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Proteins are very important molecules in our cells. They are
involved in virtually all cell functions.
Proteins do everything in the living cells. All functions of
the living organisms are related with proteins.
Each protein within the body has a specific function. Some
proteins are involved in structural support, while others are
involved in bodily movement, or in defense against germs.
Proteins vary in structure as well as function. They are
constructed from a set of 20 amino acids and have distinct
three-dimensional shapes.
Proteins are responsible for many different functions in the
living cell. It is possible to classify proteins on the basis of
their functions. Very often, proteins can carry few functions
and such proteins can be placed into different groups, but
despite this, it is possible to assign main group for each
Enzymes - catalytic activity and function
Transport Proteins - bind & carry ligands
Storage Proteins - ovalbumin, gluten, casein, ferretin
Contractile (Motor): can contract, change shape, elements
of cytoskeleton (actin, myosin, tubulin)
Structural (Support): collagen of tendons & cartilage,
elastin of ligaments (tropoelastin), keratin of hair, feathers,
& nails, fibroin of silk & webs
Defensive (Protect): antibodies (IgG), fibrinogen &
thrombin, snake venoms, bacterial toxins
Regulatory (Signal): regulate metabolic processes,
hormones, transcription factors & enhancers, growth factor
Receptors (detect stimuli): light & rhodopsin, membrane
receptor proteins and acetylcholine or insulin.
Enzymes - are proteins that facilitate biochemical reactions.
They are often referred to as catalysts because they speed up
chemical reactions.
This group of proteins probably is the biggest and most
important group of the proteins
Examples include the enzymes DNA- and RNApolymerases, dehydrogenases, lactase and pepsin.
Lactase breaks down the sugar lactose found in milk.
Pepsin is a digestive enzyme that works in the stomach to
break down proteins in food.
Catalyst: inorganic or organic substance which speeds up
the rate of a chemical reaction without entering the reaction
Enzymes: organic catalysts made of protein.
Like all catalysts, enzymes work by lowering the activation
energy (Ea or ΔG‡) for a reaction, thus dramatically
increasing the rate of the reaction.
Most enzyme reaction rates are millions of times faster than
those of comparable un-catalyzed reactions.
most enzyme names end in -ase
Many enzymes catalyze reactions without help, but some
require an additional non-protein component called a cofactor.
Co-factors may be inorganic ions such as Fe2+, Mg2+, Mn2+,
or Zn2+, or consist of organic or metalloorganic molecules
knowns as co-enzymes.
Enzyme activity can be affected by other molecules.
Inhibitors are molecules that decrease enzyme activity;
activators are molecules that increase activity.
Many drugs and poisons are enzyme inhibitors.
Activity is also affected by temperature, chemical
environment (e.g., pH), and the concentration of substrate.
Some enzymes are used commercially, for example, in the
synthesis of antibiotics.
In addition, some household products use enzymes to speed
up biochemical reactions (e.g., enzymes in biological
washing powders break down protein or fat stains on
clothes; enzymes in meat tenderizers break down proteins,
making the meat easier to chew).
substrate: molecules upon which an enzyme acts. The
enzyme is shaped so that it can only lock up with a specific
substrate molecule.
Fructose + Glucose
Enzymes are very specific, both the enzyme and the
substrate possess specific complementary geometric shapes
that fit exactly into one another. This is often referred to as
"the lock and key" model.
However, while this model explains enzyme specificity, it
fails to explain the stabilization of the transition state that
enzymes achieve. The "lock and key" model has proven
inaccurate, and the induced fit model is the most currently
accepted enzyme-substrate-coenzyme figure.
Lock and Key Theory
Each enzyme is specific for one and ONLY one substrate (one lock - one key)
active site: part of the enzyme that fits with the substrate
Note that the active site has a specific fit for this particular substrate and no other.
This theory has some weaknesses, but it explains many basic things about enzyme
Enzymes are classified according to the reactions they
catalyze. The six classes are:
Alcohol dehydrogenase: an oxidoreductase converting
alcohols to aldehydes/ ketones.
Aminotransferases: transferases catalyzing the amino acid
degradation by removing amino groups.
Glucose-6-phosphatase: a hydrolase that removes the
phosphate group from glucose-6-phosphate, leaving glucose
and H3PO4.
Pyruvate decarboxylase: a lyase that removes CO2 from
Ribulose phosphate epimerase: an isomerase that catalyzes
the interconversion of ribulose-5-phosphate and xylulose-5phosphate.
pH: the optimum (best) in most living things is close to 7
(neutral). High or low pH levels usually slow enzyme
Temperature: strongly influences enzyme activity
optimum (best) temperature for maximum enzyme function
is usually about 35-40 C.
reactions proceed slowly below optimal temperatures
above 45 C. most enzymes are denatured (change in their
shape so the enzyme active site no longer fits with the
substrate and the enzyme can't function)
Concentrations of Enzyme and Substrate
When there is a fixed amount of enzyme and an excess of
substrate molecules the rate of reaction will increase to a
point and then level off.
This leveling off occurs because all of the enzyme is used
up and the excess substrate has nothing to combine with.
