2.4 Proteins
• Essential idea: Proteins have a very wide
range of functions in living organisms.
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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 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
2.4.U1
2.4.U2
2.4.U3
2.4.U4
2.4.U5
2.4.U6
2.4.U7
2.4.U8
2.4.A1
2.4.A2
2.4.S1
Statement
Guidance
Amino acids are linked together by condensation to
form polypeptides.
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.
Amino acids can be linked together in any
sequence giving a huge range of possible
polypeptides.
The amino acid sequence of polypeptides is coded
for by genes.
A protein may consist of a single polypeptide or
more than one polypeptide linked together.
The amino acid sequence determines the threedimensional conformation of a protein.
Living organisms synthesize many different
proteins with a wide range of functions.
Every individual has a unique proteome.
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 is
of protein functions.
not needed.
Denaturation of proteins by heat or by deviation of Egg white or albumin solutions can be used in
pH from the optimum.
denaturation experiments.
Drawing molecular diagrams to show the formation
of a peptide bond.
Re-read chapter 5 of your textbook!
• Review your chapter 5 reading guide
• Review your macromolecule matrix
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
**Remember, protein
synthesis occurs on a
ribosome
Puh-puh-puh-peptide
Puh-puh-puh-protein
Both start with P!
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 21 amino acids in eukayotes, but only 20 amino acids
are encoded by the universal genetic code. There are 23
proteinogenic amino acids, 20 in the standard genetic code and an
additional 3 that can be incorporated by special translation
mechanisms
http://commons.wikimedia.org/wiki/File:Amino_Acids.svg
Hydroxyproline is an example
of an amino acid created not
by the genetic code, but
modification, after polypeptide
formation, of proline (by the
enzyme prolyl hydroxylase).
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•
prolyl hydroxylase
2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes.
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.
**This would make a good test question!
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.
2.4.U6 The amino acid sequence determines the three-dimensional conformation of a protein.
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.
There are four levels of protein structure. Which level a protein conforms to is
determined by it’s amino acid sequence.
(Polypeptide)
• The order / sequence of the
amino acids of which the protein
is composed
• Formed by covalent peptide
bonds between adjacent amino
acids
• Controls all subsequent levels of
structure
• The chains of amino acids fold or
turn upon themselves
• Held together by hydrogen bonds
between (non-adjacent) amine
(N-H) and carboxylic (C-O) groups
• H-bonds provide a level of
structural stability
• Fibrous proteins
n.b. although you don’t need to be able to outline the 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)
• The polypeptide folds and
coils to form a complex
3D shape
• Caused by interactions
between R groups (Hbonds, disulphide
bridges, ionic bonds and
hydrophilic / hydrophobic
interactions)
• Tertiary structure may be
important for the
function (e.g. specificity
of active site in enzymes)
• Globular proteins
• The interaction
between multiple
polypeptides or
prosthetic groups
• A prosthetic group
is an inorganic
compound
involved in a
protein (e.g. the
heme group in
haemoglobin)
• Fibrous and
Globular proteins
We covered protein formation in our chapter 5 reading guide!
BUT….Lets do a simulation activity so that we can remember!
We will do this in class but if you miss class or don’t finish here is how
to access this activity. Once you start you must finish in the same
setting as the program won’t save.
• Go to this website:
http://mw.concord.org/modeler/?gclid=CMW1MDqscoCFQgGaQodqxMNFw
• You will have to download molecular workbench to
your computer
• You will see this:
• You only care about this line:
Click on this
• You will see this:
Click on this
• You will see this:
Go through all activities!
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.
Nothing can compare with the versatility of proteins. Their functionality and usage in
organisms is unrivalled.
Function
Description
There are thousands of different enzymes to catalyze specific
chemical reactions within the cell or outside it.
Actin and myosin together cause the muscle contractions used
Muscle contraction
in 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,
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.
Catalysis
Key examples
Rubisco
collagen
• 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
Cell adhesion
Membrane
transport
Hormones
Receptors
Packing of DNA
Immunity
Description
Key examples
Membrane proteins cause adjacent animal cells to stick to each
other within tissues.
Membrane proteins are used for facilitated diffusion and active
transport, and also for electron transport during cell respiration
and photosynthesis.
Some such as insulin, FSH and LH are proteins, but hormones are
Insulin
chemically very diverse.
Binding sites in membranes and cytoplasm for hormones,
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
chromosomes to condense during mitosis.
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.
Rubisco
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Full name ribulose bisphosphate carboxylase
Enzyme - catalyzes the reaction that fixes carbon
dioxide from the atmosphere
We have seen Rubisco before---it’s in the Calvin
Cycle (Photosynthesis).
• Remember, it’s a bit of a ‘pop-tart’ as it has
an affinity for both CO2 and O2 which make
photosynthesis inefficient.
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.
Insulin
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A hormone – signals many cells (e.g. liver cells) to
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
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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
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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
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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.
spider silk
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Different types of silk with different functions
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
an organism
The genome determines what proteins an organism can
possibly produce. A genome is unique to most individuals
(identical twins and clones share a genome)
Environmental factors
The environment influences what
proteins an organism needs to
produce and in what quantity.
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.
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Being a function of both the genome and the
environment to which the organism is exposed the
proteome is both variable (over time) and unique to
every individual (including identical twins and clones).
It reveals what is happening in an organism at a
particular time
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.
Q – Genome or
proteome, which is
larger? Explain the
reasons for your answer.
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
• pH can cause a protein to denature and thus affect the rate of a
reaction
• Temperature can cause a protein to denature and thus affect the rate
of a reaction
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.
Heat can cause
denaturation:
vibrations
within the
molecule breaks
intermolecular
bonds or
interactions.
A denatured protein does not normally return to its former
structure – the denaturation is permanent. Soluble proteins
often become insoluble and form a precipitate.
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
2.4.A2 Denaturation of proteins by heat or by deviation of pH from the optimum.
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.
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
Click4Biology