Biochemistry

Berg, Jeremy M.; Tymoczko, John L.; Gatto, Jr., Gregory J.; Stryer, Lubert

8 ed.

New York: W.H. Freeman and Company, 2015

p. 547

The movement of protons through the half-channels from the high proton concentration of the cytoplasm to the low proton concentration of the matrix powers the rotation of the c ring.

---

p. 601

The C₄ pathway is though to have evolved in response no more than 30 million years ago and possibly as recently as 7 million years ago.

---

p. 66

For example, the roundworm Caenorhabditis elegans has a genome of 97 million bases and about 19,000 protein-encoding genes, whereas that of the fruit fly Drosophila melanogaster contains 180 million bases and about 14,000 genes.

---

p. 335

Other L-type lectins, such as calnexin and calreticulin, are prominent chaperones in the eukaryotic endoplasmic reticulum.

---

p. 335

Other L-type lectins, such as calnexin and calreticulin, are prominent chaperones in the eukaryotic endoplasmic reticulum.

---

p. 403

PKA stimulates the expression of specific genes by phosphorylating a transcriptional activator called the cAMP response element binding (CREB) protein.

---

p. 759

Ribonucleotide reductase is an attractive target for cancer therapy and a number of clinically approved anticancer drugs mimic substrates and regulators of the enzyme.

---

p. 139

The resulting fragments are separated by a technique known as capillary electrophoresis, in which the mixture is passed through a very narrow tube containing a gel matrix at high voltage to achieve efficient separation within a short time.

---

p. 697

The treatment of carbamoyl phosphate synthetase deficiency or ornithine transcarbamoylase deficiency illustrates a different strategy for circumventing a metabolic block.

---

p. 693-694

The urea cycle begins with the coupling of free NH₃ with HCO₃^- to form carbamoyl phosphate, the committed reaction of the ure cycle, which is catalyzed by carbamoyl phosphate synthetase I.

---

p. 745

The first step in de novo pyrimidine biosynthesis is the synthesis of carbamoyl phosphate from bicarbonate and ammonia in a multistep process, requiring the cleavage of two molecules of ATP. This reaction is catalyzed by carbamoyl phosphate synthetase II (CPS II).

---

p. 607

For transketolase and transaldolase, a carbanion intermediate is stabilized by resonance.

---

p. 345

Membrane lipids can include carbohydrate moieties

---

p. 815

If carbohydrate-rich meals ara consumed after glycogen depletion, glycogen stores are rapidly restored. In addition, glycogen synthesis continues during the consumption of carbohydrate-rich meals, increasing glycogen stores far above normal. This phenomenon is called "super compensation" or, more commonly, carbo-loading.

---

p. 264

Carbon dioxide hydration and HCO₃^- dehydration ara often coupled to rapid processes, particularly transport processes.

---

p. 432

The oxidation of carbon fuels is an important source of cellular energy

---

p. 790

FIGURE 26.26 Cholesterol carbon numbering. The numbering scheme for the carbon atoms in cholesterol and other steroids.

---

p. 454

The six-carbon sugar is cleaved into two three-carbon fragments

---

p. 253

The carbon-nitrogen bond is strengthened by its double-bond character.

---

p. 413

The EGF receptor undergoes phosphorylation of its carboxyl-terminal tail

---

p. 918

There the cargo proteins are further modified--for instance, by the attachment of a O-linked carbohydrates.

---

p. 883

The U2-U6 helix is indispensable for splicing, suggesting that U2 and U6 snRNAs probably form the catalytic center of the spliceosome (Figure 29.38).

---

p. 498

The coenzymes thiamine pyrophosphate (TPP), lipoic acid, and FAD serve as catalytic cofactors, and CoA and NAD⁺are stoichiometric cofactors, cofactors that function as substrates.

---

p. 664

Let us consider one catalytic cycle of the fatty acid synthase complex (Figure 22.28).

---

p. 215

The most striking characteristics of enzymes are their catalytic power and specificity.

---

p. 896

Five groups of bases are not base-paired in this way: the 3' CCA terminal region, which is part of a region called the acceptor stem; the TxpsixC loop, which acquired its name from the sequence ribothymine-pseudouracil-cytosine; the "extra arm," which contains a variable number of residues; the DHU loop, which contains several dihydrouracil residues; and the anticodon loop.

---

p. 804

The best-studied short-term signal is cholecystokinin (CCK).

El sinònim no és neològic.

---

p. 770

CTP-phosphocholine cytidylyltransferase (CCT) catalyzes the formation of CDP-choline, the rate-limiting step in phosphatidylcholine synthesis.

---

p. 1000

Additional molecules, including a membrane-bound protein phosphatase called CD45 and a cell-surface protein called CD28, play ancillary roles in this process.

---

p. 998

Cytotoxic T cells also express a protein termed CD8 on their surfaces that is crucial for the recognition of the class I MHC-peptide complex.

---

p. 149

Complementary DNA for all mRNA that a cell contains can be made, inserted into vectors, and then inserted into bacteria. Such a collection is called a cDNA library.

