Cell Biology &

Biochemistry
 Energy Lightning
(electrical energy)
• All organisms require energy to grow,
reproduce, move and carry out fundamental
maintenance and repairs.
• Energy cannot be created or destroyed, but it
can be converted from one form to another.
• The ultimate source of energy is the sun.

The Sun is the ultimate energy

source for life on Earth

Heat (thermal energy)

Photo credit:
NASA
 Most plants are autotrophs.

Energy Producers
• Organisms which are capable of producing their
own energy are called autotrophs.

• Photosynthetic autotrophs (e.g. plants, algae

and some bacteria) convert light energy into
chemical energy.

• Chemosynthetic autotrophs derive

their energy from inorganic sources such as sulfur
or ammonia. Some bacteria
are chemoautotrophs.

Anabaena sphaerica (left) is a cyanobacterium,

and is an example of an autotrophic bacteria.
Energy Consumers
• Heterotrophs are organisms which cannot make their
own energy. All animals, fungi and some bacteria are
heterotrophs.

• Chemosynthetic heterotrophs consume

other organisms to obtain their
energy and carbon sources.

• Photosynthetic heterotrophs are

able to convert light energy, but still require organic
compounds as a carbon source.
Some bacteria are photoheterotrophs.
 Energy in Cells
Carbon dioxide + water Light energy

Oxygen Oxygen

• A summary of the energy flow Other

within a plant cell is shown Photosynthesis
Glucose uses of
here. In animal cells the * glucose

glucose* is supplied by Fuel

ADP
feeding, not photosynthesis.

• Energy not immediately stored ATP

Respiration

in chemical bonds is lost as

heat.
Water
• ATP provides the energy for
metabolic reactions, including
photosynthesis.
Carbon
Heat energy dioxide
 ATP Structure
• Adenosine triphosphate (ATP) is the universal energy carrier for cells.
• ATP is classed as a nucleotide and is composed of adenine, ribose and three
phosphate groups.
• Covalent bonds join the two terminal phosphate groups to the nucleotide.

Adenine
Phosphates

A symbolic form of
ATP (adenosine triphosphate) Ribose
 ATP Structure
NH2
Adenine
C N
Phosphate C
N
groups C H
H C C
N
N
O- O- O-
Adenine
O- P O P O P O CH2 O

H H
O O O H H

OH OH

Ribose

The chemical structure of adenosine triphosphate

(ATP), and a space filling molecule (right).

Phosphate
groups
Ribose
 The Role of ATP in Cells
ATP
• ATP can release its energy
quickly by hydrolysis of the
terminal phosphate.
• This reaction is catalyzed by
the enzyme ATPase.
ATPase
• Once ATP has released its
energy, it becomes ADP
(adenosine diphosphate).
• ADP is a low energy Pi
molecule that can be
Inorganic
recharged by adding a phosphate
phosphate.

ADP + P
 The Role of ATP in Cells
A free phosphate is
The energy released from P
ATPase released from the
the loss of a phosphate is
ATP. This may be
available for immediate
reused to regenerate
work inside the cell.
ATP from ADP again.

Adenosine Adenosine
triphosphate ATP diphosphate ADP
A high energy compound A low energy compound with
able to supply energy for no available energy to fuel
metabolic activity. metabolic activity.

In cellular respiration, glucose is

oxidized in a step-wise process that
provides the energy to make high
energy ATP from ADP.

Pi
Apart from glycolysis, these
processes occur in the mitochondria.
 Cellular Respiration
Typical
• Cellular respiration is a catabolic, energy- animal cell
yielding pathway.
• It is the process by which organisms break Cell cytosol
down energy rich molecules, such as
glucose, releasing energy for the synthesis of
ATP.

• Aerobic respiration requires oxygen.

• Forms of cellular respiration that

do not require oxygen are said to
be anaerobic.

Inner
membrane
Outer
membrane
Mitochondrion
Mitochondrion (false
colored) taken by TEM.

Magnification x 14,000
 Redox Reactions
• As well as using ATP, cells can transfer energy
through the transfer of electrons in what are called
oxidation-reduction reactions.
• Oxidation is the chemical process in which
a substance loses electrons.

• Reduction is the chemical process in which a

substance gains electrons.

• Because oxidation and reduction reactions occur

simulatenously, they are called In a fire (combustion), fuels are oxidized
redox reactions. rapidly to produce water and carbon dioxide.

• In cells, redox reactions usually involve transfer of a

hydrogen atom rather than just an electron.

• In cellular respiration, redox reactions release the

energy stored in food moleules so that ATP can
synthesized using that energy.

