Organic chemistry and Biological chemistry for Health Sciences
59-191
Lecture 19
Proteins can be classified in two groups according to their solubility.

Globular protein

Fibrous protein
Globular protein:
They are soluble in water or in water that contains salt.
Albumins-present in egg white and in blood. In the blood albumins are buffer,
transporters of water insoluble molecules of lipids or fatty acids, and carriers of metal
ions, like Cu2+.
Fibrous protein:
They are not soluble in water.
Collagens-occurs in bone, teeth, tendons, cartilage and certain ligaments
Elastins-gives elasticity to ligaments, the walls of large blood vessels like the aurota etc.
Keratins-occurs in hair, wools, horns, nails, animal hooves etc
Myosin-found in contractile muscle
ENZYMES:
Enzymes are biological catalysts whose activities often depend on cofactors made from B
vitamins or metal ions.
With the exception of a small group of catalytic RNA molecules all enzymes are proteins.
All enzyme molecules and most substrate molecules are chiral. So enantiomer of the
substrate will not bind to the enzyme. They are very specific for substrates. Enzyme
specificity means that a given enzyme acts in vivo on only one substrate or one kind of
bond.
Enzymes are most active only at a narrow range of pH that is normal to their environment
in the body. F.example
Pepsin, stomachs protein digesting enzyme, is most active at a pH of about 2, which is
roughly how acidic the stomach juices are.
Enzyme activity is highest also at a narrow range of temperature. With ordinary reactions
reaction rate increases with temperature. Although reaction rate decreases with
decreasing temperature, it is not increased in increasingly higher temperature, because
enzymes denature at high temperature.
Like other catalysts enzymes increase the reaction rate by lowering the activation energy
of the reactions. The rate enhancements brought about by enzymes are often in the range
of 7 to 14 orders of magnitude.
Catalyst speeds up the equilibration. It accelerates both the forward and reverse reaction.
Whether the equilibrium will shift to the right or to the left depend on the equilibrium
constant, on the concentrations of the reactants and products, on whether other reaction
feed substances in the equilibrium or continuously remove them; and on the temperature.
Enzymes also establish equilibria extremely rapidly.
Some enzyme requires no chemical group other than their amino acid residues for
activity. Others require an additional chemical component called a cofactor. The cofactor
may be either one or more inorganic ions, such as Fe2+ Mg2+, Mn2+, Zn2+ or a complex
organic or metalloorganic molecule called a coenzyme. Some enzymes require both a
coenzyme and one or more metal ions for activity. A cofactor or coenzyme that is
covalently bound to the enzyme is called a prosthetic group. A complete, catalytically
active enzyme together with its coenzyme and/or metal ions is called a holoenzyme. The
protein part of such an enzyme is called an apoenzyme. Coenzymes function as transient
carriers of specific functional groups.
Many vitamins, organic nutrients required in
small amounts in the diet are precursors of coenzymes.
B vitamins are used as precursor for many coenzymes. F.example, thiamine diphosphate,
a coenzyme, is a diphosphate ester of vitamin B.
Nicotinamide, another B vitamin, is part of the structure of nicotinamide adenine
dinucleotide, another important coenzyme.
Nicotinamide occurs in yet another major coenzyme, nicotinamide adenine dinucleotide
phosphate, a phosphate ester of NAD+. Both NAD+ and NADP+ are coenzymes in
biological redox reactions. They are the actual H:- ion acceptor in the oxidation reaction.
Enzymes are classified by the reactions they catalyze. Many enzymes have been named
by adding the suffix –ase to the name of their substrate or to a word or phrase describing
their activity.
F. example a hydrolase catalyses hydrolysis reaction. An esterase is a hydrolase that
cantalyzes hydrolysis of ester. A lipase works on hydrolysis of lipids. A peptidase or a
protease catalyze hydrolysis of peptide bonds.
Oxidoreductase- handles a redox equilibrium. Sometimes oxidoreductase is called a
oxidase when oxidation is the favored reaction and reductase when reduction is the
favored reaction.
Transferase-catalyses transfer of a group from one molecule to another
Kinase-a special kind of transferase that trasfers phosphate groups
Lyases-catalyzes elimination reaction that produce double bonds
Isomerase-cause conversion of a compound to its isomer
Ligase-cause the formation of bonds at the expense of chemical energy in triphosphate
like ATP
In order to catalyze a reaction substrate and enzyme molecules must fit each other
momentarily. This temporary combination is called enzyme substrate complex. It is part
of a series of chemical equilibria that carry the substrate through a number of changes
until the products of overall reaction form. So the substrate fits the enzyme like a key in
a lock. In order to fit each other they must have complementary shapes. Two kinds of
complementarity is required to form an enzyme substrate complex-geometric
complementarity and physical complementarity.
Geometric complementarity-their shapes has to be similar
Physical complementarity-concerns hydrophobic interactions, hydrogen bonds and
ionic interactions between the enzyme and the substrate in the complex.
