Enzyme

      Enzymes are protein catalysts. A catalyst is a substance that speeds up a chemical reaction without being consumed in the process, and ready to catalyze the same reaction again. Although high temperatures can increase the reaction rate, proteins are denatured at high temperatures and cannot function properly any more. In order to speed up the chemical reactions in living cells at moderate temperatures, the protein catalyst enzymes are used to lower the activation energy (Ea) barrier. Enzymes may be grouped into complexes or incorporated into membranes, specific organelle, or cytosol within the cell.



enzymes only lower Ea



      The catalyst does not affect the free energy change of a reaction or the position of equilibrium, it can only decrease the potential energy level of the transition date, therefore, allow a greater proportion of colliding reactants to reach the transition state and become products.

      Substrate is the reactant that an enzyme acts on when it catalyzed a chemical reaction, and the location where the substrate binds to an enzyme is called active site. As the substrate enters the active site on the enzyme, its functional groups come close to the functional groups of a number of amino acids, then an interaction formed between these chemical groups and causes the shape of protein changes, this is known as the induced-fit model. Normally a substrate held in active site by hydrogen bonds and ionic bonds, and an enzyme-substrate complex is created. Active site can lower activation energy by acting as a template for substrate orientation, stressing the substrates and stabilizing the transition state, providing a favorable microenvironment, or participating directly in the catalytic reaction. After the reaction finished, the products are released, and the active site is available for new substrate. Different enzymes have different optimal temperatures and PH levels; the activity of enzyme is always affected by these two environmental factors. Some enzymes also require either nonprotein cofactors, such as zinc ions and manganese ions, or organic coenzymes such as NAD+, FAD+, and NADH.

     

       Enzyme-catalyzed reactions can be saturated, which means every enzyme is used to catalyze the reaction, and no free enzymes are available for more substrates. Therefore, a catalyzed reaction proceeds cannot increase indefinitely by increasing the concentration of the substrate.

     

      Regulation of enzyme catalyzed reaction:

Enzyme inhibition:

      Competitive inhibitors are substances that compete with the substrate for an enzyme’s active site. This process is reversible and can be overcome by increasing the concentration of the substrate. Noncompetitive inhibitors are substances that attach to a binding site on an enzyme other than the active site, causing a change in the enzyme’s shape and a loss of affinity for its substrate. Allosteric inhibitor is an example of noncompetitive inhibitor, a substance that binds to an allosteric site where is a receptor site and some distance from the active site on an enzyme, and stabilized the inactive form of the enzyme. Feedback inhibition is a method to control metabolic pathways allosterically, in which a product formed later in a sequence of reactions allosterically inhibits an enzyme that catalyzed a reaction occurring earlier in the process.

feedback inhibition

Enzyme activation:

      Enzymes can also be active by using of activators. Allosteric activator is a substance that binds to an allosteric site on an enzyme and stabilized the protein conformation that keeps all the active sites available to their substrates. Cooperativity is another type of allosteric activation, by binding one substrate molecules to active site of one subunit and locking all subunits in active conformation.



cooperativity



Nucleic acid

       Nucleic acids are informational macromolecules. They are used by all organisms to store hereditary information that determines structural and functional characteristics. They are the only molecules in existence that can produce identical copies of themselves.

DNA and RNA are nucleotide polymers. A nucleotide subunit in both molecules contains a nitrogenous base, a five-carbon sugar, and a phosphate group. The only difference between their monomers is DNA contains the sugar deoxyribose, whereas RNA contains ribose.

      

Nitrogenous base in DNA: A, G, C, T

      

Nitrogenous base in RNA: A, G, C, U

C, T, U are single-ringed pyrimidines, while A, and G are larger double-ringed purines.

A single nucleotide polymer is called a strand. Covalent bonds are formed between the phosphate group of one nucleotide and the hydroxyl group attached to the number 3 carbon of the sugar on the adjacent nucleotide. A phosphate diester bond forms as the result of a condensation reaction between two –OH groups.

DNA is double stranded. The two strands are hold together by hydrogen bonds between nitrogenous bases on adjacent strands, and they are said to run antiparallel.

A—T

G—C

RNA molecules coil into a helix, but remain single stranded.

