BIOLOGICAL MOLECULES

3.1
1A: BIOLOGICAL MOLECULES
EVIDENCE FOR EVOLUTION
The variety of life is extensive but all living things share the same biological
molecules. All have a similar biochemical basis.

This supports the theory of evolution by indirect evidence that all organisms
descended from one/a few common ancestors.
MONOMERS AND POLYMERS

MONOMER - simple, basic, molecular unit from which larger molecules/polymers

are made from. E.g monosaccharides, amino acids, nucleotides.

POLYMER - large, complex molecule made up of repeating monomers joined

together. E.g starch, glycogen, cellulose, polypeptide (protein), DNA, RNA.
MAKING AND BREAKING POLYMERS

CONDENSATION REACTION HYDROLYSIS REACTION

Joins two monomers together Separates two monomers

Forms chemical bond Breaks chemical bond

Eliminating a water molecule Requires addition of a water molecule

CARBOHYDRATES
Contain carbon, hydrogen and oxygen.

Functions

● Energy
● Storage
● Strength
MONOSACCHARIDES
Simplest sugars, monomers from which larger carbohydrates are made. 3 examples all have
formula C6H12O6.

Glucose - alpha and beta glucose, OH group inverted on carbon 1. Isomers have same molecular
formula but different structure with atoms arranged in different ways.

Fructose

Galactose
DISACCHARIDES
Forms when two monosaccharides join together by a condensation reaction forming a
glycosidic bond. Hydroxyl group on one joins with a hydrogen from another to release
a water molecule for each bond. One oxygen molecule joins the two sugars.

● Maltose - glucose + glucose

● Sucrose - glucose + fructose
● Lactose - glucose + galactose
● Lactulose - galactose + fructose
POLYSACCHARIDES
Formed when more than 2 monosaccharides join together via condensation
reaction, releasing a water molecule for each glycosidic bond.

Starch, glycogen and cellulose are polysaccharides.

STARCH
FUNCTION
Found in many parts of a plant in the form of small grains. Especially large amounts occur in seeds
and storage organs, such as potato tubers. It forms an important component of food and is the
major energy source in most diets.

STRUCTURE
Made up of two polysaccharides of α-glucose: amylose (unbranched helical chains just C1-4) and
amylopectin (branched every 20 monomers, both bonds). Contains C1-4 and C1-6 glycosidic
bonds.

STRUCTURE RELATED TO FUNCTION

Helical because of angles on glycosidic bonds - compact, fit more in, good for storage
Insoluble - doesn’t affect water potential
Branched chains - more efficient hydrolysis for respiration
Large - can’t leave cell
GLYCOGEN
FUNCTION
Main storage of energy in animals, stored in muscle and liver cells.

STRUCTURE
Polysaccharide of alpha glucose with branched chains every 10 monomers. C1-4 and C1-6
glycosidic bonds.

STRUCTURE RELATED TO FUNCTION

Branched - rapid hydrolysis into glucose to meet demands of cell
Insoluble - doesn’t affect water potential
Compact - good for storage
CELLULOSE
FUNCTION
Provides structural strength in the cell walls of plants due to its strength which is a result of the many
hydrogen bonds found between the parallel chains of microfibrils. The high tensile strength of cellulose
allows it to be stretched without breaking which makes it possible for cell walls to withstand turgor
pressure. The strengthened cell walls provides support to the plant. Cellulose fibres are freely permeable
which allows water and solutes to leave or reach the cell surface membrane

STRUCTURE
Polysaccharide of beta glucose monosaccharides joined together by C1-4 glycosidic bonds. They form
straight chains. Due to the inversion of the β-glucose molecules many hydrogen bonds form between the
long chains giving cellulose it’s strength. This forms microfibrils.

