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List of Figures

Figure 1-1 The universal features of living cells.
Figure 1-2 Most animal cells have intricately folded surfaces.
Figure 1-3 Phylogeny of the three domains of life.
Figure 1-4 All organisms can be classified according to their source of energy (sunlight or oxidizable chemical compounds) and their source of carbon for the synthesis of cellular material.
Figure 1-5 Some common structural features of bacterial and archaeal cells.
Figure 1-6 Eukaryotic cell structure.
Figure 1-7 Subcellular fractionation of tissue.
Figure 1-8 The three types of cytoskeletal filaments: actin filaments, microtubules, and intermediate filaments.
Figure 1-9 Structural hierarchy in the molecular organization of cells.
Figure 1-10 The crowded cell.
Figure 1-11 Elements essential to animal life and health.
Figure 1-12 Versatility of carbon bonding.
Figure 1-13 Geometry of carbon bonding.
Figure 1-14 Some common functional groups of biomolecules.
Figure 1-15 Several common functional groups in a single biomolecule.
Figure 1-16 The organic compounds from which most cellular materials are constructed: the ABCs of biochemistry.
Figure 1-17 Representations of molecules.
Figure 1-18 Configurations of geometric isomers.
Figure 1-19 Molecular asymmetry: chiral and achiral molecules.
Figure 1-20 Enantiomers and diastereomers.
Louis Pasteur 1822–1895
Figure 1 Pasteur separated crystals of two stereoisomers of tartaric acid and showed that solutions of the separated forms rotated plane-polarized light to the same extent but in opposite directions. These dextrorotatory and levorotatory forms were later shown to be the (R,R) and (S,S) isomers represented here.
Figure 1-21 Conformations.
Figure 1-22 Complementary fit between a macromolecule and a small molecule.
Figure 1-23 Stereoisomers have different effects in humans.
Figure 1-24 Some energy transformations in living organisms.
J. Willard Gibbs, 1839–1903
Figure 1-25 Adenosine triphosphate (ATP) provides energy.
Figure 1-26 Energy coupling in mechanical and chemical processes.
Figure 1-27 Energy changes during a chemical reaction.
Figure 1-28 The central roles of ATP and NAD(P)H in metabolism.
Figure 1-29 Two ancient scripts.
Figure 1-30 Complementarity between the two strands of DNA.
Figure 1-31 DNA to RNA to protein to enzyme (hexokinase).
Figure 1-32 Gene duplication and mutation: one path to generate new enzymatic activities.
Figure 1-33 Abiotic production of biomolecules.
Figure 1-34 Black smokers.
Figure 1-35 A possible “RNA world” scenario.
Figure 1-36 Landmarks in the evolution of life on Earth.
Figure 1-37 Evolution of eukaryotes through endosymbiosis.
Figure 2-1 Structure of the water molecule.
Figure 2-2 Hydrogen bonding in ice.
Figure 2-3 Common hydrogen bonds in biological systems.
Figure 2-4 Some biologically important hydrogen bonds.
Figure 2-5 Directionality of the hydrogen bond.
Figure 2-6 Water as solvent.
Figure 2-7 Amphipathic compounds in aqueous solution form structures that increase entropy.
Figure 2-8 Release of ordered water favors formation of an enzyme-substrate complex.
Figure 2-9 Water binding in hemoglobin.
Figure 2-10 Water chain in cytochrome f.
Figure 2-11 Osmosis and the measurement of osmotic pressure.
Figure 2-12 Effect of extracellular osmolarity on water movement across a plasma membrane.
Figure 2-13 Proton hopping.
Figure 2-14 The pH of some aqueous fluids.
Figure 2-15 Conjugate acid-base pairs consist of a proton donor and a proton acceptor.
Figure 2-16 The titration curve of acetic acid.
Figure 2-17 Comparison of the titration curves of three weak acids.
Figure 2-18 The acetic acid–acetate pair as a buffer system.
Figure 2-19 Ionization of histidine.
Figure 2-20 The bicarbonate buffer system. CO2
Figure 2-21 The pH optima of two enzymes.
Figure 3-1 Some functions of proteins.
Figure 3-2 General structure of an amino acid.
Margaret Oakley Dayhoff, 1925–1983
Figure 3-3 Stereoisomerism in α-amino acids.
Figure 3-4 Steric relationship of the stereoisomers of alanine to the absolute configuration of l- and d-glyceraldehyde.
Figure 3-5 The 20 common amino acids of proteins.
Figure 3-6 Absorption of ultraviolet light by aromatic amino acids.
Figure 1 The principal components of a spectrophotometer.
Figure 3-7 Reversible formation of a disulfide bond by the oxidation of two molecules of cysteine.
Figure 3-8 Uncommon amino acids.
Figure 3-9 Nonionic and zwitterionic forms of amino acids.
Figure 3-10 Titration of amino acids.
Figure 3-11 Effect of the chemical environment on pKa.
Figure 3-12 Titration curves for (a) glutamate and (b) histidine.
Figure 3-13 Formation of a peptide bond by condensation.
Figure 3-14 The pentapeptide serylglycyltyrosylalanylleucine, Ser–Gly–Tyr–Ala–Leu, or SGYAL.
Figure 3-15 Alanylglutamylglycyllysine.
Figure 3-16 Column chromatography.
Figure 3-17 Three chromatographic methods used in protein purification.
Figure 3-18 Electrophoresis.
Figure 3-19 Estimating the molecular weight of a protein.
Figure 3-20 Isoelectric focusing.
Figure 3-21 Two-dimensional electrophoresis.
Figure 3-22 Activity versus specific activity.
Figure 3-23 Levels of structure in proteins.
Figure 3-24 Amino acid sequence of bovine insulin.
Figure 3-25 Modification of the α-amino group at the amino terminus.
Figure 3-26 Breaking disulfide bonds in proteins.
Frederick Sanger, 1918–2013
Figure 3-27 Reagents used to modify the sulfhydryl groups of Cys residues.
Figure 3-28 Electrospray ionization mass spectrometry of a protein.
Figure 3-29 Obtaining protein sequence information with tandem MS.
Figure 3-30 Chemical synthesis of a peptide on an insoluble polymer support.
Figure 1 Representations of two consensus sequences.
Figure 3-31 Aligning protein sequences with the use of gaps.
Figure 3-32 A signature sequence in the EF-1α/EF-Tu protein family.
Figure 3-33 Evolutionary tree derived from amino acid sequence comparisons.
Figure 4-1 Relationship between protein structure and function.
Figure 4-2 The planar peptide group.
Linus Pauling, 1901–1994
Robert Corey, 1897–1971
Figure 4-3 Models of the α helix, showing different aspects of its structure.
Figure 4-4 Helix dipole.
Figure 4-5 The β conformation of polypeptide chains.
Figure 4-6 Structures of β turns.
Figure 4-7 Trans and cis isomers of a peptide bond involving the imino nitrogen of proline.
Figure 4-8 Ramachandran plots showing a variety of structures.
Figure 4-9 Circular dichroism spectroscopy.
Figure 4-10 Structure of hair.
Figure 4-11 Structure of collagen.
Figure 1 The Cγ-endo conformation of proline and the Cγ-exo conformation of 4-hydroxyproline.
Figure 4-12 Structure of collagen fibrils.
Figure 4-13 Structure of silk.
Figure 4-14 Globular protein structures are compact and varied.
Figure 4-15 Tertiary structure of sperm whale myoglobin.
Figure 4-16 Motifs.
Figure 4-17 Structural domains in the polypeptide troponin C.
Figure 4-18 Stable folding patterns in proteins.
Figure 4-19 Constructing large motifs from smaller ones.
Figure 4-20 Binding of the intrinsically disordered carboxyl terminus of p53 protein to its binding partners.
Figure 4-21 Organization of proteins based on motifs.
Figure 4-22 Quaternary structure of deoxyhemoglobin.
Max Perutz, 1914–2002 (left), and John Kendrew, 1917–1997
Figure 4-23 Pathways that contribute to proteostasis.
Figure 4-24 Protein denaturation.
Figure 4-25 Renaturation of unfolded, denatured ribonuclease.
Figure 4-26 A protein-folding pathway as defined for a small protein.
Figure 4-27 The thermodynamics of protein folding depicted as free-energy funnels.
Figure 4-28 Chaperones in protein folding.
Figure 4-29 Formation of disease-causing amyloid fibrils.
Figure 1 (a) Light micrograph of pyramidal cells in the human cerebral cortex. (b) A comparable section from the autopsy of a patient with Creutzfeldt-Jakob disease shows spongiform (vacuolar) degeneration, the most characteristic neurohistological feature. The yellowish vacuoles are intracellular and occur mostly in pre- and postsynaptic processes of neurons. The vacuoles in this section vary in diameter from 20 to 100 μm.
Figure 2 Structure of the globular domain of human PrP and models of the misfolded, disease-causing conformation PrPSc, and an aggregate of PrPSc.
David Baker
Figure 1 Foldit uses a video game interface to crowdsource protein-folding problems. Proteins designed in the video game can be recreated in the laboratory and studied using biochemical and structural methods.
Figure 2 The Diels-Alder reaction catalyzed by an enzyme designed by Foldit players.
Figure 4-30 Steps in determining the structure of sperm whale myoglobin by x-ray crystallography.
Figure 4-31 NMR spectra of a globin from a marine blood worm.
Figure 4-32 Structure of the chaperone protein GroEL as determined by single-particle cryo-EM.
Figure 4-33 Cryo-EM structure of human telomerase.
Eva Nogales
Kathleen Collins
Figure 5-1 Heme.
Figure 5-2 The heme group viewed from the side.
Figure 5-3 Myoglobin.
Figure 5-4 Graphical representations of ligand binding.
Figure 5-5 Steric effects caused by ligand binding to the heme of myoglobin.
Figure 5-6 Comparison of the structures of myoglobin and the β subunit of hemoglobin.
Figure 5-7 Comparison of whale myoglobin with the α and β chains of human hemoglobin.
Figure 5-8 Dominant interactions between hemoglobin subunits.
Figure 5-9 Some ion pairs that stabilize the T state of deoxyhemoglobin.
Figure 5-10 The T → R transition.
Figure 5-11 Changes in conformation near heme on O2 binding to deoxyhemoglobin.
Figure 5-12 A sigmoid (cooperative) binding curve.
Figure 1 Relationship between levels of COHb in blood and concentration of CO in the surrounding air.
Figure 2 Several oxygen-binding curves: for normal hemoglobin, for hemoglobin from an anemic individual with only 50% of her hemoglobin functional, and for hemoglobin from an individual with 50% of his hemoglobin subunits complexed with CO. The pO2 in human lungs and tissues is indicated.
Figure 5-13 Hill plots for oxygen binding to myoglobin and hemoglobin.
Figure 5-14 Two general models for the interconversion of inactive and active forms of a protein during cooperative ligand binding.
Figure 5-15 Effect of pH on oxygen binding to hemoglobin.
Figure 5-16 Effect of 2,3-bisphosphoglycerate on oxygen binding to hemoglobin.
Figure 5-17 Binding of 2,3-bisphosphoglycerate to deoxyhemoglobin.
Figure 5-18 A comparison of (a) uniform, cup-shaped, normal erythrocytes and (b) the variably shaped erythrocytes seen in sickle cell anemia, which range from normal to spiny or sickle-shaped.
Figure 5-19 Normal and sickle cell hemoglobin.
Figure 5-20 Immunoglobulin G.
Figure 5-21 Binding of IgG to an antigen.
Figure 5-22 IgM pentamer of immunoglobulin units.
Figure 5-23 Phagocytosis of an antibody-bound virus by a macrophage.
Figure 5-24 Induced fit in the binding of an antigen to IgG.
Figure 5-25 Antibodies as analytical reagents.
Figure 5-26 Myosin.
Figure 5-27 The major components of muscle.
Figure 5-28 Skeletal muscle.
Figure 5-29 Molecular mechanism of muscle contraction.
Figure 5-30 Regulation of muscle contraction by tropomyosin and troponin.
Eduard Buchner, 1860–1917
Figure 6-1 Binding of a substrate to an enzyme at the active site.
Figure 6-2 Reaction coordinate diagram.
Figure 6-3 Reaction coordinate diagram comparing enzyme-catalyzed and uncatalyzed reactions.
Figure 6-4 Complementary shapes of a substrate and its binding site on an enzyme.
Figure 6-5 An imaginary enzyme (stickase) designed to catalyze breakage of a metal stick.
Figure 6-6 Role of binding energy in catalysis.
Figure 6-7 Rate enhancement by entropy reduction.
Figure 6-8 How a catalyst circumvents unfavorable charge development during cleavage of an amide.
Figure 6-9 Amino acids in general acid-base catalysis.
Figure 6-10 The course of an enzyme-catalyzed reaction.
Figure 6-11 Initial velocities of enzyme-catalyzed reactions.
Figure 6-12 Effect of substrate concentration on the initial velocity of an enzyme-catalyzed reaction.
Left: Leonor Michaelis, 1875–1949 Right: Maud Menten, 1879–1960
Figure 6-13 Dependence of initial velocity on substrate concentration.
Figure 6-14 A double-reciprocal, or Lineweaver-Burk, plot.
Figure 6-15 Common mechanisms for enzyme-catalyzed bisubstrate reactions.
Figure 6-16 Steady-state kinetic analysis of bisubstrate reactions.
Figure 6-17 The pH-activity profiles of two enzymes.
Figure 6-18 Pre–steady state kinetics.
Figure 6-19 Competitive inhibition.
Figure 6-20 Uncompetitive inhibition.
Figure 6-21 Mixed inhibition.
Figure 6-22 Irreversible inhibition.
Figure 1 Trypanosoma brucei rhodesiense, one of several trypanosomes known to cause African sleeping sickness.
Figure 2 Mechanism of ornithine decarboxylase reaction.
Figure 3 Inhibition of ornithine decarboxylase by DFMO.
Figure 6-23 A transition-state analog.
Figure 6-24 Structure of chymotrypsin.
Figure 6-25 Pre–steady state kinetic evidence for an acyl-enzyme intermediate.
Figure 6-26 The pH dependence of chymotrypsin-catalyzed reactions.
Mechanism Figure 6-27 Hydrolytic cleavage of a peptide bond by chymotrypsin.
Mechanism Figure 6-28 Mechanism of action of HIV protease.
Figure 6-29 HIV protease inhibitors.
Figure 6-30 Induced fit in hexokinase.
Mechanism Figure 6-31 Two-step reaction catalyzed by enolase.
Figure 6-32 The transpeptidase reaction.
Figure 6-33 Transpeptidase inhibition by βlactam antibiotics.
Figure 6-34 βLactamases and βlactamase inhibition.
Figure 6-35 Subunit interactions in an allosteric enzyme, and interactions with inhibitors and activators.
Figure 6-36 The regulatory enzyme aspartate transcarbamoylase.
Figure 6-37 Substrate-activity curves for representative allosteric enzymes.
Figure 6-38 Some enzyme modification reactions.
Figure 6-39 Regulation of muscle glycogen phosphorylase activity by phosphorylation.
Figure 6-40 The conformation change brought about by phosphorylation in glycogen phosphorylase from rabbit muscle.
Figure 6-41 Multiple regulatory phosphorylations.
Figure 6-42 Activation of zymogens by proteolytic cleavage.
Figure 6-43 The function of fibrin in blood clots.
Figure 6-44 The coagulation cascades.
Figure 6-45 The royal families of Europe, and inheritance of hemophilia B.
Figure 1 The receptor for sweet-tasting substances, showing its regions of interaction (short arrows) with various sweet-tasting compounds. Each receptor subunit has seven transmembrane helices, a common feature of signaling receptors. Artificial sweeteners bind to only one of the two receptor subunits; natural sugars bind to both. TAS1R2 and TAS1R3 are the proteins encoded by the genes TAS1R2 and TAS1R3. [Information from F. M. Assadi-Porter et al., J. Mol. Biol. 398:584, 2010, Fig. 1.]
Figure 2 Stereochemical basis for the taste of two isomers of aspartame. [Information from http://chemistry.elmhurst.edu/vchembook/549receptor.html, ³ Charles E. Ophardt, Elmhurst College.]
Figure 7-1 Representative monosaccharides.
Figure 7-2 Three ways to represent the two enantiomers of glyceraldehyde.
Figure 7-3 Aldoses and ketoses.
Figure 7-4 Epimers.
Figure 7-5 Formation of hemiacetals and hemiketals.
Figure 7-6 Formation of the two cyclic forms of d-glucose.
Figure 7-7 Pyranoses and furanoses.
Figure 7-8 Conformational formulas of pyranoses.
Figure 7-9 Some hexose derivatives important in biology.
Figure 1 The nonenzymatic reaction of glucose with a primary amino group in hemoglobin begins with formation of a Schiff base, which undergoes a rearrangement to generate a stable product; this ketoamine can further cyclize to yield GHB.
Figure 2 Glycated hemoglobin, showing the hemes (red) and the glycated Lys99 residue (blue). [Data from PDB ID 3B75, N. T. Saraswathi et al., 2008.]
Figure 3 Pattern of hemoglobin (detected by its absorption at 415 nm) after electrophoretic separation of nonglycated (A0) and monoglycated (A1c) forms in a thin glass capillary. Integration of the area under the peaks allows calculation of the amount of GHB (HbA1c) as a percentage of total hemoglobin. Shown here is the profile of an individual with a normal level of HbA1c (5.9%).
Figure 4 Pathways from glycated hemoglobin to the tissue damage associated with diabetes.
Figure 7-10 Formation of maltose.
Figure 7-11 Three common disaccharides.
Figure 7-12 Homopolysaccharides and heteropolysaccharides.
Figure 7-13 Starch and glycogen.
Figure 7-14 Cellulose.
Figure 7-15 Chitin.
Figure 7-16 Different energetic conformations of a disaccharide.
Figure 7-17 Helical structure of starch (amylose).
Figure 7-18 The linear structure of cellulose chains.
Figure 7-19 Repeating units of some common glycosaminoglycans of extracellular matrix.
Figure 7-24 Molecular basis for heparan sulfate enhancement of the binding of thrombin to antithrombin.
Figure 7-20 Glycoconjugates.
Figure 7-21 Proteoglycan structure, showing the tetrasaccharide bridge.
Figure 7-22 Two families of membrane proteoglycans.
