Proteins are the machines that drive cells and, ultimately, organisms.
Proteins are composed of individual units called
amino acids.
Amino acids
all share a similiar structure. The difference between them is the
so-called "R" group. The "R" group is the cluster of atoms that give
an amino acid its particular characteristics.
Amino acids are strung together in particular sequences; a given sequence will fold up into a specific structure. If each amino acid is given a code letter (for example, leucine is "L"), then a protein sequence resembles a written word or sentence (for example, using the symbols for the amino acids some proteins spell words like "Elvis"). Some of the databases you will learn to use are meant to look for different protein sequences and to discover similarties between proteins. These are called BLAST and FASTA searches, respectively.
While an amino acid is a letter in the sequence of the protein, in the structure each amino acid letter is actually a piece of a three-dimensional jigsaw puzzle. The relationship between amino acids and protein structure can be seen by looking at a picture of two amino acids connected to form a dipeptide.
Two amino acids
connected to form a peptide.
Molecule courtesy of MacMolecule
Some of the databases you will learn to use (e.g. Swiss-Prot) show what the structures of different proteins look like.
Finally, each protein is not just a sequence and a structure, but is also a nanomachine that can perform a particular task. The letters determine the sequence, the sequence determines the structure, and the structure determines the task. For example, some proteins latch onto biochemical compounds and transform them into different compounds. These proteins are called enzymes. One such enzyme, lysozyme, is found in mucus and helps fight bacterial infections by selectively chopping bacterial cell walls into smaller fragments. Other proteins, such as insulin, are hormones. Insulin is secreted by the pancreas to stimulate the uptake of excess glucose by liver cells for conversion to glycogen. Some of the databases you will learn about (e.g. REBASE) describe the function of different protein machines.
By understanding how different proteins fold up and how they work, we can begin to understand how they work together to make up a cell. For example, scientists have recently determined what protein is damaged in the disease muscular dystrophy. Because the protein machine is damaged, both the cell and the organism are damaged. There is hope that if the damaged protein machine can be replaced by working proteins, then the onset or progression of the disease can be slowed or halted. The relationship between proteins and diseases is covered by some of the more specialized databases that you can find through this server.
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