|
|
|
|
1 The Chemical Basis Of Life |
|
|
1 | (23) |
|
1-1 What is Biochemistry? |
|
|
2 | (1) |
|
|
|
3 | (7) |
|
Cells contain four major types of biomolecules |
|
|
5 | (1) |
|
There are three major kinds of biological polymers |
|
|
6 | (4) |
|
1-3 Energy and Metabolism |
|
|
10 | (4) |
|
Enthalpy and entropy are components of free energy |
|
|
10 | (1) |
|
Δ G is less than zero for a spontaneous process |
|
|
11 | (1) |
|
Life is thermodynamically possible |
|
|
12 | (2) |
|
1-4 The Origin and Evolution of Life |
|
|
14 | (10) |
|
|
|
14 | (2) |
|
|
|
16 | |
|
Box 1-A Biochemistry Note Units Used in Biochemistry |
|
|
7 | (10) |
|
Box 1-B Biochemistry Note How Does Evolution Work? |
|
|
17 | (2) |
|
Bioinformatics Project 1 The Biochemical Literature |
|
|
19 | (5) |
|
|
|
24 | (27) |
|
2-1 Water Molecules form Hydrogen Bonds |
|
|
25 | (5) |
|
Hydrogen bonds are one type of electrostatic force |
|
|
26 | (3) |
|
Water dissolves many compounds |
|
|
29 | (1) |
|
2-2 The Hydrophobic Effect |
|
|
30 | (3) |
|
Amphiphilic molecules experience both hydrophilic interactions and the hydrophobic effect |
|
|
31 | (1) |
|
The hydrophobic core of a lipid bilayer is a barrier to diffusion |
|
|
32 | (1) |
|
|
|
33 | (8) |
|
[ H+] and [ OH-] are inversely related |
|
|
34 | (2) |
|
The pH of a solution can be altered |
|
|
36 | (1) |
|
A pK value describes an acid's tendency to ionize |
|
|
37 | (1) |
|
The pH of a solution of acid is related to the pK |
|
|
37 | (4) |
|
2-4 Tools and Techniques: Buffers |
|
|
41 | (10) |
|
Box 2-A Biochemistry Note Why Do Some Drugs Contain Fluorine? |
|
|
28 | (5) |
|
Box 2-B Biochemistry Note sweat, exercise, and sports Drinks |
|
|
33 | (2) |
|
Box 2-C Biochemistry Note Atmospheric CO2 and Ocean Acidification |
|
|
35 | (8) |
|
Box 2-D Clinical Connection Acid-Base Balance in Humans |
|
|
43 | (8) |
|
part two Molecular Structure And Function |
|
|
|
|
|
51 | (36) |
|
3-1 DNA Is the Genetic Material |
|
|
52 | (9) |
|
Nucleic acids are polymers of nucleotides |
|
|
53 | (1) |
|
Some nucleotides have other functions |
|
|
54 | (2) |
|
|
|
56 | (3) |
|
|
|
59 | (1) |
|
DNA can be denatured and renatured |
|
|
59 | (2) |
|
3-2 Genes Encode Proteins |
|
|
61 | (4) |
|
A mutated gene can cause disease |
|
|
63 | (2) |
|
|
|
65 | (5) |
|
Gene number is roughly correlated with organismal complexity |
|
|
65 | (2) |
|
Genes are identified by comparing sequences |
|
|
67 | (1) |
|
Genomic data can be linked to disease |
|
|
68 | (2) |
|
3-4 Tools and Techniques: Manipulating DNA |
|
|
70 | (17) |
|
DNA sequencing uses DNA polymerase to make a complementary strand |
|
|
70 | (2) |
|
The polymerase chain reaction amplifies DNA |
|
|
72 | (3) |
|
Restriction enzymes cut DNA at specific sequences |
|
|
75 | (1) |
|
DNA fragments are joined to produce recombinant DNA |
|
|
76 | (1) |
|
Cloned genes yield valuable products |
|
|
77 | (2) |
|
Genetically modified organisms have practical applications |
|
|
79 | (1) |
|
Gene therapy can cure some human diseases |
|
|
79 | |
|
Box 3-A Clinical Connection Discovery of the Cystic Fibrosis Gene |
|
|
64 | (10) |
|
Box 3-B Biochemistry Note DNA Fingerprinting |
|
|
74 | (7) |
|
Bioinformatics Project 2 Databases for the Storage and "Mining" of Genome Sequences |
|
|
81 | (6) |
|
|
|
87 | (34) |
|
4-1 Proteins Are Chains of Amino Acids |
|
|
89 | (7) |
|
The 20 amino acids have different chemical properties |
|
|
89 | (2) |
|
Peptide bonds link amino acids in proteins |
|
|
91 | (4) |
|
The amino acid sequence is the first level of protein structure |
