Download doc NotesForMidterm-2015

Begouen-BIOL205-Winter2015
LECTURE 2 : INTRO TO ORGANISM
(review part 5)
1) Origins
For creation of planet, size = super important.
Since appeared, matter and E interacted
H, C , He, Li  First synthetised = Pre biological synthesis (elements synthetised before life
appeared)
Then  radiation was used as an energy source and organic compounds were synthetised.
 Pre-biotic molecules complex arose = constant exchange of material and E with
environment
 Life finally appeared
!!! Life was bound to appear – a continuation of chemical evolution.
Living state = non equilibrium – always evolve:
Life needs both degradation and synthesis to occur  allows system to maintain itself and
avoid equilibrium
But (according to first law thermodynamics) system always moves towards equilibrium.
When reach equilibrium = death = no entropy
2) Chemical elements used in life
Life possible thanks to H,C,N,O ( can all form long chain of polymer = multiple
evolutionary possibilities)
 Special organisation of matter = self regulating/organising/renewing
!!Possibility that life came from Si/Ammonium !!
3) Organisms characteristics
THERMODYNAMICS CHARACT
 Can have some similar characteristic with non-living but non-living doesn’t have ALL of
them
 Are thermodynamically open (take in food + E and reject waste) but organisationally
closed + out of equilibrium
- Will exchange with enviro, but energy remains constant
Prygogine (scientist) : invented non equilibrium thermodynamics : Flow of energy in
systems , that will organize it, state is maintained by flow – If flow changed, will change
whole system allow to describes living system
-Continuously replacement of our bodies: bones = 18 months, muscles = 3 months
Organism = self organizing autopoietic system
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Organism = negative entropy : exchange with enviro but are not in equilibrium. Equilibrium
= death
HOMEOSTATIS
-Homeostasis : maintenance of internal environment VS big change in exterior one ( Ex: If
outside T go +20, inside T doesn’t change, we just sweat ) – Necessitates a feedback system
that sense the disturbance and counter interact it
Organism can be separated in conformers VS regulator (can shield itself from enviro)
Regulator maintains homeostasis by regulation
Control theory  Degrees of regulation: homeostasis is only maintained to a certain point,
after a limit, variability will change drastically. (Ex: Low T- until a certain T, body will fight
and control it. After that – hypothermia –death (fail of the system))
How it works:
Desired level = SET POINT
Deviation are sensed by a SENSOR
Sensed deviation are converted into a SIGNAL by a AMPLIFIER
Then FEEDBACK
 Negative feedback= most common
Ex: CO2 levels : Horse runs = Disturbance – CO2 rises- Nerve cells are triggered=SensorsSend signal to other part of brain hat control breathing- Signal sent to muscle - slow
breathing = return to SET POINT
 Positive feedback: Deviation is increased until unstable system that will return to set
point ex: Vomit, sneeze
!!Some animal don’t control at all (E=1)!! = Conformers
!! Some can regulate at first and then not – Some can regulate only after reaching a certain
value!!
 Different organisms = different strategies to regulate environment (but NO perfect
controller)
GROWTH
-Shape changes during growth, cannot be predicted mathematically (Allometric)
Plants always grow, not animals
Growth come with development (all change happening):
Will acquire characteristic shape (morphogenesis)
 Cells will get their specifics functions (differentiation)
Features are unique to organisms
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REPRODUCTION
Simpler reproduction = asexual
Higher = sexual: two different mating organisms and 2 different gametes. Go from haploid
to diploids
In higher plants = asexual and sexual (also Daphnea)
 Alternation of generations
4) Day to day process of organisms
ENERGY ACQUISITIONS
 Need of E to counter entropy/ drive organisation (order and complexity)
Organism  needs E and low C
Ultimate E source = SUN
Based on needs of those two, organism can be divided into groups : Autotroph vs
heterotrophs
ACQUISITION AND TRANSPORT OF MAT IN/AROUND/OUT OF ORG
 Org need material from enviro, have to be transported through membrane + some need
to be excreted + concentration gradient of ions in/out cell need to be maintained 
Transport in/out has to be strictly regulated
Different transport types:
A) Diffusion = only process if there is no air flow
B) Osmosis = special diffusion, through membrane
C) Convection = Rice in a pan
D) Transport across cell membranes
E) Endo/exocytose
A) Diffusion- a transport process
= Movements of molecule due to K energy ( !! Not to air flow= unfacilitated transport of
molecules)  random but goes away from region with higher C
 From High C to low C = down concentration gradient
Rate of diffusion changes with concentration gradiant + membrane thickness
Membrane thickness influences the diffusion coefficient
 Fast over short distance <-> very slow on long distance
Ex: O2:
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-
1microm = 10-4
1mm=100s
1m = 3 year
B) Osmosis= special diffusion
= Diffusion with special condition
Water move from one side of semi-permeable membrane to the other one
 Solvent will go through but not solute.
Goes from higher water C to lower
Speed = dependant on pore size
C) Convection
Driven by pressure difference – is used in supra-cellular distance (big one)
 Can be by air movement or in liquid – In ducts, tubes or vessels
Moved by bulk flow – need of a pressure diff between beginning and end of vessel
Flow rate (Q) = (P1-P2)/R .
R = hydraulic resistance (depends on viscosity)
 Will increase with pressure and decrease with resistance
D) Transport through cell membrane
 Many different types
Some need E: active transport process  can transport substance against C gradient
 2 types depending on ATP use (direct or not)
- ATP directly coupled = Primary active
- Just pass through protein = Secondary active
i) Both solutes in same direction = symport
ii) Opposite directions = antiport
iii) One solute in one direction = uniport
Other have no need : passive transport process  Follows C gradient . Use of channels ( can
open and close- need stimulus to open) and of carriers (proteins anchored in membrane,
binds with solute and changes membrane conformation)
E) Endo/Exocytosis
Endo = indulge, brought in
 Formation of cavity, prot comes in. Forms vesicle (separates from membrane) that will
after go freely in cytoplasm
Exo = expelled out cell
 Material is in vesicle that fuses with membrane and opens towards outside
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5) Implications of size of organism
All organism grow in size
A) Great variety
B) Being bigger doesn’t mean bigger consumption
C) Ratio CO2/size, becomes smaller as size grows
Isometric growth: Growth follows the same proportion (everything has the same pace) 
If a=2A then b=2B and c=2C
Allometric growth: can’t be mathematically measured, a=2A b=B c=3C <-> Growth = not
proportional
Surface will increase with volume but not in linear proportion, ratio will get smaller
 Metabolic proportion = Allometric
(surface ^2 and volume^3  not the same)
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LECTURE 3 –ENERGY, LIGHT AND LIFE ( 9 janv)
E= necessary for life, but where does it come from ?
1)
Food and energy requirements of plants and animals
Each org = syst of negative entropy
 Simple molecules are absorbed and then organized in more complex macromolec.
 Need of material and E to make it
Plants and animals differ in need.
- Plants receive E from Sunlight, but food from air or soil- need simple inorganic matter
- Animals receive food & E at same time
- Plants need E (sun), CO2 (air), mineral( soil) +seed  non elaborated, simple food
- Animals  complex food, made by plants/other animals
So plants = primary producers of E and food (do so through photosynthesis)
2)
Composition if sunlight and interactions light/matter
Light = both particle/wave
= Small part of electromagnetic radiation from sun, in a 400nm to 700nm
Plants Principal source E  Sun.
Energy comes from excitation of electron (induced by heating of photon)
E is inversely proportional to wavelength E= h*c/wavelength
Photons with higher energy are the one with shorter wave length  Visible light (
especially those in violet )
Interaction of light& matter depends on material’s nature & on light’s nature :
Short wavelength = high energy = too powerful, destroy stuff
Visible wavelength photons =moderate energy= cause chemical reactions, most use,
produce light and E
High wavelength=low energy= only heat and no light ( infrared lamp)
 We are mainly concerned with photons from moderate energy quanta
3) Light receptors and pigments
In light driven process, light must be absorbed by receptor. When light is in the correct
range  we can see colour  receptor now called a pigments
Pigments = conjugated to certain proteins.
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4) Action spectrum of photosynthesis + action spectrum of
pigments
Photosynthesis = process where light becomes biochemical energy
 Has an action spectrum telling us which wavelength makes the whole thing work +
receptor/pigments that absorbs this specific wavelength
 When action spectrum of light process coincides with absorption spectrum
pigment/receptor  we can say that go together towards same process
5) Site of photosynthesis  Chloroplast
Reaction summary: Light energy captured, used to take e out of water  liberates O2
e  used to create NADPH, used to reduce C
Photosynthesis characteristics
- Happens in chloroplast (organelle with double membrane)
- Where no membrane = Stroma = matrix
- Grana (Granum) = stacks of thylakoid membranes (hollow membranes , space inside
= lumen)
6) Photosynthetic pigments
In thylakoids membrane  photosynthetic pigments with conjugated protein
- Several types of pigments : chloro + carotenoid
- All eukaryotes have chloro-a , but other vary
- 4 types of chlorophyll
All pigments absorbing light: alternating double bounds. Why ?  Cloud of electron covers
it , and passes through it (pigment=good conductor)- facilitates e transmission
 electrical cord
Action spectrum: Tells us rate of process under different wavelength
 We can see that absorbance and absorption spectrum are very similar  same process
Pigments are associated with proteins; they will modify absorption spectrum
 Protein = purifier
Pigment=provider of E
Evolution O2
Photo function = to reduce C by adding e (from H)
When e are from water  O2 involved
Cyanobacteria, take e from other compounds  no e involved
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7) Three phases of photosynthesis
A) Photo physical phase: Light absorption and excitation transfer: ultrafast process :
pico second 10^-12 = path excitation transfer
B) Electrochemical phase: Electron transfer that allows NADP+NADPH and proton
production to synthetise ATP <msec = path electron transfer
C) Biochemical phase: C is captured and reduced < 1 sec = carbon path
8) Path excitation transfer
Excitation energy transferred from 1 pigment molecule to another one in higher
wavelength (lower quantum E)
EX: carotene (450nm)  chlorophyll b (650nm)
Only works one way
Lot is lost by fluorescence
9) Organization of photosynthetic machinery
Evidence of 2 photosystem
A) Transformation of 1 O2 requires 8 photons (instead of 4)
B) Red drop phenomenon  when go over 680nm , decrease in activity ( was one
phenomenon that could only work before )
C) Emerson enhancement: when we have a whole light(= white light) it works 3 times
better than separate extreme wavelength
D) Discovery of cytochrome complex: taking electron from one side and being reduced
while giving electron to other side and being oxidised (see BIOL 201)
10)
2 photosystems
Are called photosystem 1 (700nm) and photosystem 2 (680nm)
 Each organized in group and with reaction centre and antenna pigments ( each
associated with specific prot that give them special absorbance charact.
