ENCYCLOPEDIA OF PHYSICAL SCIENCE AND TECHNOLOGY: BIOCHEMISTRY
BIOENERGETICS 1 ENZYME MECHANISMS 18 FOOD COLORS 31 GLYCOCONJUGATES AND CARBOHYDRATES 47 ION TRANSPORT ACROSS BIOLOGICAL MEMBRANES 64 LIPOPROTEIN CHOLESTEROL METABOLISM 74 MEMBRANE STRUCTURE 92 NATURAL ANTIOXIDANTS IN FOODS 105 NUCLEIC ACID SYNTHESIS 113 PROTEIN FOLDING 137 PROTEIN STRUCTURE 149 PROTEIN SYNTHESIS 177 VITAMINS AND COENZYMES 199 CONTENTS BIOENERGETICS I CATABOLIC METABOLISM THE SYNTHESIS OF ATP II PHOTOSYNTHESIS III ORIGIN OF MITOCHONDRIA AND CHLOROPLASTS IV ILLUSTRATIONS OF THE USES OF ATP ION TRANSPORT BIOSYNTHESIS AND MOTILITY V CONCLUDING STATEMENTS GLOSSARY ADENOSINE 5 TRIPHOSPHATE ATP THE CARRIER OF FREE ENERGY IN CELLS BIOENERGETICS THE STUDY OF ENERGY RELATIONSHIPS IN LIVING SYSTEMS CHLOROPLASTS THE SITES OF PHOTOSYNTHESIS IN GREEN PLANTS ION TRANSPORT THE MOVEMENT OF IONS ACROSS BIOLOGICAL MEMBRANES METABOLISM THE TOTAL OF ALL REACTIONS THAT OCCUR IN CELLS CATABOLIC METABOLISM IS GENERALLY DEGRADATIVE AND EX ERGONIC WHEREAS ANABOLIC METABOLISM IS SYNTHETIC AND REQUIRES ENERGY MITOCHONDRIA SITES OF OXIDATIVE CATABOLIC METABOLISM IN CELLS PHOTOSYNTHESIS LIGHT DRIVEN SYNTHESIS OF ORGANIC MOLE CULES FROM CARBON DIOXIDE AND WATER PLASMA MEMBRANE THE BARRIER BETWEEN THE INSIDE OF CELLS AND THE EXTERNAL MEDIUM BIOENERGETICS ANAMALGAMATIONOFTHETERMBIOLOG ICAL ENERGETICS IS THE BRANCH OF BIOLOGY AND BIOCHEMISTRY THAT IS CONCERNED WITH HOW ORGANISMS EXTRACT ENERGY FROM THEIR ENVIRONMENT AND WITH HOW ENERGY IS USED TO FUEL THE MYRIAD OF LIFE S ENDERGONIC PROCESSES ORGANISMS MAY BE USEFULLY DIVIDED INTO TWO BROAD GROUPS WITH RESPECT TO HOW THEY SATISFY THEIR NEED FOR ENERGY AUTOTROPHIC ORGAN ISMS CONVERT ENERGY FROM NONORGANIC SOURCES SUCH AS LIGHT OR FROM THE OXIDATION OF INORGANIC MOLECULES TO CHEMICAL ENERGY AS HETEROTROPHIC ORGANISMS ANIMALS MUST INGEST AND BREAK DOWN COMPLEX ORGANIC MOLECULES TO PROVIDE THE ENERGY FOR LIFE INTERCONVERSIONS OF FORMS OF ENERGY ARE COMMONPLACE IN THE BIOLOGICAL WORLD IN PHOTOSYNTHESIS THE ELECTRO MAGNETIC ENERGY OF LIGHT IS CONVERTED TO CHEMICAL ENERGY LARGELY IN THE FORM OF CARBOHYDRATES WITH HIGH OVERALL EF CIENCY THE ENERGY OF LIGHT IS USED TO DRIVE OXIDATION REDUCTION REACTIONS THAT COULD NOT TAKE