some patients
True
How does H. pylori survive the acidity of the stomach?
Epithelial cells secrete carbonate to reduce acidity and H. pylori uses urease to generate ammonia
Define infection
Growth of a pathogenic microbe in/on a host (doesn’t necessarily mean symptoms or disease
Define disease
Injury of a host due to infection
Define pathogen
A microorganism that causes disease
Define opportunistic pathogen
Causes disease only under certain circumstances
Define pathogenicity
The ability of a pathogen to cause disease (yes or no, does it cause disease)
Define pathogenesis
Process by which a pathogen causes disease
Define virulence
Relative ability of a pathogen to cause disease
What are virulence factors (and give some examples)
Molecules produced by, or strategies used by, a pathogen to cause disease
e.g.
- Achieve attachment and colonization
- Evasion of the host immune system
- Invasion and dissemination (spread) to other host cells
- Acquisition of nutrients and growth
- Release into external environment (to find new hosts)
What are 3 “portals of entry” for bacteria?
- Skin (wounds or bites)
- Gut (need to survive acidic stomach)
- Mucous membranes (nose, mouth, eyes, etc.)
What is 3 things is mucous composed of?
- Mucin (made of glycoproteins and polysaccharides)
- sIgA (antibody that is secreted to try and prevent infection before pathogen even enters the body_
- Defensins (eukaryotic version of bacteriocins)
True or false: most microbes cannot penetrate mucous
True
Pathogenic virulence factors include what two things, and what is their general function?
Include flagella and enzymes that degrade mucin
What are microbial adhesins and what are they needed for?
Extracellular glycoproteins or lipoproteins that bind to host receptors
What are fimbrial adhesins?
Adhesins involved in the initial attachment of microbes to host
What are afimbrial adhesins?
Adhesins involved in the close (intimate) contact with their host
What are host pathogen receptors?
Structural or essential functional cell components, such as fibrinogen, collagen, glycoproteins, lectins, etc.
What 2 main secretion systems do pathogens use to inject proteins/toxins directly into host cells?
T3SS and T6SS
Describe how pathogenic E. coli (O157H:7) infects its host
It first injects a protein (Tir) into host cells using T3SS. Tir becomes a receptor on the host membrane for an E. coli surface adhesin (intimin) that adheres the cells tightly
How do intracellular pathogens induce phagocytosis?
Intracellular pathogens, once attached to a host cell, can induce the cell to internalize the pathogen. They do this by secreting invasins that activate host cell signaling pathways that result in reorganization of cytoskeletal actin to form pseudopod-like structures that engulf the bacterium
What happens to intracellular pathogens directly after being internalized?
Once internalized, the pathogen either escapes the phagosome before fusion with a lysosome, or prevents lysosomes from fusing with the phagosome
What are 3 ways that pathogens can evade the host immune system?
- Immunoglobulin proteases
- Antigenic variation
- Hide in plain sight
Explain how the production of immunoglobulin proteases by pathogens can help them evade the host immune system
The proteases destroy Ig proteins to evade opsonization (when a pathogen is coated with antibodies and dies)
- Also, mucin is full of sIgA so IgA protease is a major virulence factor of many intestinal pathogens bc it helps with penetrating the mucous
Explain how the production of antigenic variation by pathogens can help them evade the host immune system
Antigenic variation changes the structure of the flagella, pili/fimbriae or other surface antigens to evade antibodies. They also change the teichoic acid, LPS and peptidoglycan layers to evade defensins
Explain how pathogens can evade the immune system by hiding in plain sight (3)
- They can stop producing flagella, pili and/or fimbriae (if these are what antibodies target)
- They use polysaccharides found on host cells to build a capsule
- They coat the cell surface with host proteins
Explain how protein A specifically allows for certain pathogens to evade the immune system
Protein A is located on the surface of certain pathogens. They bind IgG and flip them so that their variable region (which usually binds antigens) are exposed. Now, the immune cells can’t recognize the antibodies
Describe how pathogens acquire nutrients through degradative enzymes
- Lipases, proteases, glycosidases, etc produced by pathogens degrade cells to that pathogens can access and use nutrients
- Phospholipases secreted by pathogens rupture host cell membranes to release nutrietns
Describe how pathogens promoting a minor immune responds helps pathogens acquire nutrients
Minor immune responses cause damage to all cells instead of the pathogen alone, and pathogen doesn’t die. The damaged host cells release nutrients
How do pathogens acquire iron? (3)
- They secrete siderophores that are proteins that bind iron with high affinity. These then travel back to pathogen receptors to provide pathogens with iron
- Certain host receptors are expressed on pathogens that steal iron from host proteins like heme, lactoferrin, etc.
- Some pathogens also degrade these host proteins to release iron.
What is iron abstinence in pathogens?
Certain pathogens use manganese as an enzyme cofactor instead of iron since iron is so limiting (avoiding the need for iron all together)
What is a pathogenicity island and what do they help with?