11)
Organisation of 2 photosynthesis
 In a Z scheme
Starts by system 2 (PS2) –excites itself with light, loses electron, E goes down , then system
1 (PS1) excites itself (incoming light) , E goes up, loses e , and finally oxidise NADP+ to
NADPH
Both system activities = synchronised
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To make up for electron loss, those remove from PS1 go to Fd and to cytochrome and then
to PS1  ATP production
12)
ATP synthesis
Protons pumped in to thylakoids membrane
Higher PH = less protons
Light reaches chloro.
Protons move from stroma (PH+) to lumen (PH-)
(????)
Experiment : Put chloro membrane in low PH buffer, PH+,
transfer thylakoids to high PH+ Pi and ADP  in dark , still gets ATP
Protons transfer from stroma to lumen  escape through ATP synthase, after every 3or 4,
ATP made
Product of light reactions
D) NADPH H will be use to reduce carbon
E) ATP  E needed to do carbon reduction
When organism take food from other organism, must break it bc :
A) Food particle too big to enter cells
B) Food entering was made according to other organism genetics  Everything must
be breaked down into monomers (so can use it)
C) Digestion provides identity to what is being eaten, if not = allergy
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LECTURE 4- CARBON ASSIMILATION
1) Photosynthetic Carbon Reduction Cycle (PCR)=Calvin cycle
Carbon reduction:
6CO2 + 12H2O Glucose + 6O2 + 6H2O + E (672kcal)
Products of light reactions
- Electrons from water
- NADPH from NADP+: reduce carbon during carbon cycle
- ATP from ADP + Pi: activates molecules of intermediates during Cavin Cycle
To incorporate atmospheric CO2  acceptor molecule is needed.
Calvin  Looked for it  Made up nobel-prize winning experiments:
 In a flat lollipop (where cells will get all light uniformly) ,we shine light for a sec , and
then kill cell by putting them in boiling methanol  no more reactions, we extract
carbohydrate
- Since CO2 was radioactive, whatever was produced thanks to it will be radioactive
and we can find it
Goal here = to find which molecule became radioactive first: it would be the acceptor.
- Paper chromatography allows to find where are products
- Radioactive shadow are noticed – to separate further, rotation of 90degrees
- To know what are all the spots  comparison with know elements ex: Sucrose
First product made was PGA, a 3 C molecule. With time increasing different carbons of the
PGA were labelled  means there is a cycle.
They then searched for a 2 C acceptor, but none was found
CCL: A 5 C uses 2 CO2 to form PGA  RuBP
So PGA initial product and RuBP CO2 acceptor.
Proof:
- In absence of light: no ATP & NADH produced PGA is not metabolized into glyceride
3 phosphate , PGA accumulates . BUT CO2 is still here  RuBP is still consumed
- In absence of CO2 but with light , RuBP not used, accumulates BUT PGA is used, consumed
as ATP and NADPH available from light reactions.
PCR cycle  3 steps
- Carboxylation
- Carbon Reduction (ATP to ADP and NADPH to NADP+)
- Regeneration of CO2 receptor (RuBP), phosphorylated with ATP to start agai
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Carboxylation ( of RubP )
Made by RUBISCO enzyme (bifunctional) = most abundant prot on planet
 catalyses first reaction in photosynthetic carbon assimilation
Very large  8 large subunits + 8 smalls
Has 2 functions=bifunctional: Adds CO2 or O2 to RuBP  carboxylation or Oxygenation
On carboxylation: unstable 6 C intermediate  splits into two 3C of 3-PGA = first product
of carboxylation.
Calvin cycle  C3 photosynthesis. ( in chloro)
VS when CO2 fixed in cytoplasm to 4C compounds then transported to chloroplast  C4.
There are 2C fixations .
Carbon Reduction :
3-PGA to 3-phosphoglycerade.
Before reduction 3-PGA has to be activated by phosphorylation using ATP  formation 1,3diPGA Reduction to G3P using NADPH.
Product light reactions ( ATP and NADPH )  used in activation and reduction of 3-PGA
Regeneration of CO2 acceptor :
 series of reaction.
G3P and DHAP form 6C . Then combine 3C and 6C BLABLABLA pleins de molecules
In the end Ru5pRuBp by ATP
!! Must know where NAPH and ATP are used !!
Photosynthetic product  can be used for export and storage :DHAP goes out of chloro for
other roles
 CCL : For each cycle : 3 ATP and 2 NADPH used
2) Photorespiration :
Comes from oxygenase function of RUBISCO, add O2 to RuBP. During evolution, efficiency of
carboxylation increased
Since O2 much higher than CO2, oxygenation should be favoured over carboxyl BUT
RUBISCO has greater affinity for CO2 than O2. One factor determining ratio = affinity of
RUBISCO for 2 competing substrates : inverse mesure of this infinity = Km
 Lower Km = greater affinity
!!To be active RUBISCO needs to bind to a CO2 !!
Photorespiration  occurs at cost of photosynthesis
Phosphoglycolate is sent to peroxisome, is oxidized to glyoxylate using O2 Then
glyoxylate amino acid glycine
Glycine  mithochondrion  release amino group. Sent back to peroxisome where is used
to convert glyoxylate to glycine
.
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Phospho decrease efficiency of photosynthesis.
Location : depends on what kind of plant it is.
3) CO2 concentrating mechanisms: C4 plants
2 experiments found out that in C4 plants (corn and sugarcane)  1st products wasn’t PGA
BUT C4 acid : MALIC & ASPARTATE acid
C3 plants  first product = PGA
To limit or decrease photorespiration :  Increase CO2 concentration around RUBISCO
C4 plants actually did so
CO2 fixed in cytoplasm of mesophyll cells  MalateBundle sheath  burst CO2
Chloroplast carry out rubsco’s fixation of CO2
Products move through plasmodesmata
C4  Concentrate CO2 at carboxylation site in BSC chloro’s stroma
- Co2 first fixed in MC cyto ( Comes from atmosphere directly into)
- Malate transported to BSC cell ,thanks to Malic enzyme NADP+ is oxydise Calvin
cycle
- Pyruvate comes back to Mc
CAM plants (Cacti)
- Same reaction as C4
- One occurs during night and other during day
- Do not open stomates during day – only in night in order not to lost H20  CO2
comes in, Malic made and stored in Vacuole , SUUUUper high C
- During day  Malic is decarboxylated  Calvin cycle
Difference between C4 and CAM
- C4 happens simultaneously in different set of plant
- CAM has a separation in time
6)Differences between C3 et C4 plants
C3  much lower Co2 concentration than C4  through stomata from atmosphere
Light compendation point (LCP) and CO2 compensation point (CCP)
 We need a CCP higher then LCP to have photosynthesis
C3 - CCP from 50 to 100 ppm Co2
C4  CCP 0-5 ppm (everything released is fixed right away )
CAM  0ppm
FINISH ENDING
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LECTURE 5: WHOLE PLANT AND CROP PHOTOSYNTHESIS.
1) Response of photosynthesis to light intensity
Minimum light intensity at photosynthetic carbon gain= carbon loss due to
respiration/photorespiration  Light compensation point (LCP)
Under LCP: plants are loosing C  will exhaust themselves to death through respi.
At LCP: Zero net photosynthesis
Over LCP: light intensity is so high that products (ATP and NADPH) not consumed fast
enough by Calvin cycle.  Photo oxidation and photo-inhibition of photosynthesis [
damage to photosynthetic machinery depending on excessive light intensity level).
Photo inhibition under moderate light excess = dynamic photo inhibition.
Rate of photosynthesis  Will slowly reach rate of optimal photosynthesis.
Whether plant = sun plant or shade plant  can be acclimatized to diff light intensity. Plant
used to a low light I  will reach stop at photosynthetic rate before plant used to a higher
light intensity
 Even if Sun plant, response to light I depends on previous exposure
 Sun and shade plant differ in response to light I  shade plants’ photosynthetic rate
saturated lot earlier.
Plant  Have avoidance/ tracking mechanism to regulate light’s absorbance.
If light to high, Chloro will hide behind each other to avoid excess light
Some plants follow sun in other to receive optimal light
 Some plants evolved to be shade-plants(shade love) or sun plants (sun loving)
2) Response of photosynthesis to CO2
!! Right now, CO2 in atmosphere  350 ppm!!
Increase CO2 associated with climate change.
HOWEVER  minimum CO2 concentration  required for plant survival.
Concentration of CO2 at which C gain = C loss  no net photosynthesis = CO2
compensation point (CCP)
CCP in C3 plants  50-100ppm
CCP in C4 plants  5-10 ppm
CCP in CAM plants  0  100% CO2 released by respiration = refixed by photosynthesis
Increase in CO2 concentration  accompanied by increase in C assimilation
This increase  more pronounced in C4 than C3
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Further increase in CO2  does not increase rate in C4  C4 photosynthesis limited by
light I not CO2 concentration.
In C3  increase in CO2 concentration diminishes photorespiration but keeps increasing
photosynthetic rate
3) Response of photosynthesis to Temperature
Rate of photosynthesis = constant between 12C and 37C in C4 plants
C3  decline in photosynthetic with increased T (between 14C and 40C)
Photorespiration  more responsive to T increase than photosynthesis decline in C3
photosynthesis due to larger increase in photorespiration than photosynthesis.
4) Response of photosynthesis to O2
Photo respiration occurs due to RUBISCO bi-function and because there is a higher O2
concentration than CO2  decrease in photoresp expected to increase photosynthesis.
C3  higher vegetative growth at reduced O2  decrease in photorespiration can
increase vegetative growth
C4  no change
Results on reproductive growth
In both C3 and C4  decrease in reproductive growth as O2 concentration is reduced.
Production of seed  requires O2 concentration.
But why does fruit/seed development requires so much O2  reproductive dev has
intensive E  requires intense respiration that only O2 concentration can support.
