Showing papers in "Annual Review of Biochemistry in 1970"

Control of Enzyme Levels in Animal Tissues

Abstract: INTRODUCTION . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . • . . . . . . . • • . . . . . . 930 PROTEIN TURNOVER AND PROBLEMS OF TERMINOLOGY . . • . • . 9 31 CRITIQUE OF METHODOLOGY . . . . . . . . . . . . . . • . . • . . . . . . . . . . . . . . . . . • . 933 WHAT IS THE BEST SYSTEM FOR STUDYING ENZYME REGULATION? . . . . . . . . • 940 Is THE DIFFERENCE IN OBSERVED ENZYME ACTIVITY DUE TO A DIFFERENCE IN THE CONTENT OF ENZYME PROTEIN? . . . • . . . . . . . . . • . . . . . . . . . . • . • . . . . .. 940

The biogenesis of mitochondria.

Abstract: INTRODUCTION 251 MITOCHONDRIAL DNA . . . . . . . . . . . . . . . . . . .. . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 SYNTHESIS AND TURNOVER OF MITOCHONDRIAL DNA . . . . .. . . .. . .. ... . .. ... 256 MITOCHONDRIAL RNA AND MITOCHONDRIAL RIBOSOMES 257 SYNTHESIS OF MITOCHONDRIAL RNA . . . . . . . . . . . . . . . . . . . . . . . . . • . . . . . . . . . .. 263 LOCALIZATION OF MITOCHONDRIAL PROTEINS AND METABOLIC TURNOVER . . . . .. 265 BIOSYNTHETIC ORIGIN OF MITOCHONDRIAL PROTEINS . . . . . . . . . . . . . . , . . . . . . . . • 271 THE FUNCTION OF MITOCHONDRIAL DNA? • • • . • • • . . • • • • . . . . . . • . . • . . • • . . . • • 274

Quaternary Structure of Proteins

Abstract: STOICHIOMETRY OF SUBUNITS. . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 DISSOCIATION METHODS . . . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Denaturants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Change of charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Binding of metabolites or s mall ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Reaction with sulfhydryl groups .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 HyBRIDIZATION .... . . . . . . . . . . . . . . . . . . • . . . . . • • • . • . . . . . • . . . .. .... ... .. . 28 TABLE OF SUBUNITS . . . ' " . . . . . . . . . . . . . . . . . . . . . . . • • . . . . . . . ..... ... . .. . 29 GEOMETRIC ARRANGEMENTS OF SUBUNITS 29 CYCLIC SYMMETRY . . . . . . . . . • • . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 DIHEDRAL SYMMETRY . . . . . . . • . . . . . . . . . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . 36 CUBIC SYMMETRY • • . • . . . . . . • . • . . . . . . . . • . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . 38 GENERAL COMMENTS . . . . . • . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 ENERGETICS OF INTERACTIONS 39 MOLECULAR STRUCTURE OF INTERFACE CONTACTS 52 FACTORS THAT MODIFY SUBUNIT INTERACTIONS S6 INTRINSIC FACTORS . . . . . . . . . . . . . . . . . . . . . . . • . . . . . . . . • . . . . . . . . . . . . . . . . . • 56 EXTRINSIC FACTORS . . . . . . • • . . . . . . • • . . • . . . • . . . . • . . . . . . . . . . . . . . . . . . . . . . . S7 CONCLUSION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S9

Chemical Synthesis of Peptides and Proteins

Abstract: CALCITONIN 847 SECRETIN . : . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 850 Fragment approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 851 Stepwise approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 852 RIBONUCLEASE A 853 RIBONUCLEASE S . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 856 CURRENT PROGRESS IN THE SYNTHESIS OF OTHER ENZYMES 857 Ribonuclease T, . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 857 Staphylococcus nuclease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 858 SPECIAL TOPICS IN P EPTIDE CHEMISTRY . . . . . . , . " ... . .. . ...... 859

The Specificity of Molecular Hybridization Reactions

Abstract: INFLUENCE OF REACTION CONDITIONS UPON SPECIFICITY • • • . . • . • • . • . . • • • . • • 136 Rates of reaction . . . . . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136 Reaction conditions and specificity . . . . . . . . . . . . . . . . . . . . . . . . . . .. . .. . ..... 137 Renaturation reactions in organic solvents . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . 138

Bacterial Cytochromes: I. Structural Aspects

Abstract: CONTENTS INTRODUCTION SOME HISTORY AND SYSTEMATICS . . . . • . . . • . . • . . . • . . • . • • . • . . • . . . • . • . . • . • . . CYTOCHROMES a . CYTOCHROMES d . CYTOCHROMES b ..... . ......... . . . . ...... . .... . . CYTOCHROMES a . ...... ..... . ... .. .... ... .. . ........ .. .... ... . . .... ..... . "P-450" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . CYTOCHROMES C • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • General remarks . Physical measurements . Primary structures . Prospectus .

Computer Applications to Biochemical Kinetics

Abstract: INTRODUCTION . . . • . . . . . • . . • . . • • • . . • . . . . . . . . . . . • . . • . • • . . . . . . . • • . . • . • . . . • . • ApPLICATION TO BIOCHEMICAL SYSTEMS . . • . . • • • • • . • • . • • • • • . • . • • • • • • . . . • . • . Glycolysis and related pathways . Control of blood glucose , . . . . . . . . . . . . . . . . . . . . . Mitochondrial systems . C ompartmentation studies . Optimation studies . Equilibrium studies . Protein synthesis . Miscellaneous systems . THEORETICAL . . . . • . . . • . • • . • • • • • • • • . • . • . • . . . • . . • • • . . • • • . • • . . . . • . • . . . . . . . . . Theorems derived with computers , .. . Biochemical oscillations . Enzyme kinetics . Allosteric control . Logical models . Input-otttput models . PROGRAMING, LANGUAGES AND METHODOLOGY . . . . . . . . . . . . . . . . . . . . . . . . . . • . . . Survey of compttter programs . Types of computers . Rate-law and matrix methods . Monte Carlo methods . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . ' " . . . . . . ' " . . . o ptimation methods . Rand chemical equilibrium program . THE ApPLICATION OF COMPUTERS TO TEACHING OF BIOCHEMISTRY . GLOSSARY

The biochemistry of RNA bacteriophage replication.

