2.1.

2 Biological Molecules
Molecular Bonding

Condensation reaction: A reaction that occurs when two molecules are joined together with the removal of
water.
Hydrolysis reaction: A reaction that occurs when a molecule is split into two smaller molecules with the
addition of water.
Almost all condensation reactions happen when two -OH groups on different molecules react together, the
covalent bonds break, and a H2O molecule is formed, this leaves the two molecules joined by covalent
bonds linked by the remaining oxygen atom. Hydrolysis is the reverse of this when a H2O molecule is added.

Monomer: A small molecule which binds to many other identical molecules to form polymer.
Polymer: A large molecule made from smaller molecules called monomers.
Condensation reactions can cause formation of polymers/dimers.
Type of Molecule Elements Monomer Polymer
Carbohydrates C, H, O Monosaccharides (glucose) Polysaccharides (starch)
Proteins C, H, O, N, S Amino acids Polypeptides/ proteins
Nucleic Acids C, H, O, N, P Nucleotides DNA/ RNA
Lipids C, H, O Not monomers/polymers as no single repeated unit.

Covalent bond: A strong chemical bond formed by the sharing of one or more electrons between two atoms
and so creating a molecule. Atoms are more stable when they have a full outer shell of electrons.

Hydrogen bond: A weak interaction that can occur wherever molecules contain a slightly negatively charged
atom bonded to a slightly positively charged hydrogen atom.
Polar molecule: A molecule with regions of negative and positive charge.
Water consists of two hydrogen atoms covalently bonded to an oxygen
atom. The oxygen has a greater number of positively charged protons in
its nucleus, and so exerts a stronger electrostatic attraction for the shared
electrons, so they are positioned close to the oxygen atom than the
hydrogens. This means the oxygen atom becomes slightly negative, and
the hydrogen atoms become slightly positive – polar.

Hydrogen bonds are weaker than covalent bonds as the charges on the atoms are weaker – weaker
electrostatic force. In some polymers, hydrogen bonds form between chains of monomers – stabilising.

Each water molecule can form 4 hydrogen bonds.

Properties of Water

1. Density:
If water was less dense aquatic organisms wouldn’t be able to float.
When water gets cooler it gets denser until 4°C. From 4°C to freezing point, because of its polar nature,
water molecules align themselves in a structure that is less dense than liquid water (molecules held further
apart).
Note: most liquids just denser as they cool, so their solid forms are denser than liquid.
Therefore, ice is less dense than water:
- Aquatic organisms have a stable environment to live in through the winter (if ice was denser it would
sink to the bottom of the pond/lake – killing aquatic organisms).
- Ponds and other bodies of water are insulated against extreme cold. Ice reduces rate of heat loss.
- Provides a surface for arctic animals (e.g. polar bears/seals) to walk on.
 2. Liquid at room temperature:
The hydrogen bonds between molecules make it more difficult for them to escape and become a gas. Even
with its hydrogen bonds water has quite a low viscosity so it can flow easily (as hydrogen bonds constantly
form and break). As it is a liquid at room temp it:
- Provides habitats for living things in rivers, lakes and seas.
- Forms a major component of tissues of living organisms.
- Provides a reaction medium for chemical reactions.
- Provides an effective transport medium (e.g. blood and vascular tissue – xylem/phloem).

3. Good solvent:
It is a good solvent for ionic solutes (NaCl) and covalent solutes (glucose). Because water is polar the positive
and negative parts of the molecule are attracted to the positive and negative parts of the solute. Water
molecules cluster around these charged parts of the solute helping to separate them and so they dissolve.
Because Water is a good solvent:
- Molecules and ions can move about and react in water. This happens in the cytoplasm (70% water).
- Molecules and ions can be transported around living things more easily whilst dissolved in water.

4. Cohesion and surface tension:

Cohesion: attraction between water molecules due to hydrogen bonding. Makes drops of water spherical.
Adhesion: attraction to other polar molecules.
Surface Tension: At the surface of water, the water molecules are hydrogen bonded to molecules below,
and hence more attracted to them than the air molecules above. This means the surface of the water
contracts (molecules pulled inwards) – giving the surface an ability to resist a force applied to it.
Because of cohesion and surface tension:
- Columns of water in plant vascular tissue are pulled up the tissue together from the roots – cohesion
and adhesion to the xylem tissue – transpiration stream
- Insects like pond-skaters can walk on water – surface tension.
- Meniscus forms as glass is polar (water molecules attracted to it – adhesion), air is non-polar to
water molecules only attracted to other water molecules resulting in surface contracting.

