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1

Biochemistry

xxx-paper name?

Enzyme structure

Description of Module
Subject Name

Biochemstry

Paper Name

14

Module Name/Title

3 Enzyme Structure

Dr
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MC Varadaraj

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Biochemistry

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Enzyme structure

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Concept Map

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Biochemistry

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Enzyme structure

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1 Enzymes
Enzymes are biological catalysts that increase the rate of reaction without affecting the reaction equilibrium
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Enzymatic reactions are also characterized by high substrate and reaction specificity and fewer side reactions
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These are:
 Primary structure
 Secondary structure
 Tertiary structure
 Quaternary structure
The enzyme structure ranges from a basic amino acid sequence to a three dimensional (3D) structure in a
folded protein
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Further, it is the 3D structure of an enzyme that determines the enzyme activities
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Biochemistry

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Enzyme structure

Fig 1
3
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1 Primary structure
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The sequence of amino acids in an enzyme is the primary structure
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2
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Biochemistry

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Enzyme structure

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In the primary structure, the constituent amino acids are linked by peptide bonds (-CONH-) bonds (Fig
3)
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3
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The peptide bond is formed between the amino group (-NH2) of one amino acid and the carboxyl group
(-COOH) of another, along with the release of water molecule
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The
different ways in which amino acids will be arranged in the chain will influence proper protein folding
for the enzyme to be functionally active
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3
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There are two types of secondary structures: helical (called α helices) and pleated
sheets (called β pleated sheets)
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The helix is right-handed in nature
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Biochemistry

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Enzyme structure

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The helix has about 3
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The pitch is 5
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Alpha helices form more readily in enzymes than any other possible conformations owing to the optimal use of
internal hydrogen bonds is made in these arrangements for attaining stability
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This structure is formed by
intermolecular hydrogen bonding between two or more straight chains
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Again, the two strands involved in the formation of beta pleated sheets can run either parallel to each other or
anti-parallel to each other
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On the other hand, if the amino groups of both chains are on the opposite side, the
chains are said to run in the opposite direction
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The anti-parallel
ß-sheet is more stable than parallel sheet owing greater alignment in the hydrogen bonds
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Difference between alpha helix and beta pleated sheet structure
Properties
Alpha helix
Beta pleated sheet
Structure
Right handed, helical
Sheet like
Formation
Formed by H bonds within the polypeptide
Formed by H bonds between two
chain
adjacent polypeptide chains
Side chains
Side Chains (R groups) orient out of the helix Side chains (R groups) are directed both
inside and outside the pleated structure
Types
Only one type
Can be of two types: parallel and
antiparallel
Preferred
Ala, Leu, Met, Phe, Glu, Gln, His, Lys, Arg
Tyr, Trp, Phe, Met, Ile, Val, Thr, Cys
amino acids
3
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3 Tertiary structure
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The arrangement of amino acids in the three dimensional space defines the tertiary structure of
enzymes
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

The various interactions involved in the formation/stabilization of a tertiary structure are Hydrogen
bonds, polar-polar interaction,

hydrophobic interaction, ionic interaction, formation of disulfide

bonds, Van der Waals forces
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

Under physiologic conditions, the side chains of amino acids which are hydrophobic in nature such as
phenylalanine or isoleucine, tend to remain buried within the protein/enzyme core, owing to their
minimal affinity for the aqueous medium
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Acidic or basic amino acid side-chains are polar in nature, and
therefore remain exposed on the enzyme surface, to allow for greater water solubility
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The interaction between these subunits is called the quaternary structure
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Fig
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Enzyme Structure Analysis
Analysis of enzyme/protein structure can be done with the help of following advanced analytical
techniques/equipments
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

The sequence of amino acids in the enzyme can be analyzed by peptide mapping, Edman degradation
or mass spectroscopy
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

The tertiary structure of an enzyme can be determined by fluorescence spectroscopy
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The amino acid sequence of enzyme is called as its primary structure
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The two types of secondary structures are helical (called α helices) and pleated sheets (called β
pleated sheets)
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Quaternary structure refers to the interaction between protein subunits
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Biochemistry

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Enzyme structure



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