Rusting is another familiar example of a

redox reaction. When iron rusts, the iron (II)
loses electrons to form iron(III) oxide.
 A Summary of
Aerobic Respiration
Glycolysis
Glycolysis Location: cytoplasm
Process: Glucose is broken down
Cell cytoplasm into two molecules of pyruvate.

Transition reaction
Transition Reaction Location: mitochondrial matrix
Process: Formation of acetyl
coenzyme A from pyruvate.

Krebs cycle
Location: mitochondrial matrix
Krebs Cycle Process: A series of reactions
producing carbon dioxide, ATP
Mitochondrion and hydrogens.

Electron transport chain

Location: mitochondrial cristae
Process: H2 is oxidised to
water using oxygen. Energy is
released as ATP.

Electron transport
chain
 Cellular Respiration
Cellular respiration can be simplified by comparing it with the
combustion reaction required to power a car.
Fuel
CAR + oxygen
Carbon dioxide,
water, kinetic energy CAR

Food Carbon dioxide,

CELL + oxygen water.
energy (ATP)
CELL

Car Cell
*Glucose is the
Petrol, diesel, Glucose* and other major fuel source for
Fuel
or gas carbohydrates, fat, protein
cellular respiration

Oxidizer Oxygen Oxygen

Location Engine Cell cytoplasm and mitochondria

Exhaust Carbon dioxide Carbon dioxide, water,

products water Energy (ATP)
 Glucose Metabolism
• The breakdown of glucose and other organic
fuels (such as fats and proteins) to simpler
molecules is exergonic.
• It releases energy for the synthesis of the high
energy molecule, ATP. Glycolysis

• Glycolysis begins glucose metabolism in all

cells. It occurs in the cytoplasm.

• Aerobic respiration uses oxygen from the

environment to completely convert the products
of glycolysis to carbon dioxide through a set of
metabolic pathways. These reactions take
place in: Krebs Cycle
• the mitochondrial matrix (Krebs cycle)

• the inner membranes of the mitochondrion

(electron transfer chain and oxidative
phosphorylation)

Electron transport
chain
 Cellular Respiration
Cristae
Electrons Electrons carried by
carried via Mitochondrial NADH and FADH2
matrix
NADH

GLYCOLYSIS KREBS ELECTRON TRANSPORT

The cytoplasm CYCLE CHAIN AND OXIDATIVE
Glucose ➙Pyruvate Matrix of the PHOSPHORYLATION
mitochondria The inner membrane of the
mitochondria

Mitochondrion

ATP ATP ATP

Substrate-level Substrate-level Oxidative

phosphorylation phosphorylation phosphorylation
 Glycolysis Cytosol

• Glycolysis comes from Greek words meaning sugar

splitting.

• Glycolysis is the first step of cellular respiration. It

converts glucose
into pyruvate.

• It occurs in the cell cytosol.

• Glycolysis has three main functions:

• Production of cellular energy sources
(ATP and NADH) for anaerobic and
aerobic respiration.

• Production of pyruvate for use in the citric acid

cycle.

• The production of intermediate carbon

This TEM image is of a human
compounds, which can be removed for other lymphocyte cell taken from bone
cellular purposes. marrow tissue. The cytosol is
clearly visible around the large
central nucleus.
Magnification X 25 710.
 Substrates for Glycolysis
• Glucose is the main fuel for glycolysis. Glycogen can also be used as a
feed substrate, but must first be converted into glucose.

• Other substrates also enter the glycolytic pathway at later phases. These
include:
• fats, which are converted into glycerol.

• proteins (as amino acids).

Glycogen Glucose

Pyruvate
Fats Glycerol

Triglyceride Proteins
Glycolysis
Alanine

Amino
acids
The Glycolysis Process
• During glycolysis, one glucose molecule (6 carbon sugar) is converted
into two pyruvate (3 carbon acid) molecules.
• Several intermediate products are produced, which may be utilized at
any time in other cellular processes.

1 x glucose (6C)

Phosphate

1 x phosphorylated
6C sugar

2 x 3C sugar phosphate
(glyceraldehyde-3-phosphate)

2 x pyruvate
 Glycolysis Yield
• For every glucose molecule,
Glucose
glycolysis yields:
2 ADP + 2Pi
• 2 ATP net
1 x glucose (6C)
• 2 NADH + 2H +

4 ATP are produced but

• 2 pyruvate 2 ATP are consumed
molecules 1 x phosphorylated
6C sugar

2 ATP

2 x 3C sugar phosphate
(glyceraldehyde-3-phosphate)

2 x pyruvate
Pyruvate 2 NADH + H+
 Glycolysis in Review
• The diagram below gives an overview of glycolysis.
• The key inputs, outputs and intermediate molecules are given.

