5.2 Determination of Three-Dimensional Structure
of Proteins
Nearly one hundred thousand structures of proteins are registered in Protein Data
Bank. More than 80% of the three-dimensional structures are determined by X-ray
crystallography, and Nuclear Magnetic Resonance (NMR) is used for determination
of protein structure in solution. Electron microscope is also used for determination of
three-dimensional protein structures. X-ray diffraction method cannot determine
position of hydrogen atoms and NMR method determines averaged structures in
solution.
5.3 Basic Concept of Enzyme
Origin of enzyme is from ‘in yeast’ because enzyme is found in yeast as substance
with catalytic function. Enzyme is protein catalyst which is synthesized by gene
expression. Enzyme has substrate specificity and distinguishes optical isomers.
There are at least three contact points between enzyme and substrate, which means
stereospecificity of enzyme. There is affinity between enzyme and substrate, and
inhibitor has affinity proportional to structural similarity to substrate, i.e. binding
constant. In a cell, substrate 1 is converted to product 1 (¼substrate 2). Substrate 2 is
converted to product 2 (¼substrate 3). These sequential reactions catalyzed by
enzyme forms metabolic pathway. Enzyme is protein, and its catalytic efficiency is
more than 10
11 -fold compared to inorganic catalyst. Chemical reactions in cells of
human body is proceeded by enzymes even at 37
C (body temperature). Catalytic
function of enzyme is lowering activation energy of chemical reaction. And chemical reaction is conversion of bonding through electron. Lowering of activation
energy is realized by overlap of electron orbitals. This is studied in quantum biology,
but it is not always easy to analyze complex reactions catalyzed by enzyme.
5.4 Chemical Reaction and Kinetics of Enzyme
5.4.1 Chemical Reaction and Enzyme
Living organism is system of regulated chemical reactions and enzyme catalyzing
chemical reaction should be mentioned for discussion of biological functions.
Chemical reaction that molecule A reacts with molecule B and generate molecule
C is explained by collision theory.
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of Proteins
Nearly one hundred thousand structures of proteins are registered in Protein Data
Bank. More than 80% of the three-dimensional structures are determined by X-ray
crystallography, and Nuclear Magnetic Resonance (NMR) is used for determination
of protein structure in solution. Electron microscope is also used for determination of
three-dimensional protein structures. X-ray diffraction method cannot determine
position of hydrogen atoms and NMR method determines averaged structures in
solution.
5.3 Basic Concept of Enzyme
Origin of enzyme is from ‘in yeast’ because enzyme is found in yeast as substance
with catalytic function. Enzyme is protein catalyst which is synthesized by gene
expression. Enzyme has substrate specificity and distinguishes optical isomers.
There are at least three contact points between enzyme and substrate, which means
stereospecificity of enzyme. There is affinity between enzyme and substrate, and
inhibitor has affinity proportional to structural similarity to substrate, i.e. binding
constant. In a cell, substrate 1 is converted to product 1 (¼substrate 2). Substrate 2 is
converted to product 2 (¼substrate 3). These sequential reactions catalyzed by
enzyme forms metabolic pathway. Enzyme is protein, and its catalytic efficiency is
more than 10
11 -fold compared to inorganic catalyst. Chemical reactions in cells of
human body is proceeded by enzymes even at 37
C (body temperature). Catalytic
function of enzyme is lowering activation energy of chemical reaction. And chemical reaction is conversion of bonding through electron. Lowering of activation
energy is realized by overlap of electron orbitals. This is studied in quantum biology,
but it is not always easy to analyze complex reactions catalyzed by enzyme.
5.4 Chemical Reaction and Kinetics of Enzyme
5.4.1 Chemical Reaction and Enzyme
Living organism is system of regulated chemical reactions and enzyme catalyzing
chemical reaction should be mentioned for discussion of biological functions.
Chemical reaction that molecule A reacts with molecule B and generate molecule
C is explained by collision theory.
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5 Structure and Function of Protein