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1021 Lecture Question bank

Cells, Tissues And Organisms (Monash University)

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1021 Lecture Question bank

Lecture 23: Salt & Water balance
What process related to amino acids releases energy?

Deamination of amino acids (breaking amino acids down into their amino groups, water, and carbon
dioxide) releases energy

What is the function of water in plasma?

It’s a solvent for carrying other substances

Describe diffusion and what it depends on.

 The movement of solutes from regions with higher solute concentration into regions with
lower solute concentration.
 Net diffusion ceases when an equilibrium concentration is reached throughout
 Diffusion of a molecule depends on its own concentration and the osmotic pressure

What is osmosis

The movement of water molecules from regions with higher water concentration into regions with
lower water concentration, through a selectively permeable membrane.

What is important about selectively permeable membranes?

They allow water to cross but not other things (e.g. solutes)

Describe the term osmolarity

 Sum of osmotically active particles in solution

 Water moves from hypo-osmotic to hyper-osmotic

Describe what happens to cells under different concentrations of water

 Hypotonic solution: E.g. cells in fresh water (<200 mOsm/L), have lots of water coming into
them. They become lysed.
 Isotonic solution: E.g. cells in human blood or saline solution (±300 mOsm/L), are normal as
there is no net movement of water.
 Hyper-osmotic environment: E.g. cells in sea water (±1000 mOsm/L), have lots of water
leaving them and become shrivelled.

What do countercurrent and concurrent exchange systems achieve?

A countercurrent system is where a substance is carried in two opposing directions within proximity
to each other. A countercurrent system can recover much more (a pressure up to 135), while the
concurrent eventually leads to an equilibrium which only recovers a partial pressure of 75.

What is osmoregulation and why is it important?

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 Osmoregulation is controlling the movement of solutes between internal fluid and

environment.
 It is important to maintain water-solute balance that is suitable for biochemistry.
 Metabolic wastes may be harmful, so it’s important that they are removed by
osmoregulation.

What is an osmoconformer and how does it behave?

 Does not adjust internal concentration.

 E.g. the spider crab, because its internal temperature change is exactly proportional with the
salt concentration of seawater.

What is an osmoregulator and how does it behave?

 Uses energy to adjust internal concentration

 E.g. the shore crab allows itself to be an osmoconformer at higher salt concentration (500
mM and higher), but at lower concentrations, it tries to keep its osmoregularity up, and is
regulating against a declining concentration of seawater.

What are nitrogenous wastes and how are they formed?

 Nitrogenous wastes are the result of the breakdown of nitrogen-containing macromolecules

(i.e. proteins into amino acids and nucleic acids into nitrogenous bases).
 This occurs through the process of deamination where the amino groups are excreted as
ammonia in aquatic animals, urea in mammals, or uric acid in birds and other
reptiles/insects.

Give more detail on the nitrogenous waste: ammonia

 NH3, NH4+
 Rapid diffusion
 Fish produce ammonia because it’s highly soluble in water, and they don’t store it because
it’s highly toxic.

Give more detail on the nitrogenous waste: urea

 Soluble in water
 Low toxicity
 Can be concentrated
 Metabolically expensive
 CO2 + NH3 + 3ATP + H2O  Urea

Give more detail on the nitrogenous waste: uric acid

 Insoluble in water
 Excreted as paste
 Relatively non-toxic
 Good water efficiency
 Most metabolically expensive to produce
 In birds and reptiles, concentration of uric acid occurs entirely in the cloaca
 Uric acid is found in egg-laying animals as it is easily excreted.
 Mammals also produce uric acid, but most don’t convert to dry waste in faeces.
 In mammals, uric acid is usually converted to allantoin

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 Excreted in urine
 Monkeys & apes (incl. humans) can’t convert uric acid to allantoin
 Primates excrete uric acid in urine
 Gout: is a painful swelling of joints caused by uric acid crystals
 Some desert dwelling mammals do excrete dry uric acid in faeces (instead of converting it to
allantoin), like the kangaroo rat.

How do invertebrates osmoregulate?

 Most invertebrates are osmoconformers

 But they aren’t ionoconformers. I.e., although they allow the total sum of osmotically active
particles in their body to match the total sum of osmotically active particles in the
environment, they don’t have the same particles.

How do marine vertebrates osmoregulate?

 Most are osmoregulators and ionoregulators.

 Tend to lose water and gain salt by osmosis
 Seawater Na+ 450 mmol/L
 Body Na+ 150-250 mmol/L
 Marine vertebrates tend to gain water and salt from food and by drinking seawater. They
then excrete salt from their gills. Osmotic water loss through their gills and other parts of
their body surface occurs. Excretion of excess ions and small amounts of water in scanty
urine from kidneys.
 Seawater is hyperosmotic to fish, and the fish is hypo-osmotic to the seawater.
 Can’t produce concentrated urine
 Chloride cells on gills.
 Elasmobranchs unusual because they’re osmoconformers (have many gills)

Describe freshwater osmoregulation

 All organisms in freshwater environments are osmoregulators, because the solute

concentration of the water is so low that if any osmoconformers were present, they’d
essentially have no internal solute concentration, which would kill them.
 Due to the low environmental osmolarity, there is a tendency to gain water and lose salts.
 Reducing permeability helps
 Active transport required
 Usually respiratory surfaces uptake ions.
 In freshwater, marine vertebrates’ uptake some ions in food, and uptake salt by gills.
Osmotic water gain through gills and other parts of body surface occurs. Large amounts of
water in dilute urine is excreted from kidneys.

Describe the mechanism of Elasmobranchs

 Elasmobranchs are osmoconformers

 They keep urea in tissues
 ±iso-osmotic

Detail how air breathing marine vertebrates osmoregulate

 Reptiles, birds, mammals have body osmolarity of about 400 mmol/L

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 Can be considered terrestrial in water balance

 Mammals use kidney to excrete salt
 Reptiles, birds use salt gland that produce very salty secretions, as their kidneys aren’t
efficient.
 Species with salt glands use a countercurrent system to control the solute concentration of
their blood.

Describe the mechanism of tubular excretory systems

 Filtrate can be produced and concentrated under high

pressure (ultra-filtration). Water and solutes can enter across
a selectively permeable membrane, while cells and proteins
can’t (they are retained in the blood)
 Selective permeability
 Filtrate is modified by secreting or reabsorbing water and
ions.
 Passive and active transport is used to concentrate filtrate.
 Excretion results in the filtrate leaving the system.

Give the main features of the kidney

 Blood transported via renal artery and vein

 Lie along vertebral column
 Highly vascularised (20-25% of blood flow)
 1000-2000L blood/day
 99% of water retained
 From image on the right, the cortex is where the
glomeruli are found, the medulla are where the loops are
found.
 Juxtamedullary nephrons set up concentration gradient
because they go down into the renal medulla.

Describe the process of excreting waste in humans

 Urinary excretion = Filtration – reabsorption + secretion

 Out of the 180L of filtrate, water, sugars, amino acids and
vitamins are reclaimed, producing 1.5L of urine.
 Refer to diagram on next page.

The vasa recta which surrounds the loop

of henle and moves in the opposite
direction to it, creating a countercurrent
exchange system. The loop of henle sets
up the concentration gradient of urine,
while the collecting duct increases the
concentration of the urine.

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How does water move out of the tubules into blood?

Aquaporin allows water to flow into the cells. Aquaporins are moved to storage vesicles when
inactive.

How is urine concentration regulated?

 The stimulus is the increase in blood osmolarity (e.g. sweating profusely).

 Signals are sent to osmoreceptors in the hypothalamus which triggers the release of ADH
from the pituitary gland.
 This can lead to increased permeability of the collecting duct, allowing H2O reabsorption,
preventing further osmolarity increase.
 Otherwise, it can lead to feelings of thirst, which leads to use quenching our thirst, reducing
the blood osmolarity to a set point.
 Both these consequences yield homeostasis, a blood osmolarity of 300 mOsm/L.

Lecture 24: Cells of the immune system

What is an immune system?

A mechanism that has evolved to protect us from being overrun by microbial pathogens.

Give example of modern diseases

 Tumour surveillance
 Autoimmune diseases
 Tissue transplantation
 Allergies

Give examples of organisms with aspects of immunity

 Plants
 Insects
 Marine sponges
 Mammals

Why do bacteria have an immune system?

Because viruses called bacteriophage, invade bacteria, causing them to develop a memory as to
what has invaded them before, allowing them to chop up the virus if it ever reinvades.

Name a recently discovered cure for cancer.

Checkpoint inhibitors.

Name the two levels of defence an immune system has

 Innate Immunity
 Adaptive immunity

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Explain innate immunity in more detail

 Comprised of external defences (skin, lysozyme in tears, mucous)

 Internal defences: phagocytic cells: neutrophils, antimicrobial proteins, inflammatory
response, natural killer cells
 Inbuilt and do not develop/mature with exposure (i.e., because it’s innate, we inherit it from
our ancestors)
 Rapid responses to a broad range of microbes.
 Early response to invasion (minutes to hours)
 Have no memory in comparison to adaptive immunity
 Uses complement as blood component to destroy pathogen
 Uses myeloid cells such as macrophage, neutrophils, basophils as cellular component to
destroy.

