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Chapter 2 - Biological Molecules
The cells of all living organisms are composed of biological molecules
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A
study of the structure of these macromolecules allows a better understanding of their functions in
living organisms
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A range of roles that relate to the properties of
water, including solvent, transport medium, coolant and as a habitat
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It makes up about 80% of a cells contents and has lots of
important function, inside and outside cells such as:
• Water is a reactant in lots of important chemical reactions, including hydrolysis
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• Most biological reactions take place in solution (e
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in the cytoplasm of eukaryotic and
prokaryotic cells) so waters pretty essential
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The fact that its a liquid and a solvent means it can easily
transport all sorts of materials, like glucose and oxygen, around plants and animals
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• Water is a habitat
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• MEMORY: Reactant, solvent, transport, temperature, habitat (Really, silly, tiny, tree, hunt)
Structure of water:
Polarity of water:
A molecule of water (H2O) is one atom of oxygen (O) joined to two atoms of hydrogen (H2) by
shared electrons
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• The unshared negative electrons on the oxygen atom give it a slight negative charge
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Hydrogen Bonding:
The slightly negative-charged oxygen atoms attract the slightly positively-charged hydrogen atoms
of other water molecules
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Properties of water:
High specific heat capacity:
• Hydrogen bonds give water a high specific heat capacity - this is the energy needed to raise 1g
of a substance by 1OC
• The hydrogen bonds between water molecules can absorb a lot of energy
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High latent heat of evaporation:
• It takes a lot of heat to break the hydrogen bonds between the water molecules
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• This is why some mammas, like up, sweat when they're too hot
• When the water evaporates, it cools the surface of the skin
Very cohesive:
•
•
•
•

Cohesion is the attraction between molecules of the same type
Water molecules are very cohesive (they stick to each other because they are polar)
This helps water to flow, making it great for transport substances
It also helps water to be transported up plant stems in the transpiration stream

Lower density when solid:
• At low temperatures water freezes - it turns from a liquid to a solid
• Water molecules are held further apart in ice than they are in liquid water, because each water
molecule forms four hydrogen bonds to other water molecules, making a lattice shape
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Good Solvent:
• A lot of important substances in biological reactions are ionic
• This means they're made form one positively-charged atom or molecule and one negativelycharged atom or molecule
• Because water is polar, the slightly positive end of a water molecule will be attracted to the
negative ion, and the slightly negative end of a water molecule will be attracted to the positive ion
• This means the ion gets surrounded by water molecules - dissolving it
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• E
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in humans, important ions can dissolve in the water in blood and then be transported around
the body
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Examples of
biological macromolecules include proteins, some carbohydrates and lipids
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Polymers:
• Most carbohydrates and all proteins are polymers
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• Monomers are small, basic molecular units
• Examples of monomers include monosaccharides and amino acids
MONOMER + MONOMER + …
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There is a break in the chemical bonds between monomers and it uses a molecule of water

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(c) the chemical elements that make up biological molecules
To include:
C, H and O for carbohydrates
C, H and O for lipids
C, H, O, N and S for proteins
C, H, O, N and P for nucleic acids
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Carbohydrates
What are carbohydrates made form:
Most carbohydrates are polymers and are made up of the same three elements: C, H and O atoms
The monomers that make up carbohydrates are called monosaccharides
MONOSACCHARIDE + MONOSCCHARIDE —> CARBOHYDRATE
Monomer + Monomer —> Polymer
There are two different types off monosaccharides; these are: Glucose and ribose
Glucose:
• Glucose is a monomer with 6 carbons
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So hydrogen is on top of alpha
glucose
Ribose:
• Ribose is a monosaccharide with 5 carbons
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• All the components of glucose is present but in a different formation and one less Carbon
• Ribose sugar is a component of RNA nucleotides

(e) the synthesis and breakdown of a disaccharide and polysaccharide by the forma on and
breakage of glycosidic bonds
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Polysaccharide Formation:
• Monosaccharides are joined together by GLYCOSIDIC bonds
• GLYCOSIDIC BONDS BETWEEN GLUCOSE MOLECULES
• During synthesis, a hydrogen atom and one monosaccharide bonds to a hydroxyl (OH) group on
the other, releasing a molecule of water
• This is a condensation reaction
• The reverse of synthesis is a hydrolysis reaction where a molecule of water breaks apart the
glycosidic bond
Disaccharide: (2 x monosaccharides joined)
• Formed when two monosaccharides are joined together (example shows two alpha glucose
molecules joining together to form maltose)