5. High specific heat capacity:

Water temperature is a measure of the KE of the molecules. Water molecules are held tightly due to
hydrogen bonds, so lots of heat energy is required to increase KE and temperature (so no rapid temp
changes) – specific heat capacity is the heat energy required to raise 1 kg of water by 1 °C (4.2kJ).
Water does not heat up/cool down quickly, it has a high specific heat capacity which is important as water is
the main component of many living things:
- Living things including prokaryotes and eukaryotes, need a stable temperature for enzyme-
controlled reactions to happen properly. Aquatic organisms need a stable environment to live in.

6. High latent heat of vaporisation:

When water evaporates, heat energy, called latent heat of vaporisation helps molecules to break away from
each other to become a gas. To break hydrogen bonds, a large amount of energy is required, therefore
water helps cool things and keep their temperature stable:
- Mammals are cooled when sweat evaporates.
- Plants are cooled when water evaporates from mesophyll cells.

7. Reactant:
Water is a reactant in photosynthesis, and hydrolysis reactions (digestion of starch, lipids and proteins). Its
properties as a reactant do not directly draw on its polarity, but its role as a reactant is extremely important
in digestion/synthesis of large biological molecules.
Carbohydrates – Monosaccharides/Disaccharides

‘Hydrated carbon’ so for every C there is one O and two H’s. They act as a source of energy (glucose), a store
of energy (starch/glycogen), and as structural units (cellulose in plants/chitin in insects).
Glycosidic bond: A bond formed between two monosaccharides by a hydrolysis reaction (across O atom).
When glycosidic bonds are formed and hydrolysed in living things, the reactions are catalysed by enzymes.

Monosaccharides:
The simplest carbohydrates, important source of energy (well suited to this role as they have many C-H
bonds). They are sugars – soluble in water/insoluble in non-polar solvents. Straight chains or ring/cyclic.

Only hexose sugars (e.g. glucose) are the monomers of more complex carbohydrates, they bond together to
form polysaccharides and disaccharides.
In solution, triose/tetrose sugars exist as straight chains, pentose/hexose are more likely to be a ring/cyclic.
Glucose has two isomers – α and β glucose. Glucose is abundant and the main form in which carbohydrates
are transported around the body in animals.
Name of sugar α-glucose β-glucose Ribose Deoxyribose
Displayed
formula

‘Alpha Romeo, O is below’

Formula C6H12O6 C6H12O6 C5H10O5 C5H10O4
Role in the Energy source. Energy source. Component of Component of
body Component of starch Component of cellulose, ribonucleic acid deoxyribonucleic
and glycogen, which provides structural (RNA), and ATP acid (DNA).
acts as energy stores. support - plant cell walls. and NAD
Type of sugar Hexose Hexose Pentose Pentose

Disaccharides:
Soluble. Common disaccharides are maltose (malt sugar) and lactose
(milk sugar) which are reducing sugars. Sucrose is a non-reducing sugar.
Disaccharides are made when two monosaccharides join – synthesis.
1. α-glucose + α-glucose -> maltose 1-4 glycosidic
2. α-glucose + fructose -> sucrose bond
3. α-glucose + β-glucose -> lactose
4. β-glucose + β-glucose -> cellobiose

To join the two monosaccharides a condensation reaction occurs to form a glycosidic bond, the two
hydroxyl groups line up next to each other and a water molecule is removed, leaving an oxygen atom to link.
Disaccharides are broken into monosaccharides by a hydrolysis reaction, addition of water. The water
provides a hydroxyl group (-OH) and a hydrogen (-H), which form the two hydroxyl groups on the ends of
the monosaccharides once the glycosidic bonds are broken.

Polysaccharides

Homopolysaccharide: Polysaccharides made solely of one kind of monomer (e.g. starch).

Hetropolysaccharide: Polysaccharides made of more than one kind of monomer.

