THE CHEMISTRY AND BIOCHEMISTRY OF NITROGEN FIXATION

By OLIVIA CLARK

TABLE OF CONTENTS CHAPTER THE FACTS OF LIFE: CHEMISTRY IS THE LOGIC OF BIOLOGICAL PHENOMENA CHAPTER WATER: THE MEDIUM OF LIFE THERMODYNAMICS OF BIOLOGICAL SYSTEMS AMINO ACIDS AND THE PEPTIDE BOND PROTEINS: THEIR PRIMARY STRUCTURE AND BIOLOGICAL FUNCTIONS PROTEINS: SECONDARY, TERTIARY, QUATERNARY STRUCTURE CARBOHYDRATES AND THE GLYCOCONJUGATES OF CELL SURFACES LIPIDS MEMBRANES AND THE MEMBRANE TRANSPORT NUCLEOTIDES AND NUCLEIC ACIDS STRUCTURE OF NUCLEIC ACIDS RECOMBINANT DNA: CLONING AND CREATION OF CHIMERIC GENES ENZYMES—KINETICS AND SPECIFICITY MECHANISMS OF ENZYME ACTION ENZYME REGULATION MOLECULAR MOTORS METABOLISM: AN OVERVIEW GLYCOLYSIS THE TRICARBOXYLIC ACID CYCLE ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION PHOTOSYNTHESIS GLUCONEOGENESIS, GLYCOGEN METABOLISM, AND THE PENTOSE PHOSPHATE PATHWAY FATTY ACID CATABOLISM LIPID BIOSYNTHESIS NITROGEN ACQUISITION AND AMINO ACID METABOLISM SYNTHESIS AND DEGRADATION OF NUCLEOTIDES METABOLIC INTEGRATION AND ORGAN SPECIALIZATION DNA METABOLISM: REPLICATION, RECOMBINATION, AND REPAIR TRANSCRIPTION AND THE REGULATION OF GENE EXPRESSION PROTEIN SYNTHESIS COMPLETING THE PROTEIN LIFE CYCLE: FOLDING, PROCESSING, AND DEGRADATION THE RECEPTION AND TRANSMISSION OF EXTRACELLULAR INFORMATION ? METABOLITES: USED TO SYNTHESIZE BUILDING BLOCK MOLECULES ? BUILDING BLOCKS: AMINO ACIDS, NUCLEOTIDES, MONOSACCHARIDES, FATTY ACIDS, GLYCEROL ? MACROMOLECULES: PROTEINS, NUCLEIC ACIDS, POLYSACCHARIDES, LIPIDS ? SUPRAMOLECULAR COMPLEXES: RIBOSOMES, CHROMOSOMES, CYTOSKELETON ? MEMBRANES: LIPID BILAYERS WITH MEMBRANE PROTEINS ? DEFINE BOUNDARIES OF CELLS AND ORGANELLES ? HYDROPHOBIC INTERACTIONS MAINTAIN STRUCTURES ? ORGANELLES: MITOCHONDRIA, CHLOROPLASTS, NUCLEI, ENDOPLASMIC RETICULUM GOLGI, ETC ? CELLS: FUNDAMENTAL UNITS OF LIFE ? LIVING STATE: GROWTH, METABOLISM, STIMULUS RESPONSE AND REPLICATION ? PROPERTIES OF BIOMOLECULES ? DIRECTIONALITY OR STRUCTURAL POLARITY ? PROTEINS: N-TERMINUS AND C-TERMINUS ? NUCLEIC ACIDS: 5’- AND 3’- ENDS ? POLYSACCHARIDES: REDUCING AND NONREDUCING ENDS ? INFORMATION CONTENT: SEQUENCE OF MONOMER BUILDING BLOCKS AND 3-DIMENSIONAL ARCHITECTURE ? 