Biological Molecules

3.
1 Biological Molecules
Contents
3.1.1 Monomers and polymers

Introduction to monomers and polymers
Condensation and hydrolysis reactions
Summary of examples
3.1.2 Carbohydrates
Introduction to carbohydrates
Monosaccharides
Disaccharides
Isomers of glucose: alpha and beta glucose
Polysaccharides
Biochemical tests: Benedict’s test
Determining glucose concentration
Biochemical tests: iodine test
3.1.3 Lipids
Triglycerides
Saturated and unsaturated fatty acids
Phospholipids
Biochemical test: emulsion test
3.1.4 Proteins
3.1.4.1 General properties of proteins
Amino acids, dipeptides and polypeptides
Structural levels of proteins and the role of bonds
Biochemical test: biuret test
3.1.4.2 Many proteins are enzymes

Introduction to enzymes
Models of enzyme action: induced-fit model
Specificity of enzymes
Factors affecting the rate of enzyme-controlled reactions
Material of @medic.coffee (not to be redistributed without permission)

3.1.5 Nucleic acids are important information-carrying molecules
3.1.5.1 Structure of DNA and RNA

Functions of DNA and RNA
Structure of DNA and RNA nucleotides and polymers
Structure of DNA structure related to its function
3.1.5.2 DNA replication

Introduction to DNA replication
Semi-conservative replication of DNA
Evidence for semi-conservative replication: Meselson and Stahl
3.1.6 ATP
Introduction to ATP
Structure of ATP
ATP / ADP condensation and hydrolysis reactions
Properties of ATP related to its function
3.1.7 Water
Water is a polar molecule
Properties of water and their importance
3.1.8 Inorganic ions

Introduction to inorganic ions

3.1.1 Monomers and polymers
What the specification says:

The variety of life, both past and present, is extensive, but the biochemical basis of life is
similar for all living things.
Monomers are the smaller units from which larger molecules are made.
Polymers are molecules made from a large number of monomers joined together.
Monosaccharides, amino acids and nucleotides are examples of monomers.
A condensation reaction joins two molecules together with the formation of a chemical bond
and involves the elimination of a molecule of water.
A hydrolysis reaction breaks a chemical bond between two molecules and involves the use of
a water molecule.
Summary of what you need to know:
Definition of monomer Examples of polymers

Definition of polymer Definition of condensation reaction
Examples of monomers Definition of hydrolysis reaction
Introduction and key terms
There are many key biological molecules that are required to build structures that enable us to
function. These structures include:
Carbohydrates Proteins
Examples: starch, glycogen, cellulose Examples: enzymes, haemoglobin
Nucleic acids Lipids

Examples: DNA, RNA Examples: triglycerides, phospholipids
Key definitions
Monomers = smaller units from which larger molecules are made

Polymers = molecules made from a large number of identical monomers joined together in a chain
Examples of monomers include: monosaccharides, amino acids and nucleotides

Examples of polymers include: polysaccharides, polypeptides and polynucleotides

Note: Lipids are not classed as polymers as they are not made up from monomers. They are made
up of fatty acids and glycerol, therefore they aren’t polymers- so don’t fall into this trap in the exam!
There are two types of reactions you need to know about: condensation and hydrolysis.
Condensation reaction = a reaction involving the elimination of a water molecule which joins two
molecules together to form a chemical bond
Hydrolysis reaction → the breaking of a chemical bond between two molecules, involving the
addition of a water molecule
A summary of the common monomers and polymers you need to know
Monomer Polymer
Condensation
(+ 2H2O)
Hydrolysis
Monosaccharides Polysaccharide (starch, glycogen, cellulose)
(glucose)
Condensation
(+ 2H2O)
Hydrolysis
Nucleotide
Nucleic acid (DNA/ RNA)
Condensation
Hydrolysis
(+ 2H2O)
Amino acid Polypeptide (protein)

Example exam question:
Describe the chemical reactions involved in the conversion of polymers to monomers and
monomers to polymers. Give two named examples of polymers and their associated
monomers to illustrate your answer. (5)
- A condensation reaction joins monomers together and forms a (chemical) bond and releases
water
- A hydrolysis reaction breaks a (chemical) bond between monomers and uses water
- A suitable example of polymers and the monomers from which they are made
- A second suitable example of polymers and the monomers from which they are made
- Reference to a correct bond within a named polymer
Top tip: Any polymer, along with its respective monomer, that we have seen so far would be
accepted in the mark scheme! Make sure to state the obvious- what type of bond is in your
chosen polymer (eg. glycosidic, peptide, phosphodiester)?

3.1.2 Carbohydrates
Monosaccharides are the monomers from which larger carbohydrates are made. Glucose,
galactose and fructose are common monosaccharides.
A condensation reaction between two monosaccharides forms a glycosidic bond.
Disaccharides are formed by the condensation of two monosaccharides:

maltose is a disaccharide formed by condensation of two glucose molecules
sucrose is a disaccharide formed by condensation of a glucose molecule and a fructose molecule
lactose is a disaccharide formed by condensation of a glucose molecule and a galactose
molecule.
Glucose has two isomers, α-glucose and β-glucose, with structures:
Polysaccharides are formed by the condensation of many glucose units.
Glycogen and starch are formed by the condensation of α-glucose.

Cellulose is formed by the condensation of β-glucose.
The basic structure and functions of glycogen, starch and cellulose. The relationship of
structure to function of these substances in animal cells and plant cells.
Biochemical tests using Benedict's solution for reducing sugars and non-reducing sugars
and iodine/potassium iodide for starch.

Definition of monosaccharide Definition of polysaccharides
Examples of monosaccharides Examples of polysaccharides
What a glycosidic bond is Structure and functions of glycogen
Definition of disaccharides Structure and functions of starch
Examples of disaccharides Structure and functions of cellulose
Isomers of glucose: alpha and beta Biochemical test for reducing sugars
Draw structures of isomers of glucose Biochemical test for non-reducing sugars
Biochemical test for starch

Introduction to carbohydrates
We saw from the previous sub-topic that carbohydrates are made up of monomers called
monosaccharides. Carbohydrates can thus be referred to as polysaccharides (since they are made
up of many monosaccharides). In very simple terms, carbohydrates can otherwise be described as
complex sugars.
These can be classified into three groups based on how many monomers they are made up of:
Monosaccharides Disaccharides Polysaccharides
Monomers from which Formed by the condensation Formed by the condensation

polysaccharides are made of 2 monosaccharides of many monosaccharides
Small Increasing size Large
A condensation reaction between any two monosaccharides will always form a glycosidic bond.
H O H H O H Condensation H O H H O H
(+ H2O)
HO OH HO OH Hydrolysis HO O OH
α-glucose α-glucose maltose
Exam tip: All sugars end in ‘ose’ (examples include: glucose, maltose, sucrose, lactose, etc)
Monosaccharides
Monosaccharide = single sugar monomer which forms larger carbohydrates / polysaccharides
There are 3 key monosaccharides you need to know:
1. Glucose
2. Fructose
3. Galactose

Disaccharides
Disaccharide = a sugar formed from two monosaccharides joined by a glycosidic bond in a

condensation reaction
There are 3 key disaccharides you need to know (and their monosaccharides):
Monosaccharides Disaccharide
Condensation
α-glucose + α-glucose maltose (reducing sugar)
Hydrolysis
Condensation
α-glucose + fructose sucrose (non-reducing sugar)
Hydrolysis
Condensation
α-glucose + galactose lactose (reducing sugar)
Hydrolysis
Exam tip: Reducing sugars are simply sugars that will donate electrons; the reverse is true for non-
reducing sugars. You don’t need to know this in much detail as it is beyond the scope of A-level. Just
make sure you know which sugars are reducing and non-reducing for the exam (see Benedict’s test)!
Isomers of glucose: alpha + beta glucose
Isomer = molecules with the same molecular formula but differently arranged atoms
Glucose has two isomers:

The main difference between the two is
6 6
that the -OH group is inverted on carbon-1
5
5
4 1
on β-glucose (circled on diagram).
4 1
3 2 3 2
Exam tip: This is the maximum level of detail that you would be expected to be able to draw in an
exam for α-glucose and β-glucose- so be sure to learn their structures!

Polysaccharides
Polysaccharides = polymers formed by many monosaccharides joined by glycosidic bonds in a

condensation reaction to form chains
There are 3 key polysaccharides you need to know:
Starch
- A polymer of α-glucose
- Function = energy store in plant cells
amylose
Structure of starch:
- Mixture of amylose and amylopectin
- Amylose = unbranched, helical + 1,4 glycosidic bonds
- Amylopectin = highly branched, 1,4 and 1,6 glycosidic bonds
How its structure is related to its function: (exam points)

- Helical structure means it is compact for storage in cell
- Large polysaccharide means it can’t leave the cell
- Insoluble in water means the water potential of the cell is unaffected
amylopectin
Glycogen The structure of

- A polymer of α-glucose glycogen is similar
- Function = energy store in animal cells to amylopectin, but
even more
Structure of glycogen branched!
- Highly branched
- 1,4 and 1,6 glycosidic bonds
Exam tip: only
How its structure is related to its function: (exam points) branched structures
- Branched structure means that ends are rapidly hydrolysed to release have both 1,4 and
glucose for respiration to provide energy 1,6 glycosidic
- Large polysaccharide means that it can’t leave the cell bonds; straight
- Insoluble in water means the water potential of the cell is unaffected chain molecules do
not!
What is the difference between 1,4 and 1,6 glycosidic bonds?

The numbers simply refer to which carbons on glucose the glycosidic bond forms between.
For instance, 1,4 glycosidic bonds occur between carbon-1 and carbon-4 on glucose.

Cellulose
- A polymer of β-glucose
- Function = provides strength and structural support to plant cell wall
Structure of cellulose
- Long, straight, unbranched chain
- 1,4 glycosidic bonds only
cellulose
- Many hydrogen bonds linking parallel strands to form microfibrils
- Hydrogen bonds strong in high numbers
Exam tip: Make
How its structure is related to its function: (exam points) sure that you
- Many hydrogen bonds forming microfibrils provide strength to plant cells walls can relate the
- Can resist turgor pressure / osmotic pressure / pulling forces structure to
- Bonds difficult to break their functions
- Resists digestion / action of microorganisms / enzymes for all three!
Exam question example:

Give two ways in which the structure of starch is similar to cellulose. (2)
(Both)
- Are polymers / polysaccharides / are made of monomers / of monosaccharides;
- Contain glucose / carbon, hydrogen and oxygen;
- Contain glycosidic bonds
- Have 1,4 links
- Hydrogen bonding (within structure)
- Neutral: references to ‘unbranched’, insoluble, formed by condensation, flexible and rigid

Give two ways in which the structure of starch is different from cellulose. (2)
(Starch) - accept converse for cellulose
- Contains α / alpha glucose
- Helical / coiled / compact / branched / not straight
- 1,6 bonds / 1,6 branching
- Glucoses / monomers same way up
- No H-bonds between molecules
- No (micro / macro) fibres / fibrils

Describe the structure of a cellulose molecule and explain how cellulose is adapted for its function
in cells. (6)
- Polymer made from β-glucose / beta-glucose
- Joined by condensation / removing molecule of water / glycosidic bond
- 1,4 links
- ‘Flipping over’ of alternate molecules
- Hydrogen bonds linking chains / long straight chains
- Cellulose makes cell walls strong / cellulose fibres are strong
- Can resist turgor pressure / osmotic pressure / pulling forces
- Bonds are difficult to break
- Resists digestion / action of microorganisms / enzymes
Biochemical tests: Benedict’s test
Benedict’s reagent can be used to test for reducing or non-reducing sugars.
Summary of reducing and non-reducing sugars:
Reducing sugars include: Non-reducing sugars include:

- All monosaccharides (glucose, fructose and galactose) - Disaccharide (sucrose)
- Some disaccharides (maltose, lactose)
Benedict’s test for reducing sugars
1. Add Benedict’s reagent to sample

2. Heat in a boiling water bath
3. Positive result = green, yellow, orange or brick-red
precipitate (depending on concentration of reducing
sugar present) Increasing reducing sugar concentration
Benedict’s test for non-reducing sugars
1. Perform Benedict’s test for reducing sugars (negative result - sample remains blue)
2. Add a few drops of dilute hydrochloric acid (to hydrolyse it into its constituent reducing sugars)
3. Heat in a boiling water bath
4. Neutralise with sodium hydrogencarbonate (adding an alkali to acid will neutralise it)
5. Add Benedict’s reagent and heat again
6. If non-reducing sugar present = green, yellow, orange or brick-red precipitate

