Topic 2 Molecular Biology

2.1 Molecules to Metabolism

2.1 Molecular biology Molecular biology is the relationship between genes and polypeptides (linear chain of
U1 explains living many amino acids)
processes in terms  DNA → mRNA → Proteins (complex and varied)
of the chemical
substances Organic molecules, especially proteins are very complex and varied, hence organic
involved. compounds have a hugely varied roles within and outside of cells

2.1 Carbon atoms can Organic Compounds

U2 form four covalent  An organic compound is a compound that contains carbon and is found in living
bonds allowing a things
diversity of stable
compounds to Carbon
exist. Carbon forms the basis of organic life due to its ability to form large and complex
molecules via covalent bonding
 Carbon atoms can form four covalent bonds, with bonds between carbon atoms
being particularly stable
 These properties allows carbon to form a wide variety of organic compounds that
are chemically stable

2.1 Life is based on Carbohydrates

U3 carbon compounds  Carbon, hydrogen and oxygen
including  Monomers follow the general formula (CH2O)x
carbohydrates,  Monomers are commonly ring-shaped molecules
lipids, proteins and  Source of energy
nucleic acids.
Lipids
Sugars include  Organic molecules that are insoluble in water (non-polar)
monosaccharides  Soluble in non-polar organic solvents
and disaccharides.
 Common lipids - triglycerides (fats), phospholipids and steroids
Only one saturated
 Used as long-term energy storage molecule
fat is expected and
its specific name is
Proteins
not necessary. The
variable radical of  Composed of one or more chains of amino acids
amino acids can be  Carbon, hydrogen, oxygen and nitrogen (some with sulphur)
shown as R. The
structure of individual Nucleic acids
R-groups does not  Chains of subunits called nucleotides
need to be  Nucleotides consist of base, sugar and phosphate groups (covalently bonded)
memorized.  Carbon, hydrogen, oxygen, nitrogen and phosphorus
 If the sugar is ribose then the nucleic acid formed is RNA
 If the sugar is deoxiribose then the nucleic acid formed is DNA

2.1 Metabolism is the Metabolism describes the totality of chemical processes that occur within a living organism
U4 web of all the in order to maintain life
enzyme-catalysed  It is the web of all enzyme-catalysed reactions that occur within a cell or organism
reactions in a cell
or organism. Metabolic reactions serve two key functions:
 They provide a source of energy for cellular processes (growth, reproduction,
etc.)
 They enable the synthesis and assimilation of new materials for use within the cell

2.1 Anabolism is the Anabolism

U5 synthesis of  Simple molecules → complex molecules
complex molecules  Formation of macromolecules from monomers
from simpler
molecules including Condensation (water releasing) makes bonds
the formation of  Anabolic reactions are those which build molecules
 macromolecules
from monomers by
condensation
reactions.

Anabolism require energy which is usually supplied in the form of ATP

2.1 Catabolism is the Catabolism

U6 breakdown of  Complex molecules → simple molecules
complex molecules  Hydrolysis of macromolecules into monomers
into simpler
molecules including Hydrolysis (water splitting) breaks bonds
the hydrolysis of  Catabolic reactions are those which break down molecules
macromolecules
into monomers.

Catabolism requires enzymes

2.1 Urea as an example Vitalism was a doctrine that dictated that organic molecules could only be synthesised by
A1 of a compound that living systems
is produced by  It was believed that living things possessed a certain “vital force” needed to make
living organisms organic molecules
but can also be  Hence organic compounds were thought to possess a non-physical element lacking
artificially from inorganic molecules
synthesised.
Vitalism as a theory has since been disproven with the discovery that organic molecules
can be artificially synthesised
 In 1828, Frederick Woehler heated an inorganic salt (ammonium cyanate) and
produced urea
 Urea is a waste product of nitrogen metabolism and is eliminated by the kidneys in
mammals
 The artificial synthesis of urea demonstrates that organic molecules are not
fundamentally different to inorganic molecules
ammonia +carbon dixoide → ammonium carbamate → urea+water
2.1 Drawing molecular Alpha-D-glucose
S1 diagrams of
glucose, ribose, a
saturated fatty acid
and a generalised
amino acid. m
Beta-D-glucose
Only the ring forms of
D-ribose, alpha–D-
glucose and beta-D-
glucose are expected
in drawings.
D-ribose

Saturated fatty acid

 Generalized amino acid

2.1 Identification of  Proteins contain the elements C, H, O and N

S2 biochemicals such  Carbohydrates and lipids contain C, H, and O but not N
as sugars, lipids or  Many proteins contain sulphur but carbohydrates and lipids do not
amino acids from  Carbohydrates contain hydrogen and oxygen atoms in a ratio of 2:1
molecular  Lipids contain less oxygen then carbohydrates
diagrams.
Triglyceride – three fatty acids joined by
Students should be a glycerol
able to recognize
from molecular
diagrams that
triglycerides,
phospholipids and
steroids are lipids.
Drawings of steroids Steroids – four linked carbon rings
are not expected.
Proteins or parts of
polypeptides should
be recognized from
molecular diagrams Phospholipids – triglyceride but with
showing amino acids phosphate
linked by peptide
bonds.
 2.2 Water
2.2 Water molecules A water molecule is formed by covalent bonds between an oxygen atom and two hydrogen
U1 are polar and atoms
hydrogen bonds  The bond between hydrogen and oxygen involves unequal sharing of electrons –
form between them it is a polar covalent bond
o Oxygen (due to having a higher electronegativity) attracts the electrons more
strongly
o The shared electrons orbit closer to the oxygen atom than the hydrogen atoms
resulting in polarity

Water is described as being polar because it has a slight charge difference across the
different poles of the molecule
 This charge difference across the molecule (dipole) allows water to form weak
associations between them (hydrogen bonds)
 Hydrogen bond is the force that forms when a hydrogen atom in one polar
molecule is attracted to a slightly negative atom of another polar covalent
molecule

2.2 Hydrogen bonding Water has the capacity to form intermolecular associations with molecules that share
U2 and bipolarity common properties
explain the  Because water is polar it will be attracted to other molecules that are polar or have
cohesive, adhesive, an ionic charge
thermal and solvent
properties of water. Cohesive Properties
 Cohesion is the ability of like molecules to stick together
Students should  Water is strongly cohesive (it will form hydrogen bonds)
know at least one
example of a benefit Adhesive Properties
to living organisms of  Adhesion is the ability of dissimilar molecules to stick together
each property of  Water will form intermolecular associations with polar and charged molecules
water. Transparency
of water and
maximum density at
4°C do not need to
be included.

Thermal properties
 High specific heat capacity (4.2 Joules)
o Hydrogen bonds restrict the motion of water molecules and increases in the
temperature of water require hydrogen bonds to be broken
o The amount of energy needed to raise the temperature of water is relatively
large
o Too cool down, water must lose relatively large amounts of energy
 High heat of vaporisation (amount of energy needed to change from a liquid to a
gas or vapour)
 o Considerable amounts of heat are needed to evaporate water, because
hydrogen bonds have to be broken
 High boiling point
o For the same reasons that water has a high latent heat of vaporization, its
boiling point is high

Solvent properties
 Water can dissolve many organic and inorganic substances that have charged or
polar regions
 The polar attraction of large quantities of water molecules can interrupt
intramolecular forces (such as ionic bonds) and resulting in the dissociation of the
atoms
 Positive atoms, e.g. Na+ end up being surrounded by the negative oxygen
regions of water molecules and the Cl- being surrounded by the positive
hydrogen region of water molecules

Property Benefits to living organisms

Cohesion Water has high surface tension, allowing small organisms to move on its
surface (e.g. Basilisk lizard)
Adhesion Water can move via capillary action against gravity (e.g. water can move up the
xylem via transpiration)
Thermal Water is an excellent coolant (e.g. sweat)
properties Water temperature remains relatively stable (thermally stable habitat for aquatic
organisms)
Solvent Water is a good transport medium (e.g. the blood system can transport soluble
properties materials in its plasma)

2.2 Substances can be Hydrophilic (substances that are chemically attracted to water)
U3 hydrophilic or  All substances that dissolve in water are hydrophilic, including polar molecules
hydrophobic. such as glucose, and particles with positive or negative charges such as sodium
and chloride ions
 Substances that water adheres to, cellulose for example, are also hydrophilic

Hydrophobic (substances that are insoluble in water)

 Molecules are hydrophobic if they do not have negative or positive charges and
are nonpolar
 All lipids are hydrophobic, including fats and oils
 Hydrophobic molecules dissolve in other solvents such as propanone (acetone)

2.2 Comparison of the Methane is a waste product of anaerobic respiration in certain prokaryotes that live in
A1 thermal properties anaerobic habitats
of water with those  Methane can be used as fuel but if allowed to escape into the atmosphere it
of methane. contributes to the greenhouse effect

Water and methane are both small molecules with atoms linked by single covalent bonds
 Water molecules are polar and can form hydrogen bonds
 Methane molecules are non-polar and do not form hydrogen bonds
o As a result their physical properties are very different

Property Methane Water

Density 0.46g per cm3 1g per cm3
Specific heat capacity 2.2 J per g per ˚C 4.2 J per g per ˚C
Latent heat of vaporisation 760 J/g 2 257 J/g
Melting point -182˚C 0˚C
Boiling point -160˚C 100˚C

2.2 Use of water as a The evaporation of water as sweat is a fundamental mechanism employed by humans as
A2 coolant in sweat. a means of cooling down
 Water requires a high latent heat of vaporisation (energy) to change state into a
gas
  This energy comes from the surface of the skin when it is hot, therefore when the
sweat evaporates the skin is cooled
 Because water has a high specific heat capacity, it absorbs a lot of thermal energy
before it evaporates
 Thus, water functions as a highly effective coolant, making it the principal
component of sweat

2.2 Modes of transport Glucose - soluble

A3 of glucose, amino Amino acids – positive and negative(polar) therefore soluble
acids, cholesterol, Cholesterol - insoluble
fats, oxygen and Fats – insoluble, carried in blood inside lipoprotein complexes
sodium chloride in Oxygen - partially soluble and that is why the body creates hemoglobin in the red cells in
blood in relation to order to support aerobic respiration
their solubility in Sodium chloride – soluble, carried in blood plasma.
water.
If they are soluble, they will travel freely in the blood (dissolved in the blood plasma)
If they are insoluble in water they form complexes with proteins in order to move through
the bloodstream
 2.3 Carbohydrates and Lipids
2.3 Monosaccharide Monosaccharides – single sugar units, energy source
U1 monomers are  Glucose
linked together by o Hexose sugar
condensation o The form of sugar that fuels respiration
reactions to form o Forms the base unit of many polymers
disaccharides and  Galactose
polysaccharide o Hexose sugar
polymers. o Less sweet
Sucrose, lactose and  Fructose
o Hexose sugar
maltose should be
included as o Sweetest naturally occurring carbohydrate (common in fruits and honey)
examples of  Ribose
disaccharides o Pentose sugar
produced by o Forms the backbone of RNA
combining
monosaccharides. Disaccharide – two monosaccharides linked together, transport from
The structure of  Maltose
starch should include o Dimer of glucose
amylose and  Lactose
amylopectin. o Glucose and galactose
 Sucrose
o Glucose and fructose

Polysaccharide – many monosaccharides linked together, storage form

Starch
cellulose Glycogen
Amylose Amylopectin
Source Plant Animal
Subunit β-glucose α-glucose
Bonds 1-4 1-4 and 1-6
Branches No Yes

Diagram

Shape Linear chains Helix Globular Globular

2.3 Fatty acids can be Fatty acids are hydrocarbon chains that are found in triglycerides and phospholipids
U2 saturated,  There is a chain of carbon atoms linked to them by single covalent bonds
monounsaturated  One end of the chain is the acid part – the carboxyl group (–COOH)
or polyunsaturated.
Saturated fatty acids
 Named examples of  No double bonds (max. no of hydrogen atoms)
fatty acids are not  Linear in structure, typically solid at room temperatures
required.
Unsaturated fatty acids
 With double bonds - either monounsaturated (1 double bond) or polyunsaturated
(1+ double bond)
 Bent in structure, typically liquid at room temperatures

2.3 Unsaturated fatty Cis-fatty acids

U3 acids can be cis or  The hydrogen atoms attached to the carbon double bond are on the same side
trans isomers.
Trans -fatty acids
 The hydrogen atoms attached to the carbon double bond are on different sides

Cis-isomers Trans-isomers

Very common in nature Rare in nature – usually artificially produced to

produce solid fats, e.g. margarine from
vegetable oils.

the hydrogen atoms are on the same side of the the hydrogen atoms are on opposite side of the
two carbon atoms two carbon atoms

The double bond causes a bend in the fatty acid The double bond does not causes a bend in
chain the fatty acid chain

Therefore cis-isomers are only loosely packed Trans-isomers can be closely packed

Triglycerides formed from cis-isomers have low Triglycerides formed from trans-isomers have
melting points – they usually liquid at room high melting points – they usually solid at room
temperature temperature

2.3 Triglycerides are Triglycerides are the largest class of lipids and function primarily as long-term energy
U4 formed by storage molecules
condensation from  Animals tend to store triglycerides as fats (solid), while plants tend to store
three fatty acids triglycerides as oils (liquid)
and one glycerol.
Triglycerides are formed when condensation reactions occur between one glycerol and
three fatty acids
  The hydroxyl groups of glycerol combine with the carboxyl groups of the fatty
acids to form an ester linkage
 This condensation reaction results in the formation of three molecules of water

