beta-chains -- Hemoglobin is made up of 4 parts, each of which is referred to as a "chain". The four chains consist of two identical chains referred to as "alpha" and two other identical chains referred to as "beta".
CLUSTAL-W -- This is a tool on the Biology Workbench that is used to align a group of protein sequences by their common elements so that they can be compared.
energetically favored -- Energetically favored is a term that refers to whether two molecules or amino acids are likely to stay near each other. To simplify thermodynamics, the amino acids that are hydrophobic (don't like water) try to associate with each other because they are not charged while water is charged. This is why cooking oil and water do not mix. The hydrophobic oil trys to stick to itself and get away from the water. The oil staying in droplets on the water is energetically favored, but the oil mixing with the water is NOT energetically favored.
glutamate -- Glutamate is one of the 20 amino acids found in biological organisms. Its three letter abbreviation is Glu, and its single-letter designation is E. Glutamate is has an acidic side chain, which means that at the pH in the body, it is negatively charged. The charge on glutamate means that it likes to be associated with water or other amino acids that have charges.
heme -- Heme groups are the part of hemoglobin that actually bind the oxygen molecules. Each heme group contains an iron atom that is held in the center of the heme. The iron is responsible for the oxygen-binding activities of hemoglobin.
hydrophobic -- The word hydrophobic can be broken into is two halves- hydro- which means water, and phobic- which means afraid. A hydrophobic amino acid is one which does not like to be near water. It avoids water by associating with other hydrophobic amino acids. Hydrophobic amino acids do not have charges. Hydrophilic amino acids (philic- means love) do like to be associated with water, and do have charges. An example of a hydrophilic amino acid is glutamate.
leucine -- Leucine is one of the 20 amino acids found in biological organisms. Its three letter abreviation is Leu and its single-letter designation is L. Leucine is very hydrophobic, so it will try to associate with other hydrophobic amino acids, such as phenyalanine or valine, in the case of sickle cell anemia.
MSA-SHADE -- This tool is found on the Biology Workbench and can be used on aligned groups of proteins (see CLUSTAL-W) to determine their similarities. It produces a color-coded output of the protein sequences. Green is for amino acids that are the same (conserved) in all the proteins examined. Yellow is for amino acids that are the same in nearly all protiens and purple means that the amino acid has the similar structure and charge but is a different amino acid.
phenyalanine -- Phenylalanine is one of the 20 amino acids found in biological organisms. Its three letter abreviation is Phe and its single-letter designation is F. Phenyalanine is highly hydrophobic, so it will try to associate with other hydrophobic amino acids, such as leucine or valine, in the case of sickle cell anemia.
PIR -- The Protein Infomation Resource (PIR) database is useful for finding resources and amino acid compositions for different proteins. PIR can be accessed through the Biology Workbench SRS Databank Search.
quaternary structure -- For proteins, there are 4 levels of structure. The first, primary structure, is composed of the amino acid sequence. The secondary structure is how the amino acids next to each other in the sequence are organized. The tertiary structure is the folded 3-D structure of the protein that allows it to perform its functions. The quaternary structure is the total protein structure that is made when all the subunits of the protein are in place.
Rasmol -- This is a molecular modeling program that was written by Roger Sayle. It is a free program. 3-D coordinates for visualizing proteins can be found in the PDBFINDER database on the Biology Workbench. Tutorials on using Rasmol can be found at http://www.umass.edu/microbio/rasmol/rastut.htm
SRS Database Search -- The SRS Search is a feature of the Biology Workbench that allows the user to find information on a topic of interest, using specific databases that may be useful. For example, if one is looking for three dimensional protein structures, the PDBFINDER (Protein Databank) database is useful.
stabilize -- The amino acids in a protein form associations with each other that try to keep hydrophobic amino acids together and separate them from the water and hydrophilic amino acids. If a hydrophobic amino acid such as valine were surrounded by water, this would be a very unstable structure. So the valine amino acids try to stay away from the water by associating with other hydrophobic amino acids such as phenylalanine and leucine.
SWISSPROT -- This is a database in Switzerland that stores the amino acid sequences that make up different proteins. SWISSPROT can be accessed through the Biology Workbench SRS Databank Search.
tetramer -- A tetramer is a protein made up of four subunits.
valine -- Valine is one of the 20 amino acids found in biological organisms. Its three letter abreviation is Val and its single-letter designation is V. Valine is one of the smallest amino acids and is also uncharged. Since it is uncharged, it is hydrophobic, which means it does not like to be near water. It would rather be associated with other hydrophobic amino acids.
wireframe -- This is a type of visualization in Rasmol. It consists of a drawing of the protein using a wireframe for the amino acids in the protein.