2.1.

2 a how hydrogen bonding occurs between water molecules, and relate this, and other
properties of water, to the roles of water for living organisms

Bonding:

 Water is composed of hydrogen and oxygen. One atom of oxygen combines with
two atoms of hydrogen by sharing electrons.
 The sharing of electrons is uneven between O2∧H . Oxygen attracts the electrons
more strongly because it is more electronegative and so it has a negatively charged
region δ- and positively charged region for H, δ+
 Water = polar molecule. Bc, it has an overall dipole (electrons unevenly
distributed)

Properties of water:

 An excellent solvent – many substances can dissolve in water:

o as it is a polar molecule, many ions will dissolve in it so chemical reactions
within cells can occur.
 A relatively high specific heat capacity
o the amount of thermal energy required to raise the temperature of 1kg of
that substance by 1°C
o The high specific heat capacity is due to the many hydrogen bonds present
in water. It takes a lot of thermal energy to break these bonds and a lot of
energy to build them
o Adv : provides suitable habitats + maintains a constant temp = optimal
enzyme activity. Water in blood plasma helps maintain constant temp.
 A relatively high latent heat of vaporisation
o In order to change state (from liquid to gas) a large amount of thermal
energy must be absorbed by water to break the hydrogen bonds and
evaporate.
o This is an adv bc only little water is required to evaporate for the organism
to lose a great amount of heat. This = cooling effect for organisms.
 Water has a high surface tension and cohesion
o Hydrogen bonds between water molecules allows for strong cohesion
between water molecules
o This allows columns of water to move through the xylem of plants and
through blood vessels in animals
o This allows columns of water to move through the xylem of plants and
through blood vessels in animals, which is known as adhesion.
 Water is less dense when a solid
 It acts as a reagent
 2.1.2 b the concept of monomers and polymers and the importance of condensation and
hydrolysis reactions in a range of biological molecules
- Monomers are the smaller units from which larger molecules are made
- Polymers are molecules made from a large number of monomers joined together in a
chain
- Macromolecules are very large molecules (polymers are macromolecules but not all
macromolecules aren’t polymers)
Condensation: A condensation reaction occurs when monomers combine together by
covalent bonds to form polymers (polymerisation) or macromolecules (lipids) and water is
removed

Hydrolysis: In the hydrolysis of polymers, covalent bonds are broken when water is added

Organic Covalent bond Diagram of bond

molecules

Carbohydrate Glycosidic
s

Proteins Peptide

Lipids Ester

Nucleic acids phosphodiester

2.1.2 c the chemical elements that make up biological molecules

All carbs have C H and O. H, and O are always present in the ratio 2:1. So presented by
Cx  (H2O)y
There are many functions of carbs. 1. Source of energy (glucose). 2. Store of energy
(glycogen). 3. Structurally important (cellulose in cell walls)
There are 3 types: monosaccharides, disaccharides, and polysaccharides. ↓

Lipids:
All contain C H and O (but proportion of O is low compared to carbs)
There are diff functions: 1. Source of energy 2. Store of energy e.g. lipids are stored in
animals as fats 3. Insulating layer e.g. thermal insulation under the skin + electrical
insulation 4. essential component of biological membranes
There are several types: triglycerides (fats and oils), phospholipids, waxes, and steroids
(such as cholesterol)
Proteins:
All contain C, H, O, N and S
There are diff functions: 1. Required for cell growth, cell repair and the replacement of
biological materials 2. Structurally important e.g. in muscles, collagen, and elastin in the
skin 3. Proteins can also act as carrier molecules in cell membranes, antibodies, enzymes,
or hormones
Nucleic Acids:
All contain C, H, O, N and P
They have one function: 1. Carrying the genetic code in all living organisms. Nucleic acids
are essential in the control of all cellular processes including protein synthesis.

2.1.2 d the ring structure and properties of glucose as an example of a hexose

monosaccharide and the structure of ribose as an example of a pentose monosaccharide

Sugars can be classified as reducing or non-reducing:

Reducing sugars can donate electrons (the carbonyl group becomes oxidised), the sugars
become the reducing agent. They’re found thru benedict’s test as they reduce the soluble
copper sulfate to insoluble brick red copper oxide. Examples of reducing: glucose, fructose
Non-reducing sugars cannot donate electrons, therefore they cannot be oxidised. To find
them out, they must be hydrolysed to break the disaccharide into two monosaccharides
before carrying out benedict’s test. Examples of non-reducing: sucrose.

Glucose

There are diff types of monosaccharides: Trioses (3C), Pentoses (5C), Hexoses (6C).
Glucose is a Hexoses. Most well-known carbohydrate monomer is glucose. It is the most
common monosaccharide, and it is important in many forms: 1. Energy source, 2.
Releasing energy for production of ATP, 3. Soluble so it’s transported in water.
Glucose exists in two forms -> alpha (α) glucose and beta (β) glucose, so known as an
isomer (isomer= same molecular formula but diff structure -> diff properties)

Ribose and Deoxyribose:

Sugars that contain five carbon molecules are described as pentose sugars. Ribose and
deoxyribose are important pentose sugars found in the nucleotides that make up RNA and
DNA. They are very similar in their structures.

2.1.2 e the synthesis and breakdown of a disaccharide and polysaccharide by the

formation and breakage of glycosidic bonds

Forming the Glycosidic Bond:

Monosaccharides are joined together to form disaccharides and polysaccharides to make
it more suitable for transport, storage and to have less influence of cell’s osmolarity.
Disaccharides and polysaccharides are formed when two hydroxyl (-OH) groups interact to
form a strong covalent bond called the glycosidic bond. Every glycosidic bond results in
one water molecule being removed (-> formed by condensation).
- Each glycosidic bond is catalysed by enzymes
specific to which OH groups are interacting
- As there are many different
monosaccharides this results in different
types of glycosidic bonds forming (e.g
maltose has a α-1,4 glycosidic bond and
sucrose has a α-1,2 glycosidic bond)

Breaking the Glycosidic Bonds:

The glycosidic bond is broken when water is added in a hydrolysis (meaning to break).
Disaccharides and polysaccharides are broken down in hydrolysis reactions. Hydrolytic
reactions are catalysed by enzymes, these are different to those present in condensation
reactions.
Sucrose = non reducing sugar which gives a neg result in Benedict’s test. When heated w
hydrochloric acid, it provides water that hydrolyses the glycosidic bond resulting in two
monosaccharides that give a pos Benedict’s test.

Common Disaccharides:

Maltose (sugar formed in breakdown if starch)

Sucrose (the main sugar produced in plants)
Lactose (a sugar found only in milk)
All three of the common examples above have the formula C12H22O11

2.1.2 f structure of starch (amylose and amylopectin), glycogen and cellulose molecules
Amylose (plant):

 Unbranched helix (linear) – stabilised by hydrogen bonds

 1,4 Glycosidic bond
 Helix shape means it can be more compact so it’s resistant
to digestion.
 Alpha glucose molecules
 Insoluble
Amylopectin (plant):

 Branched structure (every 20 monomers)

 1,4 and 1,6 glycosidic bonds
 Compact (but less than glycogen)
 Alpha glucose molecule + insoluble
Glycogen (animal):

 Branched structure (every 10 monomers)

 1,4 and 1,6 glycosidic bonds
 Very compact
 Alpha glucose molecule + insoluble
Cellulose (plant):

 Straight chain + unbranched

 1,4 glycosidic bonds
 Partially compact
 Beta glucose molecule – so it has many
hydrogen bonds (give it high tensile
strength)
 Insoluble (no osmotic effect)
 Forms fibres which increases strength of
cellulose cell walls.

2.1.2 g how the structures and properties of glucose, starch, glycogen, and cellulose
molecules relate to their functions in living organisms
Starch and glycogen are storage polysaccharides because they are compact ( so large
quantities can be stored).
They are also insoluble so that there’s no osmotic effect (unlike glucose which would
lower the water potential of a cell causing water to move into cells)
Starch: storage polysaccharide in plants specifically membrane bound organelles like
chloroplasts and amyloplasts. It takes longer to digest bc of the many monomers.
Amylopectin has many branches that can be easily hydrolysed for cellular respiration.
Glycogen: storage polysaccharide in animals since it’s more branched it’s more compact so
animals can store more of it. More branching means there’s more free ends for rapid
condensation and hydrolysis
Cellulose: main structural component in cell walls due to it’s strength bc of the many
hydrogen bonds between the parallel chains of microfibrils. High tensile strength allows it
to be stretched w/o breaking. Cellulose fibres forms a matrix which inc strength of walls.
Cellulose fibres are freely permeable which allows water to leave to reach cell surface
membrane.
2.1.2 h the structure of a triglyceride and a phospholipid as examples of macromolecules
2.1.2 i the synthesis and breakdown of triglycerides by the formation (esterification) and
breakage of ester bonds between fatty acids and glycerol
2.1.2 j how the properties of triglyceride, phospholipid and cholesterol molecules relate to
their functions in living organisms

