Cliffs biochemistry ii quick review

273 Pages·2000·3.173 MB·English

by  Frank Schmidt

CLIFFSQuICKREVIEW
Biochemistry II
By Frank Schmidt,Ph.D.
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CONTENTS
FUNDAMENTAL IDEAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
CHAPTER 1:FATTY ACID OXIDATION . . . . . . . . . . . . . . . .3
Fats and Oils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Dietary Fat Absorption. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Lipids in the bloodstream . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Tissues and lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Hydrolysis of Triacylglyerols . . . . . . . . . . . . . . . . . . . . . . . . . . 9
b eta-Oxidation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
E
Activation: Fatty Acid Fatty Acyl-CoA. . . . . . . . . . . . . . . . 10
Transport: The Role of Carnitine. . . . . . . . . . . . . . . . . . . . . . . 10
The b -Oxidation Helical Scheme for Fatty Acyl-CoA . . . . . . 12
Energy Yield from Fatty Acid Oxidation. . . . . . . . . . . . . . . . . 15
Odd-Numbered Chain and Branched Fatty Acids. . . . . . . . . . 15
Ketone Bodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
CHAPTER 2:LIPID BIOSYNTHESIS . . . . . . . . . . . . . . . . . .19
Energy Storage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Fatty Acid Biosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Initiation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Elongation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Release. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Synthesis of Triacylglycerols. . . . . . . . . . . . . . . . . . . . . . . . . . 28
Cholesterol Biosynthesis and its Control. . . . . . . . . . . . . . . . . 29
Isoprenoid Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
HMG CoAReductase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Mevalonate Squalence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Squalene fi Lanosterol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Lanosterol fi Cholesterol . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Cholesterol Transport, Uptake, and Control . . . . . . . . . . . . . . 35
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CONTENTS
CHAPTER 3:PHOTOSYNTHESIS . . . . . . . . . . . . . . . . . . . . .39
Metabolic Oxidation and Reduction . . . . . . . . . . . . . . . . . . . . 39
Overall Process of Photosynthesis. . . . . . . . . . . . . . . . . . . . . . 40
Two Photosynthetic reactions . . . . . . . . . . . . . . . . . . . . . . . 41
The chloroplast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Chlorophyll and the action spectrum
of photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Light Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Photosystem II. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Photosystem I . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Cyclic Electron Flow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Z-Scheme of Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 49
ATPSynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Carbohydrate Synthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
C-3 Photosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Energetics of Photosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . 55
Photorespiration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
C4 plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
CHAPTER 4:NITROGEN FIXATION,ASSIMILATION,
AND ELIMINATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
Reduced Nitrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
The Nitrogen Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Bacterial Nitrogenase. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Ammonium Utilization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Glutamate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Glutamine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Glutamate from glutamine. . . . . . . . . . . . . . . . . . . . . . . . . . 67
Further Fates of Incorporated Ammonia . . . . . . . . . . . . . . . . . 68
Glutamine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Carbamoyl phosphate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Urea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Biochemistry of the urea cycle . . . . . . . . . . . . . . . . . . . . . . 73
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CONTENTS
CHAPTER 5:AMINO ACID METABOLISM:CARBON . . .77
Principles of Amino Acid Metabolism. . . . . . . . . . . . . . . . . . . 77
1-Carbon Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Folic acid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Folate antagonists as antimicrobial drugs. . . . . . . . . . . . . . 80
Vitamin B12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Methyltransferases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Amino Acid Biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Nonessential amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Essential amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Biosynthesis of aromatic amino acids. . . . . . . . . . . . . . . . . 86
Pathway determination by biochemical genetics . . . . . . . . 88
Feedback inhibition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Amino acid catabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Inborn errors of amino acid metabolism. . . . . . . . . . . . . . . 92
Heme biosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
CHAPTER 6:PURINES AND PYRIMIDINES . . . . . . . . . . .95
Roles of nucleotides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Purine and Pyrimidine Structures . . . . . . . . . . . . . . . . . . . . . . 95
Salvage and Biosynthetic Pathways. . . . . . . . . . . . . . . . . . . . . 98
Salvage pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Purine biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Degradation of purine nucleotides . . . . . . . . . . . . . . . . . . 106
Pyrimidine Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Pyrimidine biosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Deoxynucleotide Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Thymidylate synthase . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Chemotherapy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
CHAPTER 7:INTEGRATED METABOLISM . . . . . . . . . .117
