Genetica per Scienze Naturali a.a prof S. Presciuttini 1. Chemical reactions in cells Thousands of biochemical reactions, in which metabolites are converted into each other and macromolecules are build up, proceed at any given instant within living cells. However, the greatest majority of these reactions would occour spontaneously at extremely low rates. Thousands of biochemical reactions, in which metabolites are converted into each other and macromolecules are build up, proceed at any given instant within living cells. However, the greatest majority of these reactions would occour spontaneously at extremely low rates.  For example, the oxidation of a fatty acid to carbon dioxide and water in a test tube requires extremes of pH, high temperatures and corrosive chemicals. Yet in the cell, such a reaction takes place smoothly and rapidly within a narrow range of pH and temperature. As another example, the average protein must be boiled for about 24 hours in a 20% HCl solution to achieve a complete breakdown. In the body, the breakdown takes place in four hours or less under conditions of mild physiological temperature and pH. How can living things perform the magic of speeding up chemical reactions many orders of magnitude, specifically those reactions they most need at any given moment? How can living things perform the magic of speeding up chemical reactions many orders of magnitude, specifically those reactions they most need at any given moment?

Genetica per Scienze Naturali a.a prof S. Presciuttini 2. Introducing enzymes The ENZYMES are the driving force behind all biochemical reactions happening in cells. The ENZYMES are the driving force behind all biochemical reactions happening in cells. Enzymes lower the energy barrier between reactants and products, thus increasing the rate of the reaction. Enzymes lower the energy barrier between reactants and products, thus increasing the rate of the reaction. Enzymes are biological catalysts. A catalyst is a species that accelerates the rate of a chemical reaction whilst remaining unchanged at the end of the reaction. Catalysis is achieved by reducing the activation energy for the reaction. Enzymes are biological catalysts. A catalyst is a species that accelerates the rate of a chemical reaction whilst remaining unchanged at the end of the reaction. Catalysis is achieved by reducing the activation energy for the reaction. Enzymes can catalyse reactions at rates typically 10 6 to times faster than the uncatalysed reaction. Enzymes can catalyse reactions at rates typically 10 6 to times faster than the uncatalysed reaction. Enzymes are very selective about substrates they act upon and also where the chemistry takes place on a substrate. Enzymes are very selective about substrates they act upon and also where the chemistry takes place on a substrate. Both the forward and reverse reactions are catalysed. A catalyst cannot change the position of thermodynamic equilibrium, only the rate at which it is attained. Both the forward and reverse reactions are catalysed. A catalyst cannot change the position of thermodynamic equilibrium, only the rate at which it is attained.

Genetica per Scienze Naturali a.a prof S. Presciuttini 3. Enzymes are proteins Enzymes are composed of proteins, and proteins are long polymers of amino acids. Amino acids all have this general formula: Enzymes are composed of proteins, and proteins are long polymers of amino acids. Amino acids all have this general formula: Amino acids have two functional groups (aminic and carbossilyc), which can react together forming covalent bonds called peptide bonds, so that they are linked head-to-tail. Amino acids have two functional groups (aminic and carbossilyc), which can react together forming covalent bonds called peptide bonds, so that they are linked head-to-tail. The side chain, or R group, can be anything from a hydrogen atom (as in the amino acid glycine) to a complex ring (as in the amino acid tryptophan). The side chain, or R group, can be anything from a hydrogen atom (as in the amino acid glycine) to a complex ring (as in the amino acid tryptophan). Each of the 20 amino acids known to occur in proteins has a different R group that gives it its unique properties. Each of the 20 amino acids known to occur in proteins has a different R group that gives it its unique properties. The linear sequence of the amino acids in a polypeptide chain constitutes the primary structure of the protein The linear sequence of the amino acids in a polypeptide chain constitutes the primary structure of the protein

Genetica per Scienze Naturali a.a prof S. Presciuttini 4. Four levels of structure of the proteins The primary structure of a protein is the sequence of amino acids in its polypeptide chain. The primary structure of a protein is the sequence of amino acids in its polypeptide chain. The secondary structure is the regular arrangement of amino acids within localized regions of the polypeptide. Two types of secondary structure are particularly common: the a helix and the b sheet. Both of these secondary structures are held together by hydrogen bonds between the CO and NH groups of peptide bonds. The secondary structure is the regular arrangement of amino acids within localized regions of the polypeptide. Two types of secondary structure are particularly common: the a helix and the b sheet. Both of these secondary structures are held together by hydrogen bonds between the CO and NH groups of peptide bonds. Tertiary structure is the folding of the polypeptide chain as a result of interactions between the side chains of amino acids that lie in different regions of the primary sequence. In most proteins, combinations of a helices and b sheets, connected by loop regions of the polypeptide chain, fold into compact globular structures called domains, which are the basic units of tertiary structure. Tertiary structure is the folding of the polypeptide chain as a result of interactions between the side chains of amino acids that lie in different regions of the primary sequence. In most proteins, combinations of a helices and b sheets, connected by loop regions of the polypeptide chain, fold into compact globular structures called domains, which are the basic units of tertiary structure. The fourth level of protein structure, quaternary structure, consists of the interactions between different polypeptide chains in proteins composed of more than one polypeptide. Hemoglobin, for example, is composed of four polypeptide chains held together by the same types of interactions that maintain tertiary structure. The fourth level of protein structure, quaternary structure, consists of the interactions between different polypeptide chains in proteins composed of more than one polypeptide. Hemoglobin, for example, is composed of four polypeptide chains held together by the same types of interactions that maintain tertiary structure.