Energy sources and stores:

Glucose is a source of energy, as it is a reactant in respiration (energy released used to make ATP).
Living things join lots of glucose molecules into polysaccharides to store energy. Plants store energy as
starch in chloroplasts and membrane-bound starch grains, humans store glycogen in cells of muscles/liver.

The structure of polysaccharides makes them good energy stores, glycogen in animals and starch
(comprising of amylose and amylopectin). They are good monosaccharide stores because:
• Glycogen/starch are compact due to coiling and folding, they occur in dense granules (starch occurs
in amyloplasts in plant cells) within the cell – more space for storage.
• Polysaccharides hold glucose molecules in chains, so they can be easily ‘snipped off’ the end of the
chain by hydrolysis reactions (always catalysed by enzymes) when required for respiration.
• Some chains are unbranched (amylose) and some are branched (amylopectin/glycogen). Branched
chains tend to be more compact but offer the chance for lots of glucose molecules to be ‘snipped
off’ by hydrolysis at the same time, when lots of energy is required quickly. The enzyme amylase is
responsible for hydrolysing 1-4 glycosidic linkages, and glucosidase hydrolyses 1-6 glycosidic linkages.
• Polysaccharides are usually less soluble than monosaccharides. If glucose dissolved in the cytoplasm
the water potential would reduce, excess water would osmose in, disrupting the cellular function.
Polysaccharides are less soluble due to their size and as the regions that can hydrogen bond are
hidden inside the molecule. Amylose may form double helix, presenting hydrophobic external
surface in contact with the water – making starch insoluble.

Type of polysaccharide (all α-glucose) Detailed structure

Amylose (plants): long chain of α-glucose. Like Coils into a spiral, held together by hydrogen bonds.
maltose, glycosidic bonds between C 1 and 4. Hydroxyl groups on the carbon 2 are situated on the
inside of the coil, making it less soluble and allowing
hydrogen bonds to maintain the coil structure.
Amylopectin (plants): like amylose (glycosidic Amylopectin also coils into a spiral, held together by
bonds between C 1 and 4, in addition branches hydrogen bonds, but branches emerge from the spiral.
formed by glycosidic bond between C 1 and 6
Glycogen (animals): like amylopectin – The 1-4 bonded chains are smaller than amylopectin,
glycosidic bonds between 1 and 4, branching therefore less tendency to coil. However, it has more
created by glycosidic bonds between 1 and 6. branches, which make it more compact and easier to
remove monomer units as there are more ends.

Polysaccharides as Structural Units – Cellulose: Amylopectin

Cellulose is a tough, insoluble, straight chain, fibrous
substance, it is a homopolysaccharide made up of β-glucose
joined by glycosidic bonds. In the condensation reaction
between the glucose molecules every other is rotated at 180
degrees so that the OH groups are next to each other.
Unlike chains of α-glucose which spiral, cellulose chains are
straight and lie side by side.
• Rotation of every other glucose molecule and the β-1-4 glycosidic bonds prevent spiralling.
• Hydrogen bonding between rotated β-glucose molecules in each chain adds strength and prevents
spiralling. Bonds form between OH groups and the O group in the ring of another molecule.
• Hydrogen bonding between rotated β-glucose molecules in different chains give the whole structure
additional strength. The hydroxyl group on carbon 2 sticks out, enabling hydrogen bonding. Bonds
form between OH group and the O atom involved in the glycosidic bond.

Microfibrils – When 60-70 cellulose chains are bound together (10-30nm diameter).
Macrofibrils – Bundles of microfibrils (approx. 400 microfibrils) which are embedded in pectins (like glue) to
form cell walls.
Structure and function of plant cell walls:
- Microfibrils & macrofibrils have high tensile strength, strong glycosidic bonds between monomers
and hydrogen bonds between chains (strong bonds = difficult to digest).
- Macrofibrils run in all directions, criss-crossing for extra strength.

Key features help the plant cell wall do its job:

- As plants do not have a rigid skeleton, each cell needs to have strength to support the whole plant.
- Space between macrofibrils for water/mineral ions to pass, making the cell wall fully permeable.
- The wall has high tensile strength, preventing the cell from bursting when turgid, and supporting the
whole plant. Turgid cells press against each other, which supports the plant’s structure.
- The cell wall protects the delicate cell membrane and cell contents.

