Biochemistry

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

8 ed.

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

p. 76

The smaller the S value, the more slowly a molecule moves in a centrifugal field.

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p. 1013

The treatment of myosin with trypsin and papain results in the formation of four fragments: two S1 fragments; heavy meromyosin (HMM) which consists of the S1 fragments and an additional region termed S2; and a fragment called light meromyosin (LMM; Figure 35.2).

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p. 258

Comparison of the S_{1 pockets of these enzymes reveals that these different specificities are due to small structural differences.}

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p. 1013

The treatment of myosin with trypsin and papain results in the formation of four fragments: two S1 fragments; heavy meromyosin (HMM) which consists of the S1 fragments and an additional region termed S2; and a fragment called light meromyosin (LMM; Figure 35.2).

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p. 941

In comparison, one of the simplest eukaryotes, Saccharomyces cerevisiae (baker's yeast), contains 16 chromosomes ranging in size from 0.2 to 2.2 Mb (Figure 32.1).

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p. 852

The Salmonella test is extensively used to help evaluate the mutagenic and carcinogenic risks of a large number of chemicals.

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p. 526

The reduction potential of this couple can be determined by measuring the electromotive force generated by an apparatus called a sample half-cell connected to a standard reference half-cell (Figure 18.5).

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p. 1046

These data are a demonstration of a structure-activity relationship (SAR); they provide an opportunity to correlate structure with function and guide design of further molecules.

El sinònim no és neològic.

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p. 370

Two are of particular interest: the sarcoplasmic reticulum Ca²⁺ATPase (or SERCA) transports Ca²⁺ out of the cytoplasm and into the sarcoplasmic reticulum of muscle cells, and the gastric H⁺-K⁺ ATPase is the enzyme responsible for pumping sufficient protons into the stomach to lower the pH to 1.0.

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p. 689

Mechanism: Pyridoxal phosphate forms Schiff base intermediates in aminotransferases

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p. 689

Indeed, even in the absence of substrate, the aldehyde group of PLP usually forms a Schiff-base linkage with the xepsilonx-amino group of a specific lysine residue at the enzyme's active site.

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p. 40

Screw sense. Describes the direction in which a helical structure rotates with respect to its axis. If, viewed down the axis of a helix, the chain turns in a clockwise direction, it has a right-handed screw sense. If the turning is counterclockwise, the screw sense is left-handed.

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p. 350

The protein components of a membrane can be readily visualized by SDS-polyacrylamide gel electrophoresis.

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p. 367

In contrast, carriers utilize the gradien of one ion to drive the transport of another against its gradient. An example of this process, termed secondary active transport, is mediated by the E. coli lactose transporter, a well-studied protein responsible for the uptake of a specific sugar from the environment of a bacterium.

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p. 84

The antibody-antigen complex on the sheet can then be detected by rinsing the sheet with a second antibody, called the secondary antibody, that is specific for the primary antibody (e.g., a goat antibody that recognizes mouse antibodies).

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p. 915-916

The other mechanism, termed the secretory pathway, directs proteins into the endoplasmic reticulum (ER), the extensive membrane system that comprises about half the total membrane of a cell, cotranslationallyxguiollargxthat is, while the protein is being synthesized.

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p. 341

Such transport systems confer on membranes the important property of selective permeability.

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p. 348

Lipid bilayers form spontaneously by a self-assembly process.

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p. 348

These hydrophobic interactions have three significant biological consequences: (1) lipid bilayers have an inherent tendency to be extensive; (2) lipid bilayers will tend to close on themselves so that there are no edges with exposed hydrocarbon chains, and so they form compartments; and (3) lipid bilayers are self-sealing because a hole in a bilayer is energetically unfavorable.

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p. 115

FIGURE 4.21 Detection of semiconservative replication of E. coli DNA by density-gradient centrifugation.

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p. 962

FIGURE 33.1 Sensory connections to the brain. Sensory nerves connect sensory organs to the brain and spinal cord.

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p. 287

The attached p-mercuribenzoate groups can be removed from the separated subunits by adding an excess of mecaptoethanol, providing isolated subunits for study.

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p. 179

The sequence-comparison methods described thus far treat all positions within a sequence equally.

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p. 370

Two are of particular interest: the sarcoplasmic reticulum Ca²⁺ATPase (or SERCA) transports Ca²⁺ out of the cytoplasm and into the sarcoplasmic reticulum of muscle cells, and the gastric H⁺-K⁺ ATPase is the enzyme responsible for pumping sufficient protons into the stomach to lower the pH to 1.0.

