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BIOL229 revision notes with multiple choice answers

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Lecture 2 - Prokaryotes, eukaryotes, the rise of
multicellularity and endosymbiosis
• Many prokaryotes are photosynthetic. They arose 3.5 billion years ago, evidence
is provided by stromatolites.
• Cyanobacteria are not truly single celled, they occur in multiple linked beaded
structures. They convert nitrogen gas into an organic form through a process
known as nitrogen fixation.
• In photosynthesis, carbon dioxide is transformed into oxygen and sugar. Water is
the reducing agent. Sulfur or Hydrogen sulphide can be the reducing agent
instead, in anoxic areas.
• Prokaryotes can also be chemotrophs and do not require light for survival. Some
use inorganic compounds as reducing agents to synthesise organic carbon and
these are known as lithotrophs. Chemotrophs can also use organic carbon
compounds to reduce CO2 into carbohydrates.
• When organic carbon is available, all prokaryotes are heterotrophs.
• Prokaryotes use flagellae to swim towards resources such as light and food.
Prokaryotes do not have an internal membrane system to concentrate
metabolites. They use the plasma membrane to generate proton gradients and in
turn produce ATP, the primary energy source for life. ATP synthase is what is used
to produce ATP.
• Many eukaryotes are only single celled organisms, but they can assemble to form
multicellular organisms through cell-cell interactions, the protist amoeba can do
this for their reproductive stage. Eukaryotes have perfected the delegation of
internal tasks, but have larger surface area to volume ratios and longer generation
times, thus attaining resources is slower compared to prokaryotes.
• Aside from ATP, there are other forms of energy: creatine phosphate (short term
energy storage in muscle), guanine triphosphate and pyrophosphate (bacteria and
plants have inherited this ability to cleave it to use it metabolically) are key
• Proton gradients are the core driving forces for creation of ATP, through ATP
synthase. Ions have to be concentrated on one side of the membrane, falling to
one side and forming a gradient. Protons cannot get through the membrane
because it is a lipid bilayer but they can flow through ATP synthase, a nanomotor
which spins.
• Animals and plants (multicellular organisms) develop in the environment, gene
expression to acclimate to conditions is called phenotypic plasticity.
Lecture 3 - Autotrophy
• Autotrophy is the process of creating food using nutrients from the environment. It
has primitive origins and still exists in modern plants.
• It is known as the reduction of carbon compounds to create nutrients, requiring
electrons and hydrogen atoms. When converting bonds, by either making and
breaking them, the processes either release energy (breaking bonds) or require
energy (making bonds). Reduction, the gain of electrons is known as the making
of bonds and oxidation, the loss of electrons is known as the breaking of bonds.
• Photoautotrophs make organic carbon compounds, reducing carbon compounds
using light. Most use water as the supplicants of H+, with the exception of
primitive bacteria.
• Photosystems have evolved to form more complex mechanisms. Primitive
bacteria only have one of two photosystems. Green and purple sulphur bacteria
use H2S as the hydrogen donor. As a consequence, oxygen is not produced. This
explains why the early atmosphere lacked oxygen.
• Chemoautotrophs can use heat in order to form reduced carbon in order to form
organic carbon. Reduced water also supplies hydrogen atoms which are used to
generate inorganic or organic hydrocarbon bonds. Primitive bacteria or archaea
used hydrogen, reduced iron and hydrogen sulphide to make hydrocarbon bonds,
and are known as lithotrophs (they are only prokaryotes). Thermal vents
commonly contain these systems, as there is no light and only heat.
Chemolithotrophic bacteria form symbiotic relationships with giant tube worms to
provide them with organic carbon.
• Cyanobacteria capture light from their filaments of individual cells, and their large
interspersed cells, called heterocysts, fix nitrogen from the atmosphere and are
widely responsible for producing the oxygen from 2%-21% through
• Cyanobacteria (blue-green algae) and all plants are modern photoautotrophs,
pigments and systems vary depending on the environment. There are two major
components: A complex membrane with intermembrane spaces (to allow for the
formation of concentration gradients) in NADPH. This is a biophysical light
reaction. A biochemical cycle called the Calvin cycle or dark reaction captures
carbon dioxide and ATP, converting it into sugars.
• Chlorophyll a is the primary pigment for photosynthesis, used by photoautotrophs
and receives light energy directly from the sun or from accessory pigments
(chlorophyll b and phycobilins).
• W2MCQ#1: What characteristics do cyanobacteria have to make them so efficient
at blooming so rapidly in lakes and waterways? Combination of photosynthetic
efficiency and the capacity to fix atmospheric nitrogen gas
• Green plants are the second major groups of photosynthetic organism. Some
plants are parasitic, and drain carbon from the other plants. Photosynthesis
occurs the green tissues of the plants, including frond leaves or fruits, and other
examples. Chloroplasts are where photosynthesis occurs. They are the membrane
organelles which once were prokaryotes, but through endosymbiosis evolved to
become organelles which can no longer be independent of the plants they are
now part of.
• In photosynthesis, light is captured by chlorophyll a, in addition to this however,
other pigments have evolved to have similar roles to chlorophyll a. Chloroplasts
contain thylakoid stacks which are membranes acting as the medium of the light
reaction. The thylakoid contains large proteins embedded as well as hydrophilic
and hydrophobic heads and tails.
• In the dark reaction, NADPH is the reducing power. It occurs in the stroma - the
interior space of the chloroplast.
• W2MCQ#2: What is the primary photosynthetic pigment in higher plants? And
correctly name a secondary pigment that transfers its captured light energy to this
primary pigment? Chlorophyll a; carotenoids
• The primary electron donor (oxidation agent, reduced compound) in
photosynthesis is water, while the final electron acceptor is NADP+, which comes
from NADPH produced in the first step: the light reaction. These reactions occur in
the thylakoids of chloroplasts.
• W2MCQ#3: What are the two main energy rich products of the light reaction? ATP
Lecture 4 - Heterotrophy
• Heterotrophy is the use of organic molecules derived by feeding on other
organisms. (heterotrophs or autotrophs). The organic molecules are extremely
• Fungi are unusual in that they contain cell walls and are morphologically similar to
plants. However, they are solely heterotrophs, similar to animals. They absorb
food, and contain enzymes which break down organic matter in decomposition.
• Modern heterotrophs arose before 500 million years ago. The most modern
appeared 540 million years ago. Half a billion years ago, the first eukaryotes arose
via symbiotic origins.
• Some large organisms eat small prey. For example, whales eat krill and algal cells.
Energy in algal cells is immensely high. When it is eaten and passed on via
organisms such as krill, energy is lost (around 90%). Short food chains, which can
skip the second step of the chain will result in less energy loss. Thus, it is a much
more sustainable option for whales.
• W2MCQ#4: What is the advantage of herbivory for the energy gained in the diets
of large mammals? energy losses in the carnivorous food chain are avoided
• Heterotrophy is at the heart of growth and survival unless autotrophy is an option,
for single celled bacteria and protists. Heterotrophic bacteria can derive carbon
skeletons through diffusion across the outer membrane or they can take up their
food via specialised recognition systems through proteins. Energy is used to
control the osmotic environment.
• Unicellular eukaryotes such as the Paramecium have an oral groove (phagosome),
through which food enters the body. They contain cilia which allow them to move
towards food sources. The contractile vacuole ejects water, forming pressure
gradients which jets them around. This works with cilia, which requires ATP in
order to function.
• Some protozoans have photosynthetic capacity while others do not.
• Amoebae, part of the kingdom protista have special mechanisms. The pseudopod
(false foot) allows of the engulfing of food. There are two mechanisms to allow for
the engulfing, phagocytosis and pinocytosis. Phagocytosis is the recognition of
ligands on the surface of the particle through receptors in the amoeba. The
receptors determine whether it is a suitable foodsource, then incorporate it into a
phagosome, then digest it. Pinocytosis is the non-specific absorption of food, the
plasma membrane invaginates, allowing for food to pass through, where it is then
• Invertebrates also have mechanisms to acquire food, these are more diverse than
those of the unicellular eukaryotes and prokaryotes. For example, the aphids
possess a stylet, which is a mouthpiece used for sucking sap, and gastropods
possess a radular apparatus which acts as a chewing mouthpiece.
• Mycorrhizal fungi feed through membrane to membrane transport, through
transport systems.
• W2MCQ#5: Name two mechanisms that unicellular organisms such as amoebae
use to acquire nutrition? phagocytosis and pinocytosis
• Large marine mammals, fish and molluscs use filter feeding in order to obtain their
food. Whales have very large plates (Gill rakers) with bristles. Fish use suspension
feeding through their gills, where food is trapped in. Filter feeders indiscriminately
filter, thus they can ingest many toxic chemicals and metals easily.
• The higher mammal stomach has highly evolved depending on their diet. Those
that need to digest celluloses or hemicelluloses have especially long stomachs
(Caecum) due to their plant diet. Cellulose is an important source of energy
because it contains pure starch which plants use as a biodegradable energy and
carbon store as well as being a source of glucose.
• Vent worms (tube worms) form symbiotic relationships with bacterial chemotrophs
in order to find food in darkness. The chemotropic bacteria break down Hydrogen
sulphide (H2S) from deep sea vents. The hydrogen reduces carbon, releases sulfur
which sinks to the ocean floor as sulphates and creates organic carbon.
• W2MCQ#6: Deep sea tube worms derive energy and reducing power from what?
volcanic vents; hydrogen sulphide
• The rumen is a complex fermenting device, using anaerobic bacteria which
produces methane, ejected from the organism. 20% of climate change is likely
due to ruminants.
Lecture 5 - Anaerobic metabolism
• The great oxidation event caused oxygen to become the basis for metabolism of
most living things.
• Prokaryotes have a better chance of surviving without oxygen because 4.6 billion
years ago they arose in an anoxic environment.
• Water filled areas are most likely prone to anoxic conditions because oxygen does
not diffuse well into water.
• Mammals that dive use an O2 binding molecule to store oxygen with them when
they dive. Aquatic plants develop aerenchyma (airspaces) through cavitation,
which allows rapid oxygen diffusion.
• Normoxia means the normal amount of oxygen in the area. Hypoxia are low
oxygen conditions, but higher than 0%. Anoxic conditions are conditions with zero
oxygen. Anaerobic is freely used to describe oxygen free areas with slight trace
Lack of oxygen kills living cells because of energy crises. Oxygen allows aerobic
respiration which degrades carbohydrates to form water. When oxygen is cut off,
95% of energy yield is lost. There are other effects of low oxygen like toxic ions
such as reduced copper, manganese and irons. Bacteria also thrive in anaerobic
environments, enabling a wider range of dangerous infections.
When oxygen is low, it is solely carbohydrates that are degraded to form carbon
dioxide and ethanol as well as ATP in plants.
W3MCQ#1: What are the principal anaerobic end products in plants? ethanol and
carbon dioxide
Fermentation cannot be sustained without sugars as substrates. Fermentation
consumes sugar faster in anaerobic conditions to compensate for low energy. A
lot of substrate has to be used to increase ATP yield by 5%.
The anaerobic product of respiration is toxic in high conditions. In plants, ethanol
takes off. Anaerobic systems cause pH to drop because of the products of
fermentation. H2S is a toxic example of an acidic byproduct. Glucose -> 2ethanol
+2CO2 + 2ATP + 2H2O.
Anaerobic respiration releases less energy than aerobic respiration, thus the
amount of produced ATP is much less than 32 ATP for one molecule of glucose,
only producing 2 ATP. This is because there is only the glycolysis stage present,
which always produces 2 ATP. Other processes of respiration, such as the TCA
cycle and Oxidative phosphorylation are cancelled.
In human muscles, anaerobic respiration produces lactic acid and ATP. Lactic acid
is waste, thus it is disposed of. Glucose -> 2Lactate + 2 ATP + 2H2O.
Fish also make anaerobic end products, secreting ethanol. Lactic acid finds its
way into the fish bloodstream and it can then be converted into pyruvic acid. Fish
can be a partially anaerobic system due to low oxygen.
In anoxia, plants and animals have strategies, known as defence and rescue. As
defence, cells lower energy use in order to rebalance ATP levels. In rescue, a few
genes are switched on to allow function for select proteins which enhance
survival. Sucrose synthase is an enzyme which hydrolyses sugars. Rice seedlings
also exhibit acclimation. Transport is also down regulated. Channel arrest is where
ion channels close, sodium is pumped out of the cell. This tried to exchange
sodium to maintain electrochemical neutrality. However energy supply is
threatened. The ATP produced by glycolysis is used to push sodium out. The cell
enters the resting phase until cells enter a favourable energy rich condition.
There are oxygen sensors in both animals and plants, however this mechanism is
clearer in animals than plants.
W3MCQ#2: What two physiological phenomena (not biochemical pathways) are
thought to help all living things survive in low oxygen conditions? defence and
Rice seedlings exhibit acclimation by fermenting carbohydrates to form ATP.