---

p. 297

6. ATP is the cellular energy currency (Chapter 15). The use of this compound as a phosphoryl-group donor links the energy status of the cell to the regulation of metabolism.

---

p. 1042

Finally, in 1965, Jack Strominger and James Park independently determined that penicillin exerts its antibiotic activity by blocking a critical transpeptidase reaction in bacterial cell-wall biosynthesis (Figure 36.15), as introduced in Section 8.5.

---

p. 774

Ceramide metabolism stimulates tumor growth

---

p. 972

The reduction in cGMP concentration causes cGMP-gated ion channels to close, leading to the hyperpolarization of the membrane and neuronal signaling.

---

p. 648

If the coactivator required by ATGL is missing or defective, a rare condition (incidence unknown) called Chanarin-Dorfman syndrome results.

---

p. 144

The cohesive-end method for joining DNA molecules can still be used in these cases by adding a short,chemically synthesized DNA linker that can be cleaved by restriction enzymes.

---

p. 1036

This relation, referred to as the Cheng-Prusoff equation, demonstrates that the IC₅₀ of a competitive inhibitor will depend on the concentration and the Michaelis constant (K_M) for the substrate S.

---

p. 1028

In their unoccupied forms, these receptors initiate a pathway leading eventually to the phosphorylation of a specific aspartate residue on a soluble protein called CheY.

---

p. 1028

Phosphorylated CheY spontaneously hydrolyzes and releases its phosphoryl group in a process accelerated by another protein, CheZ.

---

p. 584-585

Green sulfur bacteria such as Chlorobium thiosulfatophilum carry out a reaction that also seems to have appeared before oxygenic photosynthesis and is even more similar to oxygenic photosynthesis than the photosystem of R. viridis.

---

p. 417

The cholera toxin, also called choleragen, is a protein composed of two functional unitsxguiollargxa xbetax subunit that binds to GM1 gangliosides (Section 26.1) of the intestinal epithelium and a catalytic A subunit that enters the cell.

---

p. 417

The cholera toxin, also called choleragen, is a protein composed of two functional unitsxguiollargxa xbetax subunit that binds to GM1 gangliosides (Section 26.1) of the intestinal epithelium and a catalytic A subunit that enters the cell.

---

p. 784

Cholesterol metabolism must be precisely regulated to prevent atherosclerosis.

---

p. 781

Thus, cholesterol synthesis ceases when the ATP level is low.

---

p. 953

Bromodomains are also present in some components of large complexes known as chromatin-remodeling complexes or chromatin-remodeling engines.

---

p. 782

The liver then takes up the cholesterol-rich residues, known as chylomicron remnants.

---

p. 38

This preference for trans over cis can be explained by the fact that steric clashes between groups attached to the xalfax-carbon atoms hinder the formation of the cis configuration but do not arise in the trans configuration (Figure 2.20).

---

p. 502

The newly formed citryl CoA induces additional structural changes in the enzyme, causing the active site to become completely enclosed.

El sinònim no és neològic.

---

p. 56

These diseases include bovine spongiform encephalopathy (commonly referred to as mad cow disease) and the analogous diseases in other organisms, including Creutzfeldt-Jakob disease (CJD) in human beings, scrapie in sheep, and chronic wasting disease in deer and elk.

El sinònim no és neològic.

---

p. 360

One of these specialized proteins is clathrin, which polymerizes into a lattice network around the growing membrane bud, often referred to as a clathrin-coated pit (Figure 12.36).

---

p. 271

FIGURE 9.33. Stereochemistry of cleaved DNA.

---

p. 865-866

The transition from the closed promoter complex (in which DNA is double helical) to the open promoter complex (in which a DNA segment is unwound) is an essential event in transcription (Figure 29.12).

---

p. 464

The bacterium Clostridium perfringens, the cause of gangrene, is an example of an obligate anaerobe.

---

p. 654

The core of cobalamin consists of a corrin ring with a central cobalt atom (Figure 22.14).

---

p. 127

Thus, the xbetax-globin gene is split into three coding sequences (Figure 4.37).

---

p. 992

More than 10⁸ antibodies can be formed by combinatorial association and somatic mutation

---

p. 46

Myoglobin is an extremely compact molecule.

---

p. 235

As the concentration of a competitive inhibitor increases, higher concentrations of substrate are required to attain a particular reaction velocity.

---

p. 109

4.2 A Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure

---

p. 552

The complete oxidation of glucosa yields about 30 molecules of ATP

---

p. 28

3. Proteins can interact with one another and with other biological mocromolecules to form complex assemblies.

---

p. 6

The double helix can form from its components strands

---

p. 663

The xbetax-ketoacyl synthase, also called the condensing enzyme, catalyzes this condensation reaction.

---

p. 973

Color vision is mediated by three cone receptors that are homologs of rhodopsin

---

p. 224

Moreover, the substrate may bind to only certain conformations of the enzyme, in what is called conformation selection.

---

p. 1039

The oxidation reactions of xenobiotic compounds are often referred to as phase I transformations, and the conjugation reactions are referred to as phase II transformations.

