Title: Lesson 2 B.2 Proteins Function and
Structure
Learning Objectives:
– Understand the functions and structures of Proteins
– Understand how proteins are formed through condensation reactions
Introducing proteins
Proteins are a diverse group of large and complex polymer
molecules, made up of long chains of amino acids.
They have a wide range of biological roles, including:
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structural: proteins are the
main component of body
tissues, such as muscle,
skin, ligaments and hair
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catalytic: all enzymes are
proteins, catalyzing many
biochemical reactions
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signalling: many hormones and receptors are proteins
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immunological: all antibodies are proteins.
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Functions of proteins
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There are as many as ten million different protein molecules that may exist in
nature, each with a unique structure and function.
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We can classify two main types of protein:
Fibrous proteins
Globular proteins
- Structural components
- Tools that operate at the molecular level
(enzymes, carriers, receptors)
- Elongated molecules with dominant
secondary structure
- Compact spherical molecules with
dominant tertiary structure
- Insoluble in water
- Soluble in water
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Examples of the differences between fibrous and
globular
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Fibrous proteins – responsible for structure, support, and movement
Globular proteins – responsible for driving reactions of metabolism
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Fibrous proteins
Fibrous proteins are formed from parallel polypeptide chains
held together by cross-links. These form long, rope-like fibres,
with high tensile strength and are generally insoluble in water.
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collagen – the main
component of connective
tissue such as ligaments,
tendons, cartilage.
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keratin – the main
component of hard
structures such as hair,
nails, claws and hooves.
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silk – forms spiders’ webs and silkworms’ cocoons.
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Globular proteins
Globular proteins usually have a spherical shape caused
by tightly folded polypeptide chains.
The chains are usually folded so that hydrophobic groups are
on the inside, while the hydrophilic groups are on the outside.
This makes many globular proteins soluble in water.
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transport proteins – such
as haemoglobin,
myoglobin and those
embedded in membranes.
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enzymes – such as lipase
and DNA polymerase.
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hormones – such as
oestrogen and insulin.
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The general structure of amino acids
All amino acids have the same general structure: the only
difference between each one is the nature of the R group.
The R group therefore defines an amino acid.
amino
group
carboxylic
acid group
R group
The R group represents a side chain from the central ‘alpha’
carbon atom, and can be anything from a simple hydrogen
atom to a more complex ring structure.
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The structure of proteins
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Proteins are long chain molecules (polymers) present in all cells.
They are made up of 2-amino acids. (this means that the amine group
is on carbon number 2, while the carboxylic acid group is on carbon
number 1)
There are two forms of an amino acid: one that is neutral (with -NH2
and -COOH groups) and one that is zwitterionic (with -NH3+ and COO- groups).
A zwitterion has both positive and negative charge in one molecule.
The R group differs from
one amino acid to the next,
therefore the ‘R’ group is
the feature that defines the
amino acid.
There are roughly 20 naturally occurring proteins
Each is given a three-letter abbreviation, e.g. when R=H, this is called
Gly.
NOTE: A complete list of all amino acids used in proteins is given in
section 33 of the IB data booklet…
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Gly
The 20 naturally-occurring amino acids
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Amino acids can be classified according to the chemical
nature of their R group…
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- Usually based on their different polarities of the R group
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More about zwitterions…
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Amino acids are crystalline compounds with high melting points (above 200oC)
They have much greater solubility in water than in non-polar solvents
Amino acids usually move in an electric field… this suggests the amino acids contain charged
groups…
The charges are a result of acid-base behaviour…
In aqueous solution and in crystalline form, amino acids commonly exist as zwitterions (these
contain positive and negative charges within the molecule…
Zwitterions are sometimes referred to
as internal salts because charges
result from internal acid-base
reactions…
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Transfer of a proton (H+) from the acid
group to the basic group in the same
amino acid…
These zwitterion amino acids are amphoteric or amphiprotic…
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In aqueous solution they will accept and donate H+ according to changes in the pH of the
medium:
In the zwitterion it is the conjugates of
the acidic and basic groups that are
responsible for this property.
At high pH (low [H+]), reaction 1 is favoured as the –NH3+ group loses
it’s H+ and forms an anion
At low pH (high [H+]), reaction 2 is favoured as the –COO- group gains
H+ and forms an cation
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As pH affects the equilibrium position of
these reactions, it influences the charge of
an amino acid…
Summary of effects of pH on charge
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This assumes that the R group is an uncharged group…
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Positively charged at low pH
Negatively charged at high pH
Intermediate pH where there is no net charge is called the isoelectric point  will not be
able to move in an electric field
With no net charge, there is minimum mutual repulsion between molecules so will be
least soluble
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Some examples of pH of isoelectric point data…
More data can be found in section
33 in the IB data booklet…
• Uncharged R groups will have
the same isoelectric pH
• If the R group has an acidic or
basic group, then pKa and pKb
values of these groups will
influence the charge as pH
changes
• Hence lysine and aspartic acid
have different isoelectric points
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Amino acids act as pH buffers
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These equations show that amino acids act
as pH buffers
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By reacting with both H+ and OH- ions,
amino acids cause the pH to be resistant
to change to the addition of small amounts
of acid or alkali (refer back to chapter 8 or
see next 2 slides for a refresher!)
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Amino acids are important in maintaining a
constant pH in cells, as many protein
components such as enzymes are
extremely sensitive to pH
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Response to added acid and base
Addition of acid (H+)
 H+ will combine with the base COO- to form COOH (thus removing most of
the added H+)
Conjugate
Basic Salt
Added
acid
Addition of base (OH-)
 OH- will combine with the acid COOH to form COO- and H2O (thus removing
most of the added OH-)
Acid
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Added
base
As the added H+ and OH-, they do not persist in the solution  pH is largely
unchanged
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Response to added acid or alkali
Addition of acid (H+)
 H+ will combine with the base NH3 to form NH4+ (removing most of the added
H +)
2
Base
Added acid
3
Addition of base (OH-)
 OH- will combine with the acid NH4+ and form NH3 and H2O (removing most of
the OH-)
3
Conjugate Acidic Salt
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2
Added base
As the added H+ and OH- are used, they do not persist in the solution  pH is
largely unchanged.
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Peptide bonds and dipeptides
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Amino acids link together though condensation reactions
Each amino acid has an amine group, which is basic, and a carboxyl group, which is acidic.
Each one has a different R group.
Two amino acids join in a condensation reaction (where a molecule of water is lost) by a
peptide bond (or an amide link) or C(O)NH bond.
The product from this reaction would be a dipeptide and a water molecule.
Note: By convention, when
drawing amino acids:
• The free –NH2 group (Nterminal) is draw on the left
hand side of the amino acid.
• The free –COOH group (Cterminal) is drawn on the
right.
glycine
glycine
Peptides
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In your exercise book, show how a peptide bond would be formed
between two alanine amino acids (before and after).
Label the R group, amino group and carboxyl group.
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When you link three amino acids by a condensation reaction, you will make a tripeptide
and 2 molecules of water
Eventually a chain of linked amino acids known as a polypeptide will be formed from
many condensation reactions
A general equation for the synthesis of a polypeptide from its amino acids can be written
as follows:
Look up the structures of the R groups in your IB data booklet, section 33…
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What if we change the order of amino acids?
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We can link letters of the alphabet in different orders to make different words (e.g. eat, ate,
tea)
Think of different coloured beads in a necklace, we can change the order to make a different
necklace… Different combinations of amino acids can make an almost infinite variety of
proteins…
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Consider making a necklace with the choice of 20 different coloured beads, with each colour
being used as many times as you like. In each position you would have a choice of 20 different
possibilities, imagine how many different combos you would have!
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If we were building a tripeptide with a choice of 20 different amino acids, we would have
20x20x20=8000 possibilities!
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