Download Protein Synthesis

CIS Biology Team
Introduction
Proteins are probably the most important class of biochemical molecules. Proteins are the
basis for the major structural components of animal and human tissue. They also make up
many of the elements that are necessary for the body to function, such as enzymes and
antibodies. Some proteins are made in the cells of the body, while others can only be taken
in from food.
Protein Structure
Proteins are natural polymer molecules (molecules that consist of multiple subunits)
consisting of small units called amino acids. The number of amino acids in proteins may
range from two to several thousand.1 The amino acids are strung together in a linear chain,
as in this picture:
However, proteins do not usually look like a long linear chain. Rather, they commonly look
like a scrunched up mass of squiggles, like so:
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CIS Biology Team
The amino acids in the chain are held together by peptide bonds. As such, a chain of amino
acids is called a polypeptide chain. This will be further discussed in the amino acid structure
section.
It so happens that proteins have four different levels of structure. Primary structure is the
long, worm-like chain showed earlier; it is a sequence of amino acids held together by
covalent bonds.
The curling and folding of the polypeptide chains is called the secondary structure. An
polypeptide chain commonly organizes itself into either an alpha-helix or beta-pleated sheet.
These secondary structures are held together by hydrogen bonds.
In an alpha-helix, a protein chain is coiled like a loosely-coiled spring. The "alpha" means
that if you look down the length of the spring, the coiling is happening in a clockwise
direction as it goes away from you. This is a diagram of an alpha-helix, showing the individual
molecules of each amino acid:
The red ribbon running through the molecules in the diagram is merely there to help us
visualize the helix – it does not actually exist in real alpha-helices. The thin green lines in the
diagram represent the hydrogen bonds that hold the structure together.2
In beta-pleated sheets, the polypeptide chains are folded on top of each other, like so:
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In this diagram, strands A and B are anti-parallel: the two strands are in opposite
orientations. Strands B and C, however, are parallel: the two strands are in the same
orientation.3 Each strand created by the folding of the protein chain is held together by
hydrogen bonds, as indicated by the small green lines in the diagram. Because of the
structure of the protein chains, the layers of amino acid strands have a pleated appearance.
Tertiary structure is the entire three-dimensional structure of an polypeptide chain. The
alpha helices and/or beta-pleated sheets can fold over once more to form a
three-dimensional structure. The tertiary structure of a protein is what determines its
function (other than as food). If the tertiary structure of a protein is altered through either
mutation or some external force, it is considered denatured – it loses its ability to function
properly. For example, a denatured enzyme loses its catalytic powers, and a denatured
antibody can no longer bind antigen.
Here is an example of the tertiary structure of a protein:
As shown in the diagram, one protein can contain both alpha helices and beta-pleated
sheets in its structure.
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CIS Biology Team
Here is a review of the primary, secondary, and tertiary structures:
The final structure of proteins is the quaternary structure. This is the combination of two or
more polypeptide chains to form a complete unit. Some proteins are composed of identical
subunits (chains), while others exist as a singular polypeptide chain.
Amino Acid Structure
There 20 different amino acids that account for a vast array of chemical diversity. 10 of these,
called the nonessential amino acids, can be produced by the human body, while the other
10, called the essential amino acids, must be taken in through food. Failure to obtain
enough of even 1 of the 10 essential amino acids results in degradation of the body's
proteins—muscle and so forth—to obtain the one amino acid that is needed. Unlike fat and
starch, the human body does not store excess amino acids for later use—the amino acids
must be in the food every day. Plants, on the other hand, cannot take in proteins from food,
and thus are able to make all 20 amino acids.4
Amino acids have a two-carbon bond. One of the carbons is part of a group called the
carboxyl group. A carboxyl group is made up of one carbon (C), two oxygens (O), and one
hydrogen atom (H). The carboxyl group is acidic. The second carbon is a part of the amino
group. Amino means there is an NH2 group bonded to the carbon atom. One side of the
molecule is negatively charged and one side is positively charged because, in amino acids,
one hydrogen atom moves to the other end of the molecule. An extra "H" gives you a
positive charge. Behold, a diagram of an amino acid:
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CIS Biology Team
The side groups are what make each amino acid different from the others. Of the 20 used to
make proteins, there are three groups. The three groups are ionic, polar and non-polar.
These names refer to the way the side groups (sometimes called "R" groups) interact with
the environment.5 Ionic side groups are charged overall. Polar side groups have a slight
negative charge at one end and a slight positive charge at the other. Both ionic and polar
side groups are hydrophilic – they are attracted to water and tend to orient themselves in a
common direction due to their charge. Non-polar side groups, on the other hand, have little
to no charge and are hydrophobic – they are pushed away from water by the hydrophilic
side groups, giving the appearance that they repel water. Hydrophobic side groups do not
orient themselves in any particular direction.
As mentioned earlier, amino acids in a polypeptide chain are held together by peptide bonds.
A peptide bond is a covalent bond that is formed between two molecules when the carboxyl
group of one molecule reacts with the amino group of the another molecule, releasing a
molecule of water. This is called a condensation reaction and usually occurs between amino
acids. The resulting CO-NH bond is called a peptide bond, and the resulting molecule is an
amide.
A peptide bond can be broken down by hydrolysis (the adding of water). The peptide bonds
that are formed within proteins have a tendency to break spontaneously when subjected to
the presence of water. This process, however, is very slow. Living organisms use enzymes to
broken down or to form peptide bonds.6
Finally, the hydrogen bonds that hold a protein together in secondary structure naturally
occur between the C=0 and H-N. This makes such structures incredibly stable.
This concludes the section on proteins.
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CIS Biology Team
Bibliography
1.
"Proteins." Elmhurst College: Elmhurst, Illinois. N.p., n.d. Web. 21 June 2011.
<http://www.elmhurst.edu/~chm/vchembook/565proteins.html>.
2.
"Protein structure." chemguide: helping you to understand Chemistry - Main Menu.
N.p., n.d. Web. 22 June 2011.
<http://www.chemguide.co.uk/organicprops/aminoacids/proteinstruct.html>.
3.
"Protein beta-pleated sheets." The Molecular Biology Notebook Online. Rothamsted
Research, n.d. Web. 22 June 2011.
<www.rothamsted.bbsrc.ac.uk/notebook/protalbeta.htm>.
4.
"Amino Acids." The Biology Project. N.p., n.d. Web. 22 June 2011.
<http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aa.html>.
5.
"Chem4Kids.com: Biochemistry: Amino Acids." Rader's CHEM4KIDS.COM. N.p., n.d.
Web. 23 June 2011. <http://www.chem4kids.com/files/bio_aminoacid.html>.
6.
"The Peptide Bond." Peptide Guide. N.p., n.d. Web. 24 June 2011.
<http://www.peptideguide.com/peptide-bond.html>.
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