Triglycerides can be either saturated or unsaturated, depending on the composition of the

fatty acid chains
Formation of a Triglyceride

2.3 Structure and Cellulose (plants only)

A1 function of  Structural polysaccharide found in the cell wall
cellulose and  Linear molecule of β-glucose molecules linked together
starch in plants and  Condensation reactions link carbon atom 1 to carbon atom 4 on the next β-
glycogen in glucose
humans.  Hydrophilic but too large to be dissolved

Starch (plants only)

 Energy storage polysaccharide
 α-glucose molecules linked together
 Condensation reactions link carbon atom 1 to carbon atom 4 on the next α-
glucose
 Amylose – chain of α-glucose molecules unbranched and forms a helix
 Amylopectin – chain is branched (1-6 linkages), so has a more globular shape
 Amylose is harder to digest and less soluble, however, as it takes up less space, it
is the preferred storage form in plants

Glycogen (animals and fungi)

 Energy storage polysaccharide formed in the liver
 More compact than amylopectin, as it is highly branched – 1-6 linkage occur
every ~10 subunits as opposed to ~20
 α-glucose subunits linked together by both 1-4 linkages and 1-6 linkages
(branching)
 Insoluble – does not affect osmosis (too much water entering = bursting of cell)
 It is easy to add or remove extra glucose molecules

2.3 Scientific evidence Different types of fat have various effect on human health. The main concern is coronary
A2 for health risks of heart disease (CHD). In this disease the coronary arteries become partially blocked by
trans fats and fatty deposits, leading to blood clot formation and heart attacks
saturated fatty  Positive correlation has been found between saturated fatty acid intake and rates
acids. of CHD in many studies.

Regulating Blood Cholesterol levels

 Fats and cholesterol cannot dissolve in blood and are consequently packaged with
proteins (to form lipoproteins) for transport
 Low density lipoproteins (LDL) carry cholesterol from the liver to the rest of the
body, therefore is harmful
 High density lipoproteins (HDL) scavenge excess cholesterol and carry it back
 to the liver for disposal, therefore is beneficial
 Saturated fats increase LDL levels within the body, raising blood cholesterol levels
 Trans fats increase LDL levels and decrease HDL levels within the body,
significantly raising blood cholesterol levels.
 Unsaturated (cis) fats increase HDL levels within the body, lowering blood
cholesterol levels

Health Risks of High Cholesterol

 High cholesterol levels in the bloodstream may lead to the hardening and
narrowing of arteries
 When levels of LDL is too high in the blood stream > LDL particles will form
deposits in the walls of the arteries
 The increase of fat within the arterial walls leads to the clogging of arteries,
restricting blood flow
 If coronary arteries become blocked, CHD will result > includes heart attacks and
strokes

2.3 Lipids are more Property Carbohydrates

Lipids (triglycerides)
A3 suitable for long- (glycogen)
term energy Storage Short-term energy storage Long-term energy storage
storage in humans Osmolarity More effect on osmotic Less effect on osmotic
than pressure pressure
carbohydrates. Digestion More readily digested – Less easily digested – can
used for aerobic or only be used for aerobic
anaerobic respiration respiration
ATP Yield Stores half as much ATP Stores twice as much ATP
per gram (~1760kJ per per gram (~4000kJ per
100g) 100g)
Solubility Water soluble as
Water insoluble – more
monomers – easier to
difficult to transport
transport

2.3 Evaluation of Lipid Health Claims

A4 evidence and the There are two main health claims made about lipids in the diet:
methods used to  Diets rich in saturated fats and trans fats increase the risk of CHD
obtain the evidence  Diets rich in monounsaturated and polyunsaturated (cis) fats decrease the risk of
for health claims CHD
made about lipids.
These health claims are made based on evidence collected in a number of ways:
 Epidemiological studies comparing different population groups
 Intervention studies that monitor cohorts following dietary modifications
 Experimental designs utilising animal models or data based on autopsies

Evidence Supporting Health Claims

A positive correlation has been found between the intake of saturated fats and the
incidence of CHD in human populations
 Intervention studies have shown that lowering dietary intakes of saturated fats
reduces factors associated with the development of CHD (e.g. blood cholesterol
levels, blood pressure, etc.)
 In patients who died from CHD, fatty deposits in diseased arteries were found to
contain high concentrations of trans fats

Counterclaims
 Genetic factors may play a role (e.g. blood cholesterol levels only show a weak
association to dietary levels)
 Increased carbohydrate intake may cause detrimental health effects associated
with CHD (e.g. diabetes, obesity)
 Incidence of CHD dependent on a myriad of factors besides dietary intake (e.g.
exercise, access to health care, etc.)
2.3 Use of molecular
S1 visualization
software to
compare cellulose,
starch and
glycogen.

2.3 Determination of
S2 body mass index
by calculation or
use of a nomogram.
 2.4 Proteins
2.4 Amino acids are Polypeptides are chains of many amino acids that are made by linking together amino
U1 linked together by acids by condensation reactions
condensation to
form polypeptides. The condensation reaction involves the amine group (–NH2) of one amino acid and the
carboxyl group (–COOH) of another
 Water is eliminated as in all condensation reactions and a new bond is formed
between the two acids
 The covalent bond between the amino acids is called a peptide bond
2.4 There are 20 Amino acids all share a common basic structure, with a central carbon atom bound to
U2 different amino  An amine group (NH2)
acids in  A carboxylic acid group (COOH)
polypeptides  A hydrogen atom (H)
synthesized on  A variable side chain (R)
ribosomes.
Students should
know that most
organisms use the
same 20 amino acids
in the same genetic
code although there
are some exceptions.
Specific examples There are 20 different amino acids which are universal to most living organisms, and each
could be used for type of amino acid differs in the composition of the variable side chain (R) which have
illustration. distinct chemical properties:
 Some are polar
 Some are non-polar
 Some are charged
 Some contain Sulphur
2.4 Amino acids can be Ribosomes link amino acids together one at a time, until a polypeptide is fully formed
U3 linked together in  The ribosome can make peptide bonds between any pair of amino acids, so any
any sequence sequence of amino acids is possible
giving a huge range  For a polypeptide of n amino acids there are 20n possible sequences
of possible  As most natural polypeptide chains contain between 50 - 2000 amino acid
polypeptides. residues, organisms can produce a huge range of possible polypeptides
2.4 The amino acid A gene is a sequence of DNA which encodes a polypeptide sequence
U4 sequence of  The amino acid sequence of each polypeptide is stored in a coded form in the
polypeptides is base sequence of a gene
coded for by genes.
A gene sequence is converted into a polypeptide sequence via two processes:
 Transcription - making a mRNA transcript based on DNA template (occurs within
the nucleus)
 Translation - using the instruction of the mRNA transcript to link amino acids
together (occurs at the ribosome)