|
|
95 | (1) |
|
4-2 Secondary Structure: The Conformation of the Peptide Group |
|
|
96 | (3) |
|
The a helix exhibits a twisted backbone conformation |
|
|
97 | (1) |
|
The β sheet contains multiple polypeptide strands |
|
|
97 | (1) |
|
Proteins also contain irregular secondary structure |
|
|
98 | (1) |
|
4-3 Tertiary Structure and Protein Stability |
|
|
99 | (8) |
|
Proteins have hydrophobic cores |
|
|
100 | (2) |
|
Protein structures are stabilized mainly by the hydrophobic effect |
|
|
102 | (1) |
|
Cross-links help stabilize proteins |
|
|
102 | (2) |
|
Protein folding begins with the formation of secondary structures |
|
|
104 | (3) |
|
|
|
107 | (1) |
|
4-5 Tools and Techniques: Analyzing Protein Structure |
|
|
108 | (13) |
|
Chromatography takes advantage of a polypeptide's unique properties |
|
|
108 | (3) |
|
Mass spectrometry reveals amino acid sequences |
|
|
111 | (2) |
|
Protein structures are determined by X-ray crystallography, electron crystallography, and NMR spectroscopy |
|
|
113 | |
|
Box 4-A Biochemistry Note Does Chirality Matter? |
|
|
89 | (3) |
|
Box 4-B Biochemistry Note Monosodium Glutamate |
|
|
92 | (13) |
|
Box 4-C Clinical Connection Protein Misfolding and Disease |
|
|
105 | (8) |
|
Box 4-D Biochemistry Note Mass Spectrometry Applications |
|
|
113 | (2) |
|
Bioinformatics Project 3 Visualizing Three-Dimensional Protein Structures |
|
|
115 | (6) |
|
|
|
121 | (37) |
|
5-1 Myoglobin and Hemoglobin: Oxygen-Binding Proteins |
|
|
122 | (11) |
|
Oxygen binding to myoglobin depends on the oxygen concentration |
|
|
123 | (1) |
|
Myoglobin and hemoglobin are related by evolution |
|
|
124 | (2) |
|
Oxygen binds cooperatively to hemoglobin |
|
|
126 | (2) |
|
A conformational shift explains hemoglobin's cooperative behavior |
|
|
128 | (1) |
|
H+ ions and bisphosphoglycerate regulate oxygen binding to hemoglobin in vivo |
|
|
129 | (4) |
|
|
|
133 | (11) |
|
Microfilaments are made of actin |
|
|
133 | (1) |
|
Actin filaments continuously extend and retract |
|
|
134 | (2) |
|
Tubulin forms hollow microtubules |
|
|
136 | (1) |
|
Some drugs affect microtubules |
|
|
137 | (1) |
|
Keratin is an intermediate filament |
|
|
138 | (2) |
|
Collagen is a triple helix |
|
|
140 | (2) |
|
Collagen molecules are covalently cross-linked |
|
|
142 | (2) |
|
|
|
144 | (14) |
|
Myosin has two heads and a long tail |
|
|
144 | (2) |
|
Myosin operates through a lever mechanism |
|
|
146 | (1) |
|
Kinesin is a microtubule-associated motor protein |
|
|
146 | (4) |
|
Kinesin is a processive motor |
|
|
150 | |
|
Box 5-A Biochemistry Note Erythropoietin Boosts Red Blood Cell Production |
|
|
126 | (1) |
|
Box 5-B Biochemistry Note Carbon Monoxide Poisoning |
|
|
127 | (3) |
|
Box 5-C Clinical Connection Hemoglobin Mutations |
|
|
130 | (11) |
|
Box 5-D Biochemistry Note Vitamin C Deficiency Causes Scurvy |
|
|
141 | (2) |
|
Box 5-E Clinical Connection Genetic Collagen Diseases |
|
|
143 | (4) |
|
Box 5-F Biochemistry Note Myosin Mutations and Deafness |
|
|
147 | (4) |
|
Bioinformatics Project 4 Using Databases to Compare and Identify Related Protein Sequences |
|
|
151 | (7) |
|
|
|
158 | (30) |
|
|
|
159 | (3) |
|
Enzymes are usually named after the reaction they catalyze |
|
|
161 | (1) |
|
6-2 The Chemistry of Catalysis |
|
|
162 | (9) |
|
A catalyst provides a reaction pathway with a lower activation energy barrier |
|
|
164 | (1) |
|
Enzymes use chemical catalytic mechanisms |
|
|
164 | (5) |
|
The catalytic triad of chymotrypsin promotes peptide bond hydrolysis |
