Sunday, February 19, 2006

Enzymes: Come together, right now, over me.

Definition of an enzyme: Any of numerous proteins or conjugated proteins produced by living organisms and functioning as biochemical catalysts. Enzyme names almost all end in "-ase".

Definition of Catalyst: a substance that decreases the required activation energy to increase the reaction rate. Chemical composition of a catalyst is not altered by the reaction and thus a single catalyst molecule can be used over and over again.

Definition of Kinase: Any of various enzymes that catalyze the transfer of a phosphate group from a donor, such as ADP or ATP, to an acceptor. Kinases alter the shape of acceptor proteins and this change in shape changes which binding sites on the protein molecule are exposed and which other proteins are able to bind with the available sites.

Some key concepts:
Allosteric Enzymes
Conformational Change in Protein

From Enzymes are life's catalysts:
Tears convey happiness, or sadness, but they do something else as well, and exactly what was accidentally discovered in the early 1900s. A bacteriologist by the name of Alexander Fleming happened to create an inadvertent experiment when a teardrop fell into one of his bacteria cultures. It set the stage for our modern understanding of how cell processes are controlled.

Many years later the chemical in tears was isolated and described. It was an enzyme -- now called Fleming’s Lysozyme. Lyse means to break apart, zyme means enzyme.

We now know how Flemming’s Lysozyme works. First, like all enzymes, it’s a protein, a huge molecule built from a perfectly ordered assemblage of amino acid building blocks. Its chemical structure fits molecules in the bacterial cell wall like a lock and key, and once the enzyme locks on, the bacterium’s cell wall comes apart.
Enzymes often aren’t assembled by your cells until they are needed for a specific job. How does a cell know when turn on a gene for making a particular enzyme?

We know something about this turning-on of genes from experiments with bacteria. The selected subject for study: yogurt.

Yogurt is really milk, processed by some friendly bacteria. Breaking down the milk is accomplished by specific enzymes the bacteria produce.

Bacteria break down milk sugar, lactose, using an enzyme they produced called galactosidase.

When there is no lactose around the bacteria don’t bother making galactosidase, but if they encounter molecules of lactose, they start producing the enzyme.

On the bacterium’s DNA is the gene for the galactosidase enzyme. The gene has a start signal. Hanging on to it is a protein called a repressor. The repressor’s molecular structure recognizes the lactose molecule.

When a lactose molecule bonds on, the repressor releases its grip. RNA polymerase can then slip in and transcribe the galactosidase gene. Soon the bacterial ribosomes are turning out enzymes that will break down the lactose into something the bacterium can use. In the process the bacteria create a tasty treat for us.

Biology online's Enzymes and Chemical Reactions:Metabolism consists of synthesis (anabolism) and breakdown (catabolism) of organic molecules required for cell structure and function.
Chemical reactions involve: (1) the breaking of chemical bonds in reactant molecules and (2) making of new chemical bonds to form product molecules. Energy is either added or released as heat during chemical reactions.

Enzymes are protein catalysts. (A few RNA molecules also possess catalytic activity). In an enzyme-mediated reaction, an enzyme binds to reactants (substrates) to form an enzyme-substrate complex, which breaks down to release products and the enzyme. The region of the enzyme to which the substrate binds is called the active site, the shape of which determines the chemical specificity of the enzyme.

Reversibility of a Reaction: Energy released during a reaction determines reversibility of a reaction. Greater the energy released during a reaction, smaller is the probability of product molecules obtaining this energy and undergoing the reverse reaction to reform the reactants. In such a case, ratio of product to reactant concentration will be large and the reaction will tend to be irreversible.
In a reversible chemical reaction, rate of forward reaction decreases and rate of reverse reaction increases as the reaction progresses until the two are equal in a state called the chemical equilibrium, at which point there is no further change in the concentration of reactants and products.

Substances that bind to enzymes to alter their conformations and make them active. Some cofactors are trace elements. In cases where the cofactor is an organic molecule, it is called a coenzyme. Coenzymes are derived from vitamins.

From the National Science Teachers SciLink website: Vitamins are organic molecules that function in a wide variety of capacities within the body. The most prominent function is as cofactors for enzymatic reactions. The distinguishing feature of the vitamins is that they generally cannot be synthesized by mammalian cells and, therefore, must be supplied in the diet.

The Chemical level of Organization

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