C1.

3 photosynthesis
 In photosynthesis organisms are all able to make all carbon compounds they
need (carbos, proteins, lipids and nucleic acids) using only light energy, CO2 and
H20
o Energy conversion: light energy à chemical energy in carbon
compounds
 CO2 + H20 à glucose + oxygen
 Hydrogen is needed to reduce CO2 into glucose
o This hydrogen comes from the photolysis (splitting of water) à
photolysis can only happen if there is a source of light
o Hydrogen released from water as protons (+) and electrons
o 2H2O à 4 electrons + 4H(+) + O2
 Oxygen is a waste product in reaction, it stays in the
chloroplasts but when there is a very high concentration through
diffusion it goes to the leaf cells and to the outside à it is the
oxygen we breathe.
C1.3.4 Separation of pigments by chromatography
 Chloroplasts contain several types of chlorophyll (plant pigment) + other
accessory pigments
o Accessory pigments: absorb different ranges of wavelength of light à
look like different colors to us
 Pigments can be separated by chromatography
o Porous material (paper cellulose) with a spot containing pigments
extracted from leaf places in a solvent in order to run up the paper and
separate the pigments
o The different pigments are different molecules and depending on their
size they will move further up or down and later we are able to identify
the types of pigments, since every pigment has its own retardation factor
o Bigger pigments will go less up because it takes longer for them to
move through the pores of the paper (as well because of the attraction to
the stationary or mobile phase)
 A retardation factor (Rf) can then be calculated.
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C1.3.5 Absorption of specific wavelengths of light by photosynthetic pigments

How do we see colors? When an object receives light, it absorbs some wavelengths and
reflects others. The ones it reflects are the ones we see as color. A green object absorbs all
wavelengths except those of the green spectrum. A white object reflects almost all, and a black
absorbs almost all.
 The first step of photosynthesis à absorption of sunlight which involves
chemical substances à pigments
 Pigment: material which selectively absorbs certain wavelengths of light and
then reflects other wavelengths
 A photon is a particle of light with discrete quantities of energy
o Energy of a photon is related to its wavelength à long wavelength,
less energy a photon holds
o Photons are absorbed by pigment molecules, the energy photons hold
cause an electron in atom of pigment molecules to jump to a higher
energy level and when it going does it emits the light
 o A specific amount of energy is required for this to happen which is only
supplied by certain wavelengths of light
 Photosynthesis involves a range of pigments but mainly chlorophylls
o All forms of chlorophylls appear green to us because red and blue
wavelengths can excite electron in chlorophyll, but wavelengths in green
part of spectrum cannot

 Therefore most green light is reflected

The wavelengths of light absorbed by a pigment are shown on a graph called an absorption
spectrum.
X-axis shows wavelength of light in nanometers, the scale extend from 400-700 nm, the range
of wavelengths of visible light.
Y-axis shows absorption, often as percentage.
In this graph the 525 nm wavelength is absorbed which is the green color and the color emitted
is the contrary in the color wheel (red/purple) that is why this fruit is purple.

C1.3.6 Similarities and differences of absorption and action spectra

An absorption spectrum is a graph showing the percentage of light absorbed at each
wavelength by a pigment/s.
 Y-axis is used for absorption of light à in percentage or arbitrary units
 More than 1 pigment can be shown on the same graph
An action spectrum is a graph showing the rate of photosynthesis at each wavelength of
light.
 Y-axis should be used for a measure of the relative amount of photosynthesis
(%)
o This can be obtained experimentally à using O2 production or CO2
consumption as a measure of the rate of photosynthesis

o As many wavelengths as possible

should be tested so data points can be linked to a curve

C1.3.7 Experimental techniques to investigate effects of limiting factors on the rate of