Three base pairs (1 codon) of the gene are needed to code for each amino acid in the
polypeptide
2.4 A protein may Certain proteins possess a fourth level of structural organisation called a quaternary
U5 consist of a single structure
polypeptide or more  Quaternary structures are found in proteins that consist of more than
than one one polypeptide chain linked together
polypeptide linked  Alternatively, proteins may have a quaternary structure if they include inorganic
together. prosthetic groups as part of their structure
 Not all proteins will have a quaternary structure – many proteins consist of a single
polypeptide chain
2.4 The amino acid The order the amino acid sequence is called the primary structure and determines the
U6 sequence way the of chain will fold
determines the  Different amino acid sequences will fold into different configurations due to the
three-dimensional chemical properties of the variable side chains
conformation of a
protein. Amino acid sequences will commonly fold into two stable configurations, called secondary
structures
 Alpha helices occur when the amino acid sequence folds into a coil / spiral
arrangement
 Beta-pleated sheets occur when the amino acid sequence adopts a directionally-
oriented staggered strand conformation

The overall three-dimensional configuration of the protein is referred to as the tertiary

structure of the protein
 The affinity or repulsion of side chains will affect the overall shape of the
polypeptide chain and are determined by the position of specific amino acids within
a sequence
 Hence, the order of the amino acid sequence (primary structure) determines all
subsequent levels of protein folding

Fibrous proteins have structural roles whereas globular proteins are functional (active in a
cell's metabolism)
2.4 Living organisms Proteins are a very diverse class of compounds and may serve a number of different roles
U7 synthesize many within a cell, including:
different proteins  Catalysis
with a wide range of
 functions.  Muscle contraction
 Cytoskeletons
 Tensile strengthening
 Blood clotting
 Transport of nutrients and gases
 Cell adhesion
 Membrane transport
 Hormones
 Receptors
 Packing of DNA
 Immunity
2.4 Every individual has Genome influences what proteins an organism can possibly produce
U8 a unique proteome. Environmental factors influences what proteins an organism needs to produce and in
what quantity. Examples are nutrition, temperature, activity levels and anything that affect a
cell's activities

The proteome is the totality of proteins expressed within a cell, tissue or organism at a
certain time
 The proteome of any given individual will be unique, as protein expression patterns
are determined by an individual's genes

The proteome is always significantly larger than the number of genes in an individual due
to a number of factors:
 Gene sequences may be alternatively spliced following transcription to generate
multiple protein variants from a single gene
 Proteins may be modified following translation to promote further variations

2.4 Rubisco, insulin, Rubisco

A1 immunoglobulins,  Enzyme that catalyses the reaction that fixes carbon dioxide from the atmosphere,
rhodopsin, collagen providing source of carbon required by living organisms
and spider silk as  Found in high concentrations in leaves and algal cells
examples of the
range of protein Insulin
functions.  Hormone that signals cells to absorb glucose and help reduce glucose
The detailed structure concentration of the blood
of the six proteins  Secreted by β cells in the pancreas and transported by the blood
selected to illustrate
the functions of Immunoglobulins
proteins is not  Also known as antibodies
needed.  Bind to antigens on pathogens and cause a response, such as acting as a marker
to phagocytes that can engulf the pathogen

Rhodopsin
 Pigment that absorbs light, membrane protein of rod cells of the retina (light
sensitive region at the back of the eye)

Collagen
  Rope like proteins made of three polypeptide wound together
 Forms a mesh of fibres in the skin and blood vessel walls that resists tearing
 Gives strength to tendons, ligaments, skin and blood vessel walls, teeth and bones

Spider silk
 Used to makes the spokes of spider’s webs and the lifelines on which spiders
suspend themselves
 Seem like a disordered tangle, but when the silk is stretched they gradually extend,
making the silk extensive and very resistant to breaking
2.4 Denaturation of Denaturation is a structural change in a protein that results in the loss (usually permanent)
A2 proteins by heat or of its biological properties
deviation of pH from  Because the way a protein folds determines its function, any change or abrogation
the optimum. of the tertiary structure will alter its activity
Egg white or albumin  A denatured protein does not normally return to its former structure - the
solutions can be used denaturation is permanent
in denaturation
experiments.

Denaturation of proteins can usually be caused by two key conditions - temperature and
pH
Temperature
 Higher levels of thermal energy may disrupt the hydrogen bonds that hold the
protein together, the vibrations within the molecule breaks the intermolecular
bonds or interactions
 As these bonds are broken, the protein will begin to unfold and lose its capacity to
function as intended

pH
 Changing the pH will alter the charge of the protein, which in turn will alter protein
solubility and overall shape
 The charges of the R groups are changed, which breaks the ionic bonds within the
protein or cause new ionic bonds to form
2.4 Drawing molecular
S1 diagrams to show
the formation of a
peptide bond.
 2.5 Enzymes
2.5 Enzymes have an An enzyme is a globular (functional) protein that works as a catalyst by speeding up the
U1 active site to which rate of a chemical reaction without being altered themselves
specific substrates  Often called biological catalysts, as they are made by living cells and speed up
bind. biochemical reactions
 Enzymes are not changed or consumed by the reactions they catalyse and thus
can be reused

The substances that enzymes convert into products in the reactions are called substrates
 Enzymes are typically named after the molecules they react with (called
the substrate) and end with the suffix ‘-ase’
o For example, lipids are broken down by the enzyme lipase

The active Site is the region on the surface of the enzyme which binds to the substrate
molecule
 The active site and the substrate complement each other in terms of both shape
and chemical properties
 Hence only a specific substrate is capable of binding to a particular enzyme’s
active site – this is called enzyme-substrate specificity

Enzymes and Substrates

2.5 Enzyme catalysis Enzyme activity is the catalysis of a reaction by an enzyme. There are three stages:
U2 involves molecular 1. The substrate binds to the active site of the enzyme
motion and the 2. While the substrates are bound to the active site they change into different
collision of chemical substances, which are the products of the reaction
substrates with the 3. The products separate from the active site, leaving it vacant for substrates to bind
active site. again

Enzyme reactions typically occur in aqueous solutions (e.g. cytoplasm, interstitial fluid,
etc.)
 Consequently, the substrate and enzyme are usually moving randomly within the
solution (Brownian motion)
 Sometimes an enzyme may be fixed in position (e.g. membrane-bound) – this
serves to localise reactions to particular sites

Enzyme Catalysis
 Requires that the substrate to make a successful collision with the active site –
correct orientation to allow binding to active site – with the active site, due to the
random movements of both substrate and enzyme
2.5 Temperature, pH Various factors may affect the activity of enzymes, by either affecting the frequency of
U3 and substrate enzyme-substrate collisions or by affecting the capacity for the enzyme and substrate to
concentration affect interact (e.g. denaturation)
the rate of activity  Temperature, pH and substrate concentration will all influence the rate of activity of
of enzymes. an enzyme
Students should be
able to sketch graphs Temperature
to show the expected  Low temperatures result in insufficient thermal energy for the activation of an
effects of enzyme-catalysed reaction to proceed
temperature, pH and  Increasing the temperature will increase the speed and motion of both enzyme and
substrate substrate, resulting in higher enzyme activity
concentration on the  This is because a higher kinetic energy will result in more frequent collisions
activity of enzymes. between the enzymes and substrates
They should be able  At an optimal temperature (may vary for different enzymes), the rate of enzyme
to explain the activity will be at its peak
patterns or trends  Higher temperatures will cause enzyme stability to decrease, as the thermal
apparent in these energy disrupts the enzyme’s hydrogen bonds
graphs.  This causes the enzyme (particularly the active site) to lose its shape, resulting in
the loss of activity (denaturation)

pH
 Changing the pH will alter the charge of the enzyme, which in turn will alter protein
solubility and overall shape
 Changing the shape or charge of the active site will diminish its ability to bind the
substrate, abrogating enzyme function
 Enzymes have an optimal pH (may differ between enzymes) and moving outside
this range diminishes enzyme activity