---

p. 964

FIGURE 33.4 Conserved and variant regions in odorant receptors. Odorant receptors ara members of the 7TM-receptor family. The green cylinders represent the seven presumed transmembrane helices. Strongly conserved residues characteristic of this protein family are shown in blue, whereas highly variable residues are shown in red.

---

p. 317

Dihydroxyacetone and glyceraldehyde are constitutional isomers because they have identical molecular formulas but differ in how the atoms are ordered.

---

p. 925

Genomes comprise thousands of genes. Some of these genes are expressed all the time. These genes are subject to constitutive expression. Many other genes are expressed only under some circumstancesxguiollargxthat is, under a particular set of physiological conditions. These genes are subject to regulated expression.

---

p. 8

This attraction increases as two atoms come closer to each other, until they are separated by the van der Waals contact distance (Figure 1.10).

---

p. 348

Because lipid bilayers are held together by many reinforcing, noncovalent interactions (predominantly hydrophobic), they are cooperative structures.

---

p. 919

The formation of buds is facilitated by the binding of coat proteins (COPs) to the cytoplasmic side of the bud.

El sinònim no és neològic.

---

p. 536

Cytochrome c oxidase contains two heme A groups and three copper ions, arranged as two copper centers, designated A and B.

---

p. 7

The energy of an ionic interaction (sometimes called an electrostatic interaction) is given by the Coulomb energy: E = kq₁q₂/Dr, where E is the energy, q₁ and q₂ are the charges on the two atoms (in units of the electronic charge), r is the distance between the two atoms (in angstroms), D is the dielectric constant (which decreases the strenght of the Coulomb depending on the intervening solvent or medium), and k is a proportionality constant (k = 1389, for energies in units of kilojoules per mole, or 332 for energies in kilocalories per mole).

---

p. 884

FIGURE 29.39 The CTD: Coupling transcription to pre-mRNA processing.

---

p. 458

We see here the use of a covalent enzyme-bound intermediate as a mechanism of energy coupling.

---

p. 143-144

Vectors are designed to enable the rapid, covalent insertion of DNA fragments of interest.

---

p. 4

FIGURE 1.4 Covalent structure of DNA. Each unit of the polymeric structure is composed of a sugar (deoxyribose), a phosphate, and a variable base that protrudes from the sugar-phosphate backbone.

---

p. 601

To store the CO₂ until it can be used during the day, such plants make use of an adaptation called crassulacean acid metabolism (CAM), named after the genus Crassulacea (the suculents).

---

p. 601

To store the CO₂ until it can be used during the day, such plants make use of an adaptation called crassulacean acid metabolism (CAM), named after the genus Crassulacea (the suculents).

El sinònim no és neològic.

---

p. 403

PKA stimulates the expression of specific genes by phosphorylating a transcriptional activator called the cAMP response element binding (CREB) protein.

---

p. 933

Cro is a small protein that binds to the same sites as the xlambdax repressor does, but with a different order of affinity for the three sites in the right operator.

---

p. 99

The peaks apart from the diagonal (shown in red in Figure 3.45B), referred to as off-diagonal peaks or cross-peaks, provide crucial new information: they identify pairs of protons that are less that 5 xangstrommx apart.

---

p. 770

CTP-phosphocholine cytidylyltransferase (CCT) catalyzes the formation of CDP-choline, the rate-limiting step in phosphatidylcholine synthesis.

---

p. 335

C-type lectins function in a variety of cellular activities, including receptor-mediated endocytosis, a process by which soluble molecules are bound to the cell surface and subsequently internalized (Section 26.3), and cell-cell recognition.

---

p. 580

The resulting proton gradient then drives the synthesis of ATP. In this process, called cyclic photophosphorylation, ATP is generated without the concomitant formation of NADPH (Figure 19.26).

---

p. 726

Cystathionine is then deaminated and cleaved to cysteine and xalfax-ketobutyrate by cystathionine xgammax-lyase or cystathionase.

---

p. 726

This reaction is catalyzed by cystathionine xbetax-synthase.

---

p. 754

The loss of an electron generates a highly reactive cysteine thiyl radical within the active site of R1.

---

p. 747

After uridine triphosphate has been formed, it can be transformed into cytidine triphosphate by the replacement of a carbonyl group by an amino group, a reaction catalyzed by cytidine triphosphate synthetase.

---

p. 108

Similarly, the most common nucleotides that link to form RNA are nucleotid monophosphates adenylate, guanylate, cytidylate and uridylate.

---

p. 668

This reaction is catalyzed by a complex of three membrane-bound proteins: NADH-cytochrome b₅ reductase, cytochrome b₅, and stearoyl CoA desaturase (Figure 22.31).

---

p. 575

In the second half of the Q cycle, cytochrome bf reduces a molecule of plastoquinone from the Q pool to plastoquinol, taking up two protons from one side of the membrane, and then reoxidizes plastoquinol to release these protons on the other side.

---

p. 294

The irreversible attachment of a lipid group causes some proteins in signal-transduction pathways, such as Ras (a GTPase) and Src (a protein tyrosine kinase), to become affixed to the cytoplasmic face of the plasma membrane.

---