Glycogen is the major carbohydrate storage molecule found in animal cells.

The main cells glycogen

is stored in are liver and muscle cells.

Glycogen is made from the excess glucose that has been eaten and absorbed into the bloodstream.
Glucose is used in respiration, but if more glucose is eaten than the cells need for respiration it is
converted into the polymer glycogen and stored. As liver cells are responsible for removing toxins
and muscles are responsible for movement, glycogen is mainly stored in these cells to ensure they
always have access to glucose to respire and release energy

Structure of Glycogen

Glycogen is a polymer made up of α-glucose and is very similar in structure to amylopectin in starch.
The α-glucose monomers are joined together via condensation reactions and are held in place by 1,4
and 1,6 - glycosidic bonds. The key difference between the structure of glycogen and starch is that
glycogen contains more 1,6 - glycosidic bonds and is, therefore, a more branched structure.

Properties of Glycogen

Glycogen is insoluble due to the fact it is a large molecule. This is an advantage as it means it can be
stored within cells and not dissolve. Therefore it will not change the water potential of a cell nor
cause osmosis, which would otherwise cause cell lysis. The fact that glycogen is a highly branched
molecule means it has a larger surface area for enzymes to attach. This means that it is readily
hydrolysed into glucose when cells are running low on glucose. Glycogen is even more branched
than starch, therefore it is hydrolysed back into glucose more rapidly. This is essential for animals
because they have a higher metabolic rate and therefore need more glucose. For example, they may
need this glucose to provide energy to run from a predator.

Cellulose

Unlike starch and glycogen, the function of cellulose is to provide structural strength in plants.
Cellulose is located in the cell wall of plants and therefore prevents cells from bursting if they take in
excess water. Cellulose is the only polysaccharide that is made up of β-glucose monomers. These
monomers are joined by 1,4 - glycosidic bonds only. So it is unbranched.

Structure of Cellulose

These long, straight chains of β-glucose accumulate and lie parallel to each other. The parallel chains
are then held together by many hydrogen bonds, and the sheer number of hydrogen bonds provides
strength.

This structure is called a fibril. Fibrils then align in parallel and are held in place by even more
hydrogen bonds to form a cellulose fibre.

Properties Of Cellulose

Cellulose is insoluble due to the fact it is such a large molecule. This is an advantage as it will not
change the water potential of a cell and affect osmosis. Due to the large number of hydrogen bonds
in and between the fibrils, cellulose is a very strong polysaccharide

Proteins

Proteins are large polymers made up of monomers called amino acids. These amino acids are
arranged in a series of structures to create the finished 3D protein. There are up to four levels of
structural arrangements in a protein
Protein polymer chains, or polypeptides, are created on ribosomes in cells and are then further
folded and modified in the Golgi apparatus.

Proteins are large polymers, made up the monomer amino acids. There are 20 different amino acids,
but you only need to learn the general structure.

a central carbon

an amine group (NH)

a hydrogen atom

a carboxyl group (COOH)

the variable group (R group)

Amino acids join together to make the polypeptide polymer via condensation reactions and are held
together by peptide bonds.

Primary Structure

The first structure that forms in the creation of a protein is the polypeptide chain. The primary
structure is the sequence of amino acids in a polypeptide chain. The order the amino acids are
bonded in is determined by DNA. This specific order of amino acids will alter where bonds occur and
how the protein folds. Therefore, the primary structure determines the final 3D shape and the
protein's function.

Secondary Structure

The sequence of amino acids causes parts of a protein molecule to bend into an α helix or fold into
β pleated sheets. Hydrogen bonds form between the carboxyl groups of one amino acid and the
amine group of another and hold the secondary structure in place.

Tertiary Structure

The secondary structure is bent and folded to form a precise 3D shape. This unique 3D shape is held
in place by hydrogen bonds, ionic bonds and sometimes disulfide bonds. Disulfide bonds (di meaning
2) only form between the R-groups of two amino acids that contain sulfur.

Describing the tertiary structure of a protein is a 3-mark question. The 3 marks are:

The further folding of the secondary structure

To create a unique 3D structure

Held in place by hydrogen, ionic and disulfide bonds.

Make sure you always mention the bonds involved when describing protein structures, as there are
always marks for this because without these bonds the unique shapes are not maintained.

