Enzyme: Biological Catalysts

Enzymes are one of the most important forms of protein in every organism's metabolic processes. The purpose of enzymes is to speed up chemical reactions, and they are involved in almost all chemical reactions in a living organism.
The concept of enzyme is that they speed up reactions by lower the activation energy needed for that reaction but without being consumed by the reaction.

Each enzyme has its very own distinct molecules that fit into it, this molecules is referred  as the substrate. The binding site of the substrate is called the active site.

The Induced-fit Model











After the substrate binds to the active site, the enzyme will automatically change its shape to further assist in the chemical reaction. This enzyme-substrate interaction is called induced-fit model. The result is a enzyme-substrate complex,  where the chemical reaction is ready to take place. 

Inhibitors/activators
Certain enzyme will require either inorganic cofactors or organic coenzymes before they can function properly. These may bind to the active site or bind weakly with the substrate. Similarly, each enzyme has its own unique inhibitors/activators to control each enzyme activity. These chemicals can switch the enzyme between the active form/inactive form, and therefore regulating the rate of chemical reactions within a cell.

Competitive inhibitors - these inhibitors are similar to the substrate as they bind to the active site of the enzyme and therefore competing with the substrate.

 
Noncompetitive inhibitors - these inhibitors attach to another site of the enzyme and changes the shape of the enzyme, deactivating the enzyme.

Allosteric regulation- this is one method of the cell to control the rate of chemical reactions. Each enzyme has sites called allosteric sites some distance away from the active site. Binding an activator to the allosteric site will result in the stability of an enzyme in its active form. However, an allosteric inhibitor will stabilize the inactive form of the enzyme

Feedback inhibition- this is one of the major method a cell use to control its metabolic pathways. In a chain reaction, where the product of one reaction becomes the reactant of the next, the final product of the chain can act as an inhibitor that inhibits the activity of a enzyme earlier in the chain. Therefore, the increase in the concentration of products will result in the decrease in the rate of further reaction.

Macromolecules: Carbohydrates

Carbohydrates are used by organisms as an important energy source, as building materials, and also cell-to-cell identification and communication. Carbohydrates are carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio. Carbohydrates are organized into 3 groups, monosaccharides, oligosaccharides, and polysaccharides.

Monosaccharides 
These are the simplest form or sugars,they contain a single chain or carbon atoms with hydroxyl groups attached to each carbon. Monosaccharides can be formed with 3 carbons (triose), 5 (pentose), and 6 (hexose). Depending on the location of the carboxyl group, these are also categorized into aldehyde or ketone.

  

Ribose - a component of RNA

Ribulose - used in photosynthesis

Glucose - a source of energy for all cells

Galactose - a component of lactose, milk sugar

Fructose - fruit sugar

The 3 hexose sugars (glucose, galactose, and fructose) have the same chemical formula of C6H12O6, but different arrangement of atoms, these molecules are called isomers. Isomers may have the same atoms and chemical formula, but each containing its own physical and chemical properties.

Simple sugars with 5 or more carbon atoms forms a ring-shaped structure  when dissolved in water, the location of the hydroxyl group is therefore at random. Take glucose for example, if the hydroxyl group of carbon 1 ends up above the horizontal plane,   it is said to be beta-glucose. If the hydroxyl group is below the horizontal plane, the molecule is said to be alpha-glucose.

Oligosaccharides

These are sugars containing two or three monosaccharides attached to each other by covalent bonds called glycosidic linkages. 

The most important oligosaccharides are maltose, sucrose, and lactose.

  

Maltose - made by 2 alpha-glucose attached by a 1-4 glycosidic linkage. It is a disaccharide found in grains that is used in the production of beer. 

Sucrose - made from an alpha-glucose and an alpha-fructose attached by a 1-2 glycosidic linkage. Sucrose is the most common table sugar. It is used by plants to transport glucose and other simple sugars, and they are found in high concentrations in sugar cane, sugar beets, and sugar maple trees.

Lactose - a type of sugar found in milk, made by a glucose attached by a galactose.

Polysaccharides

These are complex carbohydrates (polymers composed of hundreds to thousands of monosaccharide monomers held together by glycosidic linkages). They serve as energy storage, and structural support in most organisms. 

1. Starch

This is the most significant type of energy storage in plants, they come in two different types amylose and amylopectin.

Amylose is a straight chain polymer of alpha-glucose with alpha 1-4 glycocidic linkage.

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Amylopectin are branched glucose chains with alpha 1-4 linkages and alpha 1-6 linkages. The branching makes amylopctin coils and insoluble in water. 

 

2. Glycogen

Humans store energy in the form of glycogen. Structure wise, glycogen is much like amylopectin but with much more branches. Small amounts of glycogen are found in human muscle and liver cells.

3. Cellulose
This is the major structural polysaccharide in plants, and a major component of cell walls. Unlike amylose, cellulose are a straight chain of beta-glucose held together by beta 1-4 glycosidic linkages. Adjacent cellulose chains are held together by hydrogen bonds, given them a strong structure.













4. Chitin 
This is the hard exoskeleton of insects and other animals such as crabs and lobsters, and other cell walls of many fungi. The monomer is a glucose to which a nitrogen-containing group is attached to the carbon 2 position.

Important Properties of Water

Water, in the form of H2O is probably the most important substances for all living organism on this planet due to its unique properties. To understand these properties, we must first understand some important terms in order to understand the following concepts.

Electronegativity - Assigned to each element, this represents the force of attraction an atom has to electrons. The larger the electronegativity number, the stronger the atom attracts the electrons of a covalent bond. Covalent bonds that have unequal sharing of electrons are said to be polar, and those evenly shared are non-polar. (only happens in covalent bonds)

van der Waals forces - these forces include London dispersion forces,dipole-dipole attractions, and hydrogen bonds. These forces are caused by the unequal sharing of electrons resulting in intermolecular bonds. These forces keeps molecules together in certain substances.

Universal Solvent

     Due to the reason that water is highly polar molecule, it has the ability to dissolve almost all polar materials. This is the most important reason why most organisms are mainly composed of water, its because water's ability to dissolve body's important materials and nutrients.

Cohesion 
    Water molecules have a special ability to attract one another. This is caused by the polar covalent bonding in the water molecule. The electrons shared in the water molecules stays relatively longer around the oxygen atom, and shorter around the hydrogen atoms, this is caused by oxygen's greater electronegativity. The oxygen is said to be electronegative, and the hydrogen atoms are electropositive. therefore, the oxygen of one water molecule attracts the hydrogen atom of a nearby molecule, forming an hydrogen bond.
This also results in a high surface tension in water, due to its cohesive force, many organisms can stay on the surface of water.

                                                           Adhesion
   Water can also "stick" to other polar materials by forming hydrogen bonds with them. An good example of this would be capillary action, where climbs up a narrow tube on its own. 



High Heat Capacity
      Water molecules have the ability to absorb large amounts of heat energy before its temperature would raise appreciably. Similarly, it also must lose a significant amount of heat before the temperature decreases. This ability allows organisms to keep a constant body temperature.

Density
     Water is most dense at 4 degrees Celsius, below/above 4 degrees, the hydrogen bonds between the V-shaped molecules spread the molecules apart, reducing its density. This property allows ice to float on water in the winter, also acting as an insulator, allowing aquatic organisms to live through winter.