Figure 7-23 Four types of protein interactions with NS domains of heparan sulfate.
Figure 1 A segment of proteoglycan showing the normal structure of the glycosaminoglycans (GAGs) chondroitin sulfate or dermatan sulfate (CS/DS) (top) and heparan sulfate or heparin (HS/Hep) (bottom), attached through the linkage region to a Ser residue in the core protein. When a specific biosynthetic enzyme is absent because of a mutation, the numbered elements cannot be added to the growing oligosaccharide, and the product is truncated. The dysfunctional GAGs result in several types of human disease, depending on the site of truncation: progeroid-type Ehlers-Danlos syndrome – with hyperextensible joints, fragile skin, and premature aging; short stature or frequent joint dislocations; neuropathy (nerve damage); skeletal defects; bipolar disorder or diaphragmatic hernia; and bone deformations in the form of large bone spurs.
Figure 2 Bone deformation characteristic of multiple hereditary exostoses, a disease resulting from a genetic inability to add the GlcNAc-GlcA disaccharide to the growing heparan sulfate or heparin chain (see in Fig. 1). The extra bone growth is artificially colored red in this x-ray of the humerus (upper arm bone).
Figure 7-25 Proteoglycan aggregate of the extracellular matrix.
Figure 7-26 Interactions between cells and the extracellular matrix.
Figure 7-27 Oligosaccharide linkages in glycoproteins.
Figure 7-28 Bacterial lipopolysaccharides.
Figure 7-29 Role of lectin-ligand interactions in leukocyte movement to the site of an infection or injury.
Figure 7-30 Binding site on influenza neuraminidase for N-acetylneuraminic acid and an antiviral drug.
Figure 7-31 Details of a lectin-carbohydrate interaction.
Figure 7-32 Interactions of sugar residues due to the hydrophobic effect.
Figure 7-33 Role of oligosaccharides in recognition events at the cell surface and in the endomembrane system.
Figure 7-34 Methods of carbohydrate analysis.
Figure 8-1 Structure of nucleotides.
Figure 8-2 Major purine and pyrimidine bases of nucleic acids.
Figure 8-3 Conformations of ribose.
Figure 8-4 Deoxyribonucleotides and ribonucleotides of nucleic acids.
Figure 8-5 Some minor purine and pyrimidine bases, shown as the nucleosides.
Figure 8-6 Some adenosine monophosphates.
Figure 8-7 Phosphodiester linkages in the covalent backbone of DNA and RNA.
Figure 8-8 Hydrolysis of RNA under alkaline conditions.
Figure 8-9 Tautomeric forms of uracil.
Figure 8-10 Absorption spectra of the common nucleotides.
Figure 8-11 Hydrogen-bonding patterns in the base pairs defined by Watson and Crick.
Figure 8-12 X-ray diffraction pattern of DNA fibers.
Rosalind Franklin, 1920–1958
Maurice Wilkins, 1916–2004
Figure 8-13 Watson-Crick model for the structure of DNA.
Figure 8-14 Complementarity of strands in the DNA double helix.
Figure 8-15 Replication of DNA as suggested by Watson and Crick.
Figure 8-16 Structural variation in DNA.
Figure 8-17 Comparison of A, B, and Z forms of DNA.
Figure 8-18 Palindromes and mirror repeats.
Figure 8-19 Hairpins and cruciforms.
Figure 8-20 DNA structures containing three or four DNA strands.
Figure 8-21 Bacterial mRNA.
Figure 8-22 Typical right-handed stacking pattern of single-stranded RNA.
Figure 8-23 Secondary structure of RNAs.
Figure 8-24 Base-paired helical structures in an RNA.
Figure 8-25 Three-dimensional structure in RNA.
Figure 8-26 Reversible denaturation and annealing (renaturation) of DNA.
Figure 8-27 Heat denaturation of DNA.
Figure 8-28 Partially denatured DNA.
Figure 8-29 Some well-characterized nonenzymatic reactions of nucleotides.
Figure 8-30 Formation of pyrimidine dimers induced by UV light.
Figure 8-31 Chemical agents that cause DNA damage.
FIGURE 8-32 Chemical synthesis of DNA by the phosphoramidite method.
Figure 8-33 Amplification of a DNA segment by the polymerase chain reaction (PCR).
Figure 1 (a) STR loci can be analyzed by PCR. Suitable PCR primers (with an attached dye to aid in subsequent detection) are targeted to sequences on each side of the STR, and the region between them is amplified. If the STR sequences have different lengths on the two chromosomes of an individual’s chromosome pair, two PCR products of different lengths result. (b) The PCR products from amplification of up to 16 STR loci can be run on a single capillary acrylamide gel (a “16-plex” analysis). Determination of which locus corresponds to which signal depends on the color of the fluorescent dye attached to the primers used in the process and on the size range in which the signal appears (the size range can be controlled by which sequences — those closer to or more distant from the STR — are targeted by the designed PCR primers). Fluorescence is given in relative fluorescence units (RFU), as measured against a standard supplied with the kit. [(b) Information from Carol Bingham, Promega Corporation.]
Figure 8-34 DNA sequencing by the Sanger method.
Figure 8-35 Automation of DNA sequencing reactions.
Figure 8-36 Next-generation reversible terminator sequencing.
Figure 8-37 SMRT sequencing.
Figure 8-38 Sequence assembly.
Figure 8-39 Nucleoside phosphates.
Figure 8-40 The phosphate ester and phosphoanhydride bonds of ATP.
Figure 8-41 Some coenzymes containing adenosine.
Figure 8-42 Three regulatory nucleotides.
Figure 9-1 Schematic illustration of DNA cloning.
Figure 9-2 Use of restriction endonucleases in cloning.
Figure 9-3 The constructed E. coli plasmid pBR322.
Figure 9-4 Use of pBR322 to clone foreign DNA in E. coli and identify cells containing the DNA.
Figure 9-5 Bacterial artificial chromosomes (BACs) as cloning vectors.
Figure 9-6 Construction of a yeast artificial chromosome (YAC).
Figure 9-7 DNA sequences in a typical E. coli expression vector.
Figure 9-8 Regulated expression of RecA protein in a bacterial cell.
Figure 9-9 Cloning with baculoviruses.
Figure 9-10 Two approaches to site-directed mutagenesis.
Figure 9-11 Use of tagged proteins in protein purification.
Figure 9-12 Some applications of PCR.
Figure 9-13 Building a cDNA library from mRNA.
Figure 9-14 Synteny in the human and mouse genomes.
Figure 9-15 RNA-Seq.
Figure 9-16 Green fluorescent protein (GFP).
Figure 9-17 Indirect immunofluorescence.
Figure 9-18 The use of epitope tags to study protein-protein interactions.
Figure 9-19 Tandem affinity purification (TAP) tags.
Figure 9-20 Yeast two-hybrid analysis.
Figure 9-21 The CRISPR/Cas9 system for genomic engineering.
Figure 1 The X-shredder gene drive concept.
Figure 9-22 High-throughput genetic screening.
Figure 9-23 Use of CRISPR/Cas9 in high-throughput screening.
Figure 9-24 Introns and exons.
Figure 9-25 A snapshot of the human genome.
Figure 9-26 Haplotype identification.
Figure 9-27 Genomic alterations in the human lineage.
Figure 9-28 Determination of sequence alterations unique to one ancestral line.
Figure 9-29 Accelerated evolution in some human genes.
Figure 9-30 Linkage analysis in the discovery of disease genes.
Figure 9-31 The paths of human migrations.
Figure 1 Neanderthals occupied much of Europe and western Asia until about 30,000 years ago. Major Neanderthal archaeological sites are shown here. (Note that the group was named for the site at Neanderthal in Germany.)
Figure 2 This timeline shows the divergence of human and Neanderthal genome sequences (black lines) and of ancestral human and Neanderthal populations (yellow screen). Genomic data provide evidence for some intermingling of the populations up to about 45,000 years ago. Key events in human evolution are noted. [Information from J. P. Noonan et al., Science 314:1113, 2006.]
Information from The Huntington’s Disease Collaborative Research Group, Cell 72:971, 1993.
Figure 10-1 The packing of fatty acids into stable aggregates.
Figure 10-2 Glycerol and a triacylglycerol.
Figure 10-3 Fat stores in cells.
Figure 10-4 Fatty acid composition of three food fats.
Figure 10-5 Biological wax.
Figure 10-6 Some common types of storage and membrane lipids.
Figure 10-7 l-Glycerol 3-phosphate, the backbone of phospholipids.
Figure 10-8 Glycerophospholipids.
Figure 10-9 Ether lipids.
Figure 10-10 Two galactolipids of chloroplast thylakoid membranes.
Figure 10-11 Sphingolipids.
Figure 10-12 The similar molecular structures of two classes of membrane lipid.
Figure 10-13 Glycosphingolipids as determinants of blood groups.
Figure 10-14 The specificities of phospholipases.
Figure 1 Pathways for the breakdown of GM1, globoside, and sphingomyelin to ceramide. A defect in the enzyme hydrolyzing a particular step is indicated by; the disease that results from accumulation of the partial breakdown product is noted.
Figure 2 Electron micrograph of a portion of a brain cell from an infant with Tay-Sachs disease, obtained postmortem, showing abnormal ganglioside deposits in the lysosomes.
Figure 10-15 Cholesterol.
Figure 10-16 Phosphatidylinositol and its derivatives.
Figure 10-17 Arachidonic acid and some eicosanoid derivatives.
Figure 10-18 Steroids derived from cholesterol.
Figure 10-19 Vitamin D3 production and metabolism.
Figure 10-20 Dietary β-carotene and vitamin A1 as precursors of the retinoids.
Figure 10-21 Carotene-enriched rice.
Figure 10-22 Some other biologically active isoprenoid compounds or derivatives.
Figure 10-23 Lipids as pigments in plants and bird feathers.
Figure 10-24 Three polyketide natural products used in human medicine.
Figure 10-25 Common procedures in the extraction, separation, and identification of cellular lipids.
Figure 10-26 Determination of fatty acid structure by mass spectrometry.
Figure 11-1 Amphipathic lipid aggregates that form in water.
Figure 11-2 Distribution of membrane lipids across an artificial membrane.
Figure 11-3 Fluid mosaic model for plasma membrane structure.
Figure 11-4 Trafficking in the endomembrane system of an animal cell.
Figure 11-5 Lipid composition of the plasma and organelle membranes of a rat hepatocyte.
Figure 11-6 Change in lipid composition of secretory vesicles with their passage through the Golgi apparatus.
Figure 11-7 Lipid transfer protein (LTP) action.
Figure 11-8 Transbilayer disposition of glycophorin in an erythrocyte.
Figure 11-9 Integral, peripheral, and amphitropic proteins.
Figure 11-10 Monotopic proteins penetrate only one leaflet.
Figure 11-11 Bacteriorhodopsin, a membrane-spanning protein.
Figure 11-12 Lipid annuli associated with an integral protein.
Figure 11-13 Hydropathy plots.
Figure 11-14 Polytopic integral proteins with β-barrel structure.
Figure 11-15 Tyr and Trp residues of integral proteins clustering at the water-lipid interface.
Figure 11-16 Lipid-linked membrane proteins.
Figure 11-17 Two extreme states of bilayer lipids.
Figure 11-18 Motion of single phospholipids in a bilayer.
Figure 11-19 Measurement of lateral diffusion rates of lipids by fluorescence recovery after photobleaching (FRAP).
Figure 11-20 Hop diffusion of individual lipid molecules.
Figure 11-21 Restricted motion of the erythrocyte chloride-bicarbonate exchanger and glycophorin.
Figure 11-22 Membrane microdomains (rafts).
Figure 11-23 Caveolin forces inward curvature of a membrane.
Figure 11-24 Membrane fusion.
Figure 11-25 Three models for protein-induced curvature of membranes.
Figure 11-26 Membrane fusion during neurotransmitter release at a synapse.
Figure 11-27 Summary of transporter types.
Figure 11-28 Movement of solutes across a permeable membrane.
Figure 11-29 Energy changes accompanying passage of a hydrophilic solute through the lipid bilayer of a biological membrane.
Figure 11-30 Differences between channels and transporters.
Figure 11-31 Kinetics of glucose transport into erythrocytes.
Figure 11-32 Membrane topology of the glucose transporter GLUT1.
Figure 11-33 Model of glucose transport into erythrocytes by GLUT1.
Figure 1 Transport of glucose into a myocyte by GLUT4 is regulated by insulin. [Information from F. E. Lienhard et al., Sci. Am. 66 (January):86, 1992.]
Figure 11-34 Chloride-bicarbonate exchanger of the erythrocyte membrane.
Figure 11-35 Three general classes of transport systems.
Figure 11-36 Two types of active transport.
Figure 11-37 The general structure of the P-type ATPases.
Figure 11-38 Postulated mechanism of the SERCA pump.
Figure 11-39 Role of the Na+ K+ ATPase in animal cells.
Figure 11-40 Two proton pumps with similar structures.
Figure 11-41 ABC transporters.
Figure 1 Three states of the CFTR protein.
Figure 2 (a) The CFTR mutation G551D (replacement of Gly551 with Asp) results in a protein that is inserted into the membrane correctly but is defective as a Cl− channel. Addition of the potentiator drug VX-770 (ivacaftor) restores partial function to the Cl− channel. (b) The more common mutation F508del (deletion of Phe508) prevents proper folding of CFTR, causing it to be degraded in proteasomes. In the presence of a corrector drug, folding and membrane insertion can take place; addition of the potentiator drug results in partial restoration of Cl− channel activity. The channel is unstable and is degraded over time. [Information from J. P. Clancy, Sci. Transl. Med. 6:1, 2014.]
Figure 11-42 Glucose transport in intestinal epithelial cells.
Figure 11-43 Valinomycin, a peptide ionophore that binds K+.
Figure 11-44 Electrical measurements of ion-channel function.
Figure 11-45 The K+ channel of Streptomyces lividans.
Figure 12-1 Eight features of signal-transducing systems.
Figure 12-2 Four general types of signal transducers.
Figure 12-3 Epinephrine and its synthetic analogs.
Figure 12-4 Transduction of the epinephrine signal: the β-adrenergic pathway.
Figure 12-5 The GTPase switch.
Figure 12-6 Activation of cAMP-dependent protein kinase (PKA).
Figure 1 When the donor protein (CFP) is excited with monochromatic light of wavelength 433 nm, it emits fluorescent light at 476 nm (left). When the (red) protein fused with CFP interacts with the (purple) protein fused with YFP, that interaction brings CFP and YFP close enough to allow fluorescence resonance energy transfer (FRET) between them. Now, when CFP absorbs light of 433 nm, instead of fluorescing at 476 nm, it transfers energy directly to YFP, which then fluoresces at its characteristic emission wavelength, 527 nm. The ratio of light emission at 527 nm and 476 nm is therefore a measure of the extent of interaction between the red and purple proteins.
Figure 2 Measuring [cAMP] with FRET. Gene fusion creates hybrid proteins that exhibit FRET when the PKA regulatory (R) and catalytic (C) subunits are associated (low [cAMP]). When [cAMP] rises, the subunits dissociate and FRET ceases. The ratio of emission at 460 nm (dissociated) and 545 nm (complexed) thus offers a sensitive measure of [cAMP].
Figure 3 Measuring the activity of PKA with FRET. An engineered protein links YFP and CFP via a peptide that contains (1) a Ser residue surrounded by the consensus sequence for phosphorylation by PKA and (2) the 14-3-3 –Ser-binding domain. Active PKA phosphorylates the Ser residue, which docks with the 14-3-3 binding domain, bringing the fluorescence proteins close enough to allow FRET, revealing the presence of active PKA.
Figure 12-7 Epinephrine cascade.
Figure 12-8 Factors that regulate G-protein activity.
Figure 12-9 Desensitization of the β-adrenergic receptor in the continued presence of epinephrine.
Figure 12-10 Mutual exclusion of trimeric G protein and arrestin in their interaction with a GPCR.
Figure 12-11 Nucleation of supramolecular complexes by A kinase anchoring proteins (AKAPs).
Figure 1 Two types of signal-transducing guanylyl cyclase. (a) Membrane-spanning guanylyl cyclases such as the ANF and guanylin receptors are homodimers with an extracellular ligand-binding domain and an intracellular guanylyl cyclase domain. (b) A soluble heme-containing guanylyl cyclase is activated by intracellular NO.
Figure 2 Synthesis of cGMP by guanylyl cyclase and its hydrolysis by cGMP phosphodiesterase.
Figure 12-12 Ras, the G-protein prototype.
Figure 12-13 GTP hydrolysis flips the switches in Ras.
Figure 12-14 ADP-ribosylation locks Gsα in the active conformation.
Figure 12-15 Hormone-activated phospholipase C and IP3.
Figure 12-16 Proposed mechanism of action of the IP3-gatedCa2+ channel.
Figure 12-17 Calmodulin, the protein mediator of many Ca2+-stimulated enzymatic reactions.
Figure 12-18 Triggering of oscillations in intracellular [Ca2+] by extracellular signals.
Figure 12-19 Molecular consequences of photon absorption by rhodopsin in the rod outer segment.
Figure 1 Absorption spectra of purified rhodopsin and the red, green, and blue receptors of cone cells. The receptor spectra, obtained from individual cone cells isolated from cadavers, peak at about 420, 530, and 560 nm, and the maximum absorption for rhodopsin is at about 500 nm. For reference, the visible spectrum for humans is about 380 to 750 nm. [Data from J. Nathans, Sci. Am. 260 (February):42, 1989.]
Figure 2 Dalton’s eyes. [Professor J. D. Mollon, Cambridge University, Department of Experimental Psychology.]
Figure 12-20 Common features of signaling systems that detect hormones, light, smells, and tastes. GPCRs provide signal specificity, and their interaction with G proteins provides signal amplification.
Figure 12-21 Activation of the insulin-receptor tyrosine kinase by autophosphorylation.
Figure 12-22 Regulation of gene expression by insulin through a MAP kinase cascade.
Figure 12-23 Insulin action on glycogen synthesis and GLUT4 movement to the plasma membrane.
Figure 12-24 Regulation of PIP3 formation and breakdown.
Figure 12-25 Time course of phosphorylations triggered by insulin.