Other structural polysaccharides:

Bacterial cell walls: The whole structure surrounding a bacterial cell is called a peptidoglycan, made from
long polysaccharide chains that lie in parallel, cross-linked by short peptide chains.
Exoskeletons: Insect and crustacean cell walls are made from chitin (like fungi).

Lipids – Triglycerides

Lipids contain lots of carbon and hydrogen and a small amount of oxygen. They are insoluble in
water (hydrophobic), as they are non-polar, and so do not attract water molecules, but they do
dissolve in alcohol. Triglycerides, phospholipids and steroids are the most important lipids, they
are macromolecules, not polymers as they are made of different components bonded together.

Triglycerides: Made up of 3 fatty acids and glycerol: an alcohol made of 3 carbon atoms, and 3 -OH groups.

Fatty acids:
Carboxyl (-COOH) group attached to end of hydrocarbon tail. Fatty acids are acidic
as the carboxyl group ionises into a free H+ ion and a -COO- group.
Saturated: There are no C=C double bonds, straight molecule.
Unsaturated: There is one or more C=C bonds – fewer hydrogen atoms bonded
- Monounsaturated: A single C=C bond (e.g. oleic acid).
- Polyunsaturated: More than one C=C bond (e.g. linoleic acid).

Having one or more C=C bonds changes the shape of the hydrocarbon chain, giving it a kink where the
double bond is. As the kinks push the molecules apart slightly – making them more fluid. Animal lipids
contain lots of saturated fatty acids (often solid at 20°C), melting point of unsaturated is lower.

Ester bonds:
A triglyceride consists of one glycerol molecule
bonded to three fatty acids. A condensation
reaction happens between the -COOH group of the
fatty acid and the -OH group of the glycerol (water
molecule produced). The covalent bond that forms
due to this reaction is called an Ester bond.
Triglyceride formation is called esterification.

Functions of triglycerides:
• Energy source – triglycerides can be broken down in respiration (oxidised) to release energy and
generate ATP. The first step is to hydrolyse the ester bonds, then both the glycerol and the fatty
acids can be broken down completely to CO2 and H2O. Note: respiration of a lipid produces more
water than respiration of sugar.
 • Energy store – because triglycerides are insoluble in water, they can be stored without affecting the
water potential of the cell. Mammals store fat in adipose cells under the skin. Fat releases twice as
much energy per gram as glucose, as lipids have a higher proportion of hydrogen atoms than
carbohydrates and almost no oxygen.
• Insulation – Heat insulation (e.g. adipose tissue in whales “blubber” and animals preparing for
hibernation store extra fat). Electrical insulator (Myelin sheath in nerve cells). The also form the waxy
cuticle around leaves/stems of plants.
• Buoyancy – Fat is less dense than water, help keep aquatic mammals afloat.
• Protection – Humans have fat around delicate organs, such as kidneys, to act as a shock absorber.
The peptidoglycan cell wall of some bacteria is covered in a lipid-rich outer coat.

Phospholipids

Structure:
Glycerol molecule with 2 fatty acids bonded to it by ester
bonds, and instead of the third (like a triglyceride) a
phosphate group is bonded by an ester bond, formed by a
condensation reaction between the -OH groups on a
phosphoric acid molecule (H3PO4) and one of the -OH
groups of the glycerol.
- Commonly the C-chain length of the 2 fatty acids is even (e.g. 16/18) and one saturated.

When surrounded by water the phosphate group has a negative charge (O- forms from -OH that was there),
making it polar and attracted to water – hydrophilic. The fatty acid tails are non-polar and so repelled by the
water – hydrophobic. This means the phospholipid molecule is amphipathic (hydrophobic polar end and
hydrophilic non-polar end). In general, membrane lipids tend to be amphipathic, storage lipids are not.

Amphipathic phospholipids may form a layer on the surface of water with tails pointing up; or may form
micelle – tiny balls with tails tucked away inside, with heads pointing out into the surrounding water.

Phospholipid bilayer:
Membranes around cells and organelles. Formed of amphipathic phospholipids in 2 layers with tails pointing
in and hydrophilic heads on the exterior as both sides of the membrane are aqueous solutions
(cytoplasm/extracellular space). Membranes in plant and animal cells are often made of phospholipids,
bacterial membranes contain more protein.
• The individual phospholipids are free to move around in their layer but will not move to a position
where the hydrophobic tails are exposed to water – giving the membrane stability.
• The membrane is selectively permeable, only small/non-polar molecules can move through the
bilayer (e.g. O2 and CO2), polar molecules/ions cannot travel through the non-polar hydrophobic
section formed of the fatty acid tails. This gives membrane control on what enters/exits.
• Water is an exception, it is polar, but it is so small that it can travel between the phospholipids.

