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Molecular Biology
2
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Carbon is considered to be the building block of life, and makes up all organic compounds
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There are four types of carbon compounds that form the basis of all life: carbohydrates, lipids,
proteins, and nucleic acids
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Urea was discovered in the 1720s and was assumed to be a by-product of the kidneys
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In 1828, a German chemist synthesised urea artificially using silver isocyanate and ammonium
chloride
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This was very
significant as no ‘vital principal’ had been involved
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His achievement was
evidence against the theory of vitalism (falsified)
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2: Water

Polarity of Water:
Water molecules are polar
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Water molecules have two poles and there are dipoles – they show
dipolarity
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This means hydrogen
bonds form between water molecules
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Collectively, they give water its unique properties which are very important to living things
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Adhesive properties: Water molecules will also tend to stick to other molecules that are
charged or polar, this is called adhesion
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Cooling effects: Water absorbs a great deal of energy before evaporating, which makes it an
effective agent for the removal of heat and the maintenance of body temperature, as the
body can lose a lot of heat energy with only a minimal loss of water
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It forms the main component
of solutions such as cytoplasm, blood and tissue fluid
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• The simplest kind of carbohydrates are
the simple sugars or monosaccharides
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• Simple sugars are small, soluble in water and taste sweet
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3 carbon sugars = trioses
5 carbon sugars = pentoses (e
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ribose)
6 carbon sugars = hexoses (e
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glucose)

The chemical formula of a typical monosaccharide is based on the general formula CnH2nOn
where ‘n’ equals the number of carbon atoms in the monosaccharide
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Usually
one molecule is transformed into another in a series of small steps (in a long chain or cycle of
reactions)
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Anabolism = synthesis of complex molecules from simpler molecules
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This
requires ATP
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This releases ATP
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• Use water
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Condensation Reactions:
• Always bond 2 smaller subcomponents of organic molecules into larger molecules
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•
•

Anabolic reactions (part of anabolism)
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Polysaccharides:
Complex carbohydrates like starch, glycogen and cellulose are formed from hundreds of
simple sugar molecules joined to form a long chain
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Glycogen is like animal starch as it acts as an energy
store in animals
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Cellulose is found in plant cell walls
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Alpha and Beta Glucose:

Cellulose:
• Structural polysaccharide in plants
• Beta-glucose





•
•
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1,4 glycosidic bonds
H-bonds link adjacent chains
This is what makes it so strong and gives it its structural properties


Starch:
• Used as an energy store in plants
• Alpha-glucose
• 1,4 glycosidic bonds
• Causes the molecule to form a helical shape
• There are two forms of starch:
o Amylose contains only 1,4 glycosidic bonds and forms linear helices
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Glycogen:
• Insoluble compact store of glucose in animals
• Alpha-glucose units
• 1,4 and 1,6 glycosidic bonds
• Branched structure

Summary of Types of Carbohydrates:



Lipids:
• Lipids that are solid at room temperature are called fats
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• Both are made up of triglycerides
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• They are insoluble in water
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• Thermal insulation – layer of fat under the skin reduces heat loss
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Lipids as Energy Storage:
Lipids contain twice as much energy per gram than carbohydrates, so it adds half as much to
the body mass, which is important as we have to carry our energy stores around with us
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Fats are insoluble and therefore do not affect osmosis, and they are poor
conductors of heat so they can be used as insulators
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Body Mass Index (BMI):
&'(( )* +,
𝐵𝑀𝐼 =
kg/m2
2


