2.3 Biological Molecules

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CIE A Level Biology Your notes
2.3 Proteins
Contents
Amino Acids & the Peptide Bond
The Four Levels of Protein Structure
Protein Shape
Globular & Fibrous Proteins
Haemoglobin
Collagen
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Your notes
Proteins
Proteins are polymers (and macromolecules) made of monomers called amino acids
The sequence, type and number of the amino acids within a protein determines its shape and therefore
its function
Proteins are extremely important in cells because they form all of the following:
Enzymes
Cell membrane proteins (e.g. carrier)
Hormones
Immunoproteins (e.g immunoglobulins)
Transport proteins (e.g haemoglobin)
Structural proteins (e.g keratin, collagen)
Contractile proteins (e.g. myosin)
Amino acids
Amino acids are the monomers of proteins
There are 20 amino acids found in proteins common to all living organisms
The general structure of all amino acids is a central carbon atom bonded to:
An amine group -NH2
A carboxylic acid group -COOH
A hydrogen atom
An R group (which is how each amino acid differs and why amino acid properties differ e.g. whether
they are acidic or basic or whether they are polar or non-polar)
Amino Acid Structure Diagram
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The generalised structure of an amino acid

The peptide bond Your notes
In order to form a peptide bond a hydroxyl group (-OH) is lost from the carboxylic group of one amino
acid and a hydrogen atom is lost from the amine group of another amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the
nitrogen atom of the second amino acid
This is a condensation reaction so water is released
The resulting molecule is a dipeptide
When many amino acids are bonded together by peptide bonds the molecule formed is called a
polypeptide. A protein may have only one polypeptide chain or it may have multiple chains interacting
with each other
During hydrolysis reactions polypeptides are broken down to amino acids when the addition of water
breaks the peptide bonds
Peptide Bond Formation
Amino acids are bonded together by covalent peptide bonds to form a dipeptide in a condensation
reaction
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Exam Tip
Your notes
You will be expected to recognise whether an unfamiliar molecule is an amino acid or protein so look
for the functional groups (amine and carboxyl).
When asked to identify the location of the peptide bond, look for where nitrogen is bonded to a
carbon which has a double bond with an oxygen atom, note the R group is not involved in the formation
of a peptide bond.
You will also be expected to draw out the general structure of an amino acid so be sure to practise this
skill lots.
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The Four Levels of Protein Structure

Your notes
Proteins: Structures
There are four levels of structure in proteins, three are related to a single polypeptide chain and the
fourth level relates to a protein that has two or more polypeptide chains
Polypeptide or protein molecules can have anywhere from 3 amino acids (Glutathione) to more than
34,000 amino acids (Titan) bonded together in chains
Primary Structure
The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
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 whole protein)
Primary Structure Diagram
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Your notes
The primary structure of a protein. The three-letter abbreviations indicate the specific amino acid
(there are 20 commonly found in cells of living organisms)
Secondary
The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen
atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
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There are two shapes that can form within proteins due to the hydrogen bonds:
α-helix
β-pleated sheet Your notes
The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond
(between the oxygen of the carboxyl group and the hydrogen of the amine group)
The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain
are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds
Most fibrous proteins have secondary structures (e.g. collagen and keratin)
The secondary structure only relates to hydrogen bonds forming between the amino group and the
carboxyl group (the ‘protein backbone’)
The hydrogen bonds can be broken by high temperatures and pH changes
Secondary Structure Diagram
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Your notes
The secondary structure of a protein with the α-helix and β-pleated sheet shapes highlighted. The
magnified regions illustrate how the hydrogen bonds form between the peptide bonds
Tertiary Structure
Further conformational change of the secondary structure leads to additional bonds forming between
the R groups (side chains)
The additional bonds are:
Hydrogen (these are between R groups)
Disulfide(only occurs between cysteine amino acids, sometimes referred to as a disulfide bridge)
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Ionic (occurs between charged R groups)

Weak hydrophobic interactions (between non-polar R groups)
This structure is common in globular proteins such as antibodies Your notes
Tertiary Structure Diagram
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The tertiary structure of a protein with hydrogen bonds, ionic bonds, disulphide bonds and
hydrophobic interactions formed between the R groups of the amino acids
Your notes
Quaternary Structure
Occurs in proteins that have more than one polypeptide chain working together as a functional
macromolecule, for example, haemoglobin
Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein
Quaternary Structure Diagram
The quaternary structure of a protein. This is an example of haemoglobin which contains four subunits
(polypeptide chains) working together to carry oxygen
Summary of bonds in proteins table
Level
Bonds
Primary Secondary Tertiary
Peptide ✓ ✓ ✓
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✓ (only between the ✓ (only between

