BIOCHEMICAL
TECHNIQUES:
These
five tests identify the main biologically important chemical compounds. For
each test take a small amount of the substance to test, and shake it in water
in a test tube. If the sample is a piece of food, then grind it with some water
in a pestle and mortar to break up the cells and release the cell contents.
Many of these compounds are insoluble, but the tests work just as well on a
fine suspension.
- Starch (iodine test). To approximately 2 cm³ of test
solution add two drops of iodine/potassium iodide solution. A blue-black
colour indicates the presence of starch as a starch-polyiodide complex is
formed. Starch is only slightly soluble in water, but the test works well
in a suspension or as a solid.
- Reducing Sugars (Benedict's test). All monosaccharides and most
disaccharides (except sucrose) will reduce copper (II) sulphate, producing
a precipitate of copper (I) oxide on heating, so they are called reducing
sugars. Benedict’s reagent is an aqueous solution of copper (II) sulphate,
sodium carbonate and sodium citrate. To approximately 2 cm³ of test
solution add an equal quantity of Benedict’s reagent. Shake, and heat for
a few minutes at 95°C in a water bath. A precipitate indicates reducing
sugar. The colour and density of the precipitate gives an indication of
the amount of reducing sugar present, so this test is semi-quantitative.
The original pale blue colour means no reducing sugar, a green precipitate
means relatively little sugar; a brown or red precipitate means progressively
more sugar is present.
- Non-reducing Sugars (Benedict's test). Sucrose is called a non-reducing
sugarbecause it does not reduce copper sulphate, so there is no direct
test for sucrose. However, if it is first hydrolysed (broken down) to its
constituent monosaccharides (glucose and fructose), it will then give a
positive Benedict's test. So sucrose is the only sugar that will give a
negative Benedict's test before hydrolysis and a positive test afterwards.
First test a sample for reducing sugars, to see if there are any present
bef7ore hydrolysis. Then, using a separate sample, boil the test solution
with dilute hydrochloric acid for a few minutes to hydrolyse the
glycosidic bond. Neutralise the solution by gently adding small amounts of
solid sodium hydrogen carbonate until it stops fizzing, then test as
before for reducing sugars.
- Lipids (emulsion test). Lipids do not dissolve in water,
but do dissolve in ethanol. This characteristic is used in the emulsion
test. Do not start by dissolving the sample in water, but instead shake
some of the test sample with about 4 cm³ of ethanol. Decant the liquid
into a test tube of water, leaving any undissolved substances behind. If
there are lipids dissolved in the ethanol, they will precipitate in the
water, forming a cloudy white emulsion.
- Protein (biuret test). To about 2 cm³ of test solution
add an equal volume of biuret solution, down the side of the test tube. A
blue ring forms at the surface of the solution, which disappears on
shaking, and the solution turns lilac-purple, indicating protein. The
colour is due to a complex between nitrogen atoms in the peptide chain and
Cu2+ ions, so this is really a test for peptide bonds.
Chromatography:
Chromatography
is used to separate pure substances from a mixture of substances, such as a
cell extract. It is based on different substances having different solubilities
in different solvents. A simple and common form of chromatography uses filter
paper.
- Pour some solvent into a
chromatography tank and seal it, so the atmosphere is saturated with
solvent vapour. Different solvents are suitable for different tasks, but
they are usually mixtures of water with organic liquids such as ethanol or
propanone.
- Place a drop of the mixture to
be separated onto a sheet of chromatography paper near one end. This is
the origin of the chromatogram. The spot should be small
but concentrated. Repeat for any other mixtures. Label the spots with
pencil, as ink may dissolve.
- Place the chromatography sheet
into the tank so that the origin is just above the level of solvent, and
leave for several hours. The solvent will rise up the paper by capillary
action carrying the contents of the mixture with it. Any solutes dissolved
in the solvent will be partitioned between the organic solvent (the moving
phase) and the water, which is held by the paper (the stationary
phase). The more soluble a solute is in the solvent the further up the
paper it will move.
