2.

1 MOLECULES TO METABOLIS

Understandings:
Molecular biology explains living processes in terms of the chemical substances involved
Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist
Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids
Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism
Anabolism is the synthesis of complex molecules from simpler molecules including the formation of
macromolecules from monomers by condensation reactions
Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of
macromolecules into monomers

Applications and skills:

Application: Urea as an example of a compound that is produced by living organisms but can also be arti cially
synthesised
Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised amino acid
Skill: Identi cation of biochemicals such as sugars, lipids or amino acids from molecular diagrams

Guidance:
Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings
Sugars include monosaccharides and disaccharides
Only one saturated fat is expected and its speci c name is not necessary
The variable radical of amino acids can be shown as R. The structure of individual R-groups does not need to be
memorised
Students should be able to recognise from molecular diagrams that triglycerides, phospholipids and steroids are
lipids. Drawings of steroids are not expected
Proteins or parts of polypeptides should be recognised from molecular diagrams showing amino acids linked by
peptide bonds

Aims:
Aim 7: ICT can be used for molecular visualisation of carbohydrates, lipids and proteins in this sub-topic and in
2.3 and 2.4
Aim 6: Food tests such as the use of iodine to identify starch or Benedict’s reagent to identify reducing sugars
could be carried out.
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 2.1 MOLECULES TO METABOLISM

Carbon

- Carbon has a valency of 4 so it can form four covalent bonds with other atoms
- Covalent bonds are strong bonds, so the molecules formed are stable
- A molecule is two or more atoms linked by covalent bonds
- If multiple carbon atoms bond together, chains of atoms can form
- Carbon-based chains can vary in length and be linear, branched, or closed to form rings
- The structure of a molecule determines its function.
Four main classes of organic carbon compounds

- Carbohydrates / Polysaccharides = monosaccharides = carbon, hydrogen and oxyge

- Lipids / Triglycerides = glycerol + fatty acids = carbon, hydrogen and oxyge
- Proteins / Polypeptides = amino acids = carbon, hydrogen, oxygen and nitrogen (sometimes also sulphur
- Nucleic Acids = nucleotides = carbon, hydrogen, oxygen, nitrogen and phosphorus

Need to be able to draw

Metabolism, Anabolism, and Catabolism

Metabolism is all of the enzymatic reactions that take place inside a living organism. Occurs in the cytoplasm of the cell
or outside the cell

Anabolism is the synthesis of complex molecules from simpler molecules. A process that requires the input of energy.
It includes the formation of macromolecules from monomers by condensation reactions

Catabolism is the breakdown of complex molecules into simpler molecules and includes the hydrolysis of
macromolecules into monomers. The breakdown of sugars (including glycolysis) or fats to release energy are
all examples of catabolic reactions. It is a process during which energy is released

Hydrolysis reaction is the breaking of Condensation reaction refers to the reaction in which two smaller
chemical bonds by the addition of water organic molecules combine to form a larger molecule with the
molecules. accompanied formation of water or some other simple molecule.

Urea

It is a component of urine and this was where it was rst discovered. It is produced when there is an excess of amino
acids in the body, as a means of excreting the nitrogen

from the amino acids.
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 2.2 WATE

Understandings:
Water molecules are polar and hydrogen bonds form between them
Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water
Substances can be hydrophilic or hydrophobic

Applications and skills:

Application: Comparison of the thermal properties of water with those of methane
Application: Use of water as a coolant in sweat
Application: Modes of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood in
relation to their solubility in water

Guidance:
Students should know at least one example of a bene t to living organisms of each property of water
Transparency of water and maximum density at 4°C do not need to be included
Comparison of the thermal properties of water and methane assists in the understanding of the signi cance of
hydrogen bonding in water

Aims:
Aim 6: Probes can be used to determine the effect of different factors likely to in uence cooling with water.
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 2.2 WATER
Hydrogen bonding in water

- Each hydrogen atom is joined onto the oxygen atom by a covalent bond
- The shared pair of electrons forming each covalent bond is pulled towards the oxygen nucleus and away from each
hydrogen nucleus
- Thus, the oxygen has a slight negative charge ( -) and the hydrogen atoms have a slight positive charge ( +)
- The triangular shape of the molecule results in positive and negative regions (or poles)
- Polar molecules are neutral but there is an uneven distribution of charge
- Water exhibits dipolarity, as there are two poles
Hydrophilic
- Attracted to water molecules
- Include polar molecules (such as glucose
and amino acids) and ions
- Typically soluble in water

Hydrophobic
- Not attracted to water molecules
- Include non-polar molecules (such as
lipids)
- Not soluble in water.

Properties of Water

- Cohesion - This is the tendency of water molecules to stick to each other due to the hydrogen bonding between
them. Each water molecule can potentially form four hydrogen bonds with other water molecules in a tetrahedral
arrangement. Although hydrogen bonds are weak bonds, the presence of a large number of hydrogen bonds in water
gives the cohesive forces great strength. This in turn is responsible for the high surface tension of water
- e.g: Allows water to be pulled up from the roots to the leaves of plants

- Adhesion - This is the interaction that water molecules have with other (different) molecules and explains why water
molecules stick to other polar compounds by forming hydrogen bonds. Forces of adhesion are responsible for
capillary action, which is de ned as the movement of water molecules (and all the things that are dissolved in it)
within thin spaces without relying on gravity
- e.g: Capillary action generated by adhesive forces assists the pumping action of the heart to help blood move
through blood vessels.