5) Plant architecture and productivity
Most important morpho feature (determine dry matter production)  Leaf angle
Can modulate angle of shading of lower leaves by upper ones
 Amount light interception  photosynthesis= different in upper and lower leaves
Crop yield varies with leaf angle
Highest yield = reached when angle = close to 90 degrees
There has been computer simulation to see yield of leaves at diff angles.
When top leaves = horizontal and lower leaves vertical  extremely low
When top leaves =vertical and lower = horizontal  high
Leaf angle  can have important application for community level of crop yield
Ex: if a crop = vertical leaves  can have more plants per unit ground area
Since crop iels  depends on planting density  higher D = higher yield
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6)
Community level determinants of crop yield
2 important community level determinant of crop yield  Leaf Area Index (LAI) and
planting density.
LAI = ratio between total leaf surface and ground surface under leave  dimensionless
 can determine prod/plant/unit area
 Increase during crop growth until reach final size = related to dry matter accumulation
Plant density =number of plants per unit ground surface
In agriculture  controlled by seeding rate  will depend on % germination of seeds (
rarely 100%)  If %= low , higher seeding rate has to be used.
Farmers in ancient Egypt  had figured out optimal seeding rate by trials and errors
Mathematical relation between density (d) weight per plant (w) and yield (y)
Y=w*d
!!!+ see equation in book for dry weight !!!
y =density dependant
 young crop = small and far apart ,
Mature stage  plant are shading each other  Growth of one plants affected by its
neighbour. Y becomes density-independent bc increase number of plant =decrease in
weight per plant (effect=0)
LAI increase with crop growth.
LAI can be substituted for density to determine effect on weight and yield
RESEE THIS PART
7) Efficiency of energy conversion
At the level of carboxylation  to fix 6CO2/make one glucose/evolve 6O2  minimum of
48 (6*8) photons of 680 nm = required. !! = minimum, can have more (10 or 12 photons)
Input of E = 8640 KJ
Output (E stored in one glucose)=2872 KJ
Efficiency = 33% (max)
Efficiency of E conversion by a leaf  40% of Sun E is absorbable.
8% of it  lost through transmission/reflection
8% of it  heat dissipation
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19%  in metabolism
 5% of total can be converted to carbohydrate
8) Annual budget of a tree
Gross photosynthesis/ shoot respiration/root respiration  will vary according to day
time or time of the year
Low rate of metabolism in winter (C loss under the snow )
Needles respiration during night has to be subtracted to photosynthesis stuff
Annual CO2 balance for pine: 5283.3 mg
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LECTURE 6: CAPTURE, INGESTION, DIGESTION AND ABSORPTION
OF FOOD IN ANIMALS
1) Nutritional requirements obtained from food
All animal  obtain food by eating plants (directly) or by eating animals who ate plants
(indirect)  complex food requirements
Types of food components obtained by animals:
- aa  build proteins. Obtained during digestion
- Simple sugars (Glucose)  used to obtain E or to store it as glycogen. Also needed
to synthetize other molecules
- Lipids synthetize cellular membrane or source of metabolic E
- Inorganics salts  synthesis of nucleic acids + osmoregulation
- Vitamins  to assure normal function
- Water  essential solvent.
Not every chem element = essential in animal nutrition. Biological evolution= continuity of
chemical evolution certain chem elements were selected to build up prebiotics systems
and biological systems were built from it.
Animals require them in various proportions  Some can be needed to some species and
not to others.
Essential nutrients = nutrients that cannot be produced by the organism  Vitamins and
some aa.
2) Feeding methods
Unicellular organism  take up food by surface absorption  food has to be in molecular
form. Is produced by death and decay of other life form.
Unicellular fed by endocytosis.
If food taken in solid = phagocytosis
If food is dissolved =pinocytosis
Multicellular  capture food in specific ways
-Tentacles
-Sucking
-Tear
Feeding methods of bird  have to overcome certain difficulties: refractive indice of water
(apparent position of prey is not the real one) + movement of the prey.
 Possible neuro mechanisms
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3) Digestive system
Digestive system  structural organs providing contained space for digestion + accessory
digestive system secreting enzymes
Some animals: Secluded groove  long tube track opened at ends (one for ingestion and
the other one for expulsion of undigested stuff)
Those grooves  not internal to organism. Food lies outside body of organism.
Tube like structure  called digestive track/alimentary canal/gastrointestinal tract/ gut
Tube like nature  Efficient design  different regions of the tubes can be modified to
carry out temporal sequence of digestive steps as food passes through.
Digestive system  digestive track +glands (putting biochemical digestive fluids) in gut.
Throughout length of alimentary canal  cells secrete mucus that facilitate food movement
Vertebrate alimentary canal regions :
Head gut mouth part of the gut  serves to detect/ingest and breakdown food into
smaller parts . Process  increase total surface area of food particle  rapid enzyme
action.
In first part of it (mouth) : Saliva+mucus secreted . Mucus  wets food for easy handling
Saliva has bicarbonate and amylase that degrades enzymes.
 Digestion starts with mouth chewing
Foregut includes esophagus ( part of it can become crop  in some invertebrates + grain
eating and fish-eating birds have a large one for storage )
Midgut stomach and small intestine. Part where both absorption and digestion happen.
In stomach  cells secrete hydrochloric acid into lumen activates digestive enzymes
Small intestine  digestion of prot = completed & digestion of fats and digestion of
carbohydrate continues . Acidity from Stomach=neutralized
Absorption of products from digestion  takes place in small intestine
Hindgut Large intestine.  Absorption of materials and water takes place before
undigested materials is expelled. Contains microbial community to try and digest cellulose
and vitamins.
4) Digestion
=Biochemical process by which macromolecules monomers constituents
Different parts of alimentary tract digest diff components of food.
Nature of digestive enzyme  varies with part of digestive track.
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Mouth  food physically broken into pieces to increase action area of enzymes . Mouth 
several pairs of salivary glands that will secrete saliva ( with amylases – starch degrading
enzymes)
Saliva has 3 functions :
- Moisten food for easy chewing/swallowing
- Acts as solvent for food molecules  bind to taste bud, facilitates perception of taste
- Contains amylase  degrade starch into glucose
Also contains bicarbonate ions  neutralize acids in foods. In insectsenzyme invertase
that breaks down sucrose.
In some animals  saliva has special functions (contains poisons and toxins and anticoagulant)
Every day  production of 1L of saliva.
Oesophagus  Muscular tube with sphincter at each end. Food enters it as soon as
swallowed (is all or none reflex)
Food =prevented from entering into nasal/trachea passages or re-entering mouth
Digestive process from mouth continues in oesophagus. Cells on walls secrete mucus that
helps passage.
Sphincter (band of muscle tissue) controls passage from oesophagus to stomach
Stomach As food enters carbohydrate digestions continues. Cells in stomach lining
contains hydrochloric acid+pepsinogen + gastric juice (contains intrinsic factor (essential
for B12 vitamin )) . HCl in stomach lining converts pepsinogen to pepsin (active form)
Up to 3L of gastric juices produced daily, its pH=1,5=strong enough to kill a bacteria
Small intestine  Partially digested food stomachsmall intestine
First u-shapped part= duodenum. Specialized cells in it secrete enzyme that participate in
digestion/ activate other digestive enzyme
2 types of digestive secretions poured in :
- Pancreas secretes pancreatic juice by pancreatic duct. Contains unprocessed form of
prot degrading enzymes. (Contains lipase, amylase, nuclease, maltase ) +Bicarbonate
- Bile brought in by bile-duct. Produced by liver , store in bile gladder has bile fats
(essential for fat digestion)
Digestion of all fats  primarly in small intestine
pH=7 to 8
Large intestine  Digestion is already complete  large intestine will maintain water and
ionic balance . Absorbs water & ion from undigested material before expelled by defecation
Total length of gut  reflects digestibility of food that animal eats.  Herbivore’s food takes
longer to be digested than carnivore’s  Total length gut greater in herbivore.
Within particular group (bird)  length related to type of food eaten
Called Eco morphology
Gut  also contains ++ organisms: archae, bacteria, fungi, parasitic worms …  play
essential role in digestion= Mutualistic relation (both benefit)
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Their role  particularly important in herbivore bc cannot degrade cellulose ( that is
major part of plant material)  Some of the micro organisms produce cellulose and will
help org to degrade cellulose to glucose.
Can also produce Vitamins
Evolutionary conflict between organisms & food  some plants now have defense
mechanisms Ex : tannins
5) Chemical reactor theory
Digestion system can be compared to a reactor (series of bulk reactions where reactant and
catalyst mixed and products removed according to time)
 Food and enzymes mixed together and product = removed through absorption
Reactor  will influence production efficiency: size/shape/patterns
3 types of reactors
- Batch: Single vessel  Put reactants and catalyst in reactors(= enzymes, substrates)
, mix it , let it go then  empty it and extract product from content ( input and
output from same entrance). Efficiency will depend on time, the longer the reactants
are in , the more products we get. Ex: Hydra. Lost time in emptying and refilling
-
Continuous flow stirred (CSTR)  2 openings, one for input, one for output 
continuous mixing : rate digestion = rate absorption. Global rate  depends on size
input/output. Good for animal that graze for long periods. Ex: Camel. = Progressive
digestion
-
Plus flow reactors (PFR)  Shaped like a long tube. Continuous input, move
through long tube and enzymes are being added at certain places  progressive
digestion. Mixing occurs only across radius, not length. Product removed along the
way.
6) Structure and function of the herbivore gut
Cell wall = 30-55% plant tissue dry weight mainly cellulose. None of constituents 
soluble in water.
To digest cellulose  need help of microorganisms. Also carry out food fermentation.
 To pass over that, some herbivores have multi chamber stomach  slow process of
digestion w/ repetition of certain steps Ruminants – regurgitate and re-chew food from
stomach chamber: reticulum.
To get sufficient return from slow digestion  increased stomach size  Small herbivore
feed on high Q, young plant tissue vs large herbivore  feed non-selectively (have to eat
more thus larger stomach)
Ruminant stomach = digastric stomach
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1st part  Rumen and reticulum
2nd part  Omasum and abomasum
Have rich microbial population
During grazing  animal eat as much as thyey can .
Rumination happens when animal = resting  partially fermented food in rumen brought
back to mouth and re-chewed and swallowed again in Rumen (got broken in smaller pieces
 facilitates digestion &fermentation more )
Large amount of CO2 and methane CH4 are released. Expelled by burping
Dietary fiber  cellulose and else presence is important for health because of dietary fiber
7) Absorption of digested food
Small intestine  where major absorption occurs BUT water and ions  Large intestine
To maximise absorption: surface area increased in small intestine . Epithelial cell
organised into villi. Tightly organised
Most epithelial cells = absorptive but some = goblet cells and secrete mucus .