If more enzyme is available than substrate, a similar
reaction rate increase and leveling off will occur. The excess
enzyme will eventually run out of substrate molecules to
react with.
Enzymes serve a wide variety of functions inside living
They are indispensable for signal transduction and cell
regulation, often via kinases and phosphatases.
They also generate movement, with myosin hydrolysing
ATP to generate muscle contraction and also moving cargo
around the cell as part of the cytoskeleton.
Other ATPases in the cell membrane are ion pumps involved
in active transport.
Enzymes are also involved in more exotic functions, such as
luciferase generating light in fireflies.
Viruses can also contain enzymes for infecting cells, such as
the HIV integrase and reverse transcriptase, or for viral
release from cells, like the influenza virus neuraminidase.
An important function of enzymes is in the digestive
systems of animals.
Enzymes such as amylases and proteases break down large
molecules (starch or proteins, respectively) into smaller
ones, so they can be absorbed by the intestines.
Starch molecules, for example, are too large to be absorbed
from the intestine, but enzymes hydrolyse the starch chains
into smaller molecules such as maltose and eventually
glucose, which can then be absorbed.
Different enzymes digest different food substances. In
ruminants which have a herbivorous diets, microorganisms
in the gut produce another enzyme, cellulase to break down
the cellulose cell walls of plant fiber.
Antibodies are substances made by the body's immune
system in response to bacteria, viruses, fungus, animal
dander, or cancer cells.
Antibodies attach to the foreign substances so the immune
system can destroy them.
Antibodies are specific to each type of foreign substance.
For example, antibodies made in response to a tuberculosis
infection attach only to tuberculosis bacteria.
Antibodies may be made against your own tissues. This is
called an autoimmune disease.
If your immune system makes low levels of antibodies, you
may have a higher chance of developing repeated infections.
You can be born with an immune system that makes low
levels of antibodies, or your system may make low levels of
antibodies in response to certain diseases, such as cancer.
Antibodies are produced by a kind of white blood cell called
a B cell.
Antibodies occur in two forms:
membrane-bound (attached to the surface of a B cell)
Soluble (secreted by specific B cells called plasma cells)
Stimulating B Cell
When a T lymphocyte "sees" the same peptide on the
macrophage and on the B cell, the T cell stimulates the B
cell to turn on antibody production.
Antibody Production
The stimulated B cell undergoes repeated cell divisions,
enlargement and differentiation to form a clone of antibody
secreting plasma cells.
Hence. through specific antigen recognition of the invader,
clonal expansion and B cell differentiation you acquire an
effective number of plasma cells all secreting the same
needed antibody.
That antibody then binds to the bacteria making them easier
to ingest by white cells. Antibody combined with a plasma
component called "complement" may also kill the bacteria
The general structure of all antibodies is very similar
Each antibody consists of four polypeptides– two heavy
chains and two light chains held together by disulfide bonds
joined to form a "Y" shaped molecule.
The amino acid sequence
in the tips of the "Y" varies
greatly among different antibodies.
This variable region, composed of
110-130 amino acids, give the antibody
its specificity for binding antigen.
A small region at the tip of the
protein is extremely variable,
allowing millions of antibodies with
slightly different tip structures to
This region is known as the
hypervariable region.
Each of these variants can bind to a
different target, known as an
This huge diversity of antibodies
allows the immune system to
recognize an equally wide diversity
of antigens.
Neutralization of toxins
Immobilization of microorganisms
Neutralization of viral activity
Binding soluble antigen (precipitation)
Activating complement
Activation of complement
Antibodies that bind to surface antigens on, for example a
bacterium, attract the first component of the complement
cascade with their Fc* region and initiate activation of the
"classical" complement system.
This results in the killing of bacteria in two ways. First, the
binding of the antibody and complement molecules marks
the microbe for ingestion by phagocytes in a process called
opsonization; these phagocytes are attracted by certain
complement molecules generated in the complement
Secondly, some complement system components form a
membrane attack complex to assist antibodies to kill the
bacterium directly.
* The base of the Y plays a role in modulating immune cell activity. This region is called
the Fc (Fragment, crystallizable) region, and is composed of two heavy chains that
contribute two or three constant domains depending on the class of the antibody
Activation of effector cells
To combat pathogens that replicate outside cells, antibodies
bind to pathogens to link them together, causing them to
Since an antibody has at least two paratopes it can bind
more than one antigen by binding identical epitopes carried
on the surfaces of these antigens.
By coating the pathogen, antibodies stimulate effector
functions against the pathogen in cells that recognize their
Fc region.
Those cells which recognize coated pathogens have Fc
receptors which, as the name suggests, interacts with the Fc
region of IgA, IgG, and IgE antibodies.
The engagement of a particular antibody with the Fc
receptor on a particular cell triggers an effector function of
that cell; phagocytes will phagocytose, mast cells and
neutrophils will degranulate, natural killer cells will release
cytokines and cytotoxic molecules; that will ultimately
result in destruction of the invading microbe.
The Fc receptors are isotype-specific, which gives greater
flexibility to the immune system, invoking only the
appropriate immune mechanisms for distinct pathogens.
