PROTEINS

Aspects of Biochemistry
What are proteins
•Proteins are substances made up of amino acids.
•These amino acids are linked together in a long chain.
Basic structure of an amino acid
Cont’d
•All amino acids have a central carbon atom.
•Carbon atoms form covalent bonds with other atoms, in an
amino acid the central carbon atoms bonds with:
•A carboxyl group- COOH
•A hydrogen atom- H
•An amino group- NH2
•A R group- any one of a whole range of groups.
Peptide bond formation
•When two amino acids are brought close to each other they
form peptide bond.
•A peptide bond is formed due to a condensation reaction.
•Peptide bonds are very strong due to covalent bonding.
Cont’d
•As the peptide bond is formed one hydrogen atom from one
amino acid and one hydroxyl group from another join
together to form a water molecule.
Polypeptide formation
•A polypeptide is a chain of amino acids linked together by
peptide bonds.
•E.g. of molecules that are made up of polypeptides includes:
•Haemoglobin that is made up of four polypeptide chains
coiled together.
A polypeptide formation
Haemoglobin structure
Peptide bond breaking
•Polypeptides can be broken by breaking the peptide bonds.
•This happens in a hydrolysis reaction.
•This happens when proteins are digested in the stomach by
the enzyme protease.
•The reaction is catalysed by the enzyme will water breaks
and separated the bonds of two amino acids.
Peptide bond breakage
THE FIRST 20 AMINO
ACIDS
The
Nonpola
r
Amino
acids
The
polar
amino
acids
Electrically charged
Primary structure of proteins
•The amino acid sequence for a polypeptide is almost the
same.
•This sequence is called the Primary structure.
Cont’d
•Since there are 20 amino acids that can be linked together in
any order there is an infinite number of possible primary
structures (a polypeptide may contain hundreds of amino
acids)
•A change in just one amino acid in the chain makes it a
different polypeptide or protein.
•This polypeptide or protein may even behave in a different
way.
Secondary structure
•Polypeptide chains do not usually lie straight.
•Parts of the chain may coil to from a pattern called a α-helix.
•Other parts may fold differently to form β-chain.
•They arrangement make up the secondary structure of the
protein.
α-helix and β-chains
•The shape of a α-helix or the β-chain is maintained by
hydrogen bonds between different amino acids.
•In an α-helix the hydrogen bonds form between the oxygen
of the CO group of one amino acid which carries a very
small negative charge ad the hydrogen of the NH 2
• group which has a small positive charge.
•The hydrogen bonding usually takes place between amino
acids four places ahead of each other in the chain
α helix
vs
β-pleate
d sheet
Shaping the molecule
•Although hydrogen bonds are not as strong as peptide bonds
(due to small charges and hydrogen bonds not sharing
electrons) they do help to shape the molecules.
•Since there are many hydrogen bonds form they create a
force that holds the molecule in shape.
α and β chains
•In haemoglobin there are two types of polypeptide chains.
•They are α and β chains.
•The primary structure of a protein is determine by a gene.
•(A gene is a length of DNA that carries a code determining
the sequence in which amino acids be linked together on a
ribosome to form a polypeptide.)
Cont’d
Cont’d
•The total length of the α- chain in Haemoglobin is 141 amino
acids while the β- chain is 146 amino acids long.
Tertiary structure
• This involve the infolding of the chain on itself.
• The tertiary protein is held together by hydrogen bonds from the
secondary structure and three other bonds namely:
• Disulphide bonds
• Ionic bonds
• And hydrophobic interactions between R groups.
Tertiary structure of Haemoglobin
•Each of they polypeptide chains winds itself around a little
group of iron at the centre.
•This group of ions form a haem group.
•The iron ion in each of the four haem is able to bond with
two oxygen atoms thus one haemoglobin molecule can cary
eight oxygen molecule.
Cont’d
Prosthetic group
•A group such as the haem group which makes up part of a
protein is called a prosthetic group.
Globular proteins
•Haemoglobin is considered to be a globular protein since
both polypeptide chains (α and β chains) are curled up in a
ball.
•The bonds hold each protein in a very specific shape.
•This shape also determines the function of the molecule.
•The places in which bonding takes places is determined by
the primary protein.
Quaternary structure
•The interaction between the four polypeptide chains of
haemoglobin forms a quaternary structure.
•The quaternary structure is held by the same kinds of bonds
in a tertiary protein.
•The word quaternary refers to the fourth level of structure
(and not the four chains).
Cont’d
•A protein that is cross linked by just two polypeptide chains
is still quaternary.
Haemoglobin’s binding properties
•The role of haemoglobin is in oxygen transport.
•When an oxygen molecule binds to one haem molecule
there will be a small charge on each of the other polypeptide
structure.
•This makes it easier for another oxygen molecule to bid to
the other three.
Collagen- a fibrous protein
•Collagen consist of three polypeptide chains each in the
shape of a helix.
•These helical polypeptides wind around each other to form a
rope.
•In collagen, almost every three amino acid in each
polypeptide bond is glycine.
Cont’d
•Glycine is the smallest amino acid
•Its small size allows the three strands to lie close together
and form a tight coil.
•The three coils are held together by hydrogen bonds.
•Each three-stranded molecule of collagen interacts with
another running parallel to it.
Collagen bond formation
•Bonds are formed between R groups of lysine in molecules
laying next to each other
•Theses cross-link hold collagen molecules together to form
fibrils.
•The end part of the parallel molecule is staggered as to
ensure that the molecule does not have a weak spot,
Fibrin
Cont’d
•Fibrils associate to form bundles called fibres.
•Collagen has tremendous tensile strength (resistant to pull
from strong forces).
•The human Achilles tendon (made up of mostly collagen
fibres) can withstands a pulling force of 300 N per mm
Comparison of haemoglobin and collagen
•Haemoglobin globular protein that is water soluble and
found in the dissolve cytoplasm of red blood cells.
•Collagen is a fibrous protein that is insoluble in water and is
found in skin, tendons, cartilage, bones, teeth and the walls
of blood vessels.
•Haemoglobin is a functional protein.
•Collagen is a structural protein important in almost all
animals.
Comparison between globular and fibrous
proteins
•Most globular proteins are soluble in water and are
metabolically active.
•Examples of globular proteins include: enzymes, antibodies,
some hormones (insulin and glucagon)
•Globular proteins that are insoluble in water include
transporter proteins molecule found in cell membranes.
Globular vs fibrous
•Globular proteins most have a very precise shape since this
determines their function.
•They therefore have a very precise primary structure always
made in the same sequence of amino acids and of the same
length.
Globular vs fibrous
•Fibrous proteins may have a rather more variable primary
structure with a limited change of different amino acids.
•The amino acids can be joined to form chains of varying
length.
•Fibrous proteins are not soluble in water and they are not
usually metabolically active.
•Most have a structural role.
Cont’d
•Example of a fibrous protein is keratin which forms hair and
nails and is also found in the upper layer of the skin which
makes it waterproof.
•The soluble fibrous protein is fibrinogen found in blood
plasma.
•It is transformed into a insoluble protein when the blood
vessels is damaged.
Cont’d
•The fibrin fibres forms a network across the wound in which
platelets can be trapped to form a blood clot.
Solubility of proteins
•For proteins to be soluble in water they need not to be too
large.
•They also should have groups with an electrical charge on
the outside of the molecule.
•Globular proteins generally have these features.
•When the polypeptide folds in does so with the R group
carrying charges on the outside of the molecule and the
noncharged R group on the inside.
Cont’d
•Fibrous proteins are too large to be soluble in water.