Figure 12-26 Receptor tyrosine kinases. Growth factor receptors that initiate signals through Tyr kinase activity include those for insulin (INSR), vascular endothelial growth factor (VEGFR), platelet-derived growth factor (PDGFR), epidermal growth factor (EGFR), high-affinity nerve growth factor (TrkA), and fibroblast growth factor (FGFR).
Figure 12-27 Cross talk between the insulin receptor and the β-adrenergic receptor (or other GPCR).
Figure 12-28 Interaction of a PTB domain with –Tyr residue in a partner protein.
Figure 12-29 Mechanism of autoinhibition of Src and GSK3.
Figure 12-30 Some binding modules of signaling proteins.
Figure 12-31 A scaffold protein from yeast that organizes and regulates a protein kinase cascade.
Figure 12-32 Transmembrane electrical potential.
Figure 12-33 Role of voltage-gated and ligand-gated ion channels in neural transmission.
Figure 12-34 General mechanism by which steroid and thyroid hormones, retinoids, and vitamin D regulate gene expression.
Figure 12-35 The eukaryotic cell cycle.
Figure 12-36 Variations in the activities of specific CDKs during the cell cycle in animals.
Figure 12-37 Activation of cyclin-dependent protein kinases (CDKs) by cyclin and phosphorylation.
Figure 12-38 Regulation of CDK by phosphorylation and proteolysis.
Figure 12-39 Regulation of cell division by growth factors.
Figure 12-40 Regulation of passage from G1 to S by phosphorylation of pRb.
Figure 1 Unregulated division of a single cell in the colon led to a primary cancer that metastasized to the liver. Secondary cancers are seen as white patches in this liver obtained at autopsy.
Figure 2 Conserved features of the active site of protein kinases. The amino-terminal and carboxyl-terminal lobes surround the active site of the enzyme, near the catalytic loop and the site where ATP binds. The activation loop of this and many other kinases undergoes phosphorylation, then moves away from the active site to expose the substrate-binding cleft, which in this image is occupied by a specific inhibitor of this enzyme, PD318088. The P loop is essential in the binding of ATP, and the C helix must also be correctly aligned for ATP binding and kinase activity. [Data from PDB ID 1S9I, J. F. Ohren et al., Nature Struct. Mol. Biol. 11:1192, 2004.]
Figure 3 Some protein kinase inhibitors now in clinical trials or clinical use, showing their binding to the target protein. (a) Imatinib binds to the Abl kinase (an oncogene product) active site; it occupies both the ATP-binding site and a region adjacent to that site. (b) Erlotinib binds to the active site of EGFR. (c), (d) Roscovitine is an inhibitor of the cyclin-dependent kinases CDK2, CDK7, and CDK9; shown here are normal Mg2+-ATP binding at the active site (c) and roscovitine binding (d), which prevents the binding of ATP.
Figure 12-41 Multistep transition from normal epithelial cell to colorectal cancer.
Figure 12-42 Initial events of apoptosis.
A portrait by Jacques Louis David of Antoine Lavoisier (1743–1794) in the laboratory with chemist Marie Anne Pierrette Paulze (1758–1836), his wife.
Figure 13-1 Two mechanisms for cleavage of a C—C or C—H bond.
Figure 13-2 Common nucleophiles and electrophiles in biochemical reactions.
Figure 13-3 Chemical properties of carbonyl groups.
Figure 13-4 Some common reactions that form and break C—C bonds in biological systems.
Figure 13-5 Carbocations in carbon–carbon bond formation.
Figure 13-6 Isomerization and elimination reactions.
Figure 13-7 A free radical–initiated decarboxylation reaction.
Figure 13-8 Phosphoryl group transfers: some of the participants.
Figure 13-9 The oxidation levels of carbon in biomolecules.
Figure 13-10 An oxidation-reduction reaction.
Figure 13-11 Chemical basis for the large free-energy change associated with ATP hydrolysis.
Figure 13-12 Mg2+ and ATP.
Figure 13-13 Hydrolysis of phosphoenolpyruvate (PEP).
Figure 13-14 Hydrolysis of 1,3-bisphosphoglycerate.
Figure 13-15 Hydrolysis of phosphocreatine.
Figure 13-16 Hydrolysis of acetyl-coenzyme A.
Figure 13-17 Free energy of hydrolysis for thioesters and oxygen esters.
Figure 13-18 ATP hydrolysis in two steps.
Figure 13-19 Ranking of biological phosphate compounds by standard free energies of hydrolysis.
Figure 13-20 Three positions on ATP for attack by the nucleophile.
Figure 1 Important components in the firefly bioluminescence cycle.
The firefly, a beetle of the Lampyridae family.
Figure 13-21 Ping-Pong mechanism of nucleoside diphosphate kinase.
Figure 13-22 Different levels of oxidation of carbon compounds in the biosphere.
Figure 13-23 Measurement of the standard reduction potential of a redox pair.
Figure 13-24 NAD and NADP.
Figure 13-25 Dermatitis associated with pellagra.
Figure 13-26 Niacin (nicotinic acid) and its derivative nicotinamide.
Figure 13-27 Oxidized and reduced FAD and FMN.
Figure 13-28 Metabolism as a three-dimensional meshwork.
Figure 13-29 Factors affecting the activity of enzymes.
Figure 13-30 The metabolome of E. coli growing on glucose.
Figure 13-31 Comparison of Km and substrate concentration for some metabolic enzymes.
Figure 13-32 Protein phosphorylation and dephosphorylation.
Figure 13-33 Near-equilibrium and nonequilibrium steps in a metabolic pathway.
Figure 13-34 Effect of ATP concentration on the initial reaction velocity of a typical ATP-dependent enzyme.
Figure 14-1 Major pathways of glucose utilization. Although not the only possible fates for glucose, these four pathways are the most significant in most cells.
Figure 14-2 The two phases of glycolysis. For each molecule of glucose that passes through the preparatory phase (a), two molecules of glyceraldehyde 3-phosphate are formed; both pass through the payoff phase (b). Pyruvate is the end product of the second phase of glycolysis. For each glucose molecule, two ATP are consumed in the preparatory phase and four ATP are produced in the payoff phase, giving a net yield of two ATP and two NADH per molecule of glucose converted to pyruvate. The numbered reaction steps correspond to the numbered headings in the text discussion. Keep in mind that each phosphoryl group, represented here as , has two negative charges (−PO32−).
Figure 14-3 The chemical logic of the glycolytic pathway. In this simplified version of the pathway, each molecule is shown in a linear form, with carbon and hydrogen atoms not depicted, in order to highlight chemical transformations. Remember that glucose and fructose are present mostly in their cyclized forms in solution, although they are transiently present in linear form at the active sites of some of the enzymes in this pathway. The preparatory phase, steps to , converts the six-carbon glucose into two three-carbon units, each of them phosphorylated. Oxidation of the three-carbon units is initiated in the payoff phase, steps to . To produce pyruvate, the chemical steps must occur in the order shown.
Mechanism Figure 14-4 The phosphohexose isomerase reaction. The ring opening and closing reactions (steps and ) are catalyzed by an active-site His residue, by mechanisms omitted here for simplicity. The proton (light red) initially at C-2 is made more easily abstractable by electron withdrawal by the adjacent carbonyl and nearby hydroxyl groups. After its transfer from C-2 to the active-site Glu residue (a weak acid), the proton is freely exchanged with the surrounding solution; that is, the proton abstracted from C-2 in step is not necessarily the same one that is added to C-1 in step .
Mechanism Figure 14-5 The class I aldolase reaction. Note that cleavage between C-3 and C-4 depends on the presence of the carbonyl group at C-2, which is converted to an imine on the enzyme. A and B represent amino acid residues that serve as general acid (A) or base (B).
Figure 14-6 Fate of the glucose carbons in the formation of glyceraldehyde 3-phosphate. (a) The origin of the carbons in the two three-carbon products of the aldolase and triose phosphate isomerase reactions. The end product of the two reactions is glyceraldehyde 3-phosphate (two molecules). (b) Each carbon of glyceraldehyde 3-phosphate is derived from either of two specific carbons of glucose. Note that the numbering of the carbon atoms of glyceraldehyde 3-phosphate differs from that of the glucose from which it is derived. In glyceraldehyde 3-phosphate, the most complex functional group (the carbonyl) is specified as C-1. This numbering change is important for interpreting experiments with glucose in which a single carbon is labeled with a radioisotope. (See Problems 5 and 22 at the end of this chapter.)
Mechanism Figure 14-7 The glyceraldehyde 3-phosphate dehydrogenase reaction.
Mechanism Figure 14-8 The phosphoglycerate mutase reaction.
Figure 14-9 Entry of dietary glycogen, starch, disaccharides, and hexoses into the preparatory stage of glycolysis. The numbered steps are described in the text.
Figure 14-10 Conversion of galactose to glucose 1-phosphate. The conversion proceeds through a sugar-nucleotide derivative, UDP-galactose, which is formed when galactose 1-phosphate displaces glucose 1-phosphate from UDP-glucose. UDP-galactose is then converted by UDP-glucose 4-epimerase to UDP-glucose, in a reaction that involves oxidation of C-4 (light red) by NAD+, then reduction of C-4 by NADH; the result is inversion of the configuration at C-4. The UDP-glucose is recycled through another round of the same reaction. The net effect of this cycle is the conversion of galactose 1-phosphate to glucose 1-phosphate; there is no net production or consumption of UDP-galactose or UDP-glucose. Defects in the enzymes that catalyze each of these steps result in the various galactosemias shown.
Figure 14-11 Three possible catabolic fates of the pyruvate formed in glycolysis and the recycling of NADH. Red arrows follow the regeneration of NAD+ from NADH. Under aerobic conditions, pyruvate is activated to acetyl-CoA and is completely oxidized to CO2 and water through the citric acid cycle and mitochondrial oxidative phosphorylation. NADH produced in this pathway is oxidized to NAD+ through mitochondrial electron transfer. Under anaerobic conditions, pyruvate reduction to lactate or to ethanol is required to produce the NAD+ needed for glycolysis to continue. Pyruvate also serves as a precursor in many anabolic reactions, not shown here.
Figure 1 The anaerobic metabolism of glucose in tumor cells yields far less ATP (2 per glucose) than the complete oxidation to CO2 that takes place in healthy cells under aerobic conditions (~30 ATP per glucose), so a tumor cell must consume much more glucose to produce the same amount of ATP. Glucose transporters and most of the glycolytic enzymes are overproduced in tumors. Compounds that inhibit hexokinase, glucose 6-phosphate dehydrogenase, or transketolase block ATP production by glycolysis, thus depriving the cancer cell of energy and killing it.
Figure 2 Phosphorylation of 18F-labeled 2-fluoro-2-deoxyglucose by hexokinase traps the FdG in cells (as 6-phospho-FdG), where its presence can be detected by positron emission from 18F.
Figure 3 Detection of cancerous tissue by positron emission tomography (PET). The adult male patient had undergone surgical removal of a primary skin cancer (malignant melanoma). The image on the left, obtained by whole-body computed tomography (CT scan), shows the location of the soft tissues and bones. The central panel is a PET scan after the patient had ingested 18F-labeled 2-fluoro-2-deoxyglucose (FdG). Dark spots indicate regions of high glucose utilization. As expected, the brain and bladder are heavily labeled — the brain because it uses most of the glucose consumed in the body, and the bladder because the 18F-labeled 6-phospho-FdG is excreted in the urine. When the intensity of the label in the PET scan is translated into false color (the intensity increases from green to yellow to red) and the image is superimposed on the CT scan, the fused image (right) reveals cancer in the bones of the upper spine, in the liver, and in some regions of muscle, all the result of cancer spreading from the primary malignant melanoma.
Otto Warburg, 1883–1970
Francena McCorory, Olympic sprinter
Mechanism Figure 14-12 The alcohol dehydrogenase reaction.
Mechanism Figure 14-13 Thiamine pyrophosphate (TPP) and its role in pyruvate decarboxylation. (a) TPP is the coenzyme form of vitamin B1 (thiamine). The reactive carbon atom in the thiazolium ring of TPP is shown in red. In the reaction catalyzed by pyruvate decarboxylase, two of the three carbons of pyruvate are carried transiently on TPP in the form of a hydroxyethyl, or “active acetaldehyde,” group (b), which is subsequently released as acetaldehyde. (c) The thiazolium ring of TPP stabilizes carbanion intermediates by providing an electrophilic (electron-deficient) structure into which the carbanion electrons can be delocalized by resonance. Structures with this property, often called “electron sinks,” play a role in many biochemical reactions — here, facilitating carbon–carbon bond cleavage. Dietary insufficiency of thiamine causes the serious disease beriberi and the Wernicke-Korsakoff syndrome.
Figure 14-14 Beer brewing. Large breweries and microbreweries produce beers with a wide variety of flavors, the result of differences in materials and fermentation conditions.
Figure 14-15 Carbohydrate synthesis from simple precursors. The pathway from phosphoenolpyruvate to glucose 6-phosphate is common to the biosynthetic conversion of many different precursors of carbohydrates in animals and plants. The path from pyruvate to phosphoenolpyruvate leads through oxaloacetate, an intermediate of the citric acid cycle, which we discuss in Chapter 16. Any compound that can be converted to either pyruvate or oxaloacetate can therefore serve as starting material for gluconeogenesis. This includes alanine and aspartate, which are convertible to pyruvate and oxaloacetate, respectively, and other amino acids that can also yield three- or four-carbon fragments, the so-called glucogenic amino acids. Plants and photosynthetic bacteria are uniquely able to convert CO2 to carbohydrates, using the Calvin cycle, as we shall see in Section 20.4.
Figure 14-16 Opposing pathways of glycolysis and gluconeogenesis in liver. The reactions of glycolysis are on the left side, in red; the opposing pathway of gluconeogenesis is on the right, in blue. The major sites of regulation of gluconeogenesis shown here are discussed in Section 14.5.
Figure 14-17 Role of biotin in the pyruvate carboxylase reaction. The cofactor biotin is covalently attached to pyruvate carboxylase through an amide linkage to the ε-amino group of a Lys residue, forming a biotinyl-enzyme. The reaction takes place in two phases, which occur at two different sites in the enzyme. The long biotinyl-Lys arm carries the substrate from one site to the other.
Figure 14-18 Synthesis of phosphoenolpyruvate from oxaloacetate. In the cytosol, oxaloacetate is converted to phosphoenolpyruvate by PEP carboxykinase. The CO2 incorporated in the pyruvate carboxylase reaction is lost here as CO2. The decarboxylation leads to a rearrangement of electrons that facilitates attack of the carbonyl oxygen of the pyruvate moiety on the γ phosphate of GTP.
Figure 14-19 Alternative paths from pyruvate to phosphoenolpyruvate. The relative importance of the two pathways depends on the availability of lactate or pyruvate and the cytosolic requirements for NADH for gluconeogenesis. The path on the right predominates when lactate is the precursor, because cytosolic NADH is generated in the lactate dehydrogenase reaction and does not have to be shuttled out of the mitochondrion (see text).
Figure 14-20 Comparison of the kinetic properties of hexokinase IV (glucokinase) and hexokinase I. Note the much lower Km for hexokinase I. When blood glucose rises above 5 mm, hexokinase IV activity increases, but hexokinase I is already operating near Vmax and cannot respond to an increase in glucose concentration. Hexokinases I, II, and III have similar kinetic properties.
Figure 14-21 Regulation of hexokinase IV (glucokinase) by sequestration in the nucleus. The protein inhibitor of hexokinase IV is a nuclear binding protein that draws hexokinase IV into the nucleus when the fructose 6-phosphate concentration in liver is high and releases it to the cytosol when the glucose concentration is high.
Figure 14-22 Phosphofructokinase-1 (PFK-1) and its regulation. (a) Surface contour image of E. coli PFK-1, showing portions of its four identical subunits. Each subunit has its own catalytic site, where the products ADP and fructose 1,6-bisphosphate (red and yellow stick structures, respectively) are almost in contact, and its own binding sites for the allosteric regulator ATP, buried in the protein in the positions indicated. (b) Allosteric regulation of muscle PFK-1 by ATP, shown by a substrate-activity curve. At low [ATP], the K0.5 for fructose 6-phosphate is relatively low, enabling the enzyme to function at a high rate at relatively low [fructose 6-phosphate]. (Recall from Chapter 6 that K0.5 is the Km term for regulatory enzymes; when K0.5 is larger, the binding is weaker.) When [ATP] is high, K0.5 for fructose 6-phosphate is greatly increased, as indicated by the sigmoid relationship between substrate concentration and enzyme activity. (c) Summary of the regulators affecting PFK-1 activity. [(a) Data from PDB ID 1PFK, Y. Shirakihara and P. R. Evans, J. Mol. Biol. 204:973, 1988.]
Figure 14-23 Regulation of phosphofructokinase-1 (PFK-1) and fructose 1,6-bisphosphatase (FBPase-1).
Figure 14-24 Role of fructose 2,6-bisphosphate in regulation of glycolysis and gluconeogenesis. Fructose 2,6-bisphosphate (F26BP) has opposite effects on the enzymatic activities of phosphofructokinase-1 (PFK-1, a glycolytic enzyme) and fructose 1,6-bisphosphatase (FBPase-1, a gluconeogenic enzyme). (a) PFK-1 activity in the absence of F26BP (blue curve) is half-maximal when the concentration of fructose 6-phosphate is 2 mm (that is, K0.5=2 mM). When 0.13 μM F26BP is present (red curve), the K0.5 for fructose 6-phosphate is only 0.08 mm. Thus F26BP activates PFK-1 by increasing its apparent affinity for fructose 6-phosphate (see Fig. 14-23b). (b) FBPase-1 activity is inhibited by as little as 1 μM F26BP and is strongly inhibited by 25 μM. In the absence of this inhibitor (blue curve), the K0.5 for fructose 1,6-bisphosphate is 5 μM, but in the presence of 25 μM F26BP (red curve), the K0.5 is >70 μM. Fructose 2,6-bisphosphate also makes FBPase-1 more sensitive to inhibition by another allosteric regulator, AMP. (c) Summary of regulation by F26BP.
Figure 14-25 Regulation of fructose 2,6-bisphosphate level. (a) The cellular concentration of the regulator fructose 2,6-bisphosphate (F26BP) is determined by the rates of its synthesis by phosphofructokinase-2 (PFK-2) and its breakdown by fructose 2,6-bisphosphatase (FBPase-2). (b) Both enzyme activities are part of the same polypeptide chain, and they are reciprocally regulated by insulin and glucagon.
