2.

4 Proteins Essential idea: Proteins have a very wide range of

functions in living organisms.

One of the central ideas in Biology is that

structure dictates function. Above you can
see insulin in its secondary, tertiary and
quaternary structures. Polypeptides vary
hugely in the combination and number of
amino acids that they are composed from.
Even if we consider a single polypeptide it's
properties, and hence it's function, would http://www.biotopics.co.uk/as/insulinproteinstructure.html
vary greatly depending on it's level of
structure. Insulin can exist in all these forms,
but the active form, which controls blood By Chris Paine
glucose levels, is a the tertiary structure. https://bioknowledgy.weebly.com/
Understandings, Applications and Skills
Statement Guidance
2.4.U1 Amino acids are linked together by condensation
to form polypeptides.
2.4.U2 There are 20 different amino acids in polypeptides Students should know that most organisms
synthesized on ribosomes. use the same 20 amino acids in the same
genetic code although there are some
exceptions. Specific examples could be used
for illustration.
2.4.U3 Amino acids can be linked together in any
sequence giving a huge range of possible
polypeptides.
2.4.U4 The amino acid sequence of polypeptides is coded
for by genes.
2.4.U5 A protein may consist of a single polypeptide or
more than one polypeptide linked together.
2.4.U6 The amino acid sequence determines the three-
dimensional conformation of a protein.
2.4.U7 Living organisms synthesize many different
proteins with a wide range of functions.
2.4.U8 Every individual has a unique proteome.
2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, The detailed structure of the six proteins
collagen and spider silk as examples of the range selected to illustrate the functions of proteins
of protein functions. is not needed.
2.4.A2 Denaturation of proteins by heat or by deviation of Egg white or albumin solutions can be used in
pH from the optimum. denaturation experiments.
2.4.S1 Drawing molecular diagrams to show the formation
of a peptide bond.
2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the
formation of macromolecules from monomers by condensation reactions.

Example of anabolism by condensation

A ribosome condenses two

amino acids into a dipeptide
forming a peptide bond

The bonds formed are types of covalent bonds.

Bonding monomers together creates a polymer

(mono = one, poly = many)

This is also key to understanding:

• 2.4.U1 Amino acids are linked together by condensation to form polypeptides.
• 2.4.S1 Drawing molecular diagrams to show the formation of a peptide bond.

http://commons.wikimedia.org/wiki/File:Peptidformationball.svg
2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

n.b. there are 22 amino acids, but only 20 amino

acids are encoded by the universal genetic code.
http://commons.wikimedia.org/wiki/File:Amino_Acids.svg
2.4.U4 The amino acid sequence of polypeptides is coded for by genes.
2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein.
2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein.
2.4.U5 A protein may consist of a single polypeptide or more than one polypeptide linked together.
There are four levels of protein structure. Which level a protein conforms to is
determined by it’s amino acid sequence.

(Polypeptide) • The chains of amino acids fold or • The polypeptide folds and • The interaction
• The order / sequence of the turn upon themselves coils to form a complex between multiple
amino acids of which the protein • Held together by hydrogen bonds 3D shape polypeptides or
is composed between (non-adjacent) amine • Caused by interactions prosthetic groups
• Formed by covalent peptide (N-H) and carboxylic (C-O) groups between R groups (H- • A prosthetic group
bonds between adjacent amino • H-bonds provide a level of bonds, disulphide is an inorganic
acids structural stability bridges, ionic bonds and compound
• Controls all subsequent levels of • Fibrous proteins hydrophilic / hydrophobic involved in a
structure interactions) protein (e.g. the
• Tertiary structure may be heme group in
important for the haemoglobin)
function (e.g. specificity • Fibrous and
n.b. although you don’t need to be able to outline the of active site in enzymes) Globular proteins
• Globular proteins
different levels of structure for knowing of them helps to
understand the difference between globular and fibrous
proteins. This is though required knowledge for AHL
(7.3.U7 to 7.3.U10) 
2.4.U7 Living organisms synthesize many different proteins with a wide range of functions.

Nothing can compare with the versatility of proteins. Their functionality and usage in
organisms is unrivalled.

Function Description Key examples

Catalysis There are thousands of different enzymes to catalyse specific Rubisco
chemical reactions within the cell or outside it.
Actin and myosin together cause the muscle contractions used in
Muscle contraction
locomotion and transport around the body.
Cytoskeletons Tubulin is the subunit of microtubules that give animals cells
their shape and pull on chromosomes during mitosis.
Tensile Fibrous proteins give tensile strength needed in skin, tendons, collagen
strengthening ligaments and blood vessel walls.
Plasma proteins act as clotting factors that cause blood to turn
Blood clotting
from a liquid to a gel in wounds.
Transport of Proteins in blood help transport oxygen, carbon dioxide, iron
nutrients and gases and lipids.

• Key examples are outlined in more detail.

• Although a key example spider silk is not mentioned above as the table refers to uses within the
organism
2.4.U7 Living organisms synthesize many different proteins with a wide range of functions.

Function Description Key examples

Membrane proteins cause adjacent animal cells to stick to each
Cell adhesion
other within tissues.
Membrane proteins are used for facilitated diffusion and active
Membrane transport, and also for electron transport during cell respiration
transport
and photosynthesis.
Hormones Some such as insulin, FSH and LH are proteins, but hormones are Insulin
chemically very diverse.
Binding sites in membranes and cytoplasm for hormones,
Receptors neurotransmitters, tastes and smells, and also receptors for light rhodopsin
in the eye and in plants.
Histones are associated with DNA in eukaryotes and help
Packing of DNA chromosomes to condense during mitosis.
Immunity This is the most diverse group of proteins, as cells can make immunoglobulins
huge numbers of different antibodies.

Biotechnologically has allowed us to use proteins in industry examples are:

• enzymes for removing stains in clothing detergent
• monoclonal antibodies for pregnancy tests
• insulin for treating diabetics
• Disease treatments

Genetically modified organisms are often used as to produce proteins. This however is still a technically difficult and
expensive process.
2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the
range of protein functions.

• Full name ribulose bisphosphate carboxylase

Rubisco • Enzyme - catalyses the reaction that fixes carbon
dioxide from the atmosphere
• Provides the source of carbon from which all
carbon compounds, required by living organisms,
are produced.
• Found in high concentrations in leaves and algal
cells

http://upload.wikimedia.org/wikipedia/commons/b/b0/Mint-leaves-2007.jpg
http://upload.wikimedia.org/wikipedia/commons/thumb/7/74/Rubisco.png/220px-Rubisco.png
2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the
range of protein functions.

• A hormone – signals many cells (e.g. liver cells) to

Insulin absorb glucose and help reduce the glucose
concentration of the blood.
• Affected cells have receptor (proteins) on their
surface to which insulin can (reversibly) bind to.
• Secreted by β cells in the pancreas and transported
by the blood.

The pancreas of type I diabetics don’t produce

sufficient insulin therefore they must periodically
inject synthetically produced insulin to correct their
blood sugar concentration.
https://en.wikipedia.org/wiki/File:Inzul%C3%ADn.jpg
http://www.biotopics.co.uk/as/insulinproteinstructure.html
2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the
range of protein functions.

immunoglobulins

• Also known as antibodies.

• Two antigen (a molecule on the pathogen which provokes an immune
response) binding sites - one on each ‘arm’
• Binding sites vary greatly between immunoglobulins (hypervariable) to
enable them to respond a huge range of pathogens.
• Other parts of the immunoglobulin molecule cause a response, e.g.
acting as a marker to phagocytes (which engulf the pathogen)

https://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Antibody_IgG2.png/320px-Antibody_IgG2.png
2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the
range of protein functions.

rhodopsin

• A pigment that absorbs light

• Membrane protein of rod cells of the retina (light sensitive region at the
back of the eye)
• Rhodopsin consists of the opsin polypeptide surrounding a retinal
prosthetic group
• retinal molecule absorbs a single photon of light -> changes shape ->
change to the opsin -> the rod cell sends a nerve impulse to the brain
• Even very low light intensities can be detected.

http://commons.wikimedia.org/wiki/File:Rhodopsin.jpg
https://en.wikipedia.org/wiki/Retina#mediaviewer/File:Fundus_photograph_of_normal_left_eye.jpg
2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the
range of protein functions.

collagen

• A number of different forms

• All are rope-like proteins made of three
polypeptides wound together.
• About a quarter of all protein in the human
body is collagen
• Forms a mesh of fibres in skin and in blood
vessel walls that resists tearing.
• Gives strength to tendons, ligaments, skin and
blood vessel walls.
• Forms part of teeth and bones, helps to prevent
cracks and fractures to bones and teeth

https://en.wikipedia.org/wiki/Tooth_(human)#mediaviewer/File:Teeth_by_David_Shankbone.jpg
http://chempolymerproject.wikispaces.com/file/view/collagen_%28alpha_chain%29.jpg/34235269/collagen_%28alpha_chain%29.jpg
2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the
range of protein functions.

• Different types of silk with different functions

spider silk • Dragline silk is stronger than steel and tougher
than Kevlar
• When first made it contains regions where the
polypeptide forms parallel arrays (bottom)
• Some regions seem like a disordered tangle
(middle)
• When the stretched the polypeptide gradually
extends, making the silk extensible and very
resistant to breaking.

https://en.wikipedia.org/wiki/Spider_silk#mediaviewer/File:Araneus_diadematus_underside_1.jpg
https://en.wikipedia.org/wiki/Spider_silk#mediaviewer/File:Structure_of_spider_silk_thread_Modified.svg
2.4.U8 Every individual has a unique proteome.

Genome: all of the genes of a cell, a tissue or Environmental factors

an organism
The environment influences what
The genome determines what proteins an organism can proteins an organism needs to
possibly produce. A genome is unique to most individuals produce and in what quantity.
(identical twins and clones share a genome) Example factors would be
nutrition, temperature, activity
levels and anything else that
affects a cell’s activities.

Proteome: all of the proteins produced by a

cell, a tissue or an organism.

• Being a function of both the genome and the

environment to which the organism is exposed the Q – Genome or
proteome is both variable (over time) and unique to proteome, which is
every individual (including identical twins and clones).
larger? Explain the
• It reveals what is happening in an organism at a
particular time reasons for your answer.

To analyze a proteome mixtures of proteins are extracted from a

sample and are then separated by gel electrophoresis. The
background shows a stained example of gel electrophoresis.
http://proteomics.arizona.edu/sites/proteomics.arizona.edu/files/1D_Gel_CD_4.png
2.4.U8 Every individual has a unique proteome.

Q – Genome or proteome, which is larger? Explain the reasons for your

answer.

A – Proteome:
• Not all genes produce polypeptides
• Multiple polypeptides and prosthetic groups can interact
• Amino acids can be modified (e.g. Collagen)
• A polypeptide can fold into different levels of structure (e.g. insulin)

To analyze a proteome mixtures of proteins are extracted from a

sample and are then separated by gel electrophoresis. The
background shows a stained example of gel electrophoresis.
http://proteomics.arizona.edu/sites/proteomics.arizona.edu/files/1D_Gel_CD_4.png
2.4.A2 Denaturation of proteins by heat or by deviation of pH from the optimum.

The three-dimensional conformation of proteins is stabilized by bonds or

interactions between R groups of amino acids within the molecule. Most of these
bonds and interactions are relatively weak and they can be disrupted or broken. This
results in a change to the conformation of the protein, which is called denaturation.

A denatured protein does not normally return to its former

structure – the denaturation is permanent. Soluble proteins
often become insoluble and form a precipitate.
Heat can cause
denaturation:
vibrations
within the
molecule breaks
intermolecular
bonds or
interactions. Extremes of pH can cause
denaturation: charges on R groups
are changed, breaking ionic bonds
within the protein or causing new
ionic bonds to form.

http://upload.wikimedia.org/wikipedia/commons/2/22/Fried_egg%2C_sunny_side_up_%28black_background%29.PNG