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Unicellular Organisms

Proteins and Enzymes

Protein Protein Proteins commonly have 3 levels of organization in their structure (Figure 11-27), but they can combine to form the fourth level (Figure 11-28). The primary structure is the linear sequence of the amino acids joined by peptide bonds. Any number of the 20 different amino acids can be joined in any sequence (only a certain sequences are useful to the organisms). Any given protein has a characteristic sequence of amino acids.

Figure 11-27 Protein
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Figure 11-28 Quarternary Structure

The secondary structure of a protein comes about when the polypeptide chain takes a particular orientation in space. One common arrangement of the chain is the alpha helix, or right-handed coil, with 3.6 amino acids per turn. Hydrogen bonding between amino acids stabilizes the helix. Another type of secondary structure is known as the beta-pleated sheet. Such polypeptide chains are held together side by side by hydrogen bonds between the peptide chains. A protein can consist of alpha helix, beta-pleated sheet, or a mixture of the two types. The amino acids Alanine, Cysteine, Glutamic Acid, Glutamine, Histidine, Leucine, Lysine, and Methionine are found in alpha helix region; while Arginine, Aspartic Acid, Asparagine, Proline, Serine, and Valine are found in beta-pleated sheets.

The tertiary structure of a protein is its final three-dimensional shape. The tertiary shape of a protein is maintained by various types of bonding between the R groups. Covalent, ionic, and hydrogen bonding are all seen.

When two or more polypeptide chain interweave to form one molecule the protein has a quarternary structure.

The protein folds to the state of minimum energy. (See Figure 11-29a) Its sequence has to produce an unique configuration to be useful for living organism. The final shape of a protein is very important to its function. When proteins are exposed to extreme heat and pH, they undergo an irreversible change in shape called denaturation. The change occurs because the normal bonding between the R groups has been disturbed. Once a protein loses its normal shape, it is no longer able to perform its usual function.

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 11-29a, 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
Protein Folding Protein Misfolding 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 11-29b. 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 Folding
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Figure 11-29b Misfolding

A strand of RNA such as the tRNA also trends to fold into a structure similar to a protein or enzyme. This ability of the RNA has inspired the hypothetical RNA world in considering the origin of life. The single-strand RNA can fold up to various shapes, depending on the sequence of its bases. The three-dimensional structure results from hydrogen bonding between the complementary bases and between other bases. 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.

An enzyme is a special kind of protein that can accelerate chemical reaction while retaining 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 execute the reaction. The enzyme itself does not change and can be re-used again and again. 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.

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