- Thermal - Water molecules have hydrogen bonds between them, creating the cohesive property of water.
 Evaporating water involves breaking these bonds, and therefore removes energy from the surroundings. This makes
water a great coolant. Since all living organisms have to maintain a certain temperature range, water plays an
essential role in the temperature regulation of living organisms.
- High speci c heat capacit
- High latent heat of vaporisatio
- High boiling poin
- e.g: Evaporation of sweat from body surfaces involves heat loss, which brings about a cooling effect.

- Solvent - Due to the bipolarity of each water molecule, water is a polar solvent. Polar molecules and ions are soluble
- e.g: Water dissolves mineral ions in the soil and transports it along xylem vessels from the roots to all parts of the
plant. 

Modes of transport in blood

- Glucose and amino acids
- Both are polar molecules and soluble in the blood plasm
- Cholesterol and fats
- These are non-polar and are insoluble in blood plasma. Following absorption, cholesterol and fats form droplets
surrounded by proteins and phospholipids so they can be transported in the blood
- Oxygen
- Is small and non-polar. Some oxygen can dissolve in the blood plasma but not in suf cient quantities. Hemoglobin
has the role of transporting oxygen in red blood cells
- Sodium Chloride
- Sodium chloride is soluble in the blood plasma and is transported as Na+ and Cl- ions.
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 2.3 CARBOHYDRATES AND LIPID

Understandings:
Monosaccharide monomers are linked together by condensation reactions to form disaccharides and
polysaccharide polymers
Fatty acids can be saturated, monounsaturated or polyunsaturated
Unsaturated fatty acids can be cis or trans isomers
Triglycerides are formed by condensation from three fatty acids and one glycerol

Applications and skills:

Application: Structure and function of cellulose and starch in plants and glycogen in humans
Application: Scienti c evidence for health risks of trans fats and saturated fatty acids
Application: Lipids are more suitable for long-term energy storage in humans than carbohydrates
Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about
lipids
Skill: Use of molecular visualization software to compare cellulose, starch and glycogen
Skill: Determination of body mass index by calculation or use of a nomogram

Guidance:
The structure of starch should include amylose and amylopectin
Named examples of fatty acids are not required
Sucrose, lactose and maltose should be included as examples of disaccharides produced by combining
monosaccharides

International-mindedness:
Variation in the prevalence of different health problems around the world could be discussed including obesity,
dietary energy de ciency, kwashiorkor, anorexia nervosa and coronary heart disease

Theory of knowledge:
There are con icting views as to the harms and bene ts of fats in diets. How do we decide between competing
views

Utilization:
Potatoes have been genetically modi ed to reduce the level of amylose to produce a more effective adhesive.
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2.3 CARBOHYDRATES AND LIPID

Glucose, fructose and ribose are all examples of monosaccharides.

Monosaccharides can be linked together to make larger molecules

• Monosaccharides are single sugar units.

• Disaccharides consist of two monosaccharides linked together. For example, maltose is made by linking two glucose
molecules together. Sucrose is made by linking a glucose and a fructose.
• Polysaccharides consist of many monosaccharides linked together. Starch, glycogen and cellulose are
polysaccharides. They are all made by linking together glucose molecules.

Condensation Reactions

When monosaccharides combine, they do so by a process called condensation. This involves the loss of an –OH from
one molecule and an –H from another molecule, which together form H2O. Thus, condensation involves the
combination of subunits and yields water. Linking together monosaccharides to form disaccharides and polysaccharides
is an anabolic process and energy has to be used to do it. ATP supplies energy to the monosaccharides and this energy
is then used when the condensation reaction occurs
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 Structure and function of polysaccharides

- Polysaccharides have an important role in the supply and storage of energy. (starch in plants, glycogen in animals
- Polysaccharides can also be used as a structural component. (cellulose in plant walls
- All these polymers have glucose as their monomer subunit. However, the latter can either be the α-D or β-D type
- The other important difference between starch, cellulose and glycogen lies in how the glycosidic bonds between the
glucose units have been formed. When the bond formed between two monomers involves the rst carbon of one
molecule and the fourth carbon of the other, a 1,4 glycosidic bond is formed. However, if the bond is formed between
the rst carbon of a molecule and the sixth carbon of another, a 1,6 glycosidic bond is formed

Cellulose
Function - cellulose molecules
associate to form the cell wall
of plant
1,4 glycosidic bonds, therefore
unbranched

Starch
Function - to store glucos
Large molecule, so insoluble
Branched structure of
amylopectin means it has many
ends, allowing it to be easily
made and broken down

Glycogen
Function - to store glucos
Large and compact, insoluble
Lots of 1,6 bonds = highly
branche
Branches allow it to be broken
down quickly, to supply glucose
for cell respiration.