|
|
169 | (2) |
|
6-3 The Unique Properties of Enzyme Catalysts |
|
|
171 | (3) |
|
Enzymes stabilize the transition state |
|
|
171 | (2) |
|
Efficient catalysis depends on proximity and orientation effects |
|
|
173 | (1) |
|
The active site microenvironment promotes catalysis |
|
|
173 | (1) |
|
6-4 Some Additional Features of Enzymes |
|
|
174 | (14) |
|
Not all serine proteases are related by evolution |
|
|
174 | (1) |
|
Enzymes with similar mechanisms exhibit different substrate specificity |
|
|
175 | (1) |
|
Chymotrypsin is activated by proteolysis |
|
|
176 | (3) |
|
Protease inhibitors limit protease activity |
|
|
179 | |
|
Box 6-A Biochemistry Note Depicting Reaction Mechanisms |
|
|
167 | (10) |
|
Box 6-B Clinical Connection Blood Coagulation Requires a Cascade of Proteases |
|
|
177 | (11) |
|
7 Enzyme Kinetics And Inhibition |
|
|
188 | (32) |
|
7-1 Introduction to Enzyme Kinetics |
|
|
189 | (2) |
|
7-2 Derivation and Meaning of the Michaelis-Menten Equation |
|
|
191 | (9) |
|
Rate equations describe chemical processes |
|
|
191 | (1) |
|
The Michaelis-Menten equation is a rate equation for an enzyme-catalyzed reaction |
|
|
192 | (3) |
|
Km is the substrate concentration at which velocity is half-maximal |
|
|
195 | (1) |
|
The catalytic constant describes how quickly an enzyme can act |
|
|
195 | (1) |
|
kcat/KM indicates catalytic efficiency |
|
|
195 | (1) |
|
KM and Vmax are experimentally determined |
|
|
196 | (2) |
|
Not all enzymes fit the simple Michaelis-Menten model |
|
|
198 | (2) |
|
|
|
200 | (20) |
|
Some inhibitors act irreversibly |
|
|
202 | (1) |
|
Competitive inhibition is the most common form of reversible enzyme inhibition |
|
|
203 | (2) |
|
Transition state analogs inhibit enzymes |
|
|
205 | (2) |
|
Other types of inhibitors affect Vmax |
|
|
207 | (2) |
|
Allosteric enzyme regulation includes inhibition and activation |
|
|
209 | (2) |
|
Several factors may influence enzyme activity |
|
|
211 | |
|
Box 7-A Clinical Connection Drug Development |
|
|
200 | (6) |
|
Box 7-B Biochemistry Note Inhibitors of HIV Protease |
|
|
206 | (6) |
|
Bioinformatics Project 5 Enzyme Inhibitors and Rational Drug Design |
|
|
212 | (8) |
|
|
|
220 | (21) |
|
|
|
221 | (6) |
|
Fatty acids contain long hydrocarbon chains |
|
|
221 | (2) |
|
Some lipids contain polar head groups |
|
|
223 | (2) |
|
Lipids perform a variety of physiological I functions |
|
|
225 | (2) |
|
|
|
227 | (3) |
|
The bilayer is a fluid structure |
|
|
227 | (3) |
|
Natural bilayers are asymmetric |
|
|
230 | (1) |
|
|
|
230 | (3) |
|
Integral membrane proteins span the bilayer |
|
|
231 | (1) |
|
An a helix can cross the bilayer |
|
|
231 | (1) |
|
A transmembrane β sheet forms a barrel |
|
|
232 | (1) |
|
Lipid-linked proteins are anchored in the membrane |
|
|
232 | (1) |
|
8-4 The Fluid Mosaic Model |
|
|
233 | (8) |
|
Membrane glycoproteins face the cell exterior |
|
|
234 | |
|
Box 8-A Biochemistry Note Omega-3 Fatty Acids |
|
|
222 | (3) |
|
Box 8-B Clinical Connection The Lipid Vitamins A, D, E, and K |
|
|
225 | (16) |
|
|
|
241 | (25) |
|
9-1 The Thermodynamics of Membrane Transport |
|
|
242 | (4) |
|
Ion movements alter membrane potential |
|
|
243 | (2) |
|
Transporters mediate transmembrane ion movement |
|
|
245 | (1) |
|
|
|
246 | (6) |
|
Porins are β barrel proteins |
|
|
246 | (1) |
|
Ion channels are highly selective |
|
|
247 | (1) |
|
Gated channels undergo conformational changes |
|
|
248 | (2) |
|
Aquaporins are water-specific pores |
|
|
250 | (1) |
|
