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. 544

The exterior column consists of one a subunit, two b subunits, and the xdeltax subunit.

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p. 685

Key components of the 19S complex are six ATPases of a type called the AAA class (ATPase associated with various cellular activities).

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p. 1014

A model for the structure of the motor domain of dynein was generated based on the structures of other AAA ATPases.

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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. 688

An abortive complex is formed on the enzyme when a product is replaced by substrate before the reaction is complete.

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p. 784

In fact, free cholesterol activates acyl CoA:cholesterol acyltransferase (ACAT), the enzyme catalyzing this reaction.

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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; [...].

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p. 663

The elongation phase of fatty acid synthesis starts with the formation of acetyl ACP and malonyl ACP. Acetyl transacylase and malonyl transacylase catalyze these reactions.

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p. 953

In addition, the acetylated lysine residues interact with a specific acetyllysine-binding domain that is present in many proteins that regulate eukaryotic transcription.

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p. 437

Consequently, acetyl CoA has a high acetyl-group-transfer potential because transfer of the acetyl group is exergonic.

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p. 953

In addition, the acetylated lysine residues interact with a specific acetyllysine-binding domain that is present in many proteins that regulate eukaryotic transcription.

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p. 770

Some phospholipids are synthesized from an activated alcohol

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p. 606

3. The resulting addition compound releases the aldose product to yield an activated glycoaldehyde unit.

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p. 769

The synthesis of phospholipids requires an activated intermediate

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p. 121

2. Activated precursors. All four ribonucleoside triphosphatesxguiollargxATP, GTP, UTP, and CTPxguiollargxare required.

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p. 748

For instance, herpes simplex infections are treated with acyclovir (acycloguanosine), which viral thymidine kinase converts into acyclovir monophosphate by adding a phosphate to the hydroxyl group of acyclovir.

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p. 650

The acyl group is transferred from the sulfur atom of coenzyme A to the hydroxyl group of carnitine to form acyl carnitine.

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p. 784

In fact, free cholesterol activates acyl CoA:cholesterol acyltransferase (ACAT), the enzyme catalyzing this reaction.

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p. 239

The transpeptidase normally forms an acyl intermediate with the penultimate D-alanine residue of the D-Ala-D-Ala peptide (Figure 8.29).

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p. 984

The adaptive immune system comprises two parallel but interrelated systems: humoral and cellular immune responses.

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p. 123

The adaptors in protein synthesis are transfer RNAs.

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p. 123

Transfer RNAs are the adaptor molecules in protein synthesis

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p. 108

Look, for example, at adenosine 5'-triphosphate (ATP; Figure 4.6). This nucleotide is tremendously important because, in addition to being a building block for RNA, it is the most commonly used energy currency.

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p. 721

The formation of asparagine from aspartate requires an adenylated intermediate

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p. 751

In accord with the use of GTP, the enzyme that promotes this conversion, adenylosuccinate synthetase, is structurally related to the G-protein family and does not contain an ATP-grasp domain.

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p. 647

Second, the phosphorylation of perilipin triggers the release of a coactivator for adipose triglyceride lipase (ATGL).

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p. 1036

A drug's response to these processes is referred to as its ADME (pronounced "add-me") properties.

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p. 474

Indeed, rapidly growing tumor cells will metabolize glucose to lactate even in the presence of oxygen, a process called aerobic glycolysis or the Warburg effect, after Otto Warburg, the biochemist who firt noted this characteristic of cancer cells in the 1920s.

El sinònim no és neològic.

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p. 78

2. Affinity tags can be fused to proteins.

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p. 111

Space-filling models of 10 base pairs of B-form and A-form DNA depict their right-handed helical structures.

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p. 805

There, one population of neurons expresses appetite-stimulating (orexigenic) peptides, called neuropeptide Y (NPY) and agouti-related peptide (AgRP).

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p. 805

There, one population of neurons expresses appetite-stimulating (orexigenic) peptides, called neuropeptide Y (NPY) and agouti-related peptide (AgRP).

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p. 805

There, one population of neurons expresses appetite-stimulating (orexigenic) peptides, called neuropeptide Y (NPY) and agouti-related peptide (AgRP).

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p. 207

One mechanism for maintaining xalfax chains in solution was revealed by the discovery of an 11-kDa protein in red blood cells called xalfax-hemoglobin stabilizing protein (AHSP).

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p. 895

Consider yeast alanyl-tRNA, so called because it will carry the amino acid alanine.

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p. 821

Alcoholic scurvy is occasionally observed because of an insufficient ingestion of vitamin C.

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p. 173

FIGURE 6.6 Alignment with gap insertion. The alignment of xalfax-hemoglobin and myoglobin after a gap has been inserted into the homoglobin xalfax sequence.

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p. 32

The larger aliphatic side chains are especially hydrophobic; that is, they tend to cluster together rather than contact water.

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p. 290

The ratio of the concentration of enzyme in the T state to that in the R state is called the allosteric constant (L).

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p. 285

Proteins displaying allosteric control are thus information transducers: their activity can be modified in response to signal molecules or to information shared among active sites.

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p. 290

This mechanism for allosteric regulation is referred to as the concerted model because the change in the enzyme is "all or none"; [...].

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p. 761

The oxidase hydroxylates allopurinol to alloxanthine (oxipurinol), which then remains tightly bound to the active site.

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p. 70

In 1951, Linus Pauling and Robert Corey proposed two periodic structures called the xalfax helix (alpha helix) and the xbetax pleated sheet (beta pleated sheet).

El sinònim no és neològic.

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p. 278

The altered conformation of myosin persists for a substancial period of time

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p. 146

FIGURE 5.13 Alternative infection modes for xlambdax phage. Lambda phage can multiply withis host and lyse (lytic pathway) or its DNA can become integrated into the host genome (lysogenic pathway), where it is dormant until activated.