3-DIMENSIONAL ARCHITECTURE AND INTERMOLECULAR INTERACTIONS (VIA COMPLEMENTARY SURFACES) OF MACROMOLECULES ARE BASED ON WEAK FORCES ? VAN DER WAALS INTERACTIONS (LONDON DISPERSION FORCES) ? INDUCED ELECTRIC INTERACTIONS THAT OCCUR WHEN ATOMS ARE CLOSE TOGETHER ? SIGNIFICANT WHEN MANY CONTACTS FORM COMPLEMENTARY SURFACES ? HYDROGEN BONDING ? DONOR AND ACCEPTOR PAIR: DIRECTION DEPENDENCE CHAPTER 1 CHEMISTRY IS THE LOGIC OF BIOLOGICAL PHENOMENA ? DONOR IS HYDROGEN COVALENTLY BONDED TO ELECTRONEGATIVE O OR N ? ACCEPTOR IS LONE PAIR ON O OR N ? IONIC INTERACTIONS ? STRONGER THAN H BONDS ? NOT DIRECTIONAL ? STRENGTH INFLUENCED BY SOLVENT PROPERTIES ? HYDROPHOBIC INTERACTIONS: OCCUR WHEN NONPOLAR GROUPS ADDED TO WATER ? WATER MOLECULES HYDROGEN BOND ? NONPOLAR GROUPS INTERFERE WITH WATER H-BONDING AND TO MINIMIZE THIS NONPOLAR GROUPS AGGREGATE ? STRUCTURAL COMPLEMENTARITY ? BIOMOLECULAR RECOGNITION DEPENDS ON STRUCTURAL COMPLEMENTARITY ? WEAK CHEMICAL FORCES RESPONSIBLE FOR BIOMOLECULAR RECOGNITION ? LIFE RESTRICTED TO NARROW RANGE OF CONDITIONS (TEMPERATURE, PH, SALT CONCENTRATION, ETC) BECAUSE OF DEPENDENCE ON WEAK FORCES DENATURATION: LOSS OF STRUCTURAL ORDER IN A MACROMOLECULE ? ENZYMES: BIOLOGICAL CATALYSTS CAPABLE OF BEING REGULATED ? CELL TYPES ? PROKARYOTES: BACTERIA AND ARCHAEA: PLASMA MEMBRANE BUT NO INTERNAL MEMBRANE-DEFINED COMPARTMENTS ? ARCHAEA INCLUDE THERMOACIDOPHILES, HALOPHILES AND METHANOGENS ? EUKARYOTES: INTERNAL MEMBRANE-DEFINED COMPARTMENTS: NUCLEI, ENDOPLASMIC RECTICULUM, GOLGI, MITOCHONDRIA, CHLOROPLASTS, VACUOLES, PEROXISOMES ? VIRUSES AND BACTERIOPHAGES: INCOMPLETE GENETIC SYSTEMS CHAPTER OBJECTIVES UNDERSTAND THE BASIC CHEMISTRY OF H, O, N AND C H FORMS A SINGLE COVALENT BOND WHEN BOUND TO AN ELECTRONEGATIVE ELEMENT, LIKE O OR N, THE ELECTRON PAIR FORMING THE COVALENT BOND IS NOT EQUALLY SHARED, GIVING RISE TO A PARTIAL POSITIVE CHARGE ON THE HYDROGEN (THIS IS THE BASIS OF H BONDS WHICH WILL BE COVERED IN THE NEXT CHAPTER) IN EXTREME CASES THE H CAN BE LOST AS A FREE PROTON O FORMS TWO COVALENT BONDS AND HAS TWO LONE PAIRS OF ELECTRONS IT IS AN ELECTRONEGATIVE ELEMENT AND WHEN BOUND TO HYDROGEN IT WILL CAUSE H TO BE PARTIALLY POSITIVELY CHARGED O IS HIGHLY REACTIVE DUE TO ITS HIGH ELECTRONEGATIVITY N FORMS UP TO THREE COVALENT BONDS AND HAS A SINGLE LONE PAIR OF ELECTRONS IT IS AN ELECTRONEGATIVE ELEMENT AND WILL CREATE A PARTIAL POSITIVE CHARGE ON A HYDROGEN BONDED TO IT C FORMS FOUR COVALENT BONDS WITH FOUR SINGLE BONDS, TETRAHEDRAL GEOMETRY IS PREDOMINANT WITH ONE DOUBLE BOND, CARBON SHOWS TRIGONAL PLANAR GEOMETRY, WITH AN ADDITIONAL PAIR OF ELECTRONS PARTICIPATING IN A PI BOND MACROMOLECULES AND SUBUNITS PROTEINS ARE FORMED FROM AMINO ACIDS COMPOSED OF C, H, O, N, AND IN SOME INSTANCES S NUCLEIC ACIDS ARE FORMED FROM NUCLEOTIDES THAT ARE COMPOSED OF PHOSPHATE, SUGAR AND NITROGENOUS BASE COMPONENTS (NUCLEOSIDES LACK PHOSPHATE) POLYSACCHARIDES ARE MADE OF