Some transport proteins alternate between conformations |
|
|
251 | (1) |
|
|
|
252 | (3) |
|
The Na, K-ATPase changes conformation as it pumps ions across the membrane |
|
|
252 | (1) |
|
ABC transporters mediate drug resistance |
|
|
253 | (1) |
|
Secondary active transport exploits existing gradients |
|
|
254 | (1) |
|
|
|
255 | (11) |
|
SNAREs link vesicle and plasma membranes |
|
|
256 | (3) |
|
Membrane fusion requires changes in bilayer curvature |
|
|
259 | |
|
Box 9-A Biochemistry Note Pores Can Kill |
|
|
248 | (9) |
|
Box 9-B Biochemistry Note Some Drugs Interfere with Neuronal Signaling |
|
|
257 | (1) |
|
Box 9-C Clinical Connection Antidepressants Block Serotonin Transport |
|
|
258 | (8) |
|
|
|
266 | (24) |
|
10-1 General Features of Signaling Pathways |
|
|
267 | (4) |
|
A ligand binds to a receptor with a characteristic affinity |
|
|
267 | (2) |
|
Most signaling occurs through two types of receptors |
|
|
269 | (1) |
|
The effects of signaling are limited |
|
|
270 | (1) |
|
10-2 G Protein Signaling Pathways |
|
|
271 | (6) |
|
G protein--coupled receptors include seven transmembrane helices |
|
|
271 | (1) |
|
The receptor activates a G protein |
|
|
272 | (1) |
|
Adenylate cyclase generates the second messenger cyclic AMP |
|
|
273 | (1) |
|
Cyclic AMP activates protein kinase A |
|
|
273 | (2) |
|
Signaling pathways are also switched off |
|
|
275 | (1) |
|
The phosphoinositide signaling pathway generates two second messengers |
|
|
276 | (1) |
|
Calmodulin mediates some Ca2+ signals |
|
|
277 | (1) |
|
10-3 Receptor Tyrosine Kinases |
|
|
277 | (4) |
|
The insulin receptor has two ligand-binding sites |
|
|
277 | (1) |
|
The receptor undergoes autophosphorylation |
|
|
278 | (3) |
|
10-4 Lipid Hormone Signaling |
|
|
281 | (9) |
|
Eicosanoids are short-range signals |
|
|
282 | |
|
Box 10-A Biochemistry Note Bacterial Quorum Sensing |
|
|
268 | (12) |
|
Box 10-B Biochemistry Note Cell Signaling and Cancer |
|
|
280 | (2) |
|
Box 10-C Biochemistry Note Oral Contraceptives |
|
|
282 | (1) |
|
Box 10-D Biochemistry Note Aspirin and Other Inhibitors of Cyclooxygenase |
|
|
283 | (7) |
|
|
|
290 | (18) |
|
|
|
291 | (3) |
|
Most carbohydrates are chiral compounds |
|
|
291 | (1) |
|
Cyclization generates α and β anomers |
|
|
292 | (1) |
|
Monosaccharides can be derivatized in many different ways |
|
|
293 | (1) |
|
|
|
294 | (5) |
|
Lactose and sucrose are the most common disaccharides |
|
|
295 | (1) |
|
Starch and glycogen are fuel storage molecules |
|
|
296 | (1) |
|
Cellulose and chitin provide structural support |
|
|
296 | (2) |
|
Bacterial polysaccharides form a biofilm |
|
|
298 | (1) |
|
|
|
299 | (9) |
|
N-linked oligosaccharides undergo processing |
|
|
299 | (1) |
|
O-linked oligosaccharides tend to be large |
|
|
300 | (1) |
|
What is the purpose of the oligosaccharide groups? |
|
|
300 | (1) |
|
Proteoglycans contain long glycosaminoglycan chains |
|
|
301 | (1) |
|
Bacterial cell walls are made of peptidoglycan |
|
|
302 | |
|
Box 11-A Biochemistry Note Cellulosic Biofuel |
|
|
297 | (4) |
|
Box 11-B Biochemistry Note The ABO Blood Group System |
|
|
301 | (2) |
|
Box 11-C Biochemistry Note Antibiotics and Bacterial Cell Walls |
|
|
303 | (5) |
|
|
|
|
12 Metabolism And Bioenergetics |
|
|
308 | (30) |
|
|
|
309 | (5) |
|
Cells take up the products of digestion |
|
|
309 | (3) |
|
Monomers are stored as polymers |
|
|
312 | (1) |
|
Fuels are mobilized as needed |
|
|
312 | (2) |
|
|
|
314 | (9) |
|
Some major metabolic pathways share a few common intermediates |
