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Unicellular Organisms

Proteins and Enzymes

Protein Mis-folding It is known that even if the gene can code a correct sequence of amino acids and the ribosome can translate the coding without error, the resulting protein can misfold and cause serious problem for the organism. As shown in Figure 11-28a, it seems that the repulsion between some key residues (a recurring unit in a polymer chain such as the amino acid in protein) such as the hydrophobic and polar residues is essential to establish a rudimentary native-like architecture (the saddle point in the diagram). Once the correct topology has been achieved, the native structure (the natural conformation of a protein) will then almost invariably be generated during the final stages of folding. There are molecular chaperones in the cell to weed out the misfolded proteins as shown in Figure 11-29a. Failure of this quality-control system entails a variety of diseases including cancer, diabetes, BSE, cystic fibrosis, Alzheimer, and Parkinson. These "protein-misfolding diseases" share the common pathological feature of aggregated misfolded protein deposits.

Figure 11-29a Protein Misfolding [view large image]

A strand of RNA such as the rRNA also trends to fold into a structure similar to a protein. This ability of the RNA has inspired the hypothetical RNA world in considering the origin of life. Such feat originates from the oxygen in the 2' position of the 5-carbon ribose that allows hydrogen bonding with another hydrogen in the sequence (Figure 11-29b,a). The DNA lacks such feature because the "deoxyribose" removes the oxygen in that place. The single-strand RNA can fold up to various shapes, depending on the sequence of its bases (see rRNA secondary structure in
RNA Folding Figure 11-29b,b). The three-dimensional structure is the result from hydrogen bonding between the complementary bases and between other bases [Figure 11-29b,c - rRNA in dark blue (small subunit) and dark red (large subunit); lighter colors represent ribosomal proteins.]. These forces twist the strand into a partial double helix with a tertiary structure. When certain strategic bonds are broken, this usually stable structure untwists to a one-dimensional form, which is more suitable for information transfer.

Figure 11-29b RNA Folding [view large image]

An enzyme is a special kind of protein that accelerates chemical reaction while retains its own structure. A chemical reaction is about two molecules coming together and altering their structures. Firstly they need a chance to approach each other, the frequency of encounter depends on the concentration of the reactants. Then they should have enough kinetic energy to overcome the potential barrier (activation energy), this energy is related to the temperature. Finally, there is a special orientation of the reactants such that the reaction would proceed much faster, sometimes a million folds faster. Such favourable condition can be created with a special material called enzyme or catalyst. The enzyme forces the reactants into a position most suitable to run the reaction. The enzyme itself does not change and can be re-used repeatedly (Figure 11-29c,a).
Catalyses For inorganic chemical reactions, enzyme may not be necessary since the inorganic molecules have high degree of symmetry. For organic chemical reaction, the symmetry for the molecules involved is much lower or none at all; therefore, most chemical processes in life depend on the assistance of the enzyme.

Figure 11-29c Catalyses [view large image]

The action of ligand adopts the same lock and key concept. It is a molecule (not protein) that binds to a receptor on the cell membrane and induces a biological or chemical response within the cell (Figure 11-29c,b).

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