Figure 14-26 Regulation of pyruvate kinase. The enzyme is allosterically inhibited by ATP, acetyl-CoA, and long-chain fatty acids (all signs of an abundant energy supply), and the accumulation of fructose 1,6-bisphosphate triggers its activation. Accumulation of alanine, which can be synthesized from pyruvate in one step, allosterically inhibits pyruvate kinase, slowing the production of pyruvate by glycolysis. The liver isozyme (L form) is also regulated hormonally. Glucagon activates cAMP-dependent protein kinase (PKA; see Fig. 15-12), which phosphorylates the pyruvate kinase L isozyme, inactivating it. When the glucagon level drops, a protein phosphatase (PP) dephosphorylates pyruvate kinase, activating it. This mechanism prevents the liver from consuming glucose by glycolysis when blood glucose is low; instead, the liver exports glucose. The muscle isozyme (M form) is not affected by this phosphorylation mechanism.
Figure 14-27 Two alternative fates for pyruvate. Pyruvate can be converted to glucose and glycogen via gluconeogenesis or oxidized to acetyl-CoA for energy production. The first enzyme in each path is regulated allosterically; acetyl-CoA, produced either by fatty acid oxidation or by the pyruvate dehydrogenase complex, stimulates pyruvate carboxylase and inhibits pyruvate dehydrogenase.
Figure 14-28 Mechanism of gene regulation by the transcription factor ChREBP. When ChREBP in the cytosol of a hepatocyte is phosphorylated on a Ser residue and a Thr residue, it cannot enter the nucleus. Dephosphorylation of —Ser by protein phosphatase PP2A allows ChREBP to enter the nucleus, where a second dephosphorylation, of —Thr, activates ChREBP so that it can associate with its partner protein, Mlx. ChREBP-Mlx now binds to the carbohydrate response element (ChoRE) in the promoter and stimulates transcription. PP2A is allosterically activated by xylulose 5-phosphate, an intermediate in the pentose phosphate pathway.
Figure 14-29 General scheme of the pentose phosphate pathway. NADPH formed in the oxidative phase is used to reduce glutathione, GSSG (see Box 14-4), and to support reductive biosynthesis. The other product of the oxidative phase is ribose 5-phosphate, which serves as a precursor for nucleotides, coenzymes, and nucleic acids. In cells that are not using ribose 5-phosphate for biosynthesis, the nonoxidative phase recycles six molecules of the pentose into five molecules of the hexose glucose 6-phosphate, allowing continued production of NADPH and converting glucose 6-phosphate (in six cycles) to CO2.
Figure 1 Role of NADPH and glutathione in protecting cells against highly reactive oxygen derivatives. Reduced glutathione (GSH) protects the cell by destroying hydrogen peroxide and hydroxyl free radicals. Regeneration of GSH from its oxidized form (GSSG) requires the NADPH produced in the glucose 6-phosphate dehydrogenase reaction.
Figure 14-30 Oxidative reactions of the pentose phosphate pathway. The end products are ribose 5-phosphate, CO2, and NADPH.
Figure 14-31 Nonoxidative reactions of the pentose phosphate pathway. (a) These reactions convert pentose phosphates to hexose phosphates, allowing the oxidative reactions to continue. Transketolase and transaldolase are specific to this pathway; the other enzymes also serve in the glycolytic or gluconeogenic pathways. (b) A schematic diagram showing the pathway from six pentoses (5C) to five hexoses (6C). Note that this involves two sets of the interconversions shown in (a). Every reaction shown here is reversible; unidirectional arrows are used only to make clear the direction of the reactions during continuous oxidation of glucose 6-phosphate. In the light-independent reactions of photosynthesis, the direction of these reactions is reversed.
Figure 14-32 The first reaction catalyzed by transketolase. (a) The general reaction catalyzed by transketolase is the transfer of a two-carbon group, carried temporarily on enzyme-bound TPP, from a ketose donor to an aldose acceptor. (b) Conversion of two pentose phosphates to a triose phosphate and a seven-carbon sugar phosphate, sedoheptulose 7-phosphate.
Figure 14-33 The reaction catalyzed by transaldolase.
Figure 14-34 The second reaction catalyzed by transketolase.
Figure 14-35 Carbanion intermediates stabilized by covalent interactions with transketolase and transaldolase. (a) The ring of TPP stabilizes the carbanion in the dihydroxyethyl group carried by transketolase. (b) In the transaldolase reaction, the protonated Schiff base formed between the ε-amino group of a Lys side chain and the substrate stabilizes the C-3 carbanion formed after aldol cleavage.
Figure 14-36 Role of NADPH in regulating the partitioning of glucose 6-phosphate between glycolysis and the pentose phosphate pathway. When NADPH is forming faster than it is being used for biosynthesis and glutathione reduction, [NADPH] rises and inhibits the first enzyme in the pentose phosphate pathway. As a result, more glucose 6-phosphate is available for glycolysis.
Figure 15-1 Glycogen granules in a hepatocyte. Glycogen β-granules appear as electron-dense particles. In liver they form larger clusters called α-granules and are often associated with tubules of the smooth endoplasmic reticulum. Four mitochondria are also evident in this micrograph.
Figure 15-2 Structure of a glycogen β-granule. Starting at a central glycogenin homodimer, glycogen chains (12 to 14 residues) extend in tiers. Inner chains (B-chains) have two (α1→6) branches each. A-chains in the outer tier are unbranched. There are in theory a maximum of 12 tiers in a mature glycogen β-granule (only 5 are shown here), consisting of about 55,000 glucose residues in a molecule of about 21 nm diameter and Mr~1 ×107.
Figure 15-3 Removal of a glucose residue from the nonreducing end of a glycogen chain by glycogen phosphorylase. This process is repetitive; the enzyme removes successive glucose residues, creating a new nonreducing end, until it reaches the fourth glucose unit from a branch point (see Fig. 15-4).
Figure 15-4 Glycogen breakdown near an (α1→6) branch point. Following sequential removal of terminal glucose residues by glycogen phosphorylase (see Fig. 15-3), glucose residues near a branch are removed in a two-step process that requires a bifunctional debranching enzyme. First, the transferase activity of the enzyme shifts a block of three glucose residues from the branch to a nearby nonreducing end, to which the segment is reattached in (α1→4) linkage. The single glucose residue remaining at the branch point, in (α1→6) linkage, is then released as free glucose by the (α1→6) glucosidase activity of the debranching enzyme. The glucose residues are shown in shorthand form.
Figure 15-5 Reaction catalyzed by phosphoglucomutase. The reaction begins with the enzyme phosphorylated on a Ser residue. In step , the enzyme donates its phosphoryl group (blue) to glucose 1-phosphate, producing glucose 1,6-bisphosphate. In step , the phosphoryl group at C-1 of glucose 1,6-bisphosphate (red) is transferred back to the enzyme, re-forming the phosphoenzyme and producing glucose 6-phosphate.
Figure 15-6 Hydrolysis of glucose 6-phosphate by glucose 6-phosphatase of the liver ER. The catalytic site of glucose 6-phosphatase faces the lumen of the ER. A glucose 6-phosphate (G6P) transporter (T1) carries the substrate from the cytosol to the lumen, where glucose 6-phosphatase releases Pi. The products, glucose and Pi, pass to the cytosol on specific transporters (T2 and T3). Glucose leaves the cell via the GLUT2 transporter in the plasma membrane.
Figure 1 The Coris in Gerty Cori’s laboratory, around 1947.
Figure 15-7 Formation of a sugar nucleotide. A condensation reaction occurs between a nucleoside triphosphate (NTP) and a sugar phosphate. The negatively charged oxygen on the sugar phosphate serves as a nucleophile, attacking the α phosphate of the nucleoside triphosphate and displacing pyrophosphate. The reaction is pulled in the forward direction by the hydrolysis of PPi by inorganic pyrophosphatase.
Figure 15-8 Glycogen synthesis. A glycogen chain is elongated by glycogen synthase. The enzyme transfers the glucose residue of UDP-glucose to the nonreducing end of a glycogen branch to make a new (α1→4) linkage.
Figure 15-9 Branch synthesis in glycogen. The glycogen-branching enzyme forms a new branch point during glycogen synthesis.
Figure 15-10 Glycogenin. (a) The protein is a homodimer. The substrate, UDP-glucose, is bound in a region near the amino terminus and is some distance from the Tyr194 residues — 15 Å from the Tyr in the same monomer, 12 Å from the Tyr in the dimeric partner. Each UDP-glucose is bound through its phosphates to a Mn2+ ion, which is essential to catalysis. Mn2+ is believed to function as an electron-pair acceptor (Lewis acid) to stabilize the leaving group, UDP. (b) Glycogenin catalyzes two distinct reactions. Initial attack by the hydroxyl group of Tyr194 on C-1 of the glucosyl moiety of UDP-glucose results in a glucosylated Tyr residue. The C-1 of another UDP-glucose molecule is now attacked by the C-4 hydroxyl group of the terminal glucose, and this sequence repeats to form a nascent glycogen molecule of eight glucose residues attached by (α1→4) glycosidic linkages. [(a) Data from PDB ID 1LL2, B. J. Gibbons et al., J. Mol. Biol. 319:463, 2002.]
Earl W. Sutherland, Jr., 1915–1974
Figure 15-11 Regulation of muscle glycogen phosphorylase by covalent modification. In the more active form of the enzyme, phosphorylase a, Ser14 residues, one on each subunit, are phosphorylated. Phosphorylase a is converted to the less active form, phosphorylase b, by enzymatic loss of these phosphoryl groups, catalyzed by phosphoprotein phosphatase 1 (PP1). Phosphorylase b can be reconverted (reactivated) to phosphorylase a by the action of phosphorylase b kinase.
Figure 15-12 Cascade mechanism of epinephrine and glucagon action. By binding to specific surface receptors, either epinephrine acting on a myocyte (left) or glucagon acting on a hepatocyte (right) activates a GTP-binding protein, Gsα. Active Gsα triggers a rise in [cAMP], activating PKA. This sets off a cascade of phosphorylations; PKA activates phosphorylase b kinase, which then activates glycogen phosphorylase. Such cascades effect a large amplification of the initial signal; the figures in pink boxes are certainly low estimates of the actual increase in number of molecules at each stage of the cascade. The resulting breakdown of glycogen provides glucose, which in the myocyte can supply ATP (via glycolysis) for muscle contraction and in the hepatocyte is released into the blood to counter the low blood glucose.
Figure 15-13 Glycogen phosphorylase of liver as a glucose sensor. Glucose binding to an allosteric site of the phosphorylase a isozyme of liver induces a conformational change that exposes its phosphorylated Ser residues to the action of phosphoprotein phosphatase 1 (PP1). This phosphatase converts phosphorylase a to phosphorylase b, sharply reducing the activity of phosphorylase and slowing glycogen breakdown in response to high blood glucose. Insulin also acts indirectly to stimulate PP1 and slow glycogen breakdown.
Figure 15-14 Effects of GSK3 on glycogen synthase activity. Glycogen synthase a, the active form, has three Ser residues near its carboxyl terminus. Their phosphorylation by glycogen synthase kinase 3 (GSK3) converts glycogen synthase to its inactive b form. Insulin favors the active a form of glycogen synthase by blocking the activity of GSK3 and activating phosphoprotein phosphatase 1 (PP1). In muscle, epinephrine activates PKA, which phosphorylates the glycogen-targeting protein Gm on a site that causes dissociation of PP1 from glycogen. Glucose 6-phosphate favors dephosphorylation of glycogen synthase by binding to it and promoting a conformation that is a good substrate for PP1.
Figure 15-15 Priming of GSK3 phosphorylation of glycogen synthase. (a) Glycogen synthase kinase 3 first associates with its substrate (glycogen synthase) by interaction between three positively charged residues (Arg96, Arg180, Lys205) and a phosphoserine residue at position +4 in the substrate. (For orientation, the Ser or Thr residue to be phosphorylated in the substrate is assigned the index 0. Residues on the amino-terminal side of this residue are numbered −1, −2, and so forth; residues on the carboxyl-terminal side are numbered +1, +2, and so forth.) This association aligns the active site of the enzyme with a Ser residue at position 0, which it phosphorylates. This creates a new priming site, and the enzyme moves down the protein to phosphorylate the Ser residue at position −4, and then the Ser at −8. (b) GSK3 has a Ser residue near its amino terminus that can be phosphorylated by PKA or PKB. This produces a “pseudosubstrate” region in GSK3 that folds into the priming site and makes the active site inaccessible to another protein substrate, inhibiting GSK3 until the priming phosphoryl group of its pseudosubstrate region is removed by PP1. Other proteins that are substrates for GSK3 also have a priming site at position +4, which must be phosphorylated by another protein kinase before GSK3 can act on them.
Figure 15-16 Glycogen-targeting protein Gm. Gm is a regulatory subunit of PP1 in muscle, and one of a family of glycogen-targeting proteins that serve as a scaffold, binding other proteins (including PP1) to glycogen particles. Gm can be phosphorylated at two different sites in response to insulin or epinephrine. Insulin-stimulated phosphorylation of Gm site 1 activates PP1, which dephosphorylates phosphorylase kinase, glycogen phosphorylase, and glycogen synthase. Epinephrine-stimulated phosphorylation of Gm site 2 by PKA causes dissociation of PP1 from the glycogen particle, preventing its access to glycogen phosphorylase and glycogen synthase. PKA also phosphorylates a protein (inhibitor 1) that, when phosphorylated, inhibits PP1. By these means, insulin stimulates glycogen synthesis and inhibits glycogen breakdown, whereas epinephrine (or glucagon in the liver) has the opposite effects.
Figure 15-17 Regulation of carbohydrate metabolism in the liver. Colored arrows indicate causal relationships between the changes they connect. For example, an arrow from ↓A to ↑B means that a decrease in A causes an increase in B. Red arrows connect events that result from high blood glucose; blue arrows connect events that result from low blood glucose.
Figure 15-18 Difference in the regulation of carbohydrate metabolism in liver and muscle. In liver, either glucagon (indicating low blood glucose) or epinephrine (signaling the need to fight or flee) has the effect of maximizing the output of glucose into the blood. In muscle, epinephrine increases glycogen breakdown and glycolysis, which together provide fuel to produce the ATP needed for muscle contraction.
Figure 16-1 Catabolism of proteins, fats, and carbohydrates in the three stages of cellular respiration. Stage 1: oxidation of fatty acids, glucose, and some amino acids yields acetyl-CoA. Stage 2: oxidation of acetyl groups in the citric acid cycle includes four steps in which electrons are abstracted. Stage 3: electrons carried by NADH and FADH2 are funneled into a chain of mitochondrial (or, in bacteria, plasma membrane–bound) electron carriers — the respiratory chain — ultimately reducing O2 to H2O. This electron flow drives the production of ATP.
Hans Krebs, 1900–1981
Figure 16-2 Coenzyme A (CoA-SH).
Figure 16-3 Overall reaction catalyzed by the pyruvate dehydrogenase complex. The five coenzymes participating in this reaction, and the three enzymes that make up the enzyme complex, are discussed in the text.
Figure 16-4 Lipoic acid (lipoate) in amide linkage with a Lys residue. The lipoyllysyl moiety is the prosthetic group of dihydrolipoyl transacetylase (E2 of the PDH complex). The lipoyl group occurs in oxidized (disulfide) and reduced (dithiol) forms and acts as a carrier of both hydrogen and an acetyl (or other acyl) group.
Figure 16-5 Structure of the pyruvate dehydrogenase complex. The complex is so big and so flexible that solving its structure required a combination of methods, including x-ray crystallography and NMR spectroscopy; once the individual pieces were solved, cryo-EM of the whole structure was used to assemble the pieces from several organisms to get this view. The core (E2) is from the gram-negative bacterium Azotobacter vinelandii. E1 and E3 are from the thermophilic gram-positive bacterium Geobacillus stearothermophilus. E1, pyruvate dehydrogenase (yellow); E2, dihydrolipoyl transacetylase (green); and E3, dihydrolipoyl dehydrogenase (red). The central core of the Azotobacter PDH complex consists of 24 copies of E2, but to simplify the structure, only six are shown here. Multiple copies of E1 and E3 surround the central core, and flexible arms (shown schematically) reach out from E2 to E1 and E3, carrying the lipoyl moiety (pink) from the active site of one enzyme to that of the next. The amino acid sequences and three-dimensional structures of individual domains show that both catalytic mechanism and structure have been conserved in evolution.
Figure 16-6 Oxidative decarboxylation of pyruvate to acetyl-CoA by the PDH complex. The fate of pyruvate is traced in red. In step pyruvate reacts with the bound thiamine pyrophosphate (TPP) of pyruvate dehydrogenase (E1) and is decarboxylated to the hydroxyethyl derivative. Pyruvate dehydrogenase also carries out step , the transfer of two electrons and the acetyl group from TPP to the oxidized form of the lipoyllysyl group of the core enzyme, dihydrolipoyl transacetylase (E2), to form the acetyl thioester of the reduced lipoyl group. Step is a transesterification in which the —SH group of CoA replaces the —SH group of E2 to yield acetyl-CoA and the fully reduced (dithiol) form of the lipoyl group. In step dihydrolipoyl dehydrogenase (E3) promotes transfer of two hydrogen atoms from the reduced lipoyl groups of E2 to the FAD prosthetic group of E3, restoring the oxidized form of the lipoyllysyl group of E2. In step the reduced FADH2 of E3 transfers a hydride ion to NAD+, forming NADH. The enzyme complex is now ready for another catalytic cycle. (Subunit colors correspond to those in Fig. 16-5.)
Figure 16-7 Reactions of the citric acid cycle. The carbon atoms shaded in pink are those derived from the acetate of acetyl-CoA in the first turn of the cycle; these are not the carbons released as CO2 in the first turn. Note that in succinate and fumarate, the two-carbon group derived from acetate can no longer be specifically denoted; because succinate and fumarate are symmetric molecules, C-1 and C-2 are indistinguishable from C-4 and C-3. The red arrows show where energy is conserved by electron transfer to FAD or NAD+, forming FADH2 or NADH+H+. Steps , , and are essentially irreversible in the cell; all other steps are reversible. The nucleoside triphosphate product of step may be either ATP or GTP, depending on which succinyl-CoA synthetase isozyme is the catalyst.