|
|
315 | (1) |
|
Many metabolic pathways include oxidation-reduction reactions |
|
|
316 | (2) |
|
Metabolic pathways are complex |
|
|
318 | (2) |
|
Human metabolism depends on vitamins |
|
|
320 | (3) |
|
12-3 Free Energy Changes in Metabolic Reactions |
|
|
323 | (15) |
|
The free energy change depends on reactant concentrations |
|
|
323 | (2) |
|
Unfavorable reactions are coupled to favorable reactions |
|
|
325 | (3) |
|
Free energy can take different forms |
|
|
328 | (2) |
|
Regulation occurs at the steps with the largest free energy changes |
|
|
330 | |
|
Box 12-A Biochemistry Note Dietary Guidelines |
|
|
311 | (8) |
|
Box 12-B Biochemistry Note The Transcriptome, the Proteome, and the Metabolome |
|
|
319 | (5) |
|
Box 12-C Biochemistry Note What Is a Calorie? |
|
|
324 | (4) |
|
Box 12-D Biochemistry Note Powering Human Muscles |
|
|
328 | (4) |
|
Bioinformatics Project 6 Metabolic Enzymes, Microarrays, and Proteomics |
|
|
332 | (6) |
|
|
|
338 | (32) |
|
|
|
339 | (15) |
|
Reactions 1--5 are the energy-investment phase of glycolysis |
|
|
341 | (4) |
|
Reactions 6--10 are the energy-payoff phase of glycolysis |
|
|
345 | (5) |
|
Pyruvate is converted to other substances |
|
|
350 | (4) |
|
|
|
354 | (3) |
|
Four gluconeogenic enzymes plus some glycolytic enzymes convert pyruvate to glucose |
|
|
355 | (1) |
|
Gluconeogenesis is regulated at the fructose bisphosphatase step |
|
|
356 | (1) |
|
13-3 Glycogen Synthesis and Degradation |
|
|
357 | (4) |
|
Glycogen synthesis consumes the free energy of UTP |
|
|
358 | (1) |
|
Glycogen phosphorylase catalyzes glycogenolysis |
|
|
359 | (2) |
|
13-4 The Pentose Phosphate Pathway |
|
|
361 | (9) |
|
The oxidative reactions of the pentose phosphate pathway produce NAD PH |
|
|
361 | (1) |
|
Isomerization and interconversion reactions generate a variety of monosaccharides |
|
|
362 | (1) |
|
A summary of glucose metabolism |
|
|
363 | |
|
Box 13-A Biochemistry Note Catabolism of Other Sugars |
|
|
349 | (3) |
|
Box 13-B Clinical Connection Alcohol Metabolism |
|
|
352 | (8) |
|
Box 13-C Clinical Connection Glycogen Storage Diseases |
|
|
360 | (10) |
|
|
|
370 | (5) |
|
14-1 The Pyruvate Dehydrogenase Reaction |
|
|
371 | (3) |
|
The pyruvate dehydrogenase complex contains multiple copies of three different enzymes |
|
|
371 | (1) |
|
Pyruvate dehydrogenase converts pyruvate to acetyl-CoA |
|
|
372 | (2) |
|
14-2 The Eight Reactions of the Citric Acid Cycle |
|
|
374 | (1) |
|
1 Citrate synthase adds an acetyl group to oxaloacetate |
|
|
375 | (1) |
|
2 Aconitase isomerizes citrate to isocitrate |
|
|
376 | (1) |
|
3 Isocitrate dehydrogenase releases the first CO2 |
|
|
377 | (1) |
|
4 α-Ketoglutarate dehydrogenase releases the second CO2 |
|
|
378 | (1) |
|
5 Succinyl-CoA synthetase catalyzes substrate-level phosphorylation |
|
|
378 | (1) |
|
6 Succinate dehydrogenase generates ubiquinol |
|
|
379 | (1) |
|
7 Fumarase catalyzes a hydration reaction |
|
|
380 | (1) |
|
8 Malate dehydrogenase regenerates oxaloacetate |
|
|
380 | (14) |
|
The citric acid cycle is an energy-generating catalytic cycle |
|
|
380 | (1) |
|
The citric acid cycle is regulated at three steps |
|
|
381 | (1) |
|
The citric acid cycle probably evolved as a synthetic pathway |
|
|
382 | (2) |
|
14-3 Anabolic and Catabolic Functions of the Citric Acid Cycle |
|
|
384 | (10) |
|
Citric acid cycle intermediates are precursors of other molecules |
|
|
384 | (1) |
|
Anaplerotic reactions replenish citric acid cycle intermediates |
|
|
385 | |
|