Genes for chromosomal virulence factors are often clustered together on pathogenicity islands, which facilitates their spread to other organisms by horizontal gene transfer
Genes for most virulence factors are located on…
Plasmids (which also facilitates spread by HGT events)
True or false: all genes for virulence are bacterial in origin
False; some of them are found on prophage DNA within the pathogen’s chromosome
Why do pathogens cause disease in general?
To acquire nutrients for growth, replication and spread
Pathogens that damage cells/tissues are said to have _____
Toxicity
What are the three major mechanisms of toxicity in general?
- Enzymes
- Toxins
- Endotoxins
Explain how enzymes act as a mechanism of toxicity
- Explain the two types of enzymes that cause toxicity
Enzymes break down components of host cells/tissues. Exoenzymes are secreted into surroundings and some enzymes can be delivered directly to host cells (through secretion systems)
Explain how toxins act as a mechanism of toxicity
- Explain the three types of toxins that cause toxicity
Toxins are protein molecules that affect host cell/tissue function. Exotoxins are secreted into the surroundings, toxins can be delivered directly to cells and enterotoxins are active in the GI tract.
Explain how endotoxins act as a mechanism of toxicity
Endotoxins are part of the cell wall structure and they elicit an immune response but are not secreted
What is an endotoxin in Gram-negative cells?
Lipid A, portion of LPS
What is an endotoxin in Gram-positive cells?
Lipoteichoic acids
Explain how tissue destroying enzymes help pathogens
Invasive pathogens produce enzymes that break down components of the extracellular matrix opening paths for microbes to spread below the epithelium.
What is hyaluronidase?
A tissue-destroying enzyme secreted by invasive pathogens (Streptococcus pyogenes) that cleaves hyaluronic acid (a polysaccharide that maintains organization of cells in tissues)
Coagulase function for pathogens?
Causes clots to form around the infection site to protect the pathogen from immune cells
Streptokinase (staphylokinase) function for pathogens?
Dissolves clots to allow the pathogen to move into deeper tissue layers (is expressed after the immune system “calms down” a bit)
What 3 bacterial species cause opportunistic infections through skin cuts/abrasions?
Staph. aureus, Staph. epidermidis, Strep. pyogenese
What causes pus formation?
Coagulase walls off the infected tissue to slow the immune response. The pathogen then secretes hemolysins and leukocidins that destroy RBCs and WBCs for nutrients, resulting in pus formation (so pus= destroyed cell tissue)
What toxin causes pus formation specifically in Staph. aureus infections? How is it treated?
Cell destruction by Staphylococcus aureus skin infections is mediated by alpha-hemolysin (S. aureus alpha-toxin)
- The toxin is a pre-forming cytotoxin that targets surrounding cells, resulting in cell lysis and resulting in pus formation.
- Treatment via antibiotics and drainage
How do pathogens colonize subcutaneous tissues? What are three diseases that are caused by this?
They use multiple adhesins to attach to ECM proteins and hyaluronidase
- Impetigo, scaled skin syndrome, strep throat
What is septicemia?
When bacteria get into the bloodstream
What are AB-type endotoxins? What is each subunit responsible for?
“Two-component” toxins.
- The B-subunit binds host cells and facilitates the transport and release of the A-component into the host cell.
- The A subunit has toxic activity (e.g. enzymatic interruption of transcription, translation, cell signaling, etc. )
What is diphtheria?
A respiratory disease that results when Corynebacterium diphtheriae colonizes the throat and upper respiratory tract
Why is diphtheria fatal if untreated?
A buildup of fibrin clots, dead cells, and an immune response results in typical swelling of the neck and pseudomembrane formation in the throat which closes off the throat as the infection gets worse (immune cells form a pseudomembrane when they’re trying to clog the bacteria)
- Also fatal if the toxin travels to the heart, liver, etc.
How is diphtheria eliminated in developed countries? How are diphtheria infections treated?
Virtually eliminated in “developed” countries that have access to the DTaP vaccine. Treatment via antibiotics
What is the best studied bacterial toxin?
Diphtheria toxin (DT)
Where is the Tox gene in DT located?
Located on a lysogenic bacteriophage (phage beta)
- So only Corynebacterium diphtheriae strains infected by this bacteriophage can produce the toxin
What type of toxin is DT?
An AB-type toxin
How does DT cause host cell death?
DT ADP-ribosylates EF-2 (ADP taken from NAD+), which stops translation, leading to host cell death
What is the reaction carries out by DT?
NAD+ + EF-2 + DT -> nicotinamide + EF-2-ADP +DT
What is botulism? How is it transmitted?
A neuromuscular disease that results when Clostridium botulinum either colonizes the GI tract or the toxin is ingested (caused by exposure via unpasteurized milk/honey/juice or improper (home) canning)
What age group is more susceptible to botulism and why?