Figure 16-8 Structure of citrate synthase. The flexible domain of each subunit undergoes a large conformational change on binding oxaloacetate, creating a binding site for acetyl-CoA. (a) Open form of the enzyme alone; (b) closed form with bound oxaloacetate and a stable analog of acetyl-CoA (carboxymethyl-CoA). In these representations one subunit is colored tan and one green.
Mechanism Figure 16-9 Citrate synthase. In the citrate synthase reaction in mammals, oxaloacetate binds first, in a strictly ordered reaction sequence. This binding triggers a conformation change that opens up the binding site for acetyl-CoA. Oxaloacetate is specifically oriented in the active site of citrate synthase by interaction of its two carboxylates with two positively charged Arg residues (not shown here).
Figure 16-10 Iron-sulfur center in aconitase. The iron-sulfur center is in red, the citrate molecule in blue. Three Cys residues of the enzyme bind three iron atoms; the fourth iron is bound to one of the carboxyl groups of citrate and also interacts noncovalently with a hydroxyl group of citrate (dashed bond). A basic residue (:B) in the enzyme helps to position the citrate in the active site. The iron-sulfur center acts in both substrate binding and catalysis. The general properties of iron-sulfur proteins are discussed in Chapter 19.
Figure 1 Effect of IRP1 and IRP2 on the mRNAs for ferritin and the transferrin receptor.
Figure 2 Two forms of cytosolic aconitase/IRP1 with two distinct functions. (a) In aconitase, the two major lobes are closed and the Fe-S cluster is buried; the protein has been made transparent here to show the Fe-S cluster. (b) In IRP1, the lobes open, exposing a binding site for the mRNA hairpin.
Mechanism Figure 16-11 Isocitrate dehydrogenase. In this reaction, the substrate, isocitrate, loses one carbon by oxidative decarboxylation.
Figure 16-12 A conserved mechanism for oxidative decarboxylation. The pathways shown employ the same five cofactors (thiamine pyrophosphate, coenzyme A, lipoate, FAD, and NAD+), closely similar multienzyme complexes, and the same enzymatic mechanism to carry out oxidative decarboxylations of pyruvate (by the pyruvate dehydrogenase complex), α-ketoglutarate (in the citric acid cycle), and the carbon skeletons of the three branched-chain amino acids, isoleucine (shown here), leucine, and valine.
Figure 16-13 The succinyl-CoA synthetase reaction. (a) In step a phosphoryl group replaces the CoA of succinyl-CoA bound to the enzyme, forming a high-energy acyl phosphate. In step the succinyl phosphate donates its phosphoryl group to a His residue of the enzyme, forming a high-energy phosphohistidyl enzyme. In step the phosphoryl group is transferred from the His residue to the terminal phosphate of GDP (or ADP), forming GTP (or ATP). (b) Active site of succinyl-CoA synthetase of Escherichia coli. The active site includes part of both the α (blue) and the β (brown) subunits. The power helices (blue, brown) place the partial positive charges of the helix dipole near the phosphate group of -His246 in the α chain, stabilizing the phosphohistidyl enzyme. The bacterial and mammalian enzymes have similar amino acid sequences and three-dimensional structures.
Figure 1 Incorporation of the isotopic carbon (14C) of the labeled acetyl group into α-ketoglutarate by the citric acid cycle. The carbon atoms of the entering acetyl group are shown in red.
Figure 2 The prochiral nature of citrate. (a) Structure of citrate; (b) schematic representation of citrate: X =—OH; Y=—COO−; Z=—CH2COO−. (c) Correct complementary fit of citrate to the binding site of aconitase. There is only one way in which the three specified groups of citrate can fit on the three points of the binding site. Thus only one of the two —CH2COO− groups is bound by aconitase.
Figure 16-14 Products of one turn of the citric acid cycle. At each turn of the cycle, three NADH, one FADH2, one GTP (or ATP), and two CO2 are released in oxidative decarboxylation reactions. Here and in several of the following figures, all cycle reactions are shown as proceeding in one direction only, but keep in mind that most of the reactions are reversible.
Figure 16-15 Role of the citric acid cycle in anabolism. Intermediates of the citric acid cycle are drawn off as precursors in many biosynthetic pathways. Shown in red are four anaplerotic reactions that replenish depleted cycle intermediates (see Table 16-2).
Mechanism Figure 16-16 The role of biotin in the reaction catalyzed by pyruvate carboxylase. Biotin is attached to the enzyme through an amide bond with the ε-amino group of a Lys residue, forming biotinyl-enzyme. Biotin-mediated carboxylation reactions occur in two phases, generally catalyzed in separate active sites on the enzyme, as exemplified by the pyruvate carboxylase reaction. In the first phase (steps to ), bicarbonate is converted to the more activated CO2, and then used to carboxylate biotin. The biotin acts as a carrier to transport the CO2 from one active site to another on an adjacent monomer of the tetrameric enzyme (step ). In the second phase (steps to ), catalyzed in this second active site, the CO2 reacts with pyruvate to form oxaloacetate.
Figure 16-17 Biological tethers. The cofactors lipoate, biotin, and the combination of β-mercaptoethylamine and pantothenate form long, flexible arms (green) on the enzymes to which they are covalently bound, acting as tethers that move intermediates from one active site to the next. The group shaded light red is, in each case, the point of attachment of the activated intermediate to the tether.
Figure 16-18 Regulation of metabolite flow from the PDH complex through the citric acid cycle in mammals. The PDH complex is allosterically inhibited when [ATP]/[ADP], [NADH]/[NAD+], and [acetyl-CoA]/[CoA] ratios are high, all of which indicate an energy-sufficient metabolic state. When these ratios decrease, allosteric activation of pyruvate oxidation results. The rate of flow through the citric acid cycle can be limited by the availability of the citrate synthase substrates, oxaloacetate and acetyl-CoA, or of NAD+, which is depleted by its conversion to NADH, slowing the three NAD+-dependent oxidation steps. Feedback inhibition by succinyl-CoA, citrate, and ATP also slows the cycle by inhibiting early steps. In muscle tissue, Ca2+ stimulates contraction and, as shown here, stimulates energy-yielding metabolism to replace the ATP consumed by contraction.
Figure 16-19 Pyruvate dehydrogenase is inactivated by phosphorylation catalyzed by pyruvate dehydrogenase kinase. The kinase is regulated by metabolites that signal the energetic state of the cell. Metabolites that accumulate in an energy-sufficient state activate PDH kinase, which phosphorylates and inactivates PDH. Pyruvate is then diverted away from the energy-yielding citric acid cycle (CAC). Metabolites indicating energy need or pyruvate accumulation have the opposite effect, keeping PDH active and sending acetyl-CoA into the CAC.
Figure 16-20 A mutant isocitrate dehydrogenase acquires a new activity. Wild-type isocitrate dehydrogenase catalyzes the conversion of isocitrate to α-ketoglutarate, but mutations that alter the binding site for isocitrate cause loss of the normal enzymatic activity and gain of a new activity: conversion of α-ketoglutarate to 2-hydroxyglutarate. Accumulation of this product inhibits histone demethylase, altering gene regulation and leading to glial cell tumors in the brain.
Figure 16-21 Effect of protein concentration on complex stability. Dilution of a solution containing a noncovalently bound protein complex — such as a metabolon consisting of three enzymes (illustrated here in red, blue, and green) — favors dissociation of the complex into its constituents.
Figure 16-22 A three-enzyme metabolon of the citric acid cycle. (a) Purified porcine enzymes malate dehydrogenase (MDH), citrate synthase (CS), and aconitase form a metabolon when combined in vitro. (b) Electrostatic modeling shows that a broad path of positive potential along the surface of a MDH-CS complex connects the active sites of MDH and CS. This path provides a channel for the passage of the negatively charged oxaloacetate (OAA) from the active site of MDH, where it is formed from l-malate, to the active site of CS, where it condenses with acetyl-CoA to form citrate. Engineered mutations that replaced a positively charged Arg residue along this path with a negatively charged Asp residue greatly reduced the rate of substrate channeling through the complex, providing evidence that the functional unit is a metabolon. [Information from B. Bulutoglu et al., ACS Chem. Biol. 11:2847, 2016. Data from PDB ID 1MLD, W. B. Gleason et al., Biochemistry 33:2078, 1994; PDB ID 1CTS, S. Remington et al., J. Mol. Biol. 158:111, 1982; PDB ID 7ACN, H. Lauble et al., Biochemistry 31:2735, 1992.]
Figure 17-1 Processing of dietary lipids in vertebrates. Digestion and absorption of dietary lipids occur in the small intestine, and the fatty acids released from triacylglycerols are packaged and delivered to muscle and adipose tissues. The eight steps are discussed in the text.
Figure 17-2 Mobilization of triacylglycerols stored in adipose tissue. When low levels of glucose in the blood trigger the release of glucagon, the hormone binds its receptor in the adipocyte membrane and thus stimulates adenylyl cyclase, via a G protein, to produce cAMP. This activates PKA, which phosphorylates the hormone-sensitive lipase (HSL) and perilipin molecules on the surface of the lipid droplet. Phosphorylation of perilipin causes dissociation of the protein CGI-58 from perilipin. CGI-58 (comparative gene identification-58), a protein closely associated with lipid droplets, then recruits adipose triacylglycerol lipase (ATGL) to the droplet surface and stimulates its lipase activity. Active ATGL converts triacylglycerols to diacylglycerols. The phosphorylated perilipin associates with phosphorylated HSL, allowing it access to the surface of the lipid droplet, where it converts diacylglycerols to monoacylglycerols. A third lipase, monoacylglycerol lipase (MGL), hydrolyzes monoacylglycerols. Fatty acids leave the adipocyte, and are transported in the blood bound to serum albumin. They are released from the albumin and enter a myocyte via a specific fatty acid transporter. In the myocyte, fatty acids are oxidized to CO2, and the energy of oxidation is conserved in ATP, which fuels muscle contraction and other energy-requiring metabolism in the myocyte.
Figure 17-3 Human serum albumin complexed with stearate. Each day the human liver releases 10–15 g of serum albumin into the bloodstream, where this workhorse protein transports many ligands, drugs, and particularly fatty acids through the blood. The structure has nooks and crannies that can carry up to seven fatty acids. Its passengers are both hydrophobic and hydrophilic, and include steroid hormones, the blood thinner warfarin, the antibiotic penicillin, the anti-inflammatory drug ibuprofen, and the anxiolytic diazepam.
Figure 17-4 Entry of glycerol into the glycolytic pathway.
Mechanism Figure 17-5 Activation of a fatty acid by conversion to a fatty acyl–CoA. Formation of the fatty acyl–CoA derivative occurs in two steps, catalyzed by fatty acyl–CoA synthetase. Hydrolysis of the pyrophosphate created in the first step of that reaction is catalyzed by inorganic pyrophosphatase. The overall reaction is highly exergonic.
Figure 17-6 Fatty acid entry into mitochondria via the acyl-carnitine/carnitine transporter. Fatty acyl–carnitine formed on the outer mitochondrial membrane moves into the matrix by passive cotransport through the inner membrane. In the matrix, the acyl group is transferred to mitochondrial coenzyme A, freeing carnitine to leave the matrix through the same transporter.
Figure 17-7 Stages of fatty acid oxidation. Stage 1: A long-chain fatty acid is oxidized to yield acetyl residues in the form of acetyl-CoA. This process is called β oxidation. Stage 2: The acetyl groups are oxidized to CO2 via the citric acid cycle. Stage 3: Electrons derived from the oxidations of stages 1 and 2 pass to O2 via the mitochondrial respiratory chain, providing the energy for ATP synthesis by oxidative phosphorylation.
Figure 17-8 The β-oxidation pathway. (a) In each pass through this four-step sequence, one acetyl residue (shaded in light red) is removed in the form of acetyl-CoA from the carboxyl end of the fatty acyl chain — in this example palmitate (C16), which enters as palmitoyl-CoA. Electrons from the first oxidation pass through electron transfer flavoprotein (ETF), and then through a second flavoprotein (ETF:ubiquinone oxidoreductase), into the respiratory chain. Electrons from the second oxidation enter the respiratory chain through NADH dehydrogenase. (b) Six more passes through the β-oxidation pathway yield seven more molecules of acetyl-CoA, the seventh arising from the last two carbon atoms of the 16-carbon chain. Eight molecules of acetyl-CoA are formed in all. The acetyl-CoA may be oxidized in the citric acid cycle, donating more electrons to the respiratory chain.
Figure 17-9 A conserved reaction sequence to introduce a carbonyl function on the carbon β to a carboxyl group. The β-oxidation pathway for fatty acyl–CoAs, the pathway from succinate to oxaloacetate in the citric acid cycle, and the pathway by which the deaminated carbon skeletons from isoleucine, leucine, and valine are oxidized as fuels — all use the same reaction sequence.
A grizzly bear prepares its hibernation nest near the McNeil River in Canada.
Figure 17-10 Oxidation of a monounsaturated fatty acid. Oleic acid, as oleoyl-CoA (Δ9), is the example used here. Oxidation requires an additional enzyme, enoyl-CoA isomerase, to reposition the double bond, converting the cis isomer to a trans isomer, an intermediate in β oxidation.
Figure 17-11 Oxidation of a polyunsaturated fatty acid. The example here is linoleic acid, as linoleoyl-CoA (Δ9,12). Oxidation requires a second auxiliary enzyme in addition to enoyl-CoA isomerase: NADPH-dependent 2,4-dienoyl-CoA reductase. The combined action of these two enzymes converts a trans-Δ2,cis-Δ4-dienoyl-CoA intermediate to the trans-Δ2-enoyl-CoA substrate necessary for β oxidation.
Figure 17-12 Oxidation of propionyl-CoA produced by β oxidation of odd-number fatty acids. The sequence involves the carboxylation of propionyl-CoA to d-methylmalonyl-CoA and conversion of the latter to succinyl-CoA. This conversion requires epimerization of d- to l-methylmalonyl-CoA, followed by a remarkable reaction in which substituents on adjacent carbon atoms exchange positions (see Box 17-2).
Figure 1
Figure 2
Figure 3
Dorothy Crowfoot Hodgkin, 1910–1994
Mechanism Figure 4
Figure 17-13 Coordinated regulation of fatty acid synthesis and breakdown. The steps are explained in the text.
Figure 17-14 Comparison of β oxidation in mitochondria and in peroxisomes and glyoxysomes.
Figure 17-15 The α oxidation of a branched-chain fatty acid (phytanic acid) in peroxisomes. Phytanic acid has a methyl-substituted β carbon and therefore cannot undergo β oxidation. The combined action of the enzymes shown here removes the carboxyl carbon of phytanic acid to produce pristanic acid, in which the β carbon is unsubstituted, allowing β oxidation. Notice that β oxidation of pristanic acid releases propionyl-CoA, not acetyl-CoA. This is further catabolized as in Figure 17-12. (The details of the reaction that produces pristanal remain controversial.)
Figure 17-16 Formation of ketone bodies from acetyl-CoA. Healthy, well-nourished individuals produce ketone bodies at a relatively low rate. When acetyl-CoA accumulates (as in starvation or untreated diabetes, for example), thiolase catalyzes the condensation of two acetyl-CoA molecules to acetoacetyl-CoA, the parent compound of the three ketone bodies. The reactions of ketone body formation occur in the matrix of liver mitochondria. The six-carbon compound β-hydroxy-β-methylglutaryl-CoA (HMG-CoA) is also an intermediate of sterol biosynthesis, but the enzyme that forms HMG-CoA in that pathway is cytosolic. HMG-CoA lyase is present only in the mitochondrial matrix.
Figure 17-17 D-β-Hydroxybutyrate as a fuel. d-β-Hydroxybutyrate, synthesized in the liver, passes into the blood and thus to other tissues, where it is converted in three steps to acetyl-CoA. It is first oxidized to acetoacetate, which is activated with coenzyme A donated from succinyl-CoA, then split by thiolase. The acetyl-CoA thus formed enters the citric acid cycle.
Figure 17-18 Ketone body formation and export from the liver. Conditions that promote gluconeogenesis (untreated diabetes, severely reduced food intake) slow the citric acid cycle (by drawing off oxaloacetate) and enhance the conversion of acetyl-CoA to acetoacetate. The released coenzyme A allows continued β oxidation of fatty acids.
Figure 18-1 Overview of amino acid catabolism in mammals.
Figure 18-2 Amino group catabolism.
Figure 18-3 Part of the human digestive (gastrointestinal) tract.
Figure 18-4 Enzyme-catalyzed transaminations.
Figure 18-5 Pyridoxal phosphate, the prosthetic group of aminotransferases.
Mechanism Figure 18-6 Some amino acid transformations at the α carbon that are facilitated by pyridoxal phosphate.
Figure 18-7 Reaction catalyzed by glutamate dehydrogenase.
Figure 18-8 Ammonia transport in the form of glutamine.
Figure 18-9 Glucose-alanine cycle.
Figure 18-10 The urea cycle and reactions that feed amino groups into the cycle.
Mechanism Figure 18-11 Nitrogen-acquiring reactions in the synthesis of urea.
Figure 18-12 Links between the urea cycle and citric acid cycle.
Figure 18-13 Synthesis of N-acetylglutamate and its activation of carbamoyl phosphate synthetase I.
Figure 18-14 Treatment for deficiencies in urea cycle enzymes.
Figure 18-15 Summary of amino acid catabolism.
Figure 18-16 Some enzyme cofactors important in one-carbon transfer reactions.
Figure 18-17 Conversions of one-carbon units on tetrahydrofolate.
Figure 18-18 Synthesis of methionine and S-adenosylmethionine in an activated-methyl cycle.
Figure 18-19 Catabolic pathways for alanine, tryptophan, cysteine, serine, glycine, and threonine.
Mechanism Figure 18-20 Interplay of the pyridoxal phosphate and tetrahydrofolate cofactors in serine and glycine metabolism.
Figure 18-21 Catabolic pathways for tryptophan, lysine, phenylalanine, tyrosine, leucine, and isoleucine.
Figure 18-22 Tryptophan as precursor.
Figure 18-23 Catabolic pathways for phenylalanine and tyrosine.
Figure 18-24 Role of tetrahydrobiopterin in the phenylalanine hydroxylase reaction.