STRUCTURE RELATED TO FUNCTION

Hydrogen bonds form between chains - collective strength to the cell wall
COMPARING POLYSACCHARIDES
 TEST FOR SUGARS - BENEDICT’S

METHOD - Reducing sugars POSITIVE RESULT

- Can donate electrons Blue → green, yellow, orange, brick red
- Glucose, fructose, galactose, maltose, lactose Semi-quantitative - depending on conc.
- Add benedict’s reagent (contains copper II sulfate) to the sample. Reduces blue copper sulfate into red
- Place in a gently boiling water bath for 5 minutes. copper oxide

METHOD - Non-reducing sugars

- Cannot donate electrons
POSITIVE RESULT
- Sucrose
Blue →brick red
- If negative from first test, needs hydrolysis into monosaccharides.
- Add hydrochloric acid then neutralise with sodium hydrogen carbonate.
(high conc sugars now as two
- Then add benedict's solution and in gently boiling water bath for 5 mins.
monosaccharides)
TEST FOR STARCH - IODINE
METHOD
Add iodine in potassium-iodide solution to the sample.

POSITIVE RESULT
orange → blue/black
LIPIDS
Contain elements C,H and O
TRIGLYCERIDES
STRUCTURE
1 molecule of glycerol attached to 3 fatty acids. Non-polar, hydrophobic.

FORMATION
Condensation reaction where a H from OH group on glycerol joins with
the OH group on the COOH to release a water molecule. This forms an
ester bond. Repeat for the other 2 fatty acids.

FUNCTION
Mainly used as storage molecules

PROPERTIES
Insoluble in water - due to hydrophobic fatty acid tails facing inwards, glycerol outwards - Ψ unaffected
Long hydrocarbon tails, lots of C-H little O - when oxidised releases energy
PHOSPHOLIPIDS
STRUCTURE
1 glycerol, 1 phosphatase group 2 fatty acid tails.
Glycerol + phosphate group are head = PO42- charged, polar, hydrophilic (attracts water), soluble
2 fatty acids tails = non polar, insoluble in water, hydrophobic (repels water)
Amphipathic - both hydrophobic and hydrophilic regions.

FORMATION
Condensation reactions between glycerol and phosphate group forming phosphate ester bond and reaction
between glycerol and fatty acids forming an ester bond, releasing water molecule per bond.

FUNCTION
Mainly phospholipid bilayer and micelles

PROPERTIES
Bilayer - hydrophilic heads attract water, tails repel, tails inwards shielded, heads outwards.
Barrier - in cell membrane to water soluble molecules, ions, charged/polar molecules.
Electrical insulator - ions can’t enter as they are charged and repel fatty acid hydrophobic tails.
Stability/fluidity - saturated fatty acids less fluid, can move past each other to keep membrane fluid to
change shape and move but never expose hydrophobic fatty acid tails.
FATTY ACIDS
All consist of a carboxyl group (COOH) and a hydrocarbon tail
which can vary (R)

Can be saturated (no double bonds, saturated with hydrogen or unsaturated (contains C=C double bond)
which causes the chain to kink. If on double bond the H are on the same side it is cis and if the H’s are on
opposite sides it is a trans unsaturated fatty acid.
TEST FOR LIPIDS - ETHANOL AND WATER
METHOD
Add ethanol to the sample.
Then add water.
Shake.

POSITIVE RESULT
White/milky emulsion

HAZARDS
Ethanol is flammable, don’t test near open flames
PROTEINS
Monomers are amino acids

Contain carbon,hydrogen, oxygen, nitrogen and some contain sulfur.

AMINO ACID STRUCTURE
NH2= amine group
COOH = carboxyl group
R = variable group

20 amino acids
Only vary in R group
Glycine - H in R group
DIPEPTIDE AND POLYPEPTIDE FORMATION
Condensation reaction between OH on carboxyl group
and H on amine group, releasing a water molecule and
forming a peptide bond.

2 amino acids - dipeptide

2+ amino acids - polypeptide

1 or more polypeptide chains is a

protein.
PRIMARY STRUCTURE OF PROTEINS
Sequence of amino acids in a polypeptide chain.

DNA of a cell determines the primary structure of a protein by instructing the cell to add certain
amino acids in specific quantities in a certain sequence.