Fatty Acids

Fatty acids are carboxylic acids, that is, they possess a -COOH (functional) group attached to a hydrocarbon chain.
They come in three basic forms: saturated, monounsaturated and polyunsaturated
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 Lipids and energy storage

The advantages of lipids over carbohydrates for energy storage are twofold; they have a higher energy content, and
they can act as thermal insulators

Fatty Acids - Condensation Reactions

Lipids - Impact on Health:

• Being overweight or obese increases the risk of developing type 2 diabetes, coronary heart disease (CHD) and
certain types of cancer
• There is considerable scienti c evidence linking the consumption of trans fats and saturated fats to the incidence of
CHD.
• The hypothesis is that the trans fats and saturated fats contribute to the formation of atherosclerotic plaques in
arteries which in turn lead to heart attack.
• This is supported by evidence obtained from patients who died from CHD that shows that high concentrations of trans
fats are present in fatty deposits in diseased arteries
• There is a strong correlation between the consumption of saturated fatty acids and the incidence of CHD.
Body Mass Index

BMI can also be found using a nomogram (opposite):

 

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 2.4 PROTEIN

Nature of science:
Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino
acids. (3.1

Understandings:
Amino acids are linked together by condensation to form polypeptides
There are 20 different amino acids in polypeptides synthesised on ribosomes
Amino acids can be linked together in any sequence giving a huge range of possible polypeptides
The amino acid sequence of polypeptides is coded for by genes
A protein may consist of a single polypeptide or more than one polypeptide linked together
The amino acid sequence determines the three-dimensional conformation of a protein
Living organisms synthesise many different proteins with a wide range of functions
Every individual has a unique proteome

Applications and skills:

Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of
protein functions
Application: Denaturation of proteins by heat or by deviation of pH from the optimum
Skill: Drawing molecular diagrams to show the formation of a peptide bond

Guidance:
The detailed structure of the six proteins selected to illustrate the functions of proteins is not needed
Egg white or albumin solutions can be used in denaturation experiments
Students should know that most organisms use the same 20 amino acids in the same genetic code although
there are some exceptions. Speci c examples could be used for illustration

Utilisation:
Proteomics and the production of proteins by cells cultured in fermenters offer many opportunities for the food,
pharmaceutical and other industries
Aims:
Aim 7: ICT can be used for molecular visualisation of the structure of proteins
Aim 8: Obtaining samples of human blood for immunological, pharmaceutical and anthropological studies is an
international endeavour with many ethical issues.
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 2.4 PROTEINS

Polypeptides

• Polypeptides are chains of linked peptides that are made by linking together amino acids by condensation reactions.
This happens on ribosomes by a process called translation.
• Polypeptides are the main component of proteins and in many proteins they are the only component. Some proteins
contain one polypeptide and other proteins contain two or more.
• 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 amino
acids, called a peptide bond.
• A dipeptide is a molecule consisting of two amino acids linked by a peptide bond. A polypeptide is a molecule
consisting of many amino acids linked by peptide bonds.

Amino Acids in Proteins

• 20 different amino acids are used by ribosomes to make polypeptides.

• Can be linked together in any sequence to form polypeptides
• The amine groups and the carboxyl groups are used up in forming the peptide bond, so it is the R groups of the amino
acids that give a polypeptide its character.
• Theoretically, 20ⁿ different types of polypeptides can be formed, where n is the number of amino acids per
polypeptide

Most organisms make proteins using the same 20 amino acids. In some cases amino acids are modi ed after a
polypeptide has been synthesised, but the initial process of linking together amino acids on ribosomes with peptide
bonds usually involves the same 20 amino acids.

Genes and Polypeptides

• Genes are the coding sections of a genome

• The amino acid sequence of each polypeptide is stored in a coded form in the base sequence of a gene
• A gene normally codes for one polypeptide, and each polypeptide has one function, however
• Genes may be alternatively spliced to generate multiple polypeptide variants
• Genes encoding tRNA sequences are transcribed but never translated
• Genes may be mutated and consequently produce an alternative polypeptide sequence
• Since genes are found in the nucleus and polypeptides are synthesised in the cytoplasm, a molecule containing the
speci c instructions, called mRNA, is rst made. This then carries the instructions for the amino acid sequence to the
ribosome (found in the cytoplasm)
• Three bases of the gene are needed to code for each amino acid in the polypeptide
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A protein may consist of a single polypeptide or more than one polypeptide linked together

Protein Conformations:

β α

• Polypeptides fold up into three-dimensional structures after being synthesised

• Most fold up into a compact, globular shape
• Each different polypeptide has a unique conformation, which gives a protein its speci c function
• The way a protein folds up depends on the sequence of amino acids
• The same polypeptide will always fold up the same way
• Intramolecular bonds link non-adjacent amino acids to form a stable three-dimensional shape
• If a protein is soluble, amino acids with hydrophilic R groups are on the outside and one with hydrophobic R groups
are in the centre.
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 The Proteome

• A proteome is all of the proteins produced by a cell, a tissue or an organism.