photosynthesis
  A limiting factor which, when in short supply, reduces the maximum rate of
photosynthesis
 CO2 + H2O à glucose + O2
 Limiting factors: CO2, light intensity and temperature
Carbon Dioxide:
 Atmospheric CO2 = 0.04%
 Below 0.01% percentage of CO2, rubisco is not able to fix CO2
 0.01% - 0.04% there is a low rate of successful collisions between CO2
molecules and the active site of the Rubisco enzyme
Light intensity (early morning, late afternoon, shady area):
 Low light intensities reduce the rate of photolysis
o O2 reduced
o Fewer high energy electrons which are needed to convert CO2 to
glucose
 Less production of carbohydrates
Temperature:
 Temperatures below 5Cº affects all enzymes involved in photosynthesis show
reduced activity
o At low temperatures there is low kinetic energy so few collisions
between enzyme and substrate take place
 More than 30Cº rubisco enzyme is less effective but not denatured
 Fewer high energy electrons due to a decreased rate of photolysis

C1.3.8 CO2 enrichment experiments as a mean of predicting future rates of photosynthesis

and plant growth
 In high light intensity and warm temps, rates of photosynthesis are frequently
limited by CO2 concentration
 More CO2 concentration à increase rates of photosynthesis since plants need
that CO2 to carry out the process
 From the industrial revolution to now the C02 concentration in the
atmosphere has rise a lot which has consequences
o Higher CO2 à increase rate of photosynthesis and plant growth
o FACE: “free air CO2 experiments” done to increase CO2 concentration
while keeping other factors unchanged
 In these experiments circles of towers are built with CO2 is
released whenever CO2 drops again it released more CO2 (“dosing
tree”)
D2.3 Water potential
Solvent properties of water

 Solvation: combination of a solvent with the molecules or ions of a solute

 Water: ‘universal solvent’ (ability to dissolve so many other molecules)
 Polar solutes dissolve due to the attraction between the partial positive and negative
charges in water molecules and solute molecules
 Positively charged ions are attracted to the partial negative oxygen pole of
water
 Negatively charged ions are attracted to the partial positive hydrogen people
of water
 When dissolving ionic compounds, H2O molecules surround the ions creating a
hydration shell
 Hydration shell: separation of solute particles and their uniform
distribution throughout solution (dissolution)
 Substances soluble in water (able to dissolve): solute
 Substance able to dissolve a solute: solvent
 Homogeneous mixture formed when a solute is dissolved in a solvent: solution

Water movement from less concentrated to more concentrated solutions:

The attraction between water and dissolved solute causes water to move from regions of
lower solute concentration to regions of higher solute concentration. (hypotonic to hypertonic
until it becomes isotonic)
2 regions are separated by a semi-permeable membrane (water can move, solute can’t): water
moves across the membrane by osmosis until both solutions have equal solute concentrations,
resulting in a state of dynamic equilibrium (homeostasis).
 Hypertonic: solution with higher solute concentration
 Hypotonic: solution with lower solute concentration

 Isoto
nic: same solute concentration
Water movement by osmosis into or out of cells
 Osmosis: net movement of water across a semi-permeable membrane (due to
attractions between solute and water)
 Diffusion: general process of particle movement from an area of higher
concentration to an area of lower concentration.
 Passive movement: no energy needed

 If a cell is placed in a hypertonic solution: water comes out of the cell, cell
shrinks
 Shrinking (develop indentations): affects cell structure and function
 If a cell is placed in a hypotonic solution: water goes in the cell, cell enlarges
(lysis: cell bursts)
  If the cell lacks a cell wall: internal pressure increases, cell bursts
 If a cell is placed in an isotonic solution: equal movement of water in and out
the cell, no change
To prevent excessive water intake, certain freshwater unicellular organisms (paramecium)
have a specialized structure called contractile vacuoles to survive their hypotonic
environments.
 These vacuoles actively take out water from cell to maintain the correct solute
concentration in the cell and prevent cellular bursting

Property Plasma membranes of plants Cell walls of plants

and animals
Main constituent Phospholipids Cellulose
Thickness Thin (5 nm or less) Thicker (250 nm - 5 µm or more)
State Liquid: allows changes of Solid: changes of position are
position (formation of vesicles), limited, constituent molecules of
molecules diffuse through the a wall don’t diffuse
membrane
Tensile strength Very low: easily torn High: hard to tear
Permeability Semi-permeable, with some Freely-permeable, unless
solutes scarcely able to pass impregnated with a waterproof
through it material (cutin, lignin…)