This affects the shape and therefore the function of the protein

The primary structure is specific for each protein (one alteration in the sequence of amino acids
can affect the function of the protein)
SECONDARY STRUCTURE OF PROTEINS
Hydrogen bonds form between amino acids close together (weak negatively charged nitrogen and
oxygen atoms interact with the weak positively charged hydrogen atoms between carboxyl group
and amine group). This causes the polypeptide chain to be coiled into an alpha helix or folded into
a beta pleated sheet.
TERTIARY STRUCTURE OF PROTEINS
Further conformational change of the secondary structure, coiled or folded further, leads to additional
bonds forming between the R groups (side chains). The additional bonds are:

Hydrogen bonds (these are between R groups)

Disulphide bridges (only occurs between cysteine amino acids)
Ionic bonds (occurs between charged R groups).
Hydrophobic interactions (between non-polar R groups)

Final 3D structure for proteins of only one polypeptide chain.

QUATERNARY STRUCTURE OF PROTEINS
The way polypeptide chains are assembled. Stabilised with hydrogen bonds, ionic bonds
and disulfide bridges.

Same polypeptide chains involved = homodimer

Different = heterodimer

Final 3D structure of proteins with more than one polypeptide chain.

RELATIONSHIP BETWEEN PROTEIN STRUCTURES
AND FUNCTION
- The sequence of amino acids is determined by the genetic code
- This effects the primary structure
- The primary structure determines how the polypeptide is coiled or folded in the secondary
structure
- It also determines where bonds form
- This affects the whole shape of the protein
- Shape of a protein determines its function

So altering the primary structure affects the tertiary structure shape which affects the function.
EXPLAIN HOW A CHANGE IN DNA BASE SEQUENCE
CAN AFFECT AN ENZYME REACTION
1. Base sequence determines sequence of amino acids in polypeptide chain/primary structure
2. 3 bases code for one amino acid
3. Primary structure determines position of bonds between R groups in the tertiary structure
4. Hydrogen, ionic bonds and disulphide bonds
5. A change in tertiary structure/ bonds changes shape of active site of the enzyme
6. Meaning the substrate can no longer bind to form an enzyme substrate complex
PROTEIN TYPES
Globular - soluble, R group folded in molecule

Fibrous - insoluble, R group exposed

Enzymes - biological catalysts

Antibodies - immune response

Transport proteins - channel/carrier proteins

Structural proteins - keratin/collages, strong, cross links

Communication proteins - chemical messengers e.g hormones

TEST FOR PROTEINS

METHOD
Biuret test

POSITIVE RESULT
Blue →purple
ENZYMES
Biological catalysts that speed up the rate of a chemical reaction.

-Catalyse a range of reactions.

-Do not get used up, can be reused.
-Intracellular - reactions inside cells.
-Extracellular - reactions outside cells.
HOW ENZYMES SPEED UP A REACTION
Lowers the activation energy by:

- Providing an alternate pathway for the reaction with lower energy

- Binding reactants at active site and positioning them correctly
- Bring reactants together so less kinetic energy is used by moving round and
trying to collide
LOCK AND KEY MODEL
1. Active site fixed shape
2. Substrate is complementary to active site
3. Binds to it
4. Forms enzyme-substrate complex
5. Enzyme catalyses reaction to form products (synthesis or split)
6. Enzyme is unchanged

Old and outdated model

INDUCED FIT MODEL
1. Active site of enzyme is not completely complementary to substrate
2. Substrate binds and distorts hydrogen bonds holding enzyme in shape
3. Active site changes shape to complete fit
4. Enzyme-substrate complex is formed
5. Enzyme catalyses reaction and releases products
6. Conformational change of the active site

Recent and accepted model

ENZYME SPECIFICITY
Only catalyse one reaction as only one substrate is complementary to the active
site.

The shape of the active site is determined by the tertiary structure which is
determined by the primary structure (sequence of amino acids in polypeptide
chain).