• Because proteins are coded by genes, a different genome will lead to a different proteome
• The proteome can change during development or in response to environmental factors.
• To nd out how many different proteins are being produced, mixtures of proteins are extracted from a sample and are
then separated into by their size and charge by two-dimensional gel electrophoresis.
• To identify whether or not a particular protein is present, antibodies to the protein that have been linked to a
uorescent marker can be used. If the cell uoresces, the protein is present.

Protein Functions

Protein Function Description

Rubisco Enzyme • Catalyses the xation of inorganic carbon dioxide from the
atmosphere into carbon compounds
• This is the rst major step in the production of organic compounds by
photosynthesis.

Insulin Hormone • Regulates blood glucose levels

• A messenger that is secreted by the pancreas and transported in the
blood.

Immunoglobin Antibody • Helps to destroy pathogens

• Produced as part of a speci c immune response.
Rhodopsin Pigment • A light sensitive pigment present in rods, a type of photoreceptor.

Collagen Structural • Collagen is a protein made of three polypeptide chains twisted around
each other
• It is strong, exible and used in ligaments, tendons, and blood
vessels.

Spider silk Structural • Spiders use silk to suspend themselves and make webs to catch prey
• It can stretch without breaking.

Denaturation of Proteins

When a protein is denatured it loses its three-dimensional shape. This results in the loss of function

Denaturation by Heat
• Heat causes the atoms within the protein to vibrate
• If the vibrations are great enough, then the intramolecular interactions between amino acids begin to break
• This results in a permanent loss of shape
- The soluble protein albumin is present in raw eggs, when the egg is cooked the albumin is denatured and
becomes insoluble

Denaturation by pH
• Each protein has a pH range in which it has its normal three-dimensional shape
• Changes away from this pH range cause intramolecular interactions between amino acids to break
• Denaturation caused by mild changes to pH can be reversible
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 2.5 ENZYME

Nature of science:
Experimental design—accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability.
(3.2

Understandings:
Enzymes have an active site to which speci c substrates bind
Enzyme catalysis involves molecular motion and the collision of substrates with the active site
Temperature, pH and substrate concentration affect the rate of activity of enzymes
Enzymes can be denatured
Immobilised enzymes are widely used in industry

Applications and skills:

Application: Methods of production of lactose-free milk and its advantages
Skill: Design of experiments to test the effect of temperature, pH and substrate concentration on the activity of
enzymes
Skill: Experimental investigation of a factor affecting enzyme activity. (Practical 3

Guidance:
Lactase can be immobilised in alginate beads and experiments can then be carried out in which the lactose in
milk is hydrolysed
Students should be able to sketch graphs to show the expected effects of temperature, pH and substrate
concentration on the activity of enzymes. They should be able to explain the patterns or trends apparent in these
graphs

Theory of knowledge:
Development of some techniques bene ts particular human populations more than others. For example, the
development of lactose-free milk available in Europe and North America would have greater bene t in Africa/Asia
where lactose intolerance is more prevalent. The development of techniques requires nancial investment.
Should knowledge be shared when techniques developed in one part of the world are more applicable in
another
Utilisation:
Enzymes are extensively used in industry for the production of items from fruit juice to washing powder.
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2.5 ENZYME

Enzymes - Overview

• Enzymes are globular proteins with a compact three-dimensional conformation

• Enzymes are biological catalysts, they speed up chemical reactions
• All the reactions of metabolism are catalysed by enzymes
• Every different metabolic reaction needs a different enzyme because enzymes are highly speci c

Enzymes - Active Site

• A region on an enzyme called the active site is where the substrate binds to the enzyme
• The shape of the active site must be complementary to the shape of the substrate
• This is called enzyme-substrate speci city. (See lock and key hypothesis
• The substrate chemically interacts with amino acids comprising the active site, therefore the substrate and the active
site must also chemically t together
• After the products are released from the active site, the enzyme can bind to another substrate
• Some enzymes have two substrates that bind to different parts of the active site

Induced Fit
• When the substrate enters the active site, it triggers a change in the three-dimensional shape of the enzyme that
allows a tighter t.
• This is called an induced t and is possible because of the exibility of the protein molecules that make up the
enzyme.
• When the enzyme and substrate(s) t together tightly, the enzyme induces the weakening of bonds within the
molecules of the substrate(s), thus reducing the activation energy needed for the reaction.
• When the enzyme-catalysed reaction is completed, the products are released from the enzyme.
Enzyme Activity

• Enzyme-catalysed reactions occur in solutions (such as the cytoplasm)

• Components of the solution are in constant, random motion
• For a reaction to occur, the substrate must collide with and bind to the active site of the enzyme
• For a reaction to start, energy input is needed
• Binding to the active site lowers the amount of energy needed to start the reaction (activation energy).

