Biology 001 Lab Report 2

Topics: Protein, Amino acid, Protein structure Pages: 12 (2721 words) Published: August 12, 2014

Separation of Proteins and Mass Analysis Using SDS PAGE
Biology 00-01L

This experiment consisted of separating proteins into polypeptides using a method called SDS PAGE which is a type of electrophoresis. The polypeptides had different masses, so each polypeptide traveled a different distance and this was an essential part of the lab which demonstrated that there exists a relationship between the distance traveled by the protein and the mass of the protein. This relationship was graphed and provided logarithmic function which could be used to find the size of an unknown protein just by measuring the distance that it traveled and plugging it to the equation. This is an important technique because the separation of proteins can reveal which polypeptides form the protein and identifying it can provide information on its purpose for its functionality and further scientific research in all types of fields such as the medical field. Introduction

Proteins are a large biological molecules that are made up of polypeptide chains. These chains connect to one another, but they are composed of smaller subunits called up amino acids. There exists 20 distinct amino acids which can be put together into sequences in the primary protein structure. In the secondary protein structure, the sequence of amino acids connect into a chain with the aid of hydrogen bonds and form repeating patterns of either beta sheet or alpha helix. In the tertiary structure, the patterns of amino acid chains combine to make a 3-dimentioal folding pattern and in the quaternary structure, these 3-dimentinal chains of amino acids combine to form a protein. Proteins are good to serve different functions in our bodies. For starters, proteins are able up act as enzymes that speed up reactions in our body. Proteins are also capable of serving as antibodies to help protect our bodies from being invaded by outside substances or organisms. They are also an important part of the nervous system because proteins receive and respond to molecular signals that come from inside or outside the organism. Proteins also serve as a boat that transports substances within the organism and they can also regulate how a gen will be interpreted. The protein serves these functions and many more.

In the laboratory experiment, proteins are denatured so that it is possible to see the primary structure of the protein. In order to achieve this, the process called electrophoresis is applied along with SDS PAGE. The way it works is by applying SDS (sodium dodecyl sulfate) to the protein and then placing the protein into the mini protean gel rig. The SDS has a negative charge due to the sulfate’s negative charge so when it is applied to the protein, the SDS provides an evenly distributed charge by mass to the protein. Then when the protein is placed into the well of the gel and then current is applied to the system -- this is the PAGE (polyacrylamide gel electrophoresis) stage -- the polypeptides move from away from the negative charge towards to positive charge and the proteins will move in proportion to their size (Dulai 2005). Since the proteins travel a distance that is proportional to their size, I predicted that the proteins with less mass will travel a longer distance than the proteins with more mass, which will travel a short distance. The proteins are moving because of the force which the electric field created by the current exerts of these negatively charge proteins. If the same force is applied to all proteins, then using Newton’s second law of thermodynamics , I can see that the proteins with a higher mass will have a lower acceleration, which means that there will be a smaller change in velocity, with then means that that there would be a smaller changer in distance traveled; the proteins with less mass will have a greater acceleration, which means that it will have a greater change in velocity, which then means that there would...

References: Davies, June L. Nature (1994) A Genome-wide Search for Human Type 1 Diabetes
Susceptibility Genes
Dulai, Kamal. UCLA (2005). Analysis of Protein Size and Subunit Composition Using
SDS- Polyacrylamide Gel Electrophoresis.
Lynch, Michael. Oxford Journals (2011). The Evolution of Multimetric Protein Assemblages
Wright, Caroline. Nature (2005). The Importance of Sequence Diversity in the Aggregation and
Evolution of Proteins.
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