Explain adaptive/ acquired immunity in more detail

 Matures only after exposure to pathogens

 Immunological memory:
o Specificity
o Memory
 Humoral response (antibodies)
 Cell-mediated response (cytotoxic lymphocytes)
 Primary immune response takes 10-14 days to mount, but secondary immune response is
faster.
 Adaptive immunity drives secondary immune response.

Order potential enemies of our immune system from the smallest to the largest

Viruses, bacteria, fungi, parasitic worms

What is the immune system’s response when we cut ourselves?

Neutrophils (the most common WBC) comes in and gobbles up any pathogen that got through the
cut. Sensors on the neutrophil tell it what it gobbled up, and this information is transferred through
the immune system.

What criteria do organisms have to meet to be considered the “enemy” of our immune system?

 Transplant rejections: blood, tissues

 If it’s different, it’s a potential threat
 Microbial pathogens
 Sometimes, even familiar components are mistaken as foreign:
o Autoimmunity: Immune response against our own tissues
 Diabetes: pancreas
 Rheumatoid arthritis: joints
 Multiple sclerosis: central nervous system

What past diseases/current diseases has the immune system protected/is protecting us from?

 Cholera
 Diphtheria
 Small pox
 Tetanus

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 Typhoid
 Cardiovascular disease
 Cancer

What are examples of common infectious diseases that have reduced tremendously?

Diphtheria, measles, mumps, pertussis, polio, rubella, tetanus, Hepatitis B

What has decreased the prevalence of these diseases?

 Better hygiene and understanding of pathogen spread

 Vaccinations
o Act of priming our immune system for a specific enemy
o Achieved by presenting the attentuated pathogen in a form that can stimulate an
immune response but not cause severe disease.
o Extremely specific, making you ready for a known enemy.

Name a disease that was eradicated by vaccinations

Small pox.

How was the small pox vaccine discovered?

Edward Jenner observed a milkmaid with the infection on her hands from milking a cow was
resistant to smallpox.

Lecture 25: Structure of the immune

system
What can the broad category of immunity be broken down into?

 Natural
 Innate
 Adaptive

Give examples of exterior defences

 Lysozyme in tears
 Commensals (a biological interaction in which members of one species gain benefits while
those of the other species neither benefit nor are harmed)
 Skin: physical barrier fatty acid commensals
 Bronchi: mucus, cilia
 Gut: acid causing rapid pH change

Outline the inflammatory response

1. E.g. a pin penetrates our skin. Chemical signals released by activated macrophages and mast
cells at the injury site cause nearby capillaries to widen and become more permeable.
2. Fluid, antimicrobial proteins, and clotting elements move from the blood to the site. Clotting
begins.

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3. Chemokines released by various kinds of cells attract more phagocytic cells from the blood
to the injury site.
4. Neutrophils and macrophages phagocytose pathogens and cell debris at the site, and the
tissue heals.

Where do all stem cells in the immune system originate? Describe the nature of this precursor

The haematopoietic stem cell, found is in the bone marrow. HSC’s continuously replicate and retain
the capacity to differentiate into other cells of the immune system (hematopoiesis).

What are the results of the bone being immunologically privileged?

If an infection occurs in the bone, due to it housing stem cells, it has evolved to prevent immune
cells from being launched within it. Hence, infections within the bone can’t be combatted.

Give an overview of all the immune cells found in the immune system

 NLMEB: “Never Let Monkeys Eat

Bananas”: Neutrophils,
Lymphocytes, Monocytes,
Eosinophils, Basophils”
 Eosinophils = “pink ladies” (apple
brand) because they stain pink,
and like ingesting worms.
 B lymphocyte each have a specific
receptor (y shaped) that once
activated, leaves the membrane
and is secreted as an antibody.
 T lymphocytes have unique t cell
receptors which are never
secreted (remain membrane-
bound).
o T cell receptor consists of an alpha and beta chain
o They can only recognize peptides of pathogens when presented in the antigen’s
groove of mhc. Otherwise, unlike B lymphocytes, they can’t recognize the native
conformation of proteins on bacterial or viral surfaces.
 Natural Killer Cells are important in getting rid of cancers, and are part of the innate immune
system.
 All WBCs in the innate immune system are granulocytes.

What are the important components in innate immunity?

 Phagocytes:
o Macrophages
o Neutrophils
o Dendritic cells
 Complement system: promotes identification of pathogens

Give a brief overview of how adaptive immunity is switched on.

 Adaptive immunity is switched on in the draining lymph node, not in tissues.

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 If dendritic cells present the right receptor, they can activate the t and b cells passing by in
the lymph node, thereby, switching on the adaptive immune system.

How is infection in the blood looked after?

By the spleen.

Give an overview of phagocytes found in the immune system.

 Macrophage: a mononuclear phagocyte

o Mature from blood monocytes
o Numerous found in many tissues: CT, gut, lungs, liver, spleen
o First line of defence, done by antigen presentation
 Granulocytes:
o Comprised of neutrophils, basophils, eosinophils
o Important in allergic reactions
o Short lived
o Abundant in blood
o Not found in tissues till recruited.

Outline the activation and response of phagocytes

 Activation through cell surface receptors (e.g. toll like receptors) which recognize bacteria
such as carbohydrates (sugars), LPS (lipopolysaccharides) gram -ive bacteria, bacterial
proteins. It can also be activated by blood born complement components.
 Responses:
o Phagocytosis: attach to their prey via surface receptors, and engulf them forming a
vacuole that fuses with a lysosome.
o Releasing mediators which cause injury to the pathogen and recruit other cells to
help clear the pathogen.

Outline the role of blood born complement in immune defence

 The complement system consists of proteins that interact with each other to enhance the
ability of antibodies and phagocytic cells to clear microbes and damaged cells from an
organism, promote inflammation, and attack the pathogen’s cell wall.

What is the size comparison of pathogens to immune cells?

Inflammatory cells can be much smaller than the invading pathogen (e.g. schistosome larva are
huge). However, the number of immune cells incorporated to terminate the pathogen is immense.

What are key characteristics of cells of the adaptive immune system?

 Develops over time, unlike the innate immune system whose activation is immediate
 Can be initiated in response to both microbial and non-microbial antigens (anything that’s
foreign)
 Antigen specific lymphocytes are identified and expanded via clonal selection, producing an
army of effector cells to eliminate target.
 They can develop a wide range of potential responses to combat foreign microbes.
 These give rise to memory cells

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What are the two main arms of the adaptive immune

system?

 B cells
o B cell receptor
o Activated B cell produces antibodies
(immunoglobulins): blood component.
These bind free antigens by “seeing shape”.
(soluble arm)
o Produced in the bone marrow
 T cells
o T cell receptor
o Uses lymphocytes as cellular component.
(cellular arm)
o Sees peptides displayed by the antigen in
MHC groove.
 Dendritic cells (part of the innate immune system)
are needed to activate the adaptive immune system.

What are the different ways in which we can visualize cells of the immune system?

 Blood smear
 Flow cytometry

What are the primary lymphoid organs

Bone marrow:

o All immune cells originate from HSCs produced in the bone marrow
o Some mature cells types are also produced in the bone marrow
o Neutrophils, B lymphocytes
 Thymus:
o T-lymphocytes (some lymphocytes can migrate to the thymus where they mature
into T cells)

What makes the adaptive immune system more specialised than the innate immune system?

 The presence of specific receptors:

o T cell receptor: TCR (cd8)
o B cell receptor: BCR (cd19)

Explain the clonal selection of B cells:

 Generates a clone of short-lived activated effector cells, and a clone of long-lived memory
cells.

This occurs in the following manner:

1. Antigen molecules bind to antigen receptors on only one of the many B cells present
2. The selected B cell proliferates, forming a clone of identical cells bearing receptors for the
antigen.

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3. Some proliferating cells develop into short-lived plasma cells that secrete antibodies specific
for the antigen.
4. Some proliferating cells develop into long-lived memory cells that can rapidly respond upon
subsequent exposure to the same antigen.

What does antigen receptor diversity mean?

 The ability the adaptive immune system to generate enough different receptors to recognize
any pathogen.

How many different receptors do we have?

 B cells: approx. 1014 different receptors

 T cells: approx. 1018 different receptors

Go into more detail about B cell receptors.

 B cell receptors are immunoglobins

or antibodies
 Made up of 4 protein chains (2 heavy
and 2 light chains)
 Surface receptors are secreted from activated B cells
(AKA plasma cell)
 2 binding sites per molecule
 Each has single specificity

Go into more detail about T cell receptors

 Made up of 2 chains: alpha and beta.

Only found as surface molecules, not
secreted.
 Recognises peptides presented by
MHC groove of APCs.
 Each cell has single specificity.
 Activated CD4 T cells help other T and B cells to become
activated.

*****EXTRA INFORMATION*****

Give an entire run down on how our immune system responds to

a foreign microbe.

E.g. Professor Slattery’s epithelial cells were infected with herpes.

