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BI1507
PROTEINS
Lecture 1
AIMS
To review:
protein functions
monomer (amino-acid) structure
polymer (polypeptide) structure
amino-acid isomerism
examples of the 20 coded amino-acids.
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REFERENCES
Purves
Edition 8 pp. 42-49.
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1 WHY STUDY PROTEINS?
A Present in all cells;
human cell contains ~104 different
proteins.
B
Their structures
(and hence functions)
are determined genetically.
DNA structure
genetic
information
stored
directs
protein structure
genetic
information
used (‘expressed’)
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C All biomolecules are made, function,
and then broken down through
reactions using protein catalysts.
D >1400 human genetic diseases are
caused by loss of/defect in particular,
single proteins.
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2 PROTEIN FUNCTIONS
Wide variety:
no other biomolecules are so versatile.
Many functions depend on interaction of
the protein with another molecule:
often the interaction is specific.
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A Enzymes
biological catalysts
very efficient
very specific
bind to reactants
(‘substrates’)
most water-soluble,
globular.
B Structural
most water-insoluble,
fibrous
e.g. hair keratin.
C Movement
e.g. muscle myosin.
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D Transport
e.g. O2-carrying
haemoglobin.
E Protective
e.g. antibodies.
F Hormones
e.g. insulin.
G Storage
e.g. milk casein.
H Receptors
e.g. retina rhodopsin.
I
Gene regulation
some proteins bind to DNA
and switch genes on or off.
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What is it about protein structure that
allows such versatility?
A surprise(?):
In general terms,
all proteins have the same molecular
structure.
All are linear polymers
made of -amino-acid monomers.
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3 MONOMER (AMINO-ACID)
STRUCTURE
[See: Purves, p. 42.]
Note
 carbon;
 amino group;
 carboxyl group;
side-chain (R group), which is
different in different amino-acids.
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4 POLYMER (POLYPEPTIDE)
STRUCTURE
[See:
Note
Purves, p. 44.]
peptide (amide) bond,
made by water elimination
(later BI1505 lectures
show how it is made in cells);
amino
(N terminus);
carboxy
(C terminus).
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The polymer is called a ‘polypeptide’.
How big are proteins?
Total monomers
present
insulin
51
lysozyme
129
haemoglobin
574
glutamate
dehydrogenase
~8300
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No. of
polypeptides
2
1
4
~40
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5 AMINO-ACID ISOMERISM
 carbon has 4 different groups attached,
arranged tetrahedrally.
2 ways in which they can be arranged in
space,
giving 2 (optical) isomers,
the L- and D- forms.
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Amino-acid isomers:
[See:
Note
the
two,
Purves, pp. 40-41.]
non-superimposable,
mirror-image structures.
Only L-isomers occur in proteins.
It is not clear why this evolutionary
‘decision’ was made.
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6 EXAMPLES OF THE 20 CODED
AMINO-ACIDS
>300 amino-acids are found in nature.
Just 20 are used to make proteins.
Examples of the 20
A Simplest
glycine
[See: Purves, p. 43.]
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B Non-polar (hydrophobic)
alanine
phenylalanine
[See: Purves, p. 43.]
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C Polar (hydrophilic)
serine
[See: Purves, p. 43.]
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D Charged at pH 7 (hydrophilic)
glutamate
lysine
[See: Purves, p. 43.]
E S-containing
cysteine
[See: Purves, p. 43.]
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Why (these) 20?
Only they are genetically coded
(by particular DNA triplet code-words).
20, combined in various ways,
are enough to generate
a very large number of protein structures
(and hence functions).
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BI1507
PROTEINS
Lecture 2
AIMS
To review:
levels of protein structure
compound proteins
the link between DNA structure and
protein function.
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1 LEVELS OF PROTEIN STRUCTURE
A PRIMARY
= sequence of amino-acids.
Each protein has a unique,
genetically coded sequence.
With 20 possible occupants for each
position, a very large number of
sequences is theoretically possible;
e.g. for a polypeptide
of 100 amino-acids,
20100 (= 1.27 x 10130) are possible.
