Lecture 2: Prokaryotes, eukaryote, the rise of multicellurarity and endosymbiosis
Readings: Animal Physiology Ch 1 Biology of plants Ch 8,9,28
Prokaryotes - reducing agent is water in plant photosynthesis
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Chemotrophs – Inorganic compounds as a source to reducing power to synthesise organic carbon (lithotrophs).
e.g. carbon dioxide + hydrogen sulphide  carbohydrate + water + sulphur. Others use organic carbon
compounds to reduce CO2 to carbohydrate e.g. fatty acids or lipids left from other living cells
The rise of Eukaryotes
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Heterotrophs that consume organic compounds or autotrophs that photosynthesise.
The consequences of endosymbiosis & multicellularity
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These confer metabolic flexibility on cells and tissues: The separation of function inside cells leading to a
capacity to concentrate substances and enabling catalysis & The specialisation of physiology between tissues
e.g. sensory, reproductive
Multicellular cell-cell interaction: amoeba Dictyostelium discoideum, assembles into a multicellular structure
for the reproductive stage. Some cells die to allow the generation of new spores.
Functional specialisations: Basidiomycetes (mushrooms), the complexity and diversity of flowers and animal
sensory cells. Transport mechanisms, specifically circulatory systems in animals (blood and lymphatic) and longdistance transport elements in plants (xylem and phloem).
Energy and life; energy IS life
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Thermodynamics dictate that energy must be inserted to sustain and build living organisms. Polymers and
pumps absorb energy and lower entropy.
Forms of chemical energy (e.g., creatine phosphate in the liver, GTP, pyrophosphate).
These high-energy molecules are present in small amounts (less than 10 mM) and turn over very quickly, with
the ATP pool disappearing and being re-formed every 4 seconds. We see no change in the total pool size when
normal homeostasis operates but, in a crisis, the ATP is gone very quickly.
Making energy in an aerobic world - ATP synthase
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Proton gradients are the core energy source in living things; they form from protons stripped off respired
carbohydrates (in respiration) or from the protons released during the light reaction of photosynthesis.
ATP synthase allows protons to pass through a channel in the protein complex and in turn, make ATP out of
ADP by adding a phosphate.
Animals, development and environment
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Environment modifies gene expression (acclimation) – phenotypic plasticity.
Animals have strict developmental ‘programs’ but are also modified by the environment, both in the short term
through effects imposed over the life cycle (e.g. sex determination in reptiles) and in the long term through
natural selection (e.g. gestation periods of related species).
Plants, development and environment
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Plants have even great need for developmental programs and high levels of phenotypic plasticity as they
cannot move. Polyploidy brings robustness and versatility through multiple allelic variations.
Acclimation and adaption
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Acclimation is directed by gene activity to perform physiological functions.
Acclimatization e.g. seasons – morphological changes
Adaptation – genetic complement over generations – better adaptation
Lecture 3: Autotrophy
What is autotrophy?
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The generation of chemically reduced carbon compounds. ‘Reduction’ requires a source of electrons and
hydrogen atoms.
The Gibbs Free Energy (in this case, the energy invested in a chemical bond) is greater for the reduced form
of carbon (98 kcal per mole in the hydrocarbon bond) than the oxidised form of carbon (78 kcal per mole).
Hence, making the bond requires input of energy and breaking it releases energy.
Photoautotrophs make organic carbon in light
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Organisms that can use light to drive the formation of organic carbon compounds (‘reduced carbon’).
They are extensive taxonomically, including photosynthetic bacteria right through to the Protists (including
algae such as seaweeds), lower plants (mosses, ferns) right up to the flowering plants.
Most use water (H2O) to supply the hydrogen atoms and electrons (= reducing power) required for reduction
of carbon but primitive bacteria are an exception.
The ancient green and purple sulphur (sulfur) bacteria are anaerobic phototrophs, using hydrogen from H2S
(not water) to reduce carbon. Their pigments confer colour. The end-products smell strongly, often of sulphur.
The green and purple non-sulphur bacteria use organic compounds as a source of reduction power (e.g. lipids).
Chemoautotrophs – making organic carbon in the dark
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Lithotrophs - organisms that can use energy sources other than light from their environment to drive the
formation of organic carbon compounds (‘reduced carbon’).
Chemo lithotrophic bacteria can form symbiotic relationships with giant tube worms, providing them with
organic carbon
Cyanobacteria (misnomer, blue-green algae) - Prokaryotes
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Highly efficient photosynthesises, having given rise to the first large biomass on the planet and oxygenation of
the atmosphere starting about 3.5 billion years ago
Green plants – this major group of photosynthetic organisms uses chloroplasts as photosynthetic organelles
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Green plants photosynthesise and therefore drive the Biosphere. Some plants are actually parasitic (e.g.
mistletoes), others reproduce underground, stealing organic carbon from other plants, but the vast majority
are true autotrophs in the sunlight.
Photosynthesis – details of the light reaction
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This is a thylakoid membrane but just remember this – there are two products of photosynthesis – ATP (energy)
and NADPH (reducing power)
NADPH arises from Photosystem I, using H+ from the splitting of water.
Integration of photosynthetic reactions
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Light and Dark Reactions are integrated to convert light energy to hydrocarbon bonds, and these
transformations also interact with other cell organelles. Compounds are shifted about, generating new carbon
skeletons and controlling the redox state of the cell
Photosynthesis is responsive to environmental conditions: light, temperature and CO2
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chlorophyll fluorescence, a measure of Light Reaction activity.
Lecture 4: Heterotrophy
What is heterotrophy?
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use of organic molecules derived by feeding on other heterotrophs, or autotrophs.
These organic molecules are extremely diverse – lipids, proteins, nucleic acids, plant cells walls and a vast array
of carbohydrates, all with carbon-rich skeletons ultimately derived from photosynthesis or chemotrophic
activity.