Effects on water movement on cells with a cell wall:

 Entry of water: high pressure. Cell wall is strong enough to prevent bursting
 Cell is swollen, turgid (healthy)
 Loss of water: low pressure. The plasma membrane no longer pushes against the cell
wall (plasmolysis)
 Plasmolysis: can cause irreversible damage, can lead to the death of the cell.
 Cell is flaccid. Leaves and stems bend downwards (wilting)
Medical applications of isotonic solutions:
 Hypertonic solutions: damage humans by dehydrating them
 Hypotonic solutions: cause human to swell and burst

 Isotonic solutions are used during medical procedures. Usually, an isotonic sodium
chloride solution is used: “normal saline”
 Used to rinse wounds and skin abrasions
 Safely introduced to a patient’s blood system via an intravenous drip
 Used to keep areas of damaged skin moistened prior to skin grafts
 Used as the basis for eye drops
 Frozen to the consistency of slush to transport donor organs (heart, kidney…)
to the hospital where the transplant is to be done
C.1.2 CELLULAR RESPIRATION
ATP molecule
Nucleotides are the subunits of RNA and DNA; they consist of 3 parts

1. A nitrogen-containing
base
2. A five-carbon sugar
3. One or more phosphate groups

ATP is a nucleotide with an adenine base, five carbon sugar ribose and 3 phosphate groups.
 The phosphate groups are in a chain and they are all negative charged
ATP is the energy currency of cell since its used for energy storage and for energy transfer
between processes and different parts of cell.
ATP properties:
 Soluble in water à can move freely through cytoplasm and aqueous solutions
in cell
 Stable at pH levels close to neutral (like cytoplasm around 7)
 ATP can’t pass freely through phospholipid bilayer of membrane à can’t
diffuse therefore its movement can be controlled

 The 3rd phosphate group can be

removed and reattached by hydrolysis and condensation reactions:

 Hydrolysis ATP to ADP (molecule of 1 adenine+2 phosphates+ribose) releases

small amounts of energy à this energy is enough for many processes in cell
o If more energy release à excess à wasted by turning into heat
Life processes within cells that ATP supplies with energy
Cells need energy for 3 main types of activities:
1. Synthesizing macromolecules
 Anabolic reactions that link monomers into polymers would be endothermic
and therefore need the energy from the conversion of ATP to ADP
 1 or more ATP molecules used every time a monomer is linked to growing
polymer
2. Active transport
 Pumping ions or other particles across membrane against concentration
gradient requires energy from ATP
 Energy used to cause reversible change in shape of pump protein
 ATP used to cause the change from the more stable to the less stable
conformation
 o The change back from the more stable to less stable doesn’t need
energy
3. Movements
 Cells require energy from ATP for movement
 Large amount of energy, more ATP molecules are needed to change the shape
of a cell
ATP to ADP
 The phosphate released from ATP to APD it can link to another molecules such
as the protein pump for active transport
o When phosphate detaches from this molecule à energy is released
o This energy causes a change in the molecule à for example in active
transport the conformational change
 Energy required to convert ADP + phosphate back to ATP
o This energy comes from :
 Cell respiration à energy released by oxidizing carbohydrates,
fats or proteins
 The quantity of ATP within a cell is very small, if its all used up à the processes
that require energy stop.
 Without ATP, cells start to degrade within minutes à damage irreparable à
death
o This is prevented by continual regeneration of ATP from ADP +
phosphate
 Energy transfer from ATP à ADP is not 100% efficient some energy lost
transformed to heat