2 ADP + 2Pi

Glycogen
1 x glucose (6C)

Glycerol 1 x phosphorylated
6C sugar

2 ATP
Fat
s
2 x 3C sugar phosphate
(glyceraldehyde-3-phosphate)
Proteins

2 x pyruvate
Amino acids
2 NADH + H+
Transition Reaction
Pyruvate
• A transition reaction is required to link
glycolysis to the Krebs cycle.

• In the transition reaction, the pyruvate

molecules produced as the end product of Pyruvate
glycolysis are converted to acetyl
coenzyme A.
• This occurs in the matrix
of the mitochondrion.

• During the reaction a carbon is removed as 1C (as CO2)

carbon dioxide.
NADH + H+

• Coenzyme A (CoA) picks up the remaining 2-

carbon fragment of the pyruvate to form Acetyl Coenzyme A
acetyl coenzyme A (right).

Acetyl coenzyme A
The Krebs Cycle
• The Krebs cycle (or citric acid cycle) is the
second step in the process of cellular
respiration.
• The Krebs cycle occurs in the matrix of the
mitochondria.

The mitochondrial matrix is

where pyruvate is transformed
into acetyl coenzyme A.

This TEM cross section through

a single mitochondrion shows
the folded inner membrane and
the matrix (arrowed).
 The Krebs Cycle
Acetyl coenzyme A

Acetyl Coenzyme A

Acetyl group
• Acetyl coenzyme A is the feed molecule
for the Krebs cycle. CoA

• Acetyl CoA is split releasing the Acetyl

(2 Coenzyme A
2-carbon acetyl group. Coenzyme A is carbons)
formed.

• The acetyl compound combines with

oxaloacetate (a 4 carbon compound) to
form citrate (a
6 carbon compound).

• Oxaloacetate is regenerated via a number Oxaloacetate

of steps as two carbon groups are (4 carbons) Citrate
(6 carbons)
subsequently lost as carbon dioxide.

2 carbons
(as CO2)
Citrate
Carbon
 The Krebs Cycle Yield
• Two turns are required to completely oxidize one Acetyl Coenzyme A
glucose molecule.

• Two turns of the Krebs cycle yields:

CoA
• 4 CO2
Acetyl
• (2 carbons)
2 ATP

• 6 NADH + H+

• 2 FADH2

• The Krebs cycle yields a small amount of energy in

the form of ATP, but a lot of potential energy in the
form of reducing power in NADH and FADH. Oxaloacetate
(4 carbons) Citrate
• The energy value from the Krebs cycle is realized (6 carbons)
when the NADH and FADH2 molecules (which act
as electron carriers) are used to generate ATP in the
next stage of glucose metabolism.
2 carbons
(as CO2)
1 ATP
3 1 FADH2
This diagram
NADHrepresents one turn of the Krebs
cycle. Actual yields are doubled as two turns are
required to oxidize glucose completely.
Electron Transport Chain
• The electron transport chain (ETC) is the final
stage in cellular respiration.

• The electron transport chain is a series of hydrogen

and electron carriers, located on the membranes of
the mitochondrial cristae.

• This final stage involves oxidative phosphorylation

and ATP generation.

This TEM cross section

through a single mitochondrion
shows the outer membrane
and the inner cristae (arrowed)
 Electron Transport Chain
• The electron transport chain consists of many linked proteins embedded in the cristae.

• These proteins are electron carriers and alternately reduced and oxidized as they
accept and donate electrons

NADH-Q reductase Cytochrome Inter-membrane space

C reductase
Ubiquinon Cristae membrane
e

Cytochrome C

Cytochrome C
oxidase

Mitochondrial matrix
 Electron Transport Chain
• Electrons from glycolysis and the Krebs cycle are transported to the electron
transport chain as NADH and FADH2. The hydrogens or electrons donated from
NADH and FADH2 are passed from one carrier protein to the next.

• Oxygen is the final electron acceptor in the chain, and it is reduced to water.

• The electron transport chain yields 34 ATP and water.

H+ H+ Inter-membrane space
H+ H+ High H+ concentration

H+ H+
H+ H+ H+

e- e-
e-

FADH2 e- H2O
NADH + H +
NAD+
FAD
(water)
H+ Mitochondrial matrix H+
Low H+ concentration
2H + ½O2
H+
(oxygen)
 Chemiosmosis
• The energy released from the electrons is used
to transport hydrogen ions (H+) across the
membrane. This results in the establishment of a
proton gradient.

• The proton gradient couples the electron

transport to ATP synthesis by a process called The inter-membrane space
is the site of chemiosmosis
chemiosmosis. in the mitochondrion.

• Chemiosmosis takes place in the inter-

membrane space of the mitochondria and is the
process where electron transport is coupled to
ATP synthesis.
 H+

s
membrane

Inter-membrane space
High H+ concentration

Mitochondrial matrix
Low H+ concentration
Chemiosmosis
• Energy from the oxidation of NADH + H+ and FADH2 (in the electron
transport chain) is used to move protons against their
concentration gradient (from a low H+ concentration to a high H+
concentration).
• The protons move from the mitochondrial matrix into the

H+

H+
H+
H+

H +
H+

H +
H+

Carrier protein

H+
H+
Outer mitochondrial
inter- membrane

H +
H+

H+

Inner mitochondrial
membrane
 Chemiosmosis
• The protons flow back down their concentration gradient via an enzyme called ATP
synthase. This molecule uses the energy released from the H+ flow to produce ATP.

• This coupling of H +
production to ATP production is shown below.

H+ H+ H+ Inter-membrane space
H+ H+ H+ High H+ concentration
H+
H+
H+ H+ H+
H+ H+
Cytochrome H+
NADH-Q C reductase
reductase
e- e-
e
-
Cytochrome C
Ubiquinon
e
Cytochrome
C oxidase ATP
synthase
NADH FADH2 e-
NAD +
FAD
+ H+
H+
H
+

H2O
H + ADP + Pi
Mitochondrial matrix ATP
Low H+ concentration H+
2H + ½O2
 Respiration Quotient
Tap (closed during
experiment)
• In small animals or germinating Syringe

seeds, the rate of cellular Manometer

respiration can be measured containing
colored liquid
using a simple respirometer.
• A respirometer is a sealed Calibrated
scale
unit.

• Carbon dioxide (CO2) produced

by the respiring tissues is
absorbed by soda lime.

• The volume of oxygen

consumed is detected by fluid
displacement in a manometer.
Filter
paper

In this simple respirometer, small

invertebrates are contained in a
perforated gauze basket and the volume Perforated
gauze basket
of oxygen consumed is measured by fluid
Soda lime solution Soda lime solution
displacement in the manometer.
(absorbs CO2) (absorbs CO2)
 Respiratory Quotient
• The respiration quotient (RQ) can be used as an indication of the primary fuel source for
cellular respiration and metabolism, for example, fat or carbohydrate.

• The respiratory quotient (RQ) is the simple ratio of the amount of CO 2 produced during
cellular respiration to the amount of oxygen consumed:
CO2 produced RQ Substrate
RQ
= O2 consumed
Carbohydrate with some
>1.0

More oxygen required for oxidation

• Different substrates produce typical RQ values anaerobic metabolism

when respired (table right): 1.0 Carbohydrates, e.g. glucose

• The oxidation of pure carbohydrate

produces an RQ of 1.0. 0.9 Protein

• Organisms usually respire a mix of substrates 0.7 Fat

(RQ values of 0.8-0.9).
Fat with associated
0.5
carbohydrate synthesis

Carbohydrate with associated

0.3
Germinating seeds organic acid synthesis
typically respire a mix of
fats and carbohydrates RQs are lower in substrates requiring
more oxygen for their complete oxidation
 Measuring Respiration
• The graph below shows RQ values obtained from respirometer experiments of
germinating wheat seeds (Triticum sativum). The RQ values reveal the
substrates utilized for respiration.
• Low RQ values in early germination indicate fat is being utilized.

• RQ values of closer to 1.0 in later stages of germination indicate

carbohydrate is the primary fuel source.

Modified after Clegg and MacKean 1994

Fat is the primary
respiratory substrate
during early germination

Later in germination,
carbohydrates are the
primary fuel for respiration
 Anaerobic Pathways
• All organisms can metabolize glucose
anaerobically (without oxygen) using
glycolysis in the cytoplasm.

Alan Wheals, University of Bath

• Fermentation pathways for glucose
metabolism do not use oxygen as a final
electron acceptor.

• The energy yield from fermentation is low, Alcoholic fermentation in yeast,

(Saccharomyces cerevisiae), is the basis
and few organisms can obtain sufficient of the brewing and baking industries.

energy for their needs this way. Fermentation is distinct from anaerobic
respiration. Respiration always involves
• An alternative electron acceptor is required hydrogen ions passing down a chain of
carriers to a terminal acceptor and this
in the absence of oxygen, or glycolysis will does not happen in fermentation. In
anaerobic respiration, the terminal H+
stop. acceptor is a molecule other than oxygen,
e.g. Fe2+ or nitrate.
• In alcoholic fermentation the electron
acceptor is ethanal.
Lactic Acid Fermentation
• Glycolysis can continue in the absence of Glucos
e
oxygen by reducing pyruvate to lactic acid. C6H12O6 2 ADP
This process is called lactic acid
fermentation.
2 ATP
Net
• Lactic acid is toxic and this pathway cannot
continue indefinitely. NAD.H2
• The liver converts the lactic acid back into a
2 x pyruvate
harmless respiratory intermediate.
CH3COCOOH

• Lactic acid fermentation occurs in

the skeletal muscle of mammals.
Lactic Acid Fermentation
Animal tissues
Lactic acid
Pyruvate CH3CHOHCOOH

waste
NAD.H2 NAD+ product

Skeletal muscle
 Alcoholic Fermentation
• Yeasts respire aerobically when oxygen is available Glucos
e
but can use alcoholic fermentation when it is not. C6H12O6 2 ADP

• Such organisms are called facultative anaerobes.

2 ATP
• At ethanol levels above 12-15%, fermentation is Net

toxic to the yeast cells. Alcoholic fermentation cannot

NAD.H2
be used indefinitely.
2 x pyruvate
• The root cells of plants also use fermentation as a CH3COCOOH
pathway when oxygen is unavailable.

• As ethanol is toxic, it must be Alcoholic

Fermentation
converted back to respiratory Yeast, higher plant cells
Ethanal + CO2 Ethanol
intermediates and respired CH3CH2OH
CH3CHO
aerobically to reduce its levels. gaseous
waste NAD.H2 NAD+
product
 Alcoholic Fermentation
• Alcoholic fermentation is carried out by yeasts
and some types of bacteria.

• The by-products of alcoholic fermentation (ethanol

and carbon dioxide) form the basis of the brewing
and baking industries.

Bread (above) rises during baking as a

result of the carbon dioxide given off during
alcoholic fermentation.

Alcoholic beverages such as beer (left),

derive their alcohol content from the ethanol
produced from alcoholic fermentation.
 Facultative
Anaerobic
Metabolism
• Facultative anaerobic metabolism

Athletics NZ
occurs when organisms or tissues can
produce ATP using aerobic respiratory
During short, hard muscular efforts,
pathways when oxygen is present, and human muscle performs anaerobically.

anaerobic pathways if oxygen is absent.

• Examples of facultative anaerobes

include the bacteria Listeria and
Salmonella, and some yeasts, e.g.
Saccharomyces.

• Vertebrate skeletal muscle is facultatively

anaerobic because it has the ability to

CDC
Salmonella is a facultative anaerobe
generate ATP for a short time in the
 Obligate Anaerobes
• Some organisms respire only in the absence
of oxygen; oxygen is toxic to them. Such
organisms are called obligate anaerobes.

• Some are bacterial pathogens and the by-

products of their metabolism are highly toxic
and cause diseases such as tetanus,
gangrene (right), and botulism.

• Obligate anaerobes generate ATP using

various fermentative pathways or anaerobic
respiration in which the terminal electron
acceptor is a molecule other than oxygen.

CDC
The bacterium Yesinia pestis (left),
causes bubonic plague. Gangrene
(seen in the hand above) is a common
manifestation of the plague.
CDC
 Aerobic & Anaerobic
Pathways Compared
Anaerobic Pathways
Aerobic
Respiration Alcoholic Lactic acid
fermentation fermentation
Oxygen Ethanal Pyruvate

H+ acceptor

Products CO2 + water Ethanol + CO2 Lactic acid

Phosphorylation Substrate level

Substrate level Substrate level
type and oxidative

Most energy is
Toxic when ethanol Lactic acid is toxic and
Comments produced during the
levels are >12-15% must be removed
Krebs cycle
 Photosynthesis
• Photosynthesis is the action of transforming sunlight energy into
chemical energy. Photosynthesis produces:
• energy for use by the autotroph and for use later down the food
chain.
Water and nutrients
• oxygen gas, essential
(via the roots) for the survival of advanced life forms.

Sugar Sunlight
(to rest of the plant)

Carbon dioxide gas

(through stomata)

Oxygen gas
(through stomata) Light
6CO2 + 12H2O C6H12O6 = 6O2 + 6H2O
Chlorophyll
A Summary of Photosynthesis
• A basic overview of photosynthesis is presented in the diagram below.

Carbon
Water Raw materials
dioxide
ADP

Light Dependent ATP

Light Independent Main
Phase Phase product
Solar
energy Process: Energy Capture Process: Carbon fixation Glucose
via Photosystems I and II via the Calvin cycle
NADP.H2
Location: Grana Location: Stroma

NADP

Oxygen By-products Water

 Photosynthesis

• Photosynthesis is carried out by plants, algae,

some bacteria and some protists.

• In plants and photosynthetic protists,

photosynthesis takes place in membrane-bound
A plant mesophyll cell with
organelles called chloroplasts.
a chloroplast highlighted.
• Chloroplasts are filled with a green pigment
called chlorophyll. This is what gives plants
their green coloring.