Box 14-A Clinical Connection Mutations in Citric Acid Cycle Enzymes |
|
|
382 | (4) |
|
Box 14-B Biochemistry Note The Glyoxylate Pathway |
|
|
386 | (8) |
|
15 Oxidative Phosphorylation |
|
|
394 | (26) |
|
15-1 The Thermodynamics of Oxidation-Reduction Reactions |
|
|
395 | (4) |
|
Reduction potential indicates a substance's tendency to accept electrons |
|
|
396 | (1) |
|
The free energy change can be calculated from the change in reduction potential |
|
|
397 | (2) |
|
15-2 Mitochondrial Electron Transport |
|
|
399 | (9) |
|
Mitochondrial membranes define two compartments |
|
|
399 | (2) |
|
Complex I transfers electrons from NADH to ubiquinone |
|
|
401 | (2) |
|
Other oxidation reactions contribute to the ubiquinol pool |
|
|
403 | (1) |
|
Complex III transfers electrons from ubiquinol to cytochrome c |
|
|
403 | (3) |
|
Complex IV oxidizes cytochrome C and reduces O02 |
|
|
406 | (2) |
|
|
|
408 | (2) |
|
Chemiosmosis links electron transport and oxidative phosphorylation |
|
|
408 | (1) |
|
The proton gradient is an electrochemical gradient |
|
|
409 | (1) |
|
|
|
410 | (10) |
|
ATP synthase rotates as it translocates protons |
|
|
410 | (2) |
|
The binding change mechanism explains how ATP is made |
|
|
412 | (1) |
|
The P: O ratio describes the stoichiometry of oxidative phosphorylation |
|
|
412 | (1) |
|
The rate of oxidative phosphorylation depends on the rate of fuel catabolism |
|
|
413 | |
|
Box 15-A Biochemistry Note Free Radicals and Aging |
|
|
407 | (6) |
|
Box 15-B Biochemistry Note Uncoupling Agents Prevent ATP Synthesis |
|
|
413 | (7) |
|
|
|
420 | (22) |
|
16-1 Chloroplasts and Solar Energy |
|
|
422 | (3) |
|
Pigments absorb light of different wavelengths |
|
|
422 | (2) |
|
Light-harvesting complexes transfer energy to the reaction center |
|
|
424 | (1) |
|
|
|
425 | (7) |
|
Photosystem II is a light-activated oxidation-reduction enzyme |
|
|
425 | (1) |
|
The oxygen-evolving complex of Photosystem II oxidizes water |
|
|
426 | (2) |
|
Cytochrome b6ƒ links Photosystems I and II |
|
|
428 | (1) |
|
A second photooxidation occurs at Photosystem I |
|
|
428 | (3) |
|
Chemiosmosis provides the free energy for ATP synthesis |
|
|
431 | (1) |
|
|
|
432 | (10) |
|
Rubisco catalyzes CO2 fixation |
|
|
432 | (2) |
|
The Calvin cycle rearranges sugar molecules |
|
|
434 | (2) |
|
The availability of light regulates carbon fixation |
|
|
436 | (1) |
|
Calvin cycle products are used to synthesize sucrose and starch |
|
|
436 | |
|
Box 16-A Biochemistry Note The C4 Pathway |
|
|
433 | (9) |
|
|
|
442 | (33) |
|
17-1 Fatty Acid Oxidation |
|
|
445 | (8) |
|
Fatty acids are activated before they are degraded |
|
|
445 | (1) |
|
Each round of B oxidation has four reactions |
|
|
446 | (3) |
|
Degradation of unsaturated fatty acids requires isomerization and reduction |
|
|
449 | (1) |
|
Oxidation of odd-chain fatty acids yields propionyl-CoA |
|
|
450 | (1) |
|
Some fatty acid oxidation occurs in peroxisomes |
|
|
450 | (3) |
|
17-2 Fatty Acid Synthesis |
|
|
453 | (10) |
|
Acetyl-CoA carboxylase catalyzes the first step of fatty acid synthesis |
|
|
454 | (1) |
|
Fatty acid synthase catalyzes seven reactions |
|
|
455 | (2) |
|
Other enzymes elongate and desaturate newly synthesized fatty acids |
|
|
457 | (2) |
|
Fatty acid synthesis can be activated and inhibited |
|
|
459 | (2) |
|
Acetyl-CoA can be converted to ketone bodies |
|
|
461 | (2) |
|
17-3 Synthesis of Other Lipids |
|
|
463 | (12) |
|
Triacylglycerols and phospholipids are built from acyl-CoA groups |
|
|
463 | (3) |
|