Adults are usually protected from C. botulinism, but young children and immunocompromised people are vulnerable because they don’t have the immune system or the gut microbiota to fight it.
How is the botulism toxin (BoNT) absorbed?
Absorbed in the stomach/small intestine and enters the bloodstream where it targets motor neurons at neuromuscular junctions
What does the botulism toxin (BoNT) cause in its host?
Flaccid paralysis - the host cannot initiate muscle contraction
True or false: Once the botulism toxin (BoNT) is bound to its target, it can still be treated with antibiotics and antitoxin
False; botulism is treated via antibiotics and antitoxin, but once the toxin is bound to its target, there is no treatment - if the body doesn’t replace the neuron, the damage is permanent.
What is the most potent bacterial toxin known?
BoNT
Where are Bot genes located?
On the C. botulinum chromosome, plasmids and prophage
What type of toxin is BoNT?
An AB-type neurotoxin
Explain how BoNT causes disease
The various BoNT A-subunits are endoproteases that cleave various SNARE proteins. The synaptic vesicles then can’t merge with the cell membrane to release acetylcholine into the synaptic cleft where they normally initiate muscle contraction (muscle cells not stimulated by acetylcholine can’t contract)
What causes tetanus?
Tetanus is a neuromuscular disease that results when Clostridium tetani colonizes a deep tissue wound (skin clots it off causing an anaerobic environment where they thrive)
- The tetanus toxin diffuses into the bloodstream where it targets the inhibitory neurons of motor neurons which then causes spastic paralysis (lockjaw)
True or false: Once the tetanus toxin is bound to its target, it can still be treated with antibiotics and antitoxin
False; tetanus is treated via antibiotics and antitoxin, but once the toxin is bound to its target, there is no treatment - if the body doesn’t replace the neuron, the damage is permanent.
How is tetanus eliminated in developed countries?
Virtually eliminated in “developed” countries that have access to the DTaP vaccine
How does the tetanus toxin (TeNT) relate to BoNT?
Shares homology with BoNT, but targets different receptors
Where are Tet genes located?
On a plasmid
What type of toxin is TeNT?
An AB-type neurotoxin
Explain how TeNT causes disease
The TeNT A-subunit is an endoprotease that cleaves SNARE proteins. Synaptic vesicles can’t merge with the cell membrane to release glycine into the synaptic cleft where they normally inhibit motor neurons. So uninhibited motor neurons constantly release acetylcholine, and muscles are locked in a contracted state.
What is the “aP” in DTaP?
Pertussis (whopping cough)
What is pertussis and how is it caused?
A respiratory disease that results when Bordetella pertussis colonize cilitated cells of the lung respiratory tract
What does Bordetella pertussis secrete and how?(2)
- Colonized cells secrete pertussis toxin (PT), an AB-type toxin, through T4SS
- Tracheal cytotoxin (TCT), an endotoxin which kills ciliated cells that keep lung tissue free of debris
What is Cholera and what causes it?
An intestinal disease that results when Vibrio cholerae colonize the small intestine (exposure via food and/or water contaminated with human feces)
What does the Cholera toxin target?
Intestinal epithelial cells
What does Cholera result in?
Severe diarrhea resulting in life-threatening dehydration and electrolyte loss
How is Cholera treated?
With rehydration therapy and antibiotics
True or false: Cholera is virtually eliminated in “developed” countries that have access to clean drinking water
True
The cholera toxin (CT) shares homology with…
Enterotoxins of pathogenic E. coli and Shigella
Where is the ctx gene (codes for cholera toxin) located?
On a prophage (so strains without the prophage are completely fine)
What type of toxin is CT?
A hexameric AB-type toxin (AB5)
What is the mechanism of disease by CT?
The CT A-subunit ADP-ribosylates the alpha-subunit of Gs proteins. Gs then constitutively activates adenylate cyclase resulting in increased cAMP levels. cAMP activates cAMP-dependent protein kinase (PKA) signaling pathways. This results in the cell stopping absorption of Na+ and Cl- from the intestinal lumen and actively pumps Cl- and HCO3- into the lumen. Water follows concentration gradient, causing diarrhea
What is a superantigen?
Excreted toxin proteins that induce a massive immune response that damages the host (so its our own immune system that does most of the damage, not the bacteria)
- The massive immune response induces high fever, low blood pressure, organ dysfunction/failure, system shock (severe multiorgan failure) and death
Superantigens bind to immune cells and…
Indiscriminately activate them
What are two examples of bacteria that code for superantigens? What disease do they cause specifically?
Staphylococcus aureus, which produces Toxic Shock Syndrome Toxin (TSST-1)
Streptococcus pyogenes, which produces Exotoxin A that is involved in scarlet fever and streptococcal TSS
Define endotoxins
Permanent compounds of the pathogens outer cell surface that elicit an immune response
If endotoxins aren’t excreted, how may they spread systemically?
