The document outlines the structure and function of proteins, explaining how amino acids are linked to form polypeptides and how the sequence of these amino acids determines protein conformation. It discusses the roles of proteins in various cellular processes, their synthesis by ribosomes, and the significance of primary, secondary, tertiary, and quaternary structures. Key examples of protein functions such as catalysis, transport, and immune response are also provided, emphasizing the unique characteristics of every individual's proteome and the influence of environmental factors.

1. Proteins (2.4)
IB Diploma Biology
Essential Idea: Proteins have a diverse range of
function that is reflected in their structure

2. Amino Group (-NH2)
Carboxylic Acid Group (-COOH)
A generalized amino acid
The amino group is one of the
reasons why nitrogen is an
important element in living things.
The carboxylic acid group contains an
oxygen double-bonded to the carbon
and a hydroxyl group (-OH) that can be
lost to form new bonds.
The basic structure of the amino acids is common. There are 22 different protein-making
amino acids, though only 20 are coded for in genetic code. Each has its own unique R-group.
Some are polar, others non-polar and their different properties determine their interactions
and the shape of the final protein.

4. this one
(glycine)

5. 2.4.1 Amino acids are linked together by condensation to form polypeptides.
Example of Anabolism by Condensation: The bonds formed are types of
covalent bonds.
Bonding monomers together
creates a polymer (mono = one,
poly = many)

6. 2.4.11 Draw molecular diagrams showing the formation of a peptide bond.

7. 2.4.11 Draw molecular diagrams showing the formation of a peptide bond.

8. 2.4.2 There are twenty different amino acids in polypeptides synthesized on ribosomes.

9. “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.”
2.4.2 There are twenty different amino acids in polypeptides synthesized on ribosomes.

10. Ribosomes are the molecules within
cells that facilitate the formation of
peptide bonds and hence where
polypeptides are synthesized
peptide bond
2.4.2 There are twenty different amino acids in polypeptides
synthesized on ribosomes.

11. 2.4.3 Amino acids can be linked together in any sequence giving a huge
range of possible polypeptides.

12. 2.4.3 Amino acids can be linked together in any sequence giving a huge
range of possible polypeptides.

13. 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.
2.4.3 Amino acids can be linked together in any sequence giving a huge
range of possible polypeptides.

14. https://en.wikipedia.org/wiki/File:Peptide_syn.png
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.
peptide bond
Q – Where does the messenger RNA come from?
2.4.4 The amino acid sequence of polypeptides is coded for by genes.

15. 2.4.4 The amino acid sequence of polypeptides is coded for by genes.

16. 2.4.5 A protein may consist of a single polypeptide or more than one
polypeptide linked together.
Number of
Polypeptides
Example Description
1 Lysozyme
Enzymes in secreted body fluids that kills bacteria by
breaking down the peptidoglycan in their cell walls
3 Collagen
Strong, elastic structural protein found in connective
tissues (skin, bone, muscle, tendons, ligaments)
4 Hemoglobin
Transport protein in red blood cells; Hemoglobin binds
oxygen from the lungs and releases it into tissues with
lower oxygen concentration
Collagen
Hemoglobin
Lysozyme

17. 2.4.6 The amino acid sequence determines the three dimensional
conformation of a protein.
Polypeptides, or chains of amino acids, are the
base (or primary) level of protein structure.
But before they are functional, they must fold
into specific structures based on the order /
structure of their amino acid sequence.
Remember, different amino acids have
different chemical properties (i.e. polar /
hydrophilic, non-polar / hydrophobic, +/-
charged, sulfur-containing, carbon rings, etc.)
The way that these different amino acids
interact with each other and their surrounding
environment (water) determines 3D shape
HL Students: Prepare to learn more in a few
slides!!

18. 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).
NOTE: 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.
2.4.6 The amino acid sequence determines the three dimensional
conformation of a protein.

19. 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
A denatured protein does not normally return to its former
structure – the denaturation is usually permanent. Soluble
proteins often become insoluble and form a precipitate.
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.
2.4.10 Explain the denaturation of proteins by heat or deviation of pH
from the optimum.

20. Thermophiles are organisms (often Archaea) 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
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.
2.4.10 Explain the denaturation of proteins by heat or deviation of pH
from the optimum.

21. Function Description Key Examples
Catalysis
There are thousands of different enzymes to catalyze specific
chemical reactions within the cell or outside it.
Rubisco
Muscle
contraction
Actin and myosin together cause the muscle contractions used in
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
strengthening
Fibrous proteins give tensile strength needed in skin, tendons,
ligaments and blood vessel walls.
Collagen
Blood clotting
Plasma proteins act as clotting factors that cause blood to turn from
a liquid to a gel in wounds.
Transport of
nutrients & gases
Proteins in blood (i.e. Hemoglobin) help transport oxygen, carbon
dioxide, iron and lipids.
Nothing can compare with the versatility of proteins. Their functionality and usage in
organisms is unrivalled.
• Key examples are outlined in more detail.
• Although a key example spider silk is not mentioned above as the table refers to uses within organism
2.4.7 Living organisms synthesize many different proteins with a wide
range of functions.

22. Function Description Key Examples
Cell adhesion
Membrane proteins cause adjacent animal cells to stick to each
other within tissues.
Membrane
transport
Membrane proteins are used for facilitated diffusion and active
transport, and also for electron transport during cell respiration
and photosynthesis.
Hormones
Some such as insulin, FSH and LH are proteins, but hormones are
chemically very diverse.
Insulin
Receptors
Binding sites in membranes and cytoplasm for hormones,
neurotransmitters, tastes and smells, and also receptors for light in
the eye and in plants.
Rhodopsin
Packing of DNA
Histones are associated with DNA in eukaryotes and help
chromosomes to condense during mitosis.
Immunity
This is the most diverse group of proteins, as cells can make huge
numbers of different antibodies.
Immunoglobulins
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
• Lactase for producing lactose-free dairy products
• Disease treatments
Genetically modified organisms are often used as to produce proteins. This however is still a technically difficult and
expensive process.
2.4.7 Living organisms synthesize many different proteins with a wide
range of functions.

23. Rubisco
• Full name ribulose bisphosphate
carboxylase
• Enzyme - catalyzes the reaction that
fixes carbon dioxide from the
atmosphere (i.e. takes the carbon
from CO2 and builds it into Glucose)
• 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 within photosynthetic
organisms
2.4.9 Identify rubisco, insulin, immunoglobulins, rhodopsin, collagen,
and spider silk as examples of the range of protein functions.

24. • A hormone – signals many cells (e.g. liver
cells) to absorb glucose and help lower
the glucose concentration of the blood
• Affected cells have receptor (proteins) on
their surface to which insulin can 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.
Insulin
2.4.9 Identify rubisco, insulin, immunoglobulins, rhodopsin, collagen,
and spider silk as examples of the range of protein functions.

25. 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 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 (white blood cells)
2.4.9 Identify rubisco, insulin, immunoglobulins, rhodopsin, collagen,
and spider silk as examples of the range of protein functions.

26. Rhodopsin
• A pigment that absorbs light
• Membrane receptor protein of rod cells of the retina (light
sensitive region at the back of the eye)
• Retinal molecule absorbs a single photon of light -> changes
shape -> the rod cell sends a nerve impulse to the brain
• Even very low light intensities can be detected.
2.4.9 Identify rubisco, insulin, immunoglobulins, rhodopsin, collagen,
and spider silk as examples of the range of protein functions.

27. Collagen
• A number of different forms; all are
helical, 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 fibers 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 to bones and teeth
2.4.9 Identify rubisco, insulin, immunoglobulins, rhodopsin, collagen,
and spider silk as examples of the range of protein functions.

28. Spider silk • Different types of silk with
different functions
• Dragline silk is stronger than steel
and tougher than Kevlar
• When the stretched the
polypeptide gradually extends,
making the silk extensible and
very resistant to breaking.
2.4.9 Identify rubisco, insulin, immunoglobulins, rhodopsin, collagen,
and spider silk as examples of the range of protein functions.

29. 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.
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)
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
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…
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.
Q – Genome or proteome,
which is larger?
2.4.8 Every individual has a unique proteome.

30. 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
Q – Genome or proteome, which is larger? Explain the reasons for your
answer.
A – Proteome:
• Not all genes produce polypeptides, but…
• The same gene can be spliced and translated in numerous ways
• 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)
2.4.8 Every individual has a unique proteome.

31. PRIMARY STRUCTURE:
• 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
• Chain of amino acids called
a polypeptide
7.3.7 The sequence and number of amino acids in the polypeptide is
the primary structure.

32. 7.3.8 The secondary structure is the formation of alpha helices and
beta pleated sheets stabilized by hydrogen bonds.
SECONDARY 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
• Fibrous proteins

33. 7.3.9 The tertiary structure is the further folding of the polypeptide
stabilized by interactions between R groups (side-chains).
TERTIARY STRUCTURE:
• The polypeptide folds and coils to
form a complex 3D shape
• Caused by interactions between R
groups (H-bonds, disulfide 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

34. 7.3.10 The quaternary structure exists in proteins with more than one
polypeptide chain.
QUATERNARY STRUCTURE:
• 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 hemoglobin)
• Fibrous and Globular proteins

35. Bibliography / Acknowledgments
Jason de Nys
Chris Paine