Proteins

Madalitso Muhakeya
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• Proteins are made up of polypeptide chains of amino
acids.
• The structure of an amino acid consists of an amino
functional group, a carboxyl group at end and a
side chain shown by the R.
• There are 20 naturally occurring 'R' groups, which
corresponds to 20 different amino acids. Each
different amino acid has a specific name.
• For example, Alanine's 'R' group consists of CH3.
• Plants make all the amino acids they need
themselves, as long as they can obtain nitrate from
the soil, which is then converted to amino groups and
bonded to the products of photosynthesis.
 Essential amino acids
Reading Assignment: Definition and examples
 Non-essential amino
acids
• Reading assignment: Definition and examples
Amino acids are toxic as they cannot be
stored in the animal body so they must be
excreted from the body in a process called
deamination. In animals, this occurs in the
liver, where amino acids are converted to
urea and pass out in the urine.
 Generic structure of any amino
acid.
 Peptide Bonds

• Amino acids can be joined together, forming

peptide bonds.
• All amino acids are joined in exactly the same
way. A Condensation reaction forms a covalent
bond between the monomers, between the
amino group of one and the acid group of
another. When two amino acids are joined
together in this way, a dipeptide molecule is
formed
Condensation of two amino acids to form a dipeptide
Amino groups.
 Protein Structure
• There are four protein structural types as below:
1. Primary Structure
• Proteins are made up of polypeptide chains, which are amino acids joined
together with peptide bonds.
• The unique sequence of amino acids that make up a protein or polypeptide
chain is called the Primary Structure.
• Primary Structure is the unique sequence of amino acids that makes up
a protein or polypeptide chain.
• Peptide bonds are created by enzyme-catalysed condensation reactions
and broken down by enzyme-catalysed hydrolysis reactions.
• Breaking down proteins is important in many areas of the body, not merely
in digestion. For example, in hormone regulation, cells that are targeted by
hormones contain enzymes to break down those hormones. This stops
their effects from being permanent and allows them to be controlled.
 Secondary
Structure
• After synthesis, polypeptide chains are folded or
pleated into different shapes, called their
Secondary Structure.
• Two common examples of secondary structures
are Alpha Helices and Beta Pleated Sheets.
• Secondary structure is held together by many
Hydrogen bonds, overall giving the shape great
stability.
• Secondary Structure is the way in which the
primary structure of a polypeptide chain folds
The alpha helix an example of
the secondary structure of
protein
 Tertiary Structure
• The final 3D structure of a protein is its Tertiary
Structure, which pertains to the shaping of the
secondary structure. This may involve coiling or
pleating, often with straight chains of amino acids in
between.
• Tertiary Structure is the final 3D structure of a protein,
entailing the shaping of a secondary structure.
• Tertiary structure is held together by four different
bonds and interactions:
• Disulphide Bonds – This is where two Cysteine amino
acids are found together, a strong double bond (S=S) is
formed between the Sulphur atoms within the Cysteine
monomers.
• Ionic Bonds - If two oppositely charged 'R' groups (+ve
and -ve) are found close to each other, an ionic bond
forms between them.
• Hydrogen Bonds - Your typical everyday hydrogen
bonds.
• Hydrophobic and Hydrophilic Interactions - Some
amino acids may be hydrophobic while others are
hydrophilic. In a water based environment, a globular
protein will orientate itself such that its hydrophobic parts
• The tertiary structure can be broken by the
action of heat.
• Increasing the kinetic energy of protein with a
tertiary structure makes it vibrate more, and so
the bonds that maintain its shape (which are
mainly weak, non-covalent bonds) will be more
likely to break.
• When a protein loses its shape in this way it is
said to be denatured. Even when cool the
protein will not (or is highly unlikely to) form its
original complex shape.
Proteins with a 3D structure fall into two main types:

• Globular - These tend to form ball-like structures where

hydrophobic parts are towards the centre and
hydrophilic parts are towards the edges, which makes
them water soluble. They usually have metabolic roles,
for example: enzymes in all organisms, plasma
proteins and antibodies in mammals.
• Fibrous - These proteins form long fibres and mostly
consist of repeated sequences of amino acids which are
insoluble in water. They usually have structural roles,
such as: Collagen in bone and cartilage, Keratin in
fingernails and hair.
 An example of a
tertiary protein
 Quaternary Structure
• Some proteins are made up of multiple polypeptide
chains, sometimes with an inorganic component (for
example, a haem group in haemoglogin) called a
Prosthetic Group. These proteins will only be able to
function if all subunits are present.
• Quaternary Structure is the structure formed when two
or more polypeptide chains join together, sometimes
with an inorganic component, to form a protein.
 Summary of types of protein
types
 Haemoglobin and Collagen
• Haemoglobin is a water soluble globular protein
which is composed of two α polypeptide chains,
two β polypeptide chains and an inorganic
prosthetic haem group. Its function is to carry
oxygen around in the blood, and it is facilitated
in doing so by the presence of the haem group
which contains a Fe2+ ion, onto which the oxygen
molecules can bind.
 Collagen
Collagen is a fibrous protein consisting of three
polypeptide chains wound around each other. Each of the
three chains is a coil itself. Hydrogen bonds form between
these coils, which are around 1000 amino acids in length,
which gives the structure strength. This is important given
collagen's role, as structural protein. This strength is
increased by the fact that collagen molecules form further
chains with other collagen molecules and form covalent
cross links with each other, which are staggered along the
molecules to further increase stability. Collagen molecules
wrapped around each other to form collagen fibrils which
themselves form collagen Fibres.
 Collagen serves many roles:
• form the structure of bones,
• makes up cartilage and connective tissue,
• prevents blood that is being pumped at high
pressure from bursting the walls of arteries,
• is the main component of tendons, which
connect skeletal muscles to bones.
Difference between Haemoglobin and
Collagen
• Basic Shape - haemoglobin is globular while collagen is fibrous
• Solubility - Haemoglobin is soluble in water while Collagen is insoluble
• Amino Acid Constituents - Haemoglobin contains a wide range of amino
acids while Collagen has 35% of its primary structure is made up of
Glycine
• Prosthetic Group - Haemoglobin contains a haem prosthetic group while
collagen doesn't possess a prosthetic group
• Tertiary Structure - Much of the haemoglobin molecule is wound into α
helices while much of the collagen molecule is made up of left handed
helix structures
 Reading Assignment
• Explain the biological functions of proteins