Immunology - Midterm ONE

HTHSCI 3I03

What are antibodies made by?

B cells

What are antibodies?

Proteins that bind to specific targets

What is immunology?

A complex web of cells and molecules that work together to regulate almost every bodily function AND protect us from disease.

Why do we understand so little about immunology?

It is a very young field! Started in the 60s.

How long does vaccine development usually take?

From concept to federal approval, often it takes 10-15 years.

What is a vaccine?

a substance that builds preventative immune protection against a specific infection

Two main kinds of vaccines

Inactivated (killed) and Attenuated (weakened)

Inactivated (killed) vaccines

uses a version of a germ that has been killed or rendered inactive with heat, chemicals, or radiation so it cannot cause disease

Attenuated (weakened) vaccines

use a live, but weakened, version of a germ to trigger a strong, long-lasting immune response without causing severe disease

Poliovirus

• Infects nerve cells and causes paralysis

• Eradicated completely thanks to Jonas Salk

Plague of Athens

• Athens was at war with Sparta in 430 BC

• Spartans were better warriors, but Athens had walls (big ones)

• But a plague hit Athens, killis 25-33% of their populations

  • because of this we got the earliest description of immunity - ‘for no one was every attacked for a second time, or not with a fatal result’

Theory for disease before germs

“bad air” caused disease, if you upset god he would send bad air

John Snow

In 1854 he noticed that all cases of cholera in London were centered around one water pump, and suggested that it was the cause. He also suggested to boil the water to get rid of the disease (he was right!)

Louis Pasteur

1860-1864

• really bummed that wine and beer spoils

• did a series of experiments and determined that microorganisms were the cause

• found out that heating liquids and allowing them to cool stopped spoiling by killing the microorganisms (process called pasteurization)

Robert Koch

Used microscopy and developed culture techniques to generate pure cultures of bacteria and took the first ever published pic of Anthrax.

Giving anthrax bacteria to animals causes symptoms of anthrax… GERM THEORY PROVEN!

Koch’s Postulates

1. A specific microorganism is always associated with a given disease.

2. The microorganism can be isolated from the diseased animal and grown in pure culture in the laboratory.

3. The cultured microbe will cause disease when transferred to a healthy animal.

4. The same type of microorganism can be isolated from the newly infected animal.

Louis Pasteur - chickens

Chickens given weakened bacteria, adn became immune! This led to inactivated vaccines. Salk used this in his Polio vaccine.

Paul Ehrlich

1900, horse suffered infection, take the serum from horse blood and give to humans, ???, cure dyptheria!

Paul Ehrlich thought immunity was…

1. Adaptive (responds to infection)

2. Humoral (its in our humours, aka. blood)

He was right, and was talking about (not that he knew) antibodies!

Eli Metchnikoff thought immunity was

Innate (pre-programmed and simple)

Cellular (cells confer protection)

Two major arms of immunity

First vaccine

Reported in 1796, and in widespread use by the 1800s. The smallpox vaccine (we eradicated smallpox)!

Edward Jenner

1796

noticed that local milkmaids who had caught cowpox—a mild, non-fatal disease passed from cows—seemed immune to the devastating smallpox outbreaks sweeping through England

used fluid from cowpox lesions to create immunity against the deadly smallpox virus

put into a little boy, and then gave him smallpox twice (lucky him- the boy was fine)

Variolation

Taking smallpox from one person and giving it to another, hoping for a mild infection.

The practice was brought over to England by Lady Mary Wortley Montagu, who saw the practice while travelling in the Ottoman Empire (Turkey).

Variolation was practiced in China, India, and others in the 16th century.

Who are the immune cells?

White blood cells

Where do immune cells come from?

Bone marrow —> stem cell __> red blood cells, platelets, white blood cells

Differentiation

a cell changing from one type to another

Cell fates

when a cell is choosing how it will differentiate, this is the “end” cell type

What is a cell?

An individual unit of an organism.

Except red blood cells, all cells have a nucleus.

The nucleus contains DNA.

How are immune cells different if they have the same DNA?

When a gene is transcribed and translated into a protein, we say that the gene is expressed.

Gene expression

The “choice” to express different proteins

How do we define cells?

Based on what they make, with a general focus on whats on the surface of the cell (because its easy to study)

How do we denote if a cell expresses a protein?

A plus, and say it is positive for the protein! E.g. Antibody⁺ cell

How do we denote if a cell does NOT expresses a protein?