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p. 969

The amiloride-sensitive sodium channel belongs to a superfamily having common structural features, including two hydrophobic membrane-spanning regions, intracellular amino and carboxyl termini, and a large, extracellular region with conserved cysteine-rich domains.

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p. 899

Aminoacyl-tRNA synthetases have highly discriminating amino acid activation sites

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p. 714

Amino acid biosynthesis is intimately connected with nutrition because many higher organisms, including human beings, have lost the ability to synthesize some amino acids and must therefore obtain adequate quantities of these essential amino acids in their diets.

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p. 123

For the moment, it suffices to note that tRNAs contain an amino acid-attachment site and a template-recognition site.

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p. 914

Other aminoglycoside antibiotics such as neomycin, kanamycin, and gentamycin interfere with the interaction between tRNA and the 16S rRNA of the 30S subunit (p. 906) of bacterial ribosomes.

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p. 682

Digestion if further enhanced by proteolytic enzymes, such as aminopeptidase N, that are located in the plasma membrane of the intestinal cells.

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p. 905

A clue to the mechanism of initiation was the finding that nearly half the amino-terminal residues of proteins in E. Coli are methionine.

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p. 671

AMP-activated protein kinase (AMPK) converts the carboxylase into an inactive form by modifying three serine residues.

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p. 348

Membrane formation is a consequence of the amphipathic nature of the molecules.

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p. 671

AMP-activated protein kinase (AMPK) converts the carboxylase into an inactive form by modifying three serine residues.

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p. 869

Rifampicin is a semisynthetic derivative of rifamycins, which are derived from a strain of Amycolatopsis that is related to the bacterium that causes strep throat.

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p. 976

The amino-terminal 1150 amino acids consist almost exclusively of 29 ankyrin repeats (Figure 33.34).

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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.

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p. 995

Importantly, the antigen-binding specificity is conserved in class switching because the entire V_HDJ_H gene is translocated in an intact form.

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p. 42

FIGURE 2.31 An antiparallel xbetax sheet. Adjacent xbetax strands run in opposite directions, as indicated by the arrows.

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p. 995

One of the most potent activators of apoptosis, cytochrome c, exits the mitochondria and interacts with apoptotic peptidase-activating factor 1 (APAF-1), which leads to the formation of the apoptosome.

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p. 914

Apolipoprotein B (apo B) plays an important role in the transport of triacylglycerols and cholesterol by forming an amphipathic spherical shell around the lipids carried in lipoprotein particles (Section 26.3).

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p. 990

Apolipoprotein B (apo B) plays an important role in the transport of triacylglycerols and cholesterol by forming an amphipathic spherical shell around the lipids carried in lipoprotein particles (Section 26.3).

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p. 896

One of the most potent activators of apoptosis, cytochrome c, exits the mitochondria and interacts with apoptotic peptidase-activating factor 1 (APAF-1), which leads to the formation of the apoptosome.

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p. 995

One of the most potent activators of apoptosis, cytochrome c, exits the mitochondria and interacts with apoptotic peptidase-activating factor 1 (APAF-1), which leads to the formation of the apoptosome.

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p. 42

Consider, for example, argininosuccinase deficiency. This defect can be partly bypassed by providing a surplus os arginine in the diet and restricting the total protein intake.

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p. 558

Thus, the miRNAs serve as guide RNAs that determine the specificity of the Argonaute complex (Figure 32.27).

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p. 32

Two amino acids with relatively simple aromatic side chains are part of the fundamental repertoire.

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p. 516

FIGURE 17.22 Arsenite poisoning. Arsenite inhibits the pyruvirate dehydrogenase complex by inactivating the dihydrolipoamide component of th transacetylase.

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p. 585

Artificial photosynthetic systems may provide clean, renewable energy

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p. 292

FIGURE 10.14 Effect of CTP and ATP on ATCase kinetics.

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p. 647

Second, the phosphorylation of perilipin triggers the release of a coactivator for adipose triglyceride lipase (ATGL).

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p. 971

In essence, the light energy of a photon is converted into atomic motion.

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p. 460

We will contrast this manner of ATP formation with the formation of ATP from ionic gradients in chapters 18 and 19.

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p. 376

Thus, ABC transporters use a substantially different mechanism from the P-type ATPases to couple the ATP hydrolysis reaction to conformational changes.

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p. 542

An alternative proposal was that electron transfer aids the formation of an activated protein conformation, which then drives ATP synthesis.

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p. 551

This ATP-ADP exchange is energetically expensive; about a quarter of the proton-motive force generated by the respiratory chain is consumed by this exchange process.

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p. 277

FIGURE 9.44 Myosin ATPase Transition-State Analog. The structure of the transition-state analog formed by treating the myosin ATPase domain with ADP and vanadate (VO₄^3-) in the presence of magnesium.

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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. 367

Two types of ATP-driven pumps, P-type ATPases and the ATP-binding cassette (ABC) transporters, undergo conformational changes on ATP binding and hydrolysis that cause a bound ion to be transported across the membrane.

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p. 557

ATP-ADP translocase is specifically inhibited by very low concentrations of atractyloside (a plant glycoside) or bongkrekic acid (an antibiotic from a mold).

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p. 139

DNA probes and genes can be synthesized by automated solid-phase methods

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p. 320

Axial bonds are nearly perpendicular to the average plane of the ring, whereas equatorial bonds are nearly parallel to this plane.

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p. 1051

An important example is the use of thiopurine drugs such as 6-thioguanine, 6-mecaptopurine, and azothioprine to treat diseases including leukemia, immune disorders, and inflammatory bowel disease.

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