When cells lyse or even grow/divide, little bits of peptidoglycan shed
How does the immune system respond to endotoxins?
Releases pyrogenic (fever) cytokines, as well as inducing increased heart rate, diarrhea/vomiting, low blood pressure, and inflammation
What can large quantities of endotoxin result in?
Blood clotting, organ dysfunction/failure, endotoxic shock (SEPTIC SHOCK) and death
What portion of LPS is toxic?
Lipid A
How is LPS soluble?
Due to its polysaccharide portion
What symptoms does lipid A of LPS cause? What can large doses cause?
Fever and general inflammation
Large doses can cause tachycardia and blood coagulation (forming clots within the vascular system)
Other than LPS, what is another example of an endotoxin?
Lipoteichoic acid
- As the cell is putting lipoteichoic acid into its cell wall, some may float away and act as endotoxins
Define immunology
The study of the components and processes used to resits pathogens and fight disease
Define immunity
The ability of an organism to resist infection
Describe the innate immune system in general
The automatic ability to recognize and destroy a pathogen (or its products).
- Fast acting (hours) but non-specific
True or false: innate immunity requires previous exposure to a pathogen and its products
False
Lysozyme?
- What type of defence is it and explain it
An INNATE DEFENSE. In tears and other secretions that dissolve bacterial cell walls (chops up peptidoglycan)
Mucus/cilia?
- What type of defence is it and explain it
An INNATE DEFENSE in lungs and trachea. Suspend and move microorganisms out of the body
Skin?
- What type of defence is it and explain it
An INNATE DEFENSE, is a physical barrier
What role do the blood and lymphatic systems play in immunity (in general)?
Distribute immune cells/molecules throughout the body
Blood is pumped by the heart through _____ to ______ and returns to heart through ______
Arteries, capillaries, veins
In blood capillary beds, lymph…
Drains across surrounding tissue and into lymph capillary beds
Lymph is pumped via lymph ducts, through…
Lymph nodes and back into the blood
What is a lymph node?
A secondary lymphoid organ. Lymphocyte-filled tissues that sample the LYMPH for pathogens, toxins, activated immune cells
Function of the spleen?
Lymphocyte-filled tissues that sample the BLOOD for pathogens, toxins, activated immune cells
What are Mucosa-Associated Lymphoid Tissues (MALTs)?
Patches of lymphocyte-filled tissue that sample the mucosa for pathogens, toxins, activated immune cells
What 2 organs are the primary lymphoid organs?
Bone marrow and thymus
Function of the primary lymphoid organs?
Where lymphocytes develop
Define hematopoiesis
Process by which hematopoietic stem cells, in the bone marrow, differentiate into more specific cell types
What activates hematopoiesis?
Cytokines (cell chemicals). They stimulate hematopoiesis if they make it into the bone marrow
Hematopoietic stem cells mostly differentiate into…
- What is 0.1% of the cells in circulation?
Erythrocytes (most of the cells in circulation are red blood cells, 99+%)
- 0.1% of the cells in circulation are leukocytes (WBCs)
Hematopoietic stem cells differentiate into which 2 lineages?
Lymphoid cells and myeloid cells
Lymphoid cells are cells involved in (innate/adaptive) immunity
- Specifically describe which processes they’re involved in
Adaptive immunity
- Cell (WBCs directly attack) and antibody-mediated (WBCs indirectly attack) immunity
Myeloid cells are cells involved in (innate/adaptive) immunity
- Specifically describe which processes they’re involved in
Innate immunity
- Phagocytosis and inflammation
What 2 innate immunity cells are involved in antigen presentation?
Dendritic cells and macrophages
What cell type originating from a lymphoid precursor is actually part of innate immunity>
Natural killer cells
What 4 cells are granulocytes and what immune system do they belong to?
Neutrophils, eosinophils, basophils and mast cells. They are part of innate immunity
What are the two myeloid antigen-presenting cells (APCs) and what immune system do they belong to?
Macrophages and dendritic cells, belong to the innate immune system
What is the main difference between macrophages and dendritic cells?
Macrophages associate with tissues/organs (e.g. lungs, skin, etc) and “wait” in tissues for infection, while dendritic cells associate with epithelial cells (e.g. skin, mucosa, etc)
APC function?
Phagocytose foreign cells/molecules and present antigens on class II major histocompatibility complex (MHC II) cell surface receptors
(Macrophages/dendritic cells) stay in tissues to fight infection
Macrophages
(Macrophages/dendritic cells) move to lymphoid tissue to activate the adaptive immune response
Dendritic cells
What are two phagocytic granulocytes in the innate immune system?
Neutrophils and eosinophils
Neutrophils are also known as…
Polymorphonuclear leukocyte - PMN
What is the most abundant WBC (which cells do the most work if the immune system becomes activated)?
Neutrophils
How do eosinophils differ from neutrophils?