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Disaccharide examples (need to know composition):
Condensation reactions occur between these monosaccharides to produce the polymers below:
• Sucrose = α-glucose + fructose
• Maltose = α-glucose + α-glucose
• Lactose = β-glucose + galactose

Hydrolysis of these disaccharides will release the two components of them (i
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hydrolysis of
maltose will produce two α-glucose molecules)
Polysaccharide: (2< Monosaccharides joined):
A polysaccharide is formed when MORE than two monosaccharides join together with glycosidic
bonds:

(f) the structure of starch (amylose and amylopectin), glycogen and cellulose molecules

Starch:
• Main energy store in plants
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• The angles of the glycosidic bonds give it a coiled structure, like a cylinder
• This makes it compact and really good for storage because of this, as more fits into a
small space
2) Amylopectin: (LOTS OF BRANCHES ON CHAINS OF α-glucose)
• Is a long, branched chain of α-glucose
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• Animal cells get energy from glucose to, but store excess glucose as glycogen (another
polysaccharide of α-glucose)
• Its structure is very similar to amylopectin, except that it has loads more side branches coming
off it
• Loads of branches means that stored glucose can be easily released quickly as enzymes can get
to the glycosidic bonds easily
• Very compact molecule which is important for storage
Cellulose: (LOTS OF β-glucose BONDED BY HYDROGEN BONDS)
• Cellulose is the major component of cell walls in plants
• Its made of long unbranched chains of β-glucose
• When β-glucose molecules bond, they form straight
cellulose chains
• These cellulose chains are linked together by HYDROGEN
BONDS to form strong fibres called MICROFIBRILS
• The structure of cellulose means that enzymes cannot get
to the glycosidic bonds and break it down
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Amylose:
• Has its glycosidic bonds angled to give it a coiled shape, this is great for storage
molecules as it means a lot of glucose can fit into a smaller space
Amylopectin:
• Has branches on it which means that enzymes can get down to the glycosidic bonds
easily and break the polysaccharide apart to release glucose rapidly
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Cellulose:
• Cellulose consists of chains of cellulose joined together by strong hydrogen bonds
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(h) the structure of a triglyceride and a phospholipid as examples of macromolecules
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Lipids:
• Lipids are macromolecules (complex molecule with a large molecular mass)
• They all contain the chemical elements, Hydrogen, Carbon and Oxygen
• There are three types of lipid you need to know about - triglycerides, phospholipids and
cholesterol
Triglycerides: (FATTY ACID ATTACHED TO GLYCEROL VIA ESTER BOND)
• Have one molecule of glycerol and three molecules of fatty acids attached on to it
• They’re synthesised by the formation of an ester bond between each fatty acid and the glycerol
molecule
(i) the synthesis and breakdown of triglycerides by the forma on (esterification) and breakage of
ester bonds between fatty acids and glycerol

Fatty Acid
Glycerol

Ester bond:
• One triglyceride has three ester bonds
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• The fatty acid is ‘saturated’ with hydrogen
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• The ring structure has a polar hydroxyl (OH) group attached to it

(j) how the properties of triglyceride, phospholipid and cholesterol molecules relate to their
functions in living organisms
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Triglycerides:
• In animals and plants triglycerides are used
as energy storage molecules
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• Triglycerides are good for storage because
they have long hydrocarbon tails which
contain lots of chemical energy - a lot of
energy is subsequently released when these
are broken down