A minus, and say it is negative for the protein! E.g. Antibody⁻ cell

What does phenotype define?

Function (what the cells make defines what the cells do)

Cell types

(Usually protein) markers that define an entire “lineage” of cells

Cellular program/transcriptional progran

the collection of everything made by the cell

How is immunity achieved?

By cells communicating with one another (exchange of signals)

True or false: Immune cells send and receive signals to non-immune cells in their environment.

TRUE!

How do immune cells communicate?

Molecular interactions that occur through receptors and ligands. “Locks and Keys”.

1. Direct communication between receptors.

2. Indirect communication via soluble mediators.

True or false: Cells can only respond to a ligand if they express the appropriate receptor!

TRUE!

Cognate pair

Matching ligand and receptor.

How do receptor interactions change gene expression?

How do we name receptors?

Cluster of Differentiation/Classification Determinant (CD) and then an official designation using numbers… there are now over 370 known CD molecules

Cytokine

Signalling molecule that makes a cell move or change

Interleukins

Molecules that signal between immune cells. Named with ‘IL’ and a number as well.

What are the major differences between innate and adaptive immunity?

• Innate: immediate, broad, relatively low energy

  • macrophages, neutrophils, etc.

• Adaptive: delayed, highly specific, relatively high energy

  • T cells + B cells

• Adaptive immunity is induced by innate immunity

• Adaptive = potent + systemic

What is the first line of defense?

Intrinsic barriers / epithelial cells

• Skin

• Mucosal barriers

• Prevent pathogens from entering

• Skin is difficult to penetrate and consists largely of dead, low-nutrient cells with antimicrobials.

Think: Wall of the castle.

What are the major entry points for pathogens?

Back:

• Skin → cuts/broken barriers

• Respiratory tract

• Digestive tract

• Urinary/reproductive tract

• Blood

Places where the protective barrier is thinner/wet or can be breached.

What do macrophages do?

• Major sentinel cells

• Detect pathogens

• Eliminate pathogens through phagocytosis

• Phagocytosis = essentially “eating” pathogens

• Part of the innate immune response.

Think: Castle guards waiting at the wall.

If sentinel cells handle most pathogens, why do we need more immune responses?

Every pathogen has mechanisms for evading the immune system.

If pathogens couldn't evade sentinel cells:
→ sentinel cells would usually be enough
→ infections would often go unnoticed.

What are neutrophils and why are they important?

• Part of induced innate immunity

• Recruited when local defenses are overwhelmed

• Have toxic granules

• Very potent at clearing pathogens

• BUT their toxicity can also damage our own tissues.

Think: Nearby guards called in to help.

What fundamental problem must the immune system balance?

Protection ↔ Energy cost

The immune system needs to provide enough protection without continuously maintaining massive numbers of highly active immune cells.

What do dendritic cells do?

1. Sample their surroundings using macropinocytosis

2. Detect/sample antigens

3. Travel from infection site → lymph node

4. Present antigen

5. Activate T cells

6. Initiate the adaptive immune response.

Think: Messenger running from the battlefield to the barracks.

What is antigen presentation?

Dendritic cell + MHC + antigen → T cell activation

The dendritic cell presents pathogen-derived antigen to T cells using MHC.

Why are lymph nodes important for adaptive immunity?

• Most adaptive immune cells rest in lymph nodes

• Lymph nodes are positioned centrally for broad coverage

• Lymphatic vessels sample fluid from tissues and bring information to lymph nodes

• This allows adaptive immune cells to be activated in response to infection.

What happens to adaptive immune cells after an infection?

• Most adaptive immune cells die shortly after infection

• Some survive as memory cells

• Memory cells continue monitoring and remembering the pathogen

• This allows the immune system to respond to future exposure.

Remember: This is the basis for the historian analogy.

What is the long-term antibody response?

• Some B cells differentiate into plasma cells

• Plasma cells produce antibodies

• A small number of plasma cells can produce high antibody titres for decades

• Antibodies equip sentinel cells to better kill/clear pathogens.

Walk through the immune response from pathogen entry → adaptive response (maybe even write it out on paper?)

1. Pathogen enters
↓
2. Intrinsic barriers fail
↓
3. Macrophages / dendritic cells detect pathogen
↓
4. Macrophages + sentinel cells respond
↓
5. Cytokines recruit neutrophils
↓
6. Neutrophils attack pathogen
↓
7. Dendritic cells travel to lymph node
↓
8. Dendritic cells activate T cells
↓
9. T cells activate B cells
↓
10. T cells return to infection site
↓
11. B cells → plasma cells
↓
12. Plasma cells produce antibodies
↓
13. Some adaptive cells become memory cells

What is the Lord of the Rings/castle analogy for the immune system?

Castle	Immune system

Wall	Intrinsic barriers / skin

Castle guards

Sentinel cells / macrophages

Nearby guards

Recruited innate immunity / neutrophils

Messenger

Dendritic cells

Barracks

Lymph nodes

Army	Adaptive immunity / T & B cells

Why is skin an inhospitable environment?

• No receptors for attachment.

• Very low water content.

• Dead cells do not allow viral replication

Mucous membranes

Interface with the external environment

• Ocular mucosa

• Gastrointestinal mucosa

• Respiratory mucus

• Urogenital mucosa

Mucus

• Acts as a lubricant

• Traps pathogens

• Keeps pathogens away from epithelial cells

• Provides a niche for commensal microbes

Our intrinsic barriers

Microbiological Barrier

Our microbiome, the “healthy” bacteria that coat most of our surfaces

How does the microbiome protect us?

1. Competition

Our commensals have evolved

to live in the environment of the

tissue. Pathogens struggle to

compete to live in the pH of our

tissues using the food sources

we create.

2. Crowding

They cover almost every inch,

leaving very little space for

pathogens to find a niche!

3. Antimicrobials (Peptides, enzymes, fatty acids)

Bacteria fight each other using

proteins that they evolved to be

competitive. These kill pathogens

while sparing commensals.

How is our relationship with microbes symbiotic?

We give them a home and they digest food we cannot, provide immune defence, create substances that regulate out mood and other functions.

Dysbiosis

improper composition of bacteria or improper diversity, can predispose to infection

What is dybiosis associated with

IBD, IBS, Obesity, Diabetes, Autoimmunity, Cardiovascular Disease, Cancer,

Allergy, Asthma, Mood Disorders, Pregnancy Complications and many many

more

What is the primary overall objective of the immune system?

Homeostasis (balancing external pressures to keep the inside separate from the outside).

Name examples of external pressures that force our body systems to change.

Infection, heat, cold, hunger, toxins, mental stress/studying

How is the mouth (buccal mucosa) structurally adapted to its barrier function?

It features a stratified epithelium (resembling skin) designed to withstand mechanical abrasion during eating.

How is the small intestinal mucosa structurally adapted to its function?

It possesses only a single layer of epithelial cells to maximize nutrient absorption while remaining joined by tight junctions

How is the lung alveolar epithelium specialized for its function?

It consists of a single, extremely thin layer of specialized epithelial cells (Type I and Type II pneumocytes) to maximize gas exchange

What functions does mucosal mucus provide in defense?

It acts as a mechanical lubricant, traps pathogens, physically separates microbes from epithelial surfaces, and provides an ecological niche for commensal flora

What is the defense role of tight junctions between epithelial cells?

They seal intercellular spaces to prevent paracellular entry and migration of pathogens into underlying tissues

How do desquamation and epithelial shedding protect the skin and gut?

By continuously sloughing off attached and infected cells:

• Skin: $\sim1000\text{ cells/cm}^2/\text{hour}$ ($<span style="line-height: 1.15;">$\sim 5 \times 10^8\text{ cells/day}$</span>) from the 15–20 cell layers of the stratum corneum.</p></li><li><p><strong>Intestine:</strong>$\sim 10\text{--}100\text{ billion cells/day}$$ shed from villus tips as enterocytes migrate from crypt stem cells.

What role do fluid and air flow play in physical defense?

Air flow: Dislodges microbes from the skin surface.

Peristalsis: Drives contents through the gut to prevent adherence and expels them via feces.

Tears / lacrimal flow: Flushes microbes away from the ocular surface into tear ducts and the nasal cavity.

How do active expulsion reflexes protect the respiratory and digestive tracts?

Sneezing & Coughing: Rapidly clear irritants, toxins, and microbes out of the airway.

Vomiting (emesis): Forcefully ejects ingested pathogens and toxins from the stomach.

How does the mucociliary escalator function in the airway?

Coordinated ciliary beating sweeps pathogen-laden mucus upward from the lower airways (or down from nasal passages) into the pharynx, where it is swallowed and degraded by gastric acid

What are the four general mechanisms by which chemical barriers protect us?