Abstract: INTRODUCTION . PROPERTIES OF THE RNA PHAGE . Properties of the particles .... . Physical properties of the RNA ....... ' " . . , ........ , .. .... ... . ..... . Genetic proPerties of the RNA . Properties of the coat protein .... . Properties of the maturation ("An) protein . ADSORPTION AND PENETRATION . TRANSLATION .. TRANSLATION IN VIVO .... " TRANSLATION IN VITRO . . . . . . . . . . . . . . . . . . . . . .. ... .. . RegUlation of translation . . ......... . .. . Polarity . The repressor role of coat protein . Independent translation of maturation protein . REPLICATION .. RNA REPLICATION IN VIVO .... ' " . . . . . . . ' ...... , .... ...... . RNA REPLICATION IN VITRO " .' . ....... , ..... ........ . RNA bacteriophage RNA polymerase ..... " . ..... . Properties of the Q/3 RNA polymerase . Host cell factors . Enzyme binding of RNA . The complementary strand . Replicative complex . Synthesis of viral RNA . Repl ication of other templates . ASSEMBLY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 528 528 528 529 532 533 533 534 535 535 537 538 538 540 541 541 541 543 543 544 545 545 546 546 547 548 548

Enzymes of nucleic acid metabolism

Abstract: INTRODUCTION INTERCONVERSIONS OF PYRIMIDINE NUCLEOTIDES . Phosphorylation of nucleotides . Biosynthesis of cytidine triphosphate . Reduction of ribonucleotides . Biosynthesis of thymidylate . PYRIMIDINE NUCLEOTIDE METABOLISM AFTER T-EvEN PHAGE INFECTION . . . . Biosynthesis of deo�y-5-hydro�ymethylcytidine triphosphate . CytosVne versus hydro�ymethylcytosine ., . . , .. . . . . . , ... . . . . . . . , . . . . . . . . . Biosynthesis of thymidine triphosphate . Nonessential pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Reduction of ribonucleotides . . . . . . . .. . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . DEGRADATION OF HOST DNA AFTER T-EvEN PHAGE INFECTION . ..... .. . .. . . Intermediates in the degradation of host DNA . Role of bacterial nucleases . Role of phage-induced nucleases .' . . . . . . . . . . . . . . . .

RNA sequence analysis.

Abstract: FRACTIONATION AND PURIFICATION OF RNA 228 Transfer RNA 228 Ribosomal RNA ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 230 Viral RNA 230 SEPARATION AND ISOLATION OF POLYNUCLEOTIDES 231 Physical methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 231 End group methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 232 Other methods.... ......... ...... ... ......... ... ... ... ..... ..... ...... 234 FRACTIONATION OF OLIGONUCLEOTIDES • • . . . . . . . . . . . . . . . • . . . . . . . . . . . . . . . . . . 235 METHODS OF CLEAVAGE .. . . . • . . . . .... ... ... .. ... ... ...... ... ... . .. . .. .... 237 Cleavage with enzymes . ........ . ........ 237 Chemical modification of enzymic cleavage. 240 Chemical cleavage .. . . . . . 241 CHARACTERIZATION OF OLIGOAND POLYNUCLEOTIDES . . ..... . . . . . . .. . . ..... 241

Neurochemistry: At the Crossroads of Neurobiology

Abstract: INTRODUCTION . . . . . • . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 778 A VERY ELEMENTARY MODEL OF BEHAVIOR 779 LEVEL 1: A GENERAL DESCRIPTION OF THE ORGANISM IN ITs ENVIRONMENT .779 LEVEL 2: WHERE PSYCHOLOGY, PHYSIOLOGY, AND NEUROENDOCRINOLOGY MEET 780 A guided tour through the model of behavior . . . . . . . . . . . . . . . . . . . . . . . .. 780 Learning to modify the environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 784 Learning to ignore the environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 785 LEVEL 3: \VHERE BIOCHEMISTRY, PHYSIOLOGY, AND NEUROENDOCRINOLOGY MEET . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . • . . . • . 786 Entry of information into the organism . . . .. . . . .. . . . .. . . . . . ... . . ... . 786 Neurons: the structural units of neural circuits 787 Synapses: the nodal points of neural circuits ... ' ... .. ... ... ... ..... .. 789 Model of synaptic relationships at a single neuron with one excitatory and inhibitory input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 792 Presynaptic events ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 792 Sequence of excitatory and inhibitory transmitter events . . . . . . . . . . . . . 794 Cross-reg'ulation between the excitatory and inhibitory systems. . . . . . .. 7% Altered sensitivity of neuronal membranes . . . . . . . . . . . . . . . . . . . . . . . . . 797 Behavioral search for achievement of transm'itter balance. .. . . . . . . . ... . .. 798 LEVEL 4: THE REALM OF THE BIOCHEMIST AND MOLECULAR AND CELL BIOLOGIST; MECHANISMS OF PLASTIC CHANGE AT SYNAPSES. . . . . . . . . . . • . . .. 799 Hypothetical time-relations of changes in synaptic connectivity resulting from use and disuse of synapse 800