Triglyceride
They are non-polar, hydrophobic molecules.
Structure: made of the monomers glycerol and fatty acids.
(glycerol is an alcohol whilst fatty acids contain methyl
group at one end of hydrocarbon.)
Fatty Acids vary in two ways: 1. Length of hydrocarbon 2.
Saturated (no C=C) or unsaturated (there’s a C=C).
Unsaturated can be either polyunsaturated which is where
there is more than one C=C or monounsaturated where
there is only one C=C
Synthesis and Breakdown of Triglycerides: they are
formed by esterification. An ester bond forms when
the hydroxyl group from glycerol bonds with the
carboxyl group from fatty acid. Formation of the
ester bond = condensation reaction. For each
reaction, 3 fatty acids join to one glycerol to form a
triglyceride.
Properties and Functions:
1. Energy storage-> long hydrocarbon chains contain
little oxygen (=triglycerides r v reduced) so when
oxidised (oxidation= loss of hydrogen so triglyceride is
undergoing hydrolysis.) during cellular respiration
these bonds break + release energy used to produce
ATP. Store more energy per gram than carbs and
proteins.
2. Hydrophobic/insoluble-> do not cause osmotic water
uptake in cells so more triglycerides can be stored as
energy stores.
3. Insulation-> prevent heat loss or electrical insulations in neurones (myelin sheath)
4. Buoyancy-> The low density of fat tissue increases the ability of animals to float more
easily
5. Protection-> humans have fat around internal organs to act as a shock absorber
Phospholipids
Structure: formed from the monomers glycerol and fatty acids. They are amphipathic –
hydrophobic + hydrophilic. This means phospholipids form monolayers or bilayers in
water.
There are only two fatty acids for one glycerol molecule
because one of the fatty acid molecules has been replaced
by a phosphate ion  (PO43-). The phosphate is polar so it’s
soluble in water (hydrophilic) and the fatty acids are non-
polar so its insoluble in water (hydrophobic)
Properties and Functions:
1. Hydrophobic core-> from the fatty acids act as
a barrier against water-soluble molecules.
2. Hydrophilic phosphate head-> bc of the
phosphate ions allows cell membrane to be used
to compartmentalisation (enables cells to
organise specific roles into organelles, helps
efficiency.)
3. Fluidity-> fluidity of the cell membrane depends on saturated (less fluid) or unsaturated
(more fluid)
4. Control of membrane protein orientation-> weak hydrophobic interactions between
phospholipids + membrane proteins hold the proteins within membrane but still allow
movement within layers.

Cholesterol:
Found in the cell membrane of eukaryotic cells. They have hydrophobic and hydrophilic
regions. Molecules of cholesterol are synthesised in the liver and transported via the
blood. Cholesterol affects the permeability and fluidity of the cell membrane.

 It disrupts the close-packaging of phospholipids, increasing the flexibility of the

membrane.
 It acts as a barrier, fitting the spaces between
phospholipids-> prevents water-soluble substances
from diffusing across the membrane.
Cholesterol molecules are used to produce steroid-
based hormones e.g. oestrogen, progesterone etc.
2.1.2 k the general structure of an amino acid
A central carbon atom bonded to

 An amine group −N H 2
 A carboxylic group -COOH
 A hydrogen atom
 An R group (which is how amino acids differ)
2.1.2 l the synthesis and breakdown of dipeptides and polypeptides, by the formation and
breakage of peptide bonds
Formation of Peptide Bonds:
Condensation reaction-> a hydroxyl is lost from the carboxylic group of one amino acid
and a hydrogen atom is lost from the amine group of another amino acid – to form water.
The remaining carbon atom from the first amino acid bonds to nitrogen of the second one.
Dipeptides formed by condensation of 2 amino acids. Polypeptides formed by
condensation of 3 or more amino acids-> e.g. proteins.
Breakage of Peptide Bonds:
Hydrolysis reaction: water is added to the dipeptide or polypeptide to break the peptide
bonds.