PLACE IN THE DARK LIGHT ENERGY ALSO POWERS THE GENERATION OF A PROTON ELECTROCHEMICAL POTENTIAL ACROSS THE GREEN PHOTOSYNTHETIC 1 FIGURE 1 CENTRAL ROLE OF ADENOSINE 5 TRIPHOSPHATE ATP IN METABOLISM CATABOLIC DEGRADATIVE METABOLISM IS EXERGONIC AND PROVIDES THE ENERGY NEEDED FOR THE SYNTHESIS OF ATP FROM ADENOSINE 5 DIPHOSPHATE ADP AND INORGANIC PHOSPHATE PI THE EXERGONIC HYDROLYSIS OF ATP IN TURN POWERS THE ENDERGONIC PROCESSES OF ORGANISMS MEMBRANE THUS ELECTRICAL WORK IS AN INTEGRAL PART OF PHO TOSYNTHESIS CHEMICAL ENERGY IS USED IN ALL ORGANISMS TO DRIVE THE SYNTHESIS OF LARGE AND SMALL MOLECULES MOTILITY AT THE MICROSCOPIC AND MACROSCOPIC LEVELS THE GENERA TION OF ELECTROCHEMICAL POTENTIALS OF IONS ACROSS CELLULAR MEMBRANES AND EVEN LIGHT EMISSION AS IN RE IES GIVEN THE DIVERSITY IN THE FORMS OF LIFE IT MIGHT BE EX PECTED THAT ORGANISMS HAVE EVOLVED MANY MECHANISMS TO DEAL WITH THEIR NEED FOR ENERGY TO SOME EXTENT THIS EX PECTATION IS THE CASE ESPECIALLY FOR ORGANISMS THAT LIVE IN EXTREME ENVIRONMENTS HOWEVER THE SIMILARITIES AMONG ORGANISMS IN THEIR BIOENERGETIC MECHANISMS ARE AS OR EVEN MORE STRIKING THAN THE DIFFERENCES FOR EXAMPLE THE SUGAR GLUCOSE IS CATABOLIZED BROKEN DOWN BY A PATHWAY THAT IS THE SAME IN THE ENTERIC BACTERIUM ESCHERICHIA COLI AS IT IS IN HIGHER ORGANISMS ALL ORGANISMS USE ADENOSINE 5 TRIPHOSPHATE ATP AS A CENTRAL INTERMEDIATE IN ENERGY METABOLISM ATP ACTS IN A WAY AS A CURRENCY OF FREE EN ERGY THE SYNTHESIS OF ATP FROM ADENOSINE 5 DIPHOSPHATE ADP AND INORGANIC PHOSPHATE PI IS A STRONGLY EN DERGONIC REACTION THAT IS COUPLED TO EXERGONIC REACTIONS SUCH AS THE BREAKDOWN OF GLUCOSE ATP HYDROLYSIS IN TURN POWERS MANY OF LIFE S PROCESSES THE CENTRAL ROLE OF ATP IN BIOENERGETICS IS ILLUSTRATED IN FIG 1 PARTIAL STRUC TURES OF SEV METABOLISM ARE SHOWN IN FIG 2 ERAL COMPOUNDS THAT PLAY IMPORTANT ROLES IN IN THIS ARTICLE THE ELEMENTS OF ENERGY METABOLISM WILL BE DISCUSSED WITH EMPHASIS ON HOW ORGANISMS SATISFY THEIR ENERGETIC REQUIREMENTS AND ON HOW ATP HYDROLYSIS DRIVES OTHERWISE UNFAVORABLE REACTIONS I CATABOLIC METABOLISM THE SYNTHESIS OF ATP METABOLISM MAY BE DE NED AS THE TOTAL OF ALL THE CHEM ICAL REACTIONS THAT OCCUR IN ORGANISMS GREEN PLANTS CAN SYNTHESIZE ALL THE THOUSANDS OF COMPOUNDS