Chapter 4
Biological Molecules
- Proteins -
Teacher : Mahmoud Rawajbeh
9th grade (MYP level 4 )
Introduction :
What is a
protein ?
• Proteins are an essential part of
a balanced diet. They are found in
meat, fish, cheese, eggs and
nuts. They are made up of amino
acids joined into long polymer
molecules.
• During digestion, the body breaks
proteins down the amino acids
they are made of. These then re-
join in the body to make human
protein.
• In our bodies these proteins could
be enzymes; collagen in skin, bones
and teeth; keratin in hair;
hemoglobin to carry oxygen around
our body; or hormones.
Proteins building blocks (Amino
acids)
• 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.
• Because all genes code for proteins, all of the
reactions necessary for life are dependent on the
function of proteins.
Amino Acids
• Amino acids are the monomers of proteins.
• There are 20 common amino acids. They all have the same general
molecular structure as shown in Figure next slide.
• Each amino acid differs by having a different R group. The body
needs all 20 amino acids to make these proteins. It can make 11 of
these by itself, leaving nine to be obtained from food.
• Not all foods contain all of these nine amino acids in adequate
amounts, so some care is needed in making sure we eat a variety of
protein rich foods.
R – group
Structure of an Amino acid
• Every amino acid has a central carbon atom to which are attached four
different chemical groups (Figure Below):
• 1. Amino group (-): a basic group from which part of the name amino acid is
derived.
• 2. Carboxyl group (-COOH): an acid group which gives the amino acid the
rest of its name.
• 3. Hydrogen atom (-H).
• 4. R-group: a variety of different chemical groups ranging from a single
hydrogen atom as in glycine (amino acid) to a double ring structure, as in
tyrosine, each amino acid has a different R-group.
Different types of amino acids (do not
memorize)
Peptide Bond
• The figure below shows how amino acid monomers can combine
to form a dipeptide by the removal of a water molecule in a
condensation reaction.
• The two amino acids then become linked by a covalent bond
between the carbon atom of one amino acid and the nitrogen
atom of the other, this bond is called (peptide bond).
• The peptide bond can be broken by hydrolysis (the addition
of water).
The four levels of proteins structure:
• Through a series of condensation reactions, many amino acid monomers can be
joined together in a process called (Polymerization).
• The resulting chain of many hundreds of amino acids is called a polypeptides.
• 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.
• The amino acid sequence is not random but determined by the genetic information (a
sequence of nucleotides stored in DNA).
• Dipeptides are formed from two amino acids
• Tripeptides are formed from three amino acids
• Oligopeptides (oligo: few) less than 10 peptides
• Polypeptides equal or more than 10 peptide
The primary structure of
proteins:
• 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 Figure : The primary structure of a protein. The three-
letter abbreviations indicate the specific amino acid
sequence of amino acids can affect
Secondary Structure
• 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.
• There are two shapes that can form within proteins due to the
hydrogen bonds:
• α-helix
• β-pleated sheet
• 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
Secondary Structure Diagram
The α-helix shape
occurs when the •The β-pleated
hydrogen bonds form sheet shape forms
between when the protein folds
every fourth peptide so that two parts of
bond (between the the polypeptide
oxygen of the chain are parallel to
carboxyl group and each other enabling
the hydrogen of the hydrogen bonds to
amine group) form between parallel
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)
• Ionic (occurs between charged R groups)
• Weak hydrophobic interactions (between non-polar R groups)
• This structure is common in globular proteins such as antibodies
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 Figure :The quaternary structure of a protein. This is an example of
protein. haemoglobin which contains four subunits (polypeptide chains) working
together to carry oxygen
Protein Denaturation:
• Denaturation is a structural change in a protein that results in
the loss (usually permanent) of its biological properties.
• Because the way a protein folds determines its function, any
change or repeal of the tertiary structure will alter its activity.
• Denaturation of proteins can usually be caused by two key
conditions: temperature and pH
Protein Structure: Effect of pH & Temperature
• Proteins structure is sensitive to changes in the environment,
particularly temperature and pH changes.
• The precise structure of a protein is dependent on the ionic interactions,
hydrogen bonds and other intermolecular forces between polypeptide chains
being intact.
• Denaturation may occur by temperature and pH extremes that interfere with
these bonds
• Denaturation is the irreversible change of protein conformation (structure).
• The bonds that form between different R groups are relatively
weak (compared to the peptide bonds that hold the amino acids in sequence).
• These bonds can be broken easily, which can cause the conformation of the
protein to change and denaturation.
• The altered protein shape may affect its function, physical state and
general usefulness in its original role.
Effect of pH and Temperature
• A certain pH is considered as an optimum for a
particular protein, because at that pH, the protein's 3D
structure is not denatured.
• Denaturation is almost always irreversible
• The protein cannot be re-formed in its original conformation
by reversing the change in conditions
• However, small denaturations and renaturations are
possible in certain proteins to respond to small fluctuations in
pH e.g. haemoglobin
Classes of proteins:
Globular & Fibrous Proteins
• There are two main classes of protein tertiary structure:
Globular proteins
Fibrous
proteins are
generally, have a
generally composed
more compact and
of long and narrow
rounded shape and
strands and have a
have functional
structural role
roles
(they are somethi
(they do somethin
ng)
g)
Fibrous Vs Globular Proteins
The following are specific examples of the different
functions of proteins:
Function Example Description
A component of the connective tissue of animals (most
Structure Collagen
abundant protein in mammals)
Hormones Protein produced by the pancreas and triggers a
Insulin
reduction in blood glucose levels
Antibodies produced by plasma cells that are capable
Immunity Immunoglobulins of targeting specific antigens
Transport Hemoglobin A protein found in red blood cells that is responsible
for the transport of oxygen
sensation A pigment in the photoreceptor cells of the retina (in
Rhodopsin
the eye) that is responsible for the detection of light
Actin Thin filaments involved in the contraction of muscle fibers
Movement Myosin Thick filaments involved in the contraction of muscle fibers
Enzymes Amylase A protein that break down starch into the disaccharide
Maltose