Substrate Concentration

• Increasing substrate concentration causes more frequent collisions between the substrate and the active site
• This increases enzyme activity.
• At a certain substrate concentration, a maximum enzyme activity is reached.
Denaturation of Enzymes
Temperature: pH:

• As temperature increases so does the movement of • The optimum pH is the maximum enzyme activity
the substrate and enzyme molecules • Changes away from the optimum pH cause enzyme
• More frequent collisions occur between the substrate activity to reduce
and the active sites of the enzymes • Subtle changes in pH may interfere with chemical
• Enzyme activity increases (doubles every 10ºC) interactions between the enzyme and the active site
• The optimum temperature is the maximum enzyme • This slows enzyme activity
activity • Greater changes to the pH will cause intramolecular
• As the temperature increases, vibrations in the interactions to break
enzyme molecule increase, causing intramolecular • This causes the active site to change shape,
interactions to break meaning substrate can no longer bind to it
• This causes the active site to change shape, • The enzyme is denatured.
meaning the substrate can no longer bind to it
• The enzyme is denatured
• The lower the enzyme activity, the greater the
proportion of enzymes denatured.
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 Rate of Enzyme Activity

You should be able to sketch graphs to show the

expected effects of temperature, pH and substrate
concentration on the activity of enzymes.
You should also be able to explain the patterns or
trends apparent in these graphs.

Lactose-Free Milk

• Lactose is a disaccharide found in milk

• Lactose catalyses the hydrolysis of lactose to glucose and galactose
• Lactase can be puri ed from microorganisms that live in milk

Method 1
• Add lactase (an enzyme) to milk

Method 2
• Immobilise lactase in alginate beads
• Many beads can then be placed into a syringe barrel to form a column of beads
• Milk ows through the column at a controlled rate to produce lactose-free milk

Advantages of Lactose-Free milk

• Some people are lactose-intolerant
• Milk containing glucose and galactose is sweeter
• Making yoghurt is quicker
• Makes smoother ice cream.
Immobilising Enzymes

Methods of immobilising enzymes

• Adsorption - enzyme attached to surface of an absorbing agent, such as glass beads
• Entrapment - the enzyme is trapped within gels or bres (such as alginate beads)
• Cross-linking - the enzymes are chemically linked together to form aggregates

Advantages of Immobilisation:
• Enzyme can easily be re-used many times
• No need to isolate enzymes from products
• Immobilised enzymes are more stable (less likely to denature)
• The reaction can be immediately stopped by removing the enzyme.
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 2.6 STRUCTURE OF DNA AND RN

Nature of science:
Using models as representation of the real world—Crick and Watson used model making to discover the structure of
DNA. (1.10

Understandings:
The nucleic acids DNA and RNA are polymers of nucleotides
DNA differs from RNA in the number of strands present, the base composition and the type of pentose
DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between
complementary base pairs

Applications and skills:

Application: Crick and Watson’s elucidation of the structure of DNA using model making
Skill: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons
and rectangles to represent phosphates, pentoses and bases

Guidance:
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 of
the purine and pyrimidine bases do not need to be recalled, nor the numbers of hydrogen bonds between the
base pairs

Theory of knowledge:
The story of the elucidation of the structure of DNA illustrates that cooperation and collaboration among scientists
exists alongside competition between research groups. To what extent is research in secret ‘anti-scienti c’? What
is the relationship between shared and personal knowledge in the natural sciences?
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 2.6 STRUCTURE OF DNA AND RNA

Nucleotides

A nucleotide is made up of three parts joined by covalent bonds

1. A phosphate grou
2. A pentose (5 carbon) sugar
3. A nitrogenous base

The nucleotide units link together through a phosphodiester

bond (a covalent bond) to form a single strand, a polynucleotide.
The phosphodiester bond is always formed between the phosphate
group attached to the 5'-C of one sugar and the hydroxyl (OH)
group attached to the 3'-C of another sugar

3' and 5' refer to the carbon position on the sugar in DNA. Carbon 1 is attached to the base and from there on carbon
atoms are counted in a clockwise direction.

DNA
• Complementary base pairing means
- Guanine always pairs with Cytosin
- Adenine always pairs with Thymine.
• DNA normally forms an alpha helix (meaning right turning).
• The two strands are antiparallel.
- One strand runs from 5' to 3', and the other strand runs in the opposite direction, from 3' to 5’

Crick and Watson used X-ray diffraction patterns of DNA to solve the structure of DNA by building a model.
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 2.7 DNA REPLICATION, TRANSCRIPTION AND TRANSLATIO

Nature of science:
Obtaining evidence for scienti c theories—Meselson and Stahl obtained evidence for the semi-conservative replication of
DNA. (1.8

Understandings:
The replication of DNA is semi-conservative and depends on complementary base pairing
Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds
DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template
Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase
Translation is the synthesis of polypeptides on ribosomes
The amino acid sequence of polypeptides is determined by mRNA according to the genetic code
Codons of three bases on mRNA correspond to one amino acid in a polypeptide
Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA

Applications and skills:

Application: Use of Taq DNA polymerase to produce multiple copies of DNA rapidly by the polymerase chain
reaction (PCR)
Application: Production of human insulin in bacteria as an example of the universality of the genetic code allowing
gene transfer between species
Skill: Use a table of the genetic code to deduce which codon(s) corresponds to which amino acid
Skill: Analysis of Meselson and Stahl’s results to obtain support for the theory of semi-conservative replication of
DNA
Skill: Use a table of
mRNA codons and
their corresponding
amino acids to
deduce the
sequence of amino
acids coded by a
short mRNA strand
of known base
sequence
Skill: Deducing the
DNA base
sequence for the
mRNA strand