Quaternary Structure

A protein that is made up of more than one polypeptide chain has a quaternary structure. It is still
folded into a 3D shape and held by hydrogen, ionic and disulphide bonds. Haemoglobin is an
example which is made up of 4 polypeptide chains.
In the diagram of haemoglobin, you can also see extra molecules attached that are not part of the
polypeptide chains. Any group that is attached to a protein, but is not made up of amino acids, is
known as a prosthetic group. The heme group, containing iron, is the prosthetic group in
haemoglobin. A protein that has a prosthetic group can be described as a conjugated protein, which
simply means a non-protein group is added onto it.

Enzymes

The active site is specific and unique in shape due to the specific folding and bonding in the tertiary
structure of the protein. Due to this specific active site, enzymes can only attach to substrates that
are complementary in shape.

All reactions require a certain amount of energy before they occur. This is known as the activation
energy. When enzymes attach to the substrate they can lower the activation energy needed for the
reaction to occur, and therefore speed up the reaction.

Lock and Key Model

This model suggests that the enzyme is like a lock and that the substrate is like a key that fits into it
due to its complementary shape. The enzyme active site is a fixed shape and due to random
collisions, the substrate can collide and attach to the enzyme. This forms an enzymesubstrate
complex. Once the enzyme-substrate complex has formed, the charged groups within the active site
are thought to distort the substrate and therefore lower the activation energy.

Induced Fit Model

This model suggests that the enzyme is like a glove and the substrate is like your hand; the empty
glove is not exactly complementary in shape to your hand, but when your hand enters, it enables the
glove to mould around your hand to become completely complementary. The enzyme active site is
induced or slightly changes shape, to mould around the substrate. The formation of the
enzymesubstrate complex involves the enzyme moulding around the substrate, which puts a strain
on the bonds and therefore lowers the activation energy.

The products are then removed, and the enzyme active site returns to its original shape. The induced
fit model is the accepted model for how enzymes function.

Factors affecting Enzymes

 Temperature
 pH s
 substrate concentration
 Enzyme concentration
 Inhibitors

Temperature

If the temperature is too low, there is not enough kinetic energy for successful collisions between
the enzyme and substrate. If the temperature is too high, enzymes denature, the active site changes
shape and enzymesubstrate complexes cannot form.
pH

Too high or too low a pH will interfere with the charges in the amino acids in the active site. This can
break the ionic and hydrogen bonds holding the tertiary structure in place and therefore the active
site changes shape. Therefore the enzyme denatures and fewer enzyme-substrate complexes form.

Substrate and Enzyme Concentration

If there is insufficient substrate, then the reaction will be slower as there will be fewer collisions
between the enzyme and substrate. If there are insufficient enzymes, then the enzyme active sites
will become saturated with substrate and unable to work any faster.

Inhibitors

Competitive inhibitors are the same shape as the substrate and can bind to the active site. This
prevents the substrate from binding and the reaction occurring. If you add more substrate this will
out-compete the inhibitor, knocking them out of the active site.

Non-competitive inhibitors

bind to the enzyme away from the active site (the allosteric site). This causes the active site to
permanently change shape, and therefore the substrate can no longer bind, regardless of how much
substrate is added.

Triglycerides

Triglycerides are formed via the condensation reactions between one molecule of glycerol and three
molecules of fatty acid. Ester bonds are formed.

The R-groups are fatty acids which can be saturated or unsaturated.

Saturated fatty acids– the hydrocarbon chain has only single bonds between carbons.

Unsaturated fatty acids – the hydrocarbon chain consists of at least one double bond between
carbons

Properties of Triglycerides

Here is how the triglyceride structure results in its properties.

Due to the large ratio of energy-storing carbon-hydrogen bonds compared to the number of carbon
atoms; a lot of energy is stored in the molecule.

Due to the high ratio of hydrogen to oxygen atoms they act as a metabolic water source.
Triglycerides can release water if they are oxidised. This is essential for animals in the desert, such as
camels.

Triglycerides do not affect water potentials and osmosis. This is because they are large and
hydrophobic, making them insoluble in water.

Lipids have a relatively low mass. Therefore a lot can be stored without increasing the mass and
preventing movement.
Phospholipids

Phospholipids are made of a glycerol molecule, two fatty acid chains and a phosphate group
(attached to the glycerol). The two fatty acids also bond to the glycerol via two condensation
reactions, resulting in two ester bonds. The hydrophilic ‘head’ of a phospholipid can attract water as
it is charged. Due to the phosphate being charged (polar), it repels other fats. The fatty acid chain is
not charged (non-polar). It is known as the hydrophobic ‘tail’ and it repels water but will mix with
fats.