Determining glucose concentration of an unknown sample
We can determine the glucose concentration of an unknown sample by producing a dilution series of
different glucose concentration, and then plotting a calibration curve.
Method:
1. Produce a dilution series of glucose solutions of known concentrations
2. Perform a Benedict’s test on each sample
- Heat with Benedict’s solution
- Use same amount of solution for each test
- Use excess Benedict’s
- Remove precipitate by filtering
3. Using a colorimeter, measure the absorbance of each sample and plot a calibration curve
- Calibrate colorimeter using unreacted Benedict’s
- Use a red filter
- Less absorbance of filtrate = more sugar present (as removed precipitate)
- Plot absorbance (y) against glucose concentration (x)
4. Repeat with unknown sample (find absorbance) and use graph to determine glucose concentration
Biochemical test: iodine test
We can test for starch by using the iodine test. iodine
Method:
1. Add iodine to sample and shake / stir
2. Positive result = blue-black colour

3.1.3 Lipids
Triglycerides and phospholipids are two groups of lipid.

Triglycerides are formed by the condensation of one molecule of glycerol and three molecules
of fatty acid.
A condensation reaction between glycerol and a fatty acid (RCOOH) forms an ester bond.
The R-group of a fatty acid may be saturated or unsaturated.
In phospholipids, one of the fatty acids of a triglyceride is substituted by a phosphate-
containing group.
The different properties of triglycerides and phospholipids related to their different structures.
The emulsion test for lipids.
Students should be able to:
recognise, from diagrams, saturated and unsaturated fatty acids

explain the different properties of triglycerides and phospholipids.
Two types of lipid: triglycerides and phospholipids

Structure of triglycerides
Bonds in triglycerides
Fatty acids can be saturated or unsaturated
Structure of phospholipids
Different properties of triglycerides and phospholipids and relate to structure
The emulsion test
Triglycerides
There are two groups of lipid we can classify them into: triglycerides and phospholipids.
Triglycerides = molecules formed by the condensation of one molecule of glycerol and

three molecules of fatty acid
Link to GCSE: You will be most familiar with seeing this type of lipid since this is the one
you learnt at GCSE!

Structure of triglycerides Ester bond
Condensation C C
C C 3H2O
C C C
C
C
C C
C
Glycerol 3 Fatty acids Triglyceride
Ester bonds = bonds formed between fatty acids and glycerol during a condensation reaction
Notice how the diagram above is very similar to the one you learnt at GCSE…but just
with a bit more extra detail than before!
Link to GCSE: Diagram showing formation of a lipid
Glycerol 3 Fatty acids Lipid
Link to organic chemistry: Zig zags are a simple way of representing a hydrocarbon tail. This
can also sometimes be represented as ‘R’.
C C C C C C C R

Properties of triglycerides related to its structure
- Main property = energy storage molecule

- High ratio of C-H bonds to C atoms in the hydrocarbon tail means that it releases more energy
than the same mass of carbohydrates
- Insoluble in water so no effect on water potential of cell
Saturated and unsaturated fatty acids
Fatty acids can be either saturated or unsaturated.
Saturated = absence of C=C bonds in hydrocarbon tail (ie. all carbons are fully saturated with
hydrogen)
Unsaturated = presence of one or more C=C bonds in hydrocarbon tail (ie. carbons are not all fully
saturated with hydrogen)
double bond
C C C C C C C C C
C
Saturated fatty acid Unsaturated fatty acid

Omega-3 fatty acids are unsaturated. What is an unsaturated fatty acid? (2)
- Double bond(s)
- (Bonds) between carbons
- Note: C=C bonds = 2 marks

Phospholipids
Phospholipids = molecules made up of one glycerol, two fatty acids and one phosphate group
(instead of another fatty acid)
General structure of a phospholipid

Instead of having three fatty acids (like
phosphate head triglycerides), one of the fatty acids is substituted
for by a phosphate group. We tend to refer to the
phosphate group as being the ‘head’ and the fatty
2 fatty acid tails acids as the ‘tails’.
Properties of phospholipids related to its structure
Main property = forms a phospholipid bilayer in cell membranes, allowing the diffusion of non-
polar and/or small molecules
Phosphate heads = polar and hydrophilic (attracted to water)

These face outwards towards the aqueous environment on either side of the membrane
Fatty acid tails = non-polar and hydrophobic (repelled by water) so face inwards
Extracellular environment
Hydrophilic = ‘water loving’, attracted to water
Hydrophobic = ‘water hating’, repelled by water
Exam tip: Make sure you are able to draw a

phospholipid bilayer (as shown in the diagram)!
Hydrophobic tail
Intracellular environment
Why is it called a phospholipid bilayer?

Remember that ‘bi’ means two-
phospholipids form ‘two layers’ in cell
membranes, thus we call it a bilayer.
Hydrophilic head

The structure of a phospholipid molecule is different from that of a triglyceride. Describe how a
phospholipid is different. (2)
3-
- Phosphate / PO4
- Instead of one of the fatty acids / and two fatty acids
Biochemical test: emulsion test for lipids
We can test for the presence of lipids in a sample using the emulsion test.
Method: Exam tip: The order in which you add

1. Add ethanol and shake (to dissolve lipids) the ethanol and water does matter in
2. Then add water the exam. So make sure you put
3. Positive result = milky / cloudy white emulsion forms ethanol first, and then water!

Some seeds contain lipids. Describe how you could use the emulsion test to show that a seed
contains lipids. (3)
- Crush / grind
- With ethanol / alcohol
- Then add water / then add to water
- Forms emulsion / goes white / cloudy

Describe how you would test a piece of food for the presence of lipid. (2)
- Dissolve in ethanol / alcohol, then add water
- White emulsion shows presence of lipid

3.1.4.1 Proteins: General properties of proteins
Amino acids are the monomers from which proteins are made. The general structure of an amino
acid as:
where NH2 represents an amine group, COOH represents a carboxyl group and R represents a side
chain. The twenty amino acids that are common in all organisms differ only in their side group.
A condensation reaction between two amino acids forms a peptide bond.
Dipeptides are formed by the condensation of two amino acids.

Polypeptides are formed by the condensation of many amino acids.
A functional protein may contain one or more polypeptides.