• In photosynthetic bacteria, the reactions of

photosynthesis take place within the
Plant chloroplast.
cell itself, not within a discrete organelle.
TEM X37,000
 The Electromagnetic
Spectrum
• Light is a form of energy known as electromagnetic radiation.

• The segment of the electromagnetic spectrum most important to life is the

narrow band between about 380 and 750 nanometres (nm).

• This radiation is known as visible light because it is detected as colors by

the human eye.

• Visible light drives photosynthesis.

Gamma Ultra
rays x-rays violet Infrared Microwave Radio waves

Visible light

38 40 45 55 65 75
0 0 0 0 0 0

Increasing Increasing
energy Wavelength (nm) wavelength
 l
Pigments & Light Absorption
• Light striking an object it is either reflected, transmitted or absorbed.

• Substances that absorb visible light are called pigments.

• The ability of a pigment to absorb particular wavelengths of
Photosynthetic Pigments
• The photosynthetic pigments of plants fall into two
categories:
• Chlorophylls, which absorb red and blue-violet light.
They are the main photosynthetic pigment in plants
and give leaves their green color (below).

• Carotenoids, which absorb strongly in the blue-

violet and appear orange, yellow, or red. They are
considered to be associate pigments. Carotenoids
give carrots their orange color (right).
Photosynthetic Pigments
• The photosynthetic pigments of the chloroplasts in
higher plants absorb blue and red light, and the leaves
therefore appear green (which is reflected).

• Plant leaves also contain accessory pigments, which

capture light outside the wavelengths captured by
chlorophyll.
Sunlight energy
Green light is
reflected

Red and blue light is Thylakoid

absorbed discs
Photosynthetic Pigments
• Each photosynthetic pigment has its own characteristic absorption
spectrum.

• Although only chlorophyll a can participate directly in the light reactions of

photosynthesis, the accessory pigments (chlorophyll b and carotenoids)
can absorb wavelengths of light that chlorophyll a cannot.

• The accessory pigments pass the energy (photons) to chlorophyll a, thus

Space filling model of the chlorophyll a
broadening the spectrum that can effectively drive photosynthesis.
molecule (left). Chlorophyll has a
porphyrin ring with a magnesium atom in
its centre and a hydrocarbon tail.
Chlorophyll a is responsible for the
green coloration of plant leaves (right).

Porphyrin ring
Hydrocarbon tail
 Absorption spectrum
• The absorption spectrum of different photosynthetic pigments provides clues
to their role in photosynthesis, since light can only perform work if it is absorbed.
Absorption spectra of photosynthetic pigments
(Relative amounts of light absorbed at different wavelengths)
8
0
Chlorophyll
b
6
0
Carotenoid
s
absorbance
Percentage

4 Chlorophyll
0 a

2
0

0
40 50 60 70
0 0 0
Wavelength (nm) 0
 Action Spectrum
• An action spectrum profiles the effectiveness of different
wavelength light in fueling photosynthesis. It is obtained by plotting
wavelength against some measure of photosynthetic rate (e.g. CO 2
production). Action spectrum for photosynthesis
Rate of photosynthesis (as percent of rate at 670 nm)

100 (Effectiveness of different wavelengths in fueling photosynthesis)

80

60

40

20 The action spectrum closely

matches the absorption spectrum
for the photosynthetic pigments.
0

400 500 600 700

Wavelength (nm)
 The Chloroplast
• The chloroplast is enclosed by
an envelope consisting of two
membranes separated by a very
narrow intermembrane space.
Thylakoid
membranes
• Membranes also divide the
interior of the chloroplast
Grana, are stacks of
into compartments: thylakoid membranes Stroma, the liquid
containing chlorophyll interior of the chloroplast
• flattened sacs called
thylakoids, which in places are
Inner
stacked into structures called membrane
grana.

• the stroma (fluid) outside

the thylakoids.
Thylakoid
sac (disc)
• They contain DNA and also
Outer
ribosomes, which are used to membrane
The Biochemistry of Sunlight

Photosynthesis CO2 H2O

• Photosynthesis is, in many ways, the reverse process of O2

respiration. The same principles of electron carriers, electron
transfer, and ATP generation through chemiosmosis apply.
• Water is split and electrons are transferred
together with hydrogen ions from water to CO2.
The CO2 is reduced to sugar.
Sugars are
• Sugar, oxygen and water are produced produced during
photosynthesis
as by-products. and utilized by
the plant.
• The electrons increase in potential energy
as they move from water to sugar. The
energy to do this is provided by light.