If there is a mutation which affects genes, the primary structure is affected. This
changes the way the polypeptide is folded and therefore affects the shape of the
protein in its tertiary structure which in turn alters the shape of the active site. This
means that the substrate will not fit and the reaction won’t be catalysed.
MEASURING ENZYME ACTIVITY
FACTORS AFFECTING ENZYME ACTIVITY
⭑ Temperature
⭑ pH
⭑ Enzyme concentration
⭑ Substrate concentration
⭑ Competitive inhibitors
⭑ Non-competitive inhibitors
TEMPERATURE
- As temperature increases, particles vibrate more as they have more kinetic
energy and move faster.
- This means collisions to form enzyme-substrate
complexes are more likely.
- The energy of collisions also increases.
- Rate increases up to the optimum temperature.
- If temperature continues to increase past the
optimum, vibrations cause hydrogen bonds to
break which are holding enzyme it its tertiary
structure.
- Enzyme denatures as the active site changes shape.
pH
- All enzymes have an optimum pH (usually pH7 but pH2 optimum for pepsin
due to being in HCl in the stomach).
- Above and below the optimum the enzyme denatures due to the H+ and OH-
ions altering the hydrogen and ionic bonds holding the enzyme in its tertiary
structure.
ENZYME CONCENTRATION
- Increasing enzyme concentration increases rate of reaction.
- More enzymes are available so collisions with substrates to form
enzyme-substrate complexes are more likely.
- If substrate concentration is limiting increasing concentration of enzymes has
no further effect.
SUBSTRATE CONCENTRATION
- Increasing substrate concentration increases rate of reaction
- As collisions to form enzyme-substrate complexes are more likely
- Increases up to saturation point where all enzyme active sites are in use
- Increasing substrate concentration after this point has no further effect
- Over the reaction substrate concentration reduces as the product is formed
- Meaning rate of reaction decreases over time
- Initial rate is highest.
- When it plateaus, reaction hasn’t stopped, the
- reaction hasn’t stopped, the rate is just constant.
COMPETITIVE INHIBITORS
- Competitive inhibitors have a similar shape to the substrate.
- Meaning it competes with the substrates to binds to the enzyme.
- Competitive inhibitors block the active site but not reaction takes place.
- This reduces the amount of enzyme-substrate complexes that can form.
- Increasing competitive inhibitors reduces rate as they take up active sites.
- Increasing substrate concentration reduces the effect of the competitive
inhibitors as collisions more likely up to a point.
NON-COMPETITIVE INHIBITORS
- They don’t compete for the active site as they have a different shape.
- They bind away from active site in allosteric site.
- This causes a permanent conformational change in the active site.
- Substrates cannot bind and form enzyme-substrate complexes as they are no
longer complementary.
- Increasing substrate concentration has no effect as the non-competitive
inhibitor doesn’t compete and alters the shape of the active sites.
REQUIRED PRACTICAL 1
1B: MORE BIOLOGICAL MOLECULES
DNA AND RNA FUNCTION
DNA (deoxyribonucleic acid)
- Stores genetic information
- Hereditary material responsible for passing genetic material from cell to cell
from generation to generation
- 3.2 billion base pairs in DNA od typical mammalian cell, infinite variety of
sequences which provides genetic diversity in living organisms

RNA (ribonucleic acid)

- Transfer genetic info
- From DNA to ribosomes to make proteins (translation)
NUCLEOTIDE STRUCTURE
Phosphate group

Pentose sugar - deoxyribose or ribose

Nitrogenous base - A,T,C,G,U

POLYNUCLEOTIDE FORMATION AND STRUCTURE
Condensation reaction between phosphate group and pentose sugar forming a
phosphodiester bond. Already an ester bond between phosphate and sugar on
one nucleotide so when new bond forms with another nucleotide there is two ester
bonds, hence the phosphodiester bond.

Forms a sugar-phosphate backbone where pentose

sugars and phosphate groups are joined in a chain.
DNA STRUCTURE
➔ Double helix structure
➔ 2 separate polynucleotide strands wound round each other
➔ Very long
➔ Coiled tightly
➔ Held by hydrogen bonds between bases
➔ Pentose sugar in nucleotides - deoxyribose
➔ Nitrogenous bases - adenine, thymine, cytosine, guanine
HOW IS DNA ADAPTED FOR ITS FUNCTION?
STRUCTURE FUNCTION

Double stranded Both strands can act as templates for

semi-conservative replication

Weak hydrogen bonds between bases Can be unzipped for replication

Complementary base pairing Accurate replication as free nucleotides complementary

exposed bases, reduce chance of mutation

Many hydrogen bonds between bases Stable / strong molecule

Double helix with sugar phosphate backbone Protects bases / H bonds/ degeneration of molecule

Long molecule Store lots of (genetic) information (that codes for

polypeptides)

Double helix (coiled) Compact, store a lot in a small space

COMPLEMENTARY BASE PAIRINGS
Helps when DNA replicate as it enables identical copies to be created as free
nucleotides bind to complementary base and reduce copying errors which cause
mutations.