Mechanisms for gaining food – prokaryotes
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Heterotrophic bacteria derive carbon skeletons by (passive) diffusion across their outer membrane, or (active)
uptake via proteins that are specialised for transport of specific molecules
Mechanisms for gaining food – unicellular eukaryotes
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Unicellular protozoa (protists) such a Paramecium have an oral groove through which food enters the organism
(e.g. yeast, bacteria). It is digested through the action of digestive enzymes and then extruded via a contractile
vacuole.
Some protozoa are phototrophs
Amoebae feed by two mechanisms
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Phagocytosis is achieved by the recognition of ligands on the surface of the particle by receptors in the amoeba,
incorporation into a phagosome and digestion. It is therefore specific and selective, enabling pathogen
recognition and removal
Pinocytosis is the non-specific absorption of food through the membrane then digestion by vacuolar enzymes.
Dictyostelium discoideum – a model for cell aggregation that is triggered by food shortage
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A slime mould that feeds as a free-living amoeba and then aggregates into a colony once food supply declines.
Spores germinate and release myxamoebae (vegetative amoebae). The bacteria that they feed on secrete folic
acid to attract the amoebae. When the food supply falls, the amoebae move together and glue themselves to
form a mobile slug with a stalk and spore body.
This is a process coordinated by the secondary signal molecule cyclic AMP (cAMP).
Acquiring food - invertebrates
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Snails are cited here as an example of invertebrates that have sophisticated and efficient feeding mechanisms
– the radular apparatus
There is a plethora of other invertebrate mouthparts that include stinging and sucking (mosquitos, aphids),
chewing (grasshoppers and other arthropods), biting and grinding (crustaceans) and filter feeding (marine
molluscs).
Suspension feeding in whales, fish & molluscs
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Marine mammals, fish, and marine invertebrates such as oysters, filter feed to maintain their heterotrophic
lifestyle.
These feeding mechanisms are not as indiscriminate as they appear – various biophysical forces are employed
to make them somewhat selective – hydrodynamics (water pressure), electrostatic and chemical attractants
and targeted grasping of small invertebrates
The higher mammalian stomach
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Mammalian stomachs are highly evolved according to the diet. Optimising the structure and function is clearly
the result of a strong selective forces in mammals; heterotrophic food acquisition is central to evolutionary
success.
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For example, the digestive tract of a rabbit has a large caecum, adapting it for a cellulosic diet by fermenting
complex carbohydrates to soluble sugars.
Ruminants – living fermenters
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Rumen of ruminant animals is an exquisitely adapted fermenting device, with unique anaerobic bacteria in the
rumen breaking down plant cell walls and manufacturing both soluble carbohydrates and amino acids for use
by the host
Symbiosis evolved to enhance food acquisition in some marine invertebrates
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Vent worms use bacteria (chemotrophs) to use H2S as an energy source to drive organic carbon supply.
Lecture 5: Anaerobic metabolism
Why is oxygen deflect a problem?
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Great Oxidation Event – metabolism for all living things
Prokaryotes have better survival mechanisms at low O2
Various adaptations and physiological processes enable oxygen acquisition in otherwise O2 -deprived places.
These can circumvent the need for metabolic adaptations, e.g. myoglobin in diving mammals, aerenchyma (gas
channels) in aquatic plants.
Evading O2 deficits – Diving mammals – myoglobin, aquatic plants develop internal air spaces (aerenchyma)
Why lack of O2 kills living cells
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Most importantly, low O2 levels cause an energy crisis.
Oxygen enables respiration in the mitochondria to degrade carbohydrates (or other organic compounds) to
carbon dioxide and yield about 36 molecules of ATP for every monosaccharide (say, glucose) that is degraded.
When oxygen supply is cut off, oxidative phosphorylation cannot synthesise ATP and fermentative pathways
take over, yielding about 5% as much energy as in air.
There are also other effects of O2 deficits but maybe they are less important in most environments – these
include toxic ions in anaerobic silt, anaerobic bacteria and hormonal changes in plants.
Toxic ions might include reduced forms of copper, manganese and iron (ferrous ions).
Hormonal changes often involve the plant hormone ethylene whose synthesis and entrapment change in
flooded conditions.
Anaerobic bacteria include Clostridium, Actinomyces
Fermentation
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Cannot be sustained without plenty of sugars as substrates – glycolysis
In 1857, Louis Pasteur discovered that in yeast cultures, fermentation consumed sugars faster than occurred in
aerated cultures. This was been shown in many anoxia-tolerant microorganisms and plants. By accelerating
sugar supply into glycolysis, ATP production increases, even though it remains a very inefficient way to make
energy.
ATP yield in anoxia might increase from about 5% of that is air to about onethird, allowing many anaerobes to
grow, such as yeast, rice and possible some invertebrates.
Hypotheses: surviving anoxia
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Defence - cells downregulate their energy use immediately they are placed in anoxia. This might involve
different biosynthetic pathways in plants and animals but energy saving is the central theme. This helps to rebalance ATP synthesis and utilisation
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Atkinson captures this homeostasis in his 1968 Biochemistry paper (right); R = regeneration of energy and U =
utilisation. Energy charge = energy state of the cell with anoxic cells are the left. As O2 is withdrawn, ATP use
(U) decreases.
Animals: a physiological account of low-oxygen tolerance
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Diving and marine animals, and molluscs, are the best examples of tolerance to low O2 levels in the
vertebrates.
Features include the use of myoglobin for binding oxygen in their muscles and the ability to use a range of
fermentative pathways.
The broad responses to low oxygen levels - decreased ATP utilisation and expression of a few vital genes – is
seen in animals and plants. Many of these genes should be the same, those involved in making enzymes that
are essential to glycolysis, transport and mobilisation of substrates for glycolysis.
Channel arrest in hepatocytes and ‘spike’ arrest in neurons.
A mega-fermentater the rumen of large herbivores
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The rumen is a huge fermenter occupied by obligate anaerobic bacteria.
The ruminal environment is anaerobic; the gases include carbon dioxide (~65%) and methane (~35%) plus
small amounts of H2 , N2 & O2
The final electron acceptor is organic sometimes inorganic compounds but not oxygen.
