Inside cells

Before protein molecules attain their native folded state they may expose hydrophobic patches to the solvent. Isolated purified proteins will aggregate during folding even at relatively low protein concentrations. Inside cells, where there are high concentrations of many different proteins, aggregation could therefore occur during the folding process. This is prevented by... 

In acidic solution at low pH, a carboxylic acid is completely undissociated and exists entirely as RCO2H- In basic solution at high pH, a carboxylic acid is completely dissociated and exists entirely as RC02 - Inside living cells, however, the pH is neither acidic nor basic but is instead buffered to nearