Biological molecules
Monomer- small molecule, many of which can be joined together to form a
polymer
Biological molecule
Carbohydrate
Proteins
Nucleic acids
Monomer
monosaccharide
Amino acids
nucleotides
Polymer
polysaccharide
Polypeptides and proteins
DNA and RNA
Condensation method which joins small molecules together to form larger ones
 water molecules lost
 new covalent bond formed
Hydrolysis method which splits larger molecules up into smaller ones
 water molecule is used
 covalent bonds are broken
Carbohydrates
 glucose-energy sources released during respiration
 starch- energy store
 cellulose- structural
Monosaccharides
Soluble in water, sweet to the taste, form crystals
Named after the number of carbon atoms e.g. triose has 3, pentose has 5
Glucose- 2 forms (isomers) Alpha and Beta (-OH group on C1 different)
Glucose forms a ring when C1 joins to C5, leaving C6 outside the ring.
Making and breaking down disaccharides
Two alpha-glucose molecules are condensed into the disaccharide maltose by
a glycosidic bond. (Hint- Glucose, Glycosidic)
Carbohydrates and energy storage
Respiration:Glucose + oxygen  carbon dioxide + water (ATP is released)
Glucose is broken down in several steps, with each stage being controlled by a
different enzyme.
Animals and plants have enzymes that can only break down alpha-glucose, the
position of the –OH group on C1, give beta glucose a different overall shape
that will not fit into the enzyme active site.
Starch
Is the energy store in plants only. It is a mixture of amylose and amylopectin.
Amylose- is made up of long chains of alpha glucose, linked C1 of one molecule
to C4 of another by a glycosidic linked (1,4 glycosidic link). The long chains coil
into springs into which iodine molecules can become trapped and turn from
yellow/brown to blue/black (iodine is a test for starch).
Amylopectin- is also made of alpha-glucose linked with 1,4 glycosidic bonds,
with 16 glycosidic branches
Amylose
amylopectin
Glycogen
Is the storage substance in animals only. It is identical to starch in that it is
made of 1-4 linked alpha glucose but the chains tend to be shorter with more
branching.
Features of starch and glycogen- good for storage as they do not dissolve in
water and so do not affect the water potential of cells. As they are made up
chains of alpha glucose and these glucose molecules can be broken off from
the ends of the chains to be used for respiration.
Carbohydrates and structural role
Cellulose- is a polymer of beta-glucose monomers which have been condensed
together. Cellulose is only found in plants and has a structural role.
In cell walls, 60-70, cellulose fibres come together to form microfibrils, and as
the glucose monomers have so many –OH groups, many hydrogen bonds form
between these groups, cross-linking them. These microfibrils, linked by
hydrogen bonds, form larger bundles called macrofibrils. Macrofibrils are
embedded in a polysaccharide glue called pectin, which makes it very strong in
cell walls.
• The way the macrofibrils are arranged allows water to move along and
through them.
• Cell wall allows water into the cell but the cellulose is so strong that the
turgor pressure does not cause the cell to burst.
• The way that macrofibrils are arranged, can determine how a cells can
change shape and how it grows.
Proteins





Are essential components of cell membranes.
Haemoglobin is a protein.
Antibodies are proteins.
All enzymes are proteins.
Hair and the surface layers of the skin are made of the protein
keratin.
 Collagen is a protein that adds strength to tissues such as bone and
the walls of arteries.
Proteins are for growth and repair
Proteins are made of subunits called amino acids (20 occur naturally, 8-10
are essential in the diet-essential amino acids). Amino acids are the same
except they have different R groups.
Amino acids-
Amino acids are joined together by condensation (loss of a water molecule)
and are joined by peptide bonds. This peptide bond can be broken by
hydrolysis and the addition of a water molecule. Two amino acids joined=
dipeptide
Primary protein structure- a unique sequence of amino acids joined
together. The types of amino acids and their sequence are determined by
the information on mRNA. The sequence of amino acids will affect the
properties of the protein e.g. if a proteins contains a number of amino acids
with hydrophobic R-groups, this final protein will be a particular shape and
could be found embedded in a membrane.
Secondary protein structure- the primary structure is fold into an alpha
helix or a beta-pleated sheet which are held in place by hydrogen bonds.
Tertiary protein structure- the secondary structure is folded into a tertiary
structure which is held in place by different types of bonds, i.e. disulphide
bonds (between 2 sulphur atoms), ionic bonds (between R groups which
are charged), hydrogen bonds (where slightly positive groups are found
close to slightly negatively charged groups), hydrophobic interactions.
The tertiary structure is important as if the protein is an enzyme, the folding
results in a particular active site which is complementary to a particular
amino acid, and for a hormone it is a specific shape to fit into a hormone
receptor of a target cell.
Globular and fibrous proteins
Protein type 3D feature
Globular
Fibrous
Roll up in a
ball
(hydrophilic
groups on
the outside
and
hydrophobic
groups on
the inside)
Form fibres
Solubility in
water
soluble
Role
Examples
Metabolic
role
Enzymes,
plasma
proteins, and
antibodies
insoluble
Structural
role
Collagen in
bone and
cartilage
Keratin
found in hair
Quaternary protein structure
Some proteins are made up of more than one polypeptide subunit e.g.
haemoglobin and insulin
Haemoglobin- made up of 4 polypeptide subunits (2 identical alpha ones
and 2 identical beta ones), and is a water-soluble globular protein. Each
polypeptide subunit has a haem group that contains a Fe2+ ion. Haem group
is responsible for blood colour, which is contains oxygen (oxyhaemoglobin),
it is bright red. Haem group is a prosthetic group
Collagen
Is a fibrous protein and is made up of three polypeptide chains wounded
around each other like a twisted rope, with hydrogen bonds holding the
chains together giving it strength. The molecule is further strengthened by
covalent cross-links linking the collagen molecules together. This results in a
collagen fibril, and many of these form a collagen fibre.
Functions of collagen In walls of arteries to prevent bursting when vessel under high pressure
 In tendons connecting muscles to bones
 Bones are collagen reinforced with minerals such as calcium and
phosphate
 Make up cartilage and connective tissue
 Cosmetic treatment (collagen injected into lips)
Comparison of haemoglobin and collagen
Haemoglobin
Globular protein
Soluble in water
Consists of a wide range of amino
acids
Contains a prosthetic group (haem)
Much is wound into alpha helix
structures
Collagen
Fibrous protein
Insoluble in water
35% of amino acids are glycine
No prosthetic group
Much of molecule is left-handed
helix structures
Lipids
Are not polymers. Consist of glycerol linked to 3 fatty acid chains
Uses:





Source of energy in respiration
Storage of energy (stored in adipose cells)
In membranes
Insulation to reduce heat loss
Protection e.g. cuticle on the surface of leaves
Some hormones are lipids
Fatty acids are joined to the glycerol by condensation, 3 water molecules are
released, and ester bonds are formed.
Lipids (triglyceride)- saturated or unsaturated?:-
In unsaturated fatty acid chains there are double bonds which cause the chain
to kink, cause the fatty acids to be pushed further apart, and the fat is more
liquid (oil). Plant lipids contain many unsaturated fatty acids and form oils e.g.
sunflower oil, olive oil.
Triglycerides have charges around the molecule equally distributed and so it is
hydrophobic.
Phospholipids
Found in biological membranes and are almost identical to triglycerides in that
they are made up of glycerol and fatty acids, except it has two fatty acids
instead of three, and has a phosphate group instead.
Phosphate head is hydrophilic and tails are hydrophobic. Fatty acids that make
up phospholipids can be saturated or unsaturated. In colder climates,
organisms have an increased number of unsaturated fatty acids to keep the
biological membranes fluid at low temperatures.
Fats can be used in respiration for energy with the ester bonds being
hydrolysed, and then the glycerol and fatty acids can be broken down to
produce ATP (twice as much as carbohydrates).
Cholesterol is a class of lipid. It is made up of four carbon-based rings. The
hormones testosterone, oestrogen and vitamin D are made from cholesterol.
Due to their lipid nature, these hormones can readily pass through lipid
bilayers to reach target receptors.
Lipid
Structure
Role
Other features
triglyceride
Glycerol + 3 fatty
acids
Stored as fat,
protective and
insulating
phospholipid
Glycerol, 2 fatty
acids + a phosphate
group
Energy store
Insoluble in water so
not affect water
potential
Hydrophobic and
hydrophilic part
ideal for membranes
cholesterol
Four carbon-based
joined rings
Fits in lipid bilayer
giving it strength
With carbohydrate
attached to
phosphate group,
may form glycolipids
Used to form steroid
hormones
Enzymes
• Organisms that secrete extracellular enzymes – e.g. fungi, secrete
enzymes externally to break down food and they then absorb the
monomers.
• Enzymes and defence mechanism- lysosomes contain enzymes which
digest bacteria that have been encapsulated in a vesicle.
Lock-and-key hypothesis- exact fit of substrate and active site
Induced-fit- as substrate goes into the active site, changes to amino acids
occur in the active site to make the fit better.
Enzymes and temperature
• Enzymes and substrate move randomly.
• At low temperatures, movement is slow so there is less likely that a
substrate will collide with the enzyme active sites
• As temperature increases, the molecules move faster and so
substrate is more likely to collide with the enzyme active site, and so
the rate of reaction increases.
• At the optimum temperature, there enough kinetic energy so that
there are frequent collisions between the enzyme active site and the
substrates, but not enough to break the bonds holding the enzyme in
its 3D shape (no denaturing).
• Over optimum temperature- kinetic energy so high that vibrations
are so great within the enzyme that bonds holding it in its 3D shape
break, meaning the enzyme begins to unravel and the active site
changes shape.
Enzyme and pH
 pH is a measure of H+ ions. These hydrogen ions can interfere with the
hydrogen and ionic bonds which hold an enzyme in its tertiary structure.
This means that if you alter the hydrogen ion concentration around an
enzyme, it can alter the shape of the enzyme and thus the active site. In
the induced-fit hypothesis, the active site relies on charges groups on
the R-groups of the amino acids that make up the active site. The
hydrogen ions are attracted to the negatively charged groups of the
active sites.
 Enzymes work in a fairly narrow pH range. When carrying out enzymecontrolled reactions at different pH values, buffers are used (to maintain
that particular pH).
Effect of substrate concentration on rate of reaction
 As the concentration of substrate increases, there is an increase in the
rate of reaction as there are more substrate molecules to collide with
the enzyme.
 There comes a point when adding more substrate does not increase the
rate of reaction, as the enzyme active sites are full all the time. The only
way to further increase the rate of reaction is to add more enzymes.
Effect of substrate concentration on rate of reaction
 When enzyme concentrations are low, reaction rate is slow as
there are less active sites for the substrate to fit into.
 Reactions rate increases as enzyme concentration increases as
there are more active site available for the substrate molecules to
fit into.
 Eventually reaction rate stays the same even when enzyme
concentration is increased, as the substrate becomes the limiting
factor.
Initial reaction rate
When the enzymes and the substrate are first mixed together, the rate
of reaction will be at its highest as there is more substrate available. As
the reaction proceeds, more product is formed so there is less substrate
available to collide with enzyme active sites.
Calculating the initial rate of reaction from a graph
Initial rate of reaction is x and this gives the amount of product in a
given time
y
Enzyme inhibitors
2 types
 Competitive
 Non-competitive
Inhibitors reduce the rate of enzyme reactions.
Competitive inhibitors- the inhibitor to the substrate and so competes with
the substrate for the active site and slows the reaction rate down.
All the substrate will eventually become product but it just takes longer. The
effect of the inhibitor can be decreased by increasing the amount of substrate.
Non-competitive inhibitors
Non-competitive inhibitors do not compete with the substrate but they attach
to the enzyme at a different place to the active site. When they do this they
alter the overall 3-D shape of the enzyme and the shape of the active site
meaning substrate can no longer fit in. If there is enough inhibitor present the
reaction can be stopped.
Coenzymes and prosthetic groups
Some enzymes can only work is a non-proteins substance is present, and these
substances are called co-factors.
Coenzymes – are small, organic, non-protein molecules that bind to the active
site for a short time, either just before or at the same time as the substrate.
They therefore take part in the reaction, and are changed but they are recycled
to take part in the reaction again. Vitamin B3 (nicotinamide) is used to make a
coenzyme for the enzyme pyruvate dehydrogenase which catalyses one of the
reactions involved in respiration. Without this, normal growth cannot happen
and a disease called pellagra develops.
Prosthestic groups- a coenzyme that is part of an enzyme molecule is called a
prosthestic group, and they contribute to the overall 3D-shape of the enzyme.
Carbonic anhydrase contains a zinc-based prosthetic group and is involved in
the production of carbonic acid from carbon dioxide and water.
Poisons and drugs- interfering with enzymes
Many poisons inhibit or overactivate enzymes e.g. potassium cyanide inhibits
cell respiration as it is a non-competitive inhibitor for cytochrome oxidase.
Ethylene glycol poisoning occurs it car antifreeze is ingested. It is broken down
in the live by alcohol dehydrogenase o form oxalic acid which is toxic. A large
dose of alcohol (ethanol) can be given which acts as a competitive inhibitor for
alcohol dehydrogenase and reduces the amount of oxalic acid produced.
Antibiotics - Can only treat bacterial infections. Penicillin inhibits bacterial
enzymes which form cross-links in bacterial cell walls- no new bacteria made.
Resistance to antibiotics is becoming a problem. Individual bacteria within a
given population could have mutated genes which lead to altered enzymes
which are capable of deactivating antibiotics. These then survive and so the
more we are using antibiotics, the more bacteria are killed that are killed to it
leaving the resistant ones.
Many strains of bacteria can produce beta-lactamase which can break down
penicillin and so penicillin is less useful than it used to be.
Snake venom- Venom is a mixture of toxins and different enzymes. These
enzymes include phosphodiesterases which affect the working of the prey
heart so blood pressure falls. Snake venom also contains acetyl cholinesterase
inhibitor. This enzyme is involved in nerve transmission so the snake venom
causes paralysis. Venom often contain ATP-ases which break down ATP in the
prey so that they lack energy.