1. Chemical reactions in cells

Genetica per Scienze Naturalia.a. 06-07 prof S. Presciuttini

1. Chemical reactions in cells

Thousands of biochemical reactionsThousands of biochemical reactions,, in which metabolites are in which metabolites are converted into each other and macromolecules are build up, converted into each other and macromolecules are build up, proceed proceed at any given instant within living cells. at any given instant within living cells. However, tHowever, the greatest he greatest majority of these reactions majority of these reactions would occourwould occour spontaneously spontaneously at at extremely low ratesextremely low rates.. For example, tFor example, the oxidation of a fatty acid to carbon dioxide and water he oxidation of a fatty acid to carbon dioxide and water in a test in a test

tube requirestube requires extremes of pH, high temperatures and corrosive chemicals. Yet extremes of pH, high temperatures and corrosive chemicals. Yet in the in the cellcell, such a reaction takes place smoothly and rapidly within a narrow , such a reaction takes place smoothly and rapidly within a narrow range of pH and temperature. range of pH and temperature. As another exampleAs another example, the average protein must , the average protein must be boiled for about 24 hours in a 20% HCl solution to achieve a complete 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 breakdown. In the body, the breakdown takes place in four hours or less under conditions of mild physiological temperature and pH.conditions of mild physiological temperature and pH.

How can living things perform the magic of speeding up chemical How can living things perform the magic of speeding up chemical reactions many orders of magnitude, specifically those reactions reactions many orders of magnitude, specifically those reactions they most need at any given moment? they most need at any given moment?


2. Introducing enzymes

The The ENZYMESENZYMES are the driving force behind all biochemical reactions are the driving force behind all biochemical reactions happening in cellshappening in cells. .

Enzymes Enzymes lower the energylower the energy barrierbarrier between reactants and products, thus between reactants and products, thus increasing the rate of the reaction.increasing the rate of the reaction.

EnzymesEnzymes are are biological catalystsbiological catalysts. . A catalyst is a species that accelerates the A catalyst is a species that accelerates the rate of a chemical reaction whilst remaining unchanged at the end of the rate of a chemical reaction whilst remaining unchanged at the end of the reaction. Catalysis is achieved by reducing the reaction. Catalysis is achieved by reducing the activation energyactivation energy for the for the reaction. reaction.

Enzymes can catalyse reactions at rates typically Enzymes can catalyse reactions at rates typically 101066 to to 10101414 times faster than times faster than the uncatalysed reactionthe uncatalysed reaction..

Enzymes are very selective about Enzymes are very selective about substratessubstrates they act upon and also they act upon and also where where the chemistry takes placethe chemistry takes place on a substrate. on a substrate.

BBoth the forward and reverse reactions are catalysed. A catalyst cannot oth the forward and reverse reactions are catalysed. A catalyst cannot change the position of thermodynamic equilibrium, only the rate at which it is change the position of thermodynamic equilibrium, only the rate at which it is attainedattained..


3. Enzymes are proteins

Enzymes areEnzymes are composed of composed of proteinproteins, and s, and proteins areproteins are long polymerslong polymers of amino acids. of amino acids. Amino acids all have thAmino acids all have thisis general formula general formula::

Amino acids have two functional groups (aminic and carbossilyc), Amino acids have two functional groups (aminic and carbossilyc), which can react together forming which can react together forming covalent bonds called covalent bonds called peptide peptide bondsbonds, so that they are linked head-to-tail. , so that they are linked head-to-tail.

The side chain, or R group, can be anything from a hydrogen atom The side chain, or R group, can be anything from a hydrogen atom (as in the amino acid (as in the amino acid glycineglycine) to a complex ring (as in the amino ) to a complex ring (as in the amino acid acid tryptophantryptophan).).

Each Each of theof the 20 amino acids known to occur in proteins ha 20 amino acids known to occur in proteins hass a a different R group that gives different R group that gives itit its unique properties. its unique properties.

The linear sequence of the amino acids in a polypeptide chain The linear sequence of the amino acids in a polypeptide chain constitutes the constitutes the primary structureprimary structure of the protein of the protein


4. Four levels of structure of the proteins The primary structure of a protein is the sequence of amino acids in its The primary structure of a protein is the sequence of amino acids in its

polypeptide chain.polypeptide chain. The secondary structure is the regular arrangement of amino acids within The secondary structure is the regular arrangement of amino acids within

localized regions of the polypeptide. Two types of secondary structure are localized regions of the polypeptide. Two types of secondary structure are particularly common: the particularly common: the aa helix and the helix and the bb sheet. Both of these secondary sheet. Both of these secondary structures are held together by hydrogen bonds between the CO and NH structures are held together by hydrogen bonds between the CO and NH groups of peptide bonds. groups of peptide bonds.

Tertiary structure is the folding of the polypeptide chain as a result of 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 interactions between the side chains of amino acids that lie in different regions of the primary sequence. In most proteins, combinations of regions of the primary sequence. In most proteins, combinations of aa helices and helices and bb sheets, connected by loop regions of the polypeptide chain, sheets, connected by loop regions of the polypeptide chain, fold into compact globular structures called domains, which are the basic fold into compact globular structures called domains, which are the basic units of tertiary structure.units of tertiary structure.

The fourth level of protein structure, quaternary structure, consists of the The fourth level of protein structure, quaternary structure, consists of the interactions between different polypeptide chains in proteins composed of interactions between different polypeptide chains in proteins composed of more than one polypeptide. Hemoglobin, for example, is composed of four more than one polypeptide. Hemoglobin, for example, is composed of four polypeptide chains held together by the same types of interactions that polypeptide chains held together by the same types of interactions that maintain tertiary structure.maintain tertiary structure.