Cholesterol

Cholesterol is a steroid alcohol (or sterol) – not made from glycerol or fatty acids. It consists of 4 carbon-
based rings or isoprene units. Only exists in eukaryotic cells, not prokaryotes.
Cholesterol is a small hydrophobic (non-polar) molecule, which means it can sit in the middle of the
hydrophobic part of the phospholipid bilayer.
Mainly made in the liver in animals and transported in the blood.
• It regulates the fluidity of the membrane, preventing it from becoming too fluid/stiff – binds to
hydrophobic tails of phospholipids, causing them to pack more closely together.
 • The steroid-based hormones (testosterone, progesterone, oestrogen and vitamin D) are all made
from cholesterol. As they are small and hydrophobic they can pass
through the hydrophobic part of the plasma membrane.

Proteins

Proteins are large polymers composed of amino acid chains. Functions:

- Structural components of animals, for example muscles.
- Tendency to adopt specific shapes makes proteins important as enzymes, antibodies and hormones.
- Carriers and pores for active transport/facilitated diffusion across a membrane.
Both plants and animals need amino acids to make proteins, animals must ingest essential amino acids to
make them, plants make them if they have access to fixed nitrogen (e.g. nitrates).

Amino Acids:
All contain N, O and H, some contain S in the R group.
Amino acids have an amino (-NH2) group, carboxyl (-COOH) group and R-group.
Radical groups are different in each amino acid (glycine has just an H atom,
whereas cysteine has CH3S). R groups vary in size and polarity with some being
hydrophobic and some hydrophilic.

When dissolved in water the amino group and carboxyl group ionise, the amino group accepts an H+ ion and
becomes NH3+, and the carboxyl group loses an H+ from the OH and becomes COO-.

Amino acids can act as buffers, at low pH (i.e. lots on H+ ions), they will accept H+ ions, in high pH they
release them. This means they have both acidic and basic properties (amphoteric). Protein chains are
affected by the amphoteric nature of amino acids, by accepting/releasing H+ ions, amino acid can help
regulate pH changes – this is known as buffering (a buffer is a substance that helps resist large pH changes).

Peptide bonds:
Covalent bonds between the N of an amino group and the C of a carboxyl
group, that joins amino acids. Formation of a peptide bond (like glycosidic
and ester) involves a condensation reaction and breaking involves
hydrolysis. Protease enzymes in digestion catalyse this hydrolysis reaction.

All amino acids join in the same way, independent of their different R
groups. Two amino acids – dipeptide, multiple - polypeptide. Proteins
consist of a polypeptide chain or multiple ones bonded together. Condensation Reaction

Protein Structure

Primary structure:
The sequence of amino acids in a molecule. The number and order of amino acids is important. The function
of a protein is determined by its structure, there are 20 possible amino acids, so lots of combinations in a
100-long chain. Changing 1 amino acid may change the structure of the whole protein.

Secondary structure:
The coiling or folding of amino acid chains – due to hydrogen bonding between different parts of the chain.
• α-helix: Coils held together by hydrogen bonds between the -NH group of one amino acid and the -
CO group of another four places ahead of it in the chain. Hydrogen bonds are within the chain.
• β-pleated sheet: Zig-zag structure held again by a -NH group hydrogen bonded to a -CO further down
the strand. Hydrogen bonds between different sheets.
Although hydrogen bonds are relatively weak, many are formed which makes these two structures stable at
optimum temp/pH. Some chains may have more than one secondary structure at different ends (insulin).

Tertiary structure:
The overall 3D shape of a protein molecule. Its shape arises due to interactions including hydrogen bonding,
disulphide bridges, ionic bonds and hydrophobic/hydrophilic interactions. The tertiary structure may adopt a
supercoiled shape – fibrous proteins, or a more spherial shape – globular proteins.

Quaternary structure:
Protein structure where a protein consists of more than one polypeptide chain (e.g. insulin). It describes
how multiple polypeptide chains are arranged to make the complete molecule. Same bonding as tertiary.