The rumen of the ruminant is a large anaerobic ecosystem. Gases in the rumen
include carbon dioxide and methane, a significant gas in climate change. The final
electron acceptor is either organic or inorganic but it is not oxygen. A major set of
end products are semi reduced compounds such as acetic acid, propionic acid
and butyric acid.
• W3MCQ#3: Ruminant animals digest vegetation by the action of anaerobic
microbes which break down complex carbohydrates to gases and volatile fatty
• Plant responses to hypoxia or anoxia include morphological anatomic and
metabolic responses. Aerenchyma is an example, which forms air spaces as an
adaptation to flood. Plants can also produce roots which allow for oxygen access.
• Acclimation and acclimatisation are both chronic (following prolonged exposure)
responses to environmental changes. However, acclimatisation is for completely
different natural environments (e.g. seasons and clines). The former is changes in
some highly defined ways (lab conditions).
Lecture 6 - Oxygenic energy generation (respiration)
• Dark respiration is respiration done in the absence of light. It is very difficult to
estimate and is in all aerobic organism’s tissue.
• Substrates for dark respiration are numerous. They are carbon skeletons from
various sources. As per the namesake, it requires no light.
• In respiration, sugars are combusted to produce CO2, water and ATP. Oxygen is
required along with the sugars.
• Sucrose comes from green plants, thus they are the primary substrate for
respiration in them. The sugars are used up in glycolysis, the main step for
respiration where bonds in sugar (C-H) are hydrolysed to form ATP. In animals,
sugar substrates vary.
• Before becoming ATP. sugars are phosphorylated and finally turned into organic
acids such as pyruvic acid, molecules with less energy than their original sugar.
Glycolysis happens in the cytoplasm of the cell/cytosol.
• After production, the organic acids are shifted into the mitochondrion if there is
oxygen present, then get broken down in the citric acid cycle AKA the Kreb’s
cycle. This happens in every eukaryotic cell which has a mitochondrion.
• Oxidative phosphorylation is the final stage of respiration where NADH is the
reducing power, which assists with the final production of ATP by the
phosphorylation of oxygen gas.
• Directly injecting lipids into the TCA cycle (citric acid cycle) causes them to yield
more energy per carbon than sugars. In lipid breakdown, lipids are directly fed,
which is why fats give twice the energy yield to sugars. TCA cycle happens in the
mitochondrial matrix.
• Respiration differs based on the presence of oxygen. In aerobic conditions, sugar
is broken down into pyruvic acid/pyruvate and then is converted into acetyl COA
where it is broken down to CO2 in the Kreb’s cycle. Anaerobic conditions break
sugars into pyruvate. From there, there are two different fermentation processes
that can occur: Alcohol fermentation, producing 2 ethanol and 2 CO2 or lactic acid
fermentation, which produces 2 lactate molecules.
• The mitochondrion has the outer and inner membranes. Cristae in the inter
membrane space between these accumulates protons, dooming a gradient,
leaking through ATP synthase to generate ATP.
• W3MCQ#4: Name two mitochondrial compartments in which (1) the TAC cycle
breaks down pyruvate and (2) high energy electrons are used to synthesise ATP.
matrix; cristae
• An elaboration into respiration leading into the final process of oxidative
phosphorylation is: Glycolysis feeds the pyruvate into the mitochondrion, there is
the Kreb’s (TCA) cycle, which releases CO2, then the reduced compounds (NADH
and FADH2) from TCA produced earlier being fed into the electron transport chain.
As the electrons lose energy, the energy is used to create ATP through ATP
synthase activation. As energy is lost, the diffusion gradient causes H+ ions
concentrated in the intermembrane space to spin and produce ATP.
• Many poisons interfere with the electron transport step. Cyanide inhibits the final
step, carbon monoxide competes with oxygen and blocks it causing the entire
system to halt.
• W3MCQ#5: Dark respiration produces two essential products that animals and
plants both need for survival. One is chemical and the other physical. adenosine
triphosphate; heat
• Respiration produces heat as a byproduct regulating temperature _________
• Most plants have slow respiration rates. In fruits, there is a high respiratory rate
called the climacteric burst, fruit ripens with respiratory bursts.
• W3MCQ#6: Respiration in plants and animals fulfils the roles of: controlling
temperature and metabolic rate, providing cellular energy and regulating redox
• Respiration provides optimal energy status in all organisms, ATP is always a
product. In animals and some plants it is used to regulate temperature by
releasing heat as a product. For warmed plants, fruit ripening accelerates and
pollination is facilitated, while producing heat, an electron transfer (redox) occurs.
• In aerobic respiration, oxygen is the final electron receptor. NADH is the final
electron donor and cycles between NAD and NADH.
Lecture 7 - Gaining resources, making energy and
regulating the living cell
• Humans mainly consist of proteins and lipids, with some minerals and even fewer
composition of nucleic acids and carbs (17%). Plant composition mainly consists
of fibre and protein with 14.4% sugars, and less minerals. Plants build themselves
out of sugars and animals build themselves out of bone structurally.
• Catabolism is the breaking down of structures. Catabolism of proteins foes not
have a high energy release. Making them (catabolism) is expensive because
converting nitrate to amino nitrogen for nitrogen acids is expensive.
• Fatty acids are very rich in energy because they consist of hydrocarbon bonds.
• Growth is an increase in biomass through acquisition of new resources. The
resources can be either organic or inorganic. The acquisition of resources requires
energy, while digesting may require even more energy. Some molecules have a
high cost to make but are essential e.g. immunoglobulins and phenols.
• Maintenance is easy to measure, but separating it from growth is difficult. It is
simply the process of keeping cells and tissues alive, regardless of whether or not
there is growth.
• Processes of growth include active ion uptake, amino acid synthesis, protein
synthesis. Maintenance includes reuptake of ions or resynthesis of proteins.
• W4MCQ#1: All living organisms must respire in order to complete their life cycle.
The resulting energy can be partitioned between: biosynthesis (growth) and
• Net costs can be calculated for making living tissue, with the cost always being
either ATP or photosynthetic carbon.
• The mechanism of chemotaxis is driven by concentration gradients. The switching
of kinases is behind the sensing mechanism.
• W4MCQ#2: List these major polymers in decreasing over of calorific value. lipids
> proteins > sugars
• Lipids are very rich in energy value because they are reduced. Next are proteins,
then carbohydrates followed by glycogen.
• W4MCQ#3: Protein and lipid discrimination in the diet would be expected to
optimise: There is an optimisation of metabolism and energy use, as proteins and
lipids are high in energy. Energy availability vs the biosynthesis of muscle
• Chemotaxis is a crucial process by heterotrophic prokaryotes and unicellular
eukaryotes in order to find food, drive by concentration gradients.
• As organisms age, less carbon is respired, there is a change over time
developmentally in the proportion of maintenance and growth. Temperature also
influences this, at the increase of temperature there is a spike of respiration
involved in growth and maintenance.
Lecture 8 - Compartmentation and homeostasis
• Transport proteins are essential for homeostasis. Transported molecules can move
through by simple diffusion (passive transport) or by active transport. Carriers
enhance the transport rates, increasing reaction rates across the membrane.
Without the transport proteins, homeostasis is not possible and the flux of ions
cannot be regulated.
• Bidirectional transport uses the anti port co-transporter integral membrane
transport to allow different molecules to move across the membrane in opposite
directions. Sugars, organic molecules, inorganic molecules and hormones can
also be transported by symporters which go in the same direction.
• W4MCQ#4: Which of these are intracellular compartments? peroxisomes,
lysosomes, nuclei, mitochondria, chloroplasts
• W4MCQ#5: Compartments in cells are considered to be important because: they
prevent enzymes from digesting the cell's metabolites, they concentrate
metabolites, some compartments store genetic information where it can be
transcribed and they store toxic compounds
• W4MCQ#6: Active transport involves the use of what resources? ATP and
generally, protons
• Active transport requires the participation of ATP as well as protons.
• In the small intestine, Na+-K+-ATPase uses ATP in order to transport Na+ out of the
cell in active transport (against the ion gradient). The Na+ electrochemical gradient
is maintained. which makes more Na+ diffuse inwards. This causes the secondary
active transport of glucose (using ATP) into the cell. There are two secondary
active transport mechanisms for vertebrates, inward diffusion of Na+ from the
cotransporter protein in the apical membrane and inward glucose transport.
• In the gill epithelium of freshwater fish, there is an active ion transport occurring.
Carbon dioxide from respiration provides protons, and water is added to form
carbonic acid (H2CO3). The H2CO3 is then broken down to bicarbonate (HCO3-), an
essential molecule which allows for the active transport of Cl- ions, through
exchange. The extra protons (H+) are exchanged for Na+ to allow for Na+ transport
inside the cell.
• The kidney is a very elaborate transport system. Pressure differences in the
Bowmans capsule’s epithelial capillaries causes waste and nitrogenous products
from the blood to diffuse through the fenestrations (gaps) of the capillaries. The
colloidal osmotic pressure drags water back into the bloodstream and the
hydrostatic pressure pushing outwards exceeds the other pressures (-1.9kPa).
Blood pressure in the glomerular capillary (+6.7kPa) + colloid osmotic pressure
(-3.5kPa) and hydrostatic pressure (-1.9kPa) = Filtration pressure = +1.3kPa.
• In terms of glucose absorption in the gut, the hummingbirds have the most
efficient glucose uptake. Herbivores have the highest glucose absorption, followed
by omnivores and then carnivores. Change in diet will change the abundance of
transport molecules.
• Plants make sugars in the leaves and need to transport sugars around. Their
transport mechanisms use phloem looking elements, the elements into which
sugars are loaded in order to transport them long distance. There is a proton
gradient (High to low) that is driven by ATPase which pushes protons out through
its pump. The pumped protons then become available to drive sucrose
symporters moving down the proton gradient, to the more sucrose rich region in
the bottom tissues of the phloem. Maple syrup is extremely sweet and is the
phloem sap. Cell to cell communication roots in plants are called plasmodesmata,
which allows passive diffusion of sucrose until the active transport stage
mentioned above has to take place.
• Another plant system is the trapping of CO2 by desert plants and orchids, leading
to malate storage in the night when stomata is open.
• Photorespiration is a complex process in plant cells with a three way interaction
between the peroxisome chloroplasts and mitochondria as a result of transporters.
This futile pathway makes no energy.
Lecture 9 - Plant symbiosis
• Symbiosis is the interaction between organisms, those that benefit both parties
are called mutualisms. Mycorrhizas are an ancient example. When plants were still
on water, the mass flow of water supplied nutrients. 400 million years ago,
Mycorrhizas allowed plants to bypass this and live on land. Many aquatic plants
also don’t because water helps in ways previously mentioned.
• In mycorrhizal symbiosis, there is an exchange of nutrients. Plants receive
phosphate, which is taken up by the fungus. The trees deliver carbohydrates to
the heterotrophic fungus. There are ectomychorrhizaes and endomychorrhizas,
the latter which is further separated into cricoid and orchid. Most
endomycorrhizas are Arbuscular (AM) mycorrhizas.
• Ectomycorrhizae are found on woody species typically on the northern
hemisphere. In these, the fungal hyphae don’t penetrate any cell walls and make
their distinguishing features called Hartig nets which are tight woven nets around
the root axis and turning them short and stubby. This allows for inorganic
nutrients, namely phosphate to be taken up by the root in greater amounts.
Endomycorrhizae are subcategorised as arbuscular (AM or vesicular mycorrhizae),
meaning bushy. Ericoids are specialised for Erica plants and orchidaceous which
are specialised for orchids. The hyphae penetrate the cortical cells, but not the
membrane of the root cell. AM have highly branched structures, thus increasing
the surface area to volume rations. Ericoid mycorrhizae are present in nutrient
poor soils containing Ammonium. Many heaths reside here. Ericoids are more
responsible for the uptake of nitrogen than the usual phosphorus. Orchidaceous
completely colonise the root cells of orchids.
Aside from nutrient uptake, mycorrhizae can also benefit in other ways, such as
increasing water uptake or inhibiting certain plant pathogens.
W5MCQ#1: There are two major types of mycorrhizae and others that are less
common variations. They are:
80% of the gas in the atmosphere is nitrogen but it is usually unavailable because
of its strong triple bond. Thunderstorms can cause the triple bond to brea
because of the excessive energy output, producing nitric acid.
Legume nodules are extensive root growths which house Rhizobium. These are
nitrogen fixing bacteria which provide plants with nitrogen. In turn, they receive
The mechanism of infection has recognition between the bacterium and the root
hair, which curls up upon bacterium attachment. Flavonoids are released by the
legume root to attract the Rhizobia. Rhizobium release signalling sugars called
Nod factors to communicate with the legume root in response, and each species
releases unique Nod factors (with a difference in the number of sugar repeats).