- When the solvent has nearly reached
the top of the paper, the paper is removed and the position of the solvent
front marked. The chromatogram may need to be developed to make the spots
visible. For example amino acids stain purple with ninhydrin.
- The chromatogram can be
analysed by measuring the distance travelled by the solvent front, and the
distance from the origin to the centre of each spot. This is used to
calculate the Rf (relative front) value for
each spot:
An Rf value is characteristic of a particular solute in a
particular solvent. It can be used to identify components of a mixture by
comparing to tables of known Rf values.
Sometimes chromatography with a single solvent is not enough to
separate all the constituents of a mixture. In this case the separation can be improved
by two-dimensional chromatography, where the chromatography paper
is turned through 90° and run a second time in a second solvent. Solutes that
didn't separate in one solvent will separate in another because they have
different solubilities.
There
are many different types of chromatography.
- Paper chromatography is the simplest, but does not always give very
clean separation.
- Thin layer chromatography (tlc) uses a thin layer of cellulose or silica
coated onto a plastic or glass sheet. This is more expensive, but gives
much better and more reliable separation.
- Column chromatography uses a glass column filled with a cellulose
slurry. Large samples can be pumped through the column and the separated
fractions can be collected for further experiments, so this is preparative
chromatography as opposed to analytical chromatography.
- High performance liquid
chromatography (HPLC) is an improved
form of column chromatography that delivers excellent separation very
quickly.
- Electrophoresis uses an electric current to separate molecules on the basis of charge. It can also be used to separate on the basis of molecular size, and as such is used in DNA sequencing.
CELL
FRACTIONATION:
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This means separating different
parts and organelles of a cell, so that they can be studied in detail. All
the processes of cell metabolism (such as respiration or photosynthesis) have
been studied in this way. The most common method of fractionating cells is to
use differential centrifugation:
A more sophisticated separation
can be performed by density gradient centrifugation. In this, the
cell-free extract is centrifuged in a dense solution (such as sucrose or
caesium chloride). The fractions don't pellet, but instead separate out into
layers with the densest fractions near the bottom of the tube. The desired
layer can then be pipetted off. This is the technique used in the
Meselson-Stahl experiment (module 2) and it is also used to separate the two
types of ribosomes. The terms 70S and 80S refer to their positions in a
density gradient.
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ENZYME
KINETICS:
This
means measuring the rate of enzyme reactions.
- Firstly you need a signal to
measure that shows the progress of the reaction. The signal should change
with either substrate or product concentration, and it should preferably
be something that can be measured continuously. Typical signals include
colour changes, pH changes, mass changes, gas production, volume changes
or turbidity changes. If the reaction has none of these properties, it can
sometimes be linked to a second reaction which does generate one of these
changes.
- If you mix your substrate with
enzyme and measure your signal, you will obtain a time-course.
If the signal is proportional to substrate concentration it will start
high and decrease, while if the signal is proportional to product it will
start low and increase. In both cases the time-course will be curved (actually
an exponential curve).
·
How do you obtain a
rate from this time-course? One thing that is not a good idea is to
measure the time taken for the reaction, for as the time-course shows it is
very difficult to say when the reaction ends: it just gradually approaches the
end-point. A better method is to measure theinitial rate - that is the initial slope of the time-course. This also
means you don't need to record the whole time-course, but simply take one
measurement a short time after mixing.
- Repeat this initial rate
measurement under different conditions (such as different substrate
concentrations) and then plot a graph of rate vs. the
factor. Each point on this second graph is taken from a separate initial
rate measurement (or better still is an average of several initial rate
measurements under the same conditions). Draw a smooth curve through the points.
Be careful not to confuse the two kinds of graph (the time-course
and rate graphs) when interpreting your data.
One useful trick is to dissolve the substrate in agar in an agar
plate. If a source of enzyme is placed in the agar plate, the enzyme will
diffuse out through the agar, turning the substrate into product as it goes.
There must be a way to distinguish the substrate from the product, and the
reaction will then show up as a ring around the enzyme source. The higher the
concentration of enzyme, the higher the diffusion gradient, so the faster the
enzyme diffuses through the agar, so the larger the ring in a given time. The
diameter of the ring is therefore proportional to the enzyme concentration.