Protein bonding

The primary structure is held together by peptide bonds. The secondary structure is primarily held together
by hydrogen bonds. The tertiary and quaternary are held together by many – between polypeptide chains.

Ionic bonds:
When the carboxyl groups and amino groups ionise into NH3+ and COO-, the strong attraction between
these positive and negative ions forms an ionic bond.

Disulfide Bridges:
The R group of the amino acids cysteine contains sulphur. Disulfide bridges are formed between the R
groups of two cysteines. They are strong covalent bonds.

Hydrophobic and hydrophilic interactions:

Hydrophobic parts of the R groups tend to associate in the centre of the polypeptide to avoid water,
hydrophilic parts are found on the edges. Hydrophobic and hydrophilic interactions cause the twisting on
the amino acid chain, which changes the shape of the protein. These interactions have a big influence as
most proteins are found surrounded by water in an organism.

Hydrogen bonds:
Between Hydrogen atoms with a slight + charge and other atoms with a slight – charge. In amino acid these
form in hydroxyl, amino and carboxyl groups. They may form between the carboxyl group of one amino acid
and the amino group of another, or between polar regions of R groups. They keep the secondary, tertiary
and quaternary structures in shape, many hydrogen bonds give a protein molecule lots of strength.

Fibrous and Globular Proteins

Fibrous Proteins:
Relatively long, thin structure, insoluble in water and metabolically inactive, often having a structural role
within an organism. Regular, repetitive sequences of amino acids – enabling them to form fibres. Formed
from parallel polypeptide chains, held together by cross links.

Collagen:
Function is to provide mechanical strength:
• Artery walls – a layer of collagen prevents bursting and allows it to withstand high pressure of blood
pumped from the heart.
• Tendons – connect bones to muscles, allowing them to pull on bones.
• Bones – made from collagen, reinforced with calcium phosphate – hardness.
• Cartilage and connective tissue.
Keratin:
Rich in cysteine so lots of disulfide bridges form between polypeptide chains. Alongside hydrogen bonding
this makes it strong.
Found in: Fingernails, hair, claws, hoofs, horns, scales, fur and feathers. Provides mechanical protection and
an impermeable barrier to infection, being waterproof, prevents entry of water born pollutants.

Elastin:
Cross-linking and coiling, makes it strong and extensible. Found in living things that need to stretch or adapt
their shape.
• Skin – stretching around bones and muscles, allows skin to return to normal shape after stretching.
• Lungs – inflating and deflating. Bladder – expanding to hold urine.
• Blood vessels – stretch and recoil as blood is pumped through them, helping to maintain pressure.

Globular Proteins:
Relatively spherical molecules, soluble in water, often have metabolic roles.
Tend to roll up into an almost spherical shape caused by highly folded polypeptide chains. Hydrophobic R
groups turned inwards towards centre, with hydrophilic parts on the exterior – this makes the molecules
soluble as water can bind to the exterior. They often have specific shapes, so they can take up roles as
enzymes, hormones (e.g. insulin) and haemoglobin.

Haemoglobin (transport protein):

The quaternary structure of haemoglobin is made up of 4 polypeptides: 2 α-globin chains and 2 β-globin
chains. Each has its own tertiary structure but fit together to form one molecule. The interactions between
the polypeptides give the molecule a specific shape. On each chain there is a space where a haem group is
held – this is a prosthetic group.
Prosthetic group: A non-protein component that forms a permanent part of a functioning protein molecule.
Conjugated protein: a protein with a prosthetic group.

Function: Carry oxygen from lungs to tissues. In the lungs an O2 molecule binds to an Fe2+ ion in each of the
haem groups, when it binds the haemoglobin turns a purple colour, from red. It is soluble.

Insulin (hormone):
Made by pancreas, 2 polypeptide chains, with different secondary structures at different ends. Both chains
fold into a tertiary structure, joined by disulfide links. Amino acids with hydrophilic R groups are on the
exterior of the molecule – soluble. Insulin binds to glycoprotein receptors on the outside of muscle and fat
cells to increase their uptake of glucose from blood, and to increase their consumption rate of glucose.