Metabolic Relationships. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Energy from Glucose. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Proteins and Fatty Acids . . . . . . . . . . . . . . . . . . . . . . . . . . 119
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CONTENTS
Exercise and Metabolism. . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Anaerobic exercise: sprinting . . . . . . . . . . . . . . . . . . . . . . 120
Aerobic metabolism: prolonged exercise . . . . . . . . . . . . . 121
Nutritional state. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Hormonal Regulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Down regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Receptor Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Cyclic AMP: ASecond Messenger . . . . . . . . . . . . . . . . . . . . 126
Action of cyclic AMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
PI System: Another Second Messanger. . . . . . . . . . . . . . . . . 129
Protein kinase C. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Receptors with Kinase Activity. . . . . . . . . . . . . . . . . . . . . . . 133
Hormone interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Hormones that Affect Gene Activity. . . . . . . . . . . . . . . . . . . 135
CHAPTER 8:DNA STRUCTURE,REPLICATION,
ANDREPAIR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .137
DNAand RNAStructures . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Sugar structures in DNAand RNA. . . . . . . . . . . . . . . . . . 140
DNAStructure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
DNAtertiary structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
DNAReplication Enzymes . . . . . . . . . . . . . . . . . . . . . . . . . . 146
DNApolymerases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Chromosomal replication . . . . . . . . . . . . . . . . . . . . . . . . . 152
Initiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Elongation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
DNARepair. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
DNArepair systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
DNARecombination and Repair. . . . . . . . . . . . . . . . . . . . . . 161
CHAPTER 9:MOLECULAR CLONING OF DNA . . . . . . .167
Gene Expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
DNAand Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
DNAHybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Restriction Enzyme Mapping . . . . . . . . . . . . . . . . . . . . . . . . 170
DNAMapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Southern Blotting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
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CONTENTS
Molecular Cloning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Plasmid vectors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
Other types of cloning vectors. . . . . . . . . . . . . . . . . . . . . . 179
Identifying Particular Sequences in a Library. . . . . . . . . . . . 181
The Polymerase Chain Reaction . . . . . . . . . . . . . . . . . . . . . . 183
DNASequence Determination. . . . . . . . . . . . . . . . . . . . . . . . 185
Genomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
CHAPTER 10:RNA AND TRANSCRIPTION . . . . . . . . . . .189
RNAInformation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
RNAFunctions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Messenger RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Transfer RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
Ribosomal RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
Other Information-Processing RNAs. . . . . . . . . . . . . . . . . . . 197
Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Transcription in Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . 198
Promoter recognition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
The transcription process. . . . . . . . . . . . . . . . . . . . . . . . . . 200
Transcriptional Control in Bacteria. . . . . . . . . . . . . . . . . . . . 204
The Lactose Operon—ACase Study in Regulation . . . . . . . 205
CHAPTER 11:PROTEIN SYNTHESIS . . . . . . . . . . . . . . . .213
Transcription and Translation . . . . . . . . . . . . . . . . . . . . . . . . 213
Fidelity in tRNAAminoacylation . . . . . . . . . . . . . . . . . . . . . 215
Initiation of Protein Synthesis . . . . . . . . . . . . . . . . . . . . . . . . 218
Elongation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
Termination of Translation. . . . . . . . . . . . . . . . . . . . . . . . . . . 224
CHAPTER 12:EUKARYOTIC GENES . . . . . . . . . . . . . . . .227
Eukaryotic Information Flow. . . . . . . . . . . . . . . . . . . . . . . . . 227
DNAand Genomes in Eukaryotes. . . . . . . . . . . . . . . . . . . . . 227
Structure of Chromatin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
Chromatin Replication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
Reverse Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
BIOCHEMISTRY II
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CONTENTS
Eukaryotic Gene Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
Ribosomal RNAsynthesis. . . . . . . . . . . . . . . . . . . . . . . . . 238
Messenger RNAtranscription. . . . . . . . . . . . . . . . . . . . . . 240
Transfer and 5S ribosomal RNAtranscription . . . . . . . . . 240
RNAProcessing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
Messenger RNAprocessing reactions. . . . . . . . . . . . . . . . 242
RNAcatalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
Eukaryotic Translation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Initiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Elongation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Protein glycosylation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Eukaryotic Transcriptional Control. . . . . . . . . . . . . . . . . . . . 253
Translational Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
CLIFFSQUICKREVIEW
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FUNDAMENTAL IDEAS
For the purpose of your review, your knowledge of the following fun-
damental ideas is assumed:
n The scope of biochemistry
n Biological energy flow
n Protein structure
n Weak interactions
n Physiological chemistry of oxygen binding
n Enzymes
n Organization of metabolism
n Glycolysis
n Tricarboxylic acid cycle
n Oxidative phosphorylation
n Carbohydrate metabolism II
If you need to review any of these topics, refer to CliffsQuickReview
Biochemistry I.
BIOCHEMISTRY II
1