Biochemistry

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

8 ed.

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

p. 905

These binding sites are called the A site (for aminoacyl) and the P site (for peptidyl). The third tRNA molecule is bound to an adjacent site called the E site (for exit).

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p. 951

These coactivators are referred to as the p160 family because of their size.

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p. 572

Both require light to energize reaction centers consisting of special pairs, called P700 for photosystem I and P680 for photosystem II, and both transfer electrons by using electron-transport chains.

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p. 572

Both require light to energize reaction centers consisting of special pairs, called P700 for photosystem I and P680 for photosystem II, and both transfer electrons by using electron-transport chains.

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p. 571

The special pair absorbs light maximally at 960 nm, and, for this reason, is often called P960 (P stands for pigment).

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p. 912

Soon after the PIC binds the mRNA, eIF-4G links eIF-4E to a protein associated with the poly(A) tail, poly(A) tail-binding protein I (PABPI; Figure 30.28).

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p. 388

The voltage-sensing paddles of K⁺ channels also are pulled into the membrane by the changed membrane potential, but more slowly than Na⁺ channel paddles.

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p. 810

Insulin resistance in muscle facilitates pancreatic failure

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p. 775

Although the details of the regulation of lipid synthesis remain to be elucidated, evidence suggests that phosphatidic acid phosphatase (PAP), working in concert with diacylglycerol kinase, plays a key role in the regulation of lipid synthesis.

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p. 541

Additionally, some prokaryotic cytochromes, such as cytochrome c₂ from the photosynthetic bacterium Rhodospirillum rubrum and cytochrome c₅₅₀ from the denitrifying bacterium Paracoccus denitrificans, closely resemble cytochrome c from tuna-heart mitochondria (Figure 18.20).

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p. 43

FIGURE 2.32 A parallel xbetax sheet. Adjacent xbetax strands run in the same direction, as indicated by the arrows. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.

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p. 162

The siRNA is loaded into an assembly of several proteins referred to as the RNA-induced silencing complex (RISC), which unwinds the RNA duplex and cleaves one of the strands, the so-called passenger strand.

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p. 514

FIGURE 17.21 PATHWAY INTEGRATION: Pathways active during exercise after a night's rest.

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p. 787

PCSK9 (proprotein convertase subtilisin/kexin type) is a protease, secreted by the liver, which plays a crucial role in the regulation of cycling of the LDL receptor.

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p. 513

In addition to increasing the amount of the proteins required for glycolysis, HIF-1 also stimulates the production of pyruvate dehydrogenase kinase (PDK).

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p. 809

PIP₃ activates the phosphatidylinositol-dependent protein kinase (PDK) (3), which in turn activates several other kinases, mos notabley Akt (4), also known as protein kinase B (PKB).

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p. 511

Deactivation is reversed by the pyruvate dehydrogenase phosphatase (PDP), of which there are two isozymic forms.

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p. 1044

A promising natural product, compactin, was discovered in a screen of compounds from a fermentation broth from Penicillium citrinum in a search for antibacterial agents.

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p. 240

FIGURE 8.31 Formation of a penicilloyl-enzyme derivative. Penicilin reacts irreversibly with the transpeptidase to inactivate the enzyme.

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p. 589

The second half of this chapter examines a pathway common to all organisms, known variously as the pentose phosphate pathway, the hexose monophosphate pathway, the phosphogluconate pathway, or the pentose shunt.

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p. 256

These observations suggest a mechanism for peptide hydrolysis (Figure 9.8).

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p. 91

This technique for protein identification is referred to as peptide mass fingerprinting.

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p. 52

FIGURE 2.55 Alternative conformations of a peptide sequence.

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p. 88

FIGURE 3.30 Peptide sequencing by tandem mass spectrometry.

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p. 260

Cysteine, aspartyl, and metalloproteases are other major classes of peptide-cleaving enzymes

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p. 95

With the use of specially developed peptide-ligation methods, proteins of 100 amino acids or more can by synthesized in very pure form.

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p. 570

The H subunit lies on the cytoplasmic side of the cell membrane, and the cytochrome subunit lies on the exterior face of the cell membrane, called the periplasmic side because it faces the perisplasm, the space between the cell membrane and the cell wall.

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p. 684

Additional degrons thought to identify proteins for degradation include cyclin destruction boxes, which are amino acid sequences that mark cell-cycle proteins for destruction, and PEST sequences, which contain the amino acid sequence proline (P, single-letter abbreviation), glutamic acid (E), serine (S), and threonine (T).

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p. 552

The phosphate carrier, which works in concert with ATP-ADP translocase, mediates the electro-neutral exchange of H₂PO₄^- for OH^-.

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p. 775

Although the details of the regulation of lipid synthesis remain to be elucidated, evidence suggests that phosphatidic acid phosphatase (PAP), working in concert with diacylglycerol kinase, plays a key role in the regulation of lipid synthesis.