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p. 723

This interconversion is catalyzed by serine hydroxymethyltransferase, a PLP enzyme that is homologous to aspartate aminotransferase.

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p. 302

However, this activation step is irreversible, and so a different mechanism is needed to terminate proteolysis. Specific protease inhibitors accomplish this task. Serpins, serine protease inhibitors, are an example of one such family of inhibitors.

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p. 872

The activity of RNA polymerase II is regulated by phosphorylation mainly on the serine residues of the CTD.

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p. 399

The xbetax-AR is a member of the largest class of cell-surface receptors, called the seven-transmembrane-helix (7TM) receptors.

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p. 830

Although hydrogen bonding contributes to the formation of this base pair, overall shape complementarity is crucial.

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p. 342

1. Membranes are sheetlike structures, only two molecules thick, that form closed boundaries between different compartments.

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p. 173

FIGURE 6.7 The generation of a shuffled sequence.

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p. 196

A sigmoid binding curve indicates that a protein exhibits a special binding behavior.

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p. 291

The sigmoidal curve for ATCase can be pictured as a composite of two Michaelis-Menten curves, one corresponding to the less-active T state and the other to the more-active R state.

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p. 242

FIGURE 8.34 Single molecule studies can reveal molecular heterogeneity.

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p. 432

Fuel molecules are more complex (Figure 15.10) than the single-carbon compounds depicted in Figure 15.9.

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p. 840

Copies of single-stranded-binding protein (SSB) bind to the unwound strands, keeping the strands separated so that both strands can serve as templates.

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p. 1021

FIGURE 35.17 Sliding-filament model. Muscle contraction depends on the motion of thin filaments (blue) relative to thick filaments (red).

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p. 278

Myosins are slow enzymes, typically turning over approximately once per second.

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p. 162

When a double-stranded RNA molecule is introduced into an appropriate cell, the RNA is cleaved by the enzyme Dicer into fragments approximately 21 nucleotides in lenght. Each fragment, termed a small interference RNA (siRNA), consists of 19 bp of double-stranded RNA and 2 bses of unpaired RNA on each 5' end.

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p. 879

FIGURE 29.32 Small regulatory RNA production. A pathway from a transcription product including a microRNA to the mature microRNA bound to an Argonaute protein. The initial transcription product, a pri-microRNA, is first cleaved to a small double-stranded RNA called a pre-microRNA. One of the strands of the pre-microRNA, the mature microRNA, is then bound by an Argonaute protein.

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p. 806

As for most questions in the exciting area of energy homeostasis, the answer is not well worked out, but recent evidence suggests that a group of proteins called suppressors of cytokine signaling (SOCS) may take part.

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p. 159

As noted earlier, although ALS-causing mutations within the SOD1 gene had been identified, the mechanism by which the mutant SOD1 protein ultimately leads to motor-neuron loss remains a mystery.

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p. 94

FIGURE 3.37 Solid-phase peptide synthesis. The sequence of steps in solid-phase synthesis is: (1) anchoring of the C-terminal amino acid to a solid resin, (2) deprotection of the amino terminus, and (3) coupling of the free amino terminus with the DCC-activated carboxyl group of the next amino acid. Steps 2 and 3 are repeated for each added amino acid. Finally, in step 4, the completed peptide is released from the resin.

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p. 140

FIGURE 5.5 Solid-phase synthesis of a DNA chain by the phosphite triester method.

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p. 413

Through its two SH3 domains, Grb2 then binds polyproline-rich polypeptides within a protein called Sos.

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p. 230

The rate constant k_cat/K_M, called the specificity constant, is a measure of catalytic efficiency because it takes into account both the rate of catalysis with a particular substrate (k_cat) and the nature of the enzyme-substrate interaction (K_M).

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p. 223

2. The spectroscopic characteristics of many enzymes and substrates change on the formation of an ES complex.

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p. 410

Phosphotyrosine residues, such as those in the IRS proteins, are recognized most often by Src homology 2 (SH2) domains (Figure 14.24).

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p. 413

The intracellular signaling cascade begins with the binding of Grb2, a key adaptor protein that contains one SH2 domain and two Src homology 3 (SH3) domains.

El sinònim no és neològic.

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p. 779

This transcription factor binds to a short DNA sequence called the sterol regulatory element (SRE) on the 5' side of the reductase gene when cholesterol levels are low, enhancing transcription of the gene.

El sinònim no és neològic.

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p. 755

Stable radicals other than tyrosyl radical are employed by other ribonucleotide reductases

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p. 583

Photosystem I and ATP synthase are located almost exclusively in unstacked regions, whereas photosystem II is present mostly in stacked regions.

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p. 111

Second, the stacked base pairs attract one another through van der Waals forces (p. 8), appropriately referred to as stacking forces, further contributing to stabilization of the helix (Figure 4.13).

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p. 526

The reduction potential of this couple can be determined by measuring the electromotive force generated by an apparatus called a sample half-cell connected to a standard reference half-cell (Figure 18.5).

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p. 864

They are known as the xguiollargx 10 sequence and the xguiollargx 35 sequence because they are centered at about 10 and 35 nucleotides upstream of the start site.

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p. 226

The steady-state assumption facilitates a description of enzyme kinetics

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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).

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p. 691

FIGURE 23.12 Stereoelectronic effects. The orientation about the NxguiollargxC_xalfax bond determines the most favored reaction catalyzed by a pyridoxal phosphate enzyme. The bond that is most nearly perpendicular to the plane of delocalized xpix orbitals (represented by dashed lines) of the pyridoxal phosphate electron sink is most easily cleaved.

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p. 951

Steroid-hormone receptors are targets for drugs

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p. 853

FIGURE 28.44 Strand invasion. This process, promoted by proteins such as RecA, can initiate recombination.

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p. 865

For example, the genome of the soil bacterium Streptomyces coelicolor encodes more than 60 s factors recognized on the basis of their amino acid sequences.

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p. 380

In 1998, Roderick MacKinnon and coworkers determined the structure of a K⁺ channel from the bacterium Streptomyces lividans by x-ray crystallography.

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p. 567

Different grana are linked by regions of thylakoid membrane called stroma lamellae (Figure 19.3).

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p. 864

Some genes are transcribed frequentlyxguiollargxas often as every 2 seconds in E. coli. The promoters of these genes are referred to as strong promoters.

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p. 903

For many years, ribosomal proteins were presumed to orchestrate protein synthesis and ribosomal RNAs were presumed to serve primarily as structural scaffolding.

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p. 787

The importance of reverse cholesterol transport is illustrate by the occurrence of mutations that inactivate a cholesterol-transport protein in endothelial cells and macrophages, ABCA1 (ATP-binding cassette transporter, subfamily A1) (Figure 13.7).

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p. 233

The defining feature of double-displacement reactions is the existence of a substituted enzyme intermediate, in which the enzyme is temporarily modified.

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p. 222

1. The first clue was the observation that, at a constant concentration of enzyme, the reaction rate increases with increasing substrate concentration until a maximal velocity is reached (Figure 8.4).

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p. 598

Fructose 6-phosphate formed from triose phosphates joins the glucose unit of UDP-glucose to form sucrose 6-phosphate (Figure 20.12).

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p. 33

Pairs of sulfhydryl groups may come together to form disulfide bonds, which are particularly important in stabilizing some proteins, as will be discussed shortly.

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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.

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p. 45

Three strands wind around one another to form a superhelical cable that is stabilized by hydrogen bonds between strands.

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p. 538

Toxic derivatives of molecular oxygen such as superoxide radicals are scavenged by protective enzymes

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p. 806

As for most questions in the exciting area of energy homeostasis, the answer is not well worked out, but recent evidence suggests that a group of proteins called suppressors of cytokine signaling (SOCS) may take part.

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p. 968

FIGURE 33.16 Evidence for a heterodimeric sweet receptor.

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p. 1015-1016

Two regions around the nucleotide-binding site (termed switch I and switch II) tightly conform to the shape of the xgammax-phosphoryl group of the ATP analog and adopt a looser conformation when the xgammax-phosphoryl group is absent (Figure 35.10).

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p. 1015-1016

Two regions around the nucleotide-binding site (termed switch I and switch II) tightly conform to the shape of the xgammax-phosphoryl group of the ATP analog and adopt a looser conformation when the xgammax-phosphoryl group is absent (Figure 35.10).

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p. 266

Studies of a synthetic analog model system provide evidence for the mechanism's plausibility.

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