 In all nucleated cells (incl epithelial cells), proteasomes chop proteins into peptides and load
them into the ER to be inserted into the groove of the mhc class 1 which goes to the surface
of the epithelium.
 Slattery’s epithelial lining will be made up of her own proteins, and the viral (herpes)
proteins in the cytosol.
 The adaptive immune system can’t do anything at this stage, as it can only be activated in
the draining lymph node.

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 Once her epithelial cells start exploding and forming blisters, macrophages (or other
phagocytic cells that are part of the innate immune system, e.g. dendritic cells, neutrophils)
will come to the site to clean it up.
 The macrophages will give some antigen (made up of Robyn’s and her grandma’s herpes
proteins) to a dendritic cell that will travel to the draining lymph node.
 The dendritic cell will then also put some of that antigen into its mhc class 1 and 2 (only
specialised antigen presenting cells have mhc class 1 and 2).
 Upon filling both mhc grooves with the virus, the dendritic cell becomes lit up.
 The dendritic cell is now travelling in the draining lymph node. T cells with the right receptor
for herpes comes past the dendritic cell and gets signal 1.
o Signal 1: It recognises the MHC and peptide. If the t cell is a cd4 t cell, it’s a helper t
cell and only recognizes peptides in the groove of mhc class 2. If the t cell is a cd8 t
cell, it’s a cytotoxic t cell and only recognises peptides in the groove of mhc class 1.
o Signal 2: The dendritic cell grabs a t cell with a cd28 receptor and they “shake
hands”.
o Signal 3: The dendritic cell releases a cytokine that tells the t cell what it needs to do.
The cd4 t cell activates the transcription of these cytokines. 1The cd4 t cell is the
orchestrator of the rest of the immune response. It can help the cd8 t cell and b cells
to become activated. The cytotoxic t cell (cd8) also needs activation from the cd4 t
cell. Once activated, cd8 t cells are lethal and will kill off viruses.
 The dendritic cell can hold small bits of the virus in a vesicle and spit it out into a b cell which
can use it to make memory cells.

Lecture 26: Function of the immune

system

Give the generic immune response to pathogen exposure:

1. Exposure to pathogen
2. Innate immunity mobilised- in built and quick (neutrophils and macrophages)
3. Pathogen (antigen) taken up by antigen presenting cells
4. Antigen presented (via mhc groove 2) to antigen-specific T cells (cd4 t cells)
5. Activation of antigen-specific B cells.
6. Adaptive immune cells go and look for the pathogen
7. Pathogen destroyed
8. Pathogen specific “effector” immune cells die of no further use
9. Formation of memory cells

What is an interesting fact about T cells?

Their frequency in circulation is very low. Hence, they have to somehow be found and activated.

Where are immune responses generated?

 In secondary lymphoid organs.

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o The lymphatic system is designed to drain antigens to local draining lymph node,
which gives the antigen and cells involved in initiating the adaptive immune
response a better chance to meet.

Outline the structure of the immune system (the organs in charge of generating an immune
response)

 Lymphoid organs
o Primary lymphoid organs:
 Thymus
 Bone marrow
o Secondary lymphoid organs:
 Peripheral lymph nodes
 Spleen
 Liver
 Skin
 Tonsils

Show how the body is constantly on alert for the need of activating its immune system

 Interstitial fluid which bathes tissues along with the WBCs within it, continually enters the
lymphatic capillaries.
 Fluid inside the lymphatic capillaries called lymph, flows through lymphatic vessels
throughout the body.
 Within the lymph nodes, microbes and foreign particles present in circulating lymph
encounter macrophages, dendritic cells, and lymphocytes which carry out defensive actions.
 Lymphatic vessels return lymph to the blood via two large ducts that drain into the veins
near the shoulders.

How do dendritic cells enter the lymph node? And how does this differ to T cells?

 Antigen presenting cells such as dendritic cells leave the infected tissue and drain into the
nearest lymph node via the afferent lymphatic vessel.
 T cells are not in infected tissue and are not draining into the lymphatic vessels or arriving in
the lymph node that way.

How do lymphocytes (another type of antigen presenting cell) circulate in the lymphatic system?

 Lymphocytes in the blood migrate out of the blood into lymph nodes via postcapillary
venules. Here, they interact with dendritic cells, get the 3 signals, and leave to find the
inflamed tissue.
 Lymphocytes leave the lymph node via the efferent lymphatics and return to the circulation
via the thoracic duct.

Refer to diagram on the right:

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When the dendritic cell presents to the t cell (mostly present in the paracortical area) and activates
it, the b cell (primary lymphoid follicle) gets a signal to make (in yellow) a secondary lymphoid follicle
that over time develops a germinal centre.

Describe the MHC restriction.

 MHC class 1 presents peptides coming from the endogenous compartment (peptides
derived from our own proteins, but they’re also presenting viral peptides.) The only t cell
that can recognize peptides in the groove of mhc class I is a cd8 t cell, making it a mhc
restriction.
 MHC class II present peptides coming from the exogenous environment. MHC class II is only
present in specialised antigen-presenting cells. (Macrophages, neutrophils, dendritic cells)
 The only immune cell able to kill an infected epithelial cell is the cytotoxic T cell (cd8).

Describe how antigen-presenting cells are different to other cells.

 APCs (dendritic cells, macrophages, B cells), have a nucleus and thus express mhc class 1. But
they also express mhc class 2 because they have an important role of gobbling things up and
presenting antigens on their surface.
 Of all APCs, dendritic cells are the only ones that can ingest antigens, present their peptides
in the groove of mhc class 2 but then also cross-present it on the groove of mhc class one.
Thus, they are the only cells that can activate the cd8 t cell.
 Due to the cross-presentation of exogenous antigens, dendritic cells can switch on both cd4
and cd8 t cells.

Describe the interaction of dendritic cells, T cells and B cells

1. After a dendritic cell engulfs and degrades an antigen, it displays bacterial antigen fragments
with a mhc class 2 on its surface. A specific helper T cell (cd4), with the help of its TCS (toll
like receptor), binds to the complex. This promotes secretion of cytokines by the dendritic
cell.
2. Proliferation of the T cell, stimulated by cytokines from both the dendritic cell and the T cell
itself, gives rise to a clone of activated helper T cells, all with receptors for the same MHC
antigen-complex.
3. The cells in this clone secrete other cytokines that help activate B cells and cytotoxic T cells.

Give an outline of T cell mediated immunity

 Effector arm is mediated by CD4 and CD8 T cells.

 Viruses (intracellular) are targeted by cytotoxic CD8 T cells. CD8 T cells kill infections better
because they are restricted to mhc class 1 which presents the peptides that are in the
infected cell.
 Intracellular pathogens such as in macrophages – CD4 T helper cells: They come up to the
infected macrophage and give lots of cytokines, and help the macrophage kill its contents.
CD4 T cells can aid macrophages, because macrophages are APCs, and hence present
antigens in the groove of mhc class 2, which CD4 T cells can attach to.
 Extracellular- humoral (antibody) with CD4 T helper: Extracellular pathogens can’t be
presented on the groove of mhc, as they’re not located within the cell. Hence, antibodies
freely flowing through the blood can recognize them.

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o Antibodies can also bind to pathogens and coat them, so their stalks are projecting
outwards. This allows macrophages with FC receptors (receptors that recognize
stalks of antibodies) to bind to them and kill the bacteria.

Describe key features of antibodies

 Part of the adaptive immune response produced by B lymphocytes.

 Group of heterogenous glycoproteins present in:
o Serum
o Secretory tissue fluids e.g., mucous and milk.
 Bind specifically to antigens.
 Antibodies see shape, and don’t recognize things in the groove of mhc.
 One b cell = one antibody specificity.

Describe the mechanism of the B cell, using the example from the previous lecture

 The b cell receptor recognizes the herpes virus (not the peptides in the groove of mhc, but
the actual shape/outside of the virus).
 The b cell in the lymph node needs to be activated by the cd4 helpter t cell.
 The t cell knows that this b cell needs to be activated because when the b cell recognises the
herpes virus in the draining lymph node, the dendritic cell gives it a small amount of antigen
which the b cell processes and presents on the groove of its mhc class 2.
 The t cell knows it should help the b cell because when receiving signal one, it was exposed
to the peptide in mhc class two by the dendritic cell. This peptide is being displayed in the
mhc class 2 groove of the b cell.
 Upon activation by the cytokines released from the t cells, b cells become an antibody
secreting factory.

Using the diagram below, describe the structure of antibodies

 4 polypeptides: 2 chains, heavy and light. In

any one antibody, heavy chains are identical
and light chains are identical.
 The red antigen recognition area doesn’t
change. It is the amino terminal and is the
antigen binding end.
 The constant region is the carboxyl terminal.
It has effector functions. This is the stalk and
it varies in structures depending on the type
of antibody.

Outline the different antibody isotypes involved

with an immune response

 The B cell first secretes IGM after an infection. As the B cell matures, it can change the
isotype or class of the antibody that it secretes.
o IGM
 A pentameter with low affinity, but it recognizes viruses and can start to kill
them.

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 Good at coating (opsonising) pathogen and stimulating phagocytosis of

coated pathogen.
 Found in serum
o IGA
 Secreted across mucosal surfaces such as gut and breast milk
 Secreted as a dimer
 Found in serum and secretions (specific transport)
o IGG
 Can bind very strongly
 Good at neutralizing toxins.
 Found in serum and other extracellular fluids (lymph), neonate
o IGE
 Stimulates the release of histamines from mast cells.
 Found beneath epithelial surfaces (respiratory, GI, skin)

Name and describe antibody effector functions

 Direct Actions of antibodies

o Binding of antibodies can result in neutralisation of antigen
o High titre (high presence) antibodies can prevent infection of cells by viruses and
bacteria.
 “Targeting mechanisms”
o Antibodies can recruit phagocytic cells to destroy pathogens

How do antibodies protect against toxins?

1. Toxins bind to cellular receptor

2. Endocytosis of toxin: receptor complex
3. Dissociation of toxin to release active chain which poisons cell
4. Antibody protects cell by blocking the binding of the toxin.

How do antibodies protect against viruses?

1. Viruses bind to receptor on cell surface.

2. Receptor-mediated endocytosis of virus
3. Acidification of endosome after endocytosis triggers fusion of virus with cell and entry of
viral DNA.
4. Antibody blocks binding to virus receptor and can also block fusion event.

How does the presentation of a virus by MHC class I lead to cd8 action?

1. Virus infects cell

2. Viral proteins begin to be synthesized in the cytosol
3. Peptide fragments of viral protein are bound by MHC class 1 in the ER.
4. Bound peptides are transported by MHC class 1 to the cell surface
5. The cytotoxic T cell (cd8) that was activated by this combination in the lymph node will
recognize it and kill the infected cell.

How does the Cytotoxic T carry out its mechanism?

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 The cytotoxic cell recognises and binds virus-infected cell

 The cytotoxic cell programs target for death, inducing DNA fragmentation
 The cytotoxic cell migrates to a new target, and target cell dies by apoptosis.
o Apoptosis (programmed cell death) can be carried out in two ways:
 Perforin: forms pores in membrane
 Granzymes: proteases which activate cell death pathway.

Lecture 26: Bacterial structure and

function
What are the different types of microorganisms?

 Bacteria
 Archaea
 Viruses
 Eukarya
o Fungi- Yeast and moulds
o Protists
o Algae

Name the order of commonest cells from largest to smallest

Human egg, most plant and animal cells, nucleus, most bacterial mitochondria, smallest bacteria,
viruses, ribosomes, proteins, lipids

What are the three domains of life?

 Eukarya
o Includes all eukaryotic organisms
o Contains four kingdoms of organisms
 Animalia: multicellular animals
 Plantae: multicellular plants
 Fungi: multicellular fungi and unicellular yeasts
 Protista: unicellular algae and protozoa
 Bacteria
o Includes all bacteria that cause human disease.
 Archaea
o Diverse group of organisms that live under extreme environmental conditions (high
salt/ temperature)

Why are humans great incubators for bacteria?

Because we carry the best nutrients and temperature for organisms to grow on.

What are the three major differences between prokaryotic and eukaryotic cells?

1. Structure of nucleus:
 Eukaryotes
i. True membrane bound nucleus
ii. Several chromosomes

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iii. Diploid (2 copies of each chromosome)

iv. Undergo mitosis/meiosis
 Prokaryotes
i. Prokaryotic nuclear material isn’t surrounded by a membrane
ii. Single circular chromosome
iii. No mitosis or meiosis
2. Intracellular organelles
 Eukaryotes: membrane bound cellular organelles
i. E.g. mitochondria, chloroplasts, golgi apparatus
 Prokaryotes: no membrane bound organelles
i. The cell membrane is the most important structure in the prokaryotic cell.
3. Cell wall structure
 There are many unique compounds in bacterial cell walls:
i. Peptidoglycan
ii. Lipopolysaccharides (in gram negatives)
iii. D-amino acids (only found in bacterial cells)

Name some common features of eukaryotic cells

 Membrane-delimited nuclei
 Membrane bound organelles that perform specific functions
 Intracytoplasmic membrane complex (endomembrane system) that serves as a transport
system
 More structurally complex and larger than bacterial or archael cells
 Eukaryotic cells can be seen under a magnification of 400X while prokaryotes can only be
seen under a magnification of 1000X

Give information of the cell structure of bacteria and archaea

 16 S rRNA show distinct difference in bacteria and Archaea

 Common features to both bacteria and archaea:
o Vary in shape and size (rods, cocci oval)
o Nucleoid material in most is not membrane bound
o Common cell organisation
 No single organism has all the structures at all times
 Same structures in both can differ at a molecular level

Give examples of each shape of bacteria

 Spheres (cocci):
o Streptococcus pneumoniae: present in our upper respiratory tract. If environmental
conditions are good, some can become opportunistic pathogens.
o Staphylococcus aureus: 20-40% of people carry S.aureus as part of their normal
flora. Present in hospitals.
 Rods (bacilli):
o E.coli: carried by every human in our gut
 Spirals:
o Campylobacter jejuni: number one organism responsible for food borne diseases.
 Comma shaped:
o Vibrio cholera: causes cholera

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Describe characteristics of archaea:

 Archaea show characteristics like Eukarya:

o Genes encoding protein: replication, transcription, translation
 They also show similarities to bacteria:
o Genes for metabolism
 Elements that are unique to Archaea:
o Unique rRNA gene structure
o Capable of methanogenesis
 Due to living in extreme environments, they are highly diverse with respect to morphology,
physiology, reproduction, ecology.
 Best known for growth in anaerobic, hypersaline, pH extremes, high-temp habitats.
 Found in marine artic temperature and tropical waters.

What are organisms grown in the body called, and why?

Mesophiles. Because when we isolate a bacterial culture from the body, we incubate it at 37
degrees. This is because we want to cultivate an organism so we mimic the conditions it best grows
in.

Compare all three domains

Name the main features of bacteria.

 Single celled microbes that reproduce by binary fission (splitting in two) although some
reproduce by budding

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 Some have flagella, allowing them to be motile

 Shape:
o Spherical, rod-liked, spiral, filamentous
 All bacteria are observed under 1000x magnification + immersion oil
 Consist of the following structures:
o Cell wall
o Flagella (some)
o Plasma membrane
o Cytoplasm
o Nuclear material
o DNA -chromosomal and plasmid
o Ribosomes
o Spores and endospores (Some)
o Capsule
o Granular structure (some)

How can the cell wall be used to distinguish between bacteria?

 Bacteria either have a cell wall or they don’t.

 Bacteria with cell wall:
o Typical gram positive (referred to as monomers)
o Typical gram negative (have an outer layer separate to the cell wall, referred to as
the second membrane)
o Acid fast bacteria

What is the role of the cell membrane in bacteria?

 Maintains bacterial shape

 Provides structural support due to presence of peptidoglycan
o Prevents bursting or collapsing due to osmotic pressure
 Can contribute to pathogenicity
 Protects the cell from toxic substances

What is peptidoglycan and what is the effect of lysozyme and penicillin on its structure?

 Mesh-like polymer of identical subunits forming long strands

 Polysaccharide bonds in peptidoglycan are hydrolysed by lysozyme.
 Transpeptide bonds in peptidoglycan are prevented from forming by penicillin

Describe the structure of peptidoglycan

 Glycan
o Made up of two alternating sugars:
o N-acetyl glucosamine (NAG)
o N-acetylmuramic acid (NAM)
o Both are similar to glucose
o NAG & NAM are covalently linked in long chains, one alternating with the other.
 Peptido
o Made up of four amino acids (tetrapeptides: L-Alanine, D-glutamic acid, meso-
Diaminopimelic acid, D-Alanine)
o Contains D- and L- amino acids

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 D-amino acids protect against degradation, as our normal peptidases only

break down L-amino acids. This is advantageous for the survival of bacteria.

Describe the nature of a typical gram positive cell wall

 Major part: thick, homogenous sheath of peptidoglycan (20 to 80nm in thickness)

 Contains large amounts of secondary cell polymers including:
o Teichoic acid
o Lipoteichoic acids
o Extend to the surface of the peptidoglycan
o Teichoic acids (amino acids) give gram + cells an overall – charge due to the
phosphodiester bonds between teichoic acid monomers.
o Not found in gram negative bacteria
 80% of the cell wall in a gram positive cell wall is made up of peptidoglycan

Describe the nature of a typical gram negative cell wall and outer membrane

 More complex
 Single thin (1-3 nm) sheet of peptidoglycan (10-20% peptidoglycan)
 Acts as a rigid protective structure
 Have a negative charge due to their outer LPS layer, while the charge in gram positives is due
to their amino acids.
 Its thinness gives the gram negative bacteria:
o Relatively greater flexibility
o But sensitive to lysis
 Well developed periplasmic space surrounds the peptidoglycan
o Space is an important reaction site for the large number of substances that enter the
cell.
 Beyond the periplasmic space, is the LPS (lipopolysaccharide layer) (not found in gram
positive)
 Outer membrane:
o A complex outer membrane containing:
 Protein (e.g. porin proteins)
 Lipoprotein (braun’s lipoprotein)
 Phospholipid
 Lipopolysaccharide (LPSs) in the upper most layer
o Lipid forms 15% of the outer membrane
o The outer membrane is connected to the cell by Braun’s lipoprotein
 Treating gram negatives with penicillin is ineffective because the peptidoglycan layer is very
thin while their outer membrane is more extensive.