Phospholipids have two charged regions, so they are polar. In water, they are positioned so that the
heads are exposed to water and the tails are not. This forms a phospholipid bilayer which makes up
the plasma membrane around cells

Biochemical tests for :

Reducing sugars

Non-reducing sugars

Starch

Proteins

Lipids

Reducing sugars

The chemical procedure for this is: 1. Add Benedict’s reagent to the sample you are testing

2. Heat

3. If a colour change of blue to yellow/green/red is observed, then this is confirmation that a

reducing sugar is present.

4. If the solution remains blue, there is no reducing sugar present.

If a substance remained blue after the Benedicts test you should do this

Mix sucrose with HCl and boil – this is acid hydrolysis and it breaks the glycosidic bond so that
sucrose is hydrolysed back into glucose and fructose. Hint – to get the mark you must state BOIL, as
below 100 C there is not enough energy to break the glycosidic bond. Cool the solution and then add
sodium hydroxide to make the solution alkaline. Benedict’s reagent only works in alkaline solutions,
which is why this stage is essential. You must cool the solution first to prevent excessive, dangerous
fizzing. Add a few drops of Benedict’s reagent and heat. If a colour change of blue to
yellow/green/red is observed, then this is confirmation that a non-reducing sugar is present.

Starch

The presence of starch can be confirmed by adding a few drops of iodine. Iodine is orange/brown in
colour when no starch is present, but it turns blue/black if starch is present.

Protein

To test for proteins you add biuret reagent (tip - do not confuse this with a burette! It is pronounced
Bi-u-ret). Biuret reagent is blue, but it will turn purple when added to a protein.
Lipids

To test for lipids, your sample must first be dissolved in ethanol. This is achieved by shaking the
sample you are testing in ethanol. Once the sample is dissolved, add distilled water and shake again.
If lipids are present, you will then observe a white emulsion.

DNA Structure

Deoxyribonucleic Acid (DNA) codes for the sequence of amino acids in the primary structure of a
protein, which in turn determines the final 3D structure and function of a protein. The DNA polymer
is a double helix shape. The monomer that makes up DNA is called a nucleotide. It is made up of
deoxyribose (a pentose sugar), a nitrogenous base and one phosphate group. The nitrogenous base
can either be guanine, cytosine, adenine and thymine.

The polymer of these nucleotides is called a polynucleotide. It is created via condensation reactions
between the deoxyribose sugar and the phosphate group, creating a phosphodiester bond.
Phosphodiester bonds are strong covalent bonds, and therefore help ensure that the genetic code is
not broken down. The polynucleotide has a sugar-phosphate ‘backbone’. This describes the strong
covalent bonds between the sugar and phosphate groups that hold the polymer together.

The DNA polymer occurs in pairs, and these pairs are joined together by hydrogen bonds between
the bases. This is how the double helix structure is created, as the two chains twist.

Hydrogen bonds can only form between complementary base pairs. This is the term given to the fact
that the base cytosine can only form hydrogen bonds with guanine and that adenine can only bond
with thymine

Adenine and thymine form 2 hydrogen bonds, whereas cytosine and guanine can form 3 hydrogen
bonds. This complementary base pairing is important to help maintain the order of the genetic code
when DNA replicates, therefore reducing the chance of mutations.

How the DNA Structure Links to its Function

Stable structure due to the sugar-phosphate backbone. (covalent bonds) and the double helix to
prevent damage.

Double-stranded so replication can occur using one strand as a template.

Weak hydrogen bonds for easy separation of the two strands in a double helix during replication.

Large molecule to carry lots of genetic information.

Complementary base pairing allows identical copies to be made.

RNA

RNA is a polymer of a nucleotide formed of ribose, a nitrogenous base and a phosphate group. The
nitrogenous bases in RNA are adenine, guanine, cytosine and uracil. RNA has the base uracil instead
of thymine. In comparison to the DNA polymer, the RNA polymer is a relatively short polynucleotide
chain and it is single-stranded.

The function of RNA is to copy and transfer the genetic code from DNA in the nucleus to the
ribosomes. Some RNA is also combined with proteins to create ribosomes.
There are three types of RNA;

mRNA

tRNA

rRNA

mRNA is a copy of a gene from DNA. mRNA is created in the nucleus and it then leaves the nucleus
to carry the copy of the genetic code of one gene to a ribosome in the cytoplasm. DNA is too large to
leave the nucleus and would be at risk of being damaged by enzymes, therefore destroying the
genetic code permanently. mRNA is much shorter because it is only the length of one gene, and can
therefore leave the nucleus as it is small enough to fit through the nuclear pores. mRNA is single-
stranded and every 3 bases in the sequence code for a specific amino acid; these three bases are
therefore called codons.

tRNA is found only in the cytoplasm. It is single-stranded but folded to create a shape that looks like
a cloverleaf shape. This cloverleaf shape is held in place by hydrogen bonds. The function of tRNA is
to attach to one of the 20 amino acids and transfer this amino acid to the ribosome to create the
polypeptide chain. Specific amino acids attach to specific tRNA molecules and this is determined by 3
bases found on the tRNA which are complementary to the 3 bases on mRNA. These are called the
anticodon because they are complementary to the codon on mRNA.

rRNA is the type of RNA that makes up the bulk of ribosomes. The rest of a ribosome is made of
protein.

Differences between the DNA and RNA monomer:

DNA contains the base thymine, whereas RNA contains uracil instead.

DNA contains the pentose sugar deoxyribose, whereas RNA contains the pentose sugar ribose.

Differences between the polymers:

DNA is much larger because it contains approximately 23,000 genes (the entire genome), whereas
RNA is much shorter because it is only the length of one gene.

DNA is double-stranded, whereas RNA is single-stranded.

Before cells divide (by mitosis or meiosis) all the DNA must replicate to provide a copy for the new
cell.

The process of DNA replication is semi-conservative replication (in the daughter DNA, one strand is
from the parental DNA and one strand is newly synthesised).

This process relies on the complementary base pairs (cytosine + guanine and thymine + adenine) and
involves the enzymes DNA helicase and DNA polymerase.

There are Stages for This replication

DNA helicase breaks the hydrogen bonds between the complementary base pairs between the two
stands within a double helix. This causes the DNA double helix to unwind.

Each of the separated parental DNA strands acts as a template. Free-floating DNA nucleotides within
the nucleus are attracted to their complementary base pairs on the template strands of the parental
DNA.
The adjacent nucleotides are joined together (to form the phosphodiester bond) by a condensation
reaction. DNA polymerase catalyses the joining together of adjacent nucleotides

The two sets of daughter DNA (the name given to the new DNA molecules) contain one strand of the
parental (original) DNA and one newly synthesised strand.

The Structure of Water

Water is an incredibly important biological molecule, which is why about 60-70% of your body is
water. Water is a polar molecule. Water has an unevenly distributed charge due to the fact that the
oxygen atom is slightly negative, and the hydrogen atoms are slightly positive. The delta ( δ ) symbol
indicates a slightly positive/negative on the diagram.

Five Key Properties of Water

Hydrogen bonds form between different water molecules between the oxygen and a hydrogen
atom. The formation of these hydrogen bonds and the fact that water is dipolar results in 5 key
properties of water:

It is a metabolite (e.g. in condensation and hydrolysis reactions).

An important solvent in reactions.

Has a high heat capacity, and it buffers temperature.

Has a large latent heat of vaporisation, providing a cooling effect with loss of water through
evaporation.

Has strong cohesion between water molecules; this supports water columns and provides surface
tension.

Metabolite

Water is involved in many reactions, such as photosynthesis, hydrolysis, and condensation

reactions. This is one reason why it is essential that approximately 90% of the plasma in the blood
and the cytoplasm in cells is largely composed of water.

Solvent

Water is a good solvent, meaning many substances dissolve in it. Polar (or charged) molecules
dissolve readily in water due to the fact water is polar. The slight positive charge on hydrogen atoms
will attract any negative ions in solutes and the slight negative charge on the oxygen atoms of water
will attract any positive ions in solutes. These polar molecules are often described as hydrophilic,
meaning they are attracted to water.