Guidance:
The different types
of DNA
polymerase do not
need to be
distinguished

Aims:
Aim 8: There are
ethical implications
in altering the
genome of an
organism in order
to produce proteins
for medical use in
humans
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 2.7 DNA REPLICATION, TRANSCRIPTION AND TRANSLATION

DNA Replication
• DNA replication occurs in the S phase of interphase
• From one parent DNA molecule, two daughter DNA molecules are made
• Each strand of the parent DNA molecule acts as a template to make a
new strand
• Each new molecule of DNA has one old strand (from the parent DNA
molecule) and one new strand
• Due to the fact that each of the parent DNA strands are complementary,
complementary base pairing ensures the two new DNA molecules will be
identical to the parent DNA molecule.

The Process
I. Helicase unwinds the double helix
II. Helicase breaks hydrogen bonds, separating the two strands of the
DNA molecule
III. Each strand acts as a template
IV. Free DNA nucleotides pair up with their complementary bases in each
template strand
V. Adenine with thymine and guanine with cytosine
VI. DNA polymerase forms each new strand by joining nucleotides together
with covalent bonds between the sugar and the phosphate. DNA
polymerase always moves along the template strand in the same
direction, adding one nucleotide at a time.
VII. Two identical DNA molecules are formed.

Polymerase Chain Reaction (PCR):

• The polymerase chain reaction (PCR) is a technique

used to make many copies of a selected DNA
sequence.
• The rst step of each PCR cycle is to separate DNA
strands by heating to 94ºC (to break the hydrogen
bonds)
• This temperature would denature DNA polymerase
isolated from nearly all organisms
• A heat-stable DNA polymerase has been isolated
from a bacterium, Thermus aquaticus, that lives in
hot volcanic springs
• Taq DNA polymerase has an optimum temperature
of 72ºC and is not denatured at 94ºC.

Transcription:

• Transcription is the synthesis of RNA, using DNA as a template, occurs in the nucleus of eukaryotic cells
• Because RNA is single-stranded, transcription only occurs along one of the two strands of DNA

The Process:
I. RNA polymerase binds to a site on the DNA at the start of a gene
II. RNA polymerase moves along the gene unwinding DNA into single strands and pairing up RNA nucleotides with
complementary bases on one strand of the DNA. There is no thymine in RNA, so uracil pairs in a complementary
fashion with adenine.
III. RNA polymerase forms covalent bonds between the RNA nucleotides
IV. The RNA separates from the DNA and the double helix reforms
V. Transcription stops at the end of the gene and the completed RNA molecule is released
VI. The product of transcription is a molecule of RNA with a base sequence that is complementary to the template
strand of DNA
VII. The DNA strand with the same base sequence as the RNA is called the sense strand. The other strand that acts as
the template and has a complementary base sequence to both the RNA and the sense strand is called the
antisense strand.
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 Transcription:

Translation

• Translation is the synthesis of a polypeptide, with an amino acid sequence determined by the base sequence of a
molecule of RNA
• Translation takes place on ribosomes
• Transfer RNA (tRNA) is involved in decoding the base sequence of mRNA into an amino acid sequence during
translation and ribosomal RNA (rRNA) is part of the structure of the ribosome

Codons
• A sequence of three bases on the mRNA is called a codon. Each codon codes for a speci c amino acid to be added
to the polypeptide.
• The sequence of the codons on the mRNA determines the amino acid sequence of the polypeptide made
• The genetic code is degenerate, which means that there are some amino acids that are encoded by more than one
codon
• There are 64 possible codons

Codons and Anticodons

• mRNA has a sequence of codons that speci es the amino acid sequence of the polypeptid
• tRNA molecules have an anticodon of three bases that binds to a complementary codon on mRNA and they carry the
amino acid corresponding to that codon
• Ribosomes act as the binding site for mRNA and tRNAs and also catalyse the assembly of the polypeptide

Process of Translation:

I. An mRNA binds to the small subunit of the ribosome

II. A molecule of tRNA with an anticodon complementary to the rst codon to be translated on the mRNA binds to the
ribosome
III. A second tRNA with an anticodon complementary to the second codon on the mRNA then binds. A maximum of two
tRNAs can be bound at the same time
IV. The ribosome transfers the amino acid carried by the rst tRNA to the amino acid on the second tRNA, by making a
new peptide bond. The second tRNA is then carrying a chain of two amino acids – a dipeptide
V. The ribosome moves along the mRNA so the rst tRNA is released, the second becomes the rst
VI. Another tRNA binds with an anticodon complementary to the next codon on the mRNA
VII. The ribosome transfers the chain of amino acids carried by the rst tRNA to the amino acid on the second tRNA, by
making a new peptide bond
VIII.The process continues along the mRNA until a stop codon is reached, when the completed polypeptide is released
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 2.8 CELL RESPIRATIO