Food molecules absorbed  passed to bold and lymph vessel  other part of body
Nature of stored food reserve  glycogen. Used as substrate to respiration ,growth/repair.
Equivalent in plant = starch
8) Digestion in insectivorous and carnivorous plants
Insectivorous plants  digestive juice similar to animals’. Pitcher like a toilet, prey tries to
lich nectar, falls into pitcher
Might be response to nitrogen-poor soil. Animal = protein supplement
9) Feeding the young
Mammals & birds produce milk.
Concentrations of constituents in milk vary . Protein concentration related to growth.
Penguins  male eats nothing for 2 month, is female doesn’t come back  starts producing
milk
10)
Coprophagy
 Since plant material = hard to digest  Small herbivore expel partially digested food
through defecation and eat it to take remaining nutrients in it.
Ex: Rabbits  2 types of feces: small and hard: low N = bad VS softer high N  consumed
and digested further
!!! Re-ingested food not mixed with previous one, kept t the end of stomach !!!
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11)
Evolutionary and ecological aspects of digestive systems
of animals
All animals  consume food  conflict between animal and food
Plant  evolved mechanisms to defend themselves  thorns, unpleasant coating /poison
Almost all  wounding response = produce signal (jasmonic+salicylic acid) , will enter
atmosphere and produce inhibitors in their leaves .
 Very effective against insects, not so sure about large herbivore
Total length digestive track = longer in herbi than carni  we can guess nature of diet by
looking at digestive track length  ecomorphology
During rumination  large amount of CO2 and CH4 produced. CH4 has hydrogen (product
of photosynthesis )  Loss of methane = loss of 12% of E from ingested food . Also cause
global warming (3% of all global warming gases)
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LECTURE 7: AEROBIC AND ANAEROBIC E PRODUCTION
1) Nature of stored food
Hexoses (6C sugar)  primary sugar product of photosynthesis. Not stored as food
material
Energy reserve = polymerized forms of glucose  glycogen and starch
Are macromolecules  not subject to usual metabolism.
Long term planning  need good reserve  large macromolecule
Under extreme starvation  fats and protein used for E production
Respiration = reversal of carbon reduction during photosynthesis
Photosynthesis  glucose produced from water & CO2 & O2 evolved. Input of 686 Kcal
Respiration  glucose oxidized to CO2 &water & H2O produced. 686 Kcal released and
packaged into ATP or heat.
Reaction = opposite of photosynthesis
2) Mobilization of stored food and glycolysis.
Starch/glycogen glucose before, later used as substrate for respiration.
Happens 2 ways:
- Glycogen/startch  glucose 1P by phosphorylase.
- Glycogen/startch  glucose  glucose 1P with 1 ATP
Glycolysis
Glucose 1P  enters series of reaction constituting glycolysis , no need for oxygen
Production of 2NADH and 2ATP for each glucose consumed
If glycolglucose (1 step)  production of 3 ATP
End product (for 1 glucose consumed) = 2 pyruvates  energy rich molecule.
3) Fate of pyruvate when O2 available: TCA cycle (Krebs)
No O2 consumption during glycolysis but AFTER, fate of glycolysis depends on if there is O2
If O2 : pyruvate  goes to mitochondria , gets decarboxylated (looses CO2)  CoA 
enters Krebs cycle  there is progressive decarboxylation  released H used to reduce
NAD+ & FAD to NADH and FADH2
 Removal of 3CO2 = breakdown of 1 molecule of pyruvate
there is also production of GTP/ATP
4) Oxidation of NADH/FADH2 + synthesis of ATP
e from NADH/FADH2 oxidation  enter electron transport chain = 4 complexes of electron
carriers, are in mitochondrion. + in the end enter ATP synthase
O2 = terminal electron acceptor, will form water ( proof that aerobic organisms need O2)
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. During same time ATP made and released into matrix.
See BIOL 201
Differences between plant and animal transport chain :
Plant  2 additional NADH dehydrogenase( one on each membrane ) + alternate oxidase (e
skips complex 3) = big O2 consumption and little ATP made=alternate respiration (
generates heat )
 prevents e- flow from complex 2 to complex 3 and further downstream.
Signal to change from one pathway to another = salicylic acid
Various chemical : can interrupt electron flow at several diff steps.
DNP  makes inner membrane leaky  prevents built up of proton concentration and
motive force ( Driving force of ATP synthesis )
5) Fate of pyruvate in O2 deficient conditions ( Hypoxia or Anoxia
) and fermentation
Glycolysis = important because even if org produces little ATP, can’t survive without oxygen
To glycolysis to occur, constant NAD+ needed.
Need of a mechanism to consumed NADH produced in glycolysis ( to regenerate NAD+ )
In animal  Lactic acid fermentation pathway !!
Fermentation: pyruvate  lactic acid by lactate dehydrogenase.
Consumes NADH and produces NAD+
Explains why rate of glycolysis increase during exercise when O2 supplies lie behind
O2 consumption  glycolysis becomes predominant for ATP production
Lactic acid (lactate)  metabolized as exercise ceases  conversion to glycogen in muscle
or send to liver where conversion to glucose ( Cori cycle )
Plants = important diff in anaerobic pyruvate metabolism : lactic acid fermentation = only
transient mechanism  Production of ethanol !!
Gluconeogenesis : Other way to remove pyruvate so glycolysis can keep going) . Close to
reverse reaction of glycolysis  regenerates glucose.
Occurs during germination of oil seeds
6) Respiratory quotient and respiratory substrates ( other than
carbohydrates )
Respiratory quitient = RQ
RQ = Volume CO2 produced/Volume CO2 consumed
Value  Depends upon substrate nature
Ex: In glucose RQ=1
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Fats  More CO2 consumption than CO@ production  RQ=0.7
When starvation  protein used as respiratory substrate RQ=0.8
Temperature = effect on RQ ( because depending on T, organism are going to use different
type of substrate )
 At low T = fats = low RQ vs higher T=carbohydrates = high RQ
!!! Reminder stored food must be breaked from macromolecules to monomer and converted
to glucose and pyruvate before being used as respiratory substrate !!
7) How much E is produced during respiration?
= how much ATP produced during anaerobic and aerobic respiration
glycolysis : net prod of 2ATP
One round of Krebs cycle  3C pyruvate = oxidised to CO2 and we get those products
3CO2
4NADH
1FADH2
1ATP/GTP for animals
And one glucose  2 pyruvates  Twice those products
During e- transportation, proton motive force drives ATP synthesis. And since NADH
contributes to proton motive force, each NADH = 3 ATP and FADH2 = 2ATP
Therefore total ATP production , for 1 Glucose ( =2 pyru)
24ATP (from 8NADH)
4 ATP ( 2 FADH2 )
2ATP/GDP
 30 ATP molecules per Krebs cycle + 2 produced during Glycolisis
TOTAL = 32 ATP
Also if 2 NADH from glycolysis enter mithocondria, ( not necessary)  6 more ATP
produced
MAX = 38 ATP
If anaerobic respiration , only ATP = from glycolysis ( NADH used to do NAD+ in order to
keep glycolysis going)  2 ATP = organism barely survives
8) Efficiency of respiration
Glucose = 686Kcal
36 ATP= 270 Kcal
 Efficiency of respiration = 39 %
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Rest of E = heat
In plant, heat produced is NOT captures = released
9) Heat production during respiration
Part of E liberated = in form of heat.
Amount of E produced/gr food  Depends on food type (Fats, prot, Carbo … )
SEE table
Heat liberated = used to maintain body T
In migration animals ( birds)  easier to carry fats over carbohydrates over long flights
because less heavy
 1Kcal of E = 1gr Glycogen = 0.11 gr of fat
!! Glycogen can be mobilised very quickly and in anaerobic conditions (NOT fat) !!
10)
Role of E produced by respiration
Part of E produced --> maintenance +repair of cell/tissue
= continuous process : In early growth , large part of E was used for growth (new
cell/tissue) . After reaching optimal size  growth requirements decrease  maintrnance
becomes predominant
11)
Role of respiratory intermediate
Glycolysis + TCA cycle  many intermediate : diverted in cellular constituents.
Ex: Glucose 6P  synthesize Glucose for wall assembly
Glycerol from 3-PGA ( glycolysis)  synthesize triglycerides and phospholipids
Acteyl CoA  Fatty acids ( and = precursor of some pigments )
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LECTURE 8: METABOLIC RATE, SIZE AND ACTIVITY
1) Metabolism
Metabolism = total sum of synthesis process and breakdown process
 Anabolism (make complex from simple), will store E =growth
& Catabolism ( Break complex in simple ) = release of E
Some E ingested won’t be harvested  thrown out = fecal lost ( = undigested and
unabsorbed)
Other part = absorbed  metabolizable E
Different functions:
prod of new tissues : can be structures that will be lost ( nails, hair) or gametes
Digestion & synthesis have a cost (empty stomach = cold, one in digestion =Warm = cost )
E released during respiration = proportional to intensity of activity
 To measure rate of activity use : measure O2 consumption and CO2 prod.
All of those  produce heat ( transfo E )
Leftover E  will be used for growth. More E taken in than used
All E = reducible to heat.
Metabolic rate = rate of E released through respiration ( Cal , Joules or Watts)  is
measured as 02 consumption (limit is that doesn’t take into account anabolic systems) 
Need conversion from one to other
1 ml O2 = 4.8 Cal
1 L O2/hour = 5.58 Watt
Energy budget animal = impact on biosphere : CH4 in ruminants contribute to warming
2) Metabolic rate: Measurements
E = produced by breakdown of food reserve during respiration (with O2 consumption)
 Metabolic rate can be measured by finding out : heat content of food consumed OR rate
of O2 consumption
Several Methods:
- Direct calorimetry : Sensitive calorimeter used to measure anount heat produced by
animal/unit time : Insulated container of know mass of water where heat from
animal goes and raises the T
-
Indirect calorimetry : Measuring each component of Organism’s energy budget.