The role of hydrogen bonds, ionic bonds and disulfide bridges in the structure of proteins.
Proteins have a variety of functions within all living organisms. The relationship between
primary, secondary, tertiary and quaternary structure, and protein function.
The biuret test for proteins.

relate the structure of proteins to properties of proteins named throughout the specification.

Be able to draw the general structure of an amino acid
How the twenty common amino acids differ - R group
Formation of peptide bonds
Dipeptides and how they are formed
Polypeptides and how they are formed
Role of hydrogen bonds, ionic bonds and disulfide bonds
Primary, secondary, tertiary and quaternary structure of proteins
The biuret test for proteins
Relate structure of proteins to properties of proteins

Amino acids, dipeptides and polypeptides
Amino acids = the monomers from which proteins / polypeptides are made
There are 20 commonly occurring amino acids amongst all organisms. The only difference
between these amino acids is their R group.
General structure of an amino acid:

‘R’ group = variable side chain / group
R
2 C C
-NH 2 = amine group
-COOH = carboxyl group
Exam tip: Make sure you know how to draw the general structure for an amino acid- this could
come up as a one or two-marker exam question!
Top tip: The amine group gives the ‘amino’ part of amino acid. The carboxyl group is an acid
group which gives the ‘acid’ part of amino acid. This may help you remember the structure!
Diagram showing an example of how the R groups differ between amino acids
C
2 C C 2 C C
alanine glycine
Exam tip: If you are asked about how amino acids differ, you can draw a diagram in the exam to
show how the R groups differ- diagrams can be awarded marks in the exam!

Key points:
- A condensation reaction between two amino acids forms a peptide bond.
- Functional proteins may contain one or more polypeptides.
Key definitions
Dipeptide = 2 amino acids joined together by a peptide bond in a condensation reaction
Polypeptide = many amino acids joined together by peptide bonds
C C C C
glycine glycine
C C C C
peptide bond
dipeptide
C C C C C C C C C C
polypeptide

Structural levels of proteins and the role of bonds
There are 4 different structural levels within proteins. These are:

This is coded for by the DNA base
Primary (1º) structure = sequence of amino acids sequence of the gene coding for this
protein
alanine serine lysine proline glycine aspartic acid
Secondary (2º) structure = folding or coiling in polypeptide chain The secondary structure
is held together by
There are 2 common structures you need be aware of: hydrogen bonds
1. Alpha-helix
2. Beta-pleated sheet
Tertiary (3º) structure = overall 3D structure of a polypeptide Exam tip: You don’t
need to know how these
The tertiary structure is held together by these bonds: bonds are formed- you
just need to be aware of
Hydrogen bonds - formed between polar C=O and N-H bonds what bonds hold
Ionic bonds - formed between the R groups together these different
Disulfide bridges - formed between cysteine groups in the R groups structures.
Quaternary (4º) structure = proteins made up of 2 or more polypeptide chains
The most common example of this that you will be familiar with is haemoglobin!
You will encounter this later in Unit 3 for Mass Transport. But here’s a quick sneak
peak of why haemoglobin has a quaternary structure:
β-pleated sheet Haemoglobin is made up of 4 polypeptides:

- 2 alpha-helices
α-helix
- 2 beta-pleated sheets
haem group attached to

Haemoglobin molecule an iron (II) ion
In the specification, it states that: ‘students should be able to relate the structure of proteins to
properties of proteins named throughout the specification’
You will encounter lots of different proteins during the course of A-level Biology, including:
- Enzymes (links to lots of different topics including ATP, digestion, photosynthesis, synapses, etc)
- Antibodies (secreted by plasma cells in the humoral response- Unit 2)
- Actin and myosin (in muscles for myofibril contraction- Unit 6)
Exam tip: As you are learning, make sure you are aware of key proteins that you can link back to
knowledge from this topic. It is a very common topic that is guaranteed to crop up in exams so
ensuring you have a solid understanding of proteins will equip you well for the rest of the course.
Biochemical test: biuret test for proteins
We can test for proteins in a sample by using biuret reagent (which tests for peptide bonds).
Method: Biuret reagent is made up of

1. Add biuret reagent / solution to sample sodium hydroxide and
2. Positive result = purple colour (if negative, remains blue) copper (II) sulfate. It is the
copper (II) ions in solution
which makes it appear blue.
Diagram showing the biuret test
Sample + biuret reagent Positive result

3.1.4.2 Proteins: Many proteins are enzymes
Each enzyme lowers the activation energy of the reaction it catalyses. The induced-fit model of
enzyme action.
The properties of an enzyme relate to the tertiary structure of its active site and its ability to
combine with complementary substrate(s) to form an enzyme-substrate complex.
The specificity of enzymes

The effects of the following factors on the rate of enzyme- controlled reactions – enzyme
concentration, substrate concentration, concentration of competitive and of non- competitive
inhibitors, pH and temperature.

appreciate how models of enzyme action have changed over time
appreciate that enzymes catalyse a wide range of intracellular and extracellular reactions that
determine structures and functions from cellular to whole-organism level.
How enzymes work → lowering activation energy

Models of enzyme action → lock and key and induced-fit
Properties of enzymes related to structure
Specificity of enzymes
Effects of factors on rate of enzyme-controlled reactions: enzyme concentration, substrate
concentration, concentration of competitive and of non- competitive inhibitors, pH and temperature
Introduction to enzymes
As you learnt at GCSE, enzymes are biological catalysts which increase the rate of reaction without
being used up themselves. They do this by lowering the activation energy of the reaction.
Enzymes catalyse a wide range of intracellular (occurring inside the Ea without
cell) and extracellular (occurring outside of the cell) reactions. enzyme
Ea with
reactants enzyme
Intracellular enzymes = produced and function inside the cell
Extracellular enzymes = secreted by cells and catalyse products
reactions outside the cell (eg. digestive enzymes in the gut)

Models of enzyme action
You will have learnt at GCSE that enzymes work via the lock and key model. However, at A-level there
is actually another model of enzyme action you need to know about- the ‘induced-fit model’.
Let’s recap what the lock and key model showed about enzyme action:
- The active site of the enzyme is a fixed shape and is complementary to one substrate only
- After a successful collision between the enzyme and substrate, an enzyme-substrate complex (ESC)
is formed, leading to a reaction
Whilst the lock and key model demonstrated the specificity of enzymes, it wasn’t entirely accurate.
And thus the induced-fit model was proposed later on, which is more widely accepted nowadays
and supported by more recent evidence.
The induced-fit model Top tip: You can think of