Nature of science:
Assessing the ethics of scienti c research—the use of invertebrates in respirometer experiments has ethical implications.
(4.5

Understandings:
Cell respiration is the controlled release of energy from organic compounds to produce ATP
ATP from cell respiration is immediately available as a source of energy in the cell
Anaerobic cell respiration gives a small yield of ATP from glucose
Aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose

Applications and skills:

Application: Use of anaerobic cell respiration in yeasts to produce ethanol and carbon dioxide in baking
Application: Lactate production in humans when anaerobic respiration is used to maximise the power of muscle
contractions
Skill: Analysis of results from experiments involving measurement of respiration rates in germinating seeds or
invertebrates using a respirometer

Guidance:
Details of the metabolic pathways of cell respiration are not needed but the substrates and nal waste products
should be known
There are many simple respirometers which could be used. Students are expected to know that an alkali is used
to absorb CO2, so reductions in volume are due to oxygen use. Temperature should be kept constant to avoid
volume changes due to temperature uctuations

Aims:
Aim 8: The ethics of the use of animals in experiments could be discussed in relation to respirometer
experiments. Large-scale use of food plants for biofuels and the resulting impact on food prices has ethical
implications.
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2.8 CELL RESPIRATION

• Cell respiration is the controlled release of energy from organic compounds in a series of reactions to form ATP
• Cell respiration occurs in every cell
• ATP is an immediate source of energy for cell processes.
Uses of ATP

• Active transpor
• Muscle contractio
• Nerve impulse
• Synaptic transmissio
• Building large molecules by condensation reactions, e.g: polypeptides

Aerobic vs Anaerobic Respiration

Feature Aerobic Respiration Anaerobic
Respiration

Oxygen required. Yes No

Substrate Glucose, lipids, or Glucose

proteins.

Final waste products. Carbon dioxide and Yeast: Ethanol and

water. carbon dioxid
Humans: Lactic acid

Cell locations of Cytoplasm and Cytoplasm

reaction. mitochondria.

ATP yield (per High Low

glucose)

Aerobic Anaerobic:

Yeast and cell respiration

• Yeast is mixed with our and water to make a dough
• Yeast starts to respire aerobically producing carbon dioxide and water
NEED TO ADD IN THE
• The oxygen is used up
• Yeast respires anaerobically producing carbon dioxide and ethanol
RESPIROMETER THING!
• Tiny pockets of carbon dioxide form in the elastic dough
• The dough rises
• When the dough is heated in the baking process, the pockets of carbon dioxide expand greatly to give the nal
product a spongy texture
• The ethanol evaporates in the baking process.
Anaerobic respiration in muscles
• An intense activity, such as sprinting, requires rapid and powerful muscle contractions over a short time
• Anaerobic respiration can be used to supply ATP to muscles during intense exercise
• Small amounts of ATP can be produced quickly, without the need of oxygen
• However, only for short periods of time (approximately one minute)
• Lactic acid (or lactate) is produce
• Lactic acid accumulates in the blood, limits the period of anaerobic respiration, and creates the oxygen debt.
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 2.9 PHOTOSYNTHESI

Nature of science:
Experimental design—controlling relevant variables in photosynthesis experiments is essential. (3.1

Understandings:
Photosynthesis is the production of carbon compounds in cells using light energy
Visible light has a range of wavelengths with violet the shortest wavelength and red the longest
Chlorophyll absorbs red and blue light most effectively and re ects green light more than other colours
Oxygen is produced in photosynthesis from the photolysis of water
Energy is needed to produce carbohydrates and other carbon compounds from carbon dioxide
Temperature, light intensity and carbon dioxide concentration are possible limiting factors on the rate of
photosynthesis

Applications and skills:

Application: Changes to the Earth’s atmosphere, oceans and rock deposition due to photosynthesis
Skill: Drawing an absorption spectrum for chlorophyll and an action spectrum for photosynthesis
Skill: Design of experiments to investigate the effect of limiting factors on photosynthesis
Skill: Separation of photosynthetic pigments by chromatograph. (Practical 4

Guidance:
Students should know that visible light has wavelengths between 400 and 700 nanometres, but they are not
expected to recall the wavelengths of speci c colours of light
Water free of dissolved carbon dioxide for photosynthesis experiments can be produced by boiling and cooling
water
Paper chromatography can be used to separate photosynthetic pigments but thin layer chromatography gives
better results
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 2.9 PHOTOSYNTHESIS

Photosynthesis is the production of organic carbon compounds in cells using light energy
• Carbon dioxide + water → glucose + oxyge
• Chlorophyll is the main light absorbing pigment in photosynthetic organisms
• Three kingdoms of organisms can photosynthesise
- Plant
- Some protoctists. E.g: alga
- Some bacteria. E.g: cyanobacteri
• In plants, the process of photosynthesis occurs in organelles called chloroplasts.

How did photosynthesis change young Earth?