Cell respiration producing ATP from energy released from carbon compounds
 Cell respiration à function performed by all living cells
 In respiration: carbon compounds are oxidized to release energy and this
energy is used to produce ATP
 The most common carbon compounds used as glucose and fatty acids à main
ones in cells
 Respiration uses oxygen à produces carbon dioxide, therefore it is necessary
for oxygen to enter cells through plasma membrane and for carbon dioxide to exit
cells (gas exchange)
 Gas exchange and cellular respiration are different processes, but they are
interdependent
o Without gas exchange, cell respiration could not continue, lack of
oxygen (need to diffuse in cell) and harmful excess of carbon dioxide in
cells

Differences between anaerobic and aerobic cell respiration in humans

Cell respiration can be performed using a variety of alternative metabolic pathways:
 Aerobic (use oxygen)
 Anaerobic (no oxygen needed)
Aerobic cell respiration Anaerobic cell respiration
Oxygen is used as an electron acceptor in Oxygen not used- other substances act as
oxidation reactions oxygen acceptors in oxidation reactions
Carbohydrates such as glucose, lipids including Only carbohydrates can be used
fats and oils and amino acids after deamination
can be used
Carbon dioxide and water are waste products Carbon dioxide plus either lactate or ethanol
are the waste products, water not produced
Yield of ATP much higher per glucose (30ATP) Yield of ATP is lower per glucose (2ATP)
Initial reactions are in the cytoplasm but more All reactions happen in the cytoplasm,
occur in mitochondria including use of oxygen mitochondria are not required

Different types of cell respiration using glucose as substrate:

 Aerobic respiration in human and other animals and plants
o Glucose + oxygen à carbon dioxide + water (+ATP)
 Anaerobic respiration in humans and other animals and some bacteria
o Glucose à lactate (+ATP)
 Anaerobic respiration in yeast and other fungi
o Glucose à ethanol + carbon dioxide
Anaerobic and aerobic in humans
 Lungs and blood system supply oxygen to most organs of the body rapidly for
aerobic respiration
 Sometimes anaerobic cell respiration is used in muscles
o Advantage of anaerobic is that it can supply ATP very rapidly over a
short time period à used when we need to maximize power of muscle
contractions à used when doing exercise
 Lactate (lactic acid) is a waste product of anaerobic respiration in muscles, to
break down the lactate this requires oxygen
o It takes several minutes for enough oxygen to be absorbed in order to
break down all the lactate
 The demand for oxygen that builds up during a period of
anaerobic respiration is called the oxygen debt
Variable affecting the rate of cell respiration
Respiration rate = variable measured/time
Variables are:
 O2 consumed
 CO2 produced
Factors that affect respiration rate:
 pH
 Temperature
 Concentration of substrates (O2, glucose)
Respirometer experiment conclusions:
o The seed use fats and proteins as the respiration substrate they release
a very small amount of CO2
o In the case of carbohydrates when they are used for respiration
substrate, equal amounts of dioxide and oxygen are evolved and
consumed
B2.1 Membrane and membrane transport
Lipid bilayers as the basis of cell membranes:
 Membranes: essential components of cells

 Bilayer of phospholipids and other amphipathic

molecules (forms a continuous sheet and controls the passage of molecules)
 Plasma membrane: border between a cell and its environment
 Membranes inside eukaryotic cells: divide the cytoplasm into compartments

 Phospholipids: phosphate head (hydrophilic) & 2 hydrocarbon tails (hydrophobic)

 The tails interact with each other to form the core of biological membranes
There are usually aqueous solutions on either side of cell membranes. The solutes nearest to
the membrane surface might penetrate between the hydrophilic phosphate heads of
phospholipids, but if they reach the hydrophobic core of the membrane they are drawn back
to the aqueous solution outside the membrane.
 Hydrophobic hydrocarbon chains (core of the membrane): don’t repel
hydrophilic solutes but they are more attracted to each other, and the solutes are
more attracted to water outside the membrane.

 Permeability: ability of a molecule to pass through a membrane

 The larger the molecule, the lower the permeability
 Depends on hydrophilic / hydrophobic nature

Simple diffusion of molecules:

 Diffusion: spreading out of particles in liquids and gases that happens because the
particles are in a continuous random motion
 Net movement of particles from the higher to the lower concentration
(movement down the concentration gradient)
 Passive process: no energy needed
 Movement of molecules results in equilibrium.