Substrate Concentration
 Increasing substrate concentration will increase the activity of a corresponding
enzyme
 More substrates mean there is an increased chance of enzyme and substrate
colliding and reacting within a given period
 After a certain point, the rate of activity will cease to rise regardless of any further
increases in substrate levels; optimum concentration of substrate molecules
 This is because the environment is saturated with substrate and all enzymes are
bound and reacting (Vmax)
2.4 Enzymes can be All enzymes possess an indentation or cavity to which the substrate can bind with high
U4 denatured. specificity – this is the active site
 The shape and chemical properties of the active site are highly dependent on
the tertiary structure of the enzyme

Like all proteins, enzyme structure can be modified by external factors such as high
temperatures and extreme pH
 Any change to the structure of the active site (denaturation) affect the enzyme’s
capacity to bind the substrate, as the active site is incompatible with the substrate

Effect of Denaturation on Enzyme Activity

2.5 Immobilised Immobilised enzymes have been fixed to a static surface in order to improve the efficiency
U5 enzymes are widely of the catalysed reaction
used in industry.  Enzyme concentrations are conserved as the enzyme is not dissolved – hence it
can be retained for reuse
 Separation of the product is more easily achieved as the enzyme remains attached
to the static surface

Immobilised enzymes are utilised in a wide variety of industrial practices:

 Biofuels – Enzymes are used to breakdown carbohydrates to produce ethanol-
based fuels
 Medicine – Enzymes are used to identify a range of conditions, including certain
diseases and pregnancy
 Biotechnology – Enzymes are involved in a number of processes, including gene
splicing
 Food production – Enzymes are used in the production and refinement of beers
and dairy products
 Textiles – Enzymes are utilised in the processing of fibres (e.g. polishing cloth)
 Paper – Enzymes assist in the pulping of wood for paper production
2.5 Methods of Lactose is a disaccharide of glucose and galactose which can be broken down by the
A1 production of enzyme lactase
lactose-free milk Historically, mammals exhibit a marked decrease in lactase production after weaning,
and its advantages. leading to lactose intolerance
Lactase can be
immobilized in Producing Lactose-Free Milk
alginate beads and Lactose-free milk can be produced by treating the milk with the enzyme lactase
experiments can then  The lactase is purified from yeast or bacteria and then bound to an inert substance
 be carried out in (such as alginate beads)
which the lactose in  Milk is then repeatedly passed over this immobilised enzyme, becoming lactose-
milk is hydrolysed. free

Scientists are currently attempting to create transgenic cows that produce lactose-free milk
 This involves splicing the lactase gene into the cow’s genome so that the lactose is
broken down prior to milking

Generation of Lactose-Free Milk Using Immobilised Enzymes

2.5 Design of
S1 experiments to test
the effect of
temperature, pH and
substrate
concentration on
the activity of
enzymes.
2.5 Experimental
S2 investigation of a
factor affecting
enzyme activity.
 2.6 Structure of DNA and RNA
2.6 The nucleic acids There are two types of nucleic acids present in cells – DNA and RNA
U1 DNA and RNA are  DNA (deoxyribonucleic acid) is a more stable double stranded form that stores the
polymers of genetic blueprint for cells
nucleotides.  RNA (ribonucleic acid) is a more versatile single stranded form that transfers the
genetic information for decoding

Nucleotides consist of three parts:

 A sugar, which has five carbon atoms, so it is a pentose sugar
 A phosphate group, which is the acidic, negatively-charged part of nucleic acids
 A base that contains nitrogen and has either one or two rings of atoms in its
structure
Comparison of DNA and RNA Nucleotides

2.6 DNA differs from DNA RNA

U2 RNA in the number Pentose sugar Deoxyribose Ribose
of strands present, Adenine (A) Adenine (A)
the base Guanine (G) Guanine (G)
composition and Base Composition
Cytosine (C) Cytosine (C)
the type of pentose. Thymine (T) Uracil (U)
Double stranded (forms a
Number of strands Single stranded
double helix)
2.6 DNA is a double Nucleic acids are composed of nucleotide monomers which are linked into a single strand
U3 helix made of two via condensation reactions (water is produced as a by-product)
antiparallel strands  The phosphate group of one nucleotide attaches to the sugar of another nucleotide
of nucleotides (at the 3’– hydroxyl (-OH) group), forming phosphodiester bonds
linked by hydrogen
bonding between Two polynucleotide chains of DNA are held together via hydrogen bonding between
complementary complementary nitrogenous bases (complementary base pairing)
base pairs.  Adenine (A) pairs with Thymine (T) via two hydrogen bonds
 Guanine (G) pairs with Cytosine (C) via three hydrogen bonds

The two strands are parallel but run in opposite directions so they are said to be
antiparallel
 One strand is orientated in the direction 5’ to 3’ (sense strand) and the other is
orientated in the direction 3’ to 5’ (antisense strand)

As the antiparallel chains lengthen, the atoms will organise themselves into the most
stable energy configuration
 This atomic arrangement results in the double-stranded DNA forming a double
helix

Organisation of DNA
2.6 Crick and Watson's The structural organisation of the DNA molecule was correctly proposed in 1953 by James
A1 elucidation of the Watson and Francis Crick
structure of DNA
using model Making DNA Models
making. Using trial and error, Watson and Crick were able to assemble a DNA model that
demonstrated the following:
 DNA strands are antiparallel and form a double helix
 DNA strands pair via complementary base pairing (A = T ; C Ξ G)
 Outer edges of bases remain exposed (allows access to replicative and
transcriptional proteins)