Cholesterol synthesis begins with acetyl-CoA |
|
|
466 | (1) |
|
Cholesterol can be used in several ways |
|
|
467 | (2) |
|
A summary of lipid metabolism |
|
|
469 | |
|
Box 17-A Biochemistry Note Fats, Diet, and Heart Disease |
|
|
458 | (2) |
|
Box 17-B Clinical Connection Inhibitors of Fatty Acid Synthesis |
|
|
460 | (15) |
|
|
|
475 | (34) |
|
18-1 Nitrogen Fixation and Assimilation |
|
|
476 | (4) |
|
Nitrogenase converts N2 to NH3 |
|
|
476 | (1) |
|
Ammonia is assimilated by glutamine synthetase and glutamate synthase |
|
|
477 | (1) |
|
Transamination moves amino groups between compounds |
|
|
478 | (2) |
|
18-2 Amino Acid Biosynthesis |
|
|
480 | (8) |
|
Several amino acids are easily synthesized from common metabolites |
|
|
481 | (1) |
|
Amino acids with sulfur, branched chains, or aromatic groups are more difficult to synthesize |
|
|
482 | (4) |
|
Amino acids are the precursors of some signaling molecules |
|
|
486 | (2) |
|
18-3 Nucleotide Biosynthesis |
|
|
488 | (6) |
|
Purine nucleotide synthesis yields IMP and then AMP and GMP |
|
|
488 | (1) |
|
Pyrimidine nucleotide synthesis yields UTP and CTP |
|
|
489 | (1) |
|
Ribonucleotide reductase converts ribonucleotides to deoxyribonucleotides |
|
|
490 | (1) |
|
Thymidine nucleotides are produced by methylation |
|
|
491 | (1) |
|
Nucleotide degradation produces uric acid or amino acids |
|
|
492 | (2) |
|
18-4 Amino Acid Catabolism |
|
|
494 | (4) |
|
Amino acids are glucogenic, ketogenic, or both |
|
|
494 | (4) |
|
18-5 Nitrogen Disposal: The Urea Cycle |
|
|
498 | (11) |
|
Glutamate supplies nitrogen to the urea cycle |
|
|
499 | (1) |
|
The urea cycle consists of four reactions |
|
|
499 | |
|
Box 18-A Biochemistry Note Transaminases in the Clinic |
|
|
480 | (4) |
|
Box 18-B Biochemistry Note Glyphosate, the Most Popular Herbicide |
|
|
484 | (3) |
|
Box 18-C Biochemistry Note Nitric Oxide |
|
|
487 | (10) |
|
Box 18-D Biochemistry Note Inborn Errors of Metabolism |
|
|
497 | (12) |
|
19 Regulation Of Mammalian Fuel Metabolism |
|
|
509 | (20) |
|
19-1 Integration of Fuel Metabolism |
|
|
510 | (5) |
|
Organs are specialized for different functions |
|
|
510 | (3) |
|
Metabolites travel between organs |
|
|
513 | (2) |
|
19-2 Hormonal Control of Fuel Metabolism |
|
|
515 | (5) |
|
Insulin is released in response to glucose |
|
|
515 | (1) |
|
Insulin promotes fuel use and storage |
|
|
516 | (1) |
|
Glucagon and epinephrine trigger fuel mobilization |
|
|
517 | (1) |
|
Additional hormones influence fuel metabolism |
|
|
518 | (1) |
|
AMP-dependent protein kinase acts as a fuel sensor |
|
|
519 | (1) |
|
19-3 Disorders of Fuel Metabolism |
|
|
520 | (9) |
|
The body generates glucose and ketone bodies during starvation |
|
|
520 | (1) |
|
Obesity has multiple causes |
|
|
521 | (1) |
|
Diabetes is characterized by hyperglycemia |
|
|
522 | (1) |
|
The metabolic syndrome links obesity and diabetes |
|
|
523 | |
|
Box 19-A Clinical Connection Cancer Metabolism |
|
|
512 | (1) |
|
Box 19-B Biochemistry Note The Intestinal Microbiome Contributes to Metabolism |
|
|
513 | (7) |
|
Box 19-C Biochemistry Note Marasmus and Kwashiorkor |
|
|
520 | (9) |
|
part four Genetic Information |
|
|
|
20 DNA Replication And Repair |
|
|
529 | (32) |
|
|
|
530 | (3) |
|
Topoisomerases alter DNA supercoiling |
|
|
531 | (2) |
|
20-2 The DNA Replication Machinery |
|
|
533 | (7) |
|
Replication occurs in factories |
|
|
533 | (1) |
|
Helicases convert double-stranded DNA to single-stranded DNA |
|
|
533 | (1) |
|
DNA polymerase faces two problems |
|
|
534 | (2) |