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p. 410

Through SH2 domains in the regulatory subunits, these enzymes bind to the IRS proteins and are drawn to the membrane where they can phophorylate PIP₂ to form phosphatidylinositol 3,4,5-trisphosphate (PIP₃)

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p. 809

PIP3 activates the phosphatidylinositol-dependent protein kinase (PDK) (3), which in turn activates several other kinases, mos notabley Akt (4), also known as protein kinase B (PKB).

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p. 117

DNA polymerase catalyzes phosphodiester-bridge formation

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p. 769

Phospholipid synthesis requires the combination of a diacylglycerol with an alcohol.

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p. 662

Both acyl carrier protein and coenzyme A include phosphopantetheine as their reactive units.

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p. 620

Pyridoxal phosphate participates in the phosphorolytic cleavage of glycogen

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p. 459

ATP is formed by phosphoryl transfer from 1,3-bisphosphoglycerate

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p. 431

TABLE 15.1 Standard free energies of hydrolysis of some phosphorylated compounds

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p. 430

Phosphoryl-transfer potential is an important form of cellular energy transformation

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p. 570

The L and M subunits form the structural and functional core of the bacterial photosynthetic reaction center (Figure 19.9).

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p. 584

The photosynthetic system of the nonsulfur purple bacterium Rhodopseudomonas viridis has most features common to oxygenic photosynthetic systems and clearly predates them.

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p. 704

The next step in the degradation of phenylalanine and tyrosine is the transamination of tyrosine to p-hydroxyphenylpyruvate (Figure 23.27).

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p. 704

The enzyme catalyzing this complex reaction, p-hydroxyphenylpyruvate hydroxylase, is called a dioxygenase because both atoms of O₂ become incorporated into the product, one on the ring and one in the carboxyl group.

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p. 643

Fatty acids have four major physiological roles.

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p. 912

Initiation begins with the formation of a ternary complex consisting of the 40S ribosome and Met-tRNA_i in association with eIF-2. The complex is called the 43S preinitiation complex (PIC).

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p. 78

For recombinant systems, a host organism that is amenable to genetic manipulation, such as the bacterium Escherichia coli or the yeast Pichia pastoris, is utilized to express a protein of interest.

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p. 809

Through SH2 domains in the regulatory subunits, these enzymes bind to the IRS proteins and are drawn to the membrane where they can phophorylate PIP₂ to form phosphatidylinositol 3,4,5-trisphosphate (PIP₃)

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p. 809

Through SH2 domains in the regulatory subunits, these enzymes bind to the IRS proteins and are drawn to the membrane where they can phophorylate PIP₂ to form phosphatidylinositol 3,4,5-trisphosphate (PIP₃)

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p. 34

TABLE 2.1 Typical pK_a values of ionizable groups in proteins

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p. 349

Another well-defined synthetic membrane is a planar bilayer membrane.

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p. 916

FIGURE 30.34 Amino-terminal signal sequences of some eukaryotic secretory and plasma-membrane proteins.

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p. 410

The amino-terminal part includes a pleckstrin homology domain, which binds phosphoinositide, and a phosphotyrosine-binding domain.

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p. 280

Myosins are a family of enzymes containing P-loop structures

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p. 621

FIGURE 21.6 PLP-Schiff-base linkage. A pyridoxal phosphate (PLP) group (red) forms a Schiff base with a lysine residue (blue) at the active site of phosphorylase, where it functions as a general acid-base catalyst.

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p. 690

The ketimine is then hydrolyzed to an xalfax-ketoacid and pyridoxamine phosphate (PMP).

El sinònim no és neològic.

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p. 1017

One end is called the barbed (plus) end, and the other is called the pointed (minus) end. The names "barbed" and "pointed" refer to the appearance of an actin filament when myosin S1 fragments are bound to it.

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p. 32

Polar amino acids. Six amino acids are polar but uncharged.

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p. 355

TABLE 12.2 Polarity scale for identifying transmembrane helices

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p. 912

Soon after the PIC binds the mRNA, eIF-4G links eIF-4E to a protein associated with the poly(A) tail, poly(A) tail-binding protein I (PABPI; Figure 30.28).

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p. 145

These vectors often feature a polylinker region that includes many unique restriction sites within its sequence.

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p. 106

FIGURE 4.1. Polymeric structure of nucleic acids.

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p. 33

Positively charged amino acids. We turn now to amino acids with complete positive charges that render them highly hydrophilic.

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p. 90

However, many proteins undergo posttranslational modifications after their syntheses.

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p. 629

Protein phosphatase 1 (PP1) removes the phosphoryl groups from phosphorylase kinase, thereby inactivating the enzyme.

El sinònim no és neològic.

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p. 296

One class of highly conserved phosphatase called PP2A suppresses the cancer-promoting activity of certain kinases.

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p. 728

Let us first follow the prephenate branch (Figure 24.13). A mutase converts chorismate into prephenate, the immediate precursor of the aromatic ring of phenylalanine and tyrosine.

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p. 877

The pre-rRNA is assembled with ribosomal proteins, as guided by processing factors, in a large ribonucleoprotein.

