Proteins are chains of amino acids.
Proteins have many important functions in cells.
Proteins are made of amino
acids, in long chains (polymers).
|A chain of amino acids; each amino
acid is represented by a red ball. The different amino acids shown are
Proline (Pro), Lysine (Lys), Phenylalanine (Phe), etc.
||A structural representation of a chain
of amino acids. Actual proteins are considerably larger, typically consisting
of hundreds or thousands of amino acids.
A short chain of amino acids is referred to as a peptide (or oligopeptide);
a long chain of many (hundreds or thousands) amino acids is referred to
as a polypeptide.
Each cell makes thousands of different KINDS of proteins.
Different kinds of proteins are composed of a different sequence
of amino acids.
For example, the first six amino acids in actin (a protein involved in
muscle contraction and the cytoskeleton) are: Methionine, then cysteine,
then aspartic acid, then asparagine, then asparagine, then valine.
The first six amino acids in beta-globin (part of hemoglobin, the protein
that transports oxygen in our blood) are: Methionine, then valine, then
glutamine, then leucine, then serine, then serine.
Proteins typically consist of MANY amino acids. For example, actin consists
of more than 300 amino acids. A complete hemoglobin molecule has around
600 amino acids. A single antibody molecule (part of the immune system)
contains about 1,400 amino acids or more.
The SAME protein consists of the SAME sequence of amino acids. For example,
if actin is a protein consisting of a chain of 376 amino acids, then EVERY
actin protein will be 376 amino acids long, and EVERY actin protein will
have the same amino acid sequence, starting with methionine, cysteine,
aspartic acid, asparagine, asparagine, and valine.
Proteins have up to four levels
Part of what makes a protein function the way it does is its particular
three-dimensional structure (shape).
The amino acid sequence of a particular protein determines its shape (also
The organization of protein structure is divided into four levels, called
primary, secondary, tertiary, and quaternary.
|The primary structure of a protein is
simply the sequence of amino acids.
The secondary structure of a protein is the initial arrangement
of the primary structure.
|Sometimes part of the amino acid sequence folds into a coil called
a helix. The diagram shows a model of the structure of a protein that contains
many helices (coils). The line (red and green) represents the amino acid
chain; it is coiled into numerous separate helices. EACH coil shown is
a separate unit of secondary structure.
|Sometimes part of the amino acid sequence folds into a sheet of parallel
strands. This diagrammed protein (a snake venom molecule) illustrates how
a long chain of amino acids (the grey and blue line) can form back-and-forth
rows called a sheet. Unlike the helices, the amino acid chain does NOT
form coils here.
|The complete protein may have some parts where the secondary structure
is a helix, and other parts where the secondary structure is a sheet. There
may also be sections where the secondary structure is neither helix nor
sheet (these sections are sometimes called random coil). Shown here is
a diagram of a special receptor on the surface of most human cells. The
protein has a "floor" of sheet structure and "sides" of alpha helix. The
shapes of the different parts of the protein form a groove (like a hot
dog bun); small molecules can bind within the groove. NOTE that each coil
and sheet is a separate region of secondary structure.
| In most proteins, once the secondary structure has formed, the
secondary structure is further arranged into clumps called tertiary
structure. Several examples of tertiary structure are visible above
. Tertiary structure is simply the grouping of different separate secondary
structures, such as multiple helices or multiple sheets or a combination
of helices and sheets.
|Quaternary Stucture: Some complete proteins actually consist
of more than one separate polypeptide (long chain of amino acids). For
example, hemoglobin consists of FOUR separate polypeptide chains - two
alpha-globin polypeptides plus two beta-globin polypeptide chains. When
multiple separate polypeptide chains are required to make the complete
protein, the protein has quaternary structure.
In summary, there are
up to four levels of protein structure:
||The amino acid sequence.
||Initial folding of the amino acid sequence into helixes and sheets.
||Arrangements and groupings of the secondary structure into clumps.
||Arrangement of separate tertiary structures, when multiple amino acid
chains are required to make a single protein.
Protein structure can
Protein primary structure
is strong and stable, because the amino acids are connected to each other
by covalent bonds.
Secondary, Tertiary, and Quaternary structure in proteins are held together
primarily by hydrogen bonds
and other weak interactions.
Small changes in structure often happen during protein functioning. In
other words, proteins can change shape. In fact, this is how many proteins
do their jobs: by moving and changing shape. For example, some enzymes
attach two substrate molecules by flexing and literally smashing the two
substrate molecules together to make a product. The particular shape of
a protein is sometimes called its conformation.
If all of the hydrogen bonds break at the same time, the protein can completely
unravel. If this happens, the protein will lose all structure except for
the primary structure. When a protein loses its structure, it is denatured.
You've probably conducted experiments in protein denaturation at home.
When eggs cook, the proteins denature, and because they are unable to re-form
the correct secondary and tertiary structure, the process is irreversible
(cooked eggs don't revert back to the liquid state when they cool). Some
proteins CAN correctly reverse the denaturation process by themselves.
An example is gelatin: you can melt Jello, let it solidify, remelt it,
and re-solidify it as many times as you want.
Allosteric Modification: The
function of some proteins is regulated by causing a conformation
change - causing a change in the three-dimensional shape of the protein.
For example, sometimes an enzyme
is activated (or inactivated) if some regulatory molecule binds to the
enzyme. When the regulatory molecule binds, it causes the enzyme to change
shape, causing it to gain (or sometimes to lose) its function. Sometimes
a protein can be turned "off" or turned "on" when a molecule binds and
causes a change in shape.
Types of Proteins: There are many different kinds of proteins in
cells. They perform a variety of functions in cells. All proteins, however,
consist of chains of amino acids arranged into secondary, tertiary, and
perhaps quaternary structure.
Enzymes - proteins that enable specific chemical reactions
to occur, such as conversion of starch to glucose. Most enzymes only catalyze
ONE kind of chemical reaction. For example, the eight chemical reactions
of glycolysis (breakdown of glucose to pyruvate) each require a
different kind of enzyme.
Transporters - Proteins that help other molecules move into
or out of cells.
Movement - Proteins move molecules within cells, and help cells
and organisms move through the world.
Structural - Proteins give cells their shape, and help the
cells of multicellular organisms stay attached. In humans, hair and nails
are mostly protein.
Other Proteins - have specialized functions. Many hormones are small
proteins. Many bacterial toxins (molecules that are released by the bacteria,
causing disease symptoms) are also proteins. Some proteins, such as receptors,
are involved in transmitting information into the cell from the outside.
Where do proteins come from?
Proteins are made by ribosomes, in the process of protein
synthesis, also called translation.
The instructions for protein synthesis - the code for the correct
order and number of amino acids for each protein - is contained
in the DNA (in the genes,
on the chromosomes).
In fact, this is a main function of the genetic material - to store the
instructions that allow the cell to make proteins.
I. The Chemistry of Life
A. The Basic Chemistry of Biology
II. The Cell
B. The Molecules of Biology
1. Water - Structure and properties,
hydrogen bonding, hydrophilic and hydrophobic, diffusion, osmosis.
2. Amino Acids and Proteins; Protein structure, conformation,
and allosteric modification (you are here).
3. Sugars and Polysaccharides
4. Nucleotides and Nucleic Acids
5. Lipids and Membranes (general
information; more detail on membranes)