The Rosalind Franklin Controversy

The final construction of a correct DNA molecule owed heavily to the X-ray crystallography
data generated by Franklin
 This data confirmed the arrangement of the DNA strands into a helical structure
2.6 Drawing simple Each nucleotide is comprised of three principal components:
S1 diagrams of the  5-carbon pentose sugar (pentagon)
structure of single  Phosphate group (circle)
nucleotides of DNA  Nitrogenous base (rectangle)
and RNA, using
circles, pentagons Both the phosphate group and nitrogenous base are attached to the central pentose sugar
and rectangles to  The nitrogenous base is attached to the 1’– carbon atom (right point)
represent  The phosphate base is attached to the 5’– carbon atom (left point)
phosphates,
pentoses and Simple Diagram of a Single Nucleotide
bases.
In diagrams of DNA
structure, the helical
shape does not need
to be shown, but the
two strands should be
shown antiparallel.
Adenine should be
shown paired with
thymine and guanine
with cytosine, but the
relative lengths need
to be recalled, nor the
numbers of hydrogen
bonds between the
base pairs.
 2.7 DNA Replication, Transcription and Translation
2.7 The replication of DNA replication is a semi-conservative process, because when a new double-stranded
U1 DNA is semi- DNA molecule is formed:
conservative and  One strand will be from the original template molecule
depends on  One strand will be newly synthesised
complementary
base pairing. The base sequence on the template strand determines the base sequence on the new
strand
 Only a nucleotide carrying a base that is complementary to the next base on the
template strand can successfully be added to the new strand

When DNA is replicated by the combined action of helicase and DNA polymerase:
 Each new strand formed will be identical to the original strand separated from the
template
 The two semi-conservative molecules formed will have an identical base
sequence to the original molecule

Conservation of Sequence by Complementary Base Pairing

2.7 Helicase unwinds The process of DNA replication is coordinated by two key enzymes – helicase and DNA
U2 the double helix polymerase
and separates the
two strands by Helicase
breaking hydrogen  Helicase unwinds the double helix and separates the two polynucleotide strands,
bonds. using ATP
 It does this by breaking the hydrogen bonds that exist between complementary
base pairs
 The two strands of the polynucleotide are separated and each act as a template
for the formation of a new strand

DNA Replication Summary

2.7 DNA polymerase DNA Polymerase
U3 links nucleotides  DNA polymerase synthesises new strands from the two parental template strands
together to form a  Free deoxynucleotide triphosphates (nucleotides with 3 phosphate groups) align
new strand, using opposite their complementary base partner
the pre-existing  DNA polymerase cleaves the two excess phosphates and uses the energy
strand as a released to link the nucleotide to the new strand
template.  DNA polymerase always moves in a 5' to 3' direction
The different types of
DNA polymerase do The process of DNA replication is done with a very high degree of fidelity – very few
not need to be mistakes are made during the process
distinguished.

2.7 Transcription is the Transcription is the synthesis of RNA, using DNA as a template (the antisense strand to
U4 synthesis of mRNA produce a copy of the sense strand)
copied from the  The enzyme RNA polymerase binds to a site on the DNA at the start of a gene
DNA base  RNA polymerase moves along the gene separating DNA into single strands and
sequences by RNA pairing up RNA nucleotides with complementary bases on the antisense strand
polymerase.  RNA polymerase form covalent bonds between the RNA molecules
 The RNA separates from the DNA and the double helix reforms
 Transcription stops at the end of the gene and the completed RNA molecule is
released

The Role of RNA Polymerase in Transcription

Gene
The sequence of DNA that is transcribed into RNA is called a gene
 The strand that is transcribed is called the antisense strand and is complementary
to the RNA sequence
 The strand that is not transcribed is called the sense strand and is identical to the
RNA sequence (with U instead of T)

2.7 Translation is the Translation is the synthesis of polypeptide, with an amino acid sequence determined by
U5 synthesis of the base sequence of a molecule of RNA
polypeptides on  Translation tales place in on ribosomes; complex structures in the cell that consist
ribosomes. of two subunits that have a binding site for each of the mRNA and tRNA

2.7 The amino acid In the genome, there are many different genes that carry the information needed to make
U6 sequence of a polypeptide with specific amino acid sequence
polypeptides is  Only certain genes are transcribed and only certain types of mRNA will be
determined by available for translation in the cytoplasm
mRNA according to
the genetic code. RNA that carries the information needed to synthesize a polypeptide is called messenger
RNA (mRNA)

Genetic Code
 The genetic code is the set of rules by which information encoded within mRNA
sequences is converted into amino acid sequences (polypeptides) by living cells
 The genetic code identifies the corresponding amino acid for each codon
combination
 As there are four possible bases in a nucleotide sequence, and three bases per
codon, there are 64 codon possibilities (43)
  The coding region of an mRNA sequence always begins with a START codon
(AUG) and terminates with a STOP codon

2.7 Codons of three Codons

U7 bases on mRNA  The base sequence of an mRNA molecule encodes the production of a
correspond to one polypeptide
amino acid in a  The mRNA sequence is read by the ribosome in triplets of bases called codons
polypeptide.  Each codon codes for one amino acid with a polypeptide chain
 The order of the codons in an mRNA sequence determines the order of amino
acids in a polypeptide chain

2.7 Translation Three components work together to synthesise polypeptides by translation:

U8 depends on  mRNA has a sequence of codons that specifies the amino acid sequence for the
complementary polypeptide
base pairing  tRNA molecules have an anticodon of three bases that binds to a complementary
between codons on codon on mRNA and they carry the amino acid corresponding to that codon
mRNA and  Ribosomes act as the binding site for mRNA and tRNAs and also catalyse the
anticodons on assembly of the polypeptide
tRNA.
1. Ribosomes bind to mRNA in the cytoplasm and move along the molecule in a 5’ –
3’ direction until it reaches a start codon (AUG)
2. Anticodons on tRNA molecules align opposite appropriate codons according to
complementary base pairing (e.g. AUG = UAC)
3. Each tRNA molecule carries a specific amino acid (according to the genetic code)
4. Ribosomes catalyse the formation of peptide bonds between adjacent amino acids
(via condensation reactions)
5. The ribosome moves along the mRNA molecule synthesising a polypeptide chain
until it reaches a stop codon, releasing the polypeptide chain

Overview of Translation

2.7 Use of Taq DNA The polymerase chain reaction (PCR) is an artificial method of replicating DNA under
A1 polymerase to laboratory conditions, used to amplify large quantities of a specific sequence of DNA from
produce multiple an initial minute sample
copies of DNA  Each reaction doubles the amount of DNA – a standard PCR sequence of 30
rapidly by the cycles creates over 1 billion copies (230)
polymerase chain
reaction (PCR). The reaction occurs in a thermal cycler and uses variations in temperature to control the
replication process via three steps:
 Denaturation – DNA sample is heated (~90ºC) to separate the two strands
 Annealing – Sample is cooled (~55ºC) to allow primers to anneal (primers
designate sequence to be copied)
 Elongation – Sample is heated to the optimal temperature for a heat-tolerant
polymerase (Taq) to function (~75ºC)

Taq polymerase is an enzyme isolated from the thermophilic

bacterium Thermus aquaticus
 This enzyme is able to function at the high temperatures used in PCR without
denaturing
  Taq polymerase extends the nucleotide chain from the primers – therefore primers
are used to select the sequence to be copied

Summary of a Single PCR Cycle

2.7 Production of The genetic code is universal – almost every living organism uses the same code
A2 human insulin in  As the same codons code for the same amino acids in all living things, genetic
bacteria as an information is transferrable between species
example of the
universality of the The ability to transfer genes between species has been utilised to produce human insulin
genetic code in bacteria (for mass production)
allowing gene  The gene responsible for insulin production is extracted from a human cell
transfer between  It is spliced into a plasmid vector (for autonomous replication and expression)
species. before being inserted into a bacterial cell
 The transgenic bacteria (typically E. coli) are then selected and cultured in a
fermentation tank (to increase bacterial numbers)
 The bacteria now produce human insulin, which is harvested, purified and
packaged for human use (i.e. by diabetics)

Insulin Production via Recombinant Gene Transfer

2.7 Use a table of the

S1 genetic code to
deduce which
codon(s)
corresponds to
which amino acid.