1. Before the reaction, the active site of the enzyme is not enzymes in the lock and
completely complementary to the substrate (ie. it doesn’t fit exactly) key model as being more
2. The active site changes shape / undergoes a conformational rigid, whereas in the
change in shape as the substrate binds, forming an ESC induced-fit model,
3. This stresses / distorts the bonds in the substrate, leading to a enzymes are more
reaction (remember that enzymes lower the activation energy)! flexible.
products
active site (not complementary) active site (complementary)
substrate
Enzyme-substrate complex
The specificity of enzymes
Key point: All enzymes are proteins- this means that what we learnt about the general properties of
proteins applies here too.
All enzymes have a specific tertiary structure and active site due to the sequence of amino acids
(primary structure) which determines the tertiary structure
Common exam question example:

Maltose is hydrolysed by the enzyme maltase. Explain why maltase catalyses this reaction. (3)
- Active site has a specific shape / tertiary structure / active site complementary to substrate
- Only maltose can bind / fit
- To form enzyme-substrate complex / E-S complex
Factors affecting rate of enzyme-controlled reactions
There are several factors affecting the rate of enzyme-controlled reactions. Some you will know from
GCSE and some will be new to you at A-level. These include:
- Enzyme concentration Exam tip: You should

- Substrate concentration A-level
be able to describe and
- Temperature explain the effects of
GCSE
- pH all five factors on the
- Concentration of competitive + non-competitive inhibitors A-level rate of reaction. Make
sure you know their
graphs too!
Enzyme concentration
Key takeaway point = generally, as enzyme concentration increases, the rate of reaction increases
(until substrate concentration becomes a limiting factor)
when substrate is in excess

Why this occurs: Rate of
- Enzyme concentration = limiting factor (when substrate is in excess) reaction
- More enzymes means that more active sites are available when substrate is
- More successful enzyme-substrate collisions → more ESC formed limiting
- Rate of reaction plateaus as substrate concentration becomes limiting factor
Enzyme concentration

Substrate concentration
Key takeaway point = generally, as substrate concentration increases, the rate of reaction increases
(until enzyme concentration becomes a limiting factor)
Why this occurs: when enzyme conc. is limiting

- Substrate concentration = limiting factor Rate of
- More successful enzyme-substrate collisions → more ESC formed reaction
- Rate of reaction plateaus when enzyme concentration becomes
limiting factor (ie. all active sites are saturated; substrate is in excess)
Temperature
Key takeaway point = generally, as temperature increases, the rate of reaction increases (until
optimum temperature is surpassed and enzymes denature)
Increase in rate of reaction occurs because:

- Increase in temperature causes an increase in kinetic energy
- More successful enzyme-substrate collisions → more ESC formed optimum temperature
Decrease in rate of reaction occurs because: Rate of

- Enzymes denature → tertiary structure and active site change reaction
shape (H-bonds / ionic bonds break)

all enzymes
- Fewer enzyme-substrate collisions + ESC formed (substrate no denatured
longer binds to active site)

- Rate of reaction becomes zero when all enzymes are denatured
Temperature
pH
Key takeaway point = generally, when pH is above or below optimum pH, rate of reaction decreases
Why this occurs: optimum pH
- Enzymes denature → tertiary structure + active site change Rate of

reaction
shape (H-bonds and ionic bonds break)
- Complementary substrate can no longer bind to active site
- Fewer enzyme-substrate collisions + ESC formed
- pH = - log10 [H+]
pH
Inhibitors: competitive and non-competitive
There are two types of inhibitor: competitive and non-competitive inhibitors. As it suggests in the
name, both inhibitors inhibit / slow down the rate of reaction.
Competitive inhibitors = molecules with a similar shape to substrate + binds to active site so
substrates cannot bind (ie. it ‘competes’ with the substrate for the active site) → fewer ESC formed
Key takeaway point = generally, increasing substrate concentration reduces the effect of competitive
inhibitors
Non-competitive inhibitors = molecules that bind to enzyme away from active site → enzyme tertiary
structure + active site changes shape so that substrate cannot bind to active site → fewer ESC formed
Key takeaway point = increasing substrate concentration has no effect on the rate of reaction as non-
competitive inhibitors causes permanent changes to the shape of the active site
Main difference between competitive and non-competitive inhibitors:

- Effects of competitive inhibitors can be overcome by adding more substrate
- But effects of non-competitive inhibitors cannot be overcome in this way
A graph depicting the effects of inhibitors

substrate
competitive
inhibitor
active site
Enzyme without inhibitor
Rate of
reaction
Enzyme with
competitive inhibitor
allosteric site
Enzyme with non-competitive inhibitor
non-competitive
inhibitor

Scientists have investigated the effects of competitive and non-competitive inhibitors of the
enzyme maltase. Describe competitive and non-competitive inhibition of an enzyme. (5)
- Inhibitors reduce binding of enzyme to substrate / prevent formation of E-S complex
- Note: Maximum of 3 marks awarded if only one type of inhibition is dealt with
(For competitive inhibition):

- Inhibitor similar shape (idea) to substrate
- (Binds) in to active site (of enzyme)
- (Inhibition) can be overcome by adding more substrate
(For non-competitive inhibition):

- Inhibitor binds to site on enzyme other than active site
- Prevents formation of active site / changes (shape of) active site
- Cannot be overcome by adding more substrate

3.1.5.1 Structure of DNA and RNA
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are important information-carrying
molecules. In all living cells, DNA holds genetic information and RNA transfers genetic
information from DNA to the ribosomes.
Ribosomes are formed from RNA and proteins.
Both DNA and RNA are polymers of nucleotides. Each nucleotide is formed from a pentose, a
nitrogen-containing organic base and a phosphate group:
The components of a DNA nucleotide are deoxyribose, a phosphate group and one of the
organic bases adenine, cytosine, guanine or thymine.
The components of an RNA nucleotide are ribose, a phosphate group and one of the organic
bases adenine, cytosine, guanine or uracil.
A condensation reaction between two nucleotides forms a phosphodiester bond.
A DNA molecule is a double helix with two polynucleotide chains held together by hydrogen
bonds between specific complementary base pairs.
An RNA molecule is a relatively short polynucleotide chain.