THEY CONTAIN ENCYCLOPEDIA OF PHYSICAL SCIENCE AND TECHNOLOGY THIRD EDITION BIOCHEMISTRY 2 FIGURE 2 SOME IMPORTANT REACTIONS IN METABOLISM SHOWN ARE THE PHOSPHORYLATION OF ADP TO ATP NAD NADH FAD FADH2 ACETATE COA AND ACETYL COA FOR CLARITY JUST THE PARTS OF THE LARGER MOLECULES THAT UNDERGO REACTION ARE SHOWN NAD NICOTI NAMIDE ADENINE DINUCLEOTIDE NADH NICOTINAMIDE ADENINE DINU CLEOTIDE REDUCED FORM FAD AVIN ADENINE DINUCLEOTIDE FADH2 AVIN ADENINE DINUCLEOTIDE REDUCED FORM COA COENZYME A AMP ADENOSINE MONOPHOSPHATE FROM CARBON DIOXIDE WATER AND INORGANIC NUTRIENTS THE DISCUSSION OF THE COMPLICATED TOPIC OF METABOLISM IS SOMEWHAT SIMPLI ED BY SEPARATION OF THE SUBJECT INTO TWO AREAS CATABOLIC AND ANABOLIC METABOLISM CATABOLIC METABOLISM IS DEGRADATIVE AND IS GENERALLY EXERGONIC ATP IS A PRODUCT OF CATABOLIC METABOLISM IN CONTRAST AN ABOLIC METABOLISM IS SYNTHETIC AND REQUIRES ATP FORTU NATELY THERE ARE RELATIVELY FEW MAJOR PATHWAYS OF ENERGY METABOLISM A GLYCOLYSIS AND FERMENTATION CARBOHYDRATES ARE A MAJOR SOURCE OF ENERGY FOR ORGANISMS THE MAJOR PATHWAY BY WHICH CARBOHYDRATES ARE DEGRADED IS CALLED GLYCOLYSIS STARCH GLYCOGEN AND OTHER CARBOHY DRATES ARE CONVERTED TO THE SUGAR GLUCOSE BY PATHWAYS THAT WILL NOT BE CONSIDERED HERE IN GLYCOLYSIS GLUCOSE A SIX CARBON SUGAR IS OXIDIZED AND CLEAVED BY ENZYMES IN THE CYTOPLASM OF CELLS TO FORM TWO MOLECULES OF PYRUVATE A THREE CARBON COMPOUND SEE FIGS 3 AND 4 THE OVERALL REACTION IS EXERGONIC AND SOME OF THE ENERGY RELEASED IS CONSERVED BY COUPLING THE SYNTHESIS OF ATP TO GLYCOLYSIS BEFORE IT MAY BE METABOLIZED GLUCOSE MUST RST BE PHOSPHORYLATED ON THE HYDROXYL RESIDUE AT POSITION 6 UNDER INTRACELLULAR CONDITIONS THE DIRECT PHOSPHORYLATION OF GLUCOSE BY PI IS AN UNFAVORABLE REACTION CHARACTERIZED BY A G 0 OF ABOUT 4 KCAL MOL AT PH 7 0 AND 25 C NOTE THAT THE BIOCHEMIST S STANDARD STATE DIFFERS FROM THAT AS USUALLY DE NED IN THAT THE ACTIVITY OF THE HYDROGEN ION IS TAKEN AS 10 7 M OR PH 7 0 RATHER THAN 1 M OR PH 0 0 PH 7 0 IS MUCH CLOSER TO THE PH IN MOST CELLS THIS PROB LEM IS NEATLY SOLVED IN CELLS BY USING ATP RATHER THAN PI AS THE PHOSPHORYL DONOR GLUCOSE ATP GLUCOSE 6 PHOSPHATE ADP THE G 0 FOR THIS REACTION WHICH IS CATALYZED BY THE EN ZYME HEXOKINASE IS APPROXIMATELY 