CARBOHYDRATES OR SUGAR MOLECULES LIPIDS ARE A CLASS OF MOSTLY NONPOLAR, MOSTLY HYDROCARBON MOLECULES MACROMOLECULAR STRUCTURES MACROMOLECULAR STRUCTURES ARE COMPOSED OF COMPLEXES OF MACROMOLECULES (IE, PROTEINS, NUCLEIC ACIDS, POLYSACCHARIDES AND LIPIDS) THE RIBOSOME, MADE UP OF PROTEIN AND RIBONUCLEIC ACID, IS A PRIME EXAMPLE ORGANELLES ORGANELLES ARE SUBCELLULAR COMPARTMENTS DEFINED BY LIPID BILAYER MEMBRANES CELL TYPES THERE ARE TWO FUNDAMENTAL CELL TYPES: EUKARYOTIC, HAVING ORGANELLES AND A DEFINED NUCLEAR REGION, AND PROKARYOTIC, LACKING ORGANELLES AND A MEMBRANE-ENCLOSED REGION OF GENETIC MATERIAL THE ARCHAEA AND BACTERIA COMPRISE THE PROKARYOTES 6M E COLI =250 E COLI PER PINHEAD B WHAT IS THE VOLUME OF AN E COLI CELL? (ASSUME IT IS A CYLINDER, WITH THE VOLUME OF A CYLINDER GIVEN BY V=?R2H, WHERE ? = 314) ANSWER: V=??R 2 ?H =314 ?08 UM ? ? ? ? ? ? 6M ? ? 18M BUT, 1 M 3 ?100 CM ? ? 15L=1 FL (FEMTOLITER) C WHAT IS THE SURFACE AREA OF AN E COLI CELL? WHAT IS THE SURFACE-TO-VOLUME RATIO OF AN E COLI CELL? ?6M ? ? ?12M 5 MG ML OR 66 UG L OR 66 NG ML F AN E COLI CELL CONTAINS ABOUT 15,000 RIBOSOMES, WHICH CARRY OUT PROTEIN SYNTHESIS ASSUMING RIBOSOMES ARE SPHERICAL AND HAVE A DIAMETER OF 20 NM (NANOMETERS), WHAT FRACTION OF THE E COLI CELL VOLUME IS OCCUPIED BY RIBOSOMES? ???R ?9M ? ? ?? ? ? ?? ?24M G MOL DSDNA TO CALCULATE THE NUMBER OF DIFFERENT PROTEINS THAT WOULD BE ENCODED BY THE E COLI CHROMOSOME: 6BP BP PROTEIN ?4,213 PROTEINS THE EXACT NUMBER CAN BE FOUND AT NCBI (HTTP://WWWNCBINLMNIHGOV/) THE GENOMES OF A NUMBER OF STRAINS OF E COLI HAVE BEEN SEQUENCED BUT THE FIRST ONE WAS K-12 STRAIN MG1655 AT NCBI, SEARCH FOR MG1655 AND VIEW HITS IN THE GENOME DATABASE THERE SHOULD BE 16 OF THEM AND NC_00913 SHOULD BE ONE OF THEM ACTIVATE THIS LINK (OR SEARCH FOR NC_00913 DIRECTLY AND THEN ACTIVATE IT) THE RETURNED PAGE SHOULD INDICATE THAT THIS STRAIN OF E COLI HAS 4,145 PROTEIN CODING GENES 4 THE DIMENSIONS OF MITOCHONDRIA AND THEIR CONSTITUENTS ASSUME THAT MITOCHONDRIA ARE CYLINDERS 15 ?M IN LENGTH AND 06 ?M IN DIAMETER A WHAT IS THE VOLUME OF A SINGLE MITOCHONDRION? CHAPTER 1 CHEMISTRY IS THE LOGIC OF BIOLOGICAL PHENOMENA ANSWER : V ???R2 ?H V ?314 ?3?10?7 M ?? ???? ?? ???? ?15M 3 ?100 CM M ? ? ? ? ? ? ? 1 L 1000 CM ?12L ?8 PL C WHAT IS THE SURFACE AREA OF A LIVER CELL? WHAT IS THE SURFACE-TO-VOLUME RATIO OF A LIVER CELL? HOW DOES THIS COMPARE TO THE SURFACE-TO-VOLUME RATIO OF AN E COLI CELL? (COMPARE THIS ANSWER TO THAT OF PROBLEM 3C) WHAT PROBLEMS MUST CELLS WITH LOW SURFACE-TO-VOLUME RATIOS CONFRONT THAT DO NOT OCCUR IN CELLS WITH HIGH SURFACE-TO-VOLUME RATIOS? 