• They form a double layer with their heads
facing out towards the water on either side
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• They are insoluble, meaning that they do not
cause water to enter the cells by osmosis
• The triglycerides bundle together as
insoluble droplets in cells because the fatty
acid tails are hydrophobic - they face
inwards, shielding themselves from the water
with the glycerol heads outfacing
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• The centre of the bilayer is hydrophobic, so
water-soluble substances cant pass easily
though it - the membrane acts as a barrier to
those substances
Cholesterol:
• In eukaryotic cells, cholesterol molecules
help to strengthen the cell membrane by
interacting with the phospholipid bilayer
• Cholesterol has a small size flattened shape
- this allows cholesterol to fit in between the
phospholipid molecules in the membrane
• They bind to the hydrophobic tails of the
phospholipids, causing them to pack more
closely together
• This helps them make the membrane less
fluid and more rigid
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(k) the general structure of an amino acid
Proteins:
What are proteins made from:
• Proteins are polymers
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• A carboxyl group (COOH)
• Amino group (-NH2)
• Variable “R” Group

All amino acids have the elements, Carbon, Hydrogen, Oxygen and Nitrogen
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(l) the synthesis and breakdown of dipeptides and polypeptides, by the forma on and breakage of
peptide bonds

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Amino acids: (JOINED TOGETHER BY PEPTIDE BONDS)
Amino acids are linked together by peptide bonds to form dipeptides or polypeptides
Dipeptide and Polypeptide formation:
A molecule of water is released during the reaction - it is a condensation reaction
The reverse of the synthesis reaction is to add a molecule of water which is a hydrolysis reaction

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(m) The levels of protein structure
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Protein Structure
• Proteins are big, complicated molecules
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• The four structural levels of a protein are held together by different kinds of bond
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• Different proteins have different sequences of amino acids, which produce changes in the
structure of the whole protein
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Secondary Structure:
• The polypeptide chain doesn't remain flat and straight
• Hydrogen bonds form between the -NH and -CO groups of the amino acids in the chain
• This makes it automatically coil into an alpha helix or fold into a beta pleated sheet

Beta Pleated Sheets
Tertiary Structure:
The coiled or folded chain of amino acids is often coiled and folded further
The tertiary structure is the final 3D structure for single chain polypeptides
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• Hydrophilic and hydrophobic interactions - When hydrophobic R groups are close together in
the protein they tend to clump together
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Quaternary Structure:
• Some proteins are made from multiple polypeptide chains, these chains are held together by
bonds
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“Haemoglobin is made of 4 polypeptide chains, bonded together”
• The quaternary structure tends to be determined by the tertiary structure of the individual
polypeptide chains being bonded together
• Because of this, it can be influenced by all the bonds mentioned in the tertiary structure
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- An opportunity to use computer modelling to investigate the levels of protein structure
within the molecule
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• In a globular protein, the hydrophilic R groups on the amino acids tend to be pushed to the
outside of the molecule
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This makes globular proteins soluble, so they're easily transported in fluids
Haemoglobin:
• Haemoglobin is a globular protein that carries oxygen around the body in red blood cells
• It is known as a conjugated protein - this means it’s a protein with a non-protein group
attached
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Insulin:
• Insulin is a hormone secreted by the pancreas
• It helps to regulate the blood glucose level
• Its solubility is important - it means it can be transported in the blood to the tissues where it
acts
• An insulin molecule consists of two polypeptide chains, which are held together by
DISULPHIDE BONDS

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• When they're in the pancreas, six of these molecules bind together to form a large, globular
structure
Enzyme: Amylase:
• Amylase is an enzyme that catalyses the breakdown of starch in the digestive system
• It is made of a single chain of amino acids
• Its secondary structure contains both alpha-helix’s and beta-pleated sheet sections
• Most enzymes are globular proteins

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(o) the properties and functions of fibrous proteins
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Fibrous Proteins:
• Fibrous proteins are tough and rope-shaped
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• They're structural proteins and are fairly unreactive (unlike many globular proteins)
Examples of fibrous proteins are:
Collagen:
• Found within animal and connective tissues, such as bone, skin and muscle
• It is a very strong molecule
• Minerals can bind to the protein to increase its rigidity (e
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in bones Ca2+)
Keratin:
• Found in many of the external surfaces of animals, such as skin, hair, nails, feathers and horns
• it can either be flexible (skin) or hard and tough (as in nails)
Elastin:
• Found within the connective tissues, such as skin, large blood vessels and some ligaments
• It is elastic, so it allows tissues to return to their original shape after they have been stretched
(p) the key inorganic ions that are involved in biological processes
To include the correct chemical symbols for the following ca ons and anions:
1- Cations: calcium ions (Ca2+), sodium ions (Na+), potassium ions (K+), hydrogen ions
(H+), ammonium ions (NH4+)
2- Anions: nitrate (NO3–), hydrogencarbonate (HCO3–), chloride (Cl –), phosphate
(PO43–), hydroxide, (OH–)
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• An inorganic ion is one which DOES NOT CONTAIN CARBON
• Inorganic ions are really important in biological processes
• The ones you need to know about are listed below:
Cations: (ION WITH POSITIVE CHARGE)
MEMORY: Cathy is positive when she irons
Cation

