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Aspects of Biochemistry
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A collection of my notes I made for aspects of biochemistry. This was a part of CAPE/A-level Biology.
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Aspects of BiochemistryWater
A water molecule consists of two H+ ions and one O2- ion. These ions
are held together by single covalent bonds. Covalent bonds are very
strong thus making it difficult to separate the hydrogen and oxygen
atoms. In the covalent bond, the electrons are pulled closer to the
oxygen atom making it slightly negative due to the oxygen atoms
higher affinity for electrons called, electronegativity. The pull of the electrons towards the oxygen atom
means that the electrons are being moved away from the hydrogen atom. This creates a slight positive
charge on the hydrogen atom. This unequal distribution of charge creates a dipole. The intermolecular
bonds between the water molecules are called hydrogen bonds. Hydrogen bonds are created between
the slightly negative oxygen atom and the slightly positive hydrogen atom of TWO SEPARATE WATER
MOLECULES. Hydrogen bonds are weak and long distance. Water molecules have an
angle of 104.5˚.
Properties of water
Water has an angle of 104.5°
due to the lone pairs of Ice: In the form of ice, water is in its solid state and so the water molecules
electrons on the oxygen atom.
continuously vibrate in the same place. As the temperature drops, the
If all pairs were bonding pairs
the molecule would have an molecules have less energy and each molecule forms 4 hydrogen bonds which
is the maximum number of hydrogen bonds that can be formed. Since the
angle of 109.5°. Each lone pair
(there are 2) decreases the freezing point of water is 0˚C. The water molecules found in ice each have 4
angle by 2.5° causing the hydrogen bonds. The formation of the maximum number of hydrogen bonds
resulting angle to be 104.5°.
causes the water molecules to spread out and cause the water to expand. This
means there is an increase in volume. Therefore, ice is less dene than liquid
water. This causes ice to float on water. Ice insulates the water below it and protects it from
further temperature changes.
Liquid water: Liquid water is denser than ice, therefore it lays below ice. The
maximum density is reached at 4˚C. Colder water at or a little higher than 4˚C
sinks due to its high density. Warmer water rises to the top. Warmer water is
located directly below ice while cold water is found lower.
Specific heat capacity: Specific heat capacity refers to the amount of energy
required to ncrease the temperature of 1g of a substance by 1˚C. Due to the
multiple hydrogen bonds in water, a large amount of heat energy is required
to break these bonds. Because so much energy is required to break these
bonds, water requires a large amount of energy to raise the temperature by
1
, 1˚C. The specific heat capacity of water is 4.2Jg-1˚C-1 (4.2 Joules are required to increase the temperature
of 1 gram od water by 1 degree Celsius.
Latent heat of vaporisation: Water has a high latent heat of vaporisation. The hydrogen bonds in water
prevent the molecules from easily breaking away and becoming a gas. Enough energy must be applied
to break all the hydrogen bonds before the molecules can separate and form water vapour. Water must
be heated to 100˚C before all the molecules have enough energy to break away. Evaporation of water
does not have to occur at 100˚C however. Some molecules have more energy than others (particularly
the surface molecules) and those will break away first.
Latent Heat of Fusion: 300J of energy is required to change 1g of ice to water (i.e., water must lose a
large amount energy to freeze). It is difficult to freeze water because of its high latent heat of fusion
causing it to generally remain as a liquid. The presence of solutes also causes water to have a high latent
heat of fusion. The presence of solutes disrupts the formation of hydrogen bonds between water
molecules making it more difficult to assume the structure taken in the ice state.
Solvent properties: Water is an excellent solvent for polar substances. The
tiny charges on it attract other molecules or ions that are oppositely
charged. The molecules and ions spread around in between the water
molecules (dissolving). Ionic compounds such as sodium chloride (NaCl) will
generally dissolve in water. Covalent compounds with small molecules and
dipoles also dissolve in water (e.g., glucose and amino acids). Quite large
covalent molecules can also dissolve in water if they have plenty of small
electrical charges (e.g., proteins and haemoglobin). Many other large
covalent compounds cannot dissolve in water (e.g., starch, cellulose, other
polysaccharides and fibrous proteins such as collagen).
Density and viscosity: Water is a relatively dense liquid due to its hydrogen
bonds which pull the molecules closer together. Water has a density of
1gcm-1. Water is fairly viscous as a lot of energy is required to push aside the
molecules which are attracted to one another and reluctant to move apart.
Cohesion and surface tension: Water molecules tend to stick together however in liquid water the
hydrogen bonds constantly form and break in a fraction of a second. The attractive force produced by
these hydrogen bonds is called cohesion. Cohesion makes it easier for water to move by mass flow.
Molecules on the surface are pulled closer than inn other parts of the water. This causes water to
occupy the least possible surface area. This is called surface tension.
pH: pH is the measure of concentration of hydrogen ions in a solution. The more H+ ions, the lower the
pH. Water is partially dissociated into hydrogen and hydroxide ions. The amount of hydrogen and
hydroxide ions is equal causing it to have a neutral pH of 7. Proteins which ‘soak up’ (remove) hydrogen
or hydroxide ions are called buffers.
Transparency: Pure water is transparent to visible wavelengths of light. Blue light is able to pass through
greater depths of water than red and green light.
Reactivity: Water is biologically significant as a metabolite as it takes part in many metabolic reactions.
(e.g., the breakdown of large polymer molecules). These are hydrolysis reactions.
2
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