- Respirometry : Most commonly used method. Meadures O2 consuption or CO2 prod
 Based on know relationship between the 2. Complication = nature of respiratory
substrate ( only carbohydrate RQ is 1 , other don’t work , CF lecture 7)
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Place animal in respirometer (close chamber ) with inlet and outlet , diff in concentration =
amount of O2 or CO2 produced or consumed
-
Double labeled water method: only method that can be used in natural habitats :
good for field ecologists ; Animal is captured and injected with marked water (
isotopes) , blood sample is taken and animal released
Since water is lost throught secretion and evaporation  concentration of labeled
isotopes declined ( O2 faster than H ) Difference between those 2 = amount of CO2 lost
= Measure of metabolism
Basal metabolic rate (BMR)  Only endothermic animal = 02 consumption by animals.
Measured when animal resting AND NOT digesting, at intermediate T
Standard metabolic rate (SMR)  Only in cold-blooded animals (ectothermic). Measured
when resting and not digesting. Diff  no heat production (need less food) , animal must
have been at medium T for a long time
Field Metabolic rate (FMR)  Metabolic rate measured in field with doubly labeled water
technique  Hydrogen is measured (by radioactivity).
Determination of BMR and SMR
 Measured with 02
3) Body size and metabolic rate at whole organism level
Larger organisms : consume more O2  Increase in size = increase in volume
BUT gaseous exchanges : occur at surface in contact with enviro
Surface increase to the square and volume to the cube
 surface proportional to V^2/3
Lagging behind of surface area : great effect on metabolic rate of whole body.
Is noticeable in MSMR ( Mass specific metabolic rate )
If we plot them  straight curve with a 0.67 slope =isometric relation
If MSMR was a line with a 1.0 slope  isometric relation. If not = Allometric
MSMR declines with body-size : -0.25 slope = Allometric
MR = aM^b
Mr = metabolic rate
A= proportionality coeff
M= body mass
B= Power function
 At whole body level, by unit of body mass , big animal consume less O2
Metabolic rate endotherm = higher than ectotherm
Mutlicell = higher MSMR than unicell
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4) Body size and tissue metabolic rate
But what about organs ? ( Where is MSMR reduction occurring )
Group of 5 kg organs  ¾ of whole body mechanism
= Heat, kidney,brain, lungs + splanchnic organs
 Some organs = metabolically more active
Muscles = 40 % body mass
Metabolic rate at whole body level =90.6 Watts
Decrease level = located everywhere, in organs, metabolic rate decline with increase in
body mass. But is different in the different organs (brain = ½, liver =1/4 )
Same can be said with the tissues.
Cell size does not differ much  What is the basis of the MSMR reduction ?
Lower mithochondria /cell in larger animals ( and it is where there is O2 consumption )
Number of e transport chain (in mithochondrion ) depends on surface area, if mitho has
higher density of chain , will consume O2 with higher rate
5) Metabolic rate and activity
Increase in activity = increase in metabolic rate ( at org level & per unit of mass )
Running :
The smaller the animal, the higher the MSMR + MSMR increases linearly with speed ( this
increase is higher for smaller animal than for larger one )
Also, small organism will have a greater cost for locomotion. Follows a line
May be due to smaller animal having a lower efficiency of muscle contracting at higher
speed.
At one point , with speed increase MSMR won’t increase linearly with it  Oxygen supplies
will start lagging behind oxygen need.
Ectoterms have a lower locomotion cost than endotherms. Net cost will rise with speed up
to a limit  speed increase beyond that limit won’t increase MSMR  reached maximum
aerobic speed ( MAS)
When at speed over MAS, additional E comes from anaerobic mechanisms ( lactic
fermentation)
MAS  cold lizard<warm lizard< mammals
 Mammals are able to move rapidly and for a long time but need to pay additional E cost
for this capacity
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Some animals  several modes/gaits of locomotion , will pick the most economical for the
speed they want to go. Ex : horse. Total cost of locomotion /unit distance declines with
speed increase.
Swimming and flying, since occur through fluids,consequences more pronounced.
Net cost of swimming increases with speed. But is not linear and increases a lot more
rapidly than running
Maximum range speed = higher speed for minimum cost of locomotion.  animals use it to
cover long distances like for feeding or migration.
Flying : U shape curve : Low speed ( Hovering) and high speed are very E costly.
 Lack of forward momemtum results in higher cost of E to support body weight.
Lower E costing speed = Minimum power speed. !!! Is not equal to maximum range speed!!
If compare all 3  running most expensive swimming less
In each one: Net metabolic cost declines with body size. MSMR increases with speed (more
steeply in smaller than in larger vertebrates)
LECTURE 9: METABOLIC RATE AND T
1) Effect of T on rate of Biological reactions.
T = reflect of thermal motions of atoms and molecules
Indeed, some reactions need a certain E to happen.
T increase = E increase (because kinetics)
Since chemical E depends on kinetic E, increase T increase chem E (exponentially)
Q10 = concept that tells us how reaction react (number time it increases )with a 10 degree
raise
Measure number of time by which rate increase by every 10c
Q10=Metabolic rate at T+10/meta rate at T
 we have to measure rate at 2 diff rate  Increase of exactly 20degrees = limitation
Solution : longer equation (see booklet )  that way, we can calculate Q10 no matter what T
increase we get = logarithm equation
Described by this equation :
Y=b*a^x
Y=rate at higher T
b=rate at lower T
a=Q10
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x=diff between 2 T /10
Can be re-written in the logarithm form :
LogR2= LogR1 + LogQ10*(T2-T1)/10
With R the reaction rate.
Value of Q10 decreases with higher T
Normally, for most chemical, biochemical and metabolic rate, Q10 value =2-3
Some reactions, don’t depend on T: photophysical  q10 =1 . They are temperature
independent.
If physical effect were T dependant  we couldn’t see well when T goes down (pigments
need light = E )
Enzyme catalyzed reactions.
Metabolism= sum of all biochemical reactions in an organism. Increase in body T should be
expected to be accompanied by increase in metabolic rate (We can see it by increase in O2
consumption) BUT is not totally true, biochem reactions  catalyzed by enzymes. Each of
them  optimal T for maximum activity (T will change enzyme confo).
 how a T change affects rate of enzymatic reaction  depends on optimum T for that
enzyme
After reaching optimum T and going over it , enzyme will get denaturised and wont work
anymore : Functional tertiary structure becomes unstable. The greater the deviation, the
faster the degradation.
Important parameter for efficiency of enzyme = binding affinity (Km) to substrate.
Km = concentration of substrate at which half-max velocity of reaction is reached.
Lower Km = more efficient enzyme  At optimum T , Km is the lowest.
Some animal regulate body T  endotherms = human = regulators
Some organism no  ectotherms ( lizards ) =conformers
Small birds  metabolic very active , have eat all time  little time to rest. During might
will lessen T so metabolic goes low and don’t have to eat  goes blue
2) Effect of T on cell structure
T affects metabolism by bringing change in membrane viscocity. Viscocity depends on how
tightly packed are phospholipid . And packaging order  depends on how mamy double
bounds fatty acids tail have,
Double bound = unsaturated  Less packed =Fluid
Simple bound = saturated = tightly packed =Viscous
T  direct effect on viscosity/fluidity
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Increase T  Increase Fluidity = less rigid
Lower T  increase Viscosity = flexible.
Mechanism evolved to compensate mechanisms of acclimation/acclimatization
Specific enzyme will introduce the double bound in fatty acid
3) Effects of T on metabolic rate
Endotherms have thermo-neutral zones where even if outside increase, metabolic rate and
body T remain constant.
MSMR increase exponentially with T
4) Acclimation and Acclimatization
Acclimatization = induction of tolerance to otherwise lethal degree of stress by being
previously exposed to a non-lethal degree of stress.
Capacity to acclimate = genotype dependant
Acclimation : carried under laboratory experience
Acclimatization : occurs in nature
!! Not to be mixed with adaptation, adaptation = evolutionary process!!
After full acclimation rate of metabolic will reach same as if in normal conditions
Effect of acclimation on metabolic rate occurs at level of individual processes. Protein
synthesis = central metabolic process  machinery protein synthesis have to acclimate in
order for whole plant to acclimate.
The longer the acclimation period the better the survival.
Physiological mechanisms
How come after long enough acclimation, cells synthetize protein at same rate at 4 and at
20c
 If whole mechanisms is indeed going slower, just have more stuff taking part into it  lot
more ribosomes, mRNAs
+ other mechanism underlying processes of acclimation and acclimatization
New forms of enzymes produced that are more efficient
 fatty acid desaturates induced , will induce double bounds in fatty acids preventing
membrane from being too rigid.
Under high T  double bounds removed to make membranes less fluids to avoid them to
melt away at high T
Acclimation requires O2 availability
At least in animals, acclimation only occurs when there is no O2 availability
 Acclimation involve active + E-requiring steps.
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LECTURE 10: CELL WATER RELATIONS AND UPTAKE OF WATER
1) Properties of water
Largest constituent of living system: 70-95% organism fresh weight
 ideal fluid = stable
Great force of cohesion between molecules
Universal solvent bc great dipole property  when added to solute, will dissolve
electrostatically combined ions. Ex: will separate NaCl into Na+ & ClDipole property = due to partial charges on its components atoms.  Can insert themselves
between diff atoms.
high heat capacity may capture heat but T won’t rise.
high latent heat of vaporization
Transparent to visible radiation
All lands plants  take up water from soil BUT 99% water taken by land plant returns to
atmosphere through transpiration.
2) Forces driving water movement
During movement  work is done  Force is involved
Water will move according to chemical potential:
 From higher chemical potential to a lower one, will be spontaneous.
Work done =Fdx
With x the distance
And force = F
 F= (difference in water potential)/distance derive
 Movement of water between 2 systems is determined by difference in their chem
potentials.
Water potential = chemical potential/ partial molal volume of water
 driving Force for water movement
will move from higher W to lower W  follows negative water gradient < or = 0
Water potential = composite force  resultant of several component force :
- Gravitational potential=Wg= Due to weight. Major part in ascent of Xylem in tall
trees
- Matric potential = Wsigma= Colloidal substance can absorb large number water
molecule. Decreases tendency to move < or = 0. Major part of water movement
within soil.
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-
Pressure potential =Wp= hydrostatic/turgor pressure. Will be > or = 0. Increases
tendency of water to move.
Osmotic potential ( Solute potential) = Wpi= due to presence of solutes. Reduces
tendency of water to move ( water molecule form shells around solutes) < or = 0.