• Photosynthesis can be summarized as the

H2O
following chemical reaction:
6CO2 + 12H2O + light energy ➙ Glucose (C6H12O6) + 6O2 + 6H2O
 Photosynthesis
• There are two phases in photosynthesis:
• The light dependent phase
(D), which occurs in the thylakoid
membranes of a chloroplast. D
• The light independent phase
(I), which occurs in the stroma I
of chloroplasts.

D
Diagrammatic
representation(top) and false
colored electron micrograph
I (left) of a plant chloroplast
showing the sites of the light
dependent and light
independent phases of
photosynthesis.
Photosynthesis in C3 Plants
• The diagram below summarizes photosynthesis in a C3 plant.
Water from the cell sap
is used as a raw material
Sunlight

ATP

NADPH + H+
Oxygen gas (from the Water is given off
break up of water as a waste product.
molecules) is given off
as a waste product.
Hydrogen (from the Carbon dioxide from the triose phosphate
break up of water air provides carbon and (a 3-carbon sugar)
molecules) is used oxygen as raw materials.
as a raw material. Carbon is fixed in the
Light independent phase
Conversion of Triose
Cellulose

Phosphate
• Triose phosphate, produced during photosynthesis, is the
base product leading to the formation of many other
molecules. It is converted to:
• Glucose, the fuel for cellular respiration; supplies energy
for metabolism.

• Cellulose, a component of plant cell walls is formed using

glucose as a building block. Starch
granule
• Starch granules act as a reserve supply of energy, to be
converted back into glucose when required.

• Disaccharides. Glucose is converted to other sugars

such as fructose, found in ripe fruit, and sucrose, found
in sugar cane.
Sucrose
• Lipids and amino acids. Lysine, an amino acid
 Photosystems
• The photosystems in green plants are protein complexes used to harvest light
energy so it can be converted into chemical energy (ATP and NADPH) in the
thylakoids of the chloroplasts

• The photosystems are associated with the light dependent phase of

photosynthesis.
Protein complex
Primary
• They absorb light energy and elevate
Protein electrons
acceptorto a higher energy level.
complex
Primary
acceptor

Light NADPH

A summary of noncyclic
Light ATP
electron flow through the
two photosystems of the
P700 light dependent phase.

P680 Photosystem I
Absorbs light
Photosystem II at 700nm
Absorbs light at Electrons lost are replaced
680 nm by electrons from PSII
 Light Dependent Phase
• When chlorophyll molecules absorb light, an electron is excited to a higher level. This
electron is replaced to photosystem II in one of two ways:
• In non-cyclic phosphorylation (below), the electrons lost to the electron transport
chain are replaced by splitting a water molecule.

• In cyclic phosphorylation electrons lost from photosystem II are replaced by

those from photosystem I. ATP is generated but not NADPH.
Light energy NADP+ + 2H+
Light energy
NADPH + H+

2e- 2e-
2e -
2e
-

Photosystem II Photosystem I
H
+
NADP+
½O2 2H+ reductase

H2O
Thylakoid space

ADP
ATP synthase
+ Pi

ATP Thylakoid membrane

H+
 Light Dependent Phase
Electron transport chain: Each electron
is passed from one electron carrier to
NADP is a hydrogen carrier
another; losing energy as it goes. This
When chlorophyll molecules picking up H+ from the
energy is used to pump hydrogen ions
absorb light, an electron is thylakoid and transporting
across the thylakoid membrane.
excited to a higher level. This them to the Calvin cycle.
electron “hole” must be filled.
Light energy NADP+ + 2H+
Light energy NADPH + H+

2e- 2e-
2e -
2e-

Photosystem I
Photosystem II H
+
NADP+ reductase
½O2 2H+ Flow of H+ back across the membrane is coupled
to ATP synthesis by chemiosmosis.
H2O

ADP
+ Pi
Photolysis of water: In non- ATP
cyclic phosphorylation, the
electrons lost to the electron H+
transport chain are replaced ATP synthase catalyzes the
by splitting a water molecule production of ATP from ADP
(photolysis) releasing oxygen and inorganic phosphate (Pi)
gas and hydrogen ions.
 Light Independent Phase
CO2

• The light independent phase

or Calvin cycle (carbon
Ribulose bisphosphate
fixation) occurs in the carboxylase (RuBisCo)

stroma of the chloroplast. RuBP: Ribulose G3P: Glycerate

bisphosphate 3-phosphate
• In the Calvin cycle, carbon ADP +
Pi NADPH
ATP
atoms from CO2 are + H+

ATP
incorporated into existing ADP +
Pi NADP
organic molecules. Ribulose phosphate

• Hydrogen (H+) is added to Triose phosphate

CO2 and a five carbon
intermediate molecule to
make carbohydrate.
The carbohydrates produced during the
Calvin cycle can be stored to provide
• The reducing power for energy for use at a later stage. Carbon
Hexose
fixation does not occur only in darkness
carbon fixation is supplied but was named because it does not
sugars
by NADPH. require light to proceed. The H+ and ATP
are supplied by the light dependent phase.
 Factors Affecting
Photosynthetic Rate

• The rate at which plants can make

food (the photosynthetic rate) is
dependent on environmental factors.
Some factors have a greater effect
than others. These include:
• the amount of light available.

