What is a Protein?

What is a Protein?


Proteins play countless roles throughout the
biological world. Some transport nutrients throughout the body. Some help the chemical reactions happen at
a faster rate. Others build the structures of the living
things. Despite this wide range of functions, all
proteins are made out of the same 21 building blocks, called amino acids. Amino acids are made of carbon, oxygen, nitrogen,
and hydrogen, and some contain sulfur atoms. Selenocysteine is the only standard amino
acid that contains a selenium atom. These atoms form an amino group, a carboxyl
group, and a side chain attached to a central carbon atom. The side chain is the only part that varies
from amino acid to amino acid and determines its properties. Hydrophobic amino acids have carbon-rich side
chains, which don’t interact well with water. Hydrophilic or polar amino acids interact
well with water. Charged amino acids interact with oppositely
charged amino acids or other molecules. Primary Structure
The primary structure of a protein is the linear sequence of amino acids as encoded
by DNA. The amino acids in a protein are joined by
peptide bonds, which link the amino group of one amino acid to the carboxyl group of
another. A water molecule is released each time a bond
is formed. The linked series of carbon, nitrogen, and
oxygen atoms make up the protein backbone. These protein chains often fold into two types
of secondary structures: alpha helices, or beta sheets. An alpha helix is a right-handed coil stabilized
by hydrogen bonds between the amine and carboxyl groups of nearby amino acids. Beta-sheets are formed when hydrogen bonds
stabilize two or more adjacent strands. The tertiary structure of a protein is the
three-dimensional shape of the protein chain. This shape is determined by the characteristics
of the amino acids making up the chain. Many proteins form globular shapes with hydrophobic
side chains sheltered inside, away from the surrounding water. Membrane-bound proteins have hydrophobic residues
clustered together on the outside, so that they can interact with the lipids in the membrane. Charged amino acids allow proteins to interact
with molecules that have complementary charges. The functions of many proteins rely on their
three-dimensional shapes. For example, hemoglobin forms a pocket to
hold heme, a small molecule with an iron atom in the center that binds oxygen. Two or more polypeptide chains can come together
to form one functional molecule with several subunits. The four subunits of hemoglobin cooperate
so that the complex can pick up more oxygen in the lungs and release it in the body. Different visual representations of proteins
can give us visual clues about the protein structure and function. This space filling diagram shows all atoms
that are making up this protein. This representation, called ribbon or cartoon
diagram shows the organization of the protein backbone and highlights the alpha helices. This surface representation shows the areas
that are accessible to water molecules. Most proteins are smaller than the wavelength
of light. For example, the hemoglobin molecule is about
6.5 nanometers in size. Hemoglobin is found in high concentration
in red blood cells. A typical red blood cell contains about 280
million hemoglobin molecules. The three-dimensional shapes of proteins determine
their function. The flexible arms of antibodies protect us
from disease by recognizing and binding to pathogens and targeting them for destruction
by the immune system. The hormone insulin is a small, stable protein
that can easily maintain its shape while traveling through the blood to regulate the blood glucose
level. Alpha Amylase is an enzyme that begins digestion
of starches in our saliva. The calcium pump is aided by magnesium and powered by ATP to move calcium ions back to the sarcoplasmic reticulum after each muscle contraction. Ferritin is a spherical protein with channels
that allow the iron atoms to enter and exit depending upon organism’s needs. On the inside ferritin forms a hollow space
interior with atoms attached to the inner wall. Ferritin stores iron in the non-toxic form. Collagen forms a strong triple helix that
is used throughout the body for structural support Collagen molecules can form elongated fibrils
which aggregate to form collagen fibers. This type of collagen is found in skin and
tendons. Learn more about the functions and 3D structures
of proteins and other molecular machines at the RCSB Protein Data Bank.