Why do gram positives stain purple and gram negatives stain pink?

 Gram positives have a thicker peptidoglycan layer, so retain the crystal violet stain.
 Gram negatives have a thinner PDG layer so they get counter-stained by safranin.

Describe in more detail the lipopolysaccharide (LPS) layer in peptidoglycan

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 The polysaccharide chains extending off the surface function as antigens and receptors
 Extremely important from a medical POV
 Two major parts of the LPS layer:
o Lipid A
 Present in organisms like salmonella. When bacterial cells are ingested and
killed in the gut, the lipid A structure (an endotoxin) is released into the
bloodstream, to cause disease.
o O specific polysaccharide side chain (O antigen). The o side chain is used to classify
microorganisms.

Describe the nature of acid fast bacterial cell wall

 Bulk of cell wall is composed of unique types of lipids.

 Acid-fast bacteria are gram positive
 Contain large amounts of lipid substances- long chains of fatty acids- mycolic acid or cord
factor (60%)
 Thus resist gram staining
 Contributes to the pathogenicity of the group
 This is the basis for the acid fast stain
o Egs: mycobacteria and nocardia
 Used in the diagnosis of tuberculosis (xray is done which shows cavitating lesions in the
lungs) and leprosy
 Ziehl-Neelsen stain or modified Kinyoun’s stain

Describe the nature of cell wall deficient bacteria

 Mycoplasmas are bacteria that naturally lack a cell wall

 The sterols present stabilize the cell membrane, making the cell resistant to lysis.
 Mycoplasmas are extremely tiny pleomorphic cells (cells that alter their shape and size
depending on the environment). (Between 0.1 to 0.5 micrometers in size)
 Varied shapes: filamentous to coccus or donut shaped.
 Mycoplasmas are present in many habitats, including plants, soil, animals
 E.g. mycoplasma pneumoniae adheres to the epithelial cells in the lungs, causing atypical
pneumonia in humans.

Describe capsule composition

 Needs staining to be seen with a light microscope

 May be composed of polysaccharides or polypeptides, or both
 These chemicals are produced within the cell and extruded on the cell’s surface
 The presence of a capsule is a feature of many pathogenic bacteria.
 Polypeptides
o Some members of the genus Bacillus (e.g. bacillus anthracis) have repeating units of
D-glutamic acid, giving them a proteinaceous capsule.

What are the functions of the capsule?

 Physical barrier that protects the cell

o From drying
o Prevent bacteriophages (viruses that target bacterial cells) from attachment and
infection.

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 Mediate attachment to solid surfaces

o S. mutans in the presence of sucrose produces a polysaccharide capsule that helps it
to attach to the dental enamel. Plaque builds up around teeth. The microorganisms
in the plaque use the sugars/nutrients that come in, to produce acid which causes
long term decay
 Helps bacteria avoid phagocytosis
o Chemicals in capsules are similar to those found in the body. Hence, they may not
activate the body’s defence mechanism upon initial infection.
o Prevent bacteria from being recognized and killed by body’s immune system.
 Posses virulence factors
o Capsules of streptococcus pneumoniae and Klebsiella pneumoniae enable these
bacteria to avoid destruction in the respiratory tract and cause pneumoniae.
o Un-encapsulated strains of these bacteria are killed by the body’s defensive cells,
preventing them from causing disease.

Outline the structural features of the cytoplasmic membrane in bacteria (plasma membrane)

 Absolute requirement for all living organisms

 Some bacteria also have internal membranes
 Plasma membrane and everything within is the protoplast
 Membrane is composed of lipids and proteins
o Lipids are structurally asymmetric: amphipathic
o Two ends: polar and non polar.
o Archaeal membranes contain lipids that lack phosphate groups and vary from group
to group.
 The cytoplasmic membrane is generally referred to as the phospholipid bilayer.

Outline key points about the proteins found in the phospholipid bilayer

 Peripheral proteins
o can attach nutrient molecules and bring them into the cell.
o Constitute 20-30% of total membrane proteins

Outline the characteristics of the nucleoid

 Not membrane bound

 Chromosome is longer than the length of the cell

Outline characteristics of plasmids

 Linear, circular, double-stranded DNA molecules capable of independent existence and

replication separate from the chromosome.
 Inherited by progeny (ancestors)

Outline the structure and function of flagella

 Motility enables cell to flee a harmful environment, move towards a favourable environment
 Prokaryotic flagella are made up of three parts:
o Long thin filament
 20nm in diameter, extend out into the cell’s environment
 Made up of many identical globular molecules of protein- flagellin

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 Molecules of flagellin are arranged in chains, forming a helix around the

hollow core
 Filament is non-membrane bound
o Hook
 At the base, the filament inserts into a curved structure
 Composed of different protein subunits
o Basal body
 Anchors the filament and hook to the cell wall by a rod and series of rings
(either two or four)
 Composed of different protein sub units
 Most complex part of the flagellum
 There are no coccus bacteria with flagella, only rod shaped

Outline the structure and function of Fimbriae

 Non-motile extensions present in some prokaryotes

 Sticky proteinaceous bristle-like projections
 A cell could have hundreds of fimbriae present
 Some gram -ive bacteria use fimbriae
o To adhere to one another
o Stick to substances in the environment
 E.g. Fimbriae are important in biofilms by helping bacteria to adhere to the substrate
 Neisseria gonorrhoeae colonise the mucous membrane of the reproductive tract. Neisseria
cells that lack fimbriae are non-pathogenic.

Outline the structure and function of Pili

 Tubules composed of proteins called pilin

 Pili are longer than fimbriae but shorter than flagella
 1-10% of bacteria have them
 Bacteria use pili to move across a substrate or towards another bacterium.
o Bacterium extrudes the pilus
o This attaches to the substrate or another bacterium
o Then the bacteria pulls itself along the pilus towards the attachment point.

Outline the process of binary fission

Outline how the arrangement of cocci determine their

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 When the arrangement of the septate/cocci occurs in planes:

o Chains
o Streptococcus species
 When it occurs in random orientation, before the cells go onto loosely form hexagonal
arrays,
o Grapey like clusters
o Staphylococcus species
 If after the original septate formation, further division occurs at right angles to the previous
one,
o Cuboidal or tetrad formation called sarcinae
o Micrococcus species

What are bacterial endospores and how are they formed?

 Formed when:
o Asymmetrical division occurs
o Nutrients are exhausted
o Conditions become unfavourable for growth
 Resistant, dormant structures associated with survival
 Produced by gram positive and gram negative bacteria
 Microscopic appearance
o Refractile: can be seen in unstained cells
o Resist staining: heating required

What makes an endospore so resistant?

 Calcium dipicolinate
 Small acid-soluble, DNA-binding proteins (SASPs)
 Dehydrated core
 Spore coat
 DNA repair enzymes

Outline the spore structure

How are endospores different from spores in fungal cultures?

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 While endospores as a means of survival, fungal spores are produced because of

sexual/asexual reproduction
 Endospore formation is termed sporulation
 Bacterial cells only give rise to one spore/endospore
 One bacterial endospore germinates to only give rise to one vegetative cell. Thus spores or
bacterial endospores are not reproductive structures.

Outline the interactions between bacteria and the human host

 Balance between pathogen attack and host defence (bacteria doesn’t want to kill its host
because it wants to keep on surviving).
 Normal flora can become pathogenic (opportunistic pathogens)
 Microorganisms in the environment can infect.
 In a healthy human, internal tissues are normally free of microorganisms (e.g. brain, CSF,
kidneys, liver)

Outline the role of normal flora

 Play a critical role in human survival

 Prevent colonization by potential pathogens
 Competition for space and nutrients
 Skin bacteria
o Produce fatty acids
 Gut bacteria
o Ferment unused energy substrates
o Produce bacteriocins and colicins (antibacterial)
o Synthesize and excrete vitamins
o Train the immune system
 Vaginal lactobacilli
o Acidic environment supresses growth of other potential inhabitants

Outline how bacteria can be beneficial

o Metabolise food products

o Provide essential growth factors
o Stimulates the immune response.

What is normal flora and where do they reside?

 Normal flora is the mixture of microbes present on a healthy human

o Resident flora: always present
 Skin
 Mouth
 Respiratory tract
 Gastrointestinal tract
 Genitourinary tract
o Transient flora: not always present
 Acquired rapidly, during and shortly after birth
 Changes continuously throughout life
 Normal flora are considered mutualistic
 They are only considered parasitic when they cause infection

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o Opportunistic pathogens:
 E.coli
 Streptococcus pneumoniae
 Candida albicans

Outline how carriers affect the spread of pathogens

 Some people carry microorganisms that are a potential source of infection for others.
 A carrier:
o Infected individual who isn’t obviously diseased
o Potential sources of infection, although sometimes people can be asymptomatic
carriers
o Acute carrier:
 Incubatory: incubating the pathogen but not yet ill
 Convalescent: recovered but has large numbers of the pathogen

Outline the mutualistic relationship of bacteria residing on the skin

 Commensal (mutualistic) microbes include both resident and transient microbiota

 Mechanically strong barrier
 Inhospitable environment
o Slightly acidic pH
o High concentration of NaCl
o Many ares low in moisture
 Inhibitory substances (e.g. lysozyme, cathelicidins)

Describe the mouth as a bacterial habitat

 Complex bacterial habitat

 500-600 different bacteria
 Saliva and food particles are potential sources of microbial nutrients.
 Saliva is not a good culture medium because it contains antibacterial substances e.g.
lysozyme
 Dental plaque (biofilms)
o Film on surface of teeth
o An environment that allows bacteria to flourish
o Attachment of salivary proteins
o Plaque often depleted of oxygen (hence, anaerobic microenvironment allows
anaerobic bacteria to grow)

Describe the stomach as a bacterial habitat

 Hostile environment for bacteria due to acidic pH=2. Thus, it forms a barrier to entry to the
intestinal tract
 Bile and pancreatic secretions inhibit growth
 Gastric mucosa: acid-tolerant Lactobacilli and Streptococci exist
 Less than 10 viable bacterial cells per ml of gastric fluid
 H.pylori found in half the human population

Describe the small intestine as a bacterial habitat

 Distant from the stomach

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 pH increases, hence bacterial numbers increase

 Duodenum: lightly colonised
 Jejunum: low levels
 Ileum: moderate levels
 Similar to colon microbiota as pH is more alkaline. E.g. many gram positive and negative
bacteria.

Describe the large intestine as a bacterial habitat

 Largest numbers of bacteria, around 400 different species, which comprise up to 30% of
faecal volume
 Oxygen depleted area
o 95-99% anaerobes predominate
o Bacteroides: strict anaerobe
o E.coli: facultative anaerobe
o Other microogranisms present: Candida albicans, protozoans

Lecture 27: How do bacteria cause

disease
What is disease? What are the types?

 An abnormal condition in the cells, tissues, organs of the body that cause symptomatic
alteration in normal bodily functions
 Hereditary disease: Type I diabetes
 Physiological disease: Cardiovascular disease
 Infectious disease: cholera, dysentery, tuberculosis

What is an infection?

 Growth of a microorganism in the body at a site where it isn’t normal present or is only
present in low numbers. If you don’t have cell and tissue damage, you don’t have disease
but you may have an infection.

Outline the different types of bacterial pathogens

 Primary pathogens:
o Bacteria that aren’t part of the normal microbiotia
o Do not require predisposing conditions to cause disease (if they get in, they are
going to cause disease, and it usually only takes a small amount to cause disease).
o E.g. Vibrio cholerae (causes cholera)
 Secondary or opportunistic pathogens
o Bacteria that may be part of the normal microbiota
o Require predisposing conditions such as a wound, altered microbiota, or an altered
immune system (brought on by antibiotics/if someone has an immunodeficiency and
they’re taking chemotherapy and their immune system is altered) to cause disease.

Define the terms pathogen, virulence, pathogenesis, virulence factor

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Pathogen:

 Microorganism with the potential to cause disease

 A species-specific property

Virulence:

 The capacity of an organism to enter a host and cause disease

 Regarded as a strain-specific property

Pathogenesis:

 The process whereby an organism enters the host and causes disease

Virulence factor:

 Factor that is produced by a pathogen and is involved in disease causation

Give examples of host defences:

 Non-specific skin and mucosal secretions

 Non-specific inflammatory responses- innate immunity
 Specific immune responses- acquired immunity

Give examples of pathogen weapons

 Pathogen weapons are virulence factors

 Adhesins that enable bacteria to bind to cell surfaces
 Factors that prevent phagocytosis
 Factors that enable intracellular survival and growth
 Toxins that functionally disrupt or kill host cells.

How do pathogens cause disease?

 Predisposing factors lead to infection by endogenous (agents that are already in our body)
agents.
 Transmission from exogenous sources (something from outside our body) or infected
individuals- epidemiology (the study of diseases and their spread).
 Entry into the human body
 Overcome host defences
 Growth and spread within the body
 Cause cell and tissue damage, which leads to symptoms.
 Spread to other members of the population

How are communicable infectious diseases transmitted?

 Direct
o Horizontal contact: Kissing, sex
o Airborne droplets: sneezing, coughing
o Vertical contact: pregnant mother passing disease onto her fetus.
o Vector: the sperm transferring a disease into the female
 Indirect
o Fecal-oral contamination

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 Contact (formites: objects or materials which are likely to carry infection

such as clothes, utensils, furniture)

Give examples of anatomical barriers to infection

 Lysozyme in tears and other secretions

 Skin (physical barrier) fatty acids, normal flora (interchangeable with microbiota)
 Stomach pH 2
 Normal flora in the bowels
 Flushing of urinary tract
 Mucus, cilia lining trachea
 Removal of particles by rapid passage of air over cilia in nasopharynx

Briefly overview innate and adaptive immune responses

 Innate immune responses:

o Non-specific immunity
o Use of complement system which enhances the ability of antibodies and
macrophages to kill pathogen and breaks down the pathogen membrane.
o Phagocytosis
o Inflammation
 Adaptive or acquired immune responses
o Specific immunity
o Antibodies (humoral arm)
o Cell-mediated immunity (cell-mediated arm)

Why do bacteria like growing in human hosts?

 Human bodies provide:

o Organic nutrients and growth factors
o Constant physical environment
 pH, temperature osmotic pressure
 Different regions/organs differ chemically and physically
o Provide different selective environments where certain species are favoured over
others
 Staphyloccocus aureus on the skin
 Escherichia coli in the GI tract

Outline the bacterial pathogenesis process

1. Exposure to pathogens
2. Adherence to skin of mucosa
3. Penetration or invasion through epithelium
4. Colonization and growth via production of virulence factors
5. Cell and tissue damage via toxicity and invasiveness (further growth)

Describe the mechanism of adhesins as virulence factors

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 Adhesins are proteins or macromolecules on the bacterial cell surface that mediate binding
to receptors on host cells.
 E.g. pili or fibriae
o Rod shaped structures, hollow cylinder ordered helical array of protein subunits
o Sub unit called pilin
o Tip of pillus mediates adhesion

Name a disease that relies on adhesin virulence factors

 Traveller’s Diarrhoea
 Fimbriae are essential for disease
 Bacteria: enterotoxigenic Escherichia coli (entero=intestine)
 CFA I/II= fimbrial colonisation factor antigens.

Give examples of other bacterial virulence factors that enhance immune evasion

 Capsules
o “slime layer” surround bacteria
o Comprised of polysaccharides
o Protect bacteria from complement system (break down of their cell membrane and
attack from antibodies and phagocytes)
o Can also act as adhesins.
 Other factors
o Proteins that block antibody binding
 Protein A from Staphylococcus aureus (gram +)

Describe the mode of action of protein A

 Binds Fc component (the tail region of antibodies that interact

with cell surface receptors and proteins of the complement
system) of antibodies.
 “reverse binding effect”
 Prevents phagocytosis because antibodies don’t opsonize the
pathogen, so doesn’t attract macrophages/neutrophils to site.
 Staph aureus binds antibodies so that the variable region that
isn’t recognized by the complement system is facing upwards so the bacterial cell is hidden
from the immune and complement system.

Outline the phagocytic process

 Performed by dedicated phagocytic cells: macrophages and neutrophils

 Antibodies and complement opsonize the bacteria (make it more obvious to phagocytes)
 Phagocytes extend their membrane around the pathogen and ingest it by endocytosis. The
enclosed pathogen is now a phagosome.
 The phagocytic cell with the phagosome fuses with the lysosome.
 The pathogen is killed by oxygen dependent and independent pathways.
o E.g. staphlycoccus aureus is killed by haemolysin
o Salmonella Typhimurium is killed by apoptosis

What are bacterial defences against phagocytosis?

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 Prevent complement activation

 Prevent antibody binding
 Coat themselves with host protein
o E.g. protein A by S aureus
o Produce a protective capsule
 Survive in the phagocyte by preventing phagosome-lysosome fusion
o Pathogen prevents maturation of phagolysosome
o Pathogen avoids exposure to toxic lysosomal components
o Phagosome fails to acidify
 Survive in the phagocyte by producing antioxidants and/or preventing the respiratory burst
o Pathogen may produce catalase (breaks down H2O2)
o Pathogen prevents activation of respiratory burst
 E.g. salmonella typhimurium prevents assembly of NADPH oxidase
 Survive in the phagocyte by escaping to the cytoplasm
o Pathogen avoids toxic lysosomal contents
 E.g. shigella spp.

Name the mechanism of invasins as virulence factors.

 Invasins enable bacterial cells to invade host cells

 This enables bacteria to avoid phagocytic cells, immune cells, and antibodies
 Cells provide a rich source of nutrients
 Enables dissemination to deeper tissues

Give examples of the different intracellular niches bacteria select.