1. Direct membrane disruption and killing

2. Growth and metabolic inhibition

3. Enzymatic destruction/denaturation of proteins and toxins

4. Nurturing and supporting commensal microbiota

What non-immune physiological secretions double as chemical barriers?

Pulmonary Surfactants: Lower surface tension in alveoli; potently disrupt microbial membranes and denature proteins.

Pepsin / Gastric Proteases: Digest dietary protein; enzymatically destroy microbial structural proteins and toxins.

Lysozyme (Tears & Saliva): Cleanses debris and breaks down microbial cell wall/surface components

How do Defensins differ from Cathelicidins in humans?

Defensins: Multiple variants; some are constitutively expressed, while others are induced during inflammation.

Cathelicidins: Only one human variant exists (LL-37), which is constitutively expressed by epithelial cells across all barrier tissues.

What is the step-by-step mechanism of pore formation by antimicrobial peptides?

1. Electrostatic attraction and the transmembrane electric field pull cationic peptides into the negatively charged lipid bilayer.

2. Aggregated peptides insert and form transmural pores.

3. Intracellular contents leak out, destroying membrane polarization and ion gradients (shutting down ATP synthesis), leading to cell lysis.

Aside from membrane lysis, how do antimicrobial peptides (AMPs) neutralize pathogens?

In high concentrations, AMPs disrupt electrostatic charges and folding patterns of bacterial proteins and toxins, denaturing them in a manner analogous to acidic pH.

What are the three primary mechanisms by which commensal bacteria protect against colonization?

Competition: Better adapted to consume available nutrients and thrive at local tissue pH.

Crowding: Cover mucosal niches completely, leaving no adherence space.

Antimicrobial production: Produce bacteriocins, fatty acids, and enzymes that selectively kill competing pathogens.

hat mutual benefits define our symbiotic relationship with commensal bacteria?

Host provides sheltered niches and food; commensals digest indigestible fibers, bolster immune defense, and generate metabolic byproducts/neurotransmitters that regulate host physiology and mood.

How does microbial diversity in the vaginal tract uniquely compare to other mucosal sites?

Most mucosal tissues (oral cavity, gut, skin) thrive on high species diversity, whereas the vaginal tract is dominated almost entirely by a single genus: Lactobacillus.

What is microbial dysbiosis, and what health conditions is it correlated with?

An improper composition or loss of microbial diversity that compromises barrier integrity. It correlates with IBD, IBS, obesity, diabetes, cardiovascular disease, autoimmunity, mood disorders, and cancer (though whether it is causative or symptomatic remains under study).

How do commensal bacteria survive chemical barriers that destroy pathogens?

They have co-evolved specific structural modifications in their membranes and cell walls to resist local enzymes, surfactants, and AMPs, and are metabolically adapted to low pH and fatty acid consumption.

How does Vibrio cholerae breach mucosal barriers?

Secretes mucinase to degrade host mucin polymers, allowing it to swim through the mucus layer instead of becoming trapped.

How does Helicobacter pylori survive the stomach's chemical barrier?

Produces urease to generate basic ammonia, which neutralizes gastric hydrochloric acid in its immediate microenvironment.

How does Pseudomonas aeruginosa neutralize host antimicrobial peptides?

Secretes an elastase enzyme that enzymatically degrades the host cathelicidin peptide LL-37.

How does Shigella flexneri circumvent mechanical epithelial barriers?

Directly targets and disrupts epithelial tight junctions, increasing paracellular permeability to slip past the cell layer.

How does Bordetella pertussis disable respiratory clearance?

Releases a tracheal cytotoxin that paralyzes and destroys ciliated epithelial cells, shutting down the mucociliary escalator.

Where does the complement system sit within the broader immune system?

It is the humoral branch of the innate immune system (evolutionarily conserved, hard-wired, and non-cellular).

Where are complement proteins synthesized, and how do they reach peripheral barriers?

Synthesized constitutively by the liver, secreted continuously into the blood circulation, and distributed from plasma into tissues.

What is a zymogen, and how does C3 exemplify this?

An inactive precursor protein requiring enzymatic cleavage for activation. Native C3 is inert until cleaved into active fragments: C3a and C3b.

What is a complement "convertase"?

An active multi-protein complement complex (such as C4b2a) that acts as an enzyme to cleave downstream complement factors (such as converting C3 into C3a and C3b).