appreciate that the relative simplicity of DNA led many scientists to doubt that it carried the
genetic code.
Main functions of DNA and RNA Structure of DNA molecule and how it relates
Recall what ribosomes are made up of to its function
Structure of nucleotide monomers Structure of RNA molecule
Identify structure of nucleotide from a diagram Compare structure of DNA and RNA
Structure of a DNA nucleotide Appreciate that the simplicity of the genetic
Structure of a RNA nucleotide code let many scientists to doubt that it
Condensation reactions between nucleotides carried the genetic code
forms phosphodiester bonds

Function of DNA and RNA
- DNA holds genetic information

- RNA transfers genetic information from DNA to ribosomes Exam tip: Make sure to learn what’s
in the highlighted box- this is a
common one-marker question in
Key point: Ribosomes are formed from RNA and proteins exams!
Structure of DNA and RNA nucleotides and polymers
Remember from the ‘Monomers and polymers’ unit that nucleotides are the monomers which make up
nucleic acids, such as DNA and RNA.
Each nucleotide contains: Structure of a nucleotide:
- A pentose sugar (5-carbon sugar) phosphate base

- A nitrogenous base
- A phosphate group
DNA or RNA nucleotides are joined pentose sugar

together by condensation reactions,
forming phosphodiester bonds
Structure of a single DNA nucleotide (monomer) Structure of a single RNA nucleotide (monomer)
phosphate phosphate base

base
(A, T, C, G) (A, U, C, G)
deoxyribose (sugar) ribose (sugar)
The 4 DNA nitrogenous bases include: The 4 RNA nitrogenous bases include:
- Adenine (A) - Adenine (A)
- Thymine (T) - Uracil (U)
- Cytosine (C) - Cytosine (C)
- Guanine (G) - Guanine (G)

Structure of a DNA molecule (polynucleotide / polymer)
hydrogen bond You need to know the number of

hydrogen bonds that form between
complementary base pairs in DNA:
phosphodiester
bond
- 2 H-bonds between A and T
- 3 H-bonds between C and G
Exam tip: This could easily come up

as a one-marker question so be sure
to memorise this!
Summary of the structure and differences between DNA and RNA
DNA RNA
Structure Structure
Double stranded Single stranded - one polynucleotide only
Structure (in detail) Structure (in detail)
- 2 polynucleotide strands run anti-parallel Single RNA polynucleotide strand

to each other to form a double helix
- Polynucleotide chains are held together by
hydrogen bonds between specific
complementary base pairs (A-T and C-G)
Main differences Main differences
- Double stranded - Single stranded

- Longer - Shorter
- Pentose sugar = deoxyribose - Pentose sugar = ribose
- Base = thymine (T) - Base = uracil (U) instead of thymine
Exam tip: You may be asked to compare the structure of DNA and RNA in your exam. Mark schemes
and examiners can be specific so make sure you are explicit when drawing comparisons. Getting into
the habit of using phrases such as ‘whereas’, ‘but’ or ‘on the other hand’ is good practice for this.

Structure of DNA related to its function
Whilst it isn’t explicitly mentioned in the specification, you may be asked to relate the structure of DNA
to its function, which is to carry genetic information.
Here are some key exam points that you can mention for this:
Double stranded → both strands can act as a template for semi-conservative replication
(more about this in the next sub-topic)
Weak hydrogen bonds between bases → can be unzipped for DNA replication
Complementary base pairing → ensures accurate replication
Many hydrogen bonds between bases → makes DNA a stable, strong molecule
Double helix with sugar-phosphate backbone → protects bases / hydrogen bonds
Long molecule → stores lots of genetic information (coding for polypeptides)
Double helix (coiled) → makes DNA a compact molecule
Maths application
Ensure you can use your knowledge of complementary base pairing to work out the frequency of
bases in an exam question.

Fill out the table with the percentages of each base. (2)
- First mark for getting % T correct

A C T G - Second mark for getting % of C and G correct
% 28 22 28 22 Remember: A always pairs with T and

C always pairs with G!

3.1.5.2 DNA replication

The semi-conservative replication of DNA ensures genetic continuity between generations of cells.
The process of semi-conservative replication of DNA in terms of:

unwinding of the double helix
breakage of hydrogen bonds between complementary bases in the polynucleotide strands
the role of DNA helicase in unwinding DNA and breaking its hydrogen bonds
attraction of new DNA nucleotides to exposed bases on template strands and base pairing
the role of DNA polymerase in the condensation reaction that joins adjacent nucleotides.

evaluate the work of scientists in validating the Watson–Crick model of DNA replication
Purpose of semi-conservative replication

Process of semi-conservative replication
Evaluate the work of scientists in validating the Watson-crick model of DNA replication
Introduction to DNA replication
You will have learnt from GCSE that DNA replication occurs during interphase in the cell cycle.
cytokinesis
DNA replication occurs in the nucleus of the cell since mitosis
that’s where DNA is stored.
But why is DNA replication so important?
It ensures that the whole genome is passed on accurately from

the parent cell to its daughter cells during cell division. This
ensures genetic continuity between generations of cells.
It is important because cells in our bodies undergo cell division interphase

regularly to replace themselves. DNA replication is also
important for growth of organisms.

Semi-conservative replication of DNA
DNA replicates semi-conservatively in cells. Here’s where the A-level knowledge comes in!
Semi-conservative replication = each new strand formed contains one strand from the original DNA
strand and one new strand
Key exam points:
1. DNA helicase breaks H-bonds between bases, unwinding the double helix
2. To form two strands which both act as templates
3. Free floating DNA nucleotides are attracted to exposed bases via specific complementary base
pairing, H-bonds form (A-T, C-G)
4. DNA polymerase joins adjacent nucleotides on new strand by condensation
5. Forming phosphodiester bonds (= sugar phosphate backbone)
DNA polymerase
complementary base pairing
free-floating DNA
nucleotides
original DNA strand

DNA helicase
original strand
new strand
Exam tip: Make sure to chromosome

learn these exam points
as semi-conservative
replication crops up as a
very common 5-6 marker
question! cell nucleus

Evidence for semi-conservative replication: Meselson and Stahl
These are simply different isotopes of nitrogen- you