Chemical Symbol

Examples of roles in biological processes

Calcium

Ca2+

• Involved in the transmission of neutron impulses and the
release of insulin from the pancreas
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g
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g
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The iodine test for starch:
If you want to test for the presence of starch in a sample, you do the
iodine test
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All sugars can be classed as either reducing or non-reducing
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the test differs depending on the type of sugar you are testing to
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g
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Method:
1
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Heat the solution in a test tube
3
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Now add Benedict's solution
5
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Medium conc
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Test strips for Glucose:
• Glucose can also be tested for using test strips coats in a reagent
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(r) quantitative methods to determine the concentration of a chemical substance in a solution
- To include colorimetry and the use of biosensors (an outline only of the mechanism is
required)
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What is a colorimeter:
• A colorimeter is a device used to measure the strength of a coloured solution by seeing how
much light passes through it
• A colorimeter measures absorbances
• The more concentrated the colour of a solution, the higher the absorbance is
• To find out the glucose concentration of an unknown solution, you first need to make up several
solutions of known glucose concentration
• Then measure the absorbance in these solutions
• Finally plot these absorbances on a graph to make a calibration curve
• You can then use the calibration curve to estimate the concentration of the glucose in the
unknown solution
• Its easier to measure the concentration of the blue Benedict’s solution that left after the test
• So the higher the glucose concentration, the lower the absorbance is
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Method:
1) line up 5 test tubes in a rack
2) Add 10cm3 of the initial 40mM sucrose solution to the first test tube and 5 cm3 of distilled water
to the other four test tubes
3) Then, using a pipette, draw 5cm3 of the solution form the first test tube and add it to the distilled
water in the second test tube and mix throughly
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5mM
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Heres
how:
Do a Benedict's test on each solution (using the same amount of water and Benedict's solution in
each)
Remove any precipitate -either leave it for 24 hours to settle or centrifuge them

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Use a colorimeter to measure the absorbance of the Benedict’s solution remaining in each tube
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1) Switch the colorimeter on and allow 5 minutes for it to stabilise
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Put the cuvette into the colorimeter
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Calibrate the machine to 0
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g
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• The electrical signal is then processed and can be used to work out other information
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• the electrical signal is then processed to work out the initial glucose concentration
(s) (i)
the principles and uses of paper and thin layer chromatography to separate biological molecules /
compounds
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Chromatography:
• Chromatography is used to separate stuff in a mixture - once its operated out, you can often
identify components
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• There are quite a few different types of chromatography - yo only need to know about paper
chromatography and thin-layer chromatography
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In both paper and thin-layer chromatography
the mobile phase is a liquid solvent, such as ethanol or water
• A stationary phase - Where the molecules cant move
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In thin-layer chromatography the stationary phase is a thin layer of
solid or silica gel, on a glass or plastic plate
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An Rf value is the ratio of the distance travelled by a spot to the distance travelled by the solvent
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(ii) practical investigations to analyse biological solutions using paper or thin layer chromatography
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Identifying unknown molecules:
In the exam you might be asked how chromatography can be used to identify the biological
molecules in a mixture
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The
gloves will stop any amino acids from on your skin getting onto the chromatography paper
Method:
1) Draw a pencil line nat the bottom of the chromatography paper and put a concentrated drop of
the mixture onto it
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This should be done in a fume cupboard
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4) When the solvent’s nearly reached the top, take the paper out and mark the solvent front with a
pencil
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5) Amino acid aren't coloured
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Calculate the Rf value of spot X
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3cm
Distance travelled by the solvent = 8
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3 / 8
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