As the substrate molecule binds to the enzyme, the molecular groups of the substrate
induce the enzyme molecule to adjust its shape to achieve the best fit. The initial contact
with substrate and enzyme may cause changes in tertiary structure in the polypeptide of
the protein. Such changes that induce stresses in the polypeptide, force the enzyme to
modify its shape further. This phenomenon is called induced fit.
The sequence of amino acid residues in the enzymes that bind the substrate is called the
binding site of the enzyme. These amino acids have side chain with shapes and polar
sites complementary to the substrate. Other groups in the enzymes that handle the actual
catalysis of the reaction are called the catalytic site. Catalytic sites are often supplied by
coenzyme.
The fit achieved by enzyme and substrate in E-S complex is not perfect. Intermolecular
force between the substrate and the enzyme, that was used to form the E-S distort and
stretch chemical bonds in the substrate to improve the fit. The chemical energy for this
distortion is provided by the gain in overall stability in the complex. The result of such
changes is the conversion of initial enzyme-substrate complex, E-S, into a substrate
activated complex, E-S*. In E-S* the substrate molecule has reached a unique condition
of both shape and internal energy called its transition state. The perfecting of the
enzyme substrate fit in the transition state largely accounts for the high catalytic power
of the enzyme.
The reaction rate is sensitive to the reactant concentration. In many reactions involving
two species, doubling the initial concentration of one of the reactant by keeping the other
one constant double the reaction rate. In an enzyme catalyzed reaction doubling the
initial concentration of the substrate at some fixed initial enzyme concentration, doubles
the reaction rate. But this rate enhancement levels off at a very high concentration of the
substrate. The reason for the leveling off is that we now have enough substrate to saturate
the active sites of all the enzyme molecules. Any additional substrate molecule has to
wait its turns.
The relationship between V, [E0] and [S] for the enzyme-catalyzed reaction is given by
the following reaction:
k[E0][S]
V=
KM + [S]
k= proportionality constant
KM = Michaelis constant
When [S] is very low, V = k/KM [E0][S], the velocity of the reaction is directly
proportional to the concentration of the substrate.
When [S] is very high, Vm = k[E0]
But [E0] is a constant, the concentration of the enzyme and k is constant. So the
maximum velocity must be a constant. Thus at high values of [S], the rate of enzyme
catalyzed reaction must level off at maximum.
When [S] is equal to KM
V = ½ Vm
So KM is the substrate concentration at which the reaction rate reaches one half of
the maximum rate.
Regulation of enzymes:
Enzyme activity is regulated in order to control the reactions in the cell. Enzymes are
usually regulated in the first step, formation of the enzyme substrate complex. Many
enzymes do not show a sharp linear increase of initial reaction rate at a low substrate
concentration. So they give a sigmoid plot when initial rate is plotted against the initial
substrate concentration. These enzymes remain inactive until a sufficient concentration of
substrate forces them into active form.
Enzymes with sigmoidal rate curves consist of two or more subunits. Each subunit
contains a catalytic site that is inactive in the absence of a substrate. When the substrate
interacts with one of those catalytic sites it induces a conformational change in that
subunit to fit the substrate properly. This conformational change also induces similar
conformational change in the other subunits to cause the other catalytic site become
active. Now the same enzyme molecule can accept the substrate much more easily than
first. The phenomenon of one active site being activated by an event happening elsewhere
in the enzyme is called allosteric activation. So enzymes subunits cooperate each other to
cause the full activation of the enzyme. In order to start this activation process certain
concentration of substrate is required.
Substances called effectors that are not substrates activate the catalytic sites of some
enzymes. When effectors bind to a site distinct from catalytic site they induce a
configurational change in the enzyme molecule that activates the enzyme. The effectors
may, for example, be a molecule whose own metabolism needs the products made by the
enzyme it activates.
Two of the important effectors are calmodulin, a protein found in most cells and troponin,
another protein found in muscle cell. They can only activate enzymes when they are
activated themselves by Ca2+. Cells control their Ca2+ ion levels by active transport
mechanism mediated by nerve signals.
A nerve signal opens the protein channel in the membrane to pump Ca2+ inside that binds
to calmodulin or troponin. Once the effector is activated, it can activate an enzyme or
cause muscle contraction. When the signal is over, the channels close and the Ca2+ ions
are pumped back out through a different channel.
Some enzymes are activated by removal of short polypeptide units from its sequence.
These enzymes are synthesized in their inactive form called zymogens or proenzymes.
They have several more amino acid residues that need to be removed to expose the active
site of the enzyme to render it active.
F.example
Trypsin, which helps to digest protein, is synthesized in its inactive form trypsinogen. A
compound called enteropeptidase that is released from the upper intestine converts it to
trypsin (active enzyme) by deleting a small polypeptide unit in trypsinogen after a protien
rich meal.