Figure 18-25 Alternative pathways for catabolism of phenylalanine in phenylketonuria.
Figure 18-26 Catabolic pathways for arginine, histidine, glutamate, glutamine, and proline.
Figure 18-27 Catabolic pathways for methionine, isoleucine, threonine, and valine.
Figure 1 Children with a mutation (red X) that inactivates the enzyme methylmalonyl-CoA mutase cannot degrade isoleucine, methionine, threonine, and valine normally.
Figure 18-28 Catabolic pathways for the three branched-chain amino acids: valine, isoleucine, and leucine.
Figure 18-29 Catabolic pathway for asparagine and aspartate.
Figure 19-1 The chemiosmotic mechanism for ATP synthesis in mitochondria.
Figure 19-2 Biochemical anatomy of a mitochondrion.
Albert L. Lehninger, 1917–1986
Figure 19-3 Ubiquinone (Q, or coenzyme Q).
Figure 19-4 Prosthetic groups of cytochromes.
Figure 19-5 Iron-sulfur centers.
Figure 19-6 Method for determining the sequence of electron carriers.
Figure 19-7 Separation of functional complexes of the respiratory chain.
Figure 19-8 Structure of Complex I (NADH:ubiquinone oxidoreductase).
Figure 19-9 Structure of Complex II (succinate dehydrogenase).
Figure 19-10 Structure of Complex III (cytochrome bc1 complex).
Figure 19-11 The Q cycle, shown in two stages.
Figure 19-12 Structure of Complex IV (cytochrome oxidase).
Figure 19-13 Path of electrons through Complex IV.
Figure 19-14 A respirasome composed of Complexes I, III, and IV.
Figure 19-15 Paths of electron transfer to ubiquinone in the respiratory chain.
Figure 19-16 Summary of the flow of electrons and protons through the four complexes of the respiratory chain.
Figure 19-17 Proton-motive force.
Figure 19-18 ROS formation in mitochondria and mitochondrial defenses.
Figure 19-19 Chemiosmotic model.
Peter Mitchell, 1920–1992
Figure 19-20 Coupling of electron transfer and ATP synthesis in mitochondria.
Henry Lardy, 1917–2010
Figure 19-21 Two chemical uncouplers of oxidative phosphorylation.
Figure 19-22 Evidence for the role of a proton gradient in ATP synthesis.
Figure 19-23 Catalytic mechanism of F1.
Figure 19-24 Reaction coordinate diagrams for ATP synthase and for a more typical enzyme.
Figure 19-25 Mitochondrial ATP synthase complex.
nit and two b subunits, which anchor the FoF1 complex in the membrane and act as a stator (the stationary part of a rotary system), holding the α and β subunits in place.
Figure 19-26 Binding-change model for ATP synthase.
Figure 19-27 Experimental demonstration of rotation of Fo and γ.
Figure 19-28 A model for proton-driven rotation of the c ring.
Figure 19-29 Species differences in number of c subunits in the c ring of the Fo complex.
Figure 19-30 Adenine nucleotide and phosphate translocases.
Figure 19-31 Malate-aspartate shuttle.
Figure 19-32 Glycerol 3-phosphate shuttle.
Figure 1 Eastern skunk cabbage.
Figure 2 Electron carriers of the inner membrane of plant mitochondria.
>[Data from PDB ID 1OHH, E. Cabezon et al., Nat. Struct. Biol. 10:744, 2003.]
Figure 19-34 Regulation of gene expression by hypoxia-inducible factor (HIF-1) to reduce ROS formation.
Figure 19-35 Regulation of ATP-producing pathways.
Figure 19-36 Two mechanisms of thermogenesis in mitochondria.
Figure 19-37 Mitochondria of adrenal gland, specialized for steroid synthesis.
Figure 19-38 Path of electron flow in mitochondrial cytochrome P-450 reactions in adrenal gland.
Figure 19-39 Role of cytochrome c in apoptosis.
Figure 19-40 Mitochondrial genes and mutations.
Figure 19-41 Rotation of bacterial flagella by proton-motive force.
Figure 19-42 Heteroplasmy in mitochondrial genomes.
Figure 19-43 Paracrystalline inclusions in MERRF syndrome mitochondrion.
Figure 19-44 A mitochondrial defect prevents insulin secretion.
Figure 20-1 Assimilation of CO2 provides all of the carbon a plant needs.
Figure 20-2 The chemiosmotic mechanism for ATP synthesis in chloroplasts and mitochondria.
Figure 20-3 Chloroplast structure. (a) Schematic diagram. (b) Colorized electron micrograph at high magnification, showing the highly organized thylakoid membrane system.
Figure 20-4 Electromagnetic radiation.
Figure 20-5 Primary and secondary photopigments.
Figure 20-6 Absorption of visible light by photopigments.
Figure 20-7 Two ways to determine the action spectrum for photosynthesis.
Figure 20-8 Organization of photosystems in the thylakoid membrane.
Figure 20-9 The light-harvesting complex LHCII of the pea.
Figure 20-10 Exciton and electron transfer.
Figure 20-11 Functional Modules of Photosynthetic Machinery in Purple Bacteria and Green Sulfur Bacteria.
Figure 20-12 Integration of photosystems I and II in chloroplasts.
Figure 20-13 Structure of photosystem II of the cyanobacterium Thermosynechococcus vulcanus.
Figure 20-14 Electron transfer through photosystem II of the cyanobacterium Synechococcus elongatus.
Figure 20-15 Structure of photosystem I in the cyanobacterium Synechococcus elongatus.
Figure 20-16 The path of electrons through PSI.
Figure 20-17 Electron and proton flow through the cytochrome b6f complex.
Figure 20-18 Localization of PSI and PSII in thylakoid membranes.
Figure 20-19 Electron transfer in PSI and PSII is balanced through state transitions.
Figure 20-20 Water-splitting activity of the oxygen-evolving center.
Figure 20-21 Proton and electron circuits during photophosphorylation.
Figure 20-22 Orientation of ATP synthase is fixed relative to the proton gradient.
Figure 20-23 The photosynthetic membranes of a cyanobacterium.
Figure 20-24 Dual roles of cytochrome b6f and cytochrome c6 in cyanobacteria reflect evolutionary origins.
Figure 20-25 Products of photosynthesis.
Figure 20-26 The three stages of CO2 assimilation in photosynthetic organisms.
Figure 20-27 Structure of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco).
Figure 20-28 Central role of Mg2+ in the active site of rubisco.
Mechanism Figure 20-29 First stage of CO2 assimilation: rubisco’s carboxylase activity.
Figure 20-30 Role of rubisco activase in carbamoylation of Lys201 of rubisco.
Figure 20-31 Third stage of CO2 assimilation.
Figure 20-32 Stoichiometry of CO2 assimilation in the Calvin cycle.
Figure 20-33 The Pi – triose phosphate antiport system of the chloroplast inner membrane.
Figure 20-34 Role of the Pi – triose phosphate antiporter in the transport of ATP and reducing equivalents.
Figure 20-35 Source of ATP and NADPH.
Figure 20-36 Activation of chloroplast fructose 1,6-bisphosphatase.
Figure 20-37 Light activation of several enzymes of the Calvin cycle.
Figure 20-38 Oxygenase activity of rubisco.
Figure 20-39 Glycolate pathway.
Figure 1 The concentration of CO2 in the atmosphere measured at the Mauna Loa Observatory in Hawaii.
Figure 2 The terrestrial carbon cycle. Carbon stocks (boxed text) are shown as gigatons (GT), and fluxes (arrows) are shown in GT per year. Animal biomass is negligible here — less than 0.5 GT. [Information from C. Jansson et al., BioScience 60:683, 2010, Fig. 1.]
Figure 20-40 CO2 assimilation in C4 plants.
Figure 20-41 Sucrose synthesis.
Figure 20-42 Fructose 2,6-bisphosphate as regulator of sucrose synthesis.
Figure 20-43 Regulation of sucrose phosphate synthase by phosphorylation.
Figure 20-44 Regulation of ADP-glucose pyrophosphorylase by 3-phosphoglycerate and Pi.
Figure 20-45 Conversion of stored fatty acids to sucrose in germinating seeds through the glyoxylate cycle.
Figure 20-46 Cellulose structure.
Figure 20-47 A model for the synthesis of cellulose.
Figure 20-48 Pools of hexose phosphates, pentose phosphates, and triose phosphates.
Figure 20-49 Movement of sucrose between source and sink tissues.
Figure 21-1 The acetyl-CoA carboxylase reaction.
Figure 21-2 Addition of two carbons to a growing fatty acyl chain: a four-step sequence.
Figure 21-3 The structure of a fatty acid synthase type I system.
Figure 21-4 The overall process of palmitate synthesis.
Figure 21-5 Acyl carrier protein (ACP).
Figure 21-6 Sequence of events during synthesis of a fatty acid.
Figure 21-7 Beginning of the second round of the fatty acid synthesis cycle.
Figure 21-8 Production of NADPH.
Figure 21-9 Subcellular localization of lipid metabolism.
Figure 21-10 Shuttle for transfer of acetyl groups from mitochondria to the cytosol.
Figure 21-11 Regulation of fatty acid synthesis.
Figure 21-12 Routes of synthesis of unsaturated fatty acids and their derivatives.
Figure 21-13 Electron transfer in the desaturation of fatty acids in vertebrates.
Figure 1 Simplified cytochrome P-450 reaction cycle.
Figure 2 Pathways of sterol biosynthesis, showing the steps requiring cytochrome P-450 enzymes.
Figure 21-14 Action of plant desaturases.
Figure 21-15 The “cyclic” pathway from arachidonate to prostaglandins and thromboxanes.
Figure 21-16 The “linear” pathway from arachidonate to leukotrienes.
Figure 21-17 Biosynthesis of phosphatidic acid.
Figure 21-18 Phosphatidic acid in lipid biosynthesis.
Figure 21-19 Regulation of triacylglycerol synthesis by insulin.
Figure 21-20 The triacylglycerol cycle.
Figure 21-21 Glyceroneogenesis.
Figure 21-22 Regulation of glyceroneogenesis.
Figure 21-23 Final stages of glycerophospholipid biosynthesis: head-group attachment.
Figure 21-24 Two general strategies for forming the phosphodiester bond of phospholipids.
Figure 21-25 Synthesis of glycerophospholipids in eukaryotes using CDP-diacylglycerol.
Figure 21-26 Pathways for phosphatidylserine and phosphatidylcholine synthesis in mammals.
Figure 21-27 Summary of the pathways for synthesis of major phospholipids and triacylglycerols in eukaryotes.
Figure 21-28 Origin of the polar head groups of phospholipids in E. coli.
Figure 21-29 The Lands cycle for phospholipid remodeling.
Figure 21-30 Synthesis of ether lipids and plasmalogens.
Figure 21-31 Biosynthesis of sphingolipids.
Figure 21-32 Origin of the carbon atoms of cholesterol.
Figure 21-33 Summary of cholesterol biosynthesis.
Figure 21-34 Formation of mevalonate from acetyl-CoA.
Figure 21-35 Conversion of mevalonate to activated isoprene units.
Figure 21-36 Formation of squalene.
Figure 21-37 Ring closure converts linear squalene to the condensed steroid nucleus.
Figure 21-38 Metabolic fates of cholesterol.
Figure 21-39 Lipoproteins.
Figure 21-40 Lipoproteins and lipid transport.
Figure 21-41 Reaction catalyzed by lecithin-cholesterol acyltransferase (LCAT).
Figure 21-42 Uptake of cholesterol by receptor-mediated endocytosis.
Michael Brown and Joseph Goldstein
Figure 21-43 Regulation of cholesterol formation balances synthesis with dietary uptake and energy state.
Figure 21-44 Regulation of cholesterol synthesis by SREBP.
Figure 21-45 Action of RXR-LXR dimer on expression of genes for lipid and glucose metabolism.
Figure 21-46 Formation of atherosclerotic plaques.
Figure 1 Statins as inhibitors of HMG-CoA reductase.
Akira Endo
Akira Endo
P. Roy Vagelos
Figure 21-47 Reverse cholesterol transport.
Figure 21-48 Some steroid hormones derived from cholesterol.
Figure 21-49 Side-chain cleavage in the synthesis of steroid hormones.
Figure 21-50 Overview of isoprenoid biosynthesis.
Figure 22-1 The global nitrogen web.
Figure 1 The anammox reactions. Ammonia and hydroxylamine are converted to hydrazine and H2O by hydrazine hydrolase, and the hydrazine is oxidized by hydrazine-oxidizing enzyme, generating N2 and protons. The protons create a proton gradient for ATP synthesis. On the anammoxosome exterior, protons are used by the nitrite-reducing enzyme, producing hydroxylamine and completing the cycle. All of the anammox enzymes are embedded in the anammoxosome membrane. [Information from L. A. van Niftrik et al., FEMS Microbiol. Lett. 233:10, 2004, Fig. 4.]
Figure 2 (a) Ladderane lipids of the anammoxosome membrane. The mechanism for synthesis of the unstable fused cyclobutane ring structures is unknown. (b) Ladderanes can stack to form a very dense, impermeable, hydrophobic membrane structure, allowing sequestration of the hydrazine produced in the anammox reactions. [Information from L. A. van Niftrik et al., FEMS Microbiol. Lett. 233:7, 2004, Fig. 3.]
Figure 3 Transmission electron micrograph of a cross section through Gemmata obscuriglobus, showing the DNA in a nucleus (N) with enclosing nuclear envelope (NE). Bacteria of the Gemmata genus (phylum Planctomycetes) do not promote the anammox reactions.
Figure 22-2 Nitrate assimilation by nitrate reductase and nitrite reductase.
Figure 22-3 Enzymes and cofactors of the nitrogenase complex. (a) The holoenzyme consists of two identical dinitrogenase reductase molecules (green), each with a 4Fe-4S redox center and binding sites for two ATP, and two identical dinitrogenase heterodimers (purple and blue), each with a P cluster (Fe-S center) and an FeMo cofactor. In this structure, ADP is bound in the ATP site, to make the crystal more stable. (b) The electron-transfer cofactors. A P cluster is shown here in its reduced (top) and oxidized (middle) forms. The FeMo cofactor (bottom) has a Mo atom with three S ligands, a His ligand, and two oxygen ligands from a molecule of homocitrate. In some organisms, the Mo atom is replaced with a vanadium atom. (Fe is shown in orange, S in yellow.) [Data from (a) PDB ID 1N2C, H. Schindelin et al., Nature 387:370, 1997; (b) Pred: PDB ID 3MIN, and Pox: PDB ID 2MIN, J. W. Peters et al., Biochemistry 36:1181, 1997; FeMo cofactor: PDB ID 1M1N, O. Einsle et al., Science 297:1696, 2002.]
Figure 22-4 Electron path in nitrogen fixation by the nitrogenase complex. Electrons are transferred from pyruvate to dinitrogenase via ferredoxin (or flavodoxin) and dinitrogenase reductase. Dinitrogenase reductase reduces dinitrogenase one electron at a time, with at least six electrons required to fix one molecule of N2. Two additional electrons are used to reduce 2H+ to H2 in a process that obligatorily accompanies nitrogen fixation in anaerobes, making a total of eight electrons required per N2 molecule. The subunit structures and metal cofactors of the dinitrogenase reductase and dinitrogenase proteins are described in the text and in Figure 22-3.
Figure 22-5 Two reasonable hypotheses for the intermediates involved in N2 reduction. In both scenarios, the FeMo cofactor (abbreviated as M here) plays a central role, binding directly to one of the nitrogen atoms of N2 and remaining bound throughout the sequence of reduction steps. [Information from L. C. Seefeldt et al., Annu. Rev. Biochem. 78:701, 2009, Fig. 9.]
Figure 22-6 Nitrogen-fixing nodules. (a) Pea plant (Pisum sativum) root nodules containing the nitrogen-fixing bacterium Rhizobium leguminosarum. The nodules are pink due to the presence of leghemoglobin; this heme protein has a very high binding affinity for oxygen, which strongly inhibits nitrogenase. (b) Artificially colorized electron micrograph of a thin section through a pea root nodule. Symbiotic nitrogen-fixing bacteria, or bacteroids (red), live inside the nodule cell, surrounded by the peribacteroid membrane (blue). Bacteroids produce the nitrogenase complex that converts atmospheric nitrogen (N2) to ammonium (NH4+); without the bacteroids, the plant is unable to utilize N2. (The cell nucleus is shown in yellow/green. Not visible in this micrograph are other organelles of the infected root cell that are normally found in plant cells.)
Figure 22-7 Subunit structure of bacterial type I glutamine synthetase. This view shows 6 of the 12 identical subunits; a second layer of 6 subunits lies directly beneath those shown. Each of the 12 subunits has an active site, where ATP and glutamate are bound in orientations that favor transfer of a phosphoryl group from ATP to the side-chain carboxyl of glutamate. In this crystal structure, ADP occupies the ATP site. [Data from PDB ID 2GLS, M. M. Yamashita et al., J. Biol. Chem. 264:17,681, 1989.]
Figure 22-8 Allosteric regulation of glutamine synthetase. The enzyme undergoes cumulative regulation by six end products of glutamine metabolism. Alanine and glycine probably serve as indicators of the general status of amino acid metabolism in the cell.
Figure 22-9 Second level of regulation of glutamine synthetase: covalent modifications. (a) An adenylylated Tyr residue. (b) Cascade leading to adenylylation (inactivation) of glutamine synthetase. AT represents adenylyltransferase; UT, uridylyltransferase. PII is a regulatory protein, itself regulated by uridylylation.
Mechanism Figure 22-10 Proposed mechanism for glutamine amidotransferases.
Figure 22-11 Overview of amino acid biosynthesis. The carbon skeleton precursors derive from three sources: glycolysis (light red), the citric acid cycle (blue), and the pentose phosphate pathway (purple).
Figure 22-12 Biosynthesis of proline and arginine from glutamate in bacteria.
Figure 22-13 Ornithine δ-aminotransferase reaction: a step in the mammalian pathway to proline.
Figure 22-14 Biosynthesis of serine from 3-phosphoglycerate and of glycine from serine in all organisms. As indicated in the text, this is only one of multiple pathways to synthesize glycine.
Figure 22-15 Biosynthesis of cysteine from serine in bacteria and plants. The origin of reduced sulfur is shown in the pathway on the right.