4 KCAL MOL THUS THE PHOSPHORYLATION OF GLUCOSE BY ATP IS AN ENERGETICALLY FA VORABLE REACTION AND IS ONE EXAMPLE OF HOW THE CHEMICAL ENERGY OF ATP MAY BE USED TO DRIVE OTHERWISE UNFAVORABLE REACTIONS GLUCOSE 6 PHOSPHATE IS THEN ISOMERIZED TO FORM FRUC TOSE 6 PHOSPHATE WHICH IN TURN IS PHOSPHORYLATED BY ATP AT THE 1 POSITION TO FORM FRUCTOSE 1 6 BISPHOSPHATE IT SEEMS ODD THAT A METABOLIC PATHWAY INVESTS 2 MOL OF ATP IN THE INITIAL STEPS OF THE PATHWAY WHEN ATP IS AN IM PORTANT PRODUCT OF THE PATHWAY HOWEVER THIS INVESTMENT PAYS OFF IN LATER STEPS FRUCTOSE 1 6 BISPHOSPHATE IS CLEAVED TO FORM TWO TRIOSE PHOSPHATES THAT ARE READILY INTERCONVERTIBLE NOTE THAT THE OXIDATION REDUCTION STATE OF THE TRIOSE PHOSPHATES IS THE SAME AS THAT OF GLUCOSE 6 PHOSPHATE AND THE FRUCTOSE PHOS PHATES ALL MOLECULES ARE PHOSPHORYLATED SUGARS IN THE NEXT STEP OF GLYCOLYSIS GLYCERALDEHYDE 3 PHOSPHATE IS OX IDIZED AND PHOSPHORYLATED TO FORM A SUGAR ACID THAT CON TAINS A PHOSPHORYL GROUP AT POSITIONS 1 AND 3 THE OXIDIZ ING AGENT NICOTINAMIDE ADENINE DINUCLEOTIDE NAD IS A WEAK OXIDANT E 0 AT PH 7 0 OF 340 MV THE OXIDA TION OF THE ALDEHYDE GROUP OF GLYCERALDEHYDE 3 PHOSPHATE TO A CARBOXYLATE IS A FAVORABLE REACTION THAT DRIVES BOTH THE OXIDATION AND THE PHOSPHORYLATION THIS IS THE ONLY OXIDATION REDUCTION REACTION IN GLYCOLYSIS THE HYDROLYSIS OF ACYL PHOSPHATES SUCH AS THAT OF POSITION 1 OF 1 3 BISPHOSPHOGLYCERATE IS CHARACTERIZED BY STRONGLY NEGATIVE G 0 VALUES THAT FOR 1 3 BISPHOS PHOGLYCERATE IS APPROXIMATELY 10 KCAL MOL WHICH IS SIGNI CANTLY MORE NEGATIVE THAN THE G 0 FOR THE HYDROL YSIS OF ATP TO ADP AND PI THUS THE TRANSFER OF THE ACYL PHOSPHATE FROM 1 3 BISPHOSPHOGLYCERATE TO ADP TO FORM 3 PHOSPHOGLYCERATE AND ATP IS A SPONTANEOUS REACTION SINCE TWO SUGAR ACID BISPHOSPHATES ARE FORMED PER GLU COSE METABOLIZED THE TWO ATP INVESTED IN THE BEGINNING OF THE PATHWAY HAVE BEEN RECOVERED IN THE NEXT STEPS OF GLYCOLYSIS THE PHOSPHATE ON THE 3 POSITION OF THE 3 PHOSPHOGLYCERATE IS TRANSFERRED TO THE HYDROXYL RESIDUE AT POSITION 2 REMOVAL OF THE ELEMENTS OF WATER FROM 2 PHOSPHOGLYCERATE RESULTS IN THE FORMATION OF AN ENOLIC PHOSPHATE COMPOUND PHOSPHO ENOL PYRUVATE ENCYCLOPEDIA OF PHYSICAL SCIENCE AND TECHNOLOGY THIRD EDITION BIOCHEMISTRY 3