12DA 5 OR ABOUT 100,000 TIMES GREATER! THE MAXIMAL INFORMATION IN EACH SET OF LIVER CELL CHROMOSOMES SHOULD BE RELATED TO THE NUMBER OF NUCLEOTIDE PAIRS IN THE CHROMOSOME SET’S DNA THIS NUMBER CAN BE OBTAINED BY DIVIDING THE TOTAL NUMBER OF NUCLEOTIDE PAIRS CALCULATED ABOVE BY 2 WHAT IS THIS VALUE? ANSWER: THE MAXIMAL INFORMATION IS 30 X 109 BP IF THIS INFORMATION IS EXPRESSED IN PROTEINS THAT AVERAGE 400 AMINO ACIDS IN LENGTH AND THREE NUCLEOTIDE PAIRS ENCODE ONE AMINO ACID IN A PROTEIN, HOW MANY DIFFERENT KINDS OF PROTEINS MIGHT A LIVER CELL BE ABLE TO PRODUCE? (IN REALITY LIVERS CELLS EXPRESS AT MOST ABOUT 30,000 DIFFERENT PROTEINS THUS, A LARGE DISCREPANCY EXISTS BETWEEN THE THEORETICAL INFORMATION CONTENT OF DNA IN LIVER CELLS AND THE AMOUNT OF INFORMATION ACTUALLY EXPRESSED) 6PROTEINS 6 THE PRINCIPLE OF MOLECULAR RECOGNITION THROUGH STRUCTURAL COMPLEMENTARITY BIOMOLECULES INTERACT WITH ONE ANOTHER THROUGH MOLECULAR SURFACES THAT ARE STRUCTURALLY COMPLEMENTARY HOW CAN VARIOUS PROTEINS INTERACT WITH MOLECULES AS DIFFERENT AS SIMPLE IONS, HYDROPHOBIC LIPIDS, POLAR BUT UNCHARGED CARBOHYDRATES, AND EVEN NUCLEIC ACIDS? ANSWER: THE AMINO ACID SIDE CHAINS OF PROTEINS CAN PARTICIPATE IN A NUMBER OF INTERACTIONS THROUGH HYDROGEN BONDING, IONIC BONDING, HYDROPHOBIC INTERACTIONS, AND VAN DER WAALS INTERACTIONS FOR EXAMPLE, THE POLAR AMINO ACIDS, ACIDIC AMINO ACIDS AND THEIR AMIDES, AND THE BASIC AMINO ACIDS ALL HAVE GROUPS THAT CAN PARTICIPATE IN HYDROGEN BONDING THOSE AMINO ACID SIDE CHAINS THAT HAVE NET CHARGE CAN FORM IONIC BONDS THE HYDROPHOBIC AMINO ACIDS CAN INTERACT WITH NONPOLAR, HYDROPHOBIC SURFACES OF MOLECULES THUS, AMINO ACIDS ARE CAPABLE OF PARTICIPATING IN A VARIETY OF INTERACTIONS A PROTEIN CAN BE FOLDED IN THREE DIMENSIONS TO ORGANIZE AMINO ACIDS INTO SURFACES WITH A RANGE OF PROPERTIES 7 THE PROPERTIES OF INFORMATIONAL MACROMOLECULES WHAT STRUCTURAL FEATURES ALLOW BIOLOGICAL POLYMERS TO BE INFORMATIONAL MACROMOLECULES? IS IT POSSIBLE FOR POLYSACCHARIDES TO BE INFORMATIONAL MACROMOLECULES? ANSWER: BIOPOLYMERS, LIKE PROTEINS AND NUCLEIC ACIDS, ARE INFORMATIONAL MOLECULES BECAUSE THEY ARE VECTORIAL MOLECULES, COMPOSED OF A VARIETY OF BUILDING BLOCKS FOR EXAMPLE, PROTEINS ARE LINEAR CHAINS OF SOME AMINO ACIDS JOINED HEAD-TO-TAIL TO PRODUCE A POLYMER WITH DISTINCT ENDS THE INFORMATION CONTENT IS THE SEQUENCE OF AMINO ACIDS ALONG THE POLYMER NUCLEIC ACIDS (DNA AND RNA) ARE ALSO INFORMATIONAL MOLECULES FOR THE SAME REASON HERE, THE BIOPOLYMER IS MADE UP OF 4 KINDS OF NUCLEOTIDES MONOSACCHARIDES CAN