 Simple diffusion across membranes: due to particles passing between phospholipids

in the membrane
 Only happens if the phospholipid bilayer is permeable to the particles.

 Non-polar particles (oxygen): diffuse through easily

 If oxygen concentration lowers inside cell due to aerobic respiration
(use of oxygen) and the concentration outside is higher, oxygen will pass into
the cell by diffusion

 Ions (positive or negative charges): can’t easily diffuse as the center of the
membrane is hydrophobic
  Ions are hydrophilic
 Polar molecules (partial positive and negative chargers over their surface):
diffuse at low rates
 Small polar particles (urea, ethanol) pass through easier than large
particles

Integral and peripheral proteins in membranes:

 Integral proteins:
 Hydrophobic on at least part of their surface (amphipathic)
 Embedded in the hydrocarbon chains in the center of the membrane
 May fit in 1 or both of the phospholipid layers
 Many are transmembrane proteins: they extend across the membrane, with
hydrophilic parts projecting through the regions of phosphate heads on either
side
 Hydrophobic regions: interact with the hydrophobic interior of the
lipid bilayer, causing them to be embedded in the bilayer.
 Hydrophilic regions: interact with the hydrophilic heads of the lipid
bilayer or the aqueous environment
 Peripheral proteins
 Hydrophilic on their surface
 Not embedded in the membrane: found in the surface
 Most of them are attached to the hydrophilic regions of integral proteins (this
attachment is often reversible)
 Some have a single hydrocarbon chain attached to them: is inserted into the
membrane, anchoring the protein to the membrane surface.
 Protein content: more active membrane, higher protein content
 Plasma membrane: protein content of 50%
 Chloroplast & mitochondria: highest protein content, 75%

 Functions of membrane proteins:

 Junctions: serve to connect and joint 2 cells together
 Enzymes: fixing to membranes localizes metabolic pathways
 Transport: responsible for facilitated diffusion and active transport
 Recognition: may function as markers for cellular identification
 Anchorage: attachment points for cytoskeleton and extracellular matrix


Transduction: function as receptors for peptide hormones

Movement of water molecules across membranes by osmosis and role of aquaporins

 Osmosis: due to differences in the concentration of substances dissolve in
water (solutes).
 Substances dissolve by forming intermolecular bonds with water molecules.
Osmosis can happen in all cells because water molecules, despite being hydrophilic, are small
enough to pass through the phospholipid bilayer. Some cells have water channels called
aquaporins, which greatly increase membrane permeability to water. (Example: root hair cells
absorb water from the soil)
Aquaporins: discovered by Peter Agre and his colleagues

 Integral proteins.
  The water channels allow the passage of water molecules but not of ions
 Bidirectional: water flows in either direction (to the interior or exterior of the
cell)
 Permit the rapid movement of water in and out of the cell: form hydrophilic
channels that span across the membrane.
 Nº of aquaporins is determined by the volume of water that needs to be
transported (kidney cells reabsorb water, they have more aquaporins)

 At its narrowest point, the channel in an

aquaporin is only slightly wider than water molecules, which therefore pass in a
single file. Positive charges at this point in the channel prevent protons (H+) from
passing through

Channel proteins for facilitated diffusion:

 Ions and polar molecules (hydrophilic): can’t easily pass between
phospholipids
 Diffusion of these substances is still possible with the help of proteins acting as
channels

 Channel protein: integral transmembrane protein

 Has a pore that connects the cytoplasm to the aqueous solution outside the
cell
 Only 1 type of particle passes through: ensured by the diameter of the pore
and chemical properties of its side (sodium ions or potassium ions, not both)
 Passive: no energy spent (diffusion)
 Bidirectional: normally from higher to lower concentration
 Cells can select which hydrophilic substances diffuse in and out by the types of
channel proteins that are synthesized and plasma membrane. Some channels can
be opened and closed, so permeability can be temporarily changed when
necessary.