• the level of carbon dioxide (CO2).

• the temperature.
 Factors Affecting
Photosynthetic Rate
Light intensity vs
• The effect of light intensity on
photosynthetic rate
90 photosynthetic rate is shown in
Rate of photosynthesis (mm3CO2 cm-2h-1)

this experiment using cucumber

80
plants.

70 • The experiment was carried out at

a constant temperature and
60
constant carbon dioxide level.

50 • The rate of photosynthesis

increases exponentially with light
40
intensity until a maximum rate is
1 2 3 4 5 6 7
Units of light intensity (arbitrary scale) achieved. At this point increasing
the light intensity has no effect on
photosynthetic rate and the rate of
 Factors Affecting
Photosynthetic Rate
• This graph shows how temperature Light intensity, CO2, and temperature
and CO2 levels affect vs photosynthetic rate
240 High CO2 at 30°C

Rate of photosynthesis (mm3CO2 cm-2h-1)

photosynthetic rate in cucumber
plants. 200
High CO2 at 20°C
• Photosynthetic rate increases as 160

the CO2 concentration increases.

120
At high concentrations, the rate of
photosynthesis begins to slow as 80 Low CO2 at 30°C

limiting factors other than CO2 40

Low CO2 at 20°C
become important.
1 2 3 4 5 6 7
• An increase in temperature Units of light intensity (arbitrary scale)
increases photosynthetic rate
because of its effect on enzyme Increasing the temperature when CO2 is
limiting has little effect on photosynthetic rate.
activity. However, temperatures
Photosynthesis in C4 Plants
• In many plants, the first detectable
compound made during
photosynthesis is a 3-carbon
compound called glycerate 3-
phosphate (3GP). Plants that
produce 3GP are termed C3 plants.
Sugar cane Maize
• In some plants, oxaloacetate, a
4-carbon molecule, is the first Sorghum

compound to be made. Plants that

produce this compound are termed
C4 plants.

• C4 plants include the tropical

monocots important as food crops:
• Sugar cane (Saccharum
officinarum)
Photosynthesis in C4 Plants
• C4 plants are capable of
high rates of photosynthesis
in high temperature-high
light environments.

• C4 plants have a high yield of

photosynthetic products
compared to C3 plants, giving them
a competitive advantage in tropical
environments.

• This characteristic is also an

advantage for commercial crop
plants such as maize and sugar
cane. C4 plants thrive in hot, humid tropical
conditions such as those found in
Hawaii (top right) and Fiji (bottom right).
Photosynthesis in C4 Plants
• C4 plants have chloroplasts in both the mesophyll and the bundle sheath
cells.

• They increase photosynthetic rates by separating Rubisco from atmospheric

oxygen, fixing carbon as 4-carbon intermediates in the mesophyll cells and
Upper epidermis cells.
using these to ferry the fixed carbon to Rubisco in the bundle-sheath
Bundle
sheath

Spongy mesophyll
VB

Palisade mesophyll

Lower epidermis

This C4 leaf cross section shows the

Stoma (CO2) entry chloroplasts within the cells of the bundle
Chloroplasts
sheath and the palisade mesophyll. Tightly
packed mesophyll cells keep oxygen away
from the bundle sheath cells, which
surround the vascular bundle (VB).
Photosynthesis in C4 Plants
CO2
A low oxygen environment is essential for
the enzyme ribulose bisphosphate
carboxylase (Rubisco) to function
optimally in the Calvin cycle. By protecting
RuBisCo from oxygen, C4 plants achieve
Oxaloacetate
high photosynthetic rates.

C4 1 Hatch and Slack pathway

PEP PEP
carboxylase Photosynthesis in the palisade
C3 mesophyll cells captures light energy in
the chloroplasts and fixes CO2 (as a 4C
Hatch-Slack Malate intermediate) in the cytoplasm. C4 plants
pathway C4 can fix large quantities of CO2 because
the enzyme PEP carboxylase has a
high affinity for CO2 and can incorporate
Pyruvate it into the 3C compound phophoenol
C3 pyruvate (PEP) at low levels.
2 Calvin cycle (bundle sheath)
+ CO2
Malate is transfered from the palisade
cells to the inner bundle sheath where it
Calvin cycle is broken down to pyruvate. CO2 is
released for use in the Calvin cycle.