Only happens when we have semi-permeable membrane
We don’t consider gravitational and matric potentials at cellular level
W=Wp+Wpi
Highest value of W = pure water = 0
3) Pressure-driven bulk flow of water over distance
Another process by which water move= Bulk flow = mass concerted movement of
molecules in response to pressure gradient. Ex: Flow of river, falling rain, water movement
through a hose.
Rate of volume flows depends on the tube radius, liquid viscosity and pressure gradiant
that drives the flow
Volume flow rate = IN THE BOOK
 Doubling radius of tube  Increase volume flow rate by a ratio of 16 (2^4)
Such pressure-driven bulk flow of water is the predominant mechanism for water
movement for xylem from roots to leaves.
4)
Diffusion and Osmosis and Molecular mechanisms involved in
water movement.
Molecule  Have inherent thermal E  Leads to diffusion (random mov)
Molecule tends to spread in all directions. Will spread in all directions from regions of high
concentration to regions of low concentration.
If during this movement encounter semi-permeable membranes = asymmetric distribution
of solute on both side  rise to osmotic potential
Movement of water facilitated by pressure will overcome molecular kinetic motion
Unidirectional flow from high pressure to low pressure  Allows for pressure-driven bulkflow over long distances.
Diffusion : un-facilitated movement of a substance due to inherent kinetic/thermal E. Is
completely random. As long as no other force: down concentration gradient.
Cannot account for transport through large distance
Osmosis : Diffusion substance through selective membrane. Water passes but not solute.
Water moves from higher to lower C. Driving force = difference in water pot.
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Water potential = measure of un-satiated thirst.
For short distance, we ignore role played by gravity and matric potential.
Within soil  matric potential plays determining role.
5) Pathway of water movement and operational forces.
Movement of water within soil over short distances.
In soil, water moves as bulk flow (solutes move with it, no membrane Wpi=0)
Also = open system  no pressure potential Wp= 0
 W=Wsigma =Matric potential.
Soil solution moves through root intercellular space up to endodermis  solution reaches
outside endodermis without encountering any membrane.
Endodermal cells have casparian strips  they force water to enter endodermal cells
Then  since we have membrane, osmotic potential (Wpi) comes into play.
Movement of water from outside endodermis to Xylem vessels
Movement of water  determined by difference in water potential between origin and
destination. (Destination < Origin)
Water and dissolved mineral content  move through free space between cells at
epidermis and cortex.
Water potential in soil = Sum (osmotic and matric) potential.
Water potential in Xylem Vessel = Sum (osmotic and pressure) potential
Once water enters xylem vessels  goes upward and escapes to transpiration
6) Determination of Water potential, Osmotic potential, Pressure
potential.
Do determine Water potential  Water flux equilibrium methods (tissue slices)
-
Cut tissue and determine weight
Place them in different solution concentration
Determine final weight
Plot the initial/final weight ratio against manitol concentration
Find solution C where there is no change in weight = 1 ratio
Since no Wp (open system)  W = Wpi
More accurate way = use of a psychrometer to determine water/osmotic potential.
Chamber with junction between 2 diff metal wires. Change in T at the junction generates
current in wires, that can be read.
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Water of know potential with drop + vapour. If have the same water potential not net
movement of water vapour.
Determination of Osmotic potential by depression of freezing point method.
Tissue is crushed and thermometer inserted. Latter is allowed to freeze. We note T when
freezing occurs.  By applying equation, we can calculate osmotic potential
 1 molal solution decreases freezing point by 1.86 C  By knowing the water freezing
point we can determine the concentration of solution
Determination of Pressure potential
 Is the most difficult to measure
2 methods :
- Manometric method (micropipette ) : Pressure pot = measure of cell turgidity
 Micropipette with known volume touches water surface  capillary rise Inserted in
cell cacuole .
Vacuole sap will go in micro pipette as aur rushes in pressure gauge . As sap comes in , air
inside is squeezed into smaller space  Note final volume and since P1V1=P2V2
 Can get final pressure = Wp
- Scholander’s Pressure bomb technique:
Twig inserted upside down in sealed metal chamber. Compressed N gaz allowed slowly in
the chamber. When droplets appear, gaz pressure chamber = pressure potential in twig.
W=Wp +Wpi.
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LECTURE 11: UPTAKE AND ASSIMILATION OF NUTRIENTS IN
PLANTS.
1) Why do organisms need minerals
Nucleic acid/proteins  have structure made with salt-bounded mineral elements.
This relationship  old as life origin.
Without presence of appropriate ions in good concentrations, many biological molecules 
dysfunctional
2) Essential elements
19 essential elements
Non mineral elements (H, C, O)
Mineral nutrients (16)  Can be categorised in macro and micro nutrients
- Macro nutrients (N,K,Ca,Mg,P…. )
- Micro nutrients
How to find out if some mineral = essential  Have 3 criteria.
Criteria =
- Essential for life cycle
- Deficiency symptom when not present
- Cannot be replaced by chemical essential elements
Difficult to determine nature for some elements because some concentration needed where
very low (Ex: Boron).
3) Macro- and Micro- nutrients
Elements  are not required in same amounts. Based on requires amount, can be macro
(large amount needed) or micro (small amount needed)
Non-mineral  Are required in quantities at least 30 x more Macro-nutrients  Required
in amounts 10 x more than micro-nutrients
4) Functions of different mineral elements
Essential elements can be grouped according to type of function they have in plant.
Some of them  Are structural part of C compounds
Other  Maintain structural Integrity
Rest  Is in ionic form  will form transient association with enzymes and other macro
molecules to maintain structural integrity.
Functional grouping of mineral elements
- nutrients part of carbon compounds  N and S
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-
Nutrients for E storage = structural integrity  P, Si, B
Remains in ionic form protein binfing + osmoregulation  K,Ca,Mg,Cl,Mn,Na
Involved in redox reactions  Fe, Zn,Cu, Ni, Mo
Minerals ions  mobile: Cl, K, Mg. Move through plant thanks to signalling mechanism
Immobile  B,Ca,Cu,Fe,S  even if deficiency somewhere won’t move
5) Availability and adequacy of mineral nutrients
Many of essential nutrients  are not available as elements: exist in soil as dissociated
salts:
Cations: attached to soil particles (they have an abundance of negative charge)
Anions: Are in solutions
 Both of their availability very influenced by pH of soil
For each nutrient  Range of optimal concentration
Below: Nutrient is deficient
Above: Concentration of nutrient = toxic.
For macronutrients, range is broad BUT is narrow for micronutrients.
When soil = deficient, plantsdeficiency symptoms. Distribution of those symptoms:
determined by fact of if mobile or immobile inside the plant.
If mobile : transported from older to younger organs. Symptoms won’t appear in younger
until older don’t have any.
6) Artificial nutrient solutions
To facilitate experimentation: artificial nutrient media for growing plants. Most widely used
= Hoagland solution
 Only for growing whole or intact plants (that can do photosynthesis)
If want to cultivate tissues or else, need to add vitamins and sugars
7) Assimilation of highly oxidized mineral nutrients
In death  all biological elements = oxidised
 Life = reduction and Death=oxidation
 Mineral elements taken up highly oxidised like NO3- , SO4 2-, H2PO4-  must be
reduced in order to be assimilated.
SO4 2-  undergoes 3 distinct process :
- Activation
- Reduction
- Assimilation or Incorporation
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Activation  use of 2 molecule of ATP, produces APS and then PAPS. Positive change in free
E , can’t happen spontaneous, happens thanks to breakdown of PP in 2 P
Reduction  APS and PAPS reduced to sulphite and then sulphide.
Assimilation  sulphide is incorporated in aa serine or homoserime  produce 2 sulfurcontaining aa : Cysteine and methionine.
Phosphate assimilation  P is added to ADP  ATP either during glycolysis in citric acid
cycle or by utilizing energy H+ motive in chloro and mithochondria
Conversion alpha-keto to succinate  accompanied by ATP synthesis in plants and GDP in
animals.
Nitrate assimilation  Nitrate taken up by the root, transported to shoot by transpiration
stream. Enters cytoplasm of root and shoot cell by nitrate/H+ symport. In cytoplasm, it is
reduced to nitrite by nitrate reductase as shown below:
Nitrite = toxic. Will be transported to cytoplasm, ferridoxin (e- carrier) used as e- donor to
reduce nitrite to ammonium  incorporated into glutamate to synthetize glutamine.
Nitrate reductase  Inducible enzyme (= activated only when nitrate available) . Activity
will appear first in the root.
Function in the form of a dimer, but each catalyzing nitrate reduction . Has a NADH + FAD
binding site near carboxy terminal.
e- flow from NADH to NAD (on C terminus) on the N-terminus. Nitrate  Nitrite
Nitrite reductase  Iron-sulfur complex bound to reducrase, takes e- from reduced
derridoxin, passes them to heme, later  nitrite  converts it to ammonium
8) Plants with special strategies to acquire mineral supplements.
Some plants  association with mycorrhizal fungi  It supplies mineral nutrients tp plant
and pant  provides carbohydrates to fungi.
This relationship establishment  requires complex signalling between them.
Plant root  requires strigolactones to stimulate growth of fungal hyplae towards root.
SEE STEPS in book.
Insectivorous and parasitic plants :
Insectivorous plants : catch insect to get protein supplement. Prot  broken down into aa.
 Plant obtain already reduced and assimilated nitrogen.
Parasitic plant, obtain all nutrients from host.
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LECTURE 12: BIOLOGICAL NITROGEN FIXATION AND
ASSIMILATION.
1) Importance of N in plant nutrition
Most important cell constituents: proteins and nucleic acid = nitrogenous derivative of
carbon backbone.
DNA/RNA = nitrogenous cell constituents
Almost all enzymes= proteins
 N essential to build, maintain and degrade living systems.
Atmosphere = 80 % N2 BUT animals/plants  don’t harvest it
Most common deficiency = N2
Bound E = 226Kcal  very hard to break
2) Abiotic fixation of atmospheric N2
In nature: Some phenomena result in fixation of atmospheric nitrogen:
Lightning breaks water & atmospheric N2  nitric acid (HNO3 )
Will wash down to earth as nitrate.
Nitrate in the soil  available to plant. Will reduce and assimilate it through activities of
nitrate reductase (cf lecture 15)
Can also be done chemically, is used in industry as the Haber process :
Under high P, and with metal catalyst and high T : Add H2
The 2 gases react conversion to ammonia
N2+3H22NH3
3)
Biological fixation of atmospheric nitrogen.