Evidence:
will have learnt about isotopes at GCSE!
1. Bacteria grown in a nutrient solution containing heavy nitrogen (15N) for several generations
2. Nitrogen incorporated into bacterial DNA bases
3. Bacteria then transferred to a nutrient solution containing light nitrogen (14N) and allowed to
grow and divide twice
4. During this process, DNA from different samples of bacteria was extracted, suspended in
solution in separate tubes and spun in a centrifuge (more on centrifugation in 3.2.1.3)
Sample 1
- DNA from bacteria grown for several generations in a nutrient solution containing 15N
- DNA molecules contain 2 heavy strands
Sample 2
- DNA from bacteria grown originally in a nutrient solution containing 15N, then transferred for
one division to a solution containing 14N
- DNA molecules contain 1 original heavy and 1 new light strand
Sample 3
- DNA from bacteria grown originally in a nutrient solution 15N

- Then transferred for two divisions to a solution containing 14N
- 50% DNA molecules contain 1 heavy and 1 new light strand, 50% contain both light strands
Top tip: Whilst you don’t need to know about the whole experiment in this much detail, make
sure you know enough to be able to answer an application-style question about it! Have a look at
diagrams or videos online which can help you visualise the whole process, if you are struggling to
get your head around this!

3.1.6 ATP

A single molecule of adenosine triphosphate (ATP) is a nucleotide derivative and is formed
from a molecule of ribose, a molecule of adenine and three phosphate groups.
Hydrolysis of ATP to adenosine diphosphate (ADP) and an inorganic phosphate group (Pi) is
catalysed by the enzyme ATP hydrolase.
The hydrolysis of ATP can be coupled to energy-requiring reactions within cells.

The inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate
other compounds, often making them more reactive.
ATP is resynthesised by the condensation of ADP and Pi. This reaction is catalysed by the
enzyme ATP synthase during photosynthesis, or during respiration.
Structure of ATP
Draw the structure of ATP
Hydrolysis of ATP → ADP + Pi
Condensation of of ADP + Pi → ATP
Properties of ATP related to its functions
Introduction to ATP
Adenosine triphosphate (ATP) is a very important energy-carrying molecule in Biology. It is involved in

many metabolic reactions, including: myofibril contraction, active transport, photosynthesis,
respiration and others which we will come to look at later on in the course.

Structure of ATP
A single molecule of ATP is made up of: adenine

ribose
- Ribose (pentose sugar)
- Adenine (nitrogenous base)
- 3 Phosphate groups
3 phosphates
Top tip: The structure of ATP
is hidden in its name-
adenosine triphosphate!
‘Adeno’ shows it contains Notice how the structure of ATP seems very similar to the
adenine, and ‘triphosphate’ nucleic acids we have seen before?
simply means it contains 3 This is the reason why ATP is sometimes called a nucleotide
phosphate groups. derivative (modified form of a nucleotide)
You will come across a similar molecule called adenosine diphosphate (ADP) very shortly. As it
suggests in the name, it is very similar in structure to ATP- except it only has two phosphates!
ATP / ADP hydrolysis and condensation reactions
ATP hydrolysis (ATP → ADP + Pi)
- Catalysed by the enzyme ATP hydrolase (sometimes called ATPase)

- Can be coupled to energy requiring reactions within cells to provide energy for active transport,
protein synthesis, myofibril contraction, etc.
- Energy is released when bonds between the inorganic phosphate groups are broken
- Inorganic phosphate released can be used to phosphorylate other compounds (eg. glucose) to
make them more reactive ie. lower the activation energy
Diagram showing the hydrolysis of ATP
breaking this bond between phosphates
(+ water )
adenosine triphosphate (ATP) adenosine diphosphate (ADP) inorganic phosphate

Condensation (ADP + Pi → ATP)
- Catalysed by the enzyme ATP synthase

- Occurs during respiration or photosynthesis (see Unit 5)
- Also known as the phosphorylation of ADP
Diagram showing this condensation reaction
forming a new bond between phosphates
(+ water )
adenosine diphosphate (ADP) inorganic phosphate adenosine triphosphate (ATP)
Properties of ATP related to its function
Main function of ATP = to provide a suitable immediate source of energy
Key exam points:

- ATP cannot be stored so is constantly being regenerated
- ATP released energy in small, manageable amounts (so not energy wasted as heat)
- Single chemical step (as only one bond is hydrolysed) so ATP releases energy immediately
- Used to phosphorylate other compounds to make them more reactive
This simply means to ‘add a phosphate’

ATP is an energy source used in many cell processes. Give two ways in which ATP is a suitable
energy source for cells to use. (2)
Any two from:
- Releases relatively small amounts of energy / little energy lost as heat
- Releases energy instantaneously / energy is readily available
- Phosphorylates other compounds, making them more reactive
- Can be rapidly re-synthesised
- Is not lost from / does not leave cells

3.1.7 Water

Water is a major component of cells. It has several properties that are important in biology. In
particular, water:
is a metabolite in many metabolic reactions, including condensation and hydrolysis reactions

is an important solvent in which metabolic reactions occur
has a relatively high heat capacity, buffering changes in temperature
has a relatively large latent heat of vaporisation, providing a cooling effect with little loss of
water through evaporation
has strong cohesion between water molecules; this supports columns of water in the tube-like
transport cells of plants and produces surface tension where water meets air.
Properties of water
Relate properties of water to its function
Water is a polar molecule
Water is a polar molecule meaning it has: The reason why oxygen is partially negative
is due to the fact that it attracts electrons
- Oxygen atoms with a partial negative charge better than hydrogen- but this is beyond
- Hydrogen atoms with a partial positive charge the scope of A-level Biology.
Because of its polar nature, hydrogen bonds can form between water molecules:
- The partially negative charged oxygen atoms attract partially positive charged
hydrogen atoms of other water molecules
- Hydrogen bonds form between water molecules
hydrogen bond
If you take A-level Chemistry, you will
become familiar with why this is in
the ‘Bonding’ unit!