1 base has 1 specific partner

A to T/U
C to G

Hydrogen bonds connect bases

- 2 hydrogen bonds between adenine and thymine/uracil
- 3 hydrogen bonds between cytosine and guanine
RNA STRUCTURE
➔ Single polynucleotide strand
➔ Shorter chain
➔ Pentose sugar in nucleotides - ribose sugar
➔ Nitrogenous bases - adenine, uracil, cytosine, guanine
DNA AND RNA COMPARISON

FEATURE DNA RNA

Shape Double helix, 2 Single polynucleotide strand

polynucleotide strands

Length Long Short

Pentose sugar Deoxyribose Ribose

Bases ATCG AUCG

DNA HISTORY AS CARRIER OF GENETIC CODE
● 1800 - DNA first observed
⤷ Doubted DNA as carrier of genetic code as has relatively simple chemical composition
⤷ Believed proteins would be carriers are more chemically varied

● 1953 - proved DNA and founded double helix

⤷ Experiments shown that DNA is carrier of genetic code
⤷ James Watson and Francis Crick founded double helix which helps DNA carry out its
function
C-ATOM ARRANGEMENT IN PENTOSE SUGAR
MOLECULES
C-atoms numbered after oxygen clockwise. Carbon-5 is outside pentose molecule.

Carbon 3 has hydroxyl (OH) group attached.

Carbon 5 has phosphate group attached.

As the strands are antiparallel, One strand runs 3’to 5’

(ends with phosphate group) and one goes
5’ to 3’ (ends with hydroxyl group)
WHY DOES DNA REPLICATE BY
SEMI-CONSERVATIVE REPLICATION?
🧬 DNA copies itself before cell division so that each new cell has the full amount of DNA.
This happens in interphase of the cell cycle, specifically the synthesis phase.

🧬 The method is called semi-conservative replication because half of the strands in each
new DNA molecule are from the original DNA molecule and half are newly
synthesised.

🧬 The semi-conservative replication of DNA ensures genetic continuity between

generations of cells. This means the cells produced by cell division inherit their genes
from their parent cells.
DNA REPLICATION ENZYMES
DNA HELICASE - unzipping, breaks hydrogen bonds to separate the polynucleotide strands.

DNA POLYMERASE - join together adjacent nucleotide.

DNA PRIMASE - catalyze the synthesis of short RNA molecules used as primers for DNA
polymerases.

DNA LIGASE - joins DNA fragments together.

STAGES OF SEMI-CONSERVATIVE DNA REPLICATION

1) DNA helicase attaches to molecule, breaks hydrogen bonds between bases on parental
DNA . 2 strands unwind from each other and separate. Each strand is a template for new
strand.
2) Free activated DNA nucleotides (3 phosphate groups) attach to complementary exposed
base pairs from original strand. Only held by hydrogen bonds between nucleotides.
3) DNA polymerase catalyses condensation reactions (loss of water) so that a phosphodiester
bond can form between the activated adjacent nucleotides to form a new polynucleotide
chain/sugar-phosphate backbone. Activated nucleotides lose 2 of their phosphate groups
which leave and provide energy for the reaction.
4) Now have 2 sets of daughter DNA each with one strand of original DNA and one newly
synthesised strand.
ROLE OF DNA LIGASE
○ DNA polymerase can only work in one direction (5’ to 3’) because the active site of the
enzyme is only complementary to the 3’ (phosphate) end so joins nucleotides at 3’ end.
○ The 5’ to 3’ strand is the leading strand as the DNA polymerase follows the DNA helicase.
○ As the strands are antiparallel, the other strand runs 3’ to 5’.

○ DNA polymerase wants to go 5’ to 3’

○ So does a section of strand then jumps to next bit leaving Okazaki fragments. This is the
lagging strand.

○ DNA ligase joins together the shorter polynucleotide strands/fragments together.