Figure 22-16 Biosynthesis of cysteine from homocysteine and serine in mammals. The homocysteine is formed from methionine.
Figure 22-17 Biosynthesis of six essential amino acids from oxaloacetate and pyruvate in bacteria: methionine, threonine, lysine, isoleucine, valine, and leucine. Some of the most complex pathways for amino acid biosynthesis are found here. Pathways are abbreviated to emphasize precursors and pathway products.
Figure 22-18 Biosynthesis of chorismate, an intermediate in the synthesis of aromatic amino acids in bacteria and plants.
Figure 22-19 Biosynthesis of tryptophan from chorismate in bacteria and plants. In E. coli, enzymes catalyzing steps and are subunits of a single complex.
Mechanism Figure 22-20 Tryptophan synthase reaction.
Figure 22-21 Biosynthesis of phenylalanine and tyrosine from chorismate in bacteria and plants. Conversion of chorismate to prephenate is a rare biological example of a Claisen rearrangement.
Figure 22-22 Biosynthesis of histidine in bacteria and plants. Atoms derived from PRPP and ATP are shaded light red and blue, respectively. Two of the histidine nitrogens are derived from glutamine and glutamate (green). Note that the derivative of ATP remaining after step (AICAR) is an intermediate in purine biosynthesis (see Fig. 22-35, step ), so ATP is rapidly regenerated.
Figure 22-23 Allosteric regulation of isoleucine biosynthesis. The first reaction in the pathway from threonine to isoleucine is inhibited by the end product, isoleucine. This was one of the first examples of allosteric feedback inhibition to be discovered.
Figure 22-24 Interlocking regulatory mechanisms in the biosynthesis of several amino acids derived from aspartate in E. coli.
Figure 22-25 Biosynthesis of δ-aminolevulinate.
Figure 22-26 Biosynthesis of heme from δ-aminolevulinate.
Figure 1 The key to Figure 22-26 identifies the defective enzyme at each step.
Figure 22-27 Bilirubin and its breakdown products.
Figure 22-28 Biosynthesis of creatine and phosphocreatine. Creatine is made from three amino acids: glycine, arginine, and methionine. This pathway shows the versatility of amino acids as precursors of other nitrogenous biomolecules.
Figure 22-29 Glutathione metabolism. (a) Biosynthesis of glutathione. (b) Oxidized form of glutathione.
Figure 22-30 Biosynthesis of two plant substances from amino acids. (a) Indole-3-acetate (auxin) and (b) cinnamate (cinnamon flavor).
Figure 22-31 Biosynthesis of some neurotransmitters from amino acids. The key step is the same in each case: a PLP-dependent decarboxylation (shaded light red).
Figure 22-32 Biosynthesis of spermidine and spermine. The PLP-dependent decarboxylation steps are shaded light red. In these reactions, S-adenosylmethionine (in its decarboxylated form) acts as a source of propylamino groups (shaded blue).
Figure 22-33 Biosynthesis of nitric oxide. The nitrogen of the NO is derived from the guanidinium group of arginine.
Figure 22-34 Origin of the ring atoms of purines. This information was obtained from isotopic experiments with 14C- or 15N-labeled precursors. Formate is supplied in the form of N10-formyltetrahydrofolate.
Figure 22-35 De novo synthesis of purine nucleotides: construction of the purine ring of inosinate (IMP). Each addition to the purine ring is shaded to match Figure 22-34. After step , R symbolizes the 5-phospho-d-ribosyl group on which the purine ring is built. Formation of 5-phosphoribosylamine (step ) is the first committed step in purine synthesis. Note that the product of step , AICAR, is the remnant of ATP released during histidine biosynthesis (see Fig. 22-22, step ). Abbreviations are given for most intermediates to simplify the naming of the enzymes. Step is the alternative path from AIR to CAIR occurring in higher eukaryotes.
Figure 22-36 Biosynthesis of AMP and GMP from IMP.
Figure 22-37 Regulatory mechanisms in the biosynthesis of adenine and guanine nucleotides in E. coli. Regulation of these pathways differs in other organisms.
Figure 22-38 De novo synthesis of pyrimidine nucleotides: biosynthesis of UTP and CTP via orotidylate. The pyrimidine is constructed from carbamoyl phosphate and aspartate. The ribose 5-phosphate is then added to the completed pyrimidine ring by orotate phosphoribosyltransferase. The first step in this pathway (not shown here; see Fig. 18-11a) is the synthesis of carbamoyl phosphate from CO2, NH4+, and ATP. In eukaryotes, the first step is catalyzed by carbamoyl phosphate synthetase II.
Figure 22-39 Channeling of intermediates in bacterial carbamoyl phosphate synthetase.
Figure 22-40 Allosteric regulation of aspartate transcarbamoylase by CTP and ATP.
Figure 22-41 Reduction of ribonucleotides to deoxyribonucleotides by ribonucleotide reductase. Electrons are transmitted (red arrows) to the enzyme from NADPH via (a) glutaredoxin or (b) thioredoxin. The sulfhydryl groups in glutaredoxin reductase are contributed by two molecules of bound glutathione (GSH; GSSG indicates oxidized glutathione). Note that thioredoxin reductase is a flavoenzyme, with FAD as a prosthetic group.
Figure 22-42 Ribonucleotide reductase.
Mechanism Figure 22-43 Proposed mechanism for ribonucleotide reductase.
Figure 22-44 Regulation of ribonucleotide reductase by deoxynucleoside triphosphates. The overall activity of the enzyme is affected by binding at the primary regulatory site (left). The substrate specificity of the enzyme is affected by the nature of the effector molecule bound at the second type of regulatory site, the substrate-specificity site (right). The diagram indicates inhibition or stimulation of enzyme activity with the four different substrates. The pathway from dUDP to dTMP is described below (see Figs 22-46, 22-47).
Figure 22-45 Oligomerization of ribonucleotide reductase induced by the allosteric inhibitor dATP.
Figure 22-46 Biosynthesis of thymidylate (dTMP). The pathways are shown beginning with the reaction catalyzed by ribonucleotide reductase.
Figure 22-47 Conversion of dUMP to dTMP by thymidylate synthase and dihydrofolate reductase. Serine hydroxymethyltransferase is required for regeneration of the N5,N10-methylene form of tetrahydrofolate. In the synthesis of dTMP, all three hydrogens of the added methyl group are derived from N5,N10-methylenetetrahydrofolate (light red and gray).
Figure 22-48 Catabolism of purine nucleotides. Note that primates excrete much more nitrogen as urea via the urea cycle (Chapter 18) than as uric acid from purine degradation. Similarly, fish excrete much more nitrogen as NH4+ than as urea produced by the pathway shown here.
Figure 22-49 Catabolism of pyrimidines. These simplified pathways show end products but no intermediates.
Figure 22-50 Allopurinol, an inhibitor of xanthine oxidase. Hypoxanthine is the normal substrate of xanthine oxidase. A slight alteration in the structure of hypoxanthine (shaded light red) yields the medically effective enzyme inhibitor allopurinol. At the active site, allopurinol is converted to oxypurinol, a strong competitive inhibitor that remains tightly bound to the reduced form of the enzyme.
George Hitchings, 1905–1998, and Gertrude Elion, 1918–1999.
Figure 22-51 Thymidylate synthesis and folate metabolism as targets of chemotherapy.
Mechanism Figure 22-52 Conversion of dUMP to dTMP and its inhibition by FdUMP.
Figure 23-1 Signaling by the neuroendocrine system.
Figure 23-2 Two general mechanisms of hormone action.
Figure 23-3 The structure of thyrotropin-releasing hormone (TRH).
Figure 23-4 Insulin.
Figure 23-5 Proteolytic processing of the pro-opiomelanocortin (POMC) precursor.
Figure 23-6 Cascade of top-down hormone release following central nervous system input to the hypothalamus.
Figure 23-7 Neuroendocrine origins of hormone signals.
Figure 23-8 Regulation of feeding behavior by two-way information flow between tissues and the hypothalamus.
Figure 23-9 Specialized metabolic functions of mammalian tissues.
Figure 23-10 Metabolic pathways for glucose 6-phosphate in the liver.
Figure 23-11 Metabolism of amino acids in the liver.
Figure 23-12 Metabolism of fatty acids in the liver.
Figure 23-13 White and brown adipose tissue.
Figure 23-14 Brown adipose tissue in infants and adults.
Figure 23-15 Energy sources for muscle contraction.
Figure 23-16 Phosphocreatine buffers ATP concentration during exercise.
Figure 1 Mitochondrial creatine kinase (mCK) transfers a phosphoryl group from ATP to creatine (Cr) to form phosphocreatine (PCr), which diffuses to sites of ATP use; at these sites, cytosolic creatine kinase (cCK) passes the phosphoryl group into ATP.
Figure 2 Spontaneous (nonenzymatic) formation of creatinine from phosphocreatine or creatine consumes a few percent of the body’s total creatine per day, which must be replaced by biosynthesis or from the diet.
Figure 3 Many body builders take supplemental creatine to supply phosphocreatine in new muscle tissue.
Figure 23-17 Metabolic cooperation between skeletal muscle and the liver: the Cori cycle.
Figure 23-18 Electron micrograph of heart muscle.
Figure 23-19 The fuels that supply ATP in the brain.
Figure 23-20 The composition of blood (by weight).
Figure 23-21 Physiological effects of low blood glucose in humans. Blood glucose levels of 40 mg/100 mL and below constitute severe hypoglycemia.
Figure 23-22 The well-fed state: the lipogenic liver.
Figure 23-23 The endocrine system of the pancreas.
Figure 23-24 Glucose regulation of insulin secretion by pancreatic β cells.
Figure 23-25 ATP-gated K+ channels in β cells.
Figure 23-26 The fasting state: the glucogenic liver.
Figure 23-27 Fuel metabolism in the liver during prolonged fasting or in uncontrolled diabetes mellitus.
Figure 23-28 Plasma concentrations of fatty acids, glucose, and ketone bodies during six weeks of starvation.
Figure 23-29 Set-point model for maintaining constant mass.
Figure 23-30 Obesity caused by defective leptin production.
Figure 23-31 Hypothalamic regulation of food intake and energy expenditure.
Figure 23-32 Hormones that control eating.
Figure 23-33 The role of AMP-activated protein kinase (AMPK) in maintaining energy homeostasis.
Figure 23-34 Formation of adiponectin and its actions through AMPK.
Figure 23-35 The mTORC1-Ragulator-Rag complex on the lysosomal surface.
Figure 23-36 A summary of mTORC1 activation signals and the cellular processes that active mTORC1 stimulates.
Figure 23-37 Mode of action of PPARs.
Figure 23-38 Metabolic integration by PPARs.
Figure 23-39 Variations in blood concentrations of glucose, ghrelin, and insulin relative to meal times.
Figure 23-40 Cannabinoids.
Figure 23-41 Effects of gut microbe metabolism on health.
Figure 1 A child with type 1 diabetes, before (left) and after (right) three months of treatment with an early preparation of insulin.
Figure 23-42 Overloading adipocytes with triacylglycerols triggers inflammation in fat tissue and ectopic lipid deposition and insulin resistance in muscle.
Figure 24-1 Bacteriophage T2 protein coat surrounded by its single, linear molecule of DNA.
Figure 24-2 Colinearity of the coding nucleotide sequences of DNA and mRNA and the amino acid sequence of a polypeptide chain.
Figure 24-3 A bacterial cell and its DNA.
Figure 24-4 DNA from a lysed E. coli cell.
Figure 24-5 Eukaryotic chromosomes.
Figure 24-6 Introns in two eukaryotic genes.
Figure 24-7 Important structural elements of a yeast chromosome.
Figure 24-8 Supercoils.
Figure 24-9 Supercoiling of DNA.
Figure 24-10 The effects of replication and transcription on DNA supercoiling.
Figure 24-11 Relaxed and supercoiled plasmid DNAs.
Figure 24-12 Effects of DNA underwinding.
Figure 24-13 Linking number, Lk.
Figure 24-14 Linking number applied to closed-circular DNA molecules.
Figure 24-15 Negative and positive supercoils.
Figure 24-16 Promotion of cruciform structures by DNA underwinding.
Figure 24-17 Visualization of topoisomers.
Mechanism Figure 24-18 The type I topoisomerase reaction.
Figure 24-19 Alteration of the linking number by a eukaryotic type IIα topoisomerase.
Figure 24-20 Plectonemic supercoiling.
Figure 24-21 Plectonemic and solenoidal supercoiling of the same DNA molecule, drawn to scale.
Figure 24-22 Changes in chromosome structure during the eukaryotic cell cycle.
Figure 24-23 Nucleosomes.
Figure 24-24 DNA wrapped around a histone core.
Figure 24-25 Chromatin assembly.
Figure 24-26 The effect of DNA sequence on nucleosome binding.
Figure 1 Shown here are the standard histones H3, H2A, and H2B and a few of the known variants.
Figure 2 A ChIP-Seq experiment is designed to reveal the genomic DNA sequences to which a particular histone variant binds.
Figure 24-27 Loops of DNA attached to a chromosomal scaffold.
Figure 24-28 Chromosomal organization in the eukaryotic nucleus.
Figure 24-29 Effects of lncRNAs on chromosome architecture and gene expression.
A calico cat.
Figure 1 (a) As Xist RNA is transcribed, it migrates to nearby regions within an X chromosome, (b) binding to proteins including SAFA (scaffold attachment factor A).
Figure 24-30 Chromosome territories.
Figure 24-31 Structure of SMC proteins.
Figure 24-32 Two current models of the possible role of condensins in chromatin condensation.
Figure 24-33 The roles of cohesins and condensins in the eukaryotic cell cycle.
Figure 24-34 E. coli nucleoids.
Figure 24-35 Looped domains of the E. coli chromosome.
Figure 25-1 Visualization of DNA replication.
Figure 25-2 Defining DNA strands at the replication fork.
Arthur Kornberg, 1918–2007
Mechanism Figure 25-3 The DNA polymerase reaction.
Figure 25-4 Elongation of a DNA chain.
Figure 25-5 Contribution of base-pair geometry to the fidelity of DNA replication.
Figure 25-6 An example of error correction by the 3’ 5’ exonuclease activity of DNA polymerase I.
Figure 25-7 Nick translation.
Figure 25-8 DNA polymerase III.
Figure 25-9 Arrangement of sequences in the E. coli replication origin, oriC. Conserved sequences for key repeated elements are shown.
Figure 25-10 Model for initiation of replication at the E. coli origin, oriC.
Figure 25-11 Synthesis of Okazaki fragments.
Figure 25-12 DNA synthesis on the leading and lagging strands.
Figure 25-13 The DNA polymerase III clamp loader.
Figure 25-14 Final steps in the synthesis of lagging strand segments.
Figure 25-15 Mechanism of the DNA ligase reaction.
Figure 25-16 Termination of chromosome replication in E. coli.
Figure 25-17 Role of topoisomerases in replication termination.
Figure 25-18 Assembly of a prereplicative complex at a eukaryotic replication origin.
Figure 25-19 Ames test for carcinogens, based on their mutagenicity.
Figure 25-20 Methylation and mismatch repair.
Figure 25-21 A model for the early steps of methyl-directed mismatch repair.
Figure 25-22 Completion of methyl-directed mismatch repair.
Figure 25-23 DNA repair by the base-excision repair pathway.
Figure 25-24 Nucleotide-excision repair in E. coli and humans.
Mechanism Figure 25-25 Repair of pyrimidine dimers with photolyase.
Figure 25-26 Example of how DNA damage results in mutations.
Figure 25-27 Direct repair of alkylated bases by AlkB.
Figure 25-28 DNA damage and its effect on DNA replication.
Barbara McClintock, 1902–1992
Figure 25-29 Recombinational DNA repair at a collapsed replication fork.
Figure 25-30 The RecBCD helicase/nuclease.
Figure 25-31 RecA protein filaments.
Figure 25-32 Resolution of a Holliday intermediate by the RuvC protein.
Figure 25-33 Meiosis in animal germ-line cells.
Figure 25-34 Recombination during prophase I in meiosis.
Figure 1 The increasing incidence of human trisomy with increasing age of the mother. [Data from T. Hassold and P. Hunt, Nat. Rev. Genet. 2:280, 2001, Fig. 6.]
Figure 25-35 The contribution of independent assortment to genetic diversity.
Figure 1 The activity and function of poly-ADP ribose polymerase in detecting DNA strand breaks and other types of damage. [Information from A. R. Chaudhuri and A. Nussenzweig, Nat. Rev. Mol. Cell Biol. 18:610, 2017, Fig. 1.]
Figure 25-36 Nonhomologous end joining.
Figure 25-37 A site-specific recombination reaction.
Figure 25-38 Effects of site-specific recombination.
Figure 25-39 DNA deletion to undo a deleterious effect of recombinational DNA repair.
Figure 25-40 Duplication of the DNA sequence at a target site when a transposon is inserted.
Figure 25-41 Two general pathways for transposition: direct (simple) and replicative.
Figure 25-42 Recombination of the V and J gene segments of the human IgG kappa light chain.
Figure 25-43 Mechanism of immunoglobulin gene rearrangement.
Figure 26-1 Transcription by RNA polymerase in E. coli.
Figure 26-2 Template and nontemplate (coding) DNA strands.
Figure 26-3 Organization of coding information in the adenovirus genome.
Figure 26-4 Structure of the σ70 RNA polymerase holoenzyme of E. coli.
Figure 26-5 Promoter recognition by RNA polymerase holoenzymes containing σ70.
Figure 1 Footprint analysis of the RNA polymerase–binding site on a DNA fragment.
Figure 2 Footprinting results of RNA polymerase binding to the lac promoter.
Figure 26-6 Transcription initiation and elongation by E. coli RNA polymerase.
Figure 26-7 Termination of transcription in E. coli.
Figure 26-8 Some common features of TATA box promoters recognized by eukaryotic RNA polymerase II.
Figure 26-9 Transcription at RNA polymerase II promoters.
Figure 26-10 Phosphorylation of the carboxyl-terminal domain (CTD) of RNA polymerase II.
Figure 26-11 Inhibition of RNA polymerase by rifampin.
Amanita phalloides, the death cap mushroom
Figure 26-12 Formation of the primary transcript and its processing during maturation of mRNA in a eukaryotic cell.