2.1.2 m the levels of protein structure

Primary structure (PS):
- Sequence of amino acids bonded by covalent peptide bonds =
primary structure
- The DNA of a cell determines the PS of a protein by instructing cell
to add certain amino acids in specific quantities in a certain
sequence-> affects shape + function.
- PS is specific for each protein (one alteration can affect function)
Secondary Structure (SS):
- Occurs when weak negatively charged nitrogen and oxygen atoms interact with the
weak positively charged hydrogen atoms to form hydrogen bonds
- There are 2 shapes that can form bc of this-> α -
helix and β -pleated sheet
- The α-helix shape occurs when H-bonds form
between every fourth peptide bonds
- The β-pleated sheet shape forms when protein
folds so that two parts of polypeptide chain are
parallel enabling H-bonds to form between
parallel peptide bonds.
- Most fibrous proteins have SS e.g. keratin and
collagen.
- SS only relates to hydrogen bonds forming
between amino group and carboxyl group.
- Hydrogen bonds can be broken by high temps.

Tertiary Structure (TS):

- When additional bonds form between the R groups (side chains)
- Additional bonds are:
o Hydrogen bonds - form between strongly polar R
groups.
o Disulphide bonds – strong covalent bonds form
between two cysteine R groups.
o Ionic bonds – forms between pos charged (-NH3+) and
neg charged (-COO-)
o Weak Hydrophobic interactions – form between non-
polar hydrophobic R groups.
- TS structure is common in globular proteins.
- Each of the 20 amino acids that make up proteins has a unique
R group so diff interactions create diff shapes and functions.
Quaternary Structure (QS):
- QS exists in proteins that have more than one
polypeptide chain working together as a functional
macromolecule, for example, haemoglobin
- Each polypeptide in QS is a ‘subunit’ of the protein.
Since proteins have 20 amino acids it would be 4
subunits
2.1.2 n the structure and function of globular proteins including a conjugated protein

STRUCTURE + FUNCTION
Globular proteins are compact, roughly spherical in shape and soluble in water

 Globular proteins for a spherical shape when folding into their TS because
o Non-polar hydrophobic R groups are orientated towards centre of protein
o Their hydrophilic R groups orientate themselves on the outside of the protein

This same orientation allows them to be soluble in water as water molecules surround polar
hydrophilic R groups-> their solubility allows them to be easily transported and be involved in
metabolic reactions
Their specific shapes means they are conjugated proteins (proteins with a non-protein
structure) that contain a prosthetic group (the group which is non-protein)

Function

Structure

HAEMOGLOBIN
Haemoglobin is a globular protein which is an oxygen-carrying pigment found in rbc. It has a
QS as there are 4 polypeptide chains. These chains are globin proteins (2 α–globins + 2 β–
globins) and each unit has a prosthetic haem group.
The four globin subunits are held by disulphide bonds and arranged so their hydrophobic R
group is facing inwards and hydrophilic is outwards.
The arrangement of the R group is important to functioning of the haemoglobin. If changes
occur to the sequence of amino acids in the subunits this can result in the properties of
haemoglobin changing.
The prosthetic haem contains iron II ion which is able to
reversibly combine with an oxygen molecule forming
oxyhaemoglobin + results in haemoglobin being bright red.
Each haemoglobin with the four haem groups can therefore
carry four oxygen molecules (eight oxygen atoms)-> oxygen
isn’t soluble so when it’s bound to the haemoglobin it can
be transported easily around the body
The presence of haem group (and F ⅇ 2+¿¿ ) enables small molecules like oxygen to be bound.
This is because as each oxygen molecule binds it alters the QS of protein which causes
haemoglobin to have a higher affinity (how easily a molecule can bind to another) and the
presence of iron II allows oxygen to reversibly bind.
 - Insulin-> it is a globular protein produced in
pancreas. Its function is the control of BGC .
- It consists of 2 polypeptide chains that are
held together by 3 disulphide bridges.

2.1.2 o the properties and functions of fibrous proteins

STRUCTURE + FUNCTION
Long strand of polypeptide chains that have cross-linkages bc of H-bonds. Bc of the large no.
of hydrophobic R groups, fibrous proteins are insoluble in water. They have a limited no. of
amino acids with the sequence being highly repetitive-> this creates very organised structures
that are strong.

TYPES OF FIBROUS PROTEINS:

Collagen:
Structure-> 3 polypeptide chains closely held by H-bonds to form a triple helix. In PS od
collagen almost every third amino acid is glycine (smallest AA w R group that has 1 H atom).
There are also covalent bonds between R groups of amino acids in interacting triple helices.
Collagen is positioned in fibrils so that there are staggered ends. When many fibrils go
together they form collagen fibres.
 Function-> flexible structural protein. Presence of many H-bonds + triple helix= great tensile
strength. Staggered ends=strength. It’s a stable protein + insoluble.