MODELS OF DNA REPLICATION
Watson and Crick worked out structure of DNA which led them to suggest ways of coping the
DNA. Their hypothesis was that DNA replicates by semi-conservative replication but both
models needed to be scientifically tested before any conclusion could be drawn.

➔ The conservative model suggested that the original DNA molecule remained intact
and that a separate daughter DNA copy was built up from new molecules of
deoxyribose, phosphate and organic bases. Of the two molecules produced, one would
be made of entirely new material while the other would be entirely original material.

➔ The semi-conservative model proposed that the original DNA molecule split into two
separate strands, each of which then replicated its mirror image (i.e. the
missing half). Each of the two new molecules would therefore have one strand of new
material and one strand of original material.
EVIDENCE FOR SEMI-CONSERVATIVE REPLICATION
Meselson and Stahl proved that DNA replicated by semi-conservative replication (Watson
and Crick’s theory) and not by conservative replication.

They bases their experiments on 3 facts:

● All bases in DNA contain nitrogen

● Nitrogen has two forms: the lighter nitrogen 14N and the heavier isotope 15N.
● Bacteria will incorporate nitrogen from their growing medium into any new DNA that
they make.

They reasoned that bacteria grown on a medium containing 14N would have DNA that was
lighter than bacteria grown on a medium containing 15N. Bacteria divide quickly so that is
why bacteria were used.
THE EXPERIMENT
1. Grow 2 sets of bacteria, one in light nitrogen and one in heavy nitrogen
2. Light is control, heavy is for investigation
3. DNA will contain the light or heavy nitrogen that it was grown in
4. Extract some DNA from both and spin in centrifuge
5. Heavy (15N) forms band at the bottom, light (14N) forms band at the top
6. Then put bacteria that was in heavy nitrogen that now has DNA containing heavy
nitrogen into light nitrogen broth to divide once (1st generation)
7. Then centrifuge again and observe the results
8. Then allow bacteria to divide again on 14N (2nd generation)
9. Each strand of double helix acts as new template for next generation
10. Extract and centrifuge again
11. Allow a 3rd division and repeat
RESULTS OF THE EXPERIMENT

GENERATION DNA RESULT/BAND LOCATION

(DNA in 14N) Control Top (100%, less dense)

G0 - DNA in 15N Bottom (100%, more dense)

G1 - DNA containing heavy Middle (100%, one strand

nitrogen grown in light nitrogen original 15N one 14N as that is
broth (2 bacteria ) what it was grown in)

G2 - DNA containing heavy Middle (50% or 2/4)

nitrogen grown in light nitrogen Top (50% or 2/4)
broth (4 bacteria)

G3 - of DNA containing heavy Middle (25% or 2/8)

nitrogen grown in light nitrogen Top (75% or 6/8)
broth (8 bacteria)
WHAT THE RESULTS WOULD SHOW IF
CONSERVATIVE REPLICATION TOOK PLACE

- No banding ever in the middle

- Bottom band
- Top band will increase in thickness after each replication
- Entirely new material for each new double helix
WHY IS ENERGY IMPORTANT?
Plants and animals need energy for biological processes to occur:
● Active transport
● DNA replication
● Cell division
● Protein synthesis
● Building larger molecules from smaller
ATP AND RESPIRATION
● Adenosine triphosphate is a nucleotide derivative. Modified form of a
nucleotide.
● It is not energy it is a store of energy .
● Energy is used to make ATP.
● Energy is released when ATP is hydrolysed
● Made from an adenine nucleotide base, ribose pentose sugar and 3
phosphate groups.

● Respiration is the release of energy from glucose.

● The energy released from glucose is used to make ATP.
● Once ATP is made, it diffuses to part of the cell that requires energy.
PROPERTIES OF ATP
1) Stores or releases only a small, manageable amount of energy at a time
meaning no energy is wasted as heat.
2) It is a small, soluble molecule so It can be easily transported around the
cell
3) It can be broken down easily to release energy instantly.
4) ATP can be remade quickly.
5) Can make other molecules more reactive by transferring one of their
phosphate groups to them in a process called phosphorylation.
6) Can’t pass out of the cell so the cell always has an immediate supply of
energy.
WHY DO WE NEED ATP IF WE HAVE GLUCOSE?
A cell cannot get its energy directly from glucose so it is broken down in respiration
in order for energy to be released.