Substrates are only partially oxidized, allowing the animal to absorb the products (acetate, propionate and
butyrate) as energy source. These are VFAs (volatile fatty acids).
Plants: a physiological account of low-oxygen tolerance
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Swamp plants, rice and maize
multiple physiological responses to inundation – morphological, anatomical and metabolic - complex process
that involves formation of air spaces by the action of ethylene gas, a hormone. This therefore requires
ethylene receptors (actually they respond to ethylene response factors) and secondary responses such as
calcium release and ultimately, cell wall breakdown.
superficial roots that can gain access to atmospheric oxygen and a full suite of fermentation pathways are
activated.
Lecture 6: Oxygenic energy generation (Respiration)
Dark mitochondrial respiration revised
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Mitochondrial respiration returns energy for the CO2 that was autotrophically fixed in photosynthesis
We therefore need to discuss the substrates and products of respiration, remembering that the simple equation
(sugars + O2  CO2 + water + ATP) ignores the intermediates that can be drawn off these pathways for growth
etc
‘Dark’ respiration (non light-dependent respiration by microbes and eukaryotes) can be considered on the
larger scale of landscapes and ecosystems (e.g. large vs small animals; rainforests vs deserts)
Energy returned for Co2 fixed
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Sucrose is the principal respiratory substrate in green plants and carbohydrates of many types supply glycolysis
in animals
CH bonds hydrolysed in mitochondria to yield ATP.
Carbohydrates are replenished from stores such as starch (plants) and glycogen (animals)
Where does respiration occur?
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Mitochondria were first shown to be the site of aerobic respiration (oxidative phosphorylation) in higher plants
Many substrates can enter glycolysis and be respired after being transformed into sugars, including starch,
fructus, proteins, lipids, sugars and amino acids
Mitochondrial genes
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The genes that encode these processes originate from endosymbiosis, partly in the once free-living
mitochondria and partly in the nucleus (just like photosynthetic genes in the chloroplast).
About 200,000 nucleotide base pairs in mitochondria are present in multiple circular chromosomes that reveal
their prokaryotic origins.
Pathways of energy production in living cells
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Energy is invested in NADH through the reducing power of the H atom and high-energy electrons.
Respiration makes some ATP (but not much directly out of enzymic reactions) and a lot of NADH (via oxidation
of hydrocarbon bonds).
This energy is fed into the cytochrome chains of the mitochondria.
Three major components: glycolysis, TCA cycle, oxidative phosphorylation
Energy is invested in NADH through the reducing power of the H atom and high-energy electrons
Respiration makes some ATP (but not much directly out of enzymic reactions) and a lot of NADH (via oxidation
of hydrocarbon bonds)
This energy is fed into the cytochrome chains of the mitochondria
Respiration also produces heat
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Heat is a necessary by-product of respiration because basic laws of thermodynamics dictate that all
transformations result in a release of heat – no motor is perfectly efficient
This heat enables homeothermy to be achieved in higher animals, which then regulate temperature according
to environment
How fast do plants respire?
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Most plant organs relatively low respiration rates. Factors that determine the rate are the demand for energy
(e.g. ion uptake), rate of substrate delivery to ‘sinks’, demand for metabolic intermediates (e.g. amino acids),
temperature and stress factors
Some plants respire so fast that carbohydrate reserves are exhausted in a matter of hours in order the attract
pollinators (e.g. Arum spadices )
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Seeds respire very slowly until rehydrated
Alternative pathway respiration
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Some plants, fungi and protozoa have an electron transport chain that can accept oxygen without the normal
yield of three ATPs for every oxygen atom reduced in normal respiration
This is achieved through a non-phosphorylating bypass in mitochondria that uses carbohydrates and makes
intermediates without making much energy (ATP)
Respiration of microbes vs plant organs
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Root and shoot apices have high respiration rates, as well as all fast growing tissues (dividing and expanding
cells) and ripening fruits.
Fruits have a climacteric rise in respiratory rate as they ripen, speeding up the production of colour and flavor
molecules
Why does dark respiration rate vary between organisms, environments and tissues?
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In animals – to maintain a constant temperature in homeotherms, to regulate temperature; in poikilotherms,
to manage metabolic rates and ambient temperature.
In all organisms – to provide optimal energy status by making ATP at a rate that matches ATP demand.
In plants – to provide optimal energy (ATP) and reducing power (NADH) levels, enabling biosynthetic rates to
to be optimized.
In plants – the warm particular organisms, facilitate pollination and ripen fruit
Photorespiration – nothing to do with mitochondria or making energy
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This is really a subject to be dealt with next week under compartmentation.
Photorespiration is a pathway of oxidative CO2 release but is biochemically unrelated to dark respiration.
Photorespiration occurs across three organelles with shuttles between them
Involves O2 reacting with RUBP and a C2 intermediate (glycolate) forming. It occurs only in the light
Lecture 7: Gaining resourses, making energy and regulating the living cell
Composition of animal and plant tissues
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Animals having higher mineral content – physiological function and metabolic processes
Growth and maintenance of cells and whole organisms
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Growth – acquisition of new resources (organic or inorganic)  energy to digest, transform, catabolise and
polymerise
Organic fraction – defence compounds in animals (immunoglobulins) and plants (phenols)
Maintenance – keeping tissues alive regardless of growth – homeostasis (proton transport and polymer
turnover. Proteins proportional to body mass.