Each legume species has receptors unique to a specific Nod factor. These root
hairs are extensions of the epidermal (epithelial in animals) layer, which curl to lead
to an infection thread where the root cortical cells undergo cell division then the
Rhizobium invade the cortical cells and the nodule grows and the root diminishes.
The bacteria, which have transformed into bacteria’s from root nodules with the
cortex cells. Then the nodule vascular tissue turns into a transport system for
nutrients, specifically Nitrogen, where the enzyme Nitrogenase reduces it.
W5MCQ#2: Nitrogen fixation is characterised best by:
W5MCQ#3: Mutualisms are best described as:
Lecture 10 - Animal symbiosis
• Every multicellular is a corporation with microbes, containing symbiotic
relationships. Cells that are eukaryotic are also symbiotic.
• The types of symbiosis are commensalism, parasitism, and mutualism. The rumen
of the cow is the biggest part of the digestive system where the symbiotic
microbes are located. There are 1011 microbial cells/mL and 100 litres in cattle,
thus 1016 microbial cells total. There are 1014 cells in humans. Microorganisms are
extraordinarily diverse. Ranging from protozoans, bacteria and fungi, these can
further have symbiotic interactions of their own. Therefore this is a very complex
• Other animals don’t have a modified stomach, but instead a hindgut, also known
as a caecum. In humans, this is the appendix and is a vestigial organ. Symbiosis
helps herbivores to digest cellulose from the caecum.
• Some birds eat plant material, while being mostly insectivores. The hoatzin is a
south american bird that eats leaves. The bacteria in the handout is in similar
concentrations compared to the rumen.
• Termites don’t have the enzymes to digest wood. Instead they rely on protozoal
symbionts that live in their gut. Lower termites all have these specific flagellated
protozoans, which they have coevolved with. In a termite digestive system, the
termites appendages first break down wood, which goes into the gut, getting
partially digested into wood fragments which go into the hindgut. The flagellates
produce enzymes which break the wood into glucose, and then short chain fatty
acids. The product is absorbed by the termites. Higher termites use bacteria
instead of protozoans for the same process. Some termites do digestion
externally, using premacerated wood inoculated by fungus, the fungus produces
fruiting bodies which the termites eat. This symbiotic relationship had a single
origin in Africa 30 million years ago.
• Attini ants also digest externally. They collect plant material, taking it back to their
nests and adding it onto a fungal garden. The fungi produces bromatia (fruiting
bodies) the ants eat. This arose 50 million years ago in one ant species, later
diverging. Ants have been shown to have coevolved with the fungus that they
work with. A weed that preys on the fungi has also coevolved. Queens of these
ants have a patch of streptomyces bacteria on their chest plate, which produces
an antibiotic which controls the fungi’s parasite.
• Symbiosis is also important in the marine environments. Coral reeds are the
largest biological phenomena on the planet. The huge range is formed by polyps
which form symbiotic relationships with single celled algae. Reefs have good light
penetration, allowing sunlight to get deep into it. The entire reef system is run on
photosynthesis. The symbiosis of symbiodinium (single celled algae) with coral
polyps is obligate. The symbiodinium are very high in biomass and supplies
between 50-90% of the energy requirements to the polyp. The energy increases
the rate of reef growth, allowing the polyp to lay down calcium. When the polyp
respires, it produces CO2, which is absorbed by the symbiodinium (zooxanthellae)
which uses it in photosynthesis to make glycerol. Glycerol supports polyp cells.
Meanwhile, calcium is absorbed and CO2 goes to make calcium carbonate. This
effect spans over 2000km.
• DNA analyses revealed symbiodinium is composed of multiple clades, rather than
being a single species. The molecular tree is roughly 50 million years ago which
corresponds with the fossil origin of corals. Thus, it can be inferred they coevolved
with each other.
• Symbiodinium also form symbiotic relationships with other organisms, which rely
on the in similar ways e.g. Cassiopea xamachana (upside down jellyfish), Tridacha
gigas (giant clam) or solitary anemones. The dinoflagellate symbiodinium give the
hosts their brightly pigmented hues.
• Coral bleaching is where symbiodinium is expelled from the coral. This can
happen due to infection, pollution, freshwater, and most notably, increased
temperatures and radiation. In these conditions, Symbiodinium cannot
photosynthesise from the disturbance, the coral then kick them out where the
coral proceeds to die from lack of nutrients. Some strains have evolved to have
higher heat tolerance.
Hydrothermal vents are the deepest part of the ocean where no light can
penetrate. It was once believed that there was no life here, but in the 1980’s, many
new ecosystems were discovered. Vent animals have many cases of symbiosis,
mainly relying on chemoautotrophy, using oxidation of inorganic molecules to
produce ATP. Vents are some of the most densely packed ecosystems in the
world, all of which require symbiosis to survive. Tubeworms and mussel beds are
heavily reliant, tubeworms lack a mouth, anus and digestive system. Instead, they
possess a trophosome, a cavity that is full of bacteria. The bacteria take sulfur,
water and oxygen to generate ATP and sulfate. The plume of the tubeworm is
haemoglobin, which binds to oxygen and sulfur, the worms grow 2 metres in six
months in a high biomass ecosystem.
Different compartments containing DNA can be incorporated into different
organisms. Sea slugs of the order sarcoglosa pierce algae with their mouthpiece
and digest most of the algae, however keep the chloroplast which helps the slugs
camouflage. Some slugs also allow continuous photosynthesis (Elysia chlorotica).
This is kleptoplasy. The morphology also changes into a leaf shape. Genetic
rearrangement occurs, with plant DNA being incorporated into the nucleus. This
allows them to control the photosynthetic process.
The spotted salamander transmits green algae in the egg case. The algae doesn’t
provide nutrients, but helps with camouflage. The algae penetrates the tissue of
the salamander and colonises the ovaries of females, passing them on to the
offspring. While passing them on, photosynthesis is omitted.
Humans have 1014 symbiotic bacteria in their guts. The macrobiotic have altered
over time. 350000 years ago, humans used fire for food. This increased calories
and reduced the size of the gut, also reducing microbial diversity in the gut.
Farming changed diet and increased starch, decreasing diversity. Food processing
also reduced gut diversity. Many modern processes decreased the diversity of gut
microbiota. This means systems will get less diverse over time, which could
impact health.
Lecture 11 - Cell division
• The G1 phase is where the cell doubles in size and organelles, enzymes and other
molecules increase in number and reach maturity. At this point there is a
checkpoint known as the G1 checkpoint, where cells are checked and the
decision is made to proceed in cell division. Stopping can be influenced by
environmental factors. In the S (synthesis phase) of the cell cycle, DNA (genetic
material) doubles and associated proteins are synthesised. G2 phase is where the
structures are set up to form a new DNA complement to be divided. A G2
checkpoint determines whether the division should proceed, which leads to
mitosis or the M phase.
• Two enzymes responsible for cell division are the cdc proteins and cyclins. p34
cdc2 is critical to the splitting of the genome. The adding and removing
phosphates (phosphorylation and dephosphorylation) in proteins is essential for
metabolism, needing ATP to toggle cdc and cyclin. The accuracy of cell division is
why life is so stable and this is all done by special enzymes.
W5MCQ#1: What phase is the DNA complement (a) synthesised and (b) divided?
the S and M phases
Prokaryotes must divide rapidly, they use cell fission to replicate. An important
note is that they do not have chromosomes. In fission, they have a DNA loop
contained in a mother cell, the cell elongates and replicates its DNA and the DNA
molecules seperate and cross membranes start forming until they form
completely. The last step is where the cross membranes pinch off to reveal
daughter cells. There are two theories that do not need to be known here.
A cytoskeleton is an intracellular network of proteins. In the chromosome,
microtubules are looped in an organised way inside the cell. The cytoskeleton
proteins are able to develop tension in long chains that can be dissolved and
reformed. They do this as a result of the supply of GTP (a close relative to ATP).
The microtubules tether chromosomes and pull them apart, through
In plant cell division, the cytoskeleton plays a key role. The microtubules of the
cytoskeleton are looped in an organised way in the cell (true for humans as well),
in order to direct the pole of growth. In preprophase, there is an assembly of
microtubules to make a prophase band, and the spindles defining where the
chromatids will migrate to. At metaphase, the mitotic spindle forms, and after the
cell division is complete, the microtubules form a phragmoplast (expanding like a
saucer from the middle of the cell to the edges) between the two daughter cells
also known as a cell plate (unique to plants in cell division) at telophase, they
pinch off to form a band in the middle (a site which directs the laying of polymers
to form the daughter cells now the chromosomes have separated to the top and
bottom side. Cytokinesis cannot occur without a cleavage furrow because plants
have tough cell walls, with is why a cell plate is formed instead.
In animal cells, the cytoskeleton plays its role in the same way, but spindle poles
are much more well defined than plants. All the negative ends of the microtubules
assemble around and the positive ends attach to the kinetochores and the
membrane pinches off. A cleavage furrow between the two daughter cells is
formed instead of a cell plate. The cytoplasm is pinched off via cytokinesis.
W6MCQ#2: Separation of the chromatids in mitosis is achieved by: attachment of
the kinetochore microtubules to the centromeres
Rates of cell division vary by the type of organism and temperature. Yeast divides
every 100 minutes, and mitosis happens in only 20 minutes. In humans, cells
divide every 20-24 hours, with mitosis taking 1 hour to divide. Cell division rates
decrease with temperature.
W6MCQ#3: Human cells divide approximately every: day
Special examples of cell division include: organelles such as mitochondria also
divide and are maternally inherited as mitochondrial DNA (mtDNA) to the offspring.
Pluripotent cells are cells have potential to differentiate to any body cell type that
can be undifferentiated forever. They undergo cell divisions but are held in the
state despite having differential potential. Asymmetric cell divisions are where the
daughter cells may be larger in size compared to the others.
Chloroplasts also perform cell division. Half the chloroplast complement goes to
one daughter and the other half to the next. They divide with a pinching of
mechanism similar to prokaryotes.
• Fucus (brown alga) is a model for asymmetric cell division, F granules are set off
for receptors so that the cell knows which way is up or down due to gravity. It
divides asymmetrically which will grow to the mature seaweed.
Lecture 12 - The formation of embryos
• Primitive species, namely invertebrates, have a different order of steps for embryo
development. Primitive sea stars for example divide to 16 cells rather than the 32
cells found in sea urchins. They proceed directly to form a blastula, then an early
gastrula, late gastrula and larva. On the other hand, once sea urchins reach 32
cells, they form a blastula, gastrula and then larva. Guiding cells are different from
the micromeres, with a different mechanism for the larva formation.
• Micromeres coordinate the formation of the embryo. They migrate through the
blastula to the gastrula. Two different types of micromeres move differently,
Skeletogenic micromeres are the large micromeres. which move to the base of the
invagination of the blastula and are on the outer corners while the small
micromeres migrate axially. Various embryogenic type (homeotic) genes will be
expressed to assist with this and at various stages of embryo formation.
• Diploidy is a powerful way of storing genetic information, many repeats of
chromosomes results in more alleles for every gene.
• The gingko trees are primitive monophyletic gymnosperms, the only species left in
their phylum and recently rediscovered. They have a strange reproductive program
where many divisions occur in the nucleus but cell plates do not form, in what is
an ancient characteristic. Thus, multiple nuclei are in the embryo and cells start to
seperate from each other with the laying of new cell walls to form a multicellular
embryo. The initial embryo accommodates 30 nuclei.
• More advanced gymnosperms e.g. pines have a transitional state where some
groups have embryos with multiple nuclei. Araucaria can have 32-64 nuclei in one
embryo. Sequoia do form cell plates immediately after mitosis.
• In angiosperms, an asymmetric cell division happens after mitosis. The
asymmetric division is crucial for the formation of the blastula. Some tissues are
maternal, which nurture the embryo. Through signalling from the diffusion
gradients, the asymmetric cell division is made possible.
• The Clavata-Wuschel feedback signalling system is responsible for the complexity
of the shoot apical meristem and the location in which genes are expressed.
• W6MCQ2#5: Asymmetric cell divisions are best characterised as: essential to set
up the first stages of development in the embryonic body
• Single gene mutations have a large effect on morphology. Cell fate maps have
been shown in corn through X rays, with a reverse genetic approach to induce
mutations in order to find which genes were responsible for the mutations. The
fate map shows that meristem cells have specific fates. Tobacco also have had
sectors of a leaf traces back to the meristem. Sectioning of tissues in meristem
shows differentiation in cell types. Laser cell ablation knocks out cells in the
longitudinal section in order, telling where the signal for development is coming
from, and the signal direction is determined (easy because plant cells are stuck
where they are). If killing of cell above makes cells proceed to develop normally,
signals are clearly coming from below the killed cell.
• Totipotency is the power of cells to differentiate into a range of all distinct tissue
types, for example an embryoid to a full plant if treated with hormones. There is a
possibility of regeneration through totipotency, with the introduction of foreign
genes/hormones. This is also the concept of stem cells.
