Molecular Biology And Biochemistry Of The Cell Biology Essay

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Describe what is meant by the primary, secondary and tertiary structures of a protein and discuss the forces that stabilise the secondary and tertiary structures

A protein is a macromolecule, consisting of subunits called amino acids. A linkage at the amino end (NH ) to the carboxyl end (COOH) of another amino acid forms biochemical polymers as a result of a condensation reaction. The R group side chain distinguishes the amino acid from one another and gives the protein its three dimensional shape and stability.

Various proteins are involved in biochemical processes within the human body. These include membrane proteins and signalling such a keratin in hair and nails.

A protein folds into particular shapes under physiological temperatures and in an aqueous solution. It is the sequence of amino acids which determines the structure of the protein and its single stable shape is known as its native conformation, depending solely on weak interactions between the different residues bound to one another by bonds. Three of those structures will be explored in greater depth.

Primary structure

The primary structure consists of a linear sequence of amino acids. It contains a number of repeating parts forming a backbone or main chain. (Berg) The three dimensional shape is always displayed from the N-terminus to the C-terminus and have charged backbone groups. From this sequence we can depict a structure of all the amino acids giving it its unique functional properties. When two amino acids are joined together the result is a dipeptide but many joined together is called a polypeptide chain. The two chains are brought together by hydrolysis resulting in a water molecule being removed. The rate of hydrolysis is extremely slow, which makes the peptide bonds kinetically stable.

Almost all amino acids are chiral and only L-isomers are the constituents of proteins. An a-amino acid consists of a central atom and linked to this is an amino group, a carboxylic group, a hydrogen and an R group (side chain). Rotation around the C=O bond is not possible and where the R group occurs in both the cis and trans orientation, it appears that the trans configuration is more favourable as steric clashes between adjacent side chains is minimized for most amino acids (99.95% probability)...........

Secondary structure and forces that stabilises the protein

Two structures, α helix and β pleated sheet were discovered by two young scientists named Linus Pauling and Robert Corey in 1951. . Like Beta sheets,α helix (which is essentially a right handed helix) is stabilized by hydrogen bonds between the NH and CO groups in the peptide chain. Hydrogen bonding allows the two strands to be segmented together. One might expect, negatively charged anions to be at the amino terminal and the positively charged cations to be at the negatively charged end (the carboxyl-terminal end) . Hydrogen had a partial positive charge which is then, in turn, attracted to a negatively charged atom such as oxygen, known as an acceptor. Hydrogen must already be attached to a negatively charged atom to create a bond; thereby creating an electrostatic interaction. When the donor and acceptor are both fully charged, the bonding energy is significantly higher and the hydrogen- bonded ion pair is called a salt bridge (Petsko & Ringe,2004). All proteins contain a hydrophobic region which points into the interior and a hydrophilic region at the surface, which may have sugars attached. The interior region makes hydrogen bonds with one another which stabilises the secondary structure. . By rotating the structure, there are 3.6 residues per turn and each turn is about 5.4 A (paper reference) and the orientations of side chains are away from the centre of the helix. The α helix is rod-like or cylindrical and differs from the β sheet which is tightly coiled. There are two forms of the β sheet, antiparallel and parallel. The antiparallel structure occurs more frequently and has an adjacent chain connecting the NH and CO through hydrogen bonding. By contrast, the parallel structure β strands run in the same direction and one amino acid is connected with two on the other adjacent strand through hydrogen bonding also (Berg, 2006)

Another force which stabilises proteins are van der Waals interactions. It involves a temporary dipole, which attracts an induced dipole of opposite charge. It is a weak interaction and may make only a small contribution to the stability of proteins. (Horton et al, 2002)

The tertiary structure and forces that stabilise the structure

The resulting form of secondary structures forming a folded protein is called the tertiary structure. The secondary structure is stabilised by hydrogen bonding, whereas the tertiary structure is mostly stabilised by non-covalent interactions-usually the hydrophobic effect between the side chains of the amino acid residues. In addition, disulfide bridges which are covalent also have a role in the stability of the tertiary structure. Disulfide bridges are able to hold the two cysteine residues together and particularly in secondary structures. The disulfide bridges are able to stabilise the protein when water interacts with the bond.

Denaturation of proteins

Protein denaturation can happen with all classes of proteins, They have a low thermodynamic stability which means that they can be denatured. The most common types of reagents for protein denaturation are urea and guanidium ion. It is thought that they disrupt hydrophobic interactions, although the mechanism is no thoroughly understood.

Post translational modification

Glycosylation is the process of addition of carbohydrates groups to specific amino acids of the protein. It can play a vital role in the physical properties such as the stability and solubility of a protein without altering the structure. It is believed that to be involved in the evasion of the immune system .For example O-Glycosyltion of threone (T) and serine (S).

In conclusion, there seems to be a range of significant forces that stabilise protein structures, providing structure to the protein, such as hydrogen bonding. We have examined the different arrangements in proteins and how they might be stabilised by these bonds. In addition, we have mentioned the reactions that happen between them. However, there also appears to be detriments to the protein structure, altering the stability of the protein. Overall, proteins are thought to be highly significant in life itself.

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