BE LINKED TO FORM POLYMERS WHEN A POLYMER IS FORMED FROM ONLY ONE KIND OF MONOSACCHARIDE, AS FOR EXAMPLE IN GLYCOGEN, STARCH, AND CELLULOSE, EVEN THOUGH THE MOLECULE IS VECTORIAL (IE, IT HAS DISTINCT ENDS) THERE IS LITTLE INFORMATION CONTENT THERE ARE, HOWEVER, A VARIETY OF MONOSACCHARIDES AND MONOSACCHARIDE DERIVATIVES THAT ARE USED TO FORM POLYSACCHARIDES FURTHERMORE, MONOSACCHARIDES CAN BE JOINED IN A VARIETY OF WAYS TO FORM BRANCH STRUCTURES BRANCHED POLYSACCHARIDES COMPOSED OF A NUMBER OF DIFFERENT MONOSACCHARIDES ARE RICH IN INFORMATION 8 THE IMPORTANCE OF WEAK FORCES IN BIOMOLECULAR RECOGNITION WHY IS IT IMPORTANT THAT WEAK FORCES, NOT STRONG FORCES, MEDIATE BIOMOLECULAR RECOGNITION? ANSWER: LIFE IS A DYNAMIC PROCESS CHARACTERIZED BY CONTINUALLY CHANGING INTERACTIONS COMPLEMENTARY INTERACTIONS BASED ON COVALENT BONDING WOULD OF NECESSITY PRODUCE STATIC STRUCTURES THAT WOULD BE DIFFICULT TO CHANGE AND SLOW TO RESPOND TO OUTSIDE STIMULI 9 INTERATOMIC DISTANCES IN WEAK FORCES VERSUS CHEMICAL BONDS WHAT IS THE DISTANCE BETWEEN THE CENTERS OF TWO CARBON ATOMS (THEIR LIMIT OF APPROACH) THAT ARE INTERACTING THROUGH VAN DER WAALS FORCES? WHAT IS THE DISTANCE BETWEEN THE CENTERS OF TWO CARBON ATOMS JOINED IN A COVALENT BOND? (SEE TABLE 14) THE LIMIT OF APPROACH OF TWO ATOMS IS DETERMINED BY THE SUM OF THEIR VAN DER WAALS RADII, WHICH ARE GIVEN IN TABLE 14 FOR TWO CARBON ATOMS THE LIMIT OF APPROACH IS (017 NM + 017 NM) 034 NM THE DISTANCE BETWEEN THE CENTERS OF TWO CARBON ATOMS JOINED IN A COVALENT BOND IS THE SUM OF THE COVALENT RADII OF THE TWO CARBONS OR (0077 NM + 0077 NM) 0154 NM CLEARLY, TWO CARBONS SHARING ELECTRONS IN A COVALENT BOND ARE CLOSER TOGETHER THAN ARE TWO CARBONS INTERACTING THROUGH VAN DER WAALS FORCES 10 THE STRENGTH OF WEAK FORCES DETERMINES THE ENVIRONMENTAL SENSITIVITY OF LIVING CELLS WHY DOES THE CENTRAL ROLE OF WEAK FORCES IN BIOMOLECULAR INTERACTIONS RESTRICT LIVING SYSTEMS TO A NARROW RANGE OF ENVIRONMENTAL CONDITIONS? ?580,074 ?536,818 BP ? X NOTE: THIS CALCULATION ASSUMES THAT GENES ESSENTIALLY DO NOT OVERLAP A SMALLER GENOME SIZE COULD BE POSSIBLE BY ALLOWING OVERLAPPING, BUT THIS WOULD CONSTRAIN THE PROTEIN SEQUENCES 14 AN ESTIMATION OF THE NUMBER OF GENES IN A VIRUS VIRUS GENOMES RANGE IN SIZE FROM APPROXIMATELY 3500 NUCLEOTIDES TO APPROXIMATELY 280,000 BASE PAIRS IF VIRAL GENES ARE ABOUT THE SAME SIZE AS M GENITALIUM GENES, WHAT IS THE MINIMUM AND MAXIMUM NUMBER OF GENES IN VIRUSES? ?252 GENES 15 INTRACELLULAR TRANSPORT OF PROTEINS THE ENDOPLASMIC RETICULUM (ER) IS A SITE OF PROTEIN SYNTHESIS PROTEINS