Lecture 13 - Growth: the pathway to maturity
• After division, daughter cells must grow to a certain threshold so that they can
divide again to form equal sized daughter cells.
• Unicellular organisms can have growth estimated by counting the number of cells.
They have very large SA/V ratios, thus transport systems are highly efficient and
they can easily acquire nutrients. Multicellular organisms must acquire nutrients
through internal transport systems such as blood and lymph in animals and xylem
and phloem in plants, because they do not have the efficiency in nutrient
acquisition unicellular organisms do.
• Exponential growth is idealised growth in the presence of infinite resources,
however this is impossible most of the time.
• W7MCQ#1: A condition of cell growth is that: a critical volume is reached before
cells divide
• Most plant cell growth is osmotically driven. The cells take up solutes (inorganic
nutrients), causing water to enter the cells. The water produces a hydrostatic
pressure which pushes on the cell wall and membrane, causing expansion.
• A variation is called tip growth, which is important in the hyphae of fungi. This is
driven by turgor pressure and the lying of extracellular constituents.
• The cell can be made to blow up like a balloon, like in microalgae. Thin long black
lines are the microtubules which are randomly arrayed within the cell. This is the
radially oriented cellulose microfibrils. The second example with transverse
microfibrils, blows up vertically. This is achieved by the microtubules being
arranged in hoops around the girth of the cell. They are directed by microtubules
(intracellular proteins) in order to lay down in the transverse particular orientation.
• Initial growth is exponential, then turns linear because of nutrient limitations.
Finally, there is senescence, where there is declining growth in tissues. Absolute
growth rate measures the absolute rate of change in a factor over time.
• Secondary growth in plants would be impossible if plants and animals were not
able to reinforce their structures. Woody plants initiate a surge of secondary
growth to provide structural strength. The reason animals reach a large size is
because gravity eventually becomes intolerably heavy and water provides
buoyancy. Animals are limited by the internal skeletons and plants are limited by
the external exoskeletons known as wood.
• W7MCQ#2: Exponential growth can be modelled mathematically by: conversion to
natural logarithms to depict linear growth with time
• Animal embryos are where exponential growth is likely. Early stages of
embryogenesis, cells grow and divide up till 16 cells. Then cells go into a pathway
of determination, they differentiate and their fate is sealed.
• Lateral growth is required for multicellular organisms to be successful. It produces
branches and limbs. Controlled mitosis pushes out lateral from the centre of the
root in plants. Genes responsible for initiating mitotic cell divisions set up the
zones of the tissue in which the cell division takes place to give rise to laterals.
• Allometrics explains that there are mathematic relationships between the size of
organs in multicellular organisms in a fixed way. The relationship can be between
the size of an organ and metabolism efficiency.
• W7MCQ#3: Allometrics is best described as: the relationship between some
metric of a body and a second process, or metric
• Apoptosis is programmed cell death, found in both plants and animals.
Sometimes growth needs to be reversed. Examples include apoptosis to remove
webbing in human hands.
Lecture 14 - Algae and lower plants
• Clamydomonas is a single celled freshwater algae which undergoes meiosis with
haploid and diploid phases. Plasmogamy is 1 of 2 stages of haploid fusing, where
the cell contents are fused. Karyogamy is the fusing of DNA to produce a diploid
zygote. This belongs the class chlorophyceae. Haploid chlamydomonas are
flagellated. Diploid phase in these is very short, typical of lower orders of algae.
• Some Chlorophyceae are non motile and colonial. At times, protection being in a
colony is greater than the ability to move by flagella. Hydrodictyon has a complex
matrix where individual cells are fused together. Chloroccocum is also a nonmotile
algae with vegetative spores and is flagellated.
• Not all algae are solely autotrophic or heterotrophic, but are hybrids, deemed as
• Diatoms are dinoflagellates abundant in the ocean. They have silicon based cell
walls, and symmetrical patterns.
• The higher brown algae (Fucus) has a fertilisation event involving sperm and egg
cell lines. The dominant phase in the life cycle of these algae is now the diploid
sporophytic phase, because these algae are advanced. Sperm cells in these algae
are motile, like in humans.
• Slime moulds are non-photosynthetic protists that eat organic matter. They have a
substantial proportion of their life cycle as amoebae, a haploid phase. Then they
undergo plasmogamy and karyogamy to produce a diploid zygote. The zygote
undergoes an assembly into a multicellular phase (Diplophase), producing
sporangium (spore producing structure) which does back to produce more
haploid spores, restarting the cycle.
• Bryophytes (mosses, liverworts) are the lowest of the land plants. They are
seedless and non vascular plants. They arose from ancestral green algae. The
moss life cycle shows an increasing domination of the haploid phase. After the
diploid phase, meiosis occurs, producing spores, then diverging into two cell lines
(male gametophyte or female gametophyte) which produces sperm cells or egg
cells which fuse in a recognition system to produce a sporophyte zygote, then
another phase of growth which is diploid and produces a mature sporophyte.
Liverworts have sperm cells embedded into the Antheridium and egg cells are
embedded into the Archegonium. This shows the increasing complexity of sexual
• Pteridophytes are plants that are seedless and vascular. Psilotums (whisk ferns)
are similar to the advanced mosses with the embedded eggs and highly
differentiated motile sperm. The diploid phase is more dominant in higher primitive
W8MCQ#1: Mosses, ferns and all higher plants distinguish themselves from algae
by: always having a dominant sporophytic (diploid) phase of growth
In advanced ferns, the mature plant is diploid. These also contain Antheridium and
Archegonium, arising from the mature gametophyte. These plants can be
Homosporous (produces one spore that is both male and female) or
Heterosporous (produces two distinct spores that are either male or female).
Algae gain nutrients by diffusion. relying on it because of a lack of an internal
transport system. At a membrane level, transport systems are highly efficient.
After meiosis they produce zoospores and have many inorganic constituents in
their cell walls, with a very hard cell wall structure. Algae arose from multiple
endosymbiotic events.
Mosses also rely on diffusion because of a lack of transport systems internally.
Mosses have the unique ability to dehydrate. They contain elaters, scales that
absorb water, hydroids which concoct water and leptoids which are pre-empting
the evolution of phloem cells.
M8MCQ#2: Water transport in the algae and mosses is distinctively different from
the fern because it relies primarily on: diffusion and surface tension
Light detectors containing pigments are present in single celled autotrophic
microalgae, which act as a light receptor. The stigma is the eyespot which works
with the light detector.
W8MCQ#3: Biological hydrogen generation relies upon: Reduced (gain of
electrons) substrates (water). 2H2O -> 2H2 + O2.
Lecture 15 - Higher plants
• Phylogeny of the gymnosperms goes back to the Devonian period, 360 mya.
Gymnosperms are ancient and highly diverse. Some lineages have died out over
time. Exctinct gymnosperms include Lycophytes and progymnosperms.
Archaeopteris (a pro gymnosperm) is at a boundary for being a gymnosperm and
a fern, with fern like leaves.
• Cordetailes died out 250 mya. Archaeopteris died out 360 mya. Extant groups
include cycads which are represented in the southern hemisphere, the conifers
which are the most successful of modern gymnosperms with thousands of
species, the gnetophytes with few species and the ginkgo which has only one
surviving species.
• The extinct plants had fern like leaves and possibly died because of inferior
transport systems during drying conditions.
• Coniferophyta have needlelike leaves and are well adapted for cold conditions.
They contain chemical antifreeze compounds that allow them to freeze in winter.
Life cycle includes pollen cones which are falloff microsporocytes. The dominant
phase in the life cycle is as a mature sporophyte in the diploid phase. There are
two types of cones, the male pollen cone and the female megasporangophyll with
embedded eggs.
• W8MCQ#4: Higher plants are distinguished from lower plants by:
• Angiosperms are widely successful because of a number of physiological
characteristics. There are at least 300,000 species and they fall into two classes:
Monocots and Dicots. Dicots have two cotyledons (leaves) emerging from
germinating leaves while the monocot has one sheath like leaf. Leaf venation
varies, in Dicots veins are netlike in order to increase light capture efficiency, with
consequences for water loss. Monocot leaves are almost always parallel in
A primitive angiosperm has radically different microsporocytes and
megasporocytes produced from their flowers. These form the male and female cell
lines respectively. A double fertilisation event occurs in both monocots and dicots,
where two male cells interact with multiple cells within the egg. This gives rise to
the diploid zygote.
Monocots have are more enclosed flower and are often self fertilising when
compared to dicots.
Dicots are more often pollinated by insects and environmental factors such as
Transport is a physiological feature apart from reproduction which has enabled
higher plants become so diverse. They achieve bi-directional transport split
between the xylem and phloem. The long distance transport of water and
nutrients is via two cell types that differ depending on the type of angiosperm or
gymnosperm. Normal angiosperms use xylem and woody dicots and
gymnosperms use tracheids. The bidirectional transport is achieved through the
primary xylem (inside the vascular bundle of the xylem are large vessels with
perforated end walls joining one vessel to the next) and thus a capacity for a long
distance transport system is achieved. Adjacent to it is the primary phloem (living
cells which transport photo assimilates from the photosynthetic sites of the leaves
down to the stems and fruits).
Primary plant tissues arise from primary meristems in the tips of the roots and
shoots. They are characterised by having vascular bundles. Earlier plants had
vascular bundles as their transport system, as vascular tissue had not evolved yet.
Secondary plant tissue arose from the characteristic of the vascular bundles of the
primary tissue joining to produce a concentric ring of dividing cells. This is seen in
woody dicots and gymnosperms.
W8MCQ#5: Long-distance transport of sap in plants is largely achieved by the
forces of:
W8MCQ#6: Sexual reproduction in angiosperms (flowering plants) differs
fundamentally from that in higher animals. For example: plants have no sex
chromosomes and can be bisexual or hermaphrodite
Lecture 16 - Animals: the extracellular matrix
• There are 200 cell types in animal tissues, but only 20 cell types in plants.
Prokaryotes have even fewer. This is due to animals needing to move and
metabolised response to stimuli.
• The generalised animal cell differs from plants in that there is not a large central
vacuole. It is highly compartmentalised, like plant cells, in order to safely harbour
enzymes and concentrate metabolism into compartments, allowing catalysis
(enzyme activity) to occur.
• The extracellular matrix is required for animal function. It provides structural and
biochemical support of surrounding cells, supporting local tissue growth to
maintenance of the entire system. It is associated in the gut with the basement
membrane (basal lamina). Blood vessels are beneath the Basal cell surface and
basement membrane, which participates in absorption of nutrients out of the gut.
Basal laminae provide physical support and tracts for the migration of cells and
are part of filtration in the kidney. The ECM crosses the membrane by two
methods: Exocytosis. where the golgi bodies fuse with the plasma membranes
causing them to join and there is an invagination with the proteins in the vesicle
membrane secreting components of the extracellular metric into the extracellular
matrix space. In endocytosis, components are endocytosed into the cell. Through
the invagination of the membrane and the production of a new endocytic vesicle,
capture is reversed in endocytosis.
Animal ECM is a network of fibrous proteins; collagen and elastin, proteoglycans
(feathery structures) that branch over hyaluronic acid threads and adhesion
proteins. Structural and adhesion proteins link components of ECM to each other.
The ECM cases cells, giving cell differentiation and allows cells to migrate. It is
involved in cell division and is essential for physical function of all connective
Fibrous proteins (Collagen for strength and Elastin for elasticity) are hydrophobic
and form a protein based scaffold which gives the matrix strength and rigidity.
Collagen is heterogenous, with multiple variations, 16 distinct forms in total.
Collagen is made analogous to Cellulose, it is manufactured inside the cell and
exocytosed out of the cell (Cellulose is endocytosed through a cellulose synthase
complex). Cellulose is derived from an α chain of collagen, which is woven into
soluble procollagen (starts off soluble in order to allow interweaving of the α
collagen chains which then get produced into a vesicle, coalescing into the golgi
body, a structure that delivers macromolecules to the membrane of the cell). An
exocytotic event then happens where the collagen chain is exocytosed into the
The fibrous proteins of collagen are produced by Gly-X-Y tripeptides. X and Y are
the amino acids proline and hydroxyproline. Lysine helps cross link polymers, to
strengthen collagen fibers. alpha collagen is trimeric (made of 3 polymers woven
into a chain). Weaving fibres together leads to a disproportionate increase in
Elastin is the other ECM structural component, critical for twisting and movement.
They are found in all vertebrates except for lampreys and hagfish. They are
synthesised initially as a protoelastin in the cell, tropoelastin chaperone complex
are participants in the assembly of the major proteins in the golgi bodies being
delivered to the extracellular matrix in the form of a growing elastic fibre. It
interacts with collagen to make a loosely structured elastin collagen complex
which allows for the strength and stretchiness which is critical for movement in
animals. These are found in ligaments and artery walls in the lungs and are found
less in the skin. These tropoelastin subunits have a microfibril sheath and its
thermodynamically relaxed form is because of its helical structure. It is rich in
glycine and proline, like collagen but has no hydroxyproline which collagen has.