Measuring respiration - The faster this organism grows (x-axis), the more of its respiration has to be devoted to
support this growth (y-axis)
Change in carbohydrates respired for maintenance through time – less carbon is respired as the organism ages
Energy generated to be partitioned is between biosynthesis (growth) and maintenance
Costs of growth and resource acquisition
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Analysis of amino acid metabolism – Maintenance (31%), Growth (69%) – shoot and root systems –
manufacturer of proteins
Net costs – the cost in energy units (ATP) and photosynthetic carbon (material cost of growth)
Using units of reducing power (NADH) and energy (ATP) – account for all construction costs – nitrogenous
compounds
Energy costs of turnover of metabolic pools for maintenance - molecular pools can turn over at different rates
Concerting biomass to energy
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Carbon based substrates to make energy in respiration:
Energy yielded by breaking down major polymers and combusting them in
respiration:
- Energy released by breaking down proteins
- Lipids are rich in energy  rick in hydrocarbon bonds
Major polymers in decreasing order  Mixed lipids, mixed proteins, mixed
carbs, hydrated glycogen
Acquisition of resources
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Energy costs of ion acquisition by cells – vacuole having different chemical
composition allowing transporters from surrounding cytosol Ca (low [])
Costs: in aqueous environment – rapid exchange of resources is critical:
- Single animal cell: relative ion concentrations inside and outside
- Gill epithelium of freshwater fish: relative ion concentrations of the two sides
- Epithelium of small intensive: glucose transport across the epithelium
Heterotrophs (nutrition from external sources) – chemotaxis, critical prokaryotes and unicellular eukaryote.
Driven by concentration gradients
Optimising resource supply – behaviour and integration of metabolism
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Ecological and evolutionary levels of organisation – escaping predator
Cellular level of organisation – contractile properties of muscle cells – rate of escape
Biochemical level of organisation – Krebs cycle. ATP (muscle contraction + rate of escape)
Behavioural food selection – Wolf spiders – consume in ways of prior intake of protein and lipid
Protein and lipid discrimination in diet would optimise biosynthesis of muscle vs the availability of energy from
respiration
Lecture 8: Compartmentation and homeostasis
Cell-level transport systems
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Transport proteins – lipid bilayer vital for homeostasis
Transport in single cells – passive (diffusion channels)
Carriers enhance transport rate across membranes: rate against eternal concentration of transported
molecule
Controlling ion balance
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Transport proteins are vital to cell homeostasis by regulating the flux of ions (and organic molecules) across
the plasma membrane and tonoplast. All membrane-bound organelles in animal and plant cells have
transporters embedded in them
Sugar transport
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Bi-directional (secondary) transport:
- Organic: sugars, amino acids, hormones
- Inorganic: phosphate, potassium
Intracellular compartments: biosynthesis (growth) and maintenance
A model animal compartment – kidneys
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Two secondary active transport systems: regulate sodium and glucose influx into epithelial cells of vertebrate
small intestine
- Na+ K+ APTase in the basolateral membrane and the Na+ electrochemical gradient – generates across
apical membrane. (Energetically unfavourable – active driven by ATP)
- Na+ - glucose cotransporter in the apical membrane, glucose transport into cell
Whole-epithelium view of active ion transport across the gill epithelium of a typical freshwater fish: CO2
provides protons and bicarbonate to energise Na+ and Cl- uptake
Lysosomes – key role in defence of exocytosis
Compartments in cells are important because: they prevent enzymes from digesting cell’s metabolites, store
toxic compounds, some compartments store genetic information to be transcribed and they concentrate
metabolites
Model plant compartments
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Mature plant cells are dominated by large vacuoles – repositories for solutes but without metabolic pathways
‘Phloem loading’ and long-distance transport in plants:
- Export to other plant parts
- Plasmodesmata (intercellular strands of living cytosol) connect adjacent cells and allow a pressure gradient
to deliver sugars to where they were used.
Active transport involves the input of ATP and generally, protons resources
Compartments enable CO2 to be concentrated at the site of fixation (Rubisco in the Calvin Cycle) in C4
photosynthesis
- Two stage mechanism: CO2 (fixed into organic acid – melate), Rubisco preventing O2 reacting with enzyme.
Single cell compartment:
- Concentrate CO2 using PEP carboxylase enzyme – located in specialised chloroplasts within cell
- Fixes CO2 into malate in other C4 plants, but within same cell, CO2 released, where Rubisco and Clvin cycle
takes over Carbohydrate production
CAM plants (orcids, cacti) – adapt to low water storing carbon overnight in vacuoles
- Stomata (open at night, closed during day)
Photorespiration is a three-way interaction between cellular compartments – inefficient process that uses
valuable light energt to make no carbohydrate and no energy. Chloroplast  Peroxisome  Mitochondrion
Lecture 9: Symbiosis in Plants
Mycorrhizas – a fungus that teams with a plant (root-fungus interaction)
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Essence of symbiosis is the exchange of recourses across adjacent membranes: the plant accepts immobile
inorganic ions from the fungus (particularly phosphate) which the plant contributes carbohydrates and other
organic molecules to the fungus.
Affects (>80%) of plants, critical for land plants.