(
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• An unsaturated fatty acid is a chain in which the maximum number of hydrogen atoms
aren’t bonded (there are double bonds)
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o Polyunsaturated – there’s multiple double bonds
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o Trans – the hydrogen atoms either side of the double bond are on opposite
sides
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4: Proteins
Types of Protein:
Fibrous proteins are long, insoluble molecules made up of parallel polypeptide chains
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Keratin found in hair, nails and hooves and
collagen found in bones, muscles and tendons are two abundant fibrous proteins
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The hormone insulin is a globular protein and so are enzymes
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Functions of Proteins:
Protein
Function
Rubisco
An enzyme vital for the fixation of carbon dioxide during photosynthesis
Immunoglobulin Antibodies which form the basis of our immunity to diseases
Collagen
A structural protein which forms skin, blood vessels and ligaments
Insulin
A hormone vital to the control of blood sugar levels
Rhodopsin
A visual pigment found in the retina which changes shape in the presence
of light
Spider Silk
A strong, fine, slightly elastic fibre produced by web-building spiders

Protein Structure:
• Primary structure: the sequence of amino acids that make up a protein
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• Tertiary structure: the three-dimensional shape, held together by ionic bonds and
disulphide bridges
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Denaturation of Proteins:
Many proteins are large molecules folded into a three-dimensional shape
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If
these bonds are broken, then the shape of the protein is changed and it loses its function
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Temperature:
• At every temperature above absolute zero, atoms vibrate
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• Eventually the movement of the atoms is so great that the weak bonds break and the
protein structure begins to break down
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If the pH increases, then there are fewer protons
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If the pH decreases, then there are more protons
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Binding to the active site brings the substrate into close physical proximity,
creating an enzyme-substrate complex
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As the enzyme is not consumed in the
reaction, after the product has formed, it can continue to work again and again, hence only
low concentrations are needed
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This can be caused by:
• Temperature
• pH

Lactose-Free Milk:
Almost all humans are born with the ability to digest lactose, a sugar found in milk
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Lactose is a disaccharide which is hydrolysed (broken down) into glucose and galactose
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People who are
lactose intolerant can only drink milk if it is lactose-free or contains the lactase enzyme
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Milk passed over this immobilised enzyme (an enzyme that has been
trapped on an inert material so that it can be used repeatedly) will become lactose-free
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• Ease of recovering the enzyme – the immobilised enzyme can easily be collected and
re-used
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• Immobilisation extends production time – especially when using proteases, which
might digest each other in reactions in solution
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• Galactose and glucose are sweeter than lactose, so less sugar needs to be added to
sweet foods containing milk, such as milkshakes or fruit yoghurt
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Because glucose and galactose are more soluble than lactose they remain dissolved,
giving a smoother texture
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2
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DNA is and incredibly long chained
molecule and just like carbohydrates and proteins it is made up of subunits called monomers
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Each nucleotide is made up of 3 molecules:
• A phosphate group
• A pentose sugar called deoxyribose
• A nitrogenous base (there are four possible bases)
o Adenine (A)
o Thymine (T)
o Cytosine (C)
o Guanine (G)
o Adenine and Thymine always pair together and Guanine and Cytosine always
pair together
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RNA:


DNA: the sugar is deoxyribose, double stranded, found in the nucleus, bases are adenine,
cytosine, guanine and thymine
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DNA Strands:
Each strand of DNA is composed of nucleotides
covalently linked
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Together, they
form an overall double helix shape
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e
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It is this feature of DNA that makes it capable of self
replication and allows it to serve as a guide for the
production of RNA
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This
means that the two single strands run in opposite
directions to each other, so they are antiparallel
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These other scientists were:
Rosalind Franklin and Maurice Wilkins who produced very clear X-ray diffraction photographs
of DNA
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Erwin Chargaff who discovered that the numbers of adenine and thymine molecules in any
given length of DNA were always equal, as was the number of cytosine and guanine
molecules
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The original double helix molecule has to be separated into 2 single strands
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Helicases are enzymes that break the hydrogen bonds between complementary base
pairs one at a time
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3
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4
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5
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6
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7
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DNA replication is a semi-conservative process because when a new double-stranded DNA
molecule is formed:
• One strand will be from the original molecule (the pre-existing DNA molecule is
always conserved)
• One strand will be newly synthesised