Pepsin (enzyme):
Digests protein in the stomach, made up of 1 polypeptide chain (no quaternary structure), but it folds into a
symmetrical tertiary structure (held together by 2 disulfide bridges and hydrogen bonding). Pepsin has few
amino acids with basic R groups, but many with acidic R groups – therefore its optimum pH is approx. 2.
There are few basic groups to accept H+ ions so they have little effect of the enzyme’s tertiary structure.

Inorganic Ions

Cofactor: A non-protein chemical compound that is needed for the protein’s biological activity (e.g.
inorganic ions).
Deficiency:
Some ions are required in large amounts – macronutrients (main elements), some in small quantities –
micronutrients (trace elements). Both humans and plants display deficiency symptoms if they do not
consume enough of a particular ion. E.g. deficiency of copper in plants causes young shoots to die black.
Cations:
Ca2+ - Increases rigidity of bone, teeth, cartilage & component of crustacean exoskeletons
- Cofactor in blood clotting.
- Activator for several enzymes (e.g. ligase), simulates insulin release from pancreas.
- Plant cell wall development, and formation of middle lamellae.
- Nervous transmission and muscle contraction.
Na+ - Regulation of osmotic pressure, maintenance of water levels in body fluid and pH.
- Affects absorption of water in the kidney (collecting duct)
- Nervous transmission and muscle contraction.
- Constituent of the vacuole, helping to maintain turgidity.
K+ - Control of water levels in body fluid and pH maintenance. Reabsorption in Loop of
Henle and collecting duct.
- Assists active transport of materials across the cell membrane.
- Activates essential enzymes needed for photosynthesis.
- Used in the stomatal opening mechanism in guard cells – healthy leaves.
- Nervous transmission and muscle contraction.
- Component of the vacuole, helping to maintain turgidity.
H+ - Regulation of blood pH, and transport of oxygen and carbon dioxide in the blood.
- Important for photosynthesis reactions that occur in thylakoid membranes.
- Hydrogen bonds.
NH4+ - Component of amino acids, proteins, vitamins, nucleic acids and chlorophyll.
(ammonium) - Nitrogen cycle.
- Maintenance of pH in the human body (dissociates to NH3 and H+).
- Some hormones are made of proteins that contain ammonium, e.g. insulin.

Anions:
NO3- - Component of amino acids, proteins, vitamins, nucleic acids and chlorophyll.
(nitrate) - Nitrogen cycle.
- Some hormones are made of proteins that contain nitrogen, e.g. insulin.
HCO3- - Acts as buffer – regulation of blood pH.
(hydrogen- - Transport of carbon dioxide into and out of the blood.
carbonate)
Cl- - Helps in the production of urine in the kidney, osmoregulation.
- Involved in ‘chloride shift’ which maintains the pH of blood during gas exchange.
- Regulates the affinity of haemoglobin to oxygen through allosteric effects on the
haemoglobin.
- Used to produce hydrochloric acid in the stomach (low pH for pepsin).
-
PO4 - Increases rigidity of bone, teeth, cartilage & component of crustacean exoskeletons.
(phosphate) (calcium phosphate).
- Component of phospholipids, ATP, nucleic acids and several important enzymes.
- Regulation of blood pH and help root growth in plants.
OH- - Regulation of blood pH.
(hydroxide) - Important in bonding between biological molecules.

Qualitative Tests for Biological Molecules

Reducing sugars – Benedict’s Reagent:

All monosaccharides and some disaccharides are reducing sugars as they reduce (give electrons too) other
molecules. Heat the sample with Benedict’s reagent, there is a colour change from blue to green to yellow
to orange to brick red. The Cu2+ ions in Benedict’s are reduced, forming red copper (I) oxide precipitate.
Test strips: dip the strip into sample solution and compare with calibration card, tells you whether a
reducing sugar is present of absent. They are often used to test for glucose in urine of diabetic patients.
Non-reducing sugars:
To test non-reducing sugars, test for a reducing sugar, then boil in HCl to hydrolyse the sucrose into glucose.
Then cool the solution and use sodium hydrogencarbonate to neutralise it, and then test for reducing sugars
with benedict’s solution. If the test is positive, the original solution had non-reducing sugars present.

Starch - iodine:
Add iodine solution (in potassium iodide) to a sample. If starch is present, colour change of yellow-brown to
blue-black. Iodine disrupts amylose helix causing colour change.