Pump proteins for active transport:

Cells absorb or pump out some substances, even though the concentration inside is already
higher than outside.
 Against the concentration gradient

Pump protein Channel proteins

Use energy (active transport) Don’t use energy (passive, don’t use
energy)
Move particles in only 1 direction Bidirectional
Against the concentration gradient Down the concentration gradient

Process carried out by pump proteins: 2 different conformations

 1. Particle enters the pump from one side of membrane to reach central
chamber.
2. The pump protein changes to other conformation: allows the particles to pass
out on the opposite side of membrane
3. Pump protein returns to original conformation
*Energy is used to change the protein from one conformation to another: active transport
 More stable to less stable conformation: requires energy
 Less stable to more stable conformation: doesn’t require energy
 ATP: supplies energy needed for active transport

 Membrane of the cell: contains many different pump proteins each of which
transfers one specific type of particle across the membrane.

Sodium-potassium pumps as an example of exchange transporters:

 Sodium potassium pump in membranes: found in neurons
 Active transport (uses ATP): goes against the concentration gradient
 Uses a sodium potassium pump protein
 Pumps out 3 sodium ions, pumps in 2 potassium ions

Sodium-dependent glucose cotransporters as an example of indirect active transport:

 Sodium glucose cotransporter: transfers a sodium ion and glucose molecule across the
plasma membrane (kidney)
 Facilitated diffusion: for the concentration gradient (higher to lower)
There will be a lot of glucose inside the cell. To take out the glucose (for more glucose to be
transferred inside), facilitated diffusion is carried out. To take out the sodium ions from the
cell, a sodium potassium pump is used.
 Indirect active transport: sodium glucose cotransporter is passive but, for the whole
process to occur, a sodium potassium pump is needed (active: uses energy)
Selectivity in membrane permeability: allows passage of particular molecules, but not others
 Semi-permeable membrane: allows passage of the solvent and certain
small solutes
 Facilitated diffusion & active transport: allow selective permeability (channel
proteins and pump proteins are specific to particular particles )
 Simple diffusion: not selective, only depends on the size and polarity of
particles

 Cell membrane: partly semi permeable and partly selectively permeable:

partially permeable

Structure and function of glycoproteins & glycolipids

 Glycoproteins: carbohydrates linked to proteins
 Conjugated proteins (protein + another chemical group)
 Carbohydrate is the non-polypeptide component
 Component of the plasma membrane: the protein part is embedded in the
membrane, the carbohydrate part is projecting out to the exterior environment
of the cell

 Glycolipids: carbohydrates linked to lipids

 Carbohydrate part: usually a monosaccharide or short chain between 2-4 sugar
units
 Lipid part: usually contains 1-2 hydrocarbon chains (fit into the hydrophobic
core of membranes)
 Occur in the plasma membrane of all eukaryotic cells: the attached
carbohydrate projects outwards into the extracellular environment of the cell

 Role of glycoproteins & glycolipids:

  Cell-to-cell recognition
 Glycoproteins: ABO glycoproteins in red blood cells
 Glycolipids: help immune system to distinguish between self and non-
self cells, so pathogens and foreign tissue can be recognized and
destroyed
 Form glycocalyx: carbohydrate-rich layer on the outer face of the plasma
membrane of animal cells, with an aqueous solution in the gaps between
carbohydrates
 Glycocalyx of adjacent cells can fuse, binding the cells together and
preventing the tissue from falling apart

Fluid mosaic model of membrane structure:

 Bilayer of phospholipids with proteins in a variety of positions (flexible membrane)
 Peripheral proteins are attached to the inner or outer surface

 Integral
proteins are embedded in the phospholipid bilayer

 Cholesterol and unsaturated fatty acids: Membrane is fluid, both layers rotate upon
each other, they change places all the time (tails aren’t fully touching each other). Unsaturated
fatty acids create spaces since they are not fully solid with allows movement.
 Phospholipids molecules are free to move laterally in each of the 2 layers of the
bilayer, so the proteins can also move (fluid mosaic model)