Antarctica during the Triassic (250 Mya) – Gymnosperm root with mycorrhizal fungus
Mycorrhizas – enabled plants to emerge onto land and use roots to extract enough inorganic nutrition
Australia has nutrient poor soils – little phosphate
Functional categories:
- Ectomycorrhizas (ECMs)
 Commonly on roots of woody plant species (Pinaceae, Betulaceae, tropical trees, Nothofagus)
 Northers coniferous and temperate deciduous forests on N-limited soils
 Structures: Mantle (dense network of hyphae sheathing root), Hartig net (complex of mycelia
growth between root cortical cells)
- Endomycorrhizas
 Arbuscular mycorrhizas – AMs
o Occur in herbaceous and some woody species, grown on P-limited soils
o Cortical cells  hyphae  arbuscules (branched structures) & terminal swellings (vesicles)
o Major interference for resource exchange (phosphate-carbon)
o Vesicles: endomycorrhizal associations – contain lipids and cytoplasm
 Ericoid mycorrhizas e.g. heather, rhododendron, Epacrids)
o Fungal hyphae forming loosely-organised web over root surface
o Release enzymes to facilitate nutrient update (N) with little hyphal ramification in soil
 Orchid mycorrhizas – coils of hyphae within roots or stems of plants
o Obligate relationship with young orchid root
o Orchid seeds can only germinate in the presence of suitable fungi
Role of mycorrhizae in plant nutrition: ectos and endos = large surface area of hyphae in soil increasing
scavenging capacity
Complex architecture of networking – small diameter of hyphae
- Highly affinity transformers – maximum absorption of orthophosphate
Defence: AM enables hosts to tolerate toxic heavy metal in soil, ECM and AM protect from pathogens and soil
biota (nematodes), AM relive negative effects of drought
Legume nodules – their formation and function
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House nitrogen fixing bacteria in the genus Rhizobium
Nodules form on roots but can also form on stems of some species
Host plants = nitrogen, bacterium = organic carbon for metabolism
Infection and nodule formation:
Rhizobium bacteria
enter the root hair
after stimulating
formation of an
infection thread
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Bacteria penetrate root
cortex, changing into
Bacteroides. Cells in cortex
and pericycle begin
dividing near Bacteroides
Nitrogen fixation is characterised best by
Bacteroides and
dividing cells of
cortex and
pericycle form a
root nodule
Nodule vascular tissue
forms, carrying
nutrients between
growing nodule and
xylem and phloem
Cyanobacterial associations
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Other nitrogen-fixing symptoms rely upon cyanobacteria and heir heterocyst
Mutualisms involving cyanobacteria and noses and cycads
Lichens
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Mutualism between algae and fungi
Mutualisms are best described as: interactions between organisms that confer benefits on each partner
Lecture 10: Animal symbiosis
The problem with cellulose
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No enzymic capability to breakdown polymer into readily usable glucose monomers
The solution: co-opt the activities of microorganisms that can digest cellulose. Hydrolysis of cellulose in an
anaerobic environment result in fatty acids that can be absorbed by the animal host as a source of energy and
carbon.
Stomach in ruminants
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The rumen houses a complex population of bacteria, protozoa and fungi, which digest cellulose, supplying fatty
acids to the host. - exhibit symbioses of their own
Hindgut fermenters – enlarged cecum holds large number of cellulolytic bacteria
Termites: cannot digest cellulose  rely on symbiosis with microorganism in heir gut or cultivating fungi on
wood fibre.
Fungus gardening termites: symbiotic fungus of pre=digested wood pulp, fungal fruiting bodies are then eaten
Fungus gardening ants: leaf-cutting ants use live plant material to fertilise fungus gardens.
Attine ants carry antibiotic producing streptomycetes – ants vertically inherit Actinomycetes, which queens
carry when founding new nests. The antimicrobial compounds produced by the Actinomycetes protect against
various pathogens, including Escovopsis.
Distribution of stony coral reefs
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Reef building corals occur between the tropics of Cancer and Capricorn.
Coral polyps have obligate symbiosis with dinoflagellates in the genus Symbiodium – photosynthetic
Basis of coral mutualism
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1.5-10x6 Symbiodinium/cm3 = the polyp biomass
Photosynthesis by Symbiodinium supplies 50-90% of the energy requirements of the coral polyp, usually as
glycerol
Presence of symbiodinium increases the rate of calcification (= reef growth)
Coral polyps supply inorganic nutrients e.g. ammonium and carbonate, coral host supplies an ideal protected
environment
Symbiodinium diversity
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Brown, spherical cells of 5-15 uM. All symbionts of marine invertebrates as a single species, Symbiodinium
microadriaticum.
Composed of eight clades (A-H). The orgins of the tree tie between early Eocene (~50-55 mya), corresponding
with the origin of the Scleractinian corals.
Symbioses with other hosts: different phyla of marine invertebrates, including Cnidaria, Mollusca, Porifera,
Platyhelminths and Foraminiferans.
Coral Bleaching
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Various stresses  bacterial infection, pollution, low salinity, increased sea temperatures and irradiance.
Diversity in symbiont might help Strains differ in their response to irradiance and temperature. Corals
containing mixed populations of symbionts may alter the ratios of these clades in response to climatic changes.
For instance, clade C gives faster growth, but clade D has higher heat tolerance.
Hydrothermal Vent Ecosystems
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Along the mid-oceanic ridges of the world’s oceans, upwelling lava comes in contact with seawater
Vent animals have bacterial symbionts: The dominant species around vents form symbiotic associations with
sulfur oxidizing bacteria. Bivalves have symbiotic bacteria in their gill tissues, and are dependent on the
symbionts for much of their nutrition. Tube worms have no mouth, gut or anus, and are totally dependent on
bacterial symbionts for nutrition.
Anatomy of Riftia: Riftia plumes collect oxygen and sulfur and deliver them to bacterial endosymbionts living
within the trophosome
Kleptoplasty: Sea slugs in the order Sacoglossa store chloroplasts from algae in their digestive epithelia. The
chloroplasts provide camouflage, and continue to photosynthesize, in some cases being able to fix enough
carbon to sustain the sea slug.
Elysia chlorotica: This sea slug steals chloroplasts from its algal food Vaucheria litorea. The chloroplasts can
survive in specific cells lining the digestive diverticula and supply the host slug with photosynthate. There is
some evidence that algal nuclear genes have been transferred into the slug genome. These may help maintain
and control chloroplast activity
Humans have about 10^14 symbiotic bacteria in their gut contents
Human physiological conditions:
Lecture 11: Cell division
The cell and its contents
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In animals, microbes & plants, cell size is highly conservative (although not the same for every cell type), while
cell number increases with organ size. New cells are required for growth.
G1 phase: cell doubles in size, organelles, enzymes, and other molecules increase in number
S phase: DNA replicated, and associated proteins synthesised, two copies of cell’s genetic information now exist
G2 phase: structures required for cell division begin to assemble; chromosomes begin to condense.