Like collagen, it is a hydrophobic molecule, cannot be soluble in order to function.
Fibronectin are large glycoproteins (uniquitous to vertebrates) that connect cells to
matrices with collagen. Without them organisms would not assume a form or have
strength. There are 20 forms of these cross linking agents which bind with heparin
sulphate and proteoglycan (sugary moieties) and align internally with the actin
filaments within the cell (plants and animals both have it).
Proteoglycans are complex branching sugar rich glycosylated branching polymers
between the structures of the extracellular matrix, where they regulate the
movement of molecules and affecting proteins and signalling molecules. There are
a number of components: Chondroitin sulfate is found in cartilage, bone and skin,
Karatin sulfate found in bones and the cornea, Darmatan sulfate found in the
tendons, Heparan sulfate found in the Basal laminae and cornea and Hyaluronic
acid is found in the cartilage. The former are vast molecules found in structural
tissues and connecting them. They are highly negatively charged because of the
side chains of sulphate, carboxyl groups and ironic acid residues. They strongly
react with cations thus they are highly hydrophilic molecules. They have repeating
polysaccharide polymers are are often 95% carbohydrate. They are synthesised in
the endoplasmic reticulum within the cell and secreted through the golgi bodies
and plasma membrane.
Hyaluron (sugar rich GAG chains) is the backbone onto the sugar rich
proteoglycans are linked. It is a member of the glucosaminoglycan family. It is
synthesised in the golgi bodies but not the plasma membrane. It doesn’t contain
sulfur but crosslinks to proteoglycan and collagen. They are huge molecules
critical for the interaction between collagen in organs such as eyes, where they
synthesise vitreous humour.
Specialised proteoglycans e.g. Aggrecan are a large protein core with chondroitin
sulphate and keratin sulphate chain with sugar rich molecules. Side chains can be
used to decorate the specialised proteoglycans. They are compressable
structures and highly rich in sugars so they can rehydrate to many times their
volume in the dry form when water is added, important for tissues that need
absorb compression and be flexible.
Cell surface receptors are embedded in the Extracellular membrane. They have to
span the lipid bilayer and contain a characteristic hydrophobic region. Cells have
to recognise each other and move towards each other during development.
Recognition on Fibronectin protein allows it to link to collagen on the ECM.
There are other structural proteins that link to the transmembrane proteins such as
thrombospondin, Willebrand factor and Tenascin. They are all critical for cell
development and disease.
W9MCQ#1: Two major strengthening polymers in plants and animals are cellulose
and collagen. They are similar in one way (A): and different in another (B): they
have polymer chains woven together to make a stronger chain but (B) one is made
of sugars, the other of amino acids
W9MCQ#2: Two major fibrous protein families in animal cells are: elastin and
W9MCQ#3: ECM is most comprehensively described as important in the
processes of: cell shape formation, cell-cell communication and many aspects of
cell function
Lecture 17 - Animal reproduction
• r selected animals are usually small animals that reach reproductive age,
reproduce quickly and are vulnerable to predators. K selected are large animals in
general and in more stable environments, longer lived and invest more energy into
offspring care as well as as have high probability of survival.
• Mates find each other through pheromones e.g. moths. Seasonality and migration
control the annual cycle of reproduction and requires a large amount of
coordination. Some animals go back to where they were born to reproduce (natal
philopatry). Function of reproductive organs can be studied.
• Asexual reproduction does exist in animals. Typical examples are corals, which
occur by budding (cloning). Stick insects, crustaceans and certain fish can have
whole unfertilised egg that develops into a whole organism genetically identical to
the mother (parthenogenesis). Parthenogenesis can happen among vertebrates,
but it is extremely rare. A case has been shown in an Eagle ray.
• Sexual reproduction is the joining of eggs from a female and sperm from a male.
Offspring will have half the genetic information of the parents.
• Sex determination differs with species. Humans have XY chromosome systems.
Presence of Y chromosome no matter what turns sex into male. Fly species also
have XY. Superficially it is similar, but XXY will be female, because XX determines
female sex. Birds have a ZW system and other insects have a haplodiploid
system. A female may be diploid and male haploid, when female with egg not
fertilised it becomes male, if fertilised it is female.
• Seasonality is very important for reproduction. Temperatures are a cue that is
used at times to determine seasonality, but it is not very reliable because seasons
don’t always have constant temperatures e.g. summer can be cold and winter can
be hot. Photoperiods are much better indicators, it is measured by the number of
hours of daylight per 24 hours. Most animals use the photoperiod, and plants.
• Some species have a circuannual clock, once a year there is a timestamp and a
cycle is locked in. It is only an approximation. Other species have a continuous
adjustment of reproductive status to current photoperiod.
• The hormone Melatonin is derived from Serotonin. It helps with hibernation, as the
more sunlight you are exposed to the less produced and the less light the more
melatonin. It is responsible for jet lag. Reproduction needs to be synchronised
with photoperiods and in a temperate climate. It’s important for the entire
community and is an interspecies affair as well as intraspecies. Climate change
cause temperatures to rise but photoperiod stays the same so decoupling
happens between those that use temperature and those that use photoperiods.
• Semelparous reproduce only once and die. Examples include salmon, octopi,
worms and mayflies. When an animal dies, it is called phenoptosis, programmed
death mediated by a neuroendocrine control mechanism which can also be
photoperiod regulated. They can also refrain from feeding and cannibalise each
other. Iteroparous animals are designed to reproduce two or more times in life.
• The reproductive output determines survival. r selected and K selected can be
optimal determining on the right environment, which is why they have both
evolved. Sea urchins can release 1 million to 20 million eggs once.
• Sequential hermaphroditism is a sex change sequentially. Examples include
clownfish. The environment and sex ratio plays a key role in pivoting this. When
male first, it is more practical if fertilisation occurs externally. A lot of fertilisation
occurs externally in fishes, allowing for easier sex change. Protoandrous are those
that start off male and Protogynous are those that start off female.
• Other mechanisms to determine sex are temperature or location of nest. Turtles
and crocodiles use this mechanism.
• Some rabbits and hares have a system where the copulation triggers the females
to go into a hormone surge. This is known as induced ovulation, and energy is
conserved. A minority of mammals have this system. Spontaneous ovulation
happens for most mammal species. Hormones are involved in these. Sperm is
continually produced, if there is a single male there is no need to produce as
much of it in comparison to male competition. Testis size can determine systems,
whether they are monogamous or polygynous.
• Embryonic diapause is a delayed implantation based on conditions, perfectly
timed with appropriate season. Only some animal species employ this.
Lecture 18 - Plant hormones
• Nanomolar quantities of ions like calcium can cause a phenotypic change,
supplication causes plant roots to bend. Calcium calmodulin is a calcium binding
protein that activates calcium pumps
• Plant hormones very effective and can work at very low concentrations, mostly at
micromolars which are 10-6 molars, rather than millimolar or molar.
• Hormones are endogenous molecules (produced inside the cell) that regulate plant
growth and development. They control many processes crucial for life, such as
stress response or flowering. They are also responsible for anoxia adaptions in
rice seedlings (one of the only plants which can grow in anoxic conditions), where
3 hormones interact, causing snorkel formation. Some hormones block cell
division that forms roots or development shoots and photosynthetic apparatuses.
Cactuses are another example. Auxin is released from the apical dome and moves
downwards in a directionally controlled polar fashion, suppressing outgrowth of
flowers and buds near the bottom of the plant. Apical dominance (dominance of
cell meristems) are what allow plants to grow tall and capture light and is caused
by the polar travel of Auxin down the plant. The more auxin, the softer the cell wall
becomes, allowing for more plasticity which allows growth to occur.
• Biosynthetic pathways synthesise hormones and are not spontaneously occurring.
Hormones can act locally or remotely and can move through plants via the xylem
and phloem and can travel over both short and long distances. Hormones can be
inhibited by both artificial or natural compounds. Auxin transport inhibitors are an
example that affect the movement of Auxin through plants, producing branches
and flowers at the stem (Flavonol and Genestone compounds block movement of
auxin down the stem) which causes budding to occur.
• Plants have no nervous system and produce multifunctional (Pleiotropic)
hormones in many locations. Animals restrict hormone production to only specific
cell types. Hormones in animals are specialised for single functions, with no
pleiotropic effects.
• Week10MCQ#1: Hormones in plants differ from those in animals in that they:
• There are five major hormone groups for plants: Auxins, Cytokinenes, ethylene,
Abscisic acid and Gibberellic acid.
• Auxins have a recurring simple double ring (indole) structure. 2,4Dichlorophenoxyacetic acid is a synthetic Auxin hormone that is used as a
• Charles Darwin initiated the discovery of auxin. He did an experiment where the
coleoptiles (sheath) of oats bent towards light. He removed the coleoptiles and
realised that without the sheath, the oat didn’t bend towards the light. He then
concluded that light perception was located in the coleoptile. Boyson-Jensen
discovered that there was a signal in the death situated opposite from the light.
They realised that what was moving was soluble in water, through the use of
gelatin. Went did a similar experiment, it was later discovered that the compound
was auxin.
• Auxin move from the hypocotyl. Plants have a strong polarity thus Auxin can only
move downwards and not upwards.
• Plants have a strong polarity thus Auxin can only move downwards and not
upwards. It has been shown that Auxin has stimulated root outgrowth via cell
expansion in the African violet. Auxin has also been known to enhance ripening in
strawberries, pineapples, grapes, cherries and other non-climacteric fruits. This is
a key example of Pleiotrophy of plant hormones.
• Cytokinins are critical in cancer research and are a major tool for biotechnology.
They cause cells to divide rapidly and can cause tumorous galls on plant tissues.
• There are many synthetic Cytokinins. Zeatin is an example of a natural Cytokinin
extracted from maize. Cytokinin levels can be genetically modified to test
phenotypic effects on plants. When Cytokinins are not bring broken down,
excessively oversized plant roots are a result. Cytokinin presence is most
commonly known to delay senescence (ageing) of plants, promoting longevity.
• Similarly to Auxin, Cytokinins travel downwards in a polar fashion. Cytokinines
trigger various signalling processes as they move through the plant body.
• Ethylene is a gaseous hormone which can diffuse into plant receptors. It is a
hydrocarbon with two double bonded carbons and four hydrogens. Ethylene has a
three step production process, this is found in apples (Climacteric fruits). In
arabidopsis, Ethylene causes stumpy mutational seedlings, and is responsible for
senesence. Plants without the ability to detect Ethylene will have tall growth
compared to Ethylene filled normal plants. Ethylene is also responsible for leaf
abscission once it is released by hormonal interaction with Auxin accumulation.
Ethylene causes cell walls in the plant petiole to soften and drop leaves. Ethylene
can cause a burst of respiration (Climacteric rise), and the burst of Ethylene
causes ripening, softening cell walls and aroma/flavour production.
• Abscisic acid (ABA) can prevent seed germination and also restricts water loss
from shoots by controlling the closing of stomates. ABA was understood through
the study of mutant populations. For example, VP14 in corn can cause precocious
growing in corn seeds, therefore seeds don’t know whether to remain dormant.
Under the control of ABA, the closing of stomates evolved 400 million years ago in
terrestrial plants. ABA is released from the Xylem sap and delivered to Stomates in
order to control their closing.
• Gibberellic acid controls lengthening and height of plant stems (internode
elongation). Suppressing GA resulted in dwarf plants which invested more energy
into making seeds, increasing food production. A downside is that these dwarf
plants have a higher nutrient requirement. Excess Gibberellic acid causes
immensely tall plants, which subsequently reduces yield. GA causes the increase
in the length of peduncles and internodes, opening up bunches and reducing
chance of infection in humidity. GA also causes hydrolytic enzymes to be
released, causing barley seeds to be converted into malt. This is effectively used
in breweries. GA also causes early flowering.
Release of GA determines the germination of plants. They switch on genes that
cause amylase to return to the endosperm and increase sugar availability. The
presence of GA significantly increases the rate of germination.
Week10MCQ#2: Which of these observations is an example of pleiotropy?
Hormone phenotypic output is reached by interactions between different
hormones, dose responses and Negative and Positive signalling to turn hormones
on and off.
Domination of certain plant hormones can determine cell wall/cell shape. Cells
can elongate in a polar fashion with the dominance of Gibberellic acid or they can
become isodiametric (spherical) with the dominance of Ethylene.
Cell culture development is controlled in an exogenous fashion by Cytokinin and
Elongation growth is best when in moderate exposure to Auxin, as shown in the
dose response curve. As such, concentration determines the magnitude of the
Week10MCQ#3: Hormone interactions are so effective because:
Brassinosteroids are steroids synthesised by plants, of which there are 40 different
types. They do not constitute main plant hormones because their function has not
been clearly determined, even though they are known to regulate growth. The
signal transduction pathway of these hormones has been elucidated.