This is because glucose is:

● Glucose is a bigger molecule and is not as easy to transfer.
● Not as easily broken down, it is a multistage process.
BREAKING ATP
When a cell needs energy ATP is broken down during a hydrolysis reaction which
requires a water molecule into ADP (adenosine diphosphate)and Pi (inorganic
phosphate). When the phosphate bond is broken, energy is released. The reaction
is catalysed by ATP hydrolase.
USING ATP
ATP hydrolysis can be ‘coupled’ to other energy-requiring processes meaning that
the energy released can be used directly to make the other reaction happen.

The released inorganic phosphate can be added to another compound

(phosphorylation), which often makes the compound more reactive. E.g. active
transport.

In a cell there’s a constant cycle between ADP and Pi , and ATP. This allows
energy to be stored and released as it’s needed.
RESYNTHESIS OF ATP
ATP can be re-synthesised in a condensation reaction between ADP and Pi . A
water molecule is lost when a new phosphate bond is formed. This happens
during both respiration and photosynthesis, and is
catalysed by the enzyme ATP synthase.
THE IMPORTANCE OF WATER
Water is vital to living organisms. It makes up about 80% of a cell’s contents and has loads
of important functions, inside and outside cells:

These are the main properties of water:

IMPORTANT METABOLITE
GOOD SOLVENT
HIGH LATENT HEAT OF VAPORISATION
HIGH SPECIFIC HEAT CAPACITY
VERY COHESIVE
STRUCTURE OF WATER: POLARITY
A molecule of water (H2O) is one atom of oxygen covalently bonded to two
atoms of hydrogen.

Because the shared negative electrons are pulled towards the oxygen atom as it is
more electronegative, the other side of each hydrogen atom is left with a slight
positive charge (delta +). The unshared negative electrons on the oxygen atom
give it a slight negative charge (delta -). This makes water a polar molecule, it has
a slight (partial) negative charge on one side and a slight (partial) positive charge
on the other.
STRUCTURE OF WATER: HYDROGEN BONDING
Hydrogen bonds are weak bonds that form between a slightly positively charged
hydrogen atom in one molecule and a slightly negatively charged oxygen atom in
another molecule as they attract each other.
PROPERTIES OF WATER: IMPORTANT METABOLITE
Many metabolic reactions involve a condensation or hydrolysis reaction.
A hydrolysis reaction requires a molecule of water to break a bond. A
condensation reaction releases a molecule of water as a new bond is formed.

Energy from ATP is released through a hydrolysis reaction.

A metabolic reaction is a chemical reaction that happens in a living organism to

keep the organism alive. A metabolite is a substance involved in a metabolic
reaction.
PROPERTIES OF WATER: GOOD SOLVENT
A solvent is a substance capable of dissolving another substance. As water is polar, the delta positive hydrogen atoms
will be attracted to the negative ion, and the delta negative oxygen atom will be attracted to the positive ion. This means the
ions will get totally surrounded by water molecules, meaning in they’ll dissolve.

This means living organisms can take up useful substances (like mineral ions) dissolved in water and these dissolved
substances can be transported around the organism’s body.

Most biological reactions take place in solution, so water’s pretty essential. Polar molecules, such as glucose, dissolve in
water because hydrogen bonds form between them and the water molecules.
PROPERTIES OF WATER: HIGH LATENT HEAT OF
VAPORISATION
Latent heat is the heat energy that’s needed to change a substance from one state to another, e.g. from a liquid to
a gas.

Water evaporates (vaporises) when the hydrogen bonds holding water molecules together are broken. This allows
the water molecules on the surface of the water to escape into the air as a gas. It takes a lot of energy (heat) to
break the hydrogen bonds between water molecules, so a lot of energy is used up when water evaporates. This
means water has a high latent heat of vaporisation — lots of heat is used to change it from a liquid to a gas.

This is useful for living organisms because it means they can use water loss through evaporation to cool down
without losing too much water. When water evaporates it carries away heat energy from a surface, which cools
the surface and helps to lower the temperature (e.g. when humans sweat to cool down).
PROPERTIES OF WATER: HIGH SPECIFIC HEAT
CAPACITY
Buffers changes in temperature.