M phase: two sets of chromosomes are separated (mitosis) and the cell divides (cytokinesis)
Mitosis – dividing the genome, cytokinesis, regulatory enzymes and cytoskeleton
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DNA levels: Rapid rise in DNA in the synthetic phase (S phase) and the even more rapid decline in the mitotic
(M) phase
Key enzymes during cell division: cdc proteins and the cyclins
p34cdc2 is critical to the period leading to splitting of the genome
In yeast, knocking out mitosis genes delays cell division so larger cells result
P34cdc2 and cyclin are switched on and off by phosphorylation events – therefore ATP is needed
Adding and removing phosphate from particular sites on proteins is very important for many aspects of
metabolism – disease, cell division, protein activation
DNA is complement at S phase when complement and M phase when divided
Basic phases of cell division: early prophase, mid-prophase, late prophase, metaphase, anaphase and telophase
Role of cytoskeleton in cell division: Interphase, preprophase band and spindle, mitotic spindle at metaphase
and phragmoplast at telophase
Organelles also need to divide: plastids & mitochondria must divide at mitosis and deliver their DNA to two
daughter cells. Specific proteins localize to mid-plastid rings to organise division of the chloroplast
Separation of chromatids in mitosis is achieved by
Microtubules are attached to chromosomes and they polymerise and de-polymerise dynamically
The mitotic phase during which chromosomes divide lasts roughly how long in human cells: 1 hour
Meiosis and production of gametes/ gametophyte
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Early prophase 1  prophase I  Late prophase I  metaphase I  Anaphase I  metaphase II  anaphase
II  late telophase II
Crossover in meiosis – the mechanism of sexual recombination
Special cases of cell division – totipotency, asymmetric division
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Organelles also divide (this is how maternal DNA from mitochondria (mtDNA) is transferred to the following
generation.
Pluripotent cells lines – they can be maintained in an undifferentiated state then triggered to make any cells
type (stem cells?).
Asymmetric cell divisions – to make multicellular organisms with functional parts e.g. Fucus (brown alga)
Pluripotency: the ability of cells to differentiate into any cell type in the developing organism
What controls the rates of cell division
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the organism – intrinsic factors.
Temperature Growth at 36°C:
- Cell cycle ~130 minutes, mitosis ~12 minutes.
- Growth at 26°C: Cell cycle ~200 minutes, mitosis ~20 minutes.
- Growth at 20°C: Cell cycle ~330 minutes, mitosis ~45 minutes.
nutrition and metabolic state of the cell
Lecture 12: The formation of embryos and cell fate
Animal embryogenesis
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Echinoderm development: Micromeres form in the sea urchin and migrate through the blastula to the gastrula
Embryogenesis: sea star being a primitive species
At different stages, asymmetric cell divisions are critical to setting up the germ cell lines and the early blastula
in the sea star
Manipulation during development: Alternative deployment of the micromerePMC GRN. (normal development)
In undisturbed embryos, only micromeres (red cells in the early embryo), or more precisely, their large daughter
cells, give rise to PMCs (red cells at the blastula stage) and the embryonic skeleton (red rods in the early larva).
Key genes that set up micromeres to form
germ cell line: 32-cell, blastula, gastrula and
larva
Cell layers develop into a variety of mature
tissues:
Meristems in plants
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Animal cells differ in the cytokinesis phase
from plants by the fact that: animal cells do
not form a cell plate Totipotency is best
described as:
Diploid evolved in higher plants and animals:
a delay in meiosis
The plant shoot apex -Ginkgo:
- Ginkgo embryos are shown here but all
gymnosperms have fascinating embryos.
Ginkgo is a primitive and monophyletic lineage.
The odd thing is that they have multinucleate embryos – many nuclei divide but new cells walls (‘cell plates’)
do not form to divide them. From dozens to a thousand new nuclei are present across the entire Kingdom,
cell walls form
Plant shoot apex – more advanced gymnosperms:
- Pinus embryos are shown here with a free nuclear stage as in most other gymnosperms.
Cell plates form at various times: after two free nuclei have formed. In Pinus and the cypresses then they
separate the nuclei with a cell plate.
In Araucaria, 32-64 nuclei can be in one embryo.
- However, in Sequoia, a cell plate forms immediately after mitosis
The importance of asymmetric cell divisions
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Angiosperms and cell fate: Development in arrowhead (Sagittaria), a monocot. Note the asymmetric cell
divisions. Some tissues are maternal, while others are filial (the product of fertilisation).
Critical zones in the shoot apical meristem of Arabidopsis: t there are various developmental genes coordinating
growth in the meristem. CLV3 is a small mobile protein that is a master control in the zones of the meristem
Asymmetric cell division are best characterised as:
Cell fate by genomics: Development is under the control of a suite of genes that we understand much better
now with modern genomic techniques. Mutation studies in animals (e.g. mouse) and plants (e.g. Arabidopsis)
Using mutants to understand cell fate: genetic control, with mutations altering the development of embryos.
Here you see the twn mutant in Arabidopsis making twinned seedlings
Irradiation studies and cell fate: f leaf and tassels within the leaf primordia
Red zones have been irradiated with x-rays and the predicted cell numbers (ACN) for each sector is given. The
fate map shows that meristem cells have specific fates
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Sector analysis in tobacco leaves:
- leaves received x-ray irradiation producing lesions in the
chlorophyll synthesis pathway.
This illustrates that leaf cells have developed according to
a fate map that is determined from early postmitotic
patterning
Cell fate in roots:
The Arabidopsis root is a perfect model for cell fate analysis.
It has very simple structure, with a single cell in each radial
layer representing an entire tissue type. Thus is can be easily manipulated
Using lasers to understand cell fate: non-genetic (mutational) approach
By killing individual cells, it is possible to learn how signaling events determine cell fate.
In this case, the signals seem to travel longitudinally along the axis of the root.
Cells in red have been ablated (zapped). They shrink then neighbouring cells in yellow/green take over a new
role.
Stem cells and the plant quiescent centre
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Cell fate – totipotency: Cells can be de-differentiated and cultured then made to produce embryoids in the
correct medium
- Concept of stem cells – cells in animals and plants that are able to give rise to any cell type given the correct
conditions.