MADE BY RIBOSOMES ASSOCIATED WITH THE ER MAY PASS INTO THE ER MEMBRANE OR ENTER THE LUMEN OF THE ER DEVISE A PATHWAY BY WHICH: A A PLASMA MEMBRANE PROTEIN MAY REACH THE PLASMA MEMBRANE B A SECRETED PROTEIN MAY BE DEPOSITED OUTSIDE THE CELL PROTEIN SYNTHESIS STARTS OUT ON RIBOSOMES LOCATED IN THE CYTOPLASM OF CELLS PROTEINS DESTINED TO BE EXCRETED OR TO BECOME MEMBRANE PROTEINS ARE SYNTHESIZED WITH A SIGNAL SEQUENCE LOCATED NEAR THE N-TERMINUS OF THE PROTEIN (PROTEIN SYNTHESIS BEGINS AT THE N-TERMINUS) THIS SIGNAL SEQUENCE DIRECTS THE RIBOSOME TO THE ENDOPLASMIC RETICULUM WHERE THE RIBOSOME DOCKS WITH THE RETICULAR MEMBRANE ENDOPLASMIC RETICULUM STUDDED WITH RIBOSOMES IS CALLED ROUGH ENDOPLASMIC RETICULUM THE SIGNAL-SEQUENCE-CONTAINING PROTEIN IS SYNTHESIZED BY ROUGH ENDOPLASMIC RETICULUM-BOUND RIBOSOMES THAT SYNTHESIZE THE PROTEIN AND SIMULTANEOUSLY EXPORT IT INTO THE LUMEN OF THE ENDOPLASMIC RETICULUM FOR A PROTEIN TO BE TRANSPORTED TO THE PLASMA MEMBRANE IT MUST BE PACKAGED INTO MEMBRANE VESICLES IN THE ENDOPLASMIC RETICULUM SINCE THE RETICULAR MEMBRANE IS SEPARATE FROM THE PLASMA MEMBRANE VESICLES FROM THE ENDOPLASMIC RETICULUM CONTAINING MEMBRANE PROTEINS DO NOT, HOWEVER, MOVE DIRECTLY TO THE PLASMA MEMBRANE RATHER THEY ARE ROUTED TO THE GOLGI APPARATUS WHERE A VARIETY OF POST-TRANSLATIONAL MODIFICATIONS OCCUR ONCE PROTEINS MOVE THROUGH THE GOLGI THEY ARE REPACKAGED INTO VESICLES THAT ARE DIRECTED TO THE PLASMA MEMBRANE SECRETED PROTEINS FOLLOW THE SAME PATHWAY BOTH MEMBRANE PROTEINS AND EXCRETED PROTEINS CONTAIN SIGNAL SEQUENCES THAT GET THEM INTO THE ENDOPLASMIC RETICULUM MEMBRANE PROTEINS CONTAIN AN ADDITIONAL DOMAIN OR DOMAINS THAT ARE HYDROPHOBIC IN NATURE AND ANCHOR THE PROTEINS INTO THE RETICULAR MEMBRANE PREPARING FOR THE MCAT® EXAM 16 BIOLOGICAL MOLECULES OFTEN INTERACT VIA WEAK FORCES (H BONDS, VAN DER WAALS INTERACTIONS, ETC) WHAT WOULD BE THE EFFECT OF AN INCREASE IN KINETIC ENERGY ON SUCH INTERACTIONS? ANSWER: WEAK FORCES ARE EASILY DISRUPTED BY INCREASES IN THE KINETIC ENERGIES OF THE INTERACTING COMPONENTS THUS, SLIGHT INCREASES IN TEMPERATURE CAN DISRUPT WEAK FORCES BIOLOGICAL MOLECULES, LIKE PROTEINS WHOSE THREE-DIMENSIONAL STRUCTURES ARE OFTEN DETERMINED BY WEAK FORCE INTERACTIONS, MAY UNDERGO CONFORMATIONAL CHANGES EVEN WITH MODEST CHANGES IN TEMPERATURE LEADING TO INACTIVATION OR LOSS OF FUNCTION 17 PROTEINS AND NUCLEIC ACIDS ARE INFORMATIONAL MACROMOLECULES WHAT ARE THE TWO MINIMAL CRITERIA FOR A LINEAR INFORMATIONAL POLYMER? ANSWER: INFORMATIONAL MACROMOLECULES MUST BE DIRECTIONAL (VECTORIAL) AND THEY