Non-polar molecules, such as lipids, cannot dissolve in water and are therefore described as
hydrophobic- they are repelled by water. The fact that so many essential polar substances dissolve in
water enables them to be transported easily around animals and plants through blood or xylem

High Specific Heat Capacity

This means that a lot of energy is required to raise the temperature of the water. This is because
some of the heat energy is used to break the hydrogen bonds between water molecules.
This is useful to organisms as it means the temperature of the water remains relatively stable, even
if the surrounding temperature fluctuates significantly. Therefore, the internal temperatures of
plants and animals should remain relatively constant despite the outside temperature, due to the
fact a large proportion of the organism is water.

This is important so that enzymes do not denature or reduce activity with temperature fluctuations.
Finally, this provides a stable environment, in terms of temperature, for aquatic organisms.

Large Latent Heat of Vaporisation

This means that a lot of energy is required to convert water in its liquid state to a gaseous state. This
is due to the hydrogen bonds, as energy is needed to break the hydrogen bonds between water
molecules to turn it into a gas.

This is advantageous to organisms as it means that water provides a significant cooling effect. For
example, when humans sweat they release water onto their skin. Large amounts of heat energy
from the skin is transferred to the water during evaporation and this provides a cooling effect.

Strong Cohesion

Cohesion is the term used to describe water molecules ‘sticking’ together by hydrogen bonds. Due to
water molecules sticking together, when water moves up the xylem in plants due to transpiration it
is as a continuous column of water. This is advantageous as it is easier to draw up a column rather
than individual molecules. Cohesion also provides surface tension to water. This enables small
invertebrates to move and live on the surface, providing them with a habitat away from predators
within the water.

ATP

ATP, or Adenosine Triphosphate, is an immediate source of energy for biological processes.

Metabolic reactions in cells must have a constant, steady supply of ATP. ATP contains three
phosphate ions that play a significant role in energy transfer. This biological molecule is essential to
metabolism, which is all the chemical reactions that take place in a cell

ATP IS MADE OUT OF:

Adenine is a nitrogenous base (meaning a base that contains nitrogen)

Ribose (a pentose sugar)

Three inorganic phosphate groups.

The phosphate groups are described as being inorganic because they do not contain any carbon
atoms. For this reason in chemical reactions the symbol to represent this is a P for phosphate and i
for inorganic -Pi

ATP is made during respiration from ADP, adenosine diphosphate, by the addition of an inorganic
phosphate via a condensation reaction which uses the enzyme ATP synthase.

ATP can be hydrolysed into ADP + Pi using the enzyme ATP hydrolase.

ATP + water --> ADP +Pi (energy)

By breaking one of the bonds between the inorganic phosphate groups in a hydrolysis reaction, a
small amount of energy is released to the surroundings, which can be used in chemical reactions.
Therefore, ATP is an immediate energy source as only one bond has to be hydrolysed to release
energy

Phosphorylation

ATP can also transfer energy to different compounds. The inorganic phosphate released during the
hydrolysis of ATP can be bonded onto different compounds to make them more reactive. This is
known as phosphorylation, and this happens to glucose at the start of respiration to make it more
reactive.

There are five key properties of ATP that make it a suitable immediate source of energy. In exam
questions, the properties of ATP and glucose can be compared to emphasise the importance of ATP
as the immediate source of energy for cells rather than glucose.

ATP releases energy in small, manageable amounts so no energy is wasted. This means that cells do
not overheat from wasted heat energy and cells are less likely to run out of resources. In comparison
to glucose, this would release large amounts of energy that could result in wasted energy.

It is small and soluble so it is easily transported around the cell. ATP can move around the cytoplasm
with ease to provide energy for chemical reactions within the cell. This is a property ATP has in
common with glucose.

Only one bond is hydrolysed to release energy, which is why energy release is immediate. Glucose
would need several bonds to be broken down to release all its energy.

It can transfer energy to another molecule by transferring one of its phosphate groups. ATP can
enable phosphorylation, making other compounds more reactive. Glucose cannot do this, as it does
not contain phosphate groups

. ATP can’t pass out of the cell; the cell always has an immediate supply of energy. ATP cannot leave
the cell, whereas glucose can. This means that all cells have a constant supply of ATP (or ADP + Pi),
but a cell can run out of glucose

Inorganic Ions

Inorganic ions dissolve to form solutions found within the cytoplasm of cells and other body fluids.
Some inorganic ions are required in high concentrations, whereas others are required in very low
concentrations. Each inorganic ion performs a different function and this is due to their different
properties.