LOWER SIX PUSAT TUISYEN KASTURI PREPARED BY

BIOLOGY LESSON 4 T.K. LEONG

TOPIC: BASIC CHEMISTRY OF A CELL (4)

BONDS USED IN PROTEIN STRUCTURE

 Amino acids combine to form proteins. They are joined together by a type of bond known as
peptide bond.

 Once these bonds have been formed, however, the protein typically folds into a particular
shape as result of four other types of bond, namely; Ionic bonds, Disulphide bonds, Hydrogen
bonds and Hydrophobic interactions.

Ionic bond Ф Acidic and basic R group exist in an ionised state at certain pHs. Acidic R
groups are negatively charged and basic R groups are positively
charged.
Ф They can therefore be attracted to each other, forming ionic bonds.
Ф In an aqueous environment this bond is much weaker than a covalent
bond and can be broken by changing the pH of the medium. This helps
to explain the disruptive effect that changes in pH can have on protein
structure.
Disulphide bond Ф The amino acid cysteine contains a sulphydryl group, -SH, in its R group.
If two molecules of cysteine line up alongside each other, neighbouring
sulphydryl groups can be oxidised and form a disulphide bond.
Ф Disulphide bonds may be formed between different chains of amino
acids or between different parts of the same chain. In the latter case the
disulphide bonds make the molecule fold into a particular shape.
Ф They are strong and not easily broken.
Hydrogen bond Ф When hydrogen is part of an OH or NH group it becomes slightly
positively charged. This is because the electrons that are shared, and
which are negatively charged, are attracted more towards a
neighbouring electronegative oxygen or nitrogen atom.
Ф Such as the O of a C=O group or the N of an NH group.
Ф C=O and NH groups occur along the length of polypeptide chains, and
they can interact to produce regular shapes.
Ф The hydrogen bond is weak, but as its occurrence is frequent, the total
effect makes a considerable contribution towards molecular stability.
Hydrophobic Ф Some R groups are non-polar and therefore hydrophobic, such as those
interaction on the amino acids tyrosine and valine.
Ф If a polypeptide chain contains a number of these groups and is in an
aqueous environment, the chain will tend to fold so that the maximum
number of hydrophobic groups come into close contact and exclude
water.
Ф The hydrophobic groups tend to point inwards towards the centre of
the roughly spherical molecule while the hydrophilic group face
outwards into the aqueous environment, making the protein soluble.

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STRUCTURE OF PROTEINS
Each protein possesses a characteristic three-dimensional shape, its conformation. There are four
separate levels of structure and organisation as follows.

Primary Structure
The primary structure is the linear sequence of amino acids in a polypeptide chain. There are
thousands of different proteins in the human body, all composed of different arrangements of the
20 fundamental amino acids. The sequence of amino acids of a protein dictates its biological
function.

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Secondary Structure
The most common secondary structure is an extended spiral ring, the α-helix, whose structure is
maintained by many hydrogen bonds which are formed between neighbouring C=O and NH
groups. A protein which is entirely α-helical, and hence fibrous, is keratin. It is the structural
protein of hair, wool, nails, claws, beaks, feather and horn. Its hardness and stretchability vary
with the degree of cross-linking by disulphide bridges between neighbouring chains.

Another type of secondary structure is the β-pleated sheet. The protein that makes silk, namely
fibrion, is entirely in this form. It is the protein used by silkworms when spinning their cocoon
threads. It is made up of a number of adjacent chains which are more extended than the
α-helices. They are arranged in a parallel fashion. They are joined together by hydrogen bonds
formed between C=O and NH groups of one chain and the NH and C=O groups of adjacent
chains.
All NH and C=O groups are involved in hydrogen bonding, so the structure is very stable and rigid.
The β-pleated sheet of silk has a high tensile strength (cannot be stretched), but the arrangement
makes the silk very supple.

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Tertiary Structure
Usually the polypeptide chain bends and folds
extensively, forming a precise, compact globular shape.
This is the protein tertiary structure and it is maintained
by the interaction of the four types of bond.

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Quaternary Structure
Many highly complex proteins consist of more than one polypeptide chain. The separate chains
are held together by hydrophobic interaction, hydrogen and ionic bonds.
Their precise arrangement is known as the quaternary structure. Example: Haemoglobin.

Denaturation and renaturation of proteins

Denaturation is the loss of the specific three-dimensional shape of a protein molecule. The
change may be temporary or permanent, but the amino acid sequence of the protein remains
unaffected. If Denaturation occurs, the molecule unfolds and can no longer perform its normal
biological function. A number of agents may cause Denaturation as follows.

Heat or radiation
e.g. infra-red or ultraviolet light.
Kinetic energy is supplied to the protein causing its atoms to vibrate violently, so disrupting the
weak hydrogen and ionic bonds. Coagulation of the protein then occurs.

Strong acids and alkalis and high concentrations of salts.

Ionic bonds are disrupted and the protein is coagulated. Breakage of peptide bonds may occur if
the protein is allowed to remain mixed with the reagent for a long period of time.

Heavy metals.
The positively charged ions of heavy metals (cations) form strong bonds with the negatively
charged carboxyl groups on the R groups of proteins and often disrupt ionic bonds. They also
reduce the protein's electrical polarity (its overall charge) and thus increase its insolubility. This
causes the protein to precipitate out of solution.

Organic solvents and detergents.

These reagents disrupt hydrophobic interactions and form bonds with hydrophobic (non-polar)
groups. This in turn causes the disruption of hydrogen bonding. When alcohol is used as a
disinfectant it functions to denature the protein of any bacteria present.

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 Nucleic Acids
1. Nucleic acids are polymers of nucleotides.

2. There are two types of nucleic acids;

(A) DNA ( deoxyribonucleic acid )
(B) RNA ( ribonucleic acid )

3. A nucleotide is made up of three components;

(i) Pentose
(ii) Nitrogenous base (purine and pyrimidine)
Purine bases : Adenine (A) and Guanine (G)
Pyrimidine bases : Thymine (T), Uracil (U) and Cytosine (C)
(iii) Phosphate group

4. Different nucleotides are joined by phosphodiester bonds to form a polynucleotide strand.

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Watson and Crick Model of DNA
 The DNA structure described by Watson and Crick model of double α-helix shown in the
figure below. It consists of two strands of polynucleotide, which coiled around each other
forming an α-helix.

 The nucleotides are of deoxyribonucleotide, which composed of bases of A, T, C and G with

deoxyribose and phosphates as backbone. The two strands of polynucleotides are
complementary to each other.
 e.g. A in one strand is bonded by hydrogen bonds with T of another strand. So C is with G.

 The two strands are anti-parallel i.e. in one strand the carbon in the pentose is arranged in 5'
to 3' pattern and the other is 3' to 5' pattern. The structure of the molecule is very stable as
the whole two strands are linked by hydrogen bonds. There are hydrophobic interactions
between the bases in the centre aided by water molecules around it. These make the molecule
very stable.

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