Lipids – emulsion test:

Mix sample with ethanol - any lipid will go into solution in ethanol (remember: lipids not soluble in water).
Filter it and pour into test tube containing water. A cloudy white emulsion indicates the presence of lipids.
This happens due to tiny lipid droplets coming out of solution when mixed with water.

Proteins – biuret test:

Place sample on a spotting tile and add biuret reagent. If a protein is present, the colour changes from light
blue to lilac/mauve. The colour is formed by a complex between the nitrogen atoms in the peptide chain
and Cu2+ ions – the test detects the presence of peptide bonds.

Quantitative Tests for Biological Molecules

Reducing sugars:
Benedict’s solution is used to test for reducing sugars, the more reducing sugar in the sample, the more
precipitate will form and there will be less Cu2+ ions. The amount of precipitate is assessed with colorimetry.

Colorimetry:
A centrifuge is used to separate the precipitate and any excess Benedict’s (the supernatant). The sample is
placed in a cuvette using a pipette, which is placed into the colorimeter. Ensure there are no fingerprints in
the cuvette as that will affect light transmission. The more precipitate the less light is transmitted through
the colorimeter. Between readings the device is zeroed by placing an appropriate blank sample to reset the
100% transmission/absorption (i.e. with water).

Calibration curves are used to find exact amounts of reducing sugar in the sample.
1. First take a series of known concentrations of sugar.
2. Use a sample from each, carry out the benedict’s test.
3. Use the colorimeter to record the percentage transmission of light through each sample.
4. Plot a graph of absorbance against concentration of sample and plot the point on it, this curve can
be used to calculate the conc of a sample when the absorbance is measured with the colorimeter.

Biosensors:
Biosensors use a biological molecule (e.g. enzyme) and take a biological or
chemical variable that cannot be measured easily. A transducer converts
the chemical/biological signals into an electrical signal.
The electrical signal is then processed and used to work out other
information.
Biosensors have many applications, e.g. detection of contaminants in
water, pathogens/toxins in food, airborne bacteria.

An example is the blood glucose biosensor. This uses the enzyme glucose oxidase to catalyse break down
blood glucose. The enzyme is oxidised by the transducer (electrodes) creating an electrical current which is a
measure of glucose concentration.
Chromatography

Used to separate a mixture – biological molecules. Made from two key components:
Stationary phase: The chromatography paper or thin-layer (molecules that can move), made from cellulose
or thin-layer chromatography plate made from plastic, covered with silica gel or AlOH.
Mobile phase: The solvent for biological molecules (molecules that can’t move), water for polar molecules,
ethanol for non-polar molecules. The mobile phase flows across or over the stationary phase, carrying
biological molecules. The longer components spend in the mobile phase, the further they travel.

Eye protection, draw line in pencil, wait until spots are dry before starting, cover beaker with watch
glass/glass plate – to prevent solvent evaporating, in a fume cupboard, measure distances vertically,
measure distances before solvent dries so it is visible or mark points and solvent front on with pencil.

What happens:
As the solvent travels up the paper or plate, the components of the solution mixture travel with it at
different speeds.
Rf value (relative distance travelled) = distance of pigment from pencil line / distance form pencil line to
solvent front (Rf =distance travelled by pigment / distance travelled by the solvent). In a repeat of the
experiment each pigment will have the same Rf value – this allows pigments to be identified.

Thin layer chromatography can be used to see colourless molecules:

1. UV light – the plates have a chemical which fluoresces under UV light, so everywhere will glow apart
from where the spots have travelled too.
2. Ninhydrin – Allow the plate to dry and spray with ninhydrin, this binds to the amino acids which are
visible as purple spots.
3. Iodine – Allow the plate to dry, place in enclosed container with iodine crystals, iodine gas forms
which binds with the molecules.

How does it work:

The speed at which the molecules move up the paper/plate depends on their solubility in the solvent,
polarity and size. The exposed -OH groups on the paper/plate make them very polar, allowing hydrogen
bond formation with molecules, alongside dipole interactions. A highly polar solute will stick to the surface
and move more slowly compared to non-polar solute.

Chromatography is also used to test for illegal drugs in athlete’s urine, analysing drugs for purity of
components, and analysis of foods to determine the presence of contaminants.