2.1.2 p the key inorganic ions that are involved in biological processes
Hydrogen ions ( H +¿¿ )-> inversly proportional to the pH value (a lot of H = low pH, vice
versa) so it regulated body pH.
Calcium ions (C a2+¿¿ )-> synapses= calcium regulate transmission of impulses from
neurone to neurone. regulates exocytosis of neurotransmitter. binds to troponin to
stimulate muscle contraction.
Iron ions ( F e 2+¿ ¿)( F e 3+¿ ¿)-> Fe(II) is found in haemoglobin and it binds to
oxygen for transportation. Transfer of electrons during respiration and photosynthesis, for
this the Fe (II) and (III) switch between oxidation states so that electrons are gained + lost.
Sodium ions ( N a+¿ ¿)-> co-transport of glucose and amino acids
across cell-surface membranes. It’s required for the transmission of nerve impulses.
Potassium ions (k + ¿¿)-> essential for nerve transmission.
allows for the reabsorption of water in the kidneys. Important role in guard cells and the
+¿¿
opening of the stomata. Ammonium ions ( N H 4 )-> intermediate ion that
forms during the deamination (removal of amine group) of proteins in the liver and
kidneys
−¿¿
Nitrate ions ( N O3 )-> present in the soil and are taken up by plants. used to make DNA,
amino acids. essential source of nitrogen for protein synthesis.
−¿¿
Hydrogencarbonate ions ( HC O3 )-> work alongside hydrogen ions in the transport of
carbon dioxide in the blood
−¿ ¿
Chloride ions (C l )-> involved in inhibitory synapses to cause hyperpolarisation.
Transport of carbon dioxide.
 3−¿¿
Phosphate ions ( P O4 )-> attatches to molecules to form phosphate molecules.
component of ATP/ADP for energy release & NADP
Hydroxide ions (O H −¿¿)-> lay a vital role in bonding between biochemical molecules and it
determines pH
2.1.2 q how to carry out and interpret the results of the following chemical tests: biuret
test for proteins. Benedict’s test for reducing and non-reducing sugars. reagent test strips
for reducing sugars. iodine test for starch. emulsion test for lipids.
Test for proteins: Add drops of Biuret solution to the food sample. + test= blue -> purple.
Test for reducing sugars: Add Benedict's solution. Heat for 5 mins. + test= blue -> red
Test for non-reducing sugars: add HCl and heat. Neutralise sol with sodium
hydrogencarbonate. Add benedicts sol. Heat in water bath. + test= orange/red precipitate.
Test for starch: Add drops of iodine solution. + test= orange-brown -> blue-black
Test for lipids: ethanol into food sample. Mixed sol added to water, fats + oils float
causing a cloudy emulsion.
2.1.2 r quantitatve methods to determine the concentraton of a chemical substance in a
solution -> PAG book
2.1.2 s (i) the principles and uses of paper and thin layer chromatography to separate
biological molecules / compounds
There are two phases in chromatography: 1. Mobile phase, 2. Stationary phase
How chromatography works: Differences solubility of each component in the mobile
phase affects how far each component can travel. Higher solubility=more up paper.
Paper chromatography-> where moblie phase = solvent +
stationary phase = chromatography paper. Method: a spot
of mixture that needs to be separated is placed on
chromatography paper + left to dry. Then suspended in a
solvent. Solvent will travel up the paper, and mixture moves
up with it at diff speeds. Larger molecules move slower than
smaller ones-> separate. This produces a chromatogram.

(ii) pracitcal investgations to analyse biological solutions using paper or

thin layer chromatography
Separating monosaccharides (MS): use paper chromatography.
Colourless molecules have to be stained. Spot of stained MS is placed
on paper. Known standard sols of diff MS are placed next to the same
spot. Suspend in solvent. Diff MS separate. Unknown MS identified by
matching +comparing with known MS solutions.
Separating amino acids (AA): using paper chromatography. Same as
MS preparation but w/o staining. Each AA will be more/less soluble.
They separate based on charge + size. Compare + match to find unknown. To view diff
spots, dry paper then spray w ninhydrin sol.
Calculating Rf value: solvent front= where solvent reached. Original line= line at bottom.
Rf=distance moved by solute ÷ distance moved by solvent. (it’s a ratio, always less than 1)