Hydrogen X amine and carboxyl the R, amine and Your notes
groups) carboxyl groups)
Disulfide X X ✓
Ionic X X ✓
Hydrophobic interactions X X ✓
Exam Tip
Familiarise yourself with the difference between the four structural levels found in proteins, noting
which bonds are found at which level. Remember that the hydrogen bonds in tertiary structures are
between the R groups whereas in secondary structures the hydrogen bonds form between the amino
and carboxyl groups.
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Protein Shape
Your notes
Proteins: Interactions & Shape
A polypeptide chain will fold differently due to the interactions (and hence the bonds that form)
between R groups. The three-dimensional configuration that forms is called the tertiary structure of a
protein
Each of the twenty amino acids that make up proteins has a unique R group and therefore many
different interactions can occur creating a vast range of protein configurations and therefore functions
Within proteins with a tertiary structure the following bonds occur:
Strong covalent disulfide
Weak hydrophobic interactions
Weak hydrogen
Ionic
Bonds in Proteins Diagram
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Your notes
The interactions that occur between the R groups of amino acids determines the shape and function of
a protein. These interactions are found within tertiary structures of proteins
Disulfide
Disulfide bonds are strong covalent bonds that form between two cysteine R groups (as this is the
only amino acid with an available sulfur atom in its R group)
These bonds are the strongest within a protein, but occur less frequently, and help stabilise the
proteins
These are also known as disulfide bridges
Can be broken by reduction
Disulfide bonds are common in proteins secreted from cells e.g. insulin
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Ionic
Ionic bonds form between positively charged (amine group -NH3+) and negatively charged Your notes
(carboxylic acid -COO-) R groups
Ionic bonds are stronger than hydrogen bonds but they are not common
These bonds are broken by pH changes
Hydrogen
Hydrogen bonds form between strongly polar R groups. These are the weakest bonds that form but
the most common as they form between a wide variety of R groups
Hydrophobic interactions
Hydrophobic interactions form between the non-polar (hydrophobic) R groups within the interior of
proteins
Exam Tip
Note that an interaction is not the same as a bond. An interaction refers to a low energy attraction
between two groups, whereas a bond is a high energy and typically involves the electrons of the
molecules concerned.
You need to be able to determine which bonds are found in tertiary structures and recognise them in
diagrams.
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Globular & Fibrous Proteins

Your notes
Proteins: Globular & Fibrous
Globular
Globular proteins are compact, roughly spherical (circular) in shape and soluble in water
Globular proteins form a spherical shape when folding into their tertiary structure because:
their non-polar hydrophobic R groups are orientated towards the centre of the protein away from
the aqueous surroundings
their polar hydrophilic R groups orientate themselves on the outside of the protein
This orientation enables globular proteins to be (generally) soluble in water as the water molecules can
surround the polar hydrophilic R groups
The solubility of globular proteins in water means they play important physiological roles as they can
be easily transported around organisms and be involved in metabolic reactions
The folding of the protein due to the interactions between the R groups results in globular proteins
having specific shapes. This also enables globular proteins to play physiological roles, for example,
enzymes can catalyse specific reactions and immunoglobulins can respond to specific antigens
Some globular proteins are conjugated proteins that contain a prosthetic group e.g. haemoglobin
which contains the prosthetic group called haem
Fibrous
Fibrous proteins are long strands of polypeptide chains that have cross-linkages due to hydrogen
bonds
They have little or no tertiary structure
Due to the large number of hydrophobic R groups fibrous proteins are insoluble in water
Fibrous proteins have a limited number of amino acids with the sequence usually being highly repetitive
The highly repetitive sequence creates very organised structures that are strong and this along with
their insolubility property, makes fibrous proteins very suitable for structural roles, e.g. keratin that
makes up hair, nails, horns and feathers and collagen which is a connective tissue found in skin, tendons
and ligaments
Fibrous vs Globular Proteins Diagram
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Your notes
Globular and fibrous protein models illustrating the roughly spherical shape of globular proteins and the
long, stranded shape of fibrous proteins
Comparison of Globular & Fibrous Tertiary Proteins Table
Globular Fibrous
Shape Roughly spherical Long strands
Irregular with a wide range of Repetitive with a limited range

Amino Acid Sequence
R groups of R groups
Function Physiological/functional Structural
Haemoglobin, insulin, Collagen, keratin, myosin, actin,