MUST BE COMPOSED OF UNIQUE BUILDING BLOCKS BOTH NUCLEIC ACIDS AND PROTEINS ARE DIRECTIONAL POLYMERS THE DIRECTIONALITY OF A SINGLE NUCLEIC ACID IS 5’ TO 3’ WHEREAS THAT OF A PROTEIN IS N-TERMINUS TO C-TERMINUS THE REPEAT UNITS IN NUCLEIC ACID POLYMERS ARE FOUR DIFFERENT NUCLEOSIDE MONOPHOSPHATES THE REPEAT UNITS IN PROTEINS ARE 20 AMINO ACIDS THE INFORMATION CONTENT OF A NUCLEIC ACID, ESPECIALLY DSDNA, IS ITS LINEAR SEQUENCE THE SAME IS TRUE FOR PROTEINS; HOWEVER, PROTEINS TYPICALLY FOLD INTO UNIQUE THREE-DIMENSIONAL STRUCTURES, WHICH SHOW BIOLOGICAL ACTIVITY ADDITIONAL PROBLEMS 1 SILICON IS LOCATED BELOW CARBON IN THE PERIODIC CHART IT IS CAPABLE OF FORMING A WIDE RANGE OF BONDS SIMILAR TO CARBON YET LIFE IS BASED ON CARBON CHEMISTRY WHY ARE BIOMOLECULES MADE OF SILICON UNLIKELY? 2 IDENTIFY THE FOLLOWING CHARACTERS OF THE GREEK ALPHABET:???????????????????????????????????????????????????????????AND?? CHAPTER 1 CHEMISTRY IS THE LOGIC OF BIOLOGICAL PHENOMENA 3 GIVE A COMMON EXAMPLE OF EACH OF THE WEAK FORCES AT WORK 4 ON A HOT DRY DAY, LEAFY PLANTS MAY BEGIN TO WILT WHY? ABBREVIATED ANSWERS 1 COVALENT SILICON BONDS ARE NOT QUITE AS STRONG AS CARBON COVALENT BONDS BECAUSE THE BONDING ELECTRONS OF SILICON ARE SHIELDED FROM THE NUCLEUS BY AN ADDITIONAL LAYER OF ELECTRONS IN ADDITION, SILICON IS OVER TWICE THE WEIGHT OF CARBON ALSO, SILICON OXIDES (ROCKS, GLASS) ARE EXTREMELY STABLE AND NOT AS REACTIVE AS CARBON 2 THESE GREEK LETTERS ARE COMMONLY USED IN BIOCHEMISTRY BUT THIS SET IS NOT THE COMPLETE GREEK ALPHABET ALPHA (?), BETA (?), GAMMA (?), DELTA (?), CAPITAL DELTA (?), EPSILON (?), ZETA (?), THETA (?), KAPPA (?), LAMBDA (?), MU (?), NU (?), PI (?), RHO (?), SIGMA (?), CAPITAL SIGMA (?), TAU (?), CHI (?), PHI (?), PSI (?), AND OMEGA (?), THE LAST LETTER OF THE GREEK ALPHABET 3 ICE IS AN EXAMPLE OF A STRUCTURE HELD TOGETHER BY HYDROGEN BONDS SODIUM AND CHLORIDE IONS ARE JOINED BY IONIC BONDS IN TABLE SALT CRYSTALS A STICK OF BUTTER IS A SOLID AT ROOM TEMPERATURE BECAUSE OF VAN DER WAALS FORCES THE ENERGETICALLY UNFAVORABLE INTERACTIONS BETWEEN WATER AND OIL MOLECULES CAUSE THE OIL TO COALESCE 4 THE TONOPLAST LOSES WATER AND BEGINS TO SHRINK CAUSING THE PLANT CELL MEMBRANE TO EXERT LESS PRESSURE ON THE CELL WALL SUMMARY THE CHAPTER BEGINS WITH AN OUTLINE OF THE FUNDAMENTAL PROPERTIES OF LIVING SYSTEMS: COMPLEXITY AND ORGANIZATION, BIOLOGICAL STRUCTURE AND FUNCTION, ENERGY TRANSDUCTION, AND SELF-REPLICATION WHAT ARE THE UNDERLYING CHEMICAL PRINCIPLES RESPONSIBLE FOR THESE PROPERTIES? THE ELEMENTAL COMPOSITION OF BIOMOLECULES IS