Biochemistry

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

8 ed.

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

p. 782

Lipoprotein particles are classified according to increasing density (Table 26.1): chylomicrons, chylomicron remnants, very low density lipoproteins (VLDLs), intermediate-density lipoproteins (IDLs), low-density lipoproteins (LDLs), and high-density lipoproteins (HDLs).

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p. 554

Mitochondria contain an evolutionarily conserved protein, inhibitory factor 1 (IF1), that specifically inhibits the potential hydrolytic activity of the F₀F₁ ATP synthase.

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p. 887

Analysis of the base sequence of the rRNA precursor suggested that the splice sites are aligned with the catalytic residues by base-pairing between the internal guide sequence (IGS) in the intron and the 5' and 3' exons (Figure 29.44).

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p. 432

ATP serves as the principal immediate donor of free energy in biological systems rather than as a long-term storage form of free energy.

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p. 242

This new in singulo method, examining one individual at a time, yields a great deal of new information but also illustrates a potential pitfall of studying individuals, be they students or enzymes: How can we be certain that the student or molecule is representative and not an outlier?

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p. 947

An important application illustrating the power of transcription factors is the development of induced pluripotent stem (iPS) cells.

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p. 224

FIGURE 8.9 Induced-fit model of enzyme-substrate binding. In this model, the enzyme changes shape on substrate binding. The active site forms a shape complementary to the substrate only after the substrate has been bound.

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p. 236

In pure noncompetitive inhibition, the K_i for the inhibitor binding to E is the same as for binding to ES complex.

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p. 554

Mitochondria contain an evolutionarily conserved protein, inhibitory factor 1 (IF1), that specifically inhibits the potential hydrolytic activity of the F₀F₁ ATP synthase.

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p. 907

Three protein initiation factors (IF1, IF2, and IF3) are essential.

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p. 874

The TATA box is often paired with an initiator element (Inr), a sequence found at the transcriptional start site, between positions -3 and +5.

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p. 874

The TATA box is often paired with an initiator element (Inr), a sequence found at the transcriptional start site, between positions -3 and +5.

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p. 812

Metabolic derangements in type 1 diabetes result from insulin insufficiency and glucagon excess

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p. 811

FIGURE 27.8 Insulin release is regulated by ATP.

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p. 810

For reasons to be presented later in the chapter, this accumulation results in insulin resistance and ultimately in pancreatic failure.

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p. 410

FIGURE 14.25 Action of a lipid kinase in insulin signaling.

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p. 808

Type 1 diabetes is also referred to as insulin-dependent diabetes, meaning that the affected person requires the administration of insulin to live.

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p. 409

These phosphorylated sites act as docking sites for other substrates, including a class of molecules referred to as insulin-receptor substrates (IRS; Figure 14.22).

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p. 7

Interatomic distances and bond lenghts are usually measured in angstrom (xangstrommx) units:

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p. 389

Gap junctions are important for intercellular communication.

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p. 912

In these mRNAs, highly structured RNA sequences called internal ribosome entry sites (IRES) facilitate 40S ribosome binding to the mRNA.

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p. 625

Muscle phosphorylase is regulated by the intracellular energy charge

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p. 318

For an aldohexose such as glucose, a single molecule provides both the aldehyde and the alcohol: the C-1 aldehyde in the open-chain form of glucose reacts with the C-5 hydroxyl group to form an intramolecular hemiacetal (Figure 11.3).

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p. 318-319

The C-2 keto group in the open-chain form a ketohexose, such as fructose, can form an intramolecular hemiketal by reacting with either the C-6 hydroxyl group to form a six-membered cyclic hemiketal or the C-5 hydroxyl group to form a five-membered cyclic hemiketal (Figure 11.4).

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p. 654

Cobalamin enzymes, which are present in most organisms, catalyze three types of reactions: (1) intramolecular rearrangements; (2) methylations, as in the synthesis of methione; and (3) the reduction of ribonucleotides to deoxyribonucleotides (Section 25.3).

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p. 304

Two means of initiating blood clotting have been described, the intrinsic pathway and the extrinsic pathway.

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p. 194-195

Thus, the protein component of myoglobin controls the intrinsic reactivity of heme, making it more suitable for reversible oxygen binding.

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p. 55

Our first example is a class of proteins referred to as intrinsically unstructured proteins (IUPs).

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p. 151

Here, we shall consider one: inverse PCR to introduce deletions into plasmid DNA (Figure 5.24).

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p. 156

The protocol for ion semiconductor sequencing is similar to pyrosequencing except that nucleotide incorporation is detected by sensitively measuring the very small changes in pH of the reaction mixture due to the release of proton upon nucleotide incorporation.

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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).

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p. 398

Some particularly important second messengers are cyclic AMP (cAMP) and cyclic GMP (cGMP), calcium ion, inositol 1,4,5-triphosphate (IP₃), and diacylglycerol (DAG; Figure 14.3).

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p. 947

These iPS cells represent powerful research tools and, potentially, a new class of therapeutic agents.

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p. 955

This stem-loop binds a 90-kDa protein, called an IRE-binding protein (IRP), that blocks the initiation of translation as the IRE binds on the 5' side of the coding region.

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p. 912

In these mRNAs, highly structured RNA sequences called internal ribosome entry sites (IRES) facilitate 40S ribosome binding to the mRNA.

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p. 753

Each R2 chain contains a tyrosyl radical with an unpaired electron delocalized onto its aromatic ring, generated by a nearby iron center consisting of two ferric (Fe³⁺) ions bridged by an oxide (O^2-) ion (Figure 25.10).

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p. 234

Reversible inhibition, in contrast with irreversible inhibition, is characterized by a rapid dissociation of the enzyme-inhibitor complex.

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p. 409

These phosphorylated sites act as docking sites for other substrates, including a class of molecules referred to as insulin-receptor substrates (IRS; Figure 14.22).

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p. 292

Isoform is a more generic term used when the protein in question is not an enzyme.

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p. 317

FIGURE 11.1 Isomeric forms of carbohydrates.

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p. 441

3. Isomerization reactions rearrange particular atoms within a molecule.

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p. 510

Isotope labeling studies have revealed that the two carbon atoms that enter each cycle are not the ones that leave.

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p. 55

Our first example is a class of proteins referred to as intrinsically unstructured proteins (IUPs).

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