Tutor profile: Martin B.
Describe the primary, secondary, tertiary and quaternary structure of a protein, including the interactions involved in each one.
The primary structure of a protein consists of the polypeptide chain of amino acids, linked together by peptide bonds (bonds between the carboxyl group of one amino acid and the amino group of another amino acid). The secondary structure of a protein consists of the arrangement of the local segments of a protein into 3-D structures. The main structural arrangements are alpha-helices and beta-pleated sheets, though beta turns omega loops are also sometimes present. These are held together by hydrogen bonds which occur due to the interaction between the positively charged proton of one molecule and an electronegative atom in another molecule. The tertiary structure of a protein is the 3-D arrangement of the entire polypeptide chain. The shape of the 3-D structure is caused by interactions of the side-chains of the amino acids. The interactions leading to this structure are hydrogen bonds, disulfide bridges (covalent bonds between cysteine side-chains), salt bridges ( ionic interactions between positively and negatively charged parts of the protein), Van der Waals forces (weak interactions between temporarily charged atoms) and hydrophobic-hydrophilic interactions ( 'water-loving' and 'water-hating' amino acid side-chains interact in a way that leaves the 'water-loving' side-chains on the inside of a protein and 'water hating' side-chains on the outside). Finally, the quaternary structure of a protein is the final protein complex made up of all the protein sub-units (who have taken adopted their tertiary structure) coming together. Though many proteins have a quaternary structure there are some that do not.
Subject: Basic Chemistry
Explain what a mass spectrometer is and how it can be used to analyze the structure and elemental composition of a molecule.
A mass spectrometer is a machine used to produce charged particles known as ions from the chemical compounds that are being investigated. The compounds are introduced into a vacuum chamber where a beam of electrons is introduced into the source. Some of the electrons will collide with the molecules being analyzed resulting in the molecules themselves loosing electrons, hence becoming positively charged. Such collisions will sometimes lead to the dissociation of the molecules into different fragments. Through analysis of the atomic weight of the ionic fragments and their relative abundance a profile of the structure and composition of the molecule(s) in the sample can be built.
Some cancer cells have a receptor in their cell-surface membrane that binds to a hormone known as growth factor. This stimulates cancer cell division. What are monoclonal antibodies and how could they be used to prevent this stimulation and inhibit tumour growth?
Monoclonal antibodies are antibodies produce by identical immune cells all derived from a single parent cell. A monoclonal antibody could be produced that has a unique tertiary structure and hence a very specific bind site. This binding site would be complementary to either the cell-surface receptor of the cancer cell or to the growth hormone. The antibody would interact with/bind to the cell surface receptor or growth hormone and prevent binding of the growth hormone to the cell surface receptor.
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