DOMINATED BY HYDROGEN, CARBON, NITROGEN AND OXYGEN THESE ARE THE LIGHTEST ELEMENTS CAPABLE OF FORMING STRONG COVALENT BONDS IN PARTICULAR, CARBON PLAYS A KEY ROLE SERVING AS THE BACKBONE ELEMENT OF ALL BIOMOLECULES IT CAN PARTICIPATE IN AS MANY AS FOUR COVALENT BONDS ARRANGED IN TETRAHEDRAL GEOMETRY AND CAN PRODUCE A VARIETY OF STRUCTURES INCLUDING LINEAR, BRANCHED, AND CYCLIC COMPOUNDS THE FOUR ELEMENTS ARE INCORPORATED INTO BIOMOLECULES FROM PRECURSOR COMPOUNDS: CO2, NH4+, NO3- AND N2 THESE PRECURSORS ARE USED TO CONSTRUCT MORE COMPLEX COMPOUNDS SUCH AS AMINO ACIDS, SUGARS, AND NUCLEOTIDES, WHICH SERVE AS BUILDING BLOCKS FOR THE BIOPOLYMERS; PROTEINS, POLYSACCHARIDES, AND NUCLEIC ACIDS, AS WELL AS FATTY ACIDS AND GLYCEROL WHICH ARE THE BUILDING BLOCKS OF LIPIDS THESE COMPLEX MACROMOLECULES ARE ORGANIZED INTO SUPRAMOLECULAR COMPLEXES SUCH AS MEMBRANES AND RIBOSOMES THAT ARE COMPONENTS OF CELLS, THE FUNDAMENTAL UNITS OF LIFE PROTEINS, NUCLEIC ACIDS AND POLYSACCHARIDES ARE BIOPOLYMERS WITH STRUCTURAL POLARITY DUE TO HEAD-TO-TAIL ARRANGEMENTS OF ASYMMETRIC BUILDING BLOCK MOLECULES IN THESE BIOPOLYMERS, THE BUILDING BLOCKS ARE HELD TOGETHER BY COVALENT BONDS, BUT THEY ASSUME AN ELABORATE ARCHITECTURE DUE TO WEAK, NONCOVALENT FORCES SUCH AS VAN DER WAALS INTERACTIONS, HYDROGEN BONDS, IONIC BONDS AND HYDROPHOBIC INTERACTIONS THE THREE- DIMENSIONAL SHAPE IS IMPORTANT FOR BIOLOGICAL FUNCTION, ESPECIALLY FOR PROTEINS AT EXTREME CONDITIONS SUCH AS HIGH TEMPERATURE, HIGH PRESSURE, HIGH SALT CONCENTRATIONS, EXTREMES OF PH, AND SO ON, THE WEAK FORCES MAY BE DISRUPTED, RESULTING IN LOSS OF BOTH SHAPE AND FUNCTION IN A PROCESS KNOWN AS DENATURATION THUS, LIFE IS CONFINED TO A NARROW RANGE OF CONDITIONS LIFE DEMANDS A FLOW OF ENERGY DURING WHICH ENERGY TRANSDUCTIONS OCCUR IN THE ORGANIZED, ORDERLY, SMALL, MANAGEABLE STEPS OF METABOLISM, EACH STEP CATALYZED BY ENZYMES THE FUNDAMENTAL UNIT OF LIFE IS THE CELL THERE ARE TWO TYPES: EUKARYOTIC CELLS WITH A NUCLEUS AND PROKARYOTIC CELLS WITHOUT A NUCLEUS PROKARYOTES ARE DIVIDED INTO TWO GROUPS, EUBACTERIA AND ARCHAEA ALL CELLS CONTAIN RIBOSOMES, WHICH ARE RESPONSIBLE FOR PROTEIN SYNTHESIS; HOWEVER, PROKARYOTIC CELLS CONTAIN LITTLE ELSE IN THE WAY OF SUBCELLULAR STRUCTURES EUKARYOTIC CELLS, FOUND IN PLANTS, ANIMALS, AND FUNGI, CONTAIN AN ARRAY OF MEMBRANE-BOUND COMPARTMENTS OR ORGANELLES, INCLUDING A NUCLEUS, MITOCHONDRIA, CHLOROPLASTS, ENDOPLASMIC RETICULUM, GOLGI APPARATUS, VACUOLES, LYSOSOMES, AND PERIXOSOMES ORGANELLES ARE INTERNAL COMPARTMENTS IN WHICH PARTICULAR METABOLIC PROCESSES ARE CARRIED OUT