Free living and symbiotic nitrogen fixing prokaryotes :
There are bacteria which fix nitrogen ( exclusive capacity) = cyanobacteria + aerobic one
:all free-living organisms
Some bacteria  live in symbiotic association  will fix N2 and receive carbon in return.
Ex: rhizobium/azorhizobium ( in legumes) .
Association can only be formed with the 1 specie  highly specific.
Nitrogen fixation  extremely sensible to O2
Nitrogen fixing enzyme (nitrogenase) only active when very low or 0 O2
N2 fixing organism  have evolved diff strategies to maintain anaerobic microclimate
around nitrogenase :
- Intense respiration (very O2 consuming = minimised O2 inhibition of nitrogenase)
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-
In photosynthetic bacteria, photosynthesis occurs in day ( = production O2) and
nitrogen fixation during night (= when O2 is not being production by system 2)
= Temporal partioning.
- In cyanobacteria  Special cells to fix N2 (called heterocysts-10 x bigger than other
cells) and other are doing photosynthesis
= Spatial partioning.
- In Leguminous plants that fix N2  roots nodule have a O2 binding protein =
Leghemoglobin  binds O2 20 x more tightly than our hemoglobin  no free O2 in
cells.
Rice  has a symbiotic system with a N2-fixing cyanobacteria: Anabaena
Symbiotic N2 fixation in higher plants :
All higher plant fixing N2 thanks to symbiosis = Legumes. Have formed symbiose with
Rizobium. One specific form of rhizobium associates with a particular specie  highly
selective.
Development of the root nodule :
1) Growing roots secrete flavonoids  attracts rhizobia
2) Exchange of sequential signals
3) Rhizobia attach themselves to young emerging root hairs + chem from the root
activate bacterial prot
4) Root curls to form small compartiment enclosing rhizobia
5) Activation of other nodulation genes by bacterial prot
6) Infection thread ( produced by bacteria) going from root hair to cortical cells of root
 mass of cells will form new nodule ( once concentration is sufficient)
7) Mature nodule = spherical and filled with rhizobia
Not in cell, is surrounded by plasma membrane (= invagination )
Synthesis of Leghemoglobin
Plant  synthesixes Globin protein
Bacterium  synthethize Heme ( contains Fe)
Symbiotic action of the two  Leghemoglobin
Nitrogenase action.
 Composed of 2 types of complex : Fe ( = iron protein complex) and MoFe
(=molybdenium-iron protein complex)/
Ferredoxin is reduced to iron prot complex  Releases e-  Latter is reduced , will bind
and we will have hydrolysis of ATP (change of confo in the process)
Since changed confo  can reduce MoFe  Latter will reduce N2 to NH3
In the last step  e- and H+ = lost to H2  will reduce efficiency by up to 60 %
Some plant  hydrogenase to be more efficient ( splits H2 and retakes e- and H+)
Overall reaction :
N2 +8e+8H+16ATP  2NH3+H2+16ADP+16Pi
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Nitrogenase  other enzymatic activities :
- Azide reduction
- Acetylene reduction
- H2 prod
Export of N2 from the nodule.
Once N2 is fixed as NH3 in nodule  needs to be exported to the rest of the plant BUT NH3
= toxic  has to be converted to other compounds that will be exported through xylem in
solution form.
Amide exporters
Temperate regions legume (pea,clover etc)  export fixed nitrogen as amides. Principle
amide exporters = asparagines and glutamine (serve as nitrogen stores)
1st : NH3 +glutamate (aa)  glutamine ( by glutamine synthase)
2nd ; amino group from glutamine + aspartarte (another aa)  asparagines (by
transaminase enzyme)
2glumatate + 2ATP + 2NH4 2glutamine( 1exported)
1Glutamine +1 ketoglutarate +NADH + H+  2 Glutamate
Glutamine+ Aspartic acid  Glutamic acid + asparagines
Other legumes  don’t synthetize amides BUT Ureide.
Ureide = exported by legumes of tropical orgin (ex:soybean, peanut)
3 major ureides = allantoic acid, allantoin and citrulline.
 Long serie of reaction before N2 is incorporated.
Allantoin  synthetised in peroxisome from uric acid.
Allantoic acid  from allantoin in endoplasmic reticulum (ER)
Citrulline from aa ornithine, site is unknown.
All of them  are released in xylem by respiration stream. Once at destination, are
metabolized to release NH4+ or NH3 ( will then be incorporated in amide as seen
previously)
4) Agricultural importance of biological N2 fixation.
180 million metric tons of N2 biologically fixed each year.
Usually, leguminous and non-leguminous crop alternate. When leguminous crop = planted
in field after leguminous crop, yield = higher
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5) Terrestrial nitrogen cycle
3 N pools
1. Atmosphere
2. Soil : After nitrification
3. Biomass ( when we die  ammonification of our bodies  ammonium release and
goes back into soil. )
Some bacteria  convert nitrate to N2
and some ammonia  nitrate =nitrification
and some nitrate to N2 =denitrifying bacterias
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LECTURE 13 : TRANSPIRATION AND DISTRIBUTION OF MATERIALS
IN PLANTS.
1)
Xylem = water-conducting tissue.
We know that water movement  through xylem tissue (will also carry sucrose,
transposable form of photosynthesis). Showed by Bark experiment:
 Removed ring (=phloem) and plant showed no sign of water deficiency + sucrose pack at
the top.
 When opposite experiment made, plant interrupted water supply to upper plant of the
plant.
 upward water movement in plants occurs through xylem vessels.
2) Structural elements of xylem  involved in upward water
movement
Each xylem vessel  made of xylem elements, each derived from a cell and put end-toend.
Xylem vessel = continuous tube formed from xylem elements.
Xylem elements  dead and hollow, have perforation plates at the end and at the sides.
In angiosperms, vessel from tube from root to shoot.
Another cell type taking place in upward water movement  tracheids = elongated,
spindle-shaped cells (also hollow and dead)  do not form long tubes but overlap with
each other along part of their length.
Gymnosperms  Only have tracheids
Angiosperms  tracheids and vessels.
Because vessel and tracheids have perforations (called bordered pits)  water can move
from one vessel to the other OR from one tracheid to another.
In vessel, secondary cell wall = laid down over primary cell wall in various patterns. (there
is also bordered pits on side walls)
Water can flow across these pits if they are aligned.
One advantage of having large number of adjacent vessel/tracheids  provide many
branched paths for water movements = Particularly helpful if there is discontinuity to water
flow within a vessel because of cavitation.
3)
Diurnal fluctuations in transpiration.
Transpiration shows diurnal fluctuations  stomata open during day and close during
night (except in CAM plants, where opposite = true).
Once water is withheld after watering, soil water potential starts declining with time
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When water potential of root & leaf  shoes diurnal fluctuations along with overall decline
with time.
4) Forces driving upward water movement.
We have seen various contributing forces: root pressure and capillary rise. We can consider
pulsation in the endodermal forces.
Root pressure.
Many manifestation  well-watered seedlings of grasses show drop of water at their tips
during mornings = guttation  result of water absorption by root during night (when little
transpiration occurs)
During night  root water potential = lower than the one of soil during night, waters enter
the roots.
Because no transpiration at night  positive hydrostatic pressure  push sap out  will
rise in manometeric tube
This pressure  can push water up to a maximum of about a meter  cannot account for
water rise in tall trees.
Capillary rise of water.
Liquids  rise in capillary tubes as function of their surface tension and density and as
function of the radius of capillary tubes.
As max capillary rise occurs and becomes stationary  forces pulling liquid up = forces
pulling it down.
Since these forces are equals  we can calculate height to which given liquid will rise.
For water: height at which it will rise = 1,49*10^-15/(radius of capillary in meters)
 Cannot account for rise of water in tall trees.
SEE book for equations.
Cohesion-Tension theory.
Water molecule bind to each other with large cohesive forces  can support very long
vertical columns. When column top = lifted up by suction, whole column rises.
 When transpiration occurs at top of plant, creates suction force that lifts whole column
of water in each xylem vessel up. (Won’t break because of the cohesion forces)
Continuity of water columns in xylem  established early during seeding development.
Water columns might break during strong winds when plant violently shaken(= appearance
of air bubbles). In tall trees = irreparable.
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Plants  have evolved excellent adaptation against occasional breaking of water column 
continuously form new xylem through secondary growth (while old one = non-functional) =
darker area in trees.
5)
Gradient of decreasing water potential from bottom to top of a
tree.
Water  goes from high potential to a low one.
As we go from soil to root to xylem to top  successive decrease in water potential.
BUT lower water potential = in the air outside.
When extreme suction, water potential can become less than 0.
Due to high P created by intense transpiration, diameter of tree decreases just after noon
and recovers in the evening.
Once water finally reaches leaf xylem, it goes from cell to cell by osmosis  finally gets
released into substomatal cavity (Large space inside stoma)
Movement of water from substomatal cavity through stoma out to the atmosphere  takes
place in vapour or gaseous form.
6)
Water movement from substomatal cavity to the atmosphere.
This movement = by diffusion, is driven by diff in water vapour concentration between
substomatal cavity and the air surrounding the leaf.
Transpiration stroma  commonly expressed as flux density ( J) or less common as total
flux rate of water loss (Q) in terms of total water loss per unit time
 See book for equations
The longer the path, the greater the resistance ( R is measured in time)
In transpi throught stomata, resistance R  2 components :
- Stomatal Resistance (Rs)
- Air resistance (Ra)
Water movement from substomatal cavity to atmosphere via stomatal opening.
Stomata resistance (Rs)
Resistance to water mov = directly proportional to length (l) of stomatal pore and inversely
proportional to cross sectional area of pore
+ resistance due to presence of water vapour in stomatal pore =1/2r
Rs= l/pi*r^2 + 1/2r
Pi*r^2 = cross sectional resistance
Resistance due to unstirred air boundary layer (Ra)
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 due to unstirred air presence , water vapour escaping 1 stoma mixes with vapour coming
out of another one  forms layer of water-saturated air
How thick  depends on length of leaf in wind and velocity of wind.
 Shorter leaf dimension in direction of wind = smaller thickness of unstirred boundary
layer and lower Ra
Smaller Ra = higher rate of transpiration
Ra = lower in plants with shorter leaf width  Transpi rate increases with decrease in leaf
width.
