User:Minxbrawl/sandbox2

Introduction
Proteins are made up of amino acids which connect by peptide bonds and form into polypeptide chains. There are four levels of protein organization: primary structure- the amino acid sequences; secondary structure- different types of folded shapes (ex: alpha helices and beta sheets); tertiary structure- includes all the different folding that happens on one polypeptide chain; quaternary structure- the combination of multiple polypeptide chains. (Note: not all proteins reach this fourth level of organization). A protein domain is a self contained protein unit that has it's own function within a protein and is folded in a tertiary structure.

A mosaic protein is protein that is made up of different protein domains, attributing to its multifunctionality; these proteins are in quaternary structure, as they are made up of multiple tertiary structured protein domains. The domains can be in different proteins, combining to create a diversity of proteins. These domains are have spread throughout the genome because they are mobile, which is why some domains can be found in a variety of proteins, even though they are seemingly unrelated. This also allows the domains to fold independently, and so they don't become deformed and unfolded in a new environment.

Development
All Proteins are transcribed and produced from blueprints in the cell, called genes. Mosaic proteins can be made when two adjacent genes are transcribed together and are therefore made into the same protein. This can benefit the protein because it makes the protein more stable and gives the protein a more complex function. For example, if the protein is an enzyme, it will be able to act more efficiently with its substrates.

Additionally, these proteins are most utilized outside of the cell membrane or on the outer side of membrane proteins. This suggests that these multifunctional proteins played a part in the development of multicellular organisms.

Examples
There are many studies comparing different mosaic proteins and their functional domains, trying to understand protein families and the overall functions of different proteins. For example, SpCRL and SpCRS proteins in sea urchins have a variety of functional domains that are also found within other proteins in the animal. By making comparisons, scientists can understand the complex roles these proteins play. Also, scientists are using the concept of mosaic proteins to improve vaccine function. Vaccines are injections of weak germ cells into the body that stimulate the body to produce antibodies specific to that germ. This ensures that the body will build an immunity, and that next time the germ is introduced, it will be more equipped to fight it off. Mosaic proteins of the germs can be designed in order to maximize antibody production and quality.

Annotated Bibliography
1."What are Protein Domains?"

-The specific author is not listed, but the website is associated with the European Molecular Biology Laboratory

The Domain of a protein is a self contained polypeptide chain with it's own function within a protein.

2. "Detection of mosaic protein mRNA in human astrocytes"

-VM Avery, DL Adrian, and DL Gordon, are the co-authors. They are from the Department of Microbiology and Infectious Diseases, Flinders Medical Centre, Bedford Park, South Australia, Australia

A mosaic protein is made up of different functional parts. They can have a variety of functions and different functional domains can be present in different proteins to create that diversity.

3. "Two cDNAs from the purple sea urchin..."

-Written by Multerer, K.A. & Smith, L.C who are Immunogenetics.

Gives examples of mosaic proteins: Two different genes in sea urchins SpCRL and SpCRS, have protein domains that are also found in other proteins within the animal. By comparing these domains to those of other proteins, it is possible to learn more about the proteins' overall functions.

4."Mosaic Explanation"

-Vaccine design paper (Fischer et al. 2007): Nature abstract or PubMed abstract (not exactly sure what this means).

Another definition of mosaic proteins is that they are artificially made proteins that use different protein domains as a template. These proteins are made for use in vaccines in order to maximize the body's immunity to a specific organism or disease. Making vaccines with these types of proteins will help the body make more efficient antibodies.

5."Vaccine Basics"

-Sources from the Centers for Disease Control and Prevention.

Vaccines are injections of weak germs which are not so harmful to the body but will stimulate your body onto making anti-bodies. These antibodies will be 'remembered' and so next time the body faces that same disease, it will be more equipped to fight it.

6. Essential Cell Biology

-Alberts- PhD from harvard and is chair in Biochem and Biophysics at UCSF, Bray- PhD form MIT and teaches at University of Cambridge, Hopkin- PhD in Biochem from Albert Einstein College of medicine, Johnson- PhD form Harvard, teaches at UCSF, Lewis- DPhil from university of Oxford, Raff- MD from Mcgill, Roberts- PhD from Cambridge, Walter- PhD from Rockefeller U in New york

Proteins are made up of polypeptides which are joined together via peptide bonds. These polypeptide chains fold up base on the non-covalent bonding relationships between the R groups in the amino acids. The structure has 4 stages: primary, secondary, tertiary, and quaternary.

7. Traut

-Thomas Traut- professor of Biochem and biohysics at UNC school of medicine

Proteins are transcribed from genes, and mosaic proteins, or proteins with multiple functions and domains, are transcribed when two separate genes that are adjacent on a chromosome combine. This can be beneficial to the proteins because it adds functions. For example, if the protein is an enzyme, it will be able to interact more efficiently with and substrates. It can also make the protein a more stable structure on the whole.

8." Directed Evolution of Proteins by Exon Shuffling"

-Joost A. Kolkman & Willem P.C. Stemmerarticle- published in nature biotechnology journal

Each of the different domains in the mosaic proteins contribute a different part to the overall function of the protein. Some domains get to be combined in different proteins because they are mobile. Their ability to fold on their own prevent proteins from being deformed. Most of the mosaic proteins are used for activity either outside of the cell or on the outer side of the cell membrane. This suggests that these multifunctional proteins played a part in the development of multicellular organisms.