This is the source of versatility
in protein structure (and function).
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B SECONDARY
= structures formed by H-bonding
between -NH and C=O groups of the
polypeptide backbone.
There are 2 main types of secondary
structure:
-helix
-sheet.
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The -helix
[See: Purves, p. 45.]
Note the groups involved in the Hbonding, and the periodicity of the helix;
that is, between one amino-acid and the
other to which it is hydrogen-bonded,
there are three intervening amino-acids in
the primary structure of the polypeptide.
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The -sheet
[See: Purves, p. 45.]
Note the groups involved in the H-bonding
and the layering effect produced.
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In many globular proteins,
including enzymes,
both -helix and -sheet may occur.
[See: Purves, p. 47, where this is
illustrated by diagrams of the
structure of lysozyme.]
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C TERTIARY
= folding of the polypeptide in space.
It involves various interactions
of R groups.
(i) van der Waals forces
Non-specific,
weak
attractions
between atoms 0.3 – 0.4 nm apart.
Structures
allowing
contacts are stabilised.
many
such
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(ii) Ionic interactions
between 2 close,
oppositely charged R groups.
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(iii) H-bonds
between R groups
or of R groups
to surrounding water molecules.
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(iv) Disulphide bonds
covalent
between 2 cysteines.
Occur particularly
in extracellular proteins.
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(v) Hydrophobic interactions
Our discussion of secondary and tertiary
structure suggests that proteins have
particular shapes largely because parts of
the polypeptide interact with other parts.
Why should a polypeptide form
H-bonds
ionic bonds
van der Waals interactions within itself,
when it can just as readily form them
with surrounding water molecules?
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The answer is that such intra-polypeptide
interactions occur in an environment
within the polypeptide from which water is
excluded.
Exclusion occurs because hydrophobic R
groups cluster.
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This
clustering
occurs
because
surrounding water molecules are then
more free to H-bond to one another.
So, in globular, water-soluble proteins,
hydrophobic R groups tend to be on the
inside of the protein, (making the waterexclusion
zones
secondary/tertiary
where
structure
the
intra-
polypeptide interactions occur),
while hydrophilic R groups tend to be on
the outside, H-bonding to water, and
making the protein water-soluble.
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In contrast,
proteins embedded in lipid membranes,
and some structural proteins,
e.g. hair keratin,
have many hydrophobic R groups on the
outside,
making the protein water-insoluble.
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D Quaternary
= occurrence of > 1 polypeptide
in the functional protein
e.g. adult human haemoglobin contains
2  polypeptides and
2  polypeptides.
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2 COMPOUND PROTEINS
contain a non-polypeptide part,
the prosthetic group,
necessary for function.
E.g. in haemoglobin,
each of the 4 polypeptides
contains a N/C heterocyclic structure
(‘haem’) with Fe attached
to which O2 binds.
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3 THE LINK BETWEEN DNA
STRUCTURE AND PROTEIN
FUNCTION
linear sequence of DNA triplet code-words
directs
linear sequence of amino-acids in
polypeptides
directs
intra-polypeptide interactions, and
interactions between polypeptide and its
environment
directs
protein shape
directs
protein interactions with other molecules
directs
protein function
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BI1507
ENZYMES
AIMS
To review:
how enzymes increase reaction rates
lysozyme as an example
control of enzyme activity
ribozymes.
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REFERENCES
Purves
pp. 125-135.
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Enzymes are:
biological catalysts
very efficient
very specific
bind to reactants (‘substrates’)
most are water-soluble,
globular proteins
nearly all biochemical
involve them.
reactions
They work in teams,
the product of one enzyme-catalysed
reaction becoming the substrate for
another.
This produces a network of metabolic
pathways in cells,
concerned with providing energy,
making necessary molecules, etc.
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1 HOW ENZYMES INCREASE
REACTION RATES
Enzymes
increase the rate of spontaneous reactions
by decreasing activation energies.
What makes a reaction spontaneous or
non-spontaneous?
Answer:
This depends on what the concentrations
of the reactants are, relative to their
concentrations at equilibrium.