Size of opening of stomatal pore  also determines the rate of transpiration.
Increase in the size of the opening will have effect on rate of water loss or on moving air 
gets bigger.
When air = still, transpiration increase with increase in opening up to 5microm but not
after  Rate of water loss = limited by thickness of unstirred boundary layer.
 When air moving = linear increase in rate of water loss with increase in the opening of
the pore.  Water loss = limited by size of pore opening.
7) Significance of transpiration
1. High water content  confers turgidity that is essential for optimal cell function and
provides physical driving force for cell expansion and thereby  growth
2. Transpirational cooling of leaves in hot environments
3. Serves as a vehicle for nutrient transport
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LECTURE 14 : DISTRIBUTION AND PHOTOSYNTHETIC PRODUCTS IN PLANTS.
1)
Identification of the phloem as the transport tissue
Bark cut experiment  Removed ring bark  after time, bark above girdle swelled up,
sugar accumulation. All parts below died.  evidence that photosynthetic products are
transported through phloem (= inner part of the bark)
Phloem = in vascular bundles. Phloem = towards outside (epidermis) and Xyleme= toward
inside (center of the stem)
During secondary growth  circular arrangement of vascular bundles = changed (most
central part of stem has to be occupied by xylem- need to increase diameter faster than
height.
More recent experiment with C14 datation confirmed that phloem was the transport
pathway for organic materials.
Cells made in dry season = smaller than those in wet season
2)
Structural features of the phloem
 Complex tissue containing several cells types. 2 major cell types =
Sieve elements: Elongated cell , with end wall
perforated with pores.
Open for transports, will form tube ,by arranging themselves end to end. Tube will run
through entire plant length. Look a little bit like Xylem but is not empty, needs system to
transport water. Need little ATP
 Filled with sieve plates, on side: Lateral sieve area
-Companion cells: Also elongated cells. Allow sucrose to pass to sieve elements Narrow
long cells next to sieve elements, will have cytoplasmic connections with them through
branched plasmodesmata.. Have a nucleus and a lot of mitochondria, do a lot of ATP. Lot of
plasmodesmata (=gap junction ) = opening between 2 cells. Some have a convoluted plasma
membrane  increase membrane surface area  increase transport.
Sieve element + Companion cells  functional complex
3)
Source and sinks organs
Keaf = source organs for photosynthate
If we do photosynthesis with radioactive carbon , C incorporated into sugar, only cells
where sugar went will show radioactivity
Phloem sap: Took insect, stucked it in phloem ???
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Found out major part = sugar and sucrose
Rate
Velocity = 0.5-2.5/min
Flux density=15g/h/cm^2
Excess in far the rates that could be obtained by diffusion  Is driven by pressure potential
Which source supplies which sink ?
Found out that bigger leaves supply only small leaves on the same side
Sucrose loading
Companion cells then apoplast of sieve elements
Protons pumped into apoplast
H+ and sucrose  cotransported by sucrose-proton symporter into cytoplasm of sieve
elements
But what force drives it  Pressure flow hypothesis
Created experiment with 2 flasks , both completely filled ( no air)
One flask = sink = Xylem
Other = source with sucrose = Phloem
Water potential lower in sucrose solution, water will enter through osmosis, so solution is
pushed out goes into sink.
As sucrose comes in, water will leave the bag by osmosis but sucrose won’t.
It all starts again
Requirements :
Sieve plate pores unobstructed
È???
Photosynthates  Unidirectional movement
Chillimg = T where ATP production almost completely stops
LECTURE 15: Water an ion balance in animals.
Water gain = Drinking/ Uptake through body surface (water or air) /Water in
food/Oxidation or metabolic water (when starch/glycogen are being degraded)
Water loss = Evaporation from body surface ….
Metabolic water : For each gr produced , gr of waters  Starch=0.56 , Fat=1.07, protein
=0.39 (urea in urine = Ureptelic) ….
House mite  Loss a lot of their weight when no water ( absorb thorug humidity)
Namib Desert Beetles : Will absorb water from fog/most air and does head stand  Water
will go down his body to his mouth
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Importance of maintaining favourable water and ion balance
Optimal cell function 
Optimal hydration degree
Optimal solutes C
 Water balance and solute/ion balance = intimately related
Loss of water  increases concentration of various ions,
Absorption of solutes/ions = water influx
Animals  osmoconformers or osmoregulator ( Don’t care about outside ions
concentration = regulator)
Animals  Looses lot of water through evaporation
Loss of water through body surface decreases with body size increase
Remember : V increase ^3 & Surface ^2
Many insects  exoskeletons ( outside body )
Cuticular melting point : When cuticule melts, water loss is crazayyy
Mammals  Can’t tolerate water loss very much
…
In burrowing animals (ex: desert)  t cooler in burrow then outside  slower water loss +
secrete very concentrated urine + Drier feces
In high animals, body -|> compartiments
Marine and Fresh water animals 
Intra-cellular
Extra cell or interstial
External bathing
Excretion of Nitrogen waste products : Ammonia, Uric acid and Urea  toxic
Animals have diff strategy to get rid of them.
Ammonioteles (Simple invertebrates, aquatic mollusc Ammonium
Uricoteles (Terrestrial mollusc, terrestrial arthropods, Reptiles, Birds)  Uric acid
Ureoteles (Mammals, some larval body fish)  Urea
Evolution of kidney  Flat worms : Have a canal where there are Flame cells  fluid form
outside body will enter through there and be filtered  after can associate with solute.
Annelids or segmented worm  Have segments that will be repeated multiple times In each
have a pair of metanephridium = Fluif enters Metanephridium through nephrostome.
Excretion = from nephridiopore
For primitive invertebrate  enters through mephrostome , long tube with very little water
loss
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Insects  different  Malpighian tubules. Just before rectum = branching in tubules. In
tubules  cells that filter body fluid. Will allow passage of only the necessary water to go
further, rest is absorbed back.
Kidney : Single filtration unit = nephrons
Glomerulus filtrates blood, takes back water and mineral
In the loop of Henle= contercurrent system
Glomerulus :
Artery bringing blood to glomerus cn contracte , will increase pressure ( by difference with
the other artery radius
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LECTURE 16 : Exchange mechanism in Animals
Breathing media  contain O2
Air as breathing medium : 21% air= O2 1L=209ml O2 = 280 mg O2
Water as breathing medium: 1L water = 7ml/10mg O2
 Much more water needed to extract needed O2
Water = 800 times more dense than air = 55 times more viscous.
Diffusion coeff of O2  Much more higher in air than in water. Molecules in air can travel
much more distance before colliding with each other
Tracheal Gas exchange system in insect
 In all insects: Have hole in body: Spiracles
Inside spiracles, atmospheric air goes everywhere in body.
2 others structures used for breathing :
Gills  Formed by evagination. Can be divided into lobes.
In tuft gills , O2 doesn’t go into lobes, lobes just
increase respiratory surface
Filament gills, water goes into every single lobe
Lamellar gills : Water and blood go in , made of
plate one behind each other. Each plate has its own circulation
Ex: Fish gills : water flows uni-directionally over exchange surface .
Each arch = isolated  Have their own filament stacking.
Made up of thin walls filled with blood capillaries . Blood will pass from one vein to the
other through arch through capillaries
 Counter-current flow of water and blood
Lungs
Many designs in nature. Lot of “experiment”
Amphibia  Have proper lungs  Formed by invagination.
Inner lining made into lobes made into lobes  increases surface area
Mammalina lungs = super efficient.
Each lungs  collection of air sac ( alveoles) stacked together
Birds = master of breathing.
Have 2 cycle of breathing (1,21,2…)
Have lungs AND air sacs
Also bones  Have air cavities  get air in bone marrow + reduce total skeleton weight
2 breathing cycle = Most efficient system
Us  Goes both way
In birds , respiration = unidirection system,
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There is one air sac before lung (anterior sacs) and another one behind (posterior sac)
1st breath  O2 inhaled directly into posterior sac
exhalation  Goes into lungs through other path
2nd breath Goes into anterior sac
1cm^3 lung = 600cm^2 surface area ( =1mL !!)
Atmospheric air  Fills interior
Diffusion distance (DeltaX) in air –breathing animals
Diffusion = very efficient on short distance = more efficient on mammals
If we reduce membrane thickness, deltaX = steeper  Increase diffusion rate
Other way = to increase diff between 2 concentration gradiant
!! pay attention to unit !!
Respiration in an egg
Average egg  10000 pores  gaz exchange + water loss
During 21 days incubation :
O2 taken in = 6L=8,6gr
CO2=4,5L=8.8 gr loss
Water vapour =11L = 8.8gr loss
If we take it to 4000 m  Less O2 availible BUT diffusion quicker because fewer molecules
to collide with (Diffusion ceff = *2)
 Total number pore decreases = Less water loss
Concurrent Flow VS Countercurrent flow of wate & blood
Concurrent : Saturation happens very quickly
,equilibrium is reached , no more reactions
Countercurrent : Whatever quantity we choose,
always higher O2 concentration in water than in blood. Can never reach equilibrium.
Ventilation and Perfusion flow :
Ventilation rate : Rate of flow of O2 rich medium over respiratory surface
Perfusion rate: Rate of blood flow over respiratory surface
Both occur through diffusion
How the fish breath ?
Mouth takes water, goes trough mouth , gets out at the gills.
At the gills : arch allow water in , thanks o increase V
Decrease Volume --. Closes mouth, open operculum , water leaves through there , O2 was
taken by gills .
CO2 more soluble in water than air  More removal by fishes
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Water being denser than air  provide structural structure to gill maintenance,
Aquatic life style  no need of strong skeleton
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FOR EXAM
Photosynthesis!!! + red drop  always here
Calvin cycle  do not need to memorize it , just RUBISCO RuBP now them
C3 C4 CAM  need to know different
Lecture 2p.30
+active (use ATP)/ passive transport
Allometric
Plasmodesmata
MEcanism of Osmosis
Lecture 3 p.5
Diagram on p14
How would you calculate light E in KJ
For Animals : MSMR !! Always here
Nitrogen fixation
Incorporation into amino acid of Serine and Homoserine !!! (Assimilation )
If not isometric  Allometric
Location or carbo/decarboxylatin
Why kerb only operate under aerobic conditions. O2 needed to be e acceptor. Without it ->
NADH and FADH2 would accumulate
Lecture 8p6  MSMR
AT THE TEST : Question on freezing water RU
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