Cells from the dorsal lip of the blastopore of a newt embryo can be transplanted and re-differentiate to a new
embryo
Totipotency is best described as: the capacity of cells to differentiate into a range of alternative tissue types
Determination in development is encoded by the nucleus (incoming signals)
Cell divisions happen at different rates to ensure supply of new cells is coordinated with requirements of growth
and differentiation
Cell divisions can give rise to embryonic structures while still attached to the parent organism
Lecture 13: Growth: the path to maturity
Growth
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Expansion in volume or mass or general accrual of resources
Cell division – reaching critical volume by growing before another diving can take place e/g/ yeast cells reaching
G1 but mitosis can occur in smaller cells
Unicellular organisms: unicells suspended in solution, growth rate = the number of dividing cells because of this
nexus between cell division and final cell size. This is true for many prokaryotes (not aggregating cells like
cyanobacteria), unicellular protists (e.g. Chlamydomonas) and fungi (e.g. yeast)
- unicells have a very large surface area to volume ratio, they can gain nutrients efficiently
- Multicellular organisms must acquire nutrients etc largely via internal transport systems such as
blood/lymph in animals and xylem/phloem in plants
- Absorption from the external medium can be rapid but diffusion to deeper tissues is slow
Cell numbers to infer growth rate: A doubling of the rate that cells divide (i.e. a halving in the half-life of each
cell) will cause a vast increase in final cell number. Cell numbers increase exponentially but cells must also
expand rapidly to achieve mature cell volumes and a new round of division = high temperatures
A condition of all growth is that
Directional growth
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Osmotically driven growth – internal (turgor) pressure must exceed threshold level before cell can expand.
Direction of cell growth = cell wall cellulosic fibrils
Root hairs and fungi ass new cell wall polymers to elongate tip
Exponential growth in complex aerial organs – fern fronds (over seasons)
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Cell division stops after days without substantial cell division, similarly in the ‘snorkel’ of germinating rice
Growth in plants: increase in area is not necessarily coupled to cell division
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Multicellularity = diversity of tissue shapes
Growth analysis for an determinate organism:
Initial phase (log phase) is exponential  linear (not all cells keep dividing at the initial rate)  senescence
((declining participation in growth form various tissues)
Absolute vs relative growth rates
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When the measure of growth is, say, number of individuals: by plotting the rate of change in numbers gives the
absolute growth rate (△N/△t). The bell-shaped curve in the previous slide shows the absolute growth rate
peaks in the mid-linear phase
However, when the rate of growth corrected for the total number of organisms in the population (N), quite a
different story emerges. In the exponential phase (the initial burst of growth), the absolute growth rate divided
by the size of the organism is constant (= relative growth rate = △N/△t × 1/N = natural log (N)/dt).
Synchrony if organ appearance: sequential leaves appear in a very predictable pattern
Secondary growth in plants
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Woody plants (lateral thickening) = increase strength. Encoded by genes leading to new polymers (lignin) and
direct polymers to the cell wall.
Exponential growth can best be modelled mathematically by
Growth in animal embryos
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Earliest stages = cells simply divide and grow until the 16-cell stage, rapid growth of embryo continues but
polarity commences with gastrulation
Net growth efficiency of pacific sardines declines with age - The metabolic rate of small animals is reflected in
the volume of food, and waste, that they consume. Therefore, changing over time as well as between taxa
Turnover of animal cells varies between organs, cell types & taxa: Rates of turnover of polymers using stable
isotopes are variable for ectotherms and a variety of organs
Lateral growth in plants and animals
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Lateral growth in plant roots (l) = involves initiation of a new dividing zone
Hydra (r) =grafts show an analogous initiation of laterals
Allometrics
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Allometrics = coordination of organ dimensions in a mathematical relationship. Moslty in telation to total body
weight.
Allometrics is best described as:
In animals: relationship between basal metabolic rate and body weight in animals is an example of ‘metabolic
allometry’.
- Within the context of morphology – organs and tissues develop in a coordinated way
- Isometry ((a one-to-one relationship) is less common that an log-log relationships such as you see here, or
non-linear relationships)
Growth of cell cultures – limiting factors
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Fermenters e.g. bacteria, yeast, plant or animal cells. Growth reflects supply of resources
In chemostat, nutrients are re-supplied at precisely the rate that they are removed by the culture, and therefore
cell growth appears to be eternal
Apoptosis – developmental phenomenon but reversing the gains from growth
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Cell death: both plants and animals e.g. duck leg (specific areas).
Lecture 14: Algae and lower plants
Phylogeny and life cycles of algae (Kingdom: Protists) and lower plants (Kingdom: Plantae)
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Protists – Chlamydomonas (a single-celled green alga)
- essential characteristics; flagellated haploid spores fuse, first the cytoplasm then the nuclei fuse
- Meiosis occurs in the zygote
- A very short diploid phase typical of lower orders
Chlorophyceae are non-motile (Chlorococcum) or colonial (Hydrodictyon)
Algal post-mitotic cell division - contrasting and increasingly advanced mechanisms of cytokinesis
Life cycle of diatoms: mainly reproduce asexually. The major cell differentiation is in the gametes
- Physiologically, these are very efficient organisms, with silicon-based cell walls
- Some are bilaterally symmetrical and others radially
Life cycle of Fucus (a brown alga) - A dominant sporophytic phase in these advanced algae
- the enclosure of the gamete-forming conceptacle
Also the dimorphic nature of the gametes, with motile sperm
Life cycle of a Plasmodium slime mold (non-photosynthetic Protists) - Slime molds (can assemble into a mature
multicellular structure, from which a new generation of spores will arise), can give rise to amoebae to carry out
a life cycle
The bryophytes – mosses (Seedless, non-vascular plants)
Moss lifecycle - more dominant sporophytes
- haploid and a diploid phase but the diploid phase is longer and produces larger structures than in the algae
Mosses, ferns and all higher plants distinguish themselves from algae by:
The ferns – Pteridophytes (Seedless vascular plants) e.g. Psilotum – the whisk fern
Advanced ferns – the mature plant is now diploid
Cell types and transport
1) Algae:
 gain nutrients by diffusion from their aqueous surroundings (very efficient transport systems, including sodium
efflux pumps)
 After meiosis, they produce zoospores, which generate gametes and then fuse to make a zygote
 many inorganic constituents in their cell walls, such as calcium carbonate and silicon dioxide
 Arise from multiple endosymbiotic events, with a pyrenoid in the chloroplast to store and release carbohydrates
 Light detectors – cells have a stigma or eyespot (Working together, the rhodopsin and the eyespot can help an
algal cell to work out light direction and transmit this to the flagellum to enable phototaxis)
2) Mosses:
 rely on diffusion too but with the beginnings of cell modifications (left) to allow water to move along surface
by capillary action
 A few mosses are aquatic, others such as Tortula are drought-tolerant
 Gaining water in mosses – Leptoids (conducting photosynthate) and hydroids (conducting water) are primitive
conducting systems but are not veins. Some mosses have elaters, scales that absorb water and allow dispersal
of spores by a twisting motion.