|
DNA polymerases share a common structure and mechanism |
|
|
536 | (1) |
|
DNA polymerase proofreads newly synthesized DNA |
|
|
537 | (1) |
|
An RNase and a ligase are required to complete the lagging strand |
|
|
538 | (2) |
|
|
|
540 | (3) |
|
Telomerase extends chromosomes |
|
|
540 | (3) |
|
Is telomerase activity linked to cell immortality? |
|
|
543 | (1) |
|
20-4 DNA Damage and Repair |
|
|
543 | (9) |
|
DNA damage is unavoidable |
|
|
543 | (4) |
|
Repair enzymes restore some types of damaged DNA |
|
|
547 | (1) |
|
Base excision repair corrects the most frequent DNA lesions |
|
|
548 | (1) |
|
Nucleotide excision repair targets the second most common form of DNA damage |
|
|
549 | (1) |
|
Double-strand breaks can be repaired by joining the ends |
|
|
550 | (1) |
|
Recombination also restores broken DNA molecules |
|
|
551 | (1) |
|
|
|
552 | (9) |
|
The fundamental unit of DNA packaging is the nucleosome |
|
|
552 | (1) |
|
Histones are covalently modified |
|
|
553 | (1) |
|
DNA also undergoes covalent modification |
|
|
554 | |
|
Box 20-A Biochemistry Note HIV Reverse Transcriptase |
|
|
541 | (3) |
|
Box 20-B Clinical Connection Cancer Is a Genetic Disease |
|
|
544 | (17) |
|
|
|
561 | (29) |
|
21-1 Transcription Initiation |
|
|
563 | (8) |
|
Chromatin remodeling may precede |
|
|
|
|
|
563 | (1) |
|
Transcription begins at promoters |
|
|
564 | (2) |
|
Transcription factors recognize eukaryotic) promoters |
|
|
566 | (1) |
|
Enhancers and silencers act at a distance from the promoter |
|
|
566 | (4) |
|
Prokaryotic operons allow coordinated gene expression |
|
|
570 | (1) |
|
|
|
571 | (5) |
|
RNA polymerase is a processive enzyme |
|
|
573 | (1) |
|
Transcription elongation requires a conformational change in RNA polymerase |
|
|
573 | (1) |
|
Transcription is terminated in several ways |
|
|
574 | (2) |
|
|
|
576 | (14) |
|
Eukaryotic mRNAs receive a 5' cap and a 3' poly(A) tail |
|
|
576 | (1) |
|
Splicing removes introns from eukaryotic genes |
|
|
576 | (3) |
|
mRNA turnover and RNA interference limit gene expression |
|
|
579 | (2) |
|
rRNA and tRNA processing includes the addition, deletion, and modification of nucleotides |
|
|
581 | |
|
Box 21-A Biochemistry Note DNA Binding Proteins |
|
|
567 | (15) |
|
Box 21-B Biochemistry Note RNA: A Versatile Molecule |
|
|
582 | (8) |
|
|
|
590 | (27) |
|
|
|
592 | (4) |
|
tRNA aminoacylation consumes ATP |
|
|
593 | (1) |
|
Some synthetases have proofreading activity |
|
|
594 | (1) |
|
tRNA anticodons pair with mRNA codons |
|
|
594 | (2) |
|
|
|
596 | (3) |
|
|
|
599 | (9) |
|
Initiation requires an initiator tRNA |
|
|
599 | (2) |
|
The appropriate tRNAs are delivered to the ribosome during elongation |
|
|
601 | (2) |
|
The peptidyl transferase active site catalyzes peptide bond formation |
|
|
603 | (3) |
|
Release factors mediate translation termination |
|
|
606 | (1) |
|
Translation is efficient in vivo |
|
|
606 | (2) |
|
22-4 Post-translational Events |
|
|
608 | (9) |
|
Chaperones promote protein folding |
|
|
608 | (1) |
|
The signal recognition particle targets some proteins for membrane translocation |
|
|
609 | (2) |
|
Many proteins undergo covalent modification |
|
|
611 | |
|
Box 22-A Biochemistry Note The Genetic Code Expanded |
|
|
595 | (9) |
|
Box 22-B Biochemistry Note Antibiotic Inhibitors of Protein Synthesis |
|
|
604 | (13) |
| Glossary |
|
617 | (12) |
| Solutions |
|
629 | |
| Answers To Practice Problems |
|
1 | (1) |
| Answers To Clinical Connection Questions |
|
1 | (1) |
| Index |
|
1 | |