Figure 26-13 The 5′ cap of mRNA.
Figure 26-14 Splicing mechanism of group II introns.
Thomas Cech
Figure 26-15 Structure of a group I intron.
Joan Steitz
Figure 26-16 Processing of pre-mRNA primary transcripts by the spliceosome.
Figure 26-17 RNA active site conservation between group II introns and the spliceosome.
Figure 26-18 Addition of the poly(A) tail to the primary RNA transcript of eukaryotes.
Figure 26-19 Overview of the processing of a eukaryotic mRNA.
Figure 1 Alternative splicing of the SMN1 and SMN2 gene transcripts in healthy individuals and in those with SMA.
Adrian Krainer
Figure 2
Figure 26-20 Alternative transcript production in eukaryotes.
Figure 26-21 Alternative processing of the calcitonin gene transcript in rats.
Figure 26-22 Some modified bases of RNA produced in posttranscriptional reactions.
Figure 26-23 Processing of pre-rRNA transcripts in bacteria.
Figure 26-24 RNA pairing with box H/ACA snoRNAs to guide pseudouridylations.
Figure 26-25 Processing of tRNAs in bacteria and eukaryotes.
Figure 26-26 Synthesis and processing of miRNAs.
Figure 26-27 Degradation of RNA in bacteria.
Figure 26-28 Essential role of the exosome in eukaryotic RNA degradation.
Figure 26-29 Retroviral infection of a mammalian cell and integration of the retrovirus into the host chromosome.
Howard Temin, 1934–1994; David Baltimore
Figure 26-30 Structure and gene products of an integrated retroviral genome.
Figure 26-31 Rous sarcoma virus genome.
Figure 26-32 The genome of HIV, the virus that causes AIDS.
Figure 26-33 Eukaryotic transposons.
Figure 26-34 Introns that move: homing and retrohoming.
Carol Greider; Elizabeth Blackburn
Figure 26-35 Telomere synthesis and structure.
Figure 26-36 Structural similarities between RNA-dependent polymerases.
Figure 26-37 Secondary structure of the self-splicing rRNA intron of Tetrahymena.
Figure 26-38 In vitro catalytic activity of L-19 IVS.
Figure 26-39 Hammerhead ribozyme.
Carl Woese, 1928–2012
Figure 26-40 Experiments supporting prebiotic synthesis of adenine from ammonium cyanide. Adenine is derived from five molecules of cyanide, denoted by shading.
Figure 1 The SELEX procedure.
Figure 2 RNA aptamer that binds ATP.
Figure 3 RNA aptamer bound to AMP.
Figure 26-41 Self-sustained replication of an RNA enzyme.
Figure 27-1 Timeline for the elucidation of protein biosynthetic pathways.
Figure 27-2 Crick’s adaptor hypothesis.
Figure 27-3 Overlapping versus nonoverlapping genetic codes.
Figure 27-4 The triplet, nonoverlapping code.
Figure 27-5 Reading frames in the genetic code.
Figure 27-6 Effect of a termination codon in a repeating tetranucleotide.
Figure 27-7 “Dictionary” of amino acid code words in mRNAs
Figure 27-8 Pairing relationship of codon and anticodon.
Figure 27-9 Translational frameshifting in a retroviral transcript.
Figure 27-10 RNA editing of the transcript of the cytochrome oxidase subunit II gene from Trypanosoma brucei mitochondria.
Figure 27-11 Deamination reactions that result in RNA editing.
Figure 27-12 RNA editing of the transcript of the gene for the apoB-100 component of LDL.
Figure 27-13 An overview of the five stages of protein synthesis.
Figure 27-14 The structure of ribosomes.
Figure 27-15 Conservation of secondary structure in the small subunit rRNAs from the three domains of life.
Figure 27-16 Summary of the composition and mass of ribosomes in bacteria and eukaryotes.
Figure 27-17 Assembly of ribosomes in eukaryotes.
Figure 27-18 General structure of tRNAs.
Mechanism Figure 27-19 Aminoacylation of tRNA by aminoacyl-tRNA synthetases.
Figure 27-20 General structure of aminoacyl-tRNAs.
Figure 27-21 Nucleotide positions in a tRNA that are recognized by aminoacyl-tRNA synthetases.
Figure 27-22 Aminoacyl-tRNA synthetases.
Figure 27-23 Structural elements of tRNAAla that are required for recognition by Ala-tRNA synthetase.
Figure 1 Selecting MjtRNATyr variants that function only with the tyrosyl-tRNA synthetase MjTyrRS.
Figure 2 A sampling of unnatural amino acids that have been added to the genetic code.
Figure 27-24 Formation of the initiation complex in bacteria.
Figure 27-25 Messenger RNA sequences that serve as signals for initiation of protein synthesis in bacteria.
Figure 27-26 Initiation of protein synthesis in eukaryotes.
Figure 27-27 Circularization of mRNA in the eukaryotic initiation complex.
Figure 27-28 First elongation step in bacteria: binding of the second aminoacyl-tRNA.
Figure 27-29 Second elongation step in bacteria: formation of the first peptide bond.
Figure 1 Rescue of stalled bacterial ribosomes by tmRNA.
Figure 27-30 Third elongation step in bacteria: translocation.
Figure 27-31 Termination of protein synthesis in bacteria.
Figure 27-32 Coupling of transcription and translation in bacteria.
Figure 27-33 Chaperonins in protein folding.
Figure 27-34 Some modified amino acid residues.
Figure 27-35 Farnesylation of a Cys residue.
Figure 27-36 Disruption of peptide bond formation by puromycin.
Figure 27-37 Amino-terminal signal sequences of some eukaryotic proteins that direct their translocation into the ER.
Figure 27-38 Directing eukaryotic proteins with the appropriate signals to the endoplasmic reticulum.
Figure 27-39 Synthesis of the core oligosaccharide of glycoproteins.
Figure 27-40 Pathway taken by proteins destined for lysosomes, the plasma membrane, or secretion.
Figure 27-41 Phosphorylation of mannose residues on lysosome-targeted enzymes.
Figure 27-42 Targeting of nuclear proteins.
Figure 27-43 Signal sequences that target proteins to different locations in bacteria.
Figure 27-44 Model for protein export in bacteria.
Figure 27-45 Summary of endocytosis pathways in eukaryotic cells.
Figure 27-46 Clathrin.
Figure 27-47 Three-step pathway by which ubiquitin is attached to a protein.
Figure 27-48 Three-dimensional structure of the eukaryotic proteasome.
Figure 28-1 Seven processes that affect the steady-state concentration of a protein.
Figure 28-2 Consensus sequence for many E. coli promoters.
Figure 28-3 Consensus sequence for promoters that regulate expression of the E. coli heat shock genes.
Figure 28-4 Common patterns of regulation of transcription initiation.
Figure 28-5 Interaction between activators/repressors and RNA polymerase in eukaryotes.
Figure 28-6 Representative bacterial operon.
Figure 28-7 Lactose metabolism in E. coli.
Figure 28-8 The lac operon.
Figure 28-9 Groups in DNA available for protein binding.
Figure 28-10 Specific amino acid residue–base pair interactions.
Figure 28-11 Helix-turn-helix.
Figure 28-12 Zinc fingers.
Figure 28-13 Homeodomains.
Figure 28-14 RNA recognition motifs (RRMs).
Figure 28-15 Leucine zippers.
Figure 28-16 Helix-loop-helix.
Figure 28-17 CRP homodimer with bound cAMP.
Figure 28-18 Positive regulation of the lac operon by CRP.
Figure 28-19 The trp operon.
Figure 28-20 Transcriptional attenuation in the trp operon.
Figure 28-21 SOS response in E. coli.
Figure 28-22 Translational feedback in some ribosomal protein operons.
Figure 28-23 Stringent response in E. coli.
Figure 28-24 Regulation of bacterial mRNA function in trans by sRNAs.
Figure 28-25 Regulation of bacterial mRNA function in cis by riboswitches.
Figure 28-26 Salmonella typhimurium.
Figure 28-27 Regulation of flagellin genes in Salmonella: phase variation.
Figure 28-28 Nucleosome ejection by a SWI/SNF remodeler.
Figure 28-29 The advantages of combinatorial control.
Figure 28-30 Eukaryotic promoters and regulatory proteins.
Figure 28-31 The components of transcriptional activation.
Figure 28-32 Regulation of transcription of GAL genes in yeast.
Figure 28-33 Transcription activators.
Figure 28-34 Mechanisms of steroid hormone receptor function.
Figure 28-35 Typical steroid hormone receptors.
Figure 28-36 Translational regulation of eukaryotic mRNA.
Figure 28-37 Gene silencing by RNA interference.
Figure 28-38 Life cycle of the fruit fly Drosophila melanogaster.
Figure 28-39 Early development in Drosophila.
Figure 28-40 Distribution of a maternal gene product in a Drosophila egg.
Figure 28-41 The Hox gene clusters and their effects on development.
Figure 28-42 Totipotent and pluripotent stem cells.
Figure 28-43 Stem cell proliferation versus differentiation and development.
Figure 1 Evolution of new beak structures to exploit new food sources.

List of Tables

Table 1-1 Molecular Components of an E. coli Cell
Table 1 Cell Fraction Requirement for Incorporation of [32P]-Phosphocholine into Lecithin
Table 2 Requirement of Nucleotides for Lecithin Synthesis from Phosphocholine
Table 2-1 Some Examples of Polar, Nonpolar, and Amphipathic Biomolecules (Shown as lonic Forms at pH 7)
Table 2-2 Solubilities of Some Gases in Water
Table 2-3 van der Waals Radii and Covalent (Single-Bond) Radii of Some Elements
Table 2-4 Four Types of Noncovalent (“Weak”) Interactions among Biomolecules in Aqueous Solvent
Table 2-5 The pH Scale
Table 3-1 Properties and Conventions Associated with the Common Amino Acids Found in Proteins
Table 3-2 Molecular Data on Some Proteins
Table 3-3 Amino Acid Composition of Two Proteins
Table 3-4 Conjugated Proteins
Table 3-5 A Hypothetical Purification Table for an Enzyme
Table 3-6 The Specificity of Some Common Methods for Fragmenting Polypeptide Chains
Table 4-1 Idealized ϕ and ψ Angles for Common Secondary Structures in Proteins
Table 4-2 Secondary Structures and Properties of Some Fibrous Proteins
Table 4-3 Approximate Proportion of α Helix and β Conformation in Some Single-Chain Proteins
Table 5-1 Protein Dissociation Constants: Some Examples and Range
Table 6-1 Some Inorganic Ions That Serve as Cofactors for Enzymes
Table 6-2 Some Coenzymes That Serve as Transient Carriers of Specific Atoms or Functional Groups
Table 6-3 International Classification of Enzymes
Table 6-4 Relationship
Table 6-5 Some Rate Enhancements Produced by Enzymes
Table 6-6 Km for Some Enzymes and Substrates
Table 6-7 Turnover Number, kcat, of Some Enzymes
Table 6-8 Enzymes for Which kcat/Km Is Close to the Diffusion-Controlled Limit (108 to 109 M−1 S−1)
Table 6-9 Effects of Reversible Inhibitors on Apparent Vmax and Apparent Km
Table 6-10 Consensus Recognition Sequences for a Few Protein Kinases
Table 7-1 Symbols and Abbreviations for Common Monosaccharides and Some of Their Derivatives
Table 7-2 Structures and Roles of Some Polysaccharides
Table 8-1 Nucleotide and Nucleic Acid Nomenclature
Table 1 Properties of the Loci Used for the CODIS Database
Table 9-1 Some Enzymes Used in Recombinant DNA Technology
Table 9-2 Recognition Sequences for Some Type II Restriction Endonucleases
Table 9-3 Commonly Used Protein Tags
Table 9-4 Methods for Discovering New Proteins and Exploring Their Functions
Table 10-1 Some Naturally Occurring Fatty Acids: Structure, Properties, and Nomenclature
Table 10-2 Eight Major Categories of Biological Lipids
Table 11-1 Glucose Transporters in Humans
Table 11-2 Some ABC Transporters in Humans
Table 11-3 Permeability Characteristics and Predominant Distribution of Known Mammalian Aquaporins
Table 12-1 Some Signals to Which Cells Respond
Table 12-2 Some Conserved Elements of Animal Signaling Systems
Table 12-3 Some Signals That Use cAMP as Second Messenger
Table 12-4 Some Signals That Act through Phospholipase C, IP3, and Ca2+
Table 12-5 Some Proteins Regulated by Ca2+ and Calmodulin
Table 12-6 Some Signals That Act through GPCRs
Table 13-1 Some Physical Constants and Units Used in Thermodynamics
Table 13-2 Relationship between Equilibrium Constants and Standard Free-Energy Changes of Chemical Reactions
Table 13-3 Relationships among Keq, G, and the Direction of Chemical Reactions
Table 13-4 Standard Free-Energy Changes of Some Chemical Reactions
Table 13-5 Total Concentrations of Adenine Nucleotides, Inorganic Phosphate, and Phosphocreatine in Some Cells
Table 13-6 Standard Free Energies of Hydrolysis of Some Phosphorylated Compounds and Acetyl-CoA (a Thioester)
Table 13-7 Standard Reduction Potentials of Some Biologically Important Half-Reactions
Table 13-8 Average Half-Life of Proteins in Mammalian Tissues
Table 13-9 Relationship between Hill Coefficient and the Effect of Substrate Concentration on Reaction Rate for Allosteric Enzymes
Table 13-10 Equilibrium Constants, Mass-Action Ratios, and Free-Energy Changes for Enzymes of Carbohydrate Metabolism
Table 13-11 Relative Changes in [ATP] and [AMP] When ATP Is Consumed
Table 14-1 Some TPP-Dependent Reactions
Table 14-2 Free-Energy Changes of Glycolytic Reactions in Erythrocytes
Table 14-3 Sequential Reactions in Gluconeogenesis Starting from Pyruvate
Table 14-4 Glucogenic Amino Acids, Grouped by Site of Entry
Table 14-5 Some of the Many Genes Regulated by Insulin
Table 1 Glycogen Storage Diseases of Humans
Table 16-1 Stoichiometry of Coenzyme Reduction and ATP Formation in the Aerobic Oxidation of Glucose via Glycolysis, the Pyruvate Dehydrogenase Complex Reaction, the Citric Acid Cycle, and Oxidative Phosphorylation
Table 16-2 Anaplerotic Reactions
Table 17.1 Yield of ATP during Oxidation of One Molecule of Palmitoyl-CoA to CO2 and H2O
Table 18-1 Nonessential and Essential Amino Acids for Humans and the Albino Rat
Table 18-2 Standard Reduction Potentials of Respiratory Chain and Related Electron Carriers
Table 19-1 Some Important Reactions Catalyzed by NAD(P)+-Linked Dehydrogenases
Table 19-2 Standard Reduction Potentials of Respiratory Chain and Related Electron Carriers
Table 19-3 The Protein Components of the Mitochondrial Respiratory Chain
Table 19-4 Agents That Interfere with Oxidative Phosphorylation
Table 19-5 ATP Yield from Complete Oxidation of Glucose
Table 19-6 Respiratory Proteins Encoded by Mitochondrial Genes in Humans
Table 20-1 Comparison of C3, C4, and CAM Plants
Table 21-1 Major Classes of Human Plasma Lipoproteins: Some Properties
Table 21-2 Apolipoproteins of the Human Plasma Lipoproteins
Table 22-1 Amino Acid Biosynthetic Families, Grouped by Metabolic Precursor
Table 23-1 Classes of Hormones
Table 23-2 Some Peptide Hormones That Act on Feeding Behavior and Fuel Selection in Mammals
Table 23-3 Effects of Insulin on Blood Glucose: Uptake of Glucose by Cells and Storage as Triacylglycerols and Glycogen
Table 23-4 Effects of Glucagon on Blood Glucose: Production and Release of Glucose by the Liver
Table 23-5 Available Metabolic Fuels in a Normal-Weight, 70 kg Man and in an Obese, 140 kg Man at the Beginning of a Fast
Table 23-6 Physiological and Metabolic Effects of Epinephrine: Preparation for Action
Table 23-7 Treatments for Type 2 Diabetes Mellitus
Table 24-1 The Sizes of DNA and Viral Particles for Some Bacterial Viruses (Bacteriophages)
Table 24-2 DNA, Gene, and Chromosome Content in Some Genomes
Table 24-3 Telomere Sequences
Table 24-4 Diversity in DNA Topoisomerases
Table 24-5 Types and Properties of the Common Histones
Table 25-1 Comparison of the Five DNA Polymerases of E. coli
Table 25-2 Subunits of DNA Polymerase III of E. coli
Table 25-3 Proteins Required to Initiate Replication at the E. coli Origin
Table 25-4 Proteins of the E. coli Replisome
Table 25-5 Types of DNA Repair Systems in E. coli
Table 26-1 Eukaryotic Nuclear RNA Polymerases
Table 26-2 Proteins Required for Initiation of Transcription at the RNA Polymerase II (Pol II) Promoters of Eukaryotes
Table 26-3 Mechanisms of RNA Splicing
Table 27-1 Incorporation of Amino Acids into Polypeptides in Response to Random Polymers of RNA
Table 27-2 Trinucleotides That Induce Specific Binding of Aminoacyl-tRNAs to Ribosomes
Table 27-3 Degeneracy of the Genetic Code
Table 1 Known Variant Codon Assignments in Mitochondria
Table 27-4 How the Wobble Base of the Anticodon Determines the Number of Codons a tRNA Can Recognize
Table 27-5 Components Required for the Five Major Stages of Protein Synthesis in E. coli
Table 27-6 RNA and Protein Components of the E. coli Ribosome
Table 27-7 The Two Classes of Aminoacyl-tRNA Synthetases
Table 27-8 Protein Factors Required for Initiation of Translation in Bacterial and Eukaryotic Cells
Table 27-9 Relationship between Protein Half-Life and Amino-Terminal Amino Acid Residue
Table 28-1 Examples of Gene Regulation by Recombination
Table 28-2 Some Enzyme Complexes That Catalyze Chromatin Structural Changes Associated with Transcription
Table 28-3 Genes of Galactose Metabolism in Yeast
Table 28-4 Hormone Response Elements (HREs) Bound by Steroid-Type Hormone Receptors

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