This is the energy needed to raise the temperature of 1kg of a substance by 1 °C.

Hydrogen bonds give water a high specific heat capacity. When water is heated, a lot of the heat energy
is used to break the hydrogen bonds between the water molecules. This means there is less heat energy
available to actually increase the temperature of the water. So water has a high specific heat capacity as it
takes a lot of energy to heat it up.

This is useful for living organisms because it means that water doesn’t experience rapid temperature
changes. This makes water a good habitat because the temperature under water is likely to be more
stable than on land. The water inside organisms also remains at a fairly stable temperature which helps
them to maintain a constant internal body temperature.

Enzyme activity is affected by temperature. Some important biological processes need enzymes to work
(e.g. digestion and respiration). These may not work properly if the organism’s temperature is not kept
fairly stable.
PROPERTIES OF WATER: VERY COHESIVE
Cohesion is the attraction between molecules of the same type (e.g. two water
molecules). Water molecules are very cohesive (they tend to stick together) because
they’re polar. Strong cohesion helps water to flow, making it great for transporting
substances.

For example, it’s how water travels in columns up the xylem (tube-like transport cells) in
plants. Strong cohesion also means that water has a high surface tension when it
comes into contact with air. This is the reason why sweat forms droplets, which
evaporate from the skin to cool an organism down. It’s also the reason that pond
skaters, and some other insects, can ‘walk’ on the surface of a pond.
QUESTIONS INVOLVING PROPERTIES OF WATER
Don’t just say polar or hydrogen bonding.

1. Good solvent
2. Cohesive (hydrogen bonding)
3. Buffers changes in temp as high specific heat capacity.
INORGANIC IONS
● An inorganic ion is one which doesn’t contain carbon (although there are
a few exceptions to this rule).
● There are inorganic ions, in solution, in the cytoplasm of cells and in the body
fluids of organisms.
● Inorganic ions perform a range of functions.
● The specific function a particular ion performs is related to its properties.
● An ion’s role determines whether it is found in high or low concentrations.
INORGANIC IONS
ION ION FORMULA FUNCTION

Iron Fe3+ Haemoglobin is a large protein that carries oxygen around the body, in the red blood
cells. It’s made up of four different polypeptide chains, each with an iron ion (Fe2+) in
the centre. It’s the Fe2+ that actually binds to the oxygen in haemoglobin so it’s a
pretty key component. When oxygen is bound, the Fe2+ ion temporarily becomes an
Fe3+ ion, until oxygen is released.

Phosphate PO43- Phosphorylation. When a phosphate ion is attached to another molecule, it’s known
as a phosphate group. DNA, RNA and ATP all contain phosphate groups. It’s the
bonds between phosphate group that store energy in ATP The phosphate groups in
DNA and RNA allow nucleotides to join up to form the polynucleotide.

Hydrogen H+ pH is calculated based on the concentration of hydrogen ions in the environment.

The more H+ present, the lower the pH (and the more acidic
the environment). Enzyme-controlled reactions are all affected by pH.

Sodium Na+ Glucose and amino acids need a bit of help crossing cell membranes. A molecule of
glucose or an amino acid can be transported into a cell (across the cell-surface
membrane) alongside sodium ions. This is known as co-transport.
EXPLAIN HOW A CHANGE IN DNA BASE SEQUENCE
CAN AFFECT AN ENZYME REACTION
1. Base sequence determines sequence of amino acids in polypeptide chain/primary structure
2. 3 bases code for one amino acid
3. Primary structure determines position of bonds between R groups in the tertiary structure
4. Hydrogen, ionic bonds and disulphide bonds
5. A change in tertiary structure/ bonds changes shape of active site of the enzyme
6. Meaning the substrate can no longer bind to form an enzyme substrate complex
SUMMARY
Monomers 2 monomers Polymer Bond Test

Carbohydrates monosaccharides Disaccharides Polysaccharides Glycosidic Benedicts

Lipids (Fatty acid + Ester/ phosphoester Ethanol

glycerol +
phosphate group)

Protein Amino acid Dipeptide Polypeptide Peptide Biuret

Nucleic acids Nucleotides Polynucleotide Phosphodiester