 Intralysosomal: low pH hydrolytic

 Intravacuolar: neutral pH
 Cytosolic

Name the mechanism of exotoxins as virulence factors

 Extoxins are protein toxins (e.g. cytotoxins) that are generally secreted which kill the host’s
cells.

Name the mechanism of endotoxins as virulence factors

 Lipopolysaccharide (LPS) component of outer membrane (OM) of gram negative bacteria.

o Dead gram -ive bacteria release endotoxin (lipid A) which activates the complement
cascade, stimulates cytokine release and thus causes fever, inflammation, shock,
blood coagulation.
 Not present in gram positive bacteria due to the lack of outer membrane and LPS

Lecture 28: Viruses and disease?

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What are generic structural features of viruses?

 Genomes
o DNA or RNA, single, or double-stranded
 Protein coat (capsid)
o Icosahedral (20 faces), helical, complex
o Single, double layers
 Envelope
o Membrane envelope may or may not be present

What are viruses?

 Packaged sets of genes in transit between host cells

 Unable to derive metabolic energy or replicate by themselves
 Hence, not actually living
 Take over metabolism of host cell
 Reproduce through self-assembly of virus-encoded components inside host cells.

How do viral cells replicate?

1. Attachment to specific receptors on the host cell

2. Capsid breaks down so genomic material and capsid proteins is in the cell
3. Host enzymes replicate the viral genome
4. Host enzymes transcribe viral genome into viral mRNA which host ribosomes use to make
more capsid proteins
5. Viral genomes and capsid proteins self-assemble into new virus particles (virions) which exit
the cell.

Give examples of the host range of different strains of viruses. What is host range determined by?

 Viruses can infect any type of cell: archaeal, eubacterial, eukaryotic

 Some viruses have a narrow host range:
o Bacteriophages (viruses that infect and replicate within bacteria and archaea): can
treat microbial infections.
o HIV, HBV (Hep B): only infect human hosts
 Some viruses have a wide host range:
o Influenza virus
o Rabies virus
o Plant viruses able to replicate in insects
 Host range is determined by
o Type of receptor on host cell surface (specificity of receptor)
o Replication factors

How are viruses classified?

 Based on their genome

o Viral genomes may be RNA or DNA and can be single or double stranded.

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Describe genome sense

 Single stranded viral RNA or DNA can be (+) or (-) sense

 The (+) sense strand is the coding strand, while the (-) sense strand is the template strand.
 The template strand (the negative sense strand) is what the mRNA is synthesized from
 The (-) sense strand is complementary to the (+) sense strand
 All mRNA are (+) sense and are recognized by ribosomes that translate them into viral
proteins

Explain the Baltimore classification system.

 Seven classes of viruses that are based on the genome of viruses.

o DNA or RNA
o Single or double stranded
o Single stranded?
 (+) or (-) sense
 Class I: dsDNA  Small pox
 Class II: ssDNA  Adeno-associated virus
 Class III: dsRNA Rotavirus
 Class IV: +ssRNA  Poliovirus
 Class V: -ssRNAInfluenza virus
 Class VI: ssRNA  HIV
 Class VII: dsDNA  Hep B

Explain retrovirus replication (e.g. HIV)

 Needs a viral enzyme: reverse transcriptase

 Reverse transcription RNA is converted to DNA without multiplying
genome number. This RNA-DNA hybrid is encoded by the virus, not
the host cell.
 Viral-derived DNA is integrated into host’s cellular genome
(collectively called the provirus).
 Two outcomes can result from the provirus:
o The proviral DNA can be converted to mRNA that can be
translated into viral proteins
o The proviral DNA can be transcribed to RNA so that even
more viruses can be formed.

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What is the temperate bacteriophage life cycle?

 The lytic cycle involves the chromosome being broken up, and being used to form an
assembly of new viral particles in the bacterial cell.

Give general facts about the Influenza Virus

 Baltimore class V, (-) sense ssRNA

 Highly transmissible, acute airborne viral infection
 Localised epidemics, global pandemics

Describe the molecular virology of Influenza A virus

 Pleomorphic, spherical, enveloped virions

 80-120 nm in diameter
 Subtypes of Influenza A virus are defined by their envelope proteins:
o Haemagglutinin (HA;H) and Neuraminidase (NA; N)
 Eg. H1N1; H3N2; H5N1
o Virions contain 8 segments of the ssRNA genome
o Encode 11 proteins

How do Influenza A viruses replicate?

1. Attachment via haemagglutinin to surface sialic acid receptors

2-3. Entry into the cell within endosomes and release of genome

4. Synthesis of +ssRNA from genomic ssRNA

5. Synthesis of viral proteins
6. Synthesis of new copies of ssRNA genome

7-9. Assembly of new virions at the plasma membrane

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10. Neuraminidase triggers release of virions by cleavage of sialic acid.

How is influenza A transmitted?

 Can be transmitted to numerous mammals.

 Antigenic drift can lead to localised epidemics
o Rapid accumulated mutations which escape vaccine-mediated immune memory.
o Antigenic drift is common to all viruses.
 Antigenic shift may lead to pandemic influenza
o The mixing of multiple strains of influenza in a single individual, producing a viral
strain that the body hasn’t previously seen, thus is much harder to combat.
o Antigenic shift is a special feature of influenza A
 Transmission via respiratory droplets:
o Long distance where a droplet nuclei (from a cough or sneeze) that is less than 5
micrometres, can be transmitted further than a metre away, leading to airborne
transmission.
o Short distance, where a droplet more than 5 micrometres is transmitted less than a
metre away.
o Direct contact, where an infected person touches another person
o Indirect contact, where an object in contact with an infected person comes into
contact with a new host.

Explain the course of influenza virus

 Enters via the mouth and nose

 Replication in the upper respiratory tract
 Infected individuals are contagious from when symptoms arise to a week later
 Symptoms: high fever, nausea, dry cough, headache, sore throat, runny nose, muscle and
joint pain
 Virus can spread to other parts of the body like GI tract, causing symptoms such as diarrhoea
 Fatal cases of infection usually result from extensive damage to lung tissues.

Outline how influenza vaccines need to act

 Seasonal vaccine prevents currently circulating strains of influenza A and B.

 Accounts for latest antigenic drift and antigenic shift.

Give examples of antiviral drugs for influenza and how they work.

 Neuraminidase inhibitors:
o Tamiflu/oseltamivir
 Inhibit release of virions from cells
 M2 ion channel blockers
o Flumadine/rimantadine
o Inhibit entry of viral RNA into cells
 These medications only work at the early stages of infections so you can block viral
replication.

Outline the replication of HIV-1 and outline how it’s different from other viruses.

1. Attachment of the virus to the host cell

2. Entry into the host cell

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3. Synthesis of viral genomes and proteins

4. Assembly of new viral particles (virions)
5. Release of virions from the host cell

BUT

HIV-1 is a +ssRNA virus that uses a dsDNA (intermediate)

Outline the importance of reverse transcriptase

 +ssRNA is reverse transcribed into dsDNA/cDNA by reverse

transcriptase

Describe the mechanism of HIV-1 transmission

 HIV-1 is usually transmitted between people via:

o Sexual intercourse
o Sharing needles between IV drug users
o Between mother and child via blood or breast milk
o Blood transfusions

What is AIDS

 Caused by HIV-1
 A deficiency of the immune system that leaves a person unable to fight other infections and
diseases.
 AIDS related death usually results from opportunistic infections and cancer

Outline a treatment of HIV

 Antiretroviral therapy

Lecture 29: Protists and disease

What are protists?

 Eukaryotes that aren’t plants, animals or fungi.

 Small organisms
 Mostly unicellular, some multicellular
 Tissue organisation isn’t as complex as in higher eukaryotes
 Free living, symbiotic, parasitic.
 Modes of reproduction:
o Sexual and asexual
o Binary fission
o Spores and cysts

Give a brief overview of the major groups of protists

 SAR: stramenopiles, Alveolates, Rhizarians

 Large, diverse group
 Defined by DNA similarities
 Includes important photosynthetic organisms such as diatoms

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 Rhizarian group includes amoeba

Describe stramenopiles in more detail

 Diatoms
o Algae
o Photosynthetic
o Unicellular
o Highly abundant
o Aquatic (salt & freshwater)
 Oomycetes
o E.g. Phytopthora
o Plant pathogens
o E.g. Irish potato famine

Describe alveolates in more detail

 Alveoli (membrane-enclosed sacs)

 Photosynthetics
 Dinoflagellates
o Two flagella
o Blooms lead to red tides (carotenoids in plastids)
o Toxin producers (in molluscs, fish/invertebrates)
 Apicomplexans
o Plasmodium- causes malaria
 Ciliates
o Cilia
o Predators
o E.g. paramecium

Describe Rhizarians in more detail

 Amoebas (move and feed via threadlike pseudopodia)

 Amoebas occur in different groups

Outline the main characteristics of malaria

 Caused by plasmodium species: SAR: Alveolates (Apicomplexa)

 The most deadly vector-borne disease
 Transmitted by Anopheles (and Culex) mosquitos

Outline the symptoms and complications of malaria

 Flu-like symptoms
 Cycles of fever, coldness, sweating
 Severe malaria is caused by plasmodium falciparum
 Complications
o Respiratory distress
o Severe anaemia
o Cerebral malaria
o In pregnant women: stillbirth, infant mortality, low birth weight

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Outline the plasmodium life cycle

1. Mozzies take a blood meal and inject sporozoites.

2. This toxin travels to the liver where it enters liver cells and infects them. The infected liver
cell is called a schizont.
3. The schizont ruptures, allowing the enclosed toxin particles to enter the bloodstream, where
their targets are RBCs.
4. The organism then grows in RBCs and can infect other RBCs.
5. It can also go through a sexual cycle where gametocytes are formed, and then meiosis, so
there is both an asexual and sexual cycle which is common in protists.
6. If we get bitten again, we have parasites going into the mozzie which is an active growth
process.

