Download UNIVERSITY REVISION GURU Covalent Bonds • Covalent bonds

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UNIVERSITY REVISION GURU
Covalent Bonds
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Covalent bonds are established due to the sharing of electrons between two or
more atoms, to form a strong molecule.
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Two atoms, covalently bonded, can form a single, double or triple bond. The
greater the bond number (i.e. single, double or triple), the stronger the interaction.
•
These bonds form angles, allowing the molecule to form a shape.
Polarity
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After two atoms react and form covalent bonds, they have polarity. This can
either be ‘Polar’ or ‘Non-polar’.
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If the electrons are equally shared between the two atoms then it is said to be
a ‘Non-polar’ molecule. This generally only occurs when the two atoms are the
same e.g. H2.
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If the electrons are not equally shared between the two atoms, then the
molecule is said to be ‘Polar’. This generally occurs when the two atoms are
different and have different electronegativities. This produces a ‘dipole’.
Non-Covalent Bonds
Ionic Bond
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When the electronegativites of 2 atoms are significantly different (se.g. between
a metal and a non-metal), electrons are transferred, producing an ionic bond. If
the electronegativities are the same or similar, electrons are shared, forming a
covalent bond.
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To produce an ionic bond, electrons must be transferred from one atom to
another, and are not shared. As such, there is no polarity.
Electrostatic Interaction
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Another form of non-covalent bonds is the formation of electrostatic interaction.
This is when there is no transfer of electrons. Instead this is the interaction
between ions, of which opposite charges attract.
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There are three different types of attractions:
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Dipole-Dipole
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Dipole-Charge
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Charge-Charge
Van Der Waals Force
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This is the weakest type of interaction between atoms. It is highly non-specific
and is created due to asymmetry of electrons around the atoms, as the electrons
are constantly changing place over time.
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During Van Der Waals force, one asymmetric atom will induce asymmetry onto
another atom.
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The strength of the force is dependent on the distance between the two atoms:
the closer the atoms get, the stronger the force. However, when the atoms
become too close, the electrons will begin to repel and the strength decreases.
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As such, the strength of bond can be demonstrated by a bell curve.
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PROTEINS, GENES AND GENETICS
Hydrogen Bonds
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Hydrogen bonds are produced between two molecules. One molecule must
contain either nitrogen, oxygen or fluoride atoms, and the other must contain a
hydrogen atom. The interaction occurs between the hydrogen atom, and any of
the aforementioned atoms.
Hydrophobic Interaction
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Since water is a polar molecule, anything that is non-polar is considered to be
hydrophobic. These non-polar molecules do not form hydrogen bonds with
water, but rather stick to themselves.
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A common example of this is oil. Oil and water do not mix, since oil is nonpolar, demonstrated by the separation of the two when attempted to be mixed.
This is known as the ‘Hydrophobic effect’.
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Hydrophobic literally means “water-fearing”.
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Fats have a long hydrocarbon chain and so, they are non-polar. Any
molecule with high amounts of carbon-carbon and carbon-hydrogen bonds will
be non-polar.
Amino Acids
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Amino acids are extremely important. They can be obtained from our diet in the
form of proteins, which are then broken down into single amino acids, ready for
us to use.
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The general structure of an amino acid is unique, in that the central carbon atom
forms four bonds with: an amine, carboxylic acid, hydrogen and a side chain.
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This side chain is always denoted as ‘R’ and can be any molecule or atom.
Figure 1.2
General structure of Amino Acid
COOH
H2N
C
H
R
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The carboxyl group and the amino group can both become ionised. This
means to say that a hydrogen atom can be transferred from the carboxyl group
to the amino group: this transfer is amphoteric.
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This transfer of the hydrogen atom forms a charged structure called a
‘zwitterion’ in the cells of our body. Amino Acids are zwitterions at
physiological pH.
Henderson-Hasselbalch Equation:
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The Henderson-Hasselbalch equation demonstrates the relationship between pH
and the acid/base system.
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UNIVERSITY REVISION GURU
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To derive the Henderson-Hasselbalch equation, consider first the equilibrium
constant, denoted by the following equation, where Ka represents Kacid:
[H+][ A–]
[ HA]
Ka =
This equation can be re-arranged in order to produce the Henderson-
Note:
Hasselblach equation, given by:
pKa is equal to pH
pH = pKa + log
when the groups are
[ A–]
.
[ HA]
ionised at 50%.
Calculation Example 1.0:
If told the pKa of the amino group is 8.5, what % are ionised at pH 6.5?
1. Using the Henderson-Hasselbach equation, insert the values we already know.
This gives: 6.5 = 8.5 + log
[A –]
[H A ]
.
2. Then rearrange the equation, giving: –2 = log
[A –]
.
[HA ]
3. Taking exponentials as an inverse of logs, gives 0.01 = log
[A –]
[HA ]
Note:
.
4. 0.01 represents the ratio between A – and HA. This ratio can be written
1
as 100
,
demonstrating that the concentration of the amino acid is 1, and the
concentration of the salt is 100.
5. Conclude that since the ratio is 1: 100 we have ionisation of 99% at this pH with
that pKa.
Isomers
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An isomer is where one structure has the same molecular formula as another
structure, but has a different chemical structure.
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There are several different types of isomers, split into two main brackets: The
first is the structural (Constitutional) isomer and the second is the Spatial
isomer (stereoisomer).
Figure 1.4
Structural Isomer
H
H O H
H H H
H
•
O
H
H
H H
H
H H H
H H H
I
II
H
H
O
H H
H
H
III
The key type of isomer considered here is a branch of the spatial isomer, named
optical isomers. The optical isomers were given their name due to that fact that
they are able to rotate plane polarised light.
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There are two forms of optical isomers, L-Isomers and D-Isomers, named after
the Latin words dexter and laevus, meaning right and left.
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A– is the amino group,
and HA is the salt.