Proteins are amino acid chains that fold into unique dimensional
structures. The shape into which a protein naturally
folds is known as its native state, which is determined
by its sequence of amino acids. Biochemists refer to
four distinct aspects of a protein's structure:
Primary structure: the amino acid sequence
Secondary structure: highly patterned sub-structures
alpha helix and beta sheet or of chain that assume no
stable shape. Secondary structures are locally defined,
meaning that there can be many different secondary motifs
present in one single protein molecule.
Tertiary structure:single protein ; the spatial relationship
of thecondary structural motifs to one another
Quaternary structure: the shape or structure that results
from the union of more than one protein molecule, usually
called subunit proteins subunits in this context, which
function as part of the larger assembly or protein complex.
In addition to these evels of structure, proteins may shift between
several siilar structures in performing their biological function.
In the context of these functional rearrangements, these tertiary
or quaternary structures are usually referred to as and transitions
between them are called conformational changes.
The primary structure is held together by covalent
peptide bonds, which are made during the process of translation.
The secondary structures are held together by hydrogen bonds. The
tertiary structure is held together primarily by hydrophobic but
hydrogen bonds, ionic interactions, and disulfide bonds are usually
involved too.process by which thestructures form is called protein
folding and is a consequence of the primary structure. The mechanism
of protein folding is not understood. Alhough polypeptide may have
more than one stable folded conformation, each conformation has
its own biological activity and only one conformation is considered
to be the active, or native conformation.The two ends of the amino
acid chain are referred to as the carboxy terminus and the amino
terminus based on the nature of the free group on each extremity.
Functions
Proteins are involved in practically every function
performed by a cell, including regulation of cellular
functions such as signal transduction and metabolism.
For example, catabolism requires enzymes termed proteases
and other enzymes such as glycosidases.
Mechanisms of protein regulations molecules and ions are able to
bind to specific sites on proteins. These sites are called binding
sites. They exhibit chemical specificity. The particle that binds
is called a ligand. The strength of ligand-protein binding is a
property of the binding site known as affinity.
Since proteins are involved in practically everyperformed
by a cell, the mechanisms for controlling these functions
therefore depend on controlling protein activity. Regulation
can involve a protein's shape concentration. Some forms
regulation include:Allosteric modulation: When the binding
of a ligand at one site on a protein affects the binding
of ligand at another site.
Covalent modulation: When the covalent modification of a protein
affects the binding of a ligand or some other aspect of the protein's
function.
Diversity
Proteins are generally large molecules, having molecular masses
of up to 3,000,000 the muscle protein titin has a single amino acid
chain 27,000 subunits long. Such long chains of amino acids are
almost universally referred to as proteins, but shorter strings
of amino acids are referred to as "polypeptides," "peptides"
or rarely, "oligopeptides". The dividing line is undefined,
though "polypeptide" usually refers to an amino acid chain
lacking tertiary structure which may be more likely to act as a
hormone , rather than as an enzyme which depends on its defined
tertiary structure for functionality.Proteins are generally classified
as soluble, filamentous or membrane-associated Nearly all the biological
catalysts known as enzymes are soluble proteins with a recent notable
execption being the discovery of ribozymes, RNA molecules with the
catalytic properties of enzymes Antibodies, the basis of the adaptive
immune system, are another example of soluble proteins. Membrane-associated
proteins include exchangers and ion channels, which move their substrates
from place to place but do not change them; receptors, which do
not modify their substrates but may simply shift shape upon binding
them. Filamentous proteins make up the cytoskeleton of cells and
much of the structure of animals: examples include tubulin, actin,
collagen and keratin, all of which are important components of skin,
, and cartilage. Another special class of proteins consists of motor
proteins such as myosin, kinesin, and dynein. These proteins are
"molecular motors," generating physical force which can
move organelles, cells, and entire muscles.
Working with proteins
Proteins are sensitive to their environment. They may only be active
in their native state, over a small pH range, and under solution
conditions with a minimum quantity electrolytes. A protein in its
native state is often described as folded. A proteinis not in its
native state is said to be denatured. Denatured proteins generally
have no well-defined secondary structure. Many proteins denature
and will not remain in solution in distilled water.
One of the more striking discoveries of the 20th century
was that the native and denatured states in many proteins were interconvertible,
that by careful control of solution conditionsdialyzing away a denaturing
chemica, a denatured protein could be converted to native form.
The issue of how proteins arrive at their native state is an important
area of biochemical study, called the study of protein folding.
Through genetic engineering, researchers can alter
the sequence and hence the structure, "targeting", susceptibility
to regulation and other properties of a protein. The genetic sequences
different proteins may be spliced together to create "chimeric"
proteins that possess properties of both. This form of tinkering
represents one of the chief tools of cell and molecular biologists
change and to probe the workings of cells. Another area of protein
research attempts to engineer proteins entirely new properties or
functions, a field known as protein engineering.Protein-protein
interactions can be screened for using two-hybrid screening.
Protein and nutrition
Protein is an important macronutrient to the human diet, supplying
the body's needs for nitrogen and amino acids. The exact amount
of dietary protein needed to satisfy these requirements may vary
widely depending on age, sex, level of physical activity, and medical
condition. However, the figure of .75g per kilogram of body weight
for a sedentary male is widely given as a daily requirement. Proteins
are found in most food but are particularly concentrated in legumes,
nuts, meat, and dairy . As it is used, much protein is converted
by protein catabolism to ammonia which, due to its toxicity, must
be converted to either urea or uric acid (in some animals) to be
excreted in Protein is the major component of muscles, tendons,
enzymes, skin, hair, eyes, and a tremendous variety of other organs
and processes.
The quality of protein intake is important because
different proteins supply essential amino acids in different proportions.
Given an adequate intake of nitrogen, the human body can manufacture
10 of the 18 amino acids from glucose. The remaining 8 amino acids
(threonine, valine, tryptophan, isoleucine, leucine, lysine, phenylalanine,
and methionine) be manufactured by the body and must be acquired
through dietary sources. Thus, they are termed essential amino acids.
Proteins possessing equal proportions of all essential amino acids
in relatively abundant quantities are often termed "complete".
Despite this suggestive label, good nutrition need not depend on
upon so-called "complete" proteins because non-complete
proteins in complementary combinations can readily complete spectrum
of essential amino acids. The present method of rating the completeness
of protein is known as the PDCAAS (Protein Digestibility Corrected
Amino Acid Score).
Protein deficiency can lead to symptoms such as fatigue,
insulin resistance, hair loss, loss of hair pigment that should
be black becomes reddish), loss of muscle mass proteins repair muscle
tissue, low body temperature, and hormonal irregularities. Severe
protein deficiency, encountered only in times of famine, is fatal.Excess
protein can cause problems as well, such as causing the immune system
to overreact, liver dysfunction from increased toxic residues, bone
loss due to increased acidity in the blood and foundering in horses.
The assumption high protein diets are bad for bones came from the
fact that calium excretion is increased when dietary protein intake
is increased. However, it has recently been shown that uptake of
calcium by the intestine is also increased and as long as calcium
intake is maintained, high protein intake may have benefits for
bone in older women [1].
Proteins can often figure in allergies and allergic
reactions to certain foods. This is because the structure of each
form of protein is slightly different, and some may trigger a response
from the immune system while others are perfectly safe. Many people
are allergic to casein, the protein in milk; gluten, the protein
in wheat and other grains; the particular proteins found in peanuts;
or those in shellfish or other seafoods. It is extremely unusual
for the same person to adversely react to more than two different
types of proteins.
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