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Water transport in the algae and mosses is distinctively different from the ferns because it relies primarily upon:
Transfer cells:
All plants have organs that are involved in carbohydrate transport
Upper cells are sporophytic (diploid) and the lower cell is the gametophyte. This boundary in the moss placenta
Applications and curiosities – why these ‘lower plants’ are vital for our survival and the Biosphere
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Copper mosses: genus Mielichhoferia and they are copper tolerant
- Found on soils rich in copper, mine tailing and in Buddhist temples where copper pipes have leached copper
into the soil
- Also some species are in cave entrances where the cells of the germinating spores (protonemata) and the
thalli glisten
Extremophile algae and mosses:
- Mosses are exceptional for their ability to survive dry and cold places
- resilience of the proteins in mosses – this is now the topic of a great deal of biotechnology research to find
these ‘dehydration proteins’
- ‘watermelon snow’ where carotenoid -rich algae are able to grow in the snow
Algae to make hydrogen fuels: Photosynthesis (and nitrogen fixation) are strong reduction reactions and
therefore, there is potential for chemical reduction of water (H2O) to hydrogen (H2)
- In anaerobic (oxygen-free) atmospheres, particular algae such as Chlamydomonas make hydrogen gas
Biological hydrogen generation relies upon:
Lecture 15: Higher plants
Phylogeny – Gymnosperms
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A diverse group of ancient plants that evolved from the ‘seed ferns’ in the late Devonian 360 mya carboniferous landscape
Phylogeny – extinct progymnosperms e.g. Lycophytes – fern allies, Seed fern and cordaites
- These primitive lycophytes and progymnosperms evolved in the Late Devonian but disappeared 125 mya
- Phylum Coniferophyta - Pines (conifers) generally have male organs higher on the tree than female cones
to facilitate fertilisation
- Other Gymnosperms - There are four extant phyla – the Coniferophyta (conifers, described above),
Ginkgophyta (ginkgo tree), Cycadohpyta (cycads), and Gnetophyta
Higher plants are distinguished from lower plants by:
Taxonomy of the Angiosperms – flowering plants
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Angiosperms (phylum Anthophyta) – there are at least 300,000 species and more to be discovered and defined
They fall into two classes – the Monocotyledons (‘monocots’) and Eudicotyledons (‘dicots’), respectively with
90,000 and 200,000 species
Basal angiosperms e.g. Nymphaea, Amborella and Magnoliids e.g. magnolia and pepper
Transport
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Higher plants have sophisticated bi-directional transport systems
- There are significant differences between the transport properties of primary and secondary plant tissues
and angiosperms vs gymnosperms
Long-distance transport of water and nutrients is via two cell types – xylem in dicots (l) and monocots (c)
and tracheids in woody dicots (see later slide) and gymnosperms (r)
- These are dead cells that conduct under suction, not pressure
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Long-distance transport of sap containing organic substrates is via phloem, which is a complex of living cells
containing membranes and organelles
- These two cell types are always found in association in primary plant tissues* in the form of vascular
bundles
Xylem operates under suction
Primary plant tissues are those tissues that arise from primary meristems. They are the immediate result of
growth and do not have thickened cell walls
- For example, leaves, new stem and root tissues and fruits and flowers are primary plant tissues
Secondary plant tissues arise from secondary growth in the roots and stems of both woody (perennial)
dicots and woody gymnosperms such as conifers and Ginkgo
- This requires the union of the concentric vascular bundles of the dicot stem to form a continuous annulus
of conducting xylem and phloem, greatly increasing sap volumes conducted
The physiology of long-distance transport:
Xylem operates under negative pressure to create a driving force for extraction of water from the soil
solution - there is a ‘self-correcting’ pathway for water transport
- Phloem operates under positive pressure, using metabolic (vs. solar) energy to drive transport or organic
molecules - this enable selective transport and resources to be delivered to tissues in which growth rate
(and carbohydrate demand) is maximal
Long-distance transport of sap in plants is largely achieved by the forces of:
Reproduction – asexual
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means of reproduction of the population but does not enhance genetic diversity because it is clonal
Reproduction – sexual
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include the whorls of petals and sepals, and the reproductive organs that include gametes resulting from
meiosis
A much more complex process, where autosomal chromosomes enable differentiation into complex sexual
organs that we see as a flower
The developmental genetics of this process, and its initiation, are highly complex and still being worked out
Homeotic genes have been best described in floral development
Sexual reproduction in angiosperms (flowering plants) differs fundamentally from that in higher animals. For
example:
Genetics is critical in sexual reproduction:
- Homeotic genes determine developmental programming
Simple variations in phenotype such as shape, colour and attractiveness to pollinators can be influenced
by very few genes as seen in these single-gene mutations in tomato
Thus, domestication of plants, for example, involves many deliberate and inadvertent selective changes
in the development of organs and even the elimination of sexual reproduction in the case of many fruits