Eosinophils are phagocytic granulocytes that specialize in attacking parasites
General function of phagocytic granulocytes? What 3 things do they secrete upon encountering a pathogen
Both release antimicrobials (defensins, proteases, lipases), cytokines and chemokines.
Both phagocytose foreign cells/molecules
What are two inflammatory granulocytes?
Basophils (blood) and mast cells (mucosal tissues)
What 3 molecules do inflammatory granulocytes secrete upon encounter with a pathogen?
Histamine, cytokines and chemokines
What do histamines cause?
Vasodilation and increases vascular permeability (which allows WBCs and lymph to leave the vasculature and enter tissue much more quickly
What do damaged cells (and immune cells in the area) do in general upon injury?
They respond to survey the damage, check for infection and initiate healing
What 2 molecules are secreted by damaged cells? Why are they secreted?
Cytokines (signalling peptides) and chemokines (chemoattractant peptides) to attract/activate immune cells and induce inflammation even if the trauma doesn’t cut through the skin
What do neutrophils do during injury?
Neutrophils (and other lymphocytes), activated by cytokines, follow the chemokine gradient and enter the damaged tissue resulting in inflammation
What is inflammation and what 4 things is it characterized by?
(Usually) localized response to injury.
- Redness, heat, swelling, and pain
The release of which class of molecules induces inflammation?
Induced by release of proinflammatory cytokines
What 5 things do proinflammatory cytokines promote?
- Hematopoieses
- Fever
- Attack and activation of immune cells
- Vasodilation
- Vascular permeability
How do neutrophils enter damaged tissue?
Lymph (way more than normal) leaves the vasculature, delivering neutrophils etc before draining into lymph capillaries
Define diapedesis
The act of WBCs leaving the vasculature and entering the damaged tissue
How do phagocytes arrive at an infection site?
By following a chemokine gradient
What do cytokines do to allow for diapedesis? What happens to phagocytes after this?
Cytokines loosen the junctions between capillary endothelial so WBCs can move. Phagocytes then squeeze between the cells and enter the damaged tissue
Describe how phagocytes recognize pathogens
Pathogens have PAMPs (like MAMPs in microbes), which are “patterns” like LPS, teichoic acid and peptidoglycan that aren’t found on the host cells.
Phagocytes have pattern recognition receptors (PRRs) that bind PAMPs
PAMP-PRR binding induces phagocytosis, cytokine production and release of defensins
What is a class of PRRs?
Toll-like receptors
Defensins?
Molecules that penetrate the cell membrane of other cells and cause cell lysis due to osmosis
True or false: neutrophils have more than one type of PRR
True
What happens to pathogens after initially being engulfed to the PAMP-PRR binding?
Binding of a PAMP with a PRR activates a signaling cascade that results in the attached microbes being internalized into a phagosome. The phagosome fuses with a lysosome forming a phagolysosome.
What 7 things do lysosomes contain?
- Lysozyme (cleaves peptidoglycan)
- Defensins (perforate membranes)
- Myeloperoxidase (forms hypochlorous acid that helps dissolve pathogens)
- Nucleases
- Proteases
- Lipases
- Reactive oxygen species (ROS)
How are neutrophils and macrophages related to purulence?
Activated neutrophils phagocytose and release antimicrobials into the surrounding tissue (they release lysosomal contents into the extracellular space)
- This results in both microbe and host cell destruction
- Most neutrophils and macrophages die at the site of infection. The build-up of dead cells, lymph and coagulation factors forms the pus associated with pyogenic skin/mucosal infections
What 3 things can cause a “cytokine storm”? What is a cytokine storm?
Septicemia (pathogens growing in the blood), superantigen toxins (TSST) and endotoxin (LPS) in the blood
- A cytokine storm is a mass release of cytokines, histamines, etc throughout the body resulting in systemic inflammation
What 3 things occur due to systemic inflammation from a cytokine storm?
- As the majority of vasculature dilates, and lymph leaves the circulatory system, blood pressure drops.
- The heart pumps harder to compensate for slower blood flow
- Organ systems fail due to lack of oxygen
What are interferons and what do they do?
Interferons are a special type of cytokine.
Before cells die, cells infected by certain viruses release special cytokines called interferon. Interferon migrate to surrounding cells and activate expression of antiviral genes to limit viral spread (through binding of a surface receptor)
The innate immune response prevents/clears a lot of infections. What are 3 reasons why some pathogens would need more than just the innate immune system?
- Capsules resist phagocytosis
- Exoenzymes allow pathogens to get to endothelial layers (e.g. hyaluronidase)
- Some pathogens are intracellular and “untouchable” by innate defenses
What is adaptive immunity in general?