Salicylic acid is a phenolic phytohormone (plant hormone). Along with Jasmonic
acid (Jasmonate class of phytohormones found in several plants), it plays a role in
the defence response of plants through a Systematic acquired resistance pathway
(SAR), from the inducing of Signal transduction pathways (lecture 23).
Lecture 19 - Animal hormones
• Animal Hormones are special, as they travel through the blood. There are three
types of hormones in animals: Steroids, peptides and amines. Steroids are derived
from cholesterol and are lipid soluble. Peptides are derived from amino acids and
are water soluble, while amines are also water soluble are are derived from
modified amino acids.
• Like plant hormones, they work at very low concentrations of less than 10-6 and
are thus very effective. However they do not work close to where they are
synthesised because they have to travel through the central nervous system and
they have more narrow concentration ranges.
• Cholesterol is first cleaved in the mitochondria in order to form steroids in a
creation pathway. Steroids are synthesised on demand by Pregenolone and
released by diffusion.
• Week10MCQ#4: Steroid hormones are…
• Insulin is a well known example of a peptide. Synthesis occurs in the beta cells of
the pancreas. They are hydrophilic and thus cannot move on their own.
• Amines undergo multiple transformations to achieve different forms.
• Thyroid hormones (Iodothyronines) are Amines (Tyrosine amino acid derived), and
like steroids, are lipid soluble and have to be transported through the blood by
carrier proteins. Other Amines and Peptides are water soluble hormones which
have to bind to the receptor on the cell membrane, with a second messenger
signalling cascade.
• The cAMP pathway is an example which transports water soluble hormones. It
starts when a hormone binds to a receptor, and the receptor changes, allowing
phosphorylation and activating g proteins. The g proteins then proceed to activate
adenyl cyclase, ATP then activates the cAMP (second messenger) in order to
activate Protein kinase A?
• The pituitary gland has two types: Posterior and Anterior. Posterior has multiple
subregions and neutrons. It is under neural control and releases vasopressin and
oxytocin directly into the bloodstream. The anterior pituitary gland is under
neurosecretory control. The Parvocellular neurons of the Anterior pituitary releases
or inhibit hormones.
• In the stress response, there are early effects and delayed effects. The early
effects include increased heart rate, increased ventilation, increased
vasoconstriction, decreased digestion and increased Glucagon. The Adrenal
cortex enhances early effects to increase fat catabolism, lower insulin and release
glucose from muscle and liver. Delayed responses include: increase in liver
glucoeoneogenesis (glucose production), increase in muscle/bone/protein
catabolism (breakdown), increase in amino acids, fatty acids and glycerol. TSH
(Thyroid stimulating hormone) and gonadotropins (stimulate gonads, essential for
sexual reproduction) are inhibited.
• Week10MCQ#5: Which is primarily a delayed physiological stress response?
• Hormones have two types of effects: Activational and Organizational. Activational
are involving already developed organs, are triggered by stimuli and are often
reversible while Organizational are hormonal effects during developing of the
body, they are genetically determined and not reversible.
• Juvenile hormone is a gonadotropin for reproductively mature insects. An increase
in JH increases pheromone production, increases oocyte development rate,
increases vitellogenin synthesis yield, and positively affects oviposition behaviour
(laying egg behaviour) and mating behaviour.
• Week10MCQ#6: Which of the following is not considered to be initiated by
increased juvenile hormone levels?
• There are two types of metamorphosis: Hemimetabolous development, where the
insect gets larger in each stage (instar) and Holometabolous development, where
the larvae metabolise into pupae and then an adult stage (e.g. butterflies/moths).
• JH can determine the identity and status of Hemimetabolous eusocial ants. The
more JH in a diploid individual, the higher the probability of becoming the queen
ant. The less JH of a diploid ant, the higher probability of becoming a female
worker. Haploid ants are the males.
Lecture 20 - Plant responses to stimuli
• Adaption is associated by genetic changes in response to selective pressures.
Acclimation is a response of the current gene combination (phenotypic plasticity),
to change expression pathways. An example is the expression of heat shock
proteins which are turned on in suitable conditions.
Common abiotic stresses include flooding, heat, cold, drought and salinity.
M11MCQ#1: How is a nastic movement different from a tropism?
Nastic movements are movements in response to an external stimulus that is not
of a particular direction.
Thigmonasty is the movement in response to touch. Touch stimulated arabidopsis
has lower growth that occurs due to upregulation. A potassium influx in touch
stimulated Mimosa causes a turgor driven closing of leaflets (from the loss of
solutes and loss of turgor pressure).
Tropisms are directional responses to stimuli. There are three main types:
Phototropism; response to light (controlled by the movement of auxin in the plant),
Gravitropism; response to gravity controlled by sensing mechanisms in the root of
the plant and Thigmotropism; the response to the touching of a solid object (found
in jungle climbing vines).
Heliotropic plants are those that can track the sun. They are built in many plants,
most of those flowers. Leaves and flowers that follow the direction of the sun can
maximise photosynthetic opportunity and pollination. Examples are sunflowers.
Mechanisms and explanation for this are not known.
Gravitropism is when roots grow downwards, statocytes mediate this by settling
on the root apex in a secondary signalling response. Gravity is detected by the
settling of the amyloplasts at the bottom of the cell.
Most plants strongly rely on light. Plants have been shown to have strong
responses to blue light, suggesting the presence of blue light receptors. Blue light
regulates the opening of stomates. It has been shown to be a light directed
response. Red light is also another cue for stomatal opening. These responses
are regulated by chromophores (red/far red light detectors attached to proteins). A
switch mechanism converts the structure of phytochrome (a chromophore
polypeptide attached to a moiety that mediates red light responses), changing the
phytochrome structure from cis to trans. From 730 nanometers (far red range),
phytochrome is switched off. Once back to the normal red range, it is switched on
again. Germination always occurs in red light, but not far red light.
Red light can regulate other processes, with Phytochrome regulating Circadian
In flooding, plants respond by developing aerenchyma (air spaces) which allow for
long distance transport of oxygen through diffusion.
Some plants need chilling events to germinate. These plants also need adaptions
to allow the tolerance of cold conditions.
W11MCQ#2: Which of these molecules is important in signal transduction?
W11MCQ#3: What two environmental variables most strongly affect switches in
plant development, such as initiation of flowering?
Lecture 21 - Response to stimuli in animals
• Animals require sensory organs to detect stimuli. Sensory receptors in the organ
convert sensory stimuli to electrical energy. The nerve impulses are transmitted to
the central nervous system, where decision making occurs and the decision is
transmitted as a signal through neurons to the effectors (response mediators)
In the animal kingdom, the nervous system is highly diverse in terms of structure
and complexity. The Hydra has interconnected nerve cells, while more complex
animals have nerves and a central nervous system connected.
The pupil response is how animals respond to light stimuli. The pupil in bright light
is dilated to protect photoreceptors against strong incident light. Dark situations
cause the pupil to inflate. This response is also found in ants, even though the eye
structure is different from vertebrates. The ant has thousands of eye units called
ommatidium. Lens constitute a section of the ommatidium, protruding out
towards the external side of the eye. Light coming from the lens is received by the
photoreceptor. In bright light conditions, pupillary pigments are close to the lens
and constrict to limit incident light entering. In dim light, pupillary pigment moves
away from the lens, then the eye can increase sensitivity to light.
Nocturnal insects contain a second class of the compound eye, called the
superposition compound eye. In these eyes, there is a clear zone beneath the
lens. The photoreceptors can receive light from multiple lenses to maximise
sensitivity. Tapetum is a constituent of nocturnal eyes that contributes to high
sensitivity, in the superposition eye it is located beneath the clear zone.
Day active (diurnal) insects include honeybees. They possess Apposition
compound eyes, which can only receive light from its own lens, there is no cross
circuitry between lenses. Light sensitivity is low and there is higher spatial
resolution. These eyes can sometimes have tapetum, the presence varies
depending on the insect type.
W11MCQ#4: Which responses do eyes show when they are exposed to bright
Chemical stimuli can be sensed as taste and smell. Chemicals can be used to
detect food, predators and mates. Female moths, for example, can release
pheromones. Males can detect the change in chemical concentration to find his
mate. Insects like ants use pheromones for trail marking. The sense of taste
allows for the discrimination of soluble stimulants that elicit feeding and
reproductive responses in animals. Taste is known as contact chemoreception.
Hairlike structures called sensilla detect taste and smell. The sensilla varies
depending on the sense type. Olfaction sensilla are mainly located on the
antennae and mouthpart. Taste sensilla are located on the legs, wings and
ovipository regions. Olefaction sensilla contain many pores (multiporous) where
chemicals combine.
Taste sensilla are uniporous, with a pore at the top of the hair structure. Chemical
receptors are located at the base of the hair structure, where the dendrite is
extended along the length of it. The mid region of the dendrites and the pores are
where chemicals align and bind with the olfaction binding protein, activating it.
The Olfaction binding protein then interacts with the receptor, sending transducer
signals to the chemoreceptors.
Mechanical stimuli is mechanical movement caused by the environment, the
animal or internal forces derived from muscle movement (touch, pressure, stretch
vibration/sound). Sound is also classified as acoustic stimuli. There are three
types of mechanoreception: tactile mechanoreception, position mechanoreception
and sound reception.
• Trichoid sensilla is used for tactile mechanoreception. It is distributed in the body
surface of insects, especially on the cercus at the rear of the insect. These consist
of hair structures and a flexible socket connected to the sensory cell. Any
touching of the hair from fluctuations in air pressure or direct touch can cause
electric signals to form in the sensory neurons. They are very sensitive and
support rapid escape behaviour.
• Position mechanoreception is another form of mechanoreception. Relative
position of the body is needed to coordinate body movement and balance.
Distribution of different mechanosensors are located in the leg. Trichoid sensilla is
also used for position mechanoreception. Flying insects posses another
mechanoreceptor called a Haltere (a mechanoreceptive organ derived from
hindwings in diptera or forewings). During flight, halteres oscillate at wing beat
frequency to sense the Coriolis force with their sensillum in order to measure body
rotations and maintain flight. Sensory information from halteres is sent to the
motor neurons, allowing for wing control.
• Sound reception is regulated by the ear, involving fluctuation in pressure
transmitted in a waveform via the movement of air or substrate. Humans can hear
sound frequencies of 20 hertz to 20000 kilohertz. Insects and invertebrates can
hear a wider range (2~100000 kilohertz). Insects often use sound for
communication. The ear in mosquitos is located on their antennae. The
mechanosensory organ is called a scolophore, which is connected to the antenna
shaft - located on the antenna base. When the shaft vibrates from sound,
scolophores are stimulated. Stimulation is greater when antennae is pointed
towards the sound source. Male mosquitoes are only sensitive to specific
frequencies caused by female wings, which allows for mating. Cicadas and
locusts have a special hearing system called a Tympanal vibration system. It is
located in the first segment of the abdomen in cicadas. In locusts it is located in
the first segment of the leg. The system consists of mechanoreceptor scolophores
ad a tympanal membrane which acts as an ear drum. Entry of sound causes the
tympanal membrane to vibrate.
• W11MCQ#5: Which of these sensilla below is best suited to detect odour?
• The last stimuli is temperature. Detection is crucial for animal survival. To avoid
temperature changes, animals migrate to optimal conditions. Insects and reptiles
are ectotherms, and bask in the sun to increase body temperature. The insect
abdomen can act as a heat sink and radiator, and regulate body temperature.
Torpor/dormancy is another strategy to avoid temperature change.
• Temperature changes are detected by thermoreceptors. In insects. some
thermoreceptors are found on the sensilla in insect antennae. Typically,
temperature and humidity receptors are present together in a single sensillum.
Many insects (Cockroaches, locusts, crickets, moths, honeybees and ants)
possess only one type of thermoreceptor on their antennae. In these, the same
thermoreceptors are excited by cooling and inhibited by warming, with cold
receptors continuously active at constant temperatures. Each antennae has
twenty thermoreceptors located inside. In fruit flies however, they possess both
hot and cold thermoreceptor neurons in their antennae. There are hot cells that
are activated by heat and cold cells activated by cold. In turn, cold conditions
inhibit hot cells and hot conditions inhibit cold cells. Australian fire beetles use fire
to oviposit. Their sensilla are located in the pit organs of their abdomen. There are
50-100 sensilla located in these pit organs. Heat induced expansion of fluid is
converted to a mechanoreceptive signal.
• W11MCQ#6: Where are thermoreceptors located in the fruit fly?
• Hairs can have thermoregulatory effects, as seen in the thermophilic Saharan
Silver ant.
Lecture 22 - Muscles and motion
• Muscles only work when they contract. The synapse is purely excitatory. Muscles
often work in pairs or groups on either side of a joint. The muscle itself is made of
fascicles. Each fascicle is a bundle of muscle fibres, the muscle fibres also known
as muscle cells or myocytes. They are very long, and exchange from tendon to
tendon. Muscle fibres are excitable cells. They can be stimulated to change
voltage and change the cell structure. Action potentials in muscle are produced
similarly to those in nerves.