Properties of water and their importance
A summary of all the properties:
High specific heat capacity
Explanation of property: Importance in Biology:

- Polar so many H-bonds form between - Good habitat for aquatic organisms (eg. lakes) as temperature is more
water molecules stable than land
- Allows water to absorb a large amount - Organisms are mostly made of water so this helps them to maintain a
of energy before its temperature changes constant internal body temperature; important for enzyme activity
High latent heat of vaporisation

- Polar so many H-bonds form between water molecules - Evaporation of small amounts of water (eg. sweat) has a
- Can absorb a lot of energy before breaking when water large cooling effect
evaporates - Helps organisms maintain a constant body temperature
Solvent

- Polar nature of water enables it to - Dissolves inorganic ions, enzymes, urea, etc.
separate (dissolve) ionic / polar - Enables reactions to occur (eg. metabolic reactions)
compounds in solution - Acts as a transport medium (eg. in xylem to transport nitrates)
Metabolite

- Water is reactive due to its - Condensation reactions releases water + forms chemical bonds (see 3.1.1)
polar nature - Hydrolysis reactions require water to break chemical bonds (see 3.1.1)
Cohesive

- Polar so many H-bonds form - Column of water doesn’t break when pulled up a narrow tube (eg. xylem during
between water molecules transpiration- see 3.3.4.2)
- Water molecules stick - Produces surface tension at an air-water surface so invertebrates can walk on
together water (eg. pond skaters)

Explain five properties that make water important for organisms. (5)
- A metabolite in condensation / hydrolysis / photosynthesis/respiration
- A solvent so (metabolic) reactions can occur
OR
A solvent so allowing transport of substances
- High heat capacity so buffers changes in temperature
- Large latent heat of vaporisation so provides a cooling effect (through evaporation)
- Cohesion (between water molecules) so supports columns of water (in plants)
- Cohesion (between water molecules) so produces surface tension supporting (small) organisms
Top tip: This is highlighted in the mark scheme since you are being asked to explain the properties
of water, as opposed to just describing them. So make sure you get into the habit of using
explanatory phrases such as ‘so’, ‘as’ or ‘because’- this way it is clear to the examiner that you have
explained the properties!
3.1.8 Inorganic ions
Inorganic ions occur in solution in the cytoplasm and body fluids of organisms, some in high
concentrations and others in very low concentrations.
Each type of ion has a specific role, depending on its properties.
Students should be able to recognise the role of ions in the following topics:
hydrogen ions and pH
iron ions as a component of haemoglobin
sodium ions in the co-transport of glucose and amino acids
and phosphate ions as components of DNA and of ATP.
Where inorganic ions occur

Where we get inorganic ions from
Know roles of the following ions: H+ ions, iron (II) ions, Na+ ions, phosphate ions
Introduction to inorganic ions
Inorganic ions occur in solution in the cytoplasm and body fluids of organisms.
- Some are found in high concentrations whilst others are found in low concentrations
- Each type of inorganic ion has a specific role, depending on its properties- these ions will be
relevant across the whole A-level course
Hydrogen ions
Role = maintain pH levels in the body
- Too much hydrogen ions = too acidic

- Too little hydrogen ions = too alkaline
- Affects the rate of enzyme-controlled reactions in the body (see 3.1.4.2)
Iron (II) ions

Role = component of haem group of haemoglobin in red blood cells, involved in
transporting oxygen around the body (as oxyhaemoglobin- see 3.3.4.1)

Sodium ions
Role = co-transport of glucose and amino acids across cell-membranes (see 3.2.1.5)
- Also involved in generating nerve impulses (see 3.6.2.1) and muscle contraction (see 3.6.3)
Phosphate ions
Role = attached to other molecules as a phosphate group
- Examples: DNA / RNA nucleotides, ATP, phospholipids, etc.

Biological Molecules

Uploaded by

Copyright:

Available Formats

You might also like

Biological Molecules

Uploaded by

Document Information

Original Description:

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Biological Molecules

Uploaded by

Copyright:

Available Formats

3.

3.1.1 Monomers and polymers

3.1.4.2 Many proteins are enzymes

Material of @medic.coffee (not to be redistributed without permission)

3.1.5.1 Structure of DNA and RNA

3.1.5.2 DNA replication

3.1.8 Inorganic ions

Material of @medic.coffee (not to be redistributed without permission)

What the specification says:

Summary of what you need to know:

Definition of monomer Examples of polymers

Introduction and key terms

Nucleic acids Lipids

Monomers = smaller units from which larger molecules are made

Examples of monomers include: monosaccharides, amino acids and nucleotides

Material of @medic.coffee (not to be redistributed without permission)

A summary of the common monomers and polymers you need to know

Amino acid Polypeptide (protein)

Material of @medic.coffee (not to be redistributed without permission)

Material of @medic.coffee (not to be redistributed without permission)

What the specification says:

Disaccharides are formed by the condensation of two monosaccharides:

Glucose has two isomers, α-glucose and β-glucose, with structures:

Polysaccharides are formed by the condensation of many glucose units.

Glycogen and starch are formed by the condensation of α-glucose.

Summary of what you need to know:

Material of @medic.coffee (not to be redistributed without permission)

Monosaccharides Disaccharides Polysaccharides

Monomers from which Formed by the condensation Formed by the condensation

Small Increasing size Large

α-glucose α-glucose maltose

Monosaccharide = single sugar monomer which forms larger carbohydrates / polysaccharides

There are 3 key monosaccharides you need to know:

Material of @medic.coffee (not to be redistributed without permission)

Disaccharide = a sugar formed from two monosaccharides joined by a glycosidic bond in a

Isomers of glucose: alpha + beta glucose

Glucose has two isomers:

Material of @medic.coffee (not to be redistributed without permission)

Polysaccharides = polymers formed by many monosaccharides joined by glycosidic bonds in a

There are 3 key polysaccharides you need to know:

How its structure is related to its function: (exam points)

Glycogen The structure of

What is the difference between 1,4 and 1,6 glycosidic bonds?

Material of @medic.coffee (not to be redistributed without permission)

Exam question example:

Exam question example:

Material of @medic.coffee (not to be redistributed without permission)

Biochemical tests: Benedict’s test

Benedict’s reagent can be used to test for reducing or non-reducing sugars.

Summary of reducing and non-reducing sugars:

Reducing sugars include: Non-reducing sugars include:

Benedict’s test for reducing sugars

1. Add Benedict’s reagent to sample

Benedict’s test for non-reducing sugars

Material of @medic.coffee (not to be redistributed without permission)

Biochemical test: iodine test

We can test for starch by using the iodine test. iodine

Material of @medic.coffee (not to be redistributed without permission)