The acquired ability to recognize and destroy a specific pathogens or its products, the “second line of defense” because it’s slower than innate immunity
- Following exposure, effectors learn to target a particular pathogen to generate a coordinated response
The adaptive immune system is (fast/slow) and (specific/non-specific)
Slow, specific
True or false: adaptive immunity confers protection against subsequent exposure and targets “self” antigens
False; it does confer protection against subsequent exposure but does not target “self” antigens
B lymphocytes (cells) mature in the ____ and then…
Bone marrow, await activation in the secondary lymphoid organs (MALT, spleen and lymph nodes)
__ cells confer humoral immunity
B
T lymphocytes (cells) mature first in the ___ and then in the ___, and then…
Bone marrow, thymus, await activation in the secondary lymphoid tissue
__ cells confer cell-mediated immunity
T
Other than T cells and B cells, what else can lymphoid precursors differentiate into?
Natural killer cells (NK)
Natural killer cells are part of ____ immunity and are responsible for…
Innate immunity, identify and destroy virus-infected and cancerous cells
Define antigen
Molecules that interact with components of the immune system (More specific than PAMPs, and smaller)
Define epitope
The specific parts of an antigen that interacts with the immune system (i.e. the specific interaction/binding sites)
True or false: antigens can have multiple epitopes
True
In the thymus, T cells are tested for their ability to react with which two things? Where do surviving T cells migrate to?
- MHC molecules
- Self-antigens
- They are destroyed if they do not interact with MHCs or if they react with self-antigens, and surviving T cells migrate to secondary lymphoid tissues (lymph nodes, spleen, MALT)
B cells are tested for their ability to react with what? Where do surviving B cells migrate to?
Self-antigens
- They are destroyed if they do react with these, and surviving B cells migrate to secondary lymphoid tissues (lymph nodes, spleen, MALT)
When a pathogen gets past the skin or mucous layer, they often first encounter…
Macrophages and dendritic cells
What two cells connect the innate immune system with the adaptive immune system?
Macrophages and dendritic cells
Once a pathogen encounters a macrophage/dendritic cell, what happens first?
PAMPs (on the pathogen) bind to PRRs (on the APC) and the pathogen is phagocytosed.
What happens after a macrophage/dendritic cell phagocytoses a pathogen?
Antigens are processed and presented on MHCII cell surface receptors
What do dendritic cells do after presenting a pathogenic antigen on their MHCs?
They enter the lymphatic system and move to a nearby lymph node (or MALT). B cells and T cells are there waiting for them
What do macrophages do after presenting a pathogenic antigen on their MHCs?
They stay in the area and “casually” continue to consume the pathogen
MHCII are only found on antigen-presenting cells (APCs), which are…(3)
- Macrophages
- Dendritic cells
- B cells
Everyone has __ versions of MHCII with variable regions that allow…
6, allows MHCII to bind different antigens
Antigens bound to MHCII are displayed on the APC cell surface where they can be recognized by ____ cells
Helper Th cells
T cell receptors (TCRs) on naïve Th cells interact with…
MHCII-epitope complexes
True or false: there is a unique Th cell for every epitope
True
True or false: A single Th cell can recognize various epitopes
False; Each Th cell has 1000s of TCRs that only recognize one specific epitope (a single T cell will only recognize one epitope)
Other than the TCRs on the Th cell, what else binds MHCII?
Th cell co-receptor (CD4) also binds MHCII to strengthen the association
Activated (effector) Th cells undergo clonal expansion to…
Replicate to form multiple copies of the epitope-specific cell
What 3 things do Th cells differentiate into upon activation?
- Th1 cells
- Th2 cells
- Memory T cells
These have the same TCR as the naïve Th cell)
After Th1 cells are produced, they…
They enter the circulation, migrate to infection sites and release cytokines that activate PHAGOCYTES (macrophages)
After Th2 cells are produced, they…
Stay in the lymphoid tissue and release cytokines that activate B CELLS
In the infected area, Th1 cells interact with…
Macrophages displaying the epitope on MHCII
What do effector Th1 cells release upon binding to the macrophages displaying the pathogen epitope on MHCII? What does this cause?
Cytokines to activate the phagocytes (macrophages become super-macrophages). This results in improved phagocytosis and causes macrophages to release their own cytokines (results in a positive feedback loop of cross activation)
Define a superantigen and the result of their presence
Excreted toxin proteins that induce a massive immune response that damages the host. They indiscriminately activate Th cells
- Results in a cytokine storm that results in toxic shock
What do superantigens form?
A bridge between MHCII complexes and TCRs regardless of bound antigen (the TCR does not have to match the antigen)
Naïve B cells have membrane-bound….
antibodies that function as B cell receptors (BCRs)
True or false: every B cell has a unique BCR that binds a specific epitope
True
Describe T cell-dependent B cell activation (5 steps)
- During an infection, the antigen is swept into the lymph which passes through MALT and lymph nodes (where mature, naïve B cells are waiting)
- When an epitope binds to a BCR, the antigen is internalized and phagocytosed
- Antigens are processed and presented on MHCII (B cells are APCs)
- T cells are also being activated, so if a Th2 cell binds the MHCII-epitope complex on the B cell, the Th2 cell releases cytokines that activate the B cell
- The B cells undergo clonal expansion into multiple copies of epitope-specific plasma cells and memory B cells
Plasma B cells produce and release…
Antibodies specific to the antigen that was recognized by the Th2 cell
What type of immunity is provided by plasma B cells?