5. The active site

Enzymes are typically Enzymes are typically large proteinslarge proteins,, which are which are structured structured specificallyspecifically for the reaction they catalyze. Their size provide sites for the reaction they catalyze. Their size provide sites for action and stability of the overall structure.for action and stability of the overall structure.

Two Two importantimportant sites within enzymes are: sites within enzymes are: The The catalytic sitecatalytic site, which is a region within the enzyme involved with , which is a region within the enzyme involved with

catalysis, andcatalysis, and The The substrate binding sitesubstrate binding site which is the specific area on the enzyme to which which is the specific area on the enzyme to which

reactants called substrates bind to.reactants called substrates bind to. The catalytic site and substrate binding site are often close or The catalytic site and substrate binding site are often close or

overlapping and collectively they are called the overlapping and collectively they are called the active siteactive site.. If the catalytic site is not near the substrate binding site it can move into If the catalytic site is not near the substrate binding site it can move into

position once the enzyme is bound to a substrate.position once the enzyme is bound to a substrate.


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.


7. Aditional components of enzymes

Often enzymes require additional components to become Often enzymes require additional components to become active. These may be:active. These may be: co-factorsco-factors: : simple cations, or small organic or simple cations, or small organic or

inorganic molecules that bind loosely to the enzyme,inorganic molecules that bind loosely to the enzyme, prosthetic groupsprosthetic groups: : similar to co-factors but more similar to co-factors but more

tightly bound to the enzyme, ortightly bound to the enzyme, or co-enzymesco-enzymes – which are more complex than co-factors – which are more complex than co-factors

and prosthetic groups, they often act as a second and prosthetic groups, they often act as a second substrate or bind covalently with the enzyme to affect substrate or bind covalently with the enzyme to affect the active site.the active site.


8. The first step of photosynthesis

PhotosynthesisPhotosynthesis. The key passage of the photosynthesis is the organication of the . The key passage of the photosynthesis is the organication of the carbon, or the fixation of COcarbon, or the fixation of CO22 . .

The COThe CO22 molecule condenses with ribulose 1,5-bisphosphate to form an unstable molecule condenses with ribulose 1,5-bisphosphate to form an unstable six-carbon compound, which is rapidly hydrolyzed to two molecules of 3-six-carbon compound, which is rapidly hydrolyzed to two molecules of 3-phosphoglycerate.phosphoglycerate.

This reaction is catalyzed by the enzyme This reaction is catalyzed by the enzyme ribulose 1,5-bisphosphate ribulose 1,5-bisphosphate carboxylase/oxygenase carboxylase/oxygenase (RUBISCO)(RUBISCO)


9. An enzyme of fundamental importance for life

The enzyme The enzyme ribulose 1,5-bisphosphate carboxylase/oxygenaseribulose 1,5-bisphosphate carboxylase/oxygenase (RUBISCO) is located (RUBISCO) is located on the stromal surface of the thylakoid membranes of chloroplasts. It comprises eight 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) 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).subunits (one shown here in blue and the others in white).

The active sites lie in the L subunits. Each L The active sites lie in the L subunits. Each L subunit contains a catalytic site and a subunit contains a catalytic site and a regulatory site. The S chains enhance the regulatory site. The S chains enhance the catalytic activity of the L chains. This enzyme catalytic activity of the L chains. This enzyme is very abundant, constituting more than 16% is very abundant, constituting more than 16% of chloroplast total protein. RUBISCO is of chloroplast total protein. RUBISCO is probably the most abundant protein in the probably the most abundant protein in the biosphere. biosphere.


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 Mg2+ ion is bound to carbamylated lysine 191. The substrates CO2 and ribulose 1,5-bisphosphate are shown bound to the active site.


11. METABOLIC PATHWAYS There are thousands of enzyme-catalyzed reactions in a cell. If the biochemical There are thousands of enzyme-catalyzed reactions in a cell. If the biochemical

reactions involved in this process were reversible, we would convert our reactions involved in this process were reversible, we would convert our macromoleculesmacromolecules back to back to metabolitesmetabolites if we stop eating even for a short period of if we stop eating even for a short period of time.time.

To prevent this from happening, our metabolism is organized in To prevent this from happening, our metabolism is organized in metabolic metabolic pathwayspathways. These pathways are a series of biochemical reactions which are, as a . These pathways are a series of biochemical reactions which are, as a whole, irreversible.whole, irreversible.

These reactions are organized in consecutive steps or pathways where the These reactions are organized in consecutive steps or pathways where the products of one reaction can become the reactants in another. Every biochemical products of one reaction can become the reactants in another. Every biochemical molecule is synthesized in a biochemical pathway with specific enzymes.molecule is synthesized in a biochemical pathway with specific enzymes.


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.)


13. PhenylketonuriaPhenylketonuria is caused by an absence or deficiency of phenylalanine hydroxylase or, more 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 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 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 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 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 acid is detected soon after birth, the baby can be placed on a special low-phenylalanine diet and develops without retardation.develops without retardation.

Because the major outflow pathway Because the major outflow pathway is blocked in phenylketonuria, the is blocked in phenylketonuria, the blood level of phenylalanine is blood level of phenylalanine is typically at least 20-fold as high as in typically at least 20-fold as high as in normal people. Minor fates of normal people. Minor fates of phenylalanine in normal people, such phenylalanine in normal people, such as the formation of phenylpyruvate, as the formation of phenylpyruvate, become major fates in become major fates in phenylketonurics.phenylketonurics.

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1. Chemical reactions in cells