The immunoglobulins can be divided into five different
classes, based on differences in the amino acid sequences in
the constant region of the heavy chains.
IgA - Alpha heavy chains:
IgA antibodies are found in areas of the body such the nose,
breathing passages, digestive tract, ears, eyes, and vagina.
IgA antibodies protect body surfaces that are exposed to
outside foreign substances.
This type of antibody is also found in saliva, tears, and
blood. About 10% to 15% of the antibodies present in the
body are IgA antibodies. A small number of people do not
make IgA antibodies.
IgG - Gamma heavy chains:
IgG antibodies are found in all body fluids. They are the
smallest but most common antibody (75% to 80%) of all the
antibodies in the body.
IgG antibodies are very important in fighting bacterial and
viral infections. IgG antibodies are the only type of antibody
that can cross the placenta in a pregnant woman to help
protect her baby.
IgM - Mu heavy chains:
IgM antibodies are the largest antibody. They are found in
blood and lymph fluid and are the first type of antibody
made in response to an infection.
They also cause other immune system cells to destroy
foreign substances. IgM antibodies are about 5% to 10% of
all the antibodies in the body.
IgE - Epsilon heavy chains:
IgE antibodies are found in the lungs, skin, and mucous
membranes. They cause the body to react against foreign
substances such as pollen, fungus spores, and animal
dander. They may occur in allergic reactions to milk, some
medicines, and some poisons.
IgE antibody levels are often high in people with allergies.
IgD - Delta heavy chains:
IgD antibodies are found in small amounts in the tissues that
line the belly or chest. How they work is not clear.
Immunoglobulin Types:
Immunoglobulins can also be classified by the type of light
chain that they have.
Light chain types are based on differences in the amino acid
sequence in the constant region of the light chain. These
differences are detected by serological means.
1. Kappa light chains
2. Lambda light chains
Storage proteins are biological reserves of metal ions and
amino acids, used by organisms. They are found in plant
seeds, egg whites, and milk.
Ferritin is an example of a storage protein that stores iron.
Iron is a component of heme, which is contained in the
transport protein hemoglobin and in cytochromes.
Some storage proteins store amino acids. Storage proteins'
amino acids are used in embryonic development of animals
or plants. Two amino acid storage proteins in animals are
casein and ovalbumin.
Seeds, particularly of leguminous plants, contain high
concentrations of storage proteins. Up to 25 percent of the
dry weight of the seed can be composed of storage proteins.
Ovalbumin is a glycoprotein with molecular weight of 45
kDa. The molecule consists of a polypeptide with up to two
phosphate groups per mole and a side chain of mannose and
glucosamine residues.
Ovalbumin is the main protein found in egg white, making
up 60-65% of the total protein.
Medicinal characteristics:
In cases where poisoning by heavy metals (such as Iron) is
suspected, ovalbumin may be administered. Ovalbumin
chelates to heavy metals and traps the metal ions within the
sulfhydryl bonds of the protein. Chelating prevents the
absorption of the metals into the gastrointestinal tract and
prevents poisoning.
Contractile proteins are proteins which participate in
contractile processes.
They include muscle proteins as well as those found in other
cells and tissues.
These proteins participate in localised contractile events in
the cytoplasm, in motile activity, and in cell aggregation
The cytoplasm of cells is a colloidal network of contractile
proteins. Actin filaments are the major components of this
network. Other contractile proteins interact with these
filaments to create structural rigidity and movement.
The structure and function of contractile proteins is striated
muscles is well characterized and thus provides a good
example for extrapolitation to an analysis of contractileprotein structure and function of nonmuscle cells. However,
the interaction of contractile proteins of various cells may
be unique.
The study of contractile proteins in cells other than muscle
has distinct difficulties:
(a) The proteins are present in much lower concentration
than in muscle, and only a few cell types are obtainable for
study in quantities comparable to muscle.
(b) Proteolysis and other detriments may be more severe in
nonmuscle cells.
(c) The organization of contractile proteins is difficult to
define in nonmuscle cells.
(d) The effort is diffuse; investigations examine a wide
variety of different, or less commonly the same, cells.
The most prominent example of a motor protein is the
muscle protein myosin which "motors" the contraction of
muscle fibers in animals.
Myosin is the protein responsible for generating muscle
Many molecules of myosin generate enough force to
contract muscle tissue.
Myosins are also vital in the process of cell division.
Structure and Function:
Most myosin molecules are composed of a head, neck, and
tail domain.
 The head domain binds the filamentous actin, and uses ATP
hydrolysis to generate force and to "walk" along the
filament towards the (+) end (with the exception of one
family member, myosin VI, which moves towards the (-)
The neck domain acts as a linker and as a lever arm for
transducing force generated by the catalytic motor domain.
The neck domain can also serve as a binding site for myosin
light chains which are distinct proteins that form part of a
macromolecular complex and generally have regulatory
The tail domain generally mediates interaction with cargo
molecules and/or other myosin subunits. In some cases, the
tail domain may play a role in regulating motor activity.
The thick myosin bands are not single myosin proteins but are made of multiple
myosin molecules. Each myosin molecule is composed of two parts: the globular
"head" and the elongated "tail". They are arranged to form the thick bands