• Before the rst photosynthetic organisms, the Earth’s atmosphere contained only small amounts of oxygen.
• About 2.3 billion years ago, oxygen began to build up in the atmosphere (up to about 2%).
• Due to vast numbers of photosynthetic bacteria (cyanobacteria).
• Before oxygen began to build up in the atmosphere, there was much iron dissolved in the oceans;
• Cyanobacteria began producing oxygen in the ocean about 3.5 billion years ago.
• The dissolved iron reacted with the oxygen to form insoluble iron oxide
• Iron oxide was deposited on the ocean oor.
• This formed rocks called banded iron formations.
• Oxygen began to build up in the atmosphere only after all the dissolved iron formed iron oxide.
• Evolution of land plants led to much greater increases in atmospheric oxygen from about 650 million years ago.

Wavelengths of Light

• Visible light is a very small fraction of the electromagnetic spectrum

• Visible light ranges from 400 nm to 700 nm
- 400 nm light has the shortest wavelength and is viole
- 700 nm has the longest wavelength and is red

Absorption spectrum shows which wavelength of visible light is absorbed by a particular photosynthetic pigment such
as chlorophyll a or b
Action spectrum shows the ef ciency of photosynthesis or rate of photosynthesis achieved over the various
wavelengths of light from the visible spectrum

Absorption spectrum for chlorophyll:

• Chlorophyll pigments mainly absorb blue and red light, and re ects green light.

Action spectrum for photosynthesis:

• The highest rates of photosynthesis are when exposed to blue and red light.
• The peaks match with the absorption spectrum, which is good evidence that chlorophyll is the main pigment
responsible for photosynthesis.
• Low rated of photosynthesis between blue and red light show that other pigments also play a role in absorbing light.
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How photosynthetic pigments are separated by chromatography:

1. Cut up leaves.
2. Grind leaves in a pestle and mortar with a pinch of sand and a few drops of propane (a solvent).
3. Draw a pencil line 3 cm from the bottom of a strip of chromatography paper or a Thin Layer Chromatography strip
(TLC will give better results).
4. With a glass capillary tube, spot the extracted pigment onto the pencil line (to achieve one small concentrated spot).
5. Add a small volume of propane to a beaker and suspend the chromatography strip in the beaker.
6. Remove the strip when the propane is near the top of the strip. Mark the distance moved by the solvent.
7. Calculate the Rf value for each spot using the following equation: Rf = distance moved by spot / distance moved by
solvent.
8. The distance travelled by each pigment depends on its solubility in the solvent used.

Reactions of Photosynthesis

Stage 1 (the light-dependent stage of photosynthesis

• Light energy, absorbed by chlorophyll, is used to split water molecules, in a process known as photolysis
• To produce ATP, hydrogen, electrons, and oxygen
• Oxygen is the waste product of photosynthesis

Stage 2 (the light-independent stage of photosynthesis

• Rubisco catalyses the xation of carbon dioxide
• The hydrogen and electrons react with carbon dioxide to produce carbohydrate molecules
• Energy is needed to enable this reaction and is supplied by ATP
• The carbohydrate produced can form glucose and other carbon compounds.
Limiting factors in Photosynthesis:

A limiting factor is the factor that is in the shortest supply, thus limiting the reaction.

In photosynthesis, the three possible limiting factors are:

1. Temperature.
2. Carbon. dioxide concentration.
3. Light intensity.

For example, if a plant is at a suitable temperature, has plentiful carbon dioxide, but the light intensity is low, light
intensity would be the limiting factor.

The effect of temperature on the rate of photosynthesis:

• As temperature increases, photosynthetic rate increases.
• Maximum rate of photosynthesis at the optimum temperature.
• At high temperatures (over 40˚C), photosynthesis slows as enzymes involved i
the reactions of photosynthesis denature.
• At high and low temperatures temperature is a limiting factor of photosynthesis.
• At the optimum temperature, another factor will be limiting the rate of reaction.
The effect of carbon dioxide concentration on the rate of photosynthesis:
• Carbon dioxide is normally present in low concentrations (0.04% in air) and the
rate of photosynthesis is low.
• There is a low frequency of collision between carbon dioxide (substrate) and
rubisco (enzyme).
• As the concentration of carbon dioxide rises, the rate of photosynthesis increases
(more frequent collisions).
• The rate of photosynthesis plateaus (when a maximum rate of carbon xation is
reached).
• increasing the concentration further will have no effect.
• Another factor is then limiting.

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The effect of light intensity on the rate of photosynthesis:

• As light intensity increases, photosynthetic rate increases.
• Light provides the energy to drive photosynthesis.
• At high light intensity, photosynthesis reaches a maximum rate (it plateaus).
• Increasing the light intensity further will have no effect on the rate.
• All the chlorophyll molecules are saturated with light.
• Another factor becomes limiting.
• Light is not typically a limiting factor for photosynthesis.
How the rate of photosynthesis is measured accurately:
• The rate of photosynthesis can be directly measured by the production of oxygen.
• Cut a piece of pondweed (such as Elodea).
• Submerge in water with the cut stem upwards.
• Oxygen bubbles form at the cut stem and rise to the surface.
• Record the number of bubbles per minute.
• Alternatively, measure the volume of oxygen produced over a period of time.