• Higher level control has two different types of neurons; upper motor neurons are
the executive control and modulate the activity of lower motor neurons. Upper
motor neurons are located in the brain stem. Lower motor neurons are located in
the brainstem and spinal chord, receiving input from upper motor neurons or
reflexes from periphery working through reflex in brainstem or spine. These
working together excite muscles. Lower motor neurons are the only neurons that
directly contact muscle cells.
• Motor pools are all collective Lower motor neurons that innervate the muscle, a
motor unit is a single lower motor neuron and joined innervated muscle fibres
which can be few or many. When activated muscle fibres contract, nervous syste,
must recruit different size motor units. Motor units that are small contact few
muscle fibres with a resulting low force. Large motor units contact 100-1000
muscle fibres, resulting in a powerful contraction. The latter is used for lifting and
rapid movement, resulting in more rapid fatigue. An increase in active motor unit
numbers is known as recruitment. Asynchronous recruitment is when motor units
contract at different intervals to prevent fatigue.
• Muscle fibre structure is long, formed by fusion of cells. Thus, there are multiple
nuclei and mitochondria (for excessive energy demand). Sarcolemma is the
plasma membrane, while the sarcoplasm is the cytoplasm. These are cylindrical at
around 50nm diameter. Myofibrils are the elongated contractile unit which
shortens muscle upon contraction. Sarcoplasmic reticulum is involved in the
excitation of the muscle via action potential coming through the nerve. Myofibrils
are highly banded and striated. The Z-line is an important band that connects
respective ends of sarcomeres. Cross section shows thin and thick filaments.
• W12MCQ#1: The elongated contractile structures within an individual muscle fibre
are called?
• Sarcomere is a subunit of myofibril and the functional unit of contraction. Each
sarcomere contracts, pulling Z-lines (discs) towards M-lines. Fine structure has
thick filament called Myosin filament and thin filament called actin filament.
Proteins support these filaments. Titin has high elasticity and supports myosin.
Nebulin supports actin. Cross section shows each thick filament is surrounded by
6 thin filaments and each thin filament is surrounded by 3 thick filaments. This
allows Actin and Myosin to interact, which is essential for the contraction process.
The thick filament (myosin filament) contains a head called a cross bridge. This
head has an actin binding site (where it binds with the thin filament) and a myosin
ATPase binding site which is important for hydrolysis of ATP and crucial for
contraction process. Head becomes a molecular motor and pulls actin filaments
across myosin top.
Actin is built by small monomers to a double helix chain, wrapped around
supporting nebulin proteins. Black dots cap of binding to myosin thick filament
cross bridge head. Actin and Myosin bind together.
If there is no regulatory structure, Myosin and Actin are free to bind which results
in uncoordinated and uneven contraction of muscle. Tropomyosin complex is a
long thread of proteins that runs across top of helix and actin binding site,
blocking binding site at the relaxed stage. Troponin complex is linked to actin and
tropomyosin as well as binding with calcium, moving tropomyosin away and
allowing myosin to bind with binding site. Calcium triggers the binding by binding
with Troponin subunit c, causing shape changes which moves tropomyosin from
its position blocking binding site.
Action potential needs to move to middle of muscle fibre, and uses T-tubules to
move there. The sarcoplasmic reticulum wraps around muscle fibre. Voltage
change triggers release of calcium from the vesicles in the sarcoplasmic reticulum
through exocytosis, ultimately causing contraction. Lateral sacs are the expansion
of the sarcoplasmic reticulum. Calcium gets pumped into the lateral sacs during
the relaxed state, ready to be released when an action potential travels down the
Lower motor neurons travel out through the spinal nerves to the muscle group,
synapsing with muscles through a specialised chemical synapse called a
neuromuscular junction. The site of synapsis is specialised, allowing reliable
response target tissue (the muscle). Multiply branched axonal terminals are known
as terminal buttons, which makes tens or hundreds of contact with muscle fibres
delivering neurotransmitters to muscle fibres. The neuromuscular junction is highly
specialised because of fine control for muscle contraction and is purely excitatory.
Many neurotransmitters are released via multiple synaptic contacts through
invaginated surfaces to muscle fibre. Acetylcholine is the released
neurotransmitter by the lower motor neuron. A burst of acetylcholine brings action
potential from the nerve terminal, contraction is guaranteed.
W12MCQ#2: The excitatory neurotransmitter released by a lower motor neuron
onto a muscle fibre at the neuromuscular junction is?
Excitation-contraction coupling links action potential from sarcolemma to muscle
contraction (release of calcium). Release from sarcoplasmic reticulum causes
changes which allows binding and contraction. The action potential travels along
membrane of muscle fibres, diving through the T-tubules and opens receptors on
flanking terminal cisternae which releases the calcium to the cytosol via the shape
change of proteins that link the terminal cisternae with the T-tubules, arising from
the passing of the action potential. At rest, Troponin is in a state that holds
tropomyosin over the binding site. Head on thick filament is cocked in a high
energy state, but inhibited from binding. once the action potential travels across,
excitation causes calcium to bind with troponin c which pulls tropomyosin away
and allows actin and myosin binding trigging contraction and the bending of the
• W12MCQ#3: Which ionic species is critical for the process of excitationcontraction coupling in muscle fibres through its action on the troponintropomyosin complex?
• The sequence of the cross bridge binding starts with the binding of the myosin
globular head, attaching to the actin binding site, triggering a power stroke where
it pivots from a cocked high energy state to a low energy state. It pulls the thin
filament over the top, and it is anchored to the Z-disk at the end of the sarcomere,
pulling it closer to the middle and happening on either end of the sarcomere
across all sarcomeres in the myofibril. The head will then detach, using ATP to go
back into the ready state and will keep binding as long as calcium is available.
• ATP is needed for cross bridge formation and power stroke formation in the cross
bridge cycle. It binds with the myosin head, causing it to detach from the actin
molecule. The enzymatic region of the head will hydrolyse ATP into ADP and
inorganic phosphate, using the chemical energy to turn it into a high energy
cocked state once again. After death, ATP will be absent resulting in the head
staying attached to the binding site causing a rigor mortis complex in the midst of
continuous calcium release.
• Filaments slide over each other, they do not get shorter. The actin is brought in
and slides over the the top of myosin in the middle. The Z-lines attached to the
actin are brought in closer to another and each of these Z-lines shortens,
shortening the myofibril and muscle.
• Each action potential generated in the muscle fibre gives rise to a twitch (a
contraction that occurs from just one action potential). The action potential is
short, lasting 1-2 milliseconds, but the twitch contraction is relatively long. All
muscle contractions are built on a single twitch contraction. This reflects the
structure of the neuromuscular junction to ensure the sequence of events occur.
The twitch can be broken down to different phases. There are three different
phases. The stimulus is the action potential generated in the muscle fibre. The
latent period is a short period where there is no obvious muscle force generation
or shortening, however the action potential is spreading out over the cell
membrane through the T-tubules and calcium release is occurring. The
contraction phase is where the calcium is triggering the binding between actin and
myosin, starting the cross bridge cycle. This can last between 10 to 100
milliseconds depending on the type of muscle involved. The muscle then enters
the third and last phase of a twitch called the relaxation phase, if no further action
potentials are being delivered. Calcium gets mopped up into the sarcoplasmic
reticulum, the rate of cross bridge cycling goes down and the muscle relaxes into
its resting state instead of shortening.
• The important consequences of the difference in duration between the twitch and
the action potential is that there can be multiple action potentials arriving within
the duration of the initial twitch. This is a process called twitch summation (wave
summation). There is a further summated twitch on top of the original twitch to
increase the tension developed in the muscle fibre, in response to a second action
potential fired before the first can result in the relaxation phase. By changing the
rate of action potential firing, the body can bring about stronger contraction. There
is a continuum of increase in muscle force depending on how fast muscle fibre is
stimulated. The stage of unfused tetanus (incomplete tetanus) and fused tetanus
are linked with the twitch summation, with the difference being that the rate of
increase in tension is brought about by difference in stimulation of the muscle.
Incomplete tetanus has a maximal cross bridge cycling for short periods because
all binding sites on actin are exposed for a short period of time due of high
concentration of calcium from multiple action potentials. A problem with
stimulating muscle that rapidly is that the muscle will fatigue. This is because of a
few reasons. The first is central fatigue, the lower motor neurons run out of
neurotransmitter in the presynaptic terminal and muscle cannot be activated.
Muscle fatigue is where the muscle cannot keep up with the contraction it is
asked to do. Lactic acid buildup occurs because its part of the ATP producing
process (anaerobic respiration) in the muscle, acidifying the inside of the muscle
fibre and changing the enzymatic activity of the myosin, making it harder to
hydrolyse ATP and slowing down the cross bridge cycle, slowing down
contraction rate. There is a depletion of energy reserves. The muscle needs to get
ATP by breaking down glucose which comes from glycogen stored in the muscle,
if it runs out the muscle can’t produce ATP and thus contract the muscle.
• There are different types of muscle fibre found in the body. Fast twitch and slow
twitch muscle fibres come about because of their behaviour. From a molecular
perspective this arises because of the nature of the myosin inside the sarcomeres.
Fast twitch muscles have a fast myosin which hydrolyses ATP much quicker than
slow twitch fibres which contain slow myosin, giving a fast or slow contraction.
Depending on which muscle in the body, there will be a different mix of these fast
and slow twitch muscles. The fast twitch muscles fatigue very quickly while the
slow twitch muscles can continue longer and fatigue slower. This comes about in
the way they generate ATP. Essentially ATP can be produced by glycolysis
(substrate level phosphorylation) or oxidative phosphorylation in the mitochondria.
The latter is very efficient, producing many ATP molecules (38). Different muscle
types use these two ATP generating mechanisms to different extents. This gives
rise to two different types of skeletal muscle fibres known as red (oxidative) and
white (glycolytic). The red fibres are packed with oxygen binding protein called
myoglobin which binds to oxygen and provides it for oxidative phosphorylation
during sustained contraction. White fibres don’t need myoglobin because they rely
on an anaerobic glycolytic process to generate ATP. The red fibres are smaller,
meaning they won’t generate as much force, but they are surrounded by
capillaries which will keep supplying oxygen to the muscles allowing for
continuous oxidative phosphorylation. The white fibres don’t have good blood
supply because they don’t need continuous supply of oxygen, however they can
pack in more myofibrils and are larger in diameter with a stronger contraction.
Glycolytic fibres will burn through ATP very rapidly, generating fast twitch and thus
generating fatigue because they can’t get rid of the glycolysis products which is
Pyruvic acid, which gets turned into lactic acid. Oxidative fibres can continue for a
long time because of the continuous oxygen, keep using up pyruvate which
becomes a substrate for the Krebs cycle, producing more ATP through aerobic
respiration. There can be four combinations between fast and slow twitch and red
and white fibres. In the human body there are only 3 types: slow red (Type I, which
are found in the smaller motor units), fast red (Type IIa, found in larger motor units)
and fast white (Type IIb, only recruited when heavy force is required such as heavy
lifting and sprinting).
Lecture 23 - Plants: defence against attacks
• The generalised response to pest attacks is generalised because of abiotic
factors and artificial compounds. The diversity is due to the number of species
(300,000). There are more than 5 million fungal species that could be potential
pathogens. Common defence pathways have evolved, with diversity in reception.
Artificial elicitors known as BABA and BTH set off priming responses, which are
the elicitation of defence compounds and hydrolytic enzymes produced. There
was a compatibility to be considered with the host and pathogen, the correct
combination results in the + sign, where the host (plant) doesn’t have resistance
and needs to mount a complex defence or the resistance gene is operating,
known as - (resistance is present and plant is adequately defended).
• Systemic Acquired resistance (SAR) is a long term resistance mechanism where
plants can mount an instantaneous response, when they do not have resistance. It
can help the individual cell under attack, and cells remote from it to produce
defence response. Plants produce volatile and non volatile compounds when
under attack/ Plants have evolved tens of thousands chemicals. For example,
Salicylic acid can accumulate upon infection which causes the synthesis and
release of volatile methyl salicylate. The transmission can be airborne (signals of
jasmonic acid and ethylene) as well as a transmissive signal through the phloem of
the vascular system. There is a coevolution of defence responses. Jasmonic acid
interacts with ethylene to set off proteinase inhibitors to block proteases the
insects release to attack the plant.
• Ethylene is involved in senescence and aspirin (salicylic acid) is involved in the
defence response, thus there are applications e.g. the application of silver which
blocks the receptor for ethylene and thus stops senescence. Aspirin/salicylic acid
sends signals that tell the plant they are under attack, inducing a defence
response which makes them toughen up their cell walls. Thus this is why cut
flowers last longer. Ethylene toughens cell walls so it becomes more physically
difficult for an insect to break through.