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p. 367

The free energy of ATP hydrolysis is used to drive the movement of ions against their concentration gradients, a process referred to as primary active transport.

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p. 83-84

An antibody that is specific for the protein of interest, called the primary antibody, is added to the sheet and reacts with the antigen.

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p. 299

6. Programmed cell death, or apoptosis, is mediated by proteolytic enzymes called caspases, which are synthesized in precursor form as procaspases.

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p. 844

TABLE 28.1 Some types of DNA polymerases. Prokaryotic Polymerases

El context és en una taula.

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p. 513

Prolyl hydroxylase 2 requires xalfax-ketoglutarate, ascorbate, and oxygen for activity.

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p. 684

Some times the N-terminal degron is exposed only after the protein is proteolytically cleaved. Such degrons are called pro-N-terminal degrons, in analogy to proenzymes (Section 10.4), because the protein must be cleaved to expose the signal.

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p. 787

PCSK9 (proprotein convertase subtilisin/kexin type) is a protease, secreted by the liver, which plays a crucial role in the regulation of cycling of the LDL receptor.

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p. 669

Prostacyclin and thromboxanes are related compounds that arise from a nascent prostaglandin. They are generated by prostacyclin synthase and thromboxane synthase, respectively.

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p. 353

The enzyme that produces prostaglandin H₂ is a homodimer with a rather complicated structure consisting primarily of xalfax helices.

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p. 353

The structure of the endoplasmic reticulum membrane-bound enzyme prostaglandin H₂ synthase-1 reveals a rather different role for xalfax helices in protein-membrane associations.

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p. 787

However, a number of recent clinical trials revealed that increased levels of HDL-bound cholesterol had no protective effects at all.

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p. 791

The cytochrome P450 system is widespread and performs a protective function

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p. 56

These fibrous protein aggregates are often referred to as amyloid forms.

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p. 646

The protein colipase (another pancreatic secretory product) must bind the lipase to the particle to permit lipid degradation.

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p. 414

Activated Ras initiates a protein kinase cascade

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p. 89

Genomic and proteomic methods are complementary

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p. 547

FIGURE 18.33 Proton path through the membrane. Each proton enters the cytoplasmic half-channel, follows a complete rotation of the c ring, and exits through the other half-channel into the matrix.

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p. 546

FIGURE 18.31 Components of the proton-conducting unit of ATP synthase.

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p. 159

This DNA version of the viral genome, called proviral DNA, can be efficiently expressed by the host cell and replicated along with normal cellular DNA.

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p. 794

7-Dehydrocholesterol (pro-vitamin D₃) is photolyzed by the ultraviolet light of sunlight to previtamin D3, which spontaneously isomerizes to vitamin D₃ (Figure 26.30).

El sinònim no és neològic.

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p. 297

In the R₂C₂ complex, this pseudosubstrate sequence of R occupies the catalytic site of C, thereby preventing the entry of protein substrates (Figure 10.16).

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p. 372

The structural results can be combined with other studies to construct a detailed mechanism for Ca²⁺ pumping by SERCA (Figure 13.5):

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p. 200

Pure hemoglobin binds oxygen much more tightly than does hemoglobin in red blood cells.

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p. 66

Starting from pure proteins, we can determine amino acid sequences and investigate biochemical functions.

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p. 200

This mechanism was discovered by comparing the oxygen-binding properties of hemoglobin in red blood cells with fully purified hemoglobin (Figure 7.16).

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p. 696

Remarkably, these steps are analogous to two consecutive steps in the purine biosynthetic pathway (Section 25.2).

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p. 760

FIGURE 25.17 Purine catabolism. Purine bases are converted first into xanthine and then into urate for excretion. Xanthine oxidase catalyzes two steps in this process.

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p. 752

When the cells were switched to growth media without purines, purine synthesis began and the enzymes became associated with one another, forming complexes dubbed purinosomes (Figure 25.8B).

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p. 752

When the cells were switched to growth media without purines, purine synthesis began and the enzymes became associated with one another, forming complexes dubbed purinosomes (Figure 25.8B).

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p. 749

De novo purine biosynthesis, like pyrimidine biosynthesis, requires PRPP but, for purines, PRTT provides the foundation on which the bases are constructerd step by step.

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p. 696

Thus, two consecutive steps in the pyrimidine biosynthetic pathway were adapted for ure synthesis.

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p. 155

In pyrosequencing, nucleotides are added to the template DNA, one at a time in a defined order.

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p. 45

Instead, the helix is stabilized by steric repulsion of the pyrrolidine ring of the proline and hydroxyproline residues (Figure 2.41).

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p. 511

Thus, pyruvate dehydrogenase is switched off when the energy charge is high.

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p. 513

In addition to increasing the amount of the proteins required for glycolysis, HIF-1 also stimulates the production of pyruvate dehydrogenase kinase (PDK).

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p. 511

Deactivation is reversed by the pyruvate dehydrogenase phosphatase (PDP), of which there are two isozymic forms.

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p. 475

More importantly, an embryonic isozyme of pyruvirate kinase, pyruvate kinase M, is also expressed.

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