Outline Archaeplastida as an example of a stramenophile

 Red and green algae, land plants

 First photosynthetic eukaryotes
 Red algae (rodophytes)
o Mostly saltwater
o Photosynthetic pigment is phycoerythrin
o Mostly multicellular
o E.g. Poryphyra, Nori
 Green algae
o Mostly freshwater
o Photosynthetic pigment is chlorophyll
o Unicellular, e.g. Chlamydomonas
o Multicellular e.g. Volvox

Outline excavata as a major group of protists

 “Excavated” feeding groove on one side of the cell body

 No plastids, highly reduced mitochondria- not as highly metabolically active as other
organisms
 Examples of pathogens
o Leishmania
o Giardia

What is Leishmaniasis, describe it in detail

 Caused by Leishmania spp

o Protist supergroups: Excavata
o Vector: sandflies
o Natural host: small rodents (gerbils)
 Cutaneous leishmaniasis: affects the skin
 Monocutaneous leishmaniasis: affects mucosal membranes
 Visceral leishmaniasis: affecting inner organs, mainly the liver and spleen

Outline the life cycle of Leishmania

1. Sandfly takes a blood meal and injects promastigote stage into the skin

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2. Promastigotes are phagocytised by macrophages

3. Promastigotes transform into amastigotes inside macrophages
4. Amastigotes multiply in cells (including macrophages) in various tissues
5. Sandfly takes a blood meal, ingesting macrophages infected with amastigotes
6. Amastigotes transform into promastigote stage in midgut
7. Divide in midgut and migrate to proboscis

Outline the disease Giardiasis

 Caused by Giardia lamblia

o Excavata (protist super group)
o Global disease
o Drinking contaminated water can cause infection (no infection)  “hikers
diarrhoea”
o Symptoms
 Diarrhea
 Nausea/vomiting
 Cramps
 Dehydration
 Chronic disease

Outline Unikonta (Amoebazoa) as a major group of protists

 Amoebas with lobe or tube-shaped pseudopodia

 Archamoeba
o No/reduced mitochondria
o E.g. Entamoeba histolytica causes amoebic dysentery

Outline the role entamoeba histolytica plays in disease

 Amoebazoans (unikonta) causes amoebic dysentery

 Symptoms: abdominal pain, (bloody) diarrhoea
 E.histolytica cysts and trophozoites passed in faeces
 Infection by ingestion of cysts via fecal-oral route
 Excystation in intestine
 Trophozoites multiply by binary fission
 If symptomatic: invade intestinal mucosa, may migrate to lungs, brain, liver, skin

Outline Unikonta (Opsithokonta) as a major groups of protists

 Diverse group of organisms that includes animals, fungi,

and protists
 Prostists include nucleariids
o Amoebas that feed on algae and bacteria
o Most closely related to fungi
o Protists include choanoflagellates
 Closest relatives to animals
 Have a flagellum with a collar

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Lecture 29: Fungi and disease

What are fungi?

 Eukaryotes with cell walls

 Unicellular (yeast) and/or multicellular filaments (hyphae or mycelia)
 Terrestrial or aquatic
 Produces spores through sexual or asexual life cycles
 Highly diverse
 Major role is decomposition of organic material
 Several pathogens

Outline fungal structure

 Typical eukaryotic features with ones to remember being:

o Cytoskeleton with actin microfilaments and tubulin-containing microtubules
o Usually in haploid state, but diploid nucleus is formed during sexual reproduction

Outline fungal reproduction

 Fungal hyphae and spores are haploid

 Sexual reproduction usually starts with pheromones
o Moulds:
 Visible mycelia
 Filamentous growth
 Mitotic spores
o Yeasts
 No mycelia, single cells
 No spores
 Reproduce by cell division or budding

Briefly outline the major fungal groups

 Zygomycetes
o E.g. mucor, bread mould
o Have mycelia that are not septate
o Multinucleated
 Ascomycetes
o E.g. Aspergillis and Penicillium (a mould commonly encountered as a decomposer of
food),
o Have mycelia that are septate (there is a septum/wall between each cell)
o Produce endogenous ascospores
 Basidiomycetes
o E.g. mushrooms and toadstools
 Tiny haploid cells- spores, are produced inside the mushroom
o Have mycelia that are septate
o Produce exogenous basidiospores

Outline the life cycle of a mushroom

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1. Two haploid mycelia of different mating types undergo plasmogamy

2. A dikaryotic mycelium forms, growing faster than, ultimately crowding out the haploid
parental mycelia.
3. Environmental changes (e.g. rain/temp change) cause dikaryotic mycelium to form
basidiocarps (mushrooms)
4. Basidiocarp gills are lined with cells called basidia
5. Karyogamy in each basidium produces a diploid nucleus which then undergoes meiosis
6. Each diploid nucleus yields four haploid nuclei, each of which develops into a basidiospore
7. When mature, the basidiospores are ejected and dispersed by the wind
8. In a suitable environment, basidiospores germinate and grow into short-lived haploid
mycelia.

Outline the ecological role of fungi

 Decomposition: fungi are the main recyclers of plant materials. They degrade organic
material, returning complex carbohydrates, lipids, proteins to their simple components
 Most vascular plants are dependent on the symbiotic fungal hyphae or mycorrhizae that
branch into plant cells.
 Fruiting bodies of mycorrhizae (forest mushrooms) are important in animal diets

Outline examples of the mutualistic nature of fungi

 Termites: digestive tract contains symbionts whose enzymes break down wood (bacteria,
protists or fungi)
 Lichen:
o Photosynthetic organisms (green algae/cyanobacteria) provides complex carbons
(and N2 if cyanobacteria)
o Held in mass of fungal hyphae: provide structure and protection

Why do leafcutter ants collect leaves?

To feed to fungi. They then feed the fungi to progeny (offspring)

What are important uses of fungi?

 They are important sources of antibiotics such as penicillin

Outline Candida infections (yeast infections): Candidiasis

 Candida albicans is the major pathogen (ascomycetes)

 Yeast that is part of normal microbiota of oral cavity, genitalia, large intestine of skin of 20%
of humans. (endogenous ascospores)
 Budding cells of varying size can form both elongated pseudohyphae and true hyphae
 Biofilm formation is important in pathogenesis
 Most common syndrome is thrush
 Causes most nosocomial fungal infections (infections that exist due to toxins in certain
locations, i.e., hospitals).
 Infections can be short-lived, superficial skin irritations overwhelming, fatal systemic
diseases.

Why is killing off fungi harder to do than bacteria?

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Fungi are eukaryotes so the processes we can target in them that won’t affect humans are limited.
One of these, is the production of their cell wall.

Outline biofilm formation by Candida albicans

 Biofilm is made up of host cells, dead cells, hyphae. Biofilms are present on pipes, river beds.
 Biofilms offer antifungal resistance, protection from host defences and thus pathogenesis
 Disperses via increased virulence and adhesive properties increasing # of metastatic sites.
 This leads to the planktonic state which leads to attachment to surfaces. Attachment to
surfaces= normal microbiota are removed

Outline Candidiasis

 Thrush: occurs as a thick, white, adherent growth on the mucous membranes of mouth and
throat
 Vulvovaginal yeast infection: painful inflammatory conditions of the genital region that
causes ulceration and whitish discharge
 Cutaneous candidiasis- occurs in very moist areas of skin and in burn patients
 Invasive candidiasis- if phagocytic system is compromised, infection spreads to organs and
causes potentially fatal infections

Outline the important features of cryptococcosis: basidiomycetes

 Cryptococcus neoformans causes cryptococcosis

 A widespread yeast that normally inhabits soil
 Polysaccharide capsule surrounds it for virulence
 Common infection in AIDS, cancer, or diabetes patients
 Infection of lungs leads to cough, fever, and lung nodules
 Dissemination (spreading) to meninges (membrane covering brain and spinal cord) and brain
can cause severe neurological disturbance and death (cryptococcal meningitis)

Outline what aspergillosis is

 Caused by members of the genus aspergillus

 Very common airborne soil fungus
 Aspergillus fumigatus: most common pathogen
 Serious opportunistic threat to AIDS, leukemia, and transplant patients
 Infection occurs in lungs. Spores germinate in lungs, forming fungal colonies which can
colonise sinuses, ear canals, eyelids, and conjunctiva.
 Invasive aspergillosis can produce necrotic pneumonia, and infection of brain, heart, and
other organs.

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