Examples
immunoglobulins, insulin fibrin
Solubility Generally soluble in water Generally insoluble in water
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Exam Tip
Your notes
To distinguish between the two proteins, learn SAFES (Shape, Amino acid sequence, Function,
Examples and Solubility).
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Haemoglobin
Your notes
The Molecular Structure of Haemoglobin
Structure
Haemoglobin is a globular protein which is an oxygen-carrying pigment found in vast quantities in red
blood cells
It has a quaternary structure as there are four polypeptide chains. These chains or subunits are globin
proteins (two α–globins and two β–globins) and each subunit has a prosthetic haem group
The four globin subunits are held together by disulphide bonds and arranged so that their
hydrophobic R groups are facing inwards (helping preserve the three-dimensional spherical shape)
and the hydrophilic R groups are facing outwards (helping maintain its solubility)
The arrangements of the R groups is important to the functioning of haemoglobin. If changes occur to
the sequence of amino acids in the subunits this can result in the properties of haemoglobin changing
This is what happens to cause sickle cell anaemia
The prosthetic haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an
oxygen molecule forming oxyhaemoglobin and results in the haemoglobin appearing bright red
Each haemoglobin with the four haem groups can therefore carry four oxygen molecules (eight
oxygen atoms)
Haemoglobin Diagram
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Your notes
The structure of haemoglobin showing the α–globin and β–globin subunits, the prosthetic haem group
with oxygen molecules bonded to form oxyhaemoglobin.
Function
Haemoglobin is responsible for binding oxygen in the lung and transporting the oxygen to tissue to be
used in aerobic respiration
As oxygen is not very soluble in water and haemoglobin is, oxygen can be carried more efficiently
around the body when bound to the haemoglobin
The presence of the haem group (and Fe2+) enables small molecules like oxygen to be bound more
easily:
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As each oxygen molecule binds, it alters the quaternary structure (due to alterations in the tertiary
structure) of the protein which causes haemoglobin to have a higher affinity for the subsequent
oxygen molecules and they bind more easily Your notes
The existence of the iron II ion (Fe2+) in the prosthetic haem group also allows oxygen to reversibly
bind as none of the amino acids that make up the polypeptide chains in haemoglobin are well suited to
binding with oxygen
Exam Tip
You need to know the structure of haemoglobin and how this relates to the function (its ability to
transport oxygen).
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Collagen
Your notes
The Molecular Structure of Collagen
Collagen is the most common structural protein found in vertebrates
In vertebrates it is the component of connective tissue which forms:
Tendons
Cartilage
Ligaments
Bones
Teeth
Skin
Walls of blood vessels
Cornea of the eye
Collagen is an insoluble fibrous protein
Structure
Collagen is formed from three polypeptide chains closely held together by hydrogen bonds to form a
triple helix (known as tropocollagen)
Each polypeptide chain is a helix shape (but not α-helix as the chain is not as tightly wound) and
contains about 1000 amino acids with glycine, proline and hydroxyproline being the most common
In the primary structure of collagen almost every third amino acid is glycine
This is the smallest amino acid with a R group that contains a single hydrogen atom
Glycine tends to be found on the inside of the polypeptide chains allowing the three chains to be
arranged closely together forming a tight triple helix structure
Along with hydrogen bonds forming between the three chains there are also covalent bonds present
Covalent bonds also form cross-links between R groups of amino acids in interacting triple helices
when they are arranged parallel to each other. The cross-links hold the collagen molecules together to
form fibrils
The collagen molecules are positioned in the fibrils so that there are staggered ends (this gives the
striated effect seen in electron micrographs)
When many fibrils are arranged together they form collagen fibres
Collagen fibres are positioned so that they are lined up with the forces they are withstanding
Collagen Diagram
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Your notes
Collagen is a fibrous structural protein that is formed by triple helices collagen molecules arranging into
collagen fibrils and finally into collagen fibres which have high tensile strength
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Function
Collagen is a flexible structural protein forming connective tissues Your notes
The presence of the many hydrogen bonds within the triple helix structure of collagen results in great
tensile strength. This enables collagen to be able to withstand large pulling forces without stretching
or breaking
The staggered ends of the collagen molecules within the fibrils provide strength
Collagen is a stable protein due to the high proportion of proline and hydroxyproline amino acids result
in more stability as their R groups repel each other
The length of collagen molecules means they take too long to dissolve in water, so collagen is
therefore insoluble in water
Comparison between Collagen & Haemoglobin Table
Collagen Haemoglobin
Number of polypeptide 4 (two alpha globin, two beta

3 (triple helix)
chains globin)
Outline (shape) Long, thin Spherical
Type of protein Fibrous Globular
Structural (forms connective

Main function Functional (transports oxygen)
tissue)
Amino acid variation Repetitive Variable
Prosthetic group No Yes (haem group)
Solubility Insoluble in water Soluble in water
Exam Tip
Use the acronym NOT MAPS to understand how the function relates to the structure of collagen and
know the difference between haemoglobin and collagen
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CIE A Level Biology Your notes

Amino Acids & the Peptide Bond

The generalised structure of an amino acid

The Four Levels of Protein Structure

Ionic (occurs between charged R groups)

✓ (only between the ✓ (only between

Globular & Fibrous Proteins

Shape Roughly spherical Long strands

Irregular with a wide range of Repetitive with a limited range

Function Physiological/functional Structural

Haemoglobin, insulin, Collagen, keratin, myosin, actin,

Solubility Generally soluble in water Generally insoluble in water

Number of polypeptide 4 (two alpha globin, two beta

Outline (shape) Long, thin Spherical

Type of protein Fibrous Globular

Structural (forms connective

Amino acid variation Repetitive Variable

Prosthetic group No Yes (haem group)

Solubility Insoluble in water Soluble in water

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