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Suppose equilibrium of the reaction
A
B
occurs when there are
5 molecules of A for every 2 molecules of B.
Now, suppose, in a particular situation,
there are
10 molecules of A for every 2 of B.
Some A is converted spontaneously into B.
A
B
then, is a ‘spontaneous’ reaction.
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If, in a different situation,
there were
3 molecules of A for every 2 of B,
then some B would be converted
spontaneously into A, and
A
B
would be a ‘spontaneous’ reaction.
[A spontaneous reaction occurs with a
-G, that is, a decrease in free energy.]
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‘Spontaneous’ does not mean
‘instantaneous’.
For the complex reaction
wood + O2
CO2 + H2O
+ smoke + ashes
the equilibrium and the ‘concentrations’
of the reactants are such that spontaneous
flow always occurs
Nevertheless, wood is generally stable over
long periods in the presence of O2.
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Why do spontaneous reactions not occur
instantaneously?
Answer:
an input of energy is needed,
to move the reactants (e.g. wood and O2)
from their fairly stable state.
This energy is the activation energy of the
reaction.
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Energy profile for a spontaneous reaction
A
[See
B
Purves, p. 126.]
Note: the axes of the graph;
the transition state, which has a
higher free energy than either A or
B;
the activation energy, which is the
difference in free energy between
the free energy of A and that of the
transition state;
the fact that B has a lower free
energy than A.
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There are 2 ways to increase the rate of a
spontaneous reaction:
1 Heat reactants
The input in energy allows passage
through the activation energy barrier.
2 Lower the activation energy barrier.
This is what enzymes do.
In terms of our ‘wood’ example:
1 burn the wood in air;
2
feed
the
shipworms.
wood
to
termites
or
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Enzymes do not
‘shift’ equilibria;
make non-spontaneous reactions
spontaneous.
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2 LYSOZYME AS AN EXAMPLE
Lysozyme is an enzyme found in
egg white, saliva, tears.
It acts as a natural antibiotic, because it
catalyses the cutting of polysaccharide
chains (made of sugar monomers) in
bacterial walls, causing the cells to lyse
(i.e. burst).
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The reaction is a hydrolysis:
and is spontaneous,
but certainly not instantaneous
(the cell wall is stable and very tough).
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This is because, for hydrolysis,
the sugars need to be distorted
before the bond between them will break.
The distorted form is called
the transition state
(look back at the energy profile diagram).
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Lysozyme has a groove
(the enzyme’s active site)
into which the chain fits precisely.
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When the enzyme binds,
it distorts the chain,
so that the transition state is easily
reached.
Once the chain is broken,
the enzyme releases it,
and can repeat the process.
Only certain chains fit the active site:
this
is
the
specificity.
origin
of
the
enzyme’s
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3 CONTROL OF ENZYME ACTIVITY
An example is feed-back inhibition.
Consider a metabolic pathway
enzyme a
A
B
Z
the function of which is to make Z.
Often, when sufficient Z is present, then,
at that concentration, it ‘feeds-back’ and
inhibits enzyme a.
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It does this by binding non-covalently to a
site
other than the active site,
causing the enzyme protein
to change shape,
so that it no longer binds (or processes)
the substrate so well.
This is called
allosteric (other site) inhibition.
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For the organism,
this means that when there is sufficient Z,
its synthesis slows.
When [Z] falls, the inhibition is relieved,
and its rate of synthesis increases.
A neat control system:
the rate of synthesis of Z depends on [Z],
and [Z] stays ~ constant in the cell.
Allosteric
occurs.
activation
of
enzymes
also
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4 RIBOZYMES
Enzymes are proteins.
We know that protein structure is directed
by DNA structure.
In fact,
sequence of bases in DNA
directs
sequence of bases in RNA
directs
amino-acid sequence in proteins.
Nowadays, protein enzymes catalyse the
synthesis of DNA, RNA,
but, before there were proteins,
how were nucleic acids made?
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In 1982,
a few RNA molecules were shown to act as
catalysts, called ‘ribozymes’.
Perhaps they are remnants of very early,
pre-protein catalysts.