2.7 Analysis of The theory that DNA replication was semi-conservative was confirmed by the Meselson-
S2 Meselson and Stahl experiment in 1958
Stahl’s results to
obtain support for Meselson and Stahl were able to experimentally test the validity of these three models
the theory of semi- using radioactive isotopes of nitrogen
conservative  Nitrogen is a key component of DNA and can exist as a heavier 15N or a
replication of DNA. lighter 14N

DNA molecules were prepared using the heavier 15N and then induced to replicate in the
presence of the lighter 14N
 DNA samples were then separated via centrifugation to determine the composition
of DNA in the replicated molecules

The results after two divisions supported the semi-conservative model of DNA replication
 After one division, DNA molecules were found to contain a mix of 15N and 14N,
disproving the conservative model
 After two divisions, some molecules of DNA were found to consist solely of 14N,
disproving the dispersive model
2.7 Use a table of
S3 mRNA codons and
their corresponding
amino acids to
deduce the
sequence of amino
acids coded by a
short mRNA strand
of known base
sequence.

2.7 Deducing the DNA mRNA → DNA

S4 base sequence for mRNA is a complementary copy of a DNA segment (gene) and consequently can be used
the mRNA strand. to deduce the gene sequence
For converting a sequence from mRNA to the original DNA code, apply the rules of
complementary base pairing:
 Cytosine (C) is replaced with Guanine (G) – and vice versa
 Uracil (U) is replaced by Adenine (A)
 Adenine (A) is replaced by Thymine (T)
 2.8 Cell respiration
2.8 Cell respiration is Cell respiration is the controlled release of energy from organic compounds to produce
U1 the controlled ATP
release of energy  Cell respiration is carried out using enzymes so that as much as possible of the
from organic energy released is retained in a usable form (ATP)
compounds to  ATP is not transferred from cell to cell and all cells require a continuous supply for
produce ATP. energy
Details of the  Therefore, cell respiration is an essential function of life in all cells
metabolic pathways
of cell respiration are C 6 H 12 O6+ 6 O2 → 6 C O2 +6 H 2 O+ ATP
not needed but the
substrates are final
waste products
should be known

2.8 ATP from cell ATP (adenosine triphosphate) is a high energy molecule that functions as an immediate
U2 respiration is source of power for cell processes
immediately  One molecule of ATP contains three covalently linked phosphate groups – which
available as a store potential energy in their bonds
source of energy in  When ATP is hydrolysed (to form ADP + Pi) the energy stored in the phosphate
the cell. bond is released to be used by the cell
 Cell respiration uses energy stored in organic molecules to regenerate ATP from
ADP + Pi

When energy from ATP is used in cells, it is ultimately all converted to heat
 Heat cannot be reused for cell activities and is eventually lost to surroundings
 Thus, cells require a continual source of ATP for cell activities

2.8 Anaerobic Both anaerobic and aerobic respiration pathways begin with the anaerobic breakdown of
U3 respiration gives a glucose in the cytoplasm by glycolysis
small yield of ATP
from glucose. Glycolysis breaks down glucose (6-C) into two molecules of pyruvate (3C), and also
produces:
 A small yield of ATP (net gain of 2 molecules)

Anaerobic Respiration
Anaerobic respiration proceeds in the absence of oxygen and results in a relatively small
 ATP yield
 Anaerobic cell respiration is useful in three situations:
o When a short but rapid burst of ATP production is needed
o When oxygen supplies run out in respiring cells
o In environments that are deficient in oxygen, for example waterlogged soils
 In animals, the pyruvate is converted into lactic acid (or lactate)
 In plants and yeasts, the pyruvate is converted into ethanol and carbon dioxide

2.8 Aerobic cell Aerobic cell respiration requires the presence of oxygen and takes place within
U4 respiration gives a the mitochondrion
small yield of ATP  Pyruvate is broken down into carbon dioxide and water, and a large amount of
from glucose. ATP is produced (~34 – 36 molecules)
 Although aerobic respiration typically begins with glycolysis in carbohydrates,
glycolysis itself is an anaerobic process

2.8 Use of anaerobic Anaerobic respiration (fermentation) involves the breakdown of carbohydrates in
A1 cell respiration in the absence of oxygen
yeasts to produce
ethanol and carbon In yeasts, fermentation results in the production of ethanol and carbon dioxide – which can
dioxide in baking. be used in food processing:
 In bread making, the kneaded dough is kept warm to encourage the yeast to respire
 The oxygen in the dough is soon used up so the yeast is forced to respire
anaerobically
 The carbon dioxide produced by anaerobic cell respiration form bubbles, causing the
dough to swell and rise
 The ethanol produced in the anaerobic cell respiration evaporates during baking

2.8 Lactate production Muscle contractions require the expenditure of high amounts of energy and thus require
A2 in humans when high levels of ATP
anaerobic
respiration is used When exercising at high intensity, the cells’ energy demands will exceed what the
to maximize the available levels of O2 can supply aerobically
power of muscle  Hence the body will begin breaking down glucose anaerobically to maximise ATP
contractions. production

This will result in an increase in the production of lactic acid, which leads to muscle fatigue
 When the individual stops exercising, oxygen levels will increase and lactate will be
converted back to pyruvate

The Effect of Exercise Intensity on Carbohydrate Consumption (and Lactate

Production)
2.8 Analysis of results A respirometer is a device that determines an organism’s respiration rate by measuring
S1 from experiments the rate of exchange of O2 and CO2
involving  The living specimen (e.g. germinating seeds or invertebrate organism) is enclosed
measurement of in a sealed container
respiration rates in  Carbon dioxide production can be measured with a data logger or by pH changes if
germinating seeds the specimen is immersed in water
or invertebrates  When an alkali is included to absorb CO2, oxygen consumption can be measured
using a as a change in pressure within the system
respirometer.  The pressure change can be detected with a data logger or via use of a U-tube
There are many manometer
sample respirometer
which could be use. Factors which may affect respiration rates include temperature, hydration, light (plants),
Student are expected age and activity levels
to know that an alkali  An increase in carbon dioxide levels will indicate an increase in respiration (CO2 is
is used to absorb a product of aerobic respiration)
CO2, so reductions in  A decrease in oxygen levels will indicate an increase in respiration (O2 is a
volume are due to requirement for aerobic respiration)
oxygen use.
Temperature should Schematic of a Simple Respirometer Designed to Measure Oxygen Uptake
be kept constant to
avoid volume
changes due to
temperature
fluctuations.
 2.9 Photosynthesis
2.9 Photosynthesis is Photosynthesis is the process by which cells synthesise organic compounds (e.g. glucose)
U1 the production of from inorganic molecules (CO2 and H2O) in the presence of sunlight
carbon compounds  This process requires a photosynthetic pigment (chlorophyll) and can only occur in
in cells using light certain organisms (plants, certain bacteria)
energy.