Genetica per Scienze Naturali a.a prof S. Presciuttini 5. The active site Enzymes are typically large proteins, which are structured specifically for the reaction they catalyze. Their size provide sites for action and stability of the overall structure. Enzymes are typically large proteins, which are structured specifically for the reaction they catalyze. Their size provide sites for action and stability of the overall structure. Two important sites within enzymes are: Two important sites within enzymes are:  The catalytic site, which is a region within the enzyme involved with catalysis, and  The substrate binding site which is the specific area on the enzyme to which reactants called substrates bind to. The catalytic site and substrate binding site are often close or overlapping and collectively they are called the active site. The catalytic site and substrate binding site are often close or overlapping and collectively they are called the active site.  If the catalytic site is not near the substrate binding site it can move into position once the enzyme is bound to a substrate.

Genetica per Scienze Naturali a.a prof S. Presciuttini 6. The “Lock-and-key” metaphor Schematic representation of the action of a hypothetical enzyme in putting two substrate molecules together. (a) In the "lock-and-key" mechanism the substrates have a complementary fit to the enzyme's active site. (b) In the induced-fit model, binding of substrates induces a conformational change in the enzyme.

Genetica per Scienze Naturali a.a prof S. Presciuttini 7. Aditional components of enzymes Often enzymes require additional components to become active. These may be: Often enzymes require additional components to become active. These may be:  co-factors: simple cations, or small organic or inorganic molecules that bind loosely to the enzyme,  prosthetic groups: similar to co-factors but more tightly bound to the enzyme, or  co-enzymes – which are more complex than co-factors and prosthetic groups, they often act as a second substrate or bind covalently with the enzyme to affect the active site.

Genetica per Scienze Naturali a.a prof S. Presciuttini 8. The first step of photosynthesis Photosynthesis. The key passage of the photosynthesis is the organication of the carbon, or the fixation of CO 2. The CO 2 molecule condenses with ribulose 1,5-bisphosphate to form an unstable six-carbon compound, which is rapidly hydrolyzed to two molecules of 3- phosphoglycerate. This reaction is catalyzed by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RUBISCO)

Genetica per Scienze Naturali a.a prof S. Presciuttini 9. An enzyme of fundamental importance for life The enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RUBISCO) is located on the stromal surface of the thylakoid membranes of chloroplasts. It comprises eight large (L) subunits (one shown in red and the others in yellow) and eight small (S) subunits (one shown here in blue and the others in white). The active sites lie in the L subunits. Each L subunit contains a catalytic site and a regulatory site. The S chains enhance the catalytic activity of the L chains. This enzyme is very abundant, constituting more than 16% of chloroplast total protein. RUBISCO is probably the most abundant protein in the biosphere.

Genetica per Scienze Naturali a.a prof S. Presciuttini 10. The active site of RUBISCO Structure of the catalytic domain of the active form of ribulose 1,5-bisphosphate carboxylase. Dark blue cylinders represent  helices and yellow arrows represent  sheets in the polypeptide. The key residues in the active site are carbamylated lysine 191, aspartate 193, and glutamate 194; a Mg 2+ ion is bound to carbamylated lysine 191. The substrates CO 2 and ribulose 1,5- bisphosphate are shown bound to the active site.

Genetica per Scienze Naturali a.a prof S. Presciuttini 11. METABOLIC PATHWAYS There are thousands of enzyme-catalyzed reactions in a cell. If the biochemical reactions involved in this process were reversible, we would convert our macromolecules back to metabolites if we stop eating even for a short period of time. There are thousands of enzyme-catalyzed reactions in a cell. If the biochemical reactions involved in this process were reversible, we would convert our macromolecules back to metabolites if we stop eating even for a short period of time. To prevent this from happening, our metabolism is organized in metabolic pathways. These pathways are a series of biochemical reactions which are, as a whole, irreversible. To prevent this from happening, our metabolism is organized in metabolic pathways. These pathways are a series of biochemical reactions which are, as a whole, irreversible. These reactions are organized in consecutive steps or pathways where the products of one reaction can become the reactants in another. Every biochemical molecule is synthesized in a biochemical pathway with specific enzymes. These reactions are organized in consecutive steps or pathways where the products of one reaction can become the reactants in another. Every biochemical molecule is synthesized in a biochemical pathway with specific enzymes.

Genetica per Scienze Naturali a.a prof S. Presciuttini 12. Metabolic pathways of phenylalanine in human One small part of the human metabolic map, showing the consequences of various specific enzyme failures. (Disease phenotypes are shown in colored boxes.)

Genetica per Scienze Naturali a.a prof S. Presciuttini 13. Phenylketonuria Phenylketonuria is caused by an absence or deficiency of phenylalanine hydroxylase or, more rarely, of its tetrahydrobiopterin cofactor. Phenylalanine accumulates in all body fluids because it cannot be converted into tyrosine. Normally, three-quarters of the phenylalanine is converted into tyrosine, and the other quarter becomes incorporated into proteins. The accumulation of phenylpyruvate leads to severe mental retardation in infants. If the high level of phenylpyruvic acid is detected soon after birth, the baby can be placed on a special low-phenylalanine diet and develops without retardation. Because the major outflow pathway is blocked in phenylketonuria, the blood level of phenylalanine is typically at least 20-fold as high as in normal people. Minor fates of phenylalanine in normal people, such as the formation of phenylpyruvate, become major fates in phenylketonurics.