This can be done for many enzymes, e.g. a protein agar plate can be used for a
protease enzyme, or a starch agar plate can be used for the
enzyme amylase.
MICROSCOPY
Of all the techniques used in biology microscopy
is probably the most important. The vast majority of living organisms are too
small to be seen in any detail with the human eye, and cells and their
organelles can only be seen with the aid of a microscope. Cells were first seen
in 1665 by Robert Hooke (who named them after monks' cells in a monastery), and
were studied in more detail by Leeuwehoek using a primitive microscope.Units of measurement. The standard SI units of measurement used in microscopy are:
|
metre |
m |
= 1 m |
|
millimetre |
mm |
= 10-3 m |
|
micrometre |
mm |
= 10-6 m |
|
nanometre |
nm |
= 10-9 m |
|
picometre |
pm |
= 10-12 m |
|
angstrom |
Å |
= 10-10 m (obsolete) |
Magnification and Resolving Power. By using more lenses microscopes can magnify by a larger amount, but this doesn't always mean that more detail can be seen. The amount of detail depends on the resolving power of a microscope, which is the smallest separation at which two separate objects can be distinguished (or resolved). It is calculated by the formula:
Different
kinds of Microscope.
Light Microscope. This
is the oldest, simplest and most widely-used form of microscopy. Specimens are
illuminated with light, which is focussed using glass lenses and viewed using
the eye or photographic film. Specimens can be living or dead, but often need
to be stained with a coloured dye to make them visible. Many different stains
are available that stain specific parts of the cell such as DNA, lipids,
cytoskeleton, etc. All light microscopes today are compound microscopes, which
means they use several lenses to obtain high magnification. Light microscopy
has a resolution of about 200 nm, which is good enough to see cells, but
not the details of cell organelles. There has been a recent resurgence in the
use of light microscopy, partly due to technical improvements, which have
dramatically improved the resolution far beyond the theoretical limit. For
example fluorescence
microscopy has a resolution
of about 10 nm, while interference
microscopy has a resolution
of about 1 nm.
Electron Microscope.
This uses a beam of electrons, rather than electromagnetic radiation, to
"illuminate" the specimen. This may seem strange, but electrons
behave like waves and can easily be produced (using a hot wire), focussed
(using electromagnets) and detected (using a phosphor screen or photographic
film). A beam of electrons has an effective wavelength of less than 1 nm, so
can be used to resolve small sub-cellular ultrastructure. The development of
the electron microscope in the 1930s revolutionised biology, allowing
organelles such as mitochondria, ER and membranes to be seen in detail for the
first time.
The main problem with the electron microscope is
that specimens must be fixed in plastic and viewed in a vacuum, and must
therefore be dead. Other problems are that the specimens can be damaged by the
electron beam and they must be stained with an electron-dense chemical (usually
heavy metals like osmium, lead or gold). Initially there was a problem of artefacts (i.e. observed
structures that were due to the preparation process and were not real), but
improvements in technique have eliminated most of these.There are two kinds of electron microscope. The transmission electron microscope (TEM) works much like a light microscope, transmitting a beam of electrons through a thin specimen and then focussing the electrons to form an image on a screen or on film. This is the most common form of electron microscope and has the best resolution. The scanning electron microscope (SEM) scans a fine beam of electron onto a specimen and collects the electrons scattered by the surface. This has poorer resolution, but gives excellent 3-dimentional images of surfaces.
- X-ray Microscope. This is an obvious improvement to the light microscope, since x-rays have wavelengths a thousand time shorter than visible light, and so could even be used to resolve atoms. Unfortunately there are no good x-ray lenses, so an image cannot be focussed, and useable x-ray microscopes do not yet exist. However, x-rays can be used without focussing to give a diffraction pattern, which can be used to work out the structures of molecules, such as those of proteins and DNA.
- Scanning
Tunnelling Microscope (or Atomic Force Microscope). This uses a very fine
needle to scan the surface of a specimen. It has a resolution of about 10
pm, and has been used to observe individual atoms for the first time.
Comparison
of Light and Electron Microscopes
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