Photosynthetic organisms use the light energy from the sun to create chemical energy
(ATP)
 This chemical energy can either be used directly by the organism or used to
synthesise organic compounds (e.g. carbohydrates, proteins and lipids)

Animals then consume these organic compounds as food and release the stored energy
via cell respiration

2.9 Visible light has a The electromagnetic spectrum is the range of all possible frequencies of electromagnetic
U2 range of radiation
wavelengths with  The Sun emits its peak power in the visible region of this spectrum (white light ~
violet the shortest 400 – 700 nm)
wavelength and red  Violet and blue are shorter wavelengths and red is the longest wavelength
the longest.

2.9 Chlorophyll Chlorophyll is a green pigment found in photosynthetic organisms that is responsible for
U3 absorbs red and light absorption
blue light most  When chlorophyll absorbs light, it releases electrons which are used to synthesise
effectively and ATP (chemical energy) (2 H 2 O → 4 e
−¿+4 H
+¿+ O2 ¿
¿
)
reflects green light
more than other
colours. There are a number of different chlorophyll molecules, each with their own absorption
Students should spectra, however collectively:
know that visible light  Chlorophyll absorbs light most strongly in the blue portion of the visible spectrum,
has wavelengths followed by the red portion
between 400 and  Chlorophyll reflects light most strongly in the green portion of the visible spectrum
700 nanometres, but (hence the green colour of leaves)
they are not
expected to recall the
wavelengths of
specific colours of
light.

2.9 Oxygen is Photosynthesis is a two-step process:

U4 produced in Step 1: Light Dependent Reactions - convert light energy from the Sun into chemical
photosynthesis energy (ATP)
from the photolysis  Light is absorbed by chlorophyll, which results in the production of ATP (chemical
of water. energy)
 Light is also absorbed by water, which is split (photolysis) to produce oxygen and
+ ¿+O 2 ¿
−¿+ 4 H ¿
hydrogen ( H 2 O→ 4 e )
 The hydrogen and ATP are used in the light independent reactions, the oxygen is
released from stomata as a waste product
 Step 2: Light Independent Reactions - use chemical energy to synthesise organic
compounds (e.g. carbohydrates)
 ATP and hydrogen are transferred to the site of the light independent reactions
 The hydrogen is combined with carbon dioxide to form complex organic
compounds (e.g. carbohydrates, amino acids, etc.)
 The ATP provides the required energy to power these anabolic reactions and fix
the carbon molecules together

2.9 Energy is needed to To convert carbon dioxide and water into carbohydrates by photosynthesis, energy is
U5 produce required
carbohydrates and  Photosynthesis is a series of chemical reactions that involves putting in energy in
other carbon the form of light – thus is an endothermic reaction
compounds from  The energy for the conversion of CO2 into carbohydrate is obtained by absorbing
carbon dioxide. light
 The energy absorbed from light does not disappear – it is converted to chemical
energy in the carbohydrates

2.9 Temperature, light Temperature

U6 intensity and  Photosynthesis is controlled by enzymes, which are sensitive to temperature
carbon dioxide fluctuations
concentration are  As temperature increases reaction rate will increase, as reactants have greater
possible limiting kinetic energy and more collisions result
factors on the rate  Above a certain temperature the rate of photosynthesis will decrease as essential
of photosynthesis. enzymes begin to denature

Light Intensity
 Light is absorbed by chlorophyll, which convert the radiant energy into chemical
energy (ATP)
 As light intensity increases reaction rate will increase, as more chlorophyll are
being photo-activated
 At a certain light intensity photosynthetic rate will plateau, as all available
chlorophyll are saturated with light
 Different wavelengths of light will have different effects on the rate of
photosynthesis (e.g. green light is reflected)
 Carbon Dioxide Concentration
 Carbon dioxide is involved in the fixation of carbon atoms to form organic
molecules
 As carbon dioxide concentration increases reaction rate will increase, as more
organic molecules are being produced
 At a certain concentration of CO2 photosynthetic rate will plateau, as the enzymes
responsible for carbon fixation are saturated

2.9 Changes to the Approximately 2.3 billion years ago, photosynthetic organisms began to saturate the
A1 Earth’s environment with oxygen, hence changing the oceans, the atmosphere and rock
atmosphere, deposition
oceans and rock
deposition due to Oceans
photosynthesis.  Earth’s oceans initially had high levels of dissolved iron (released from the crust
by underwater volcanic vents)
 When iron reacts with oxygen gas it undergoes a chemical reaction to form an
insoluble precipitate (iron oxide)
 When the iron in the ocean was completely consumed, oxygen gas started
accumulating in the atmosphere

Atmosphere
 For the first 2 billion years after the Earth was formed, its atmosphere was anoxic
(oxygen-free)
 The current concentration of oxygen gas within the atmosphere is approximately
20%

Rock Deposition
 The reaction between dissolved iron and oxygen gas created oceanic deposits
called banded iron formations (BIFs)
 This likely reflects the time when oxygen levels caused the near complete
consumption of dissolved iron levels
 As BIF deposition slowed in oceans, iron rich layers started to form on land due to
the rise in atmospheric O2 levels

Changes to Oxygen Levels on Earth

2.9 Drawing an
S1 absorption
spectrum for
chlorophyll and an
action spectrum for
photosynthesis.

2.9 Design of
S2 experiments to
investigate the
effect of limiting
factors on
photosynthesis.
Water free of
dissolved carbon
dioxide for
photosynthesis
experiments can be
produced by boiling
and cooling water.

2.9 Separation of Photosynthetic organisms do not rely on a single pigment to absorb light, but instead
S3 photosynthetic benefit from the combined action of many
pigments by  These pigments include chlorophylls, xanthophyll and carotenes
chromatograph.
(Practical 4) Chromatography is an experimental technique by which mixtures can be separated
Paper  A mixture is dissolved in a fluid (called the mobile phase) and passed through a
chromatography can static material (called the stationary phase)
be used to separate  The different components of the mixture travel at different speeds, causing them
photosynthetic to separate
pigments but thin  A retardation factor can then be calculated (Rf value = distance component travels
layer ÷ distance solvent travels)
chromatography
gives better results. Overview of the Chromatographic Separation of Photosynthetic Pigments