Antigen-specific (humoral) immunity
Antibodies are a complex of _ identical light (short/long) and _ identical heavy (short/long) peptide chains arranged into a symmetrical _ shape
Antibodies are a complex of 2 identical light (short) and 2 identical heavy (long) peptide chains arranged into a symmetrical “Y” shape
One light chain and one heavy chain in the antibody interact to form…
An antigen-binding site (Fab region)
Ig monomers are (monovalent/bivalent)
- Explain what this means
Bivalent (have two antigen binding sites)
True or false: the parts of the light and heavy chains that form the antigen binding sites are highly variable and each unique plasma cell produces one specific combination
True
Other than the Fab region, the rest of the light and heavy chains are…
- What is this region called?
Constant (Fc region)
What does the Fc region of antibodies allow for?
Allows them to interact with other immune effectors (to fight and clear the infection)
Describe IgM function and structure
Monomeric IgM functions as a B cell receptor (BCR). It is the antibody class secreted by B cells during INITIAL EXPOSURE.
- Serum IgM forms a pentamer (good or clumping antigens together)
Describe IgG function and structure
Most abundant antibody in the blood, has a higher affinity for the epitope and is good at activating many types of immune cells. Is secreted by B cells during subsequent exposure.
- Serum IgG is a monomer
Describe IgA function and structure
Serum IgA is a monomer, dimeric IgA is secreted at mucosal surfaces (sIgA)
- Binds mucin and found in tears, sweat, colostrum, milk, anything that is found outside of our cells
- Involved in preventing pathogens from reaching epithelium
Describe IgD function and structure
Serum IgD is a monomer, and monomeric IgD functions as a B cell receptor
- Don’t really know what it does, maybe involved in memory B cell activation?
Describe IgE function
Displayed on basophils and mast cell membranes, triggers release of histamine and pro-inflammatory cytokines if antigen attached to Fab portion (associated with allergies)
What is opsonization?
Pathogen is coated in antibodies.
- Marks bacterial, viral, or parasitic cellular components (i.e. O-specific antigen) for phagocytosis, complement activation or antibody-dependent cell-mediated cytotoxicity (ADCC)
In addition to the PRRs that recognize PAMPs, phagocytes have both…
C3b (complement) receptors and Fc (antibody) receptors that recognize the antibodies coating a pathogen in opsonization and engulf it.
True or false: opsonized pathogens are phagocytosed more efficiently
True
What is antibody agglutination and its function?
Agglutination clumps foreign particles together (i.e. multiple pathogens, viruses) for phagocytosis
What is antibody neutralization and its function?
Bind to parts of a pathogen and prevents toxins, viruses, microbial adhesins from interacting with their target
Describe secondary antibody response
Upon initial exposure/activation to the antigen, plasma B cells release antigen-specific IgM. Upon subsequent exposure to the same antigen, memory B cells (with epitope-specific BCRs) rapidly differentiate into plasma cells (no need for assistance from Th2 cells)
- The antibody response is much faster and more intense than the initial exposure event
Describe antibody class switching during the secondary antibody response
What is the relative concentration of antibodies compared to the primary response?
IgM either becomes:
- IgG in the serum
- IgA on mucosal surfaces
10-100x the concentration of the primary response
True or false: Being infected with the same antigen a third time is known as tertiary response
False; being infected with the same antigen 2+ times is always known as the secondary response
Describe vaccination in general
Vaccination is a deliberate antigen exposure to illicit a primary immune response to develop memory B and T cells
- If you are ever exposed to the “real” antigen, you skip to the secondary immune response
Describe live-attenuated pathogen vaccines and examples
Take pathogen and boil it, changes the pathogen structure slightly (becomes attenuated)
Ex: measles, mumps, rubella (MMR) vaccine
What is a risk of using live-attenuated pathogen vaccines?
It can fix itself using its repair mechanisms so you can actually get the disease
Describe heat/chemically-“killed” pathogen vaccines and examples
Non-functional pathogen is injected
Ex: polio and influenza
Describe altered toxins (toxoids) vaccines and an example
Chemically-modified toxins of pathogens are injected
Ex: DTaP
Describe subunit vaccines and an example
Injecting just the spike proteins or cell envelope proteins
Ex: HepB
Describe viral vector (DNA) vaccines
Deliver viral DNA into our nucleus, which is transcribed into pathogen proteins
Describe lipid nanoparticle (mRNA) vaccines
Lipid particle with mRNA in it is delivered to our cells
What 2 things must vaccines be?