ATP is another type of nucleotide, which is used to drive virtually all the energy-requiring reactions in a cell. The hydrolysis of ATP is usually coupled with an endergonic process that attached the inorganic phosphate group to another molecule directly associated with the work the cell needs to do.

Protein

Proteins are biochemical compounds consisting of one or more polypeptides folded into a fibrous or globular form. Proteins are coded by the genetic information on DNA.

There are 7 classes of protein:

Ø  Structural proteins (function in the cell membrane, muscle tissue, and the silk of spiders, fibers, and mammal hair.)

Ø  Contractile proteins (work with structural elements, provide muscular movement.)

Ø  Storage proteins (such as albumin, the main substance of egg white.)

Ø  Defensive proteins (antibodies)

Ø  Transport proteins (hemoglobin, which transport oxygen from lungs to other parts of the body.)

Ø  Enzymes (the most important class, promote and regulate the chemical reactions in the cell.)

Ø  Hormones (can act as chemical messengers such as insulin.)

Proteins are amino acid polymers folded into specific three-dimensional shapes. The functions are determined by the specific structural characteristics. An amino acid is an organic molecule, including a central carbon atom which is attached by an amino group, a carboxyl group, an H atom and a variable group of atoms called a side chain (R). There are 20 different amino acids which are different in their side chains.

*amino and carboxyl groups are ionized.

*since amino acids contain both acidic (carboxyl) and basic (amino) groups, amino acids are considered amphiprotic.

*amino acids may be polar, nonpolar, or acidic, basic, depending on the nature of their side chains.

*9 amino acids are considered essential: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

      

An amino acid polymer is called a polypeptide. The amide linkage that holds amino acids together in polypeptides are called peptide bonds. Peptide bonds are formed by a condensation reaction between the amino group of one amino acid and the carboxyl group of an adjacent amino acid.

1 A.A →a monomer;

2 A.As →dipeptide (has one bond);

Many A.As →polypeptides→protein molecule.

Primary protein:

       Primary protein is the unique sequence of amino acids in a polypeptide chain. The polypeptide chain will always have an amino at one end, called the amino terminus, and a carboxyl group at the other, called the carboxyl terminus. Each of the amino acids in a polypeptide is referred to as a residue. Primary structure is determined by the nucleotide sequence in a gene in DNA. Changing the sequence by one amino acid could alter the three-dimensional shape to the point that the protein loses function or is rendered useless.

Secondary protein:

Secondary protein contains coils and folds in a polypeptide caused by hydrogen bonds between hydrogen and oxygen atoms near the peptide bonds.

l  α helix: a type of polypeptide secondary structure characterized by a tight coil that is stabilized by hydrogen bonds.

i.e. keratin.

l  β-pleated sheet: polypeptide secondary structured that form between parallel stretched of a polypeptide and are stabilized by hydrogen bonds.

i.e. silk protein.

*α helix is more flexible than β-pleated sheet, and β-pleated sheet structure is stronger.

Tertiary protein:

Supercoiling of a polypeptide that is stabilized by side-chain interactions.

l  Hydrophobic and van der Waals interactions

l  Proline kink

l  Hydrogen bond

l  Disulfide bridge

l  Ionic bond

 

Quandary protein:

Two or more polypeptide subunits forming a functional protein.

i.e. Hemoglobin: composed of four polypeptides in tertiary structure: two identical α-chains and two identical β-chains. Each subunit has a nonproteinaceous heme group containing an iron atom that binds oxygen.

Protein denaturation:

Protein denaturation is a change in the three-dimensional shape of a protein caused by changes in temperature, PH, ionic concentration, or other environmental factors. A denatured protein cannot carry out its biological functions; all their five types of tertiary interactions are disrupted.

Use of protein denaturation:

Dangerous: prolonged fever above 39℃ could denature critical enzymes in the brain, leading to seizures and possibly death.

Useful: heat can be used to denature the proteins in hair, allowing people to temporarily straighten curly hair or curl straight hair.

Lipids and Fats

Lipid:

Lipid molecules are all hydrophobic since they contain fewer polar O-H bonds and more nonpolar C-H bonds. Lipids are used for storing energy and building membranes.

Fats:

Fats are formed by excess carbohydrate and store energy in both animals and plants. The most common fat is called triacylglycerol or triglyceride, which combined with a glycerol molecule and three fatty acids.

*Glycerol – three carbon alcohol.