Protein Synthesis:
Polypeptides are synthesised using a two step process using the base sequence of a gene
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Transcription: a strand of DNA is used as a template to create an mRNA molecule
(messenger RNA)
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Translation: the mRNA molecule binds to a ribosome and together with tRNA make a
protein from amino acids
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The DNA helix is unzipped at the position of the gene to be transcribed
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The helix is unwound by RNA polymerase, separating the DNA into two strands
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One of the strands is used as a template for mRNA (antisense strand)
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RNA nucleotides are found floating in the nucleus
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Free RNA nucleotides base pair with DNA nucleotides
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The covalent bonds on the mRNA chain are formed by RNA polymerase
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mRNA is single stranded and the base thymine is replaced by uracil
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After the mRNA is complete the molecule detaches from the DNA and leaves the
nucleus via nuclear pores in the nuclear envelope to go to the ribosomes in the
cytoplasm, where translation occurs
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The DNA helix is zipped up again by RNA polymerase
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So, every three bases codes for one
of the 20 possible amino acids
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Structure of tRNA:
Transfer RNA (tRNA) is a small molecule
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This longer section is attached
to an amino acid
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They determine
which of the 20 amino acids is attached to the tRNA
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Translation takes place on ribosomes
which are either free in the
cytoplasm or attached to the rough
endoplasmic reticulum
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mRNA moves from the nucleus and attaches to ribosome in cytoplasm
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First tRNA with amino acid and anticodon complementary to first codon joins to first
codon by base pairing codon and anticodon
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Second tRNA with amino acid joins to second codon by base pairing codon and
anticodon
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The two amino acids are now alongside each other and a peptide bond forms between
them
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Ribosome shifts along one mRNA triplet or codon
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The third tRNA enters the ribosome as the first one leaves, and the steps are repeated
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tRNA continues to bind and the polypeptide chain grows until the stop codon is
reached
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mRNA and ribosome separate and the completed polypeptide breaks free
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• It is universal – same codon codes for the same amino acid in all organisms (with a
few minor exceptions)
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8: Cell Respiration

Respiration and Breathing:
Breathing is the action of drawing air into the body (inhaling) and pushing air out (exhaling)
so that gaseous exchange can take place between the air and the blood
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Respiration is the chemical process of releasing energy from our food by breaking down
glucose and it occurs in every cell of the body
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Glucose + Oxygen à Carbon Dioxide + Water

We require the energy from cell respiration for three main types of activity:
• Synthesising large molecules like DNA, RNA and proteins
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• Moving things around inside the cell, such as chromosomes, vesicles, or in muscle cells
the protein fibres that cause muscle contraction
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Glyco = sugar
Lysis = to split
Glycolysis occurs in the cytoplasm, and breaks down one glucose molecule into two pyruvate
molecules
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Aerobic Respiration:
After glycolysis, if oxygen is present then the two pyruvate molecules will move into the
mitochondria where they will be metabolised further
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This process yields much more ATP than glycolysis or anaerobic respiration and so is much
more efficient
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It can respire either aerobically or anaerobically
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Bread is made by adding water to flour, kneading the mixture to make dough and then baking
it
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Yeast is often this ingredient
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Any oxygen in the dough is soon used up so the yeast
carries out anaerobic cell respiration
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The swelling of the dough due
to the production of bubbles of carbon dioxide is called rising
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2
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Oxygen is released as a waste product
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This is where light energy is trapped
and turned into chemical energy
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This graph shows the
absorption spectra for two
types of chlorophyll and
carotenoid pigments found
in green plants
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An action spectrum shows the rates of
photosynthesis will be higher when red and blue
light are absorbed as they provide the energy
needed for photosynthesis
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• Light independent reaction – organic compounds are made from the products of the
light dependent reactions (ATP and hydrogen)
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Effects on Photosynthesis:











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