- Safe - few side effects and shouldn’t cause autoimmunity
- Efficacious - most produce memory T and B cells
Describe how a vaccine for smallpox was developed
Jenner noticed that milkmaids often got cowpox but not smallpox. He took pus from cowpox pustules and injected it into a “young boy”. The boy was protected from smallpox
- This worked because cowpox is antigenically similar to cowpox
- Today, smallpox has been eliminated from natural spread due to a global vaccine program
What happens when intracellular pathogens and viruses directly enter cells? (3 steps)
Intracellular pathogens and viruses evade the innate and antibody response.
1. Some PAMPs bind to intracellular PRRs in the cytosol and mark them for destruction
2. As they grow and divide, intracellular pathogens release foreign proteins (antigens).
3. These antigens are directed to, and processed in a proteasome and various epitopes are presented on MHCI cell surface receptors (whether they’re self proteins or foreign)
True or false: all cells regularly degrade self proteins in proteasomes and present self antigen on MHCI
True
What cells are MHCI found on?
All nucleated cells, including APCs
True or false: everyone has multiple MHCI sub-types with variable regions that bind different antigen motifs
True
Antigens bound to MHCI are displayed on the cell surface where epitopes can be recognized by…
Cytotoxic T cells (Tc)
What are cytotoxic T cells (Tc) programmed to do in general?
Programmed to destroy cells
What strengthens the association between Tc TCRs and MHCI?
Tc cell coreceptor CD8 (DIFFERENT FROM CD28)
Explain how APCs are multitaskers
Th1 recognizes MHCII-epitope complex on APC, while Tc recognizes MHCII-epitope complex on APC
Self-reactive Tc cells are usually eliminated in the thymus, but not always. How do Tc cells not recognize healthy cells?
Only APCs have B7. B7 on the APC must bind with CD28 on the Tc cell
True or false: Tcs always need CD28 and B7 interaction
False; once activated, they only need to have MHCI-epitope interaction (specific to the pathogenic epitope)
What happens directly after Tc cells are activated?
They enter the circulation and find cells displaying the foreign epitope on MHCI.
What 3 enzymes/molecules are secreted by activated (effector) Tc cells?
- Perforins
- Granzyme
- Cytokines
Function of perforins?
Form pores in the target membrane
Function of granzyme?
Induces apoptosis in the target cell (target cells kills itself)
What is the function of the cytokines released from Tc cells?
Attracts/activates other immune cells
Activated (effector) Tc cells undergo clonal expansion and differentiate into what two cell types?
- Multiple copies of the epitope-specific T cell
- Memory T cells
What is special about memory Tc cells?
They don’t have to undergo the step with APC
Complement is part of what immune system?
The innate immune system
Define complement and its function
A set of proteins that “complement” the innate and adaptive immune systems
- enhances inflammation, phagocytosis, and pathogen lysis
What are two things that activate complement proteins?
- Antibodies coating a pathogen
- Pathogens directly
What are the steps of the complementation MAC attack (classic activation pathway)? (11 steps)
- The C1 complex binds to the Fc portion of antibodies coating a pathogen
- C1 recruits and activates C2 and C4
- C2 splits C2a and C2b
- C4 splits into C4a and C4b
- C2a and C4b bind the cell surface in close association with the C1 complex
- C2b and C4a float away (act as chemokines and attract other immune cells)
- The 2a/C4b complex recruits and activates C3 and C5
- C3 and C5 split into a’s and b’s
- C3a and C5a float away (act as chemokines)
- C3b and C5b bind the cell surface
- The C3b/C5b complex recruits C6, C7, C8 and multiple C9 proteins that form a membrane attack complex (MAC) in the pathogen membrane = cell lysis
Describe how complement proteins allow for enhanced opsonization
C3 can also be cleaved in the blood into C3a and C3b. C3b can opsonize pathogens.
- Phagocytes have C3b receptors (C3R) in addition to antibody receptors (FcR)
- Amplifies phagocytosis 10x
Why are natural killer cells part of the innate immune system if they’re produced by lymphoid progenitor cells?
They have non-specific interactions with pathogens and unhealthy cells
The presence of MHCI (with or without self antigen) has what effect on NK cell activation?
- Explain this
Inhibits NK cell activation
Many infected/cancer cells do not display MHCI (so no Tc cell response possible and without MHCI, NK cells become “suspicious”)
How are NK cells activated?
Many infected/cancer cells display stress proteins on their cell surface. Detection of stress proteins activates suspicious NK cells.
What do NK cells secrete upon activation?
Perforin and granzyme that kill the infected/cancer cell
Describe antibody-dependent cell-mediated cytotoxicity (ADCC)
Antibodies coating infected or cancerous host cells can bind to Fc receptors on NK cells, which also triggers the release of messengers that induce apoptosis in the infected/cancerous cell
Bacteria present in the blood is called ______. Bacteria growing in the blood is called _____.
Bacteremia; septicemia