• There are three main elicitors of long term responses to attack (SAR): Salicylic
acid, Jasmonic acid and ethylene. They can block and cause synthesis of the
other. The first moment of attack is determined by a receptor, the cell wall has a
moiety chopped off and that can make the plant realise it is under attack.
• Jasmonic acid is an elicitor which derives from a biosynthetic pathway. It inhibits
growth and causes senescence thus it is very pleiotropic. As an elicitor, it drives
the Acquired Systemic Response an can induce a pathway seperately from
Salicylic acid. The two proteins have reporter genes switched on only when
adding methyl jasmonate. Ethylene plays both positive and negative roles during
plant attack. It probably interacts with other elicitors as part of the defence
• W13MCQ#1: What are the three major elicitors in plants that induce the long term,
long distance Systematic Acquired Response?
• Defence responses are downstream responses. The first group is phytoalexins,
which is like immunoglobulins. They are toxic compounds plants produce to
defend themselves. These include terpenoids, glycosteroids and alkaloids. There
are also parthenogenesis related proteins such as chitinases which break down
fungal cell walls, proteinase inhibitors which are proteins that inhibit proteins that
attack proteins e.g. serpins (there are also suicide proteins, in knocking out
proteases they are no longer functional) and enzymes for cell wall linkage which
reinforces the physical defence of the cell wall. The froth of beer comes from the
barley seeds that produce serpins.
Short term responses include when plants do have resistance to the attack, and
can mount an effective response promptly. This is elicited by the production of
reactive oxygen species (free radicals). They are highly oxidative and there are
three main groups of these: peroxide, hydroxyl and superoxide and all have three
electrons. They have been shown to been signal molecules in low concentrations
for pathogen attack, thus aren’t just damaging. The pathogen hitting the cell sets
off peroxidases, causing the production of ROS molecules which set off signalling
pathways which mount a defence response e.g. Callose deposition (carbohydrate
to toughen up cell wall), lignification, cross wall linking, stiffening of the cell wall,
cell wall expansion.
PAMPS are pathogen associated molecular patterns. They are bacterial
recognition sites that trigger defence responses. They are recognised by pattern
recognition receptors. This leads to an oxidative burst which leads to a
hypersensitive response by the plant. These hypersensitive responses by the plant
are resulting from incompatible Plant and pathogen, being a feature of resistance
and thus the short term responses. Pathogens thus perish at the site of infection,
at the same time as the cells, essentially suicide.
Nitric oxide is a free radical agent, critically important in animals and plants as a
signal molecule, in conjunction with peroxide and superoxide, in causing the
hypersensitive response. Cell deaths occur when superoxide is converted to
peroxide and interacts with nitric oxide at the right concentration to get cell death
to occur. Nitrogen Oxide is a relaxant of blood vessels, yet is part of the defence
system in plants. The lack of cell death is because there is a lack of superoxide
dismutase (SOD) which allows superoxide to transform into peroxide or too much
superoxide or too much nitric oxide.
To summarise, the Hypersensitive response has an avirulent pathogen which the
plant recognises through R protein, setting off the signal transduction pathway
and sacrificing local tissue to prevent attack. This releases signals which will warn
the rest of the plant. The acquired response has a warning device which sets off a
signal transduction pathway.
W13MCQ#2: What is the fundamental differences between the hypersensitive
response to pathogen attack and Systematic Acquired Resistance?
Oomycetes are a group of eukaryotic organisms which resemble filamentous
fungi. They appeared as endophytes (symbionts of plants for part of the life cycle
with no apparent disease) of land plants 350mya. Pathogenic and benign
symbiotic organisms have been going on for a long time. Almost all of the most
heavy pathogens of plants are part of this class. Phytomixids are groups of
important Oomycetes which infect the cabbage family (brassica), cereals, peanuts.
Downy mildews are important, happen after humid warm weather and affect
multiple plants.
Pathogens also affect marine plants such as kelp and algae, chytrid rot diseases
(olpidiopsis) attack kelps.
Fungi are well known pathogens of all eukaryotes, as well as being symbiotic.
They steal carbohydrates from the plant as well as other nutrients and can
dissolve their way through lignin because of their hydrolytic enzymes. Botrytis
causes grapes to shrivel up to produce Botrytis sweet wines. Fusarium is a genus
which produces a lot of pathogenic fungi and many don’t stop until they kill the
• W13MCQ#3: Which of the following organisms would you consider to be a plant?
Lecture 24 - Introductory Immunology
• Immune system has two key functions, which are to protect against danger and to
harm the host. It tends to protect against unavoidable danger, known as
pathogens as well as cancer. And performs wound repair.
• There are three layers: Barrier defences, Innate immunity and adaptive immunity.
The immune systems are ancient and conserved between species. Innate
immunity has occurred a long time ago in multicellular organisms a long time ago.
They function in essentially the exact same way.
• Barrier defences is the first line of defence. All surfaces in contact with external
environment are lined with epithelial cells which are strongly connected to provide
a mechanical barrier to make it difficult to move through. There are also
biochemical defences via secretions such as mucous, saliva, sweat and tears
which contain substances which kills microorganisms. Stomach acid also counts
as a biochemical barrier. There are also bacteria derived chemicals produced by
the microbiome (our natural coexisting microorganisms) which prevents the
creation of biofilms by invading bacteria.
• W13MCQ#4: Considering the body’s defence mechanisms against infections,
which of the following is NOT considered part of the first line of defence?
• The innate immune system (Inflammation) is the second line of defence. There’re
dendritic cells and cells circulating in the blood, such as granulocytes (neutrophils,
basophils, eosinophils), natural killer cells and cells resident in peripheral tissue
such as macrophages which provide additional defends against bacteria by
eliminating them and cause the inflammation response. There are also soluble
factors which are used to protect the body against bacteria called the
complement system. 10% of our entire blood protein content is made by proteins
of the complement system.
• The adaptive immune system is the third line of defence. The cells involved are
called lymphocytes (T cells and B cells). They are located in lymphoid organs
(spleen, lymph nodes, tonsils, appendix) most of the time, but can move through
the blood vessels and lymph circulation. Soluble factors are also involved, these
are cytokines.
• Having both innate and adaptive immune systems is optimal for health, those
without innate immunity cannot activate adaptive immunity without an innate
response and infection is uncontrolled, getting hold of the body very quickly and
causing death. Lacking adaptive immunity shows that the infection is initially
contained by cannot be cleared.
• The differences between innate and adaptive: Innate is evolutionarily conserved
and in all multicellular organisms, it is directed against types of molecules through
pattern recognition, it is fast response with broadly reactive effectors and no
memory. The key cells are known as phagocytes. Adaptive immunity is
evolutionarily more advanced and directed against unique structures, with a slow
response and highly specific effectors. There is persisting memory that occurs
through memory B cells. The key cells are T and B lymphocytes. Within the first 12
hours of the innate immune response, phagocytes, dendritic cells, epithelial
barriers, complement and NK cells finish their job. It starts immediately after the
microbe passes the epithelial barrier. Adaptive immunity does not really have
effect until a week later. In terms of immune system, it generally refers to the
adaptive immune system.
There are more cells in the innate immune system. All the phils (Neutrophil,
Basophil, Eosinophil) contain granules (generally filled with bacteriocidal/lytic
substances) that are very quickly released. The cells arrive at the site where the
infection occurs and rapidly release the granules. It will most likely kill the majority
of pathogens but also damage cells. Macrophages are good at engulfing bacteria
and destroying them. Natural killer cells can kill other cells. The dendritic cell
serves as a link between the innate and adaptive immune system. As mentioned
before, they recognise patterns through pattern recognition receptors which
recognise shared structures of pathogens such as bacterial cell wall components,
bacteria DNA and viral components.
In the highly specific adaptive immune system, the receptors on each T or B
lymphocyte are completely unique to the other. These cells see a unique structure
known as an epitope. All lymphoid organs are connected by systemic circulation.
the main lymphoid organ is known as the thymus (above the heart) which
generates T cells and bone marrow which generates B cells (in humans and other
mammals). Secondary lymphoid organs are lymph nodes which are connected by
lymphatic vessels. B cells are generated in the Bursa of Fabricius in birds,
adjacent to the cloaca. Cartilaginous fish (sharks) don’t have bones or BoF, thus B
cells are generated in Lymphomyeloid organs.
The immune system is easier to study in larger animals. The most ingenious
organs in the entire system are the lymph nodes. These receive blood cells in a
blood flow and also receive the liquid part of the blood which is filtered through
the capillaries and it is taken up through the lymphatic capillaries and travels
through the lymph nodes with the lymph fragments. The lymph node serves as a
communication hub between T and B cells (which go through the blood
continuously and arrive into a lymph node, going in to the next one) and lymphatic
flow. Without a lymph node, an adaptive immune response cannot be mounted.
The immune system communicates through Cytokines, which are proteins,
produced by a lot of different types of cells. They work by binding to a particular
receptor and activate a cell to perform its functions. Immune Cytokines are one of
most important of many inflammatory cytokines (Cytokines which attract other
cells and sustain inflammatory response). In the inflammatory response, upon the
bacteria penetrating the skin through wounds, macrophages and dendritic cells
take them up and produce cytokines. The cytokines signal to the epithelial cells of
the blood to make the blood vessels sticky, which attracts granulocytes that stick
to the blood vessel. Once the neutrophils (granulocytes) release the granules they
can eat up (phagocytose) the bacteria and destroy it, they then die in huge
numbers and cause tissue damage through granule release. The macrophages
pick up the debris to make sure things go back to normal. Both neutrophils and
macrophages are classified as phagocytes (cells that eat). Elie Metchnikoff
discovered phagocytosis through starfish larvae.
At the same time of the inflammatory reaction, the dendritic cell alerts the higher
levels. It can travel from the peripheral tissue to the lymph nodes. It is dispatched
by the peripheral tissue to ask adaptive immunity to assist. The dendritic cell picks
up lingering fragments of the dead pathogen, then moves them to the lymph
nodes where the it encounters T cells which are activated as a result. One T cell
suited to fight the particular infection produces an army of T cells which are
released into the blood and then tissue where they fight the pathogen they are
wired to fight.
Adaptive immunity is based on clonal selection of lymphocytes with unique
antigen receptors, one T cell with a specific receptor that is specialised for fighting
a specific invading antigen will get cloned. An antigen is an antibody generator,
which can be seen by the antibody. What T and B cells can see are antigens. The
receptors for lymphocytes are unique, there are estimated a billion B cells and a
hundred billion T cells. The large diversity is because different genetic signals are
mixed in certain different combinations. Clonal selection is selecting one cell of
the total pool using shape based recognition, which is largely how the immune
system works.
B cell receptors are called antibodies and immunoglobulin. They are Y shaped and
contain 4 chains with 2 heavy chains and two light chains. Every chain made by
every single B cell is unique. There are 2 identical antigen binding sites per
molecule. Antibodies can improve with time, becoming more efficient in binding. B
cells mediate humoral responses along with antibodies. They see the antigen on
the fragment of the antigen itself and coat bacteria in preparation for phagocytosis
(opsonization). They also improve Natural killer cell killing.
There are five different antibodies in the immune system with different functions.
IgM is the main antibody that mediates the primary immune response (5
antibodies bound together), IgG mediates the secondary immune response, IgA is
in the saliva it is a secreted antibody (two bound antibodies), IgB is the B cell
receptor and IgE is on mast cells and responsible for allergic reactions. These
antibodies can bind to viruses and bacteria to neutralise them. They can also
activate additional mechanisms such as complement.
The initial antibody response is low and made slowly, but a second infection
rapidly increases the specificity and rate of response.
W13MCQ#5: Select ONE CORRECT option from the following statements about
the mouse immune system
Sharks have very small antibodies, they can use in applications where larger
antibodies cannot be used. Antibodies can be used as tools (Flow cytometry,
western blotting, as diagnostic tools in pathology) and drugs which can deplete
cells, block antibodies or activate antibodies.
The T cell receptor is simpler, there are only two chains designated as alpha and
beta. These see antigens as a small peptide which is bound to MHC (Major
Histocompatibility complex). There are two types of MHC molecules (Class I and
Class II), and two types of T cells (CD4 cells and CD8 cells). CD4 (helper) sees the
antigen presented on MHC class II and CD8 (cytotoxic) sees the antigen on MHC
class I. All cells in the body express MHC class I, thus CD8 T cells can potentially
take care of every single viral infected cells anywhere in the body. CD4 cells
cannot monitor all cells, MHC class II is typically found on the surface of antigen
presenting cells, including macrophages, dendritic cells and B cells. They help
macrophages phagocytose better, help CD8 cells kill better and allow B cells to
make better antibodies. CD8 cells can only kill infected cells by releasing toxic
• Along with the effector cells, memory T cells and B cells are synthesised. They are
long living and are able to recognise the same pathogen.
• M13MCQ#3: The Thymus is the site of development for: