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Proteins
• Learning objective
• To be able to describe how bonds are
made between amino acids forming
polypeptides
Methionine
O
Histidine
H
N
O
S
OH
H3C
OH
NH2
N
CH3
Isoleucine
NH2
O
O
Phenylalanine
H3C
OH
OH
NH2
NH2
O
O
Leucine
Tryptophan
H3C
OH
OH
CH3
NH2
NH2
NH
CH3
O
H2N
Lysine
O
Valine
OH
NH2
H3C
OH
NH2
• Proteins are the most complex and most diverse
group of biological compounds. They have an
astonishing range of different functions.
• How many can you think of?
• Structure e.g. collagen (bone, cartilage, tendon),
keratin (hair), actin (muscle)
• Enzymes e.g. amylase, pepsin, catalase, etc (>10,000
others)
• Transport e.g. haemoglobin (oxygen), transferrin
(iron)
• Pumps e.g. Na+K+ pump in cell membranes
• Motors e.g. myosin (muscle), kinesin (cilia)
• Hormones e.g. insulin, glucagon
• Receptors e.g. rhodopsin (light receptor in retina)
• Antibodies e.g. immunoglobulins
• Storage e.g. albumins in eggs and blood, caesin in
milk
• Blood clotting e.g. thrombin, fibrin
• Lubrication e.g. glycoproteins in synovial fluid
• Toxins e.g. diphtheria toxin
• Antifreeze e.g. glycoproteins in arctic flea
• and many more!
Proteins
• Proteins contain the elements C H O N & sometimes S
• They are made by condensation reactions between
amino acids forming long polypeptide chains.
• The properties of each individual protein are
determined by the aa sequence
• There are 20 different R groups, and so 20 different
amino acids e.g.
•Glycine R=H
•Alanine R=CH3
• Since each R group is slightly different, each amino
acid has different properties, and this in turn means
that proteins can have a wide range of properties
Amino acids
Draw the general
structure of an amino
acid molecule
There is a central carbon
atom (called the "alpha
carbon"), with four
different chemical
groups attached to it:
a hydrogen atom
a basic amino group
an acidic carboxyl group
a variable "R" group (or
side chain)
R
O
H
H
N
C
H
amino
C
O H
carboxyl
Amino acids are so-called because they have both amino
groups and acid groups, which have opposite charges.
At neutral pH (found in most living organisms), the
groups are ionised, so there is a positive charge at one
end of the molecule and a negative charge at the other
end.
• In a neutral solution and in a solid state
amino acids exist as a dipolar ion.
• H3N+ – CH2 – COO• The ion is formed as a result of an internal
acid base reaction the COOH group donates
a proton to the NH2 group
• This kind of ion is called a zwitterion
• Amino acids can therefore exist in three
forms depending on the pH
The charge on the amino acid changes with pH:
low pH (acid)
neutral pH
high pH (alkali)
It is these
changes in
charge with
pH that
explain the
effect of pH
on enzymes.
• Proteins are said to be amphoteric and
can act as buffers
• An amphoteric substance can act as
both an acid an a base
• Buffers resist changes in pH
Polypeptides
• Amino acids are joined together by
peptide bonds.
• The reaction involves the formation of a
molecule of water in another
condensation polymerisation reaction
Peptide bonding
H
H
R
N
C
H
C
O
O H
H
H
R
N
C
H
C
O
O H
Peptide bonding
H
H
R
N
C
H
C
O
O H
H
H
R
N
C
H
C
O
O H
Peptide bonding
H
H
R
N
C
H
C
O
H
H H
O
R
N
C
H
C
O
O H
Peptide bonding
H
H
R
N
C
C
O
H
H
R
N
C
H
C
O
O H
Peptide bond
H H
O
water
A condensation reaction
Peptide bonding
H
H
R
N
C
H
R
O
C
N
H
A dipeptide
C
H
C
O
O H
When two amino acids join together a dipeptide is
formed. Three amino acids form a tripeptide.
Many amino acids form a polypeptide. e.g.:
+NH3-Gly — Pro — His — Leu — Tyr — Ser — Trp —COO-
In a polypeptide there is always one end with a free
amino (NH3) group, called the N-terminus, and one end
with a free carboxyl (CO2) group, called the C-terminus.
• In a protein the polypeptide chain may
be hundreds of amino acids long.
• Amino acid polymerisation to form
polypeptides is part of protein
synthesis.
• It takes place in ribosomes, and is
special because it requires an RNA
template.
• The sequence of amino acids in a
polypeptide chain is determined by the
sequence of the genetic code in DNA.
• The diagram shows the structural formulae of two amino acids
Amine
group
Acid
group
R group
• Name one chemical element found in all amino acids, but not in
monosaccharides.
• Nitrogen / N (not N2)
• (ii) What type of chemical reaction occurs to form a dipeptide?
• Condensation
• (iii) Draw around the amine group, the acid group and the R
group for each amino acid and label them
• (iv) Draw the structural formula of the dipeptide formed when
these two amino acids combine.