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
glucose levels, is a the tertiary structure.
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.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

Proteins
• Contain carbon, hydrogen, oxygen and nitrogen (additionally sulphur is common
component, but it is not present in all proteins)
• Proteins are large organic compounds made of amino acids arranged into one or more
linear chains

Leucine – an amino acid

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Alanine Arginine Leucine

Here are three of

the twenty-one
amino acids found
in eukaryotes.
Identify what parts
of their structures
are identical.

http://commons.wikimedia.org/wiki/File:Alanine.png
http://commons.wikimedia.org/wiki/File:Arginine.png
http://commons.wikimedia.org/wiki/File:Leucine.png
2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Alanine Arginine Leucine

Yeah, that bit…

2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Drawn slightly differently you can see the bit that is

always the same and the R Group.
The R group is like x in an equation. It is a variable
that stands in for a bunch of different side chains

http://commons.wikimedia.org/wiki/File:AminoAcidball.svg
2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

A
sim

m
ato
pl
eH

n
bo
gr
ou

car
p

(α)
The amine

al
group (NH2)

ntr
Ce
The carboxyl
group (COOH)
n.b. this is an
acidic group

Look out for this structure

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.

Ribosomes are the molecules within

cells that facilitate the formation of
peptide bonds and hence where
polypeptides are synthesized

peptide bond

https://en.wikipedia.org/wiki/File:Peptide_syn.png
http://www.rcsb.org/pdb/education_discussion/molecule_of_the_month/images/2wdk_2wdl_front.jpg
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.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

Hydroxyproline is an
example of an amino acid
created not by the genetic

prolyl hydroxylase
code, but modification, after
polypeptide formation, of
proline (by the enzyme prolyl
hydroxylase).

• This modification of proline

increases the stability of the
collagen triple helix.
• Collagen is a a structural protein
used to provide tensile strength in
tendons, ligaments, skin and
blood vessel walls.

http://chempolymerproject.wikispaces.com/file/view/collagen_%28alpha_chain%29.jpg/34235269/collagen_%28alpha_chain%29.jpg
2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

“OMG I HAVE TO LEARN THE

NAMES OF ALL 20 !?!?”

“Relax, no you don’t, you just

need an awareness of the
concepts as outlined.”
http://commons.wikimedia.org/wiki/File:Amino_Acids.svg
2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.
2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.
2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

If a polypeptide contains just 7 amino acids there can be 207

= 1,280,000,000 possible polypeptides generated.

Given that polypeptides can contain up to 30,000 amino acids (e.g.

Titin) the different possible combinations of polypeptides are
effectively infinite.
2.4.U4 The amino acid sequence of polypeptides is coded for by genes.

peptide bond

Ribosomes are the site of

polypeptide synthesis,
but ribosomes need a
template – the
messenger RNA, which,
in turn, is translated by
transfer RNA molecules
which, in turn, carry
specific amino acids.

Q – Where does the messenger RNA come from?

https://en.wikipedia.org/wiki/File:Peptide_syn.png
2.4.U4 The amino acid sequence of polypeptides is coded for by genes.
Nature of science: Looking for patterns, trends and discrepancies - most but not all organisms assemble proteins
from the same amino acids. (3.1)

Almost all organisms use their genetic code

to produce the same 20 amino acids*. What
can you deduce from this pattern?

*What varies between organisms is how the amino acids are

combined into different polypeptides and proteins.

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.U6 The amino acid sequence determines the three-dimensional conformation of a protein. AND 2.4.U5 A
protein may consist of a single polypeptide or more than one polypeptide linked together.

Proteins may consist of a single polypeptide

or multiple polypeptides that fold together.
7.3.U7 The sequence and number of amino acids in the polypeptide is the primary structure. AND 7.3.U8 The secondary
structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding. AND 7.3.U9 The tertiary
structure is the further folding of the polypeptide stabilized by interactions between R groups. AND 7.3.U10 The quaternary
structure exists in proteins with more than one polypeptide chain.

The four levels of protein structure. The 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
n.b. although you don’t need to be able to outline the different important for the haemoglobin)
levels of structure for knowing of them helps to understand the function (e.g. specificity • Fibrous and
difference between globular and fibrous proteins. This is though of active site in enzymes) Globular proteins
• Globular proteins
required knowledge for AHL (7.3.U7 to 7.3.U10) 
2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein.

Proteins are commonly described as either

being fibrous or globular in nature.
Fibrous proteins have structural roles whereas globular proteins are
functional (active in a cell’s metabolism).

In globular proteins the hydrophobic R groups are folded into the core of the molecule, away from
the surrounding water molecules, this makes them soluble. In fibrous proteins the hydrophobic R
groups are exposed and therefore the molecule is insoluble.
2.4.U7 Living organisms synthesize many different proteins with a wide range of functions.

Usage of proteins 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.
Tubulin is the subunit of microtubules that give animals cells
Cytoskeletons
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.
Blood clotting Plasma proteins act as clotting factors that cause blood to turn
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.

Usage of proteins Nothing can compare with the versatility of proteins. Their
functionality and usage in organisms is unrivalled.
Function Description Key examples
Membrane proteins cause adjacent animal cells to stick to each
Cell adhesion
other within tissues.
Membrane Membrane proteins are used for facilitated diffusion and active
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.

The proteome
Environmental factors
Genome: all of the genes of a cell, a tissue or
The environment influences what
an organism proteins an organism needs to
produce and in what quantity.
The genome determines what proteins an organism can Example factors would be
possibly produce. A genome is unique to most individuals nutrition, temperature, activity
(identical twins and clones share a genome) 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.

The proteome
Q – Genome or proteome, which is larger? Explain the 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.

The 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.

Denaturation of proteins
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
Heat can cause often become insoluble and form a precipitate.
denaturation:
vibrations
within the
molecule breaks Extremes of pH can cause
intramolecular denaturation: charges on R groups
bonds or are changed, breaking ionic bonds
interactions. 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
2.4.A2 Denaturation of proteins by heat or by deviation of pH from the optimum.

Denaturation of proteins

The background image shows white smokers, a particular kind of hydrothermal vent
which produces very hot carbon dioxide gas. These vents can be found deep in
oceans and produce temperatures in excess of 100 °C, but life can still be found
around them.

Thermophiles are organisms (often archea or eubacteria) that live in relatively hot
conditions (45 to122 °C). In order that they can survive their proteins are stable at
the higher than normal temperatures they experience.

https://en.wikipedia.org/wiki/File:Champagne_vent_white_smokers.jpg
2.4.A2 Denaturation of proteins by heat or by deviation of pH from the optimum.

Investigating the denaturation of proteins

Available equipment:
• Waterbaths
• Albumen otherwise known as egg white
• Thermometers
• Colorimeters (optional)

Your task: determine the temperature

stability of albumen

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

Jason de Nys