WHAT IS PROTEIN?

Proteins are nature’s most important molecules and are present in all living
beings. The human body consists mostly of proteins of different structures,
dynamics and functions. Oxygen is transported to the human cells by
hemoglobin, a multidomain protein in complex with iron which coordinates the
oxygen molecule. The skin, the immune system, and muscle tissues are other
examples of protein arrangements essential to human life. The building blocks
of proteins are amino acids, small molecules mainly composed of carbon,
nitrogen, oxygen and hydrogen. There are 20 different amino acids with specific
properties that can be part of the protein structures. The sequence of the amino
acids is unique for each protein and determines its fold and the function.

PROTEIN’S STRUCTURE

The basic building blocks for polypeptides are small organic molecules called amino acids.
Amino acids can combine to form long linear chains known as polipeptides. Each type of
polypeptides chain has a unique amino acid sequence. Although a polypeptide must have the
correct amino acid sequence to perform its specific biological function, the amino acids sequence
alone does not guarantee that the polypeptide will be biologically active. The polypeptide must
fold into a specific three-dimensional structure before it can perform its biological functions.
Once folded into its biological active form, the polypeptide is termed a protein. Protein come in
various sizes and shapes. Those with thread-like shapes, the fibrous protein, tend to have
structural or mechanical roles. Those with sperichal shapes, the globular proteins, function as
enzymes, transport proteins, or antibodies. Fibrous proteins tend to be water-insoluble, while
globular proteins tend to be water-soluble.

The protein interior is usually composed of hydrophobic amino acids, which

thus avoid contact with the hydrophilic environment in the cell. At the protein
surface, polar and hydrophilic residues dominate, as they are attracted to the
polarity of the solvent. Charged amino acid side chains like those of Asp, Glu,
Lys and Arg are hydrophilic, whereas large non-charged residues such as the
aliphaticLeu, Ile and Val as well as the aromatic Phe, Tyr and Trp are
hydrophobic. The backbone of proteins, which includes the alpha carbons and
the peptide bond, is hydrophilic and is thus not favored in the hydrophobic core.
Nature has solved this problem by forming secondary structure elements from
the backbone, thus preventing their hydrophilic NH and CO groups from exposure towards the
hydrophobic surroundings. The two main secondary
structure elements, called -helix and sheet, are stabilized by hydrogen
bonding between residues that are non-adjacent in sequence.

Protein structure is the biomolecular structure of a protein molecule. Proteins are polymers —
specifically polypeptides — formed from sequences of amino acids. Each unit of a protein is
called an amino acid residue because it is the residue of every amino acid that forms the protein
by losing a water molecule. By convention, a chain under 40 residues is often identified as a
peptide, rather than a protein.[1] To be able to perform their biological function, proteins fold into
one or more specific spatial conformations, driven by a number of non-covalent interactions such
as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To
understand the functions of proteins at a molecular level, it is often necessary to determine their
three-dimensional structure. This is the topic of the scientific field of structural biology, which
employs techniques such as X-ray crystallography, NMR spectroscopy, and dual polarisation
interferometry to determine the structure of proteins.

Protein structures range in size from tens to several thousand residues.[2] By physical size,
proteins are classified as nanoparticles, between 1–100 nm. Very large aggregates can be formed
from protein subunits. For example, many thousands of actin molecules assemble into a
microfilament.

A protein may undergo reversible structural changes in performing its biological function. The
alternative structures of the same protein are referred to as different conformations, and
transitions between them are called conformational changes

Protein Function

We have seen that each type of protein consists of a precise sequence of amino acids that allows
it to fold up into a particular three-dimensional shape, or conformation. But proteins are not rigid
lumps of material. They can have precisely engineered moving parts whose mechanical actions
are coupled to chemical events. It is this coupling of chemistry and movement that gives proteins
the extraordinary capabilities that underlie the dynamic processes in living cells.
In this section, we explain how proteins bind to other selected molecules and how their activity
depends on such binding. We show that the ability to bind to other molecules enables proteins to
act as catalysts, signal receptors, switches, motors, or tiny pumps. The examples we discuss in
this chapter by no means exhaust the vast functional repertoire of proteins. However, the
specialized functions of many of the proteins you will encounter elsewhere in this book are based
on similar principles

All Proteins Bind to Other Molecules

The biological properties of a protein molecule depend on its physical interaction with other
molecules. Thus, antibodies attach to viruses or bacteria to mark them for destruction, the
enzyme hexokinase binds glucose and ATP so as to catalyze a reaction between them, actin
molecules bind to each other to assemble into actin filaments, and so on. Indeed, all proteins
stick, or bind, to other molecules. In some cases, this binding is very tight; in others, it is weak
and short-lived. But the binding always shows great specificity, in the sense that each protein
molecule can usually bind just one or a few molecules out of the many thousands of different
types it encounters. The substance that is bound by the protein—no matter whether it is an ion, a
small molecule, or a macromolecule— is referred to as a ligand for that protein (from the Latin
word ligare, meaning “to bind”).