*Fatty acid – long hydrocarbon chain containing a single carboxyl group.

Fatty acid can be either saturated or unsaturated. Saturated fatty acids only contain single bonds and make these fatty acids fit more closely together. (Like lard and butter.) Unsaturated fatty acids contain double bonds between carbon atoms, and make the fats in a form of liquid. (Like olive oil and sunflower oil.)

When a glycerol molecule reacts with three fatty acids, three –H atoms from the hydroxyl groups combined with three –OH from the carboxyl groups, and form three water molecules. The bonds between a glycerol and fatty acids are called ester bonds.

Phospholipids:

Phospholipids are made of one glycerol molecule, two fatty acids and a polar phosphate group. Since the phospholipids have both polar and nonpolar parts, they can form a bilayer and act as the main components in cell membrane. The hydrophilic head (polar phosphate group) can mix with water whereas the hydrophobic tails (nonpolar fatty acids) only can mix with each other in the center of bilayer.

Sterols:

Sterols contain four fused hydrocarbon rings and few different functional groups. Cholesterol is an important steroid component of cell membranes. Cholesterol is often converted into vitamin D and bile salts.

Waxes:

Waxes are another lipid containing long-chain fatty acids attached to alcohols or carbon rings.

Waxes are usually used to form waterproof coatings

on plants or animals.

Biological Macromolecules

There are four major classes of macromolecules in living organisms: carbohydrates, lipids, proteins, and nucleic acids. Macromolecules are large molecules which composed of a large number of repeating subunits; you can call them polymers (except lipids).
Reactions of Polymers:
Dehydration reaction (condensation reaction, anabolic reaction):
monomer(-OH) + monomer(-H) + energy → polymer + H2O
Hydrolysis (catabolic reaction):
polymer +H2O → monomer(-OH) + monomer(-H) + energy
*Enzymes can act as catalysts in both reactions.


Carbohydrates:Carbohydrates are produced by plants through the process of photosynthesis, and act as the energy source, structural compounds and raw materials. Carbohydrates can be classified into three groups: monosaccharaides, disaccharides, and polysaccharides.

Monosaccharaide: monosaccharaides are simple sugars which contain a single chain of carbon (three to seven carbon atoms), multiple hydroxyl groups, and a carbonyl group(C=O). If the carbonyl group is attached to the end of the carbon chain, it must be an aldose; if it is located on the carbon chain, it is ketoses. Aldoses and ketoses are isomers if they contain same number of carbon atoms. Ex: glucose, galactose and fructose are isomers which have the same chemical formula C6H12O6.

Disaccharide: disaccharides are sugars contain two monosaccharaides which attached to one another by glycosidic linkages. There are three major disaccharides: maltose, sucrose, and lactose.
α-glucose + α-glucose → maltose (held by an α 1-4 glycosidic linkage)
Ex: Beer
α-glucose + α-fructose → sucrose (held by an α 1-2 glycosidic linkage)
Ex: Table sugar
α-glucose + α-galactose → lactose
Ex: Milk

Polysaccharide: polysaccharides are monosaccharide polymers and held by glycosidic linkages. They can either store energy or act as a structural compound.
  1)Energy storage: excess α-glucose molecules are linked by α 1-4 glycosidic linkage in the main chain and α 1-4 glycosidic linkage at the branched points. Starch and glycogen can both be digested into single glucose by enzymes.
Starch: (in plant, monomer: α glucose) starch is a mixture of two different polysaccharides- amylose (unbranched) and amylopectin (branched).
Glycogen: (in human and animals, monomer: α glucose) the structure of glycogen is similar to amylopectin (branched). Glycogen can be transferred to energy during physical exercise.


polysaccharides

 2)Structural compound: unlike starch and glycogen, cellulose and chitin cannot be digested by the enzymes in human body, thus they are used to build cell walls or hard exoskeleton.
Cellulose: (in plant, monomer: β glucose) the monomers in cellulose are held by β1-4 glycosidic linkage. Because cellulose is a straight chain polymer and neither coiled nor branched, also have the hydroxyl groups formed hydrogen bonds between parallel molecules, cellulose can produce micro fibrils to build cell walls.
Chitin: (in animals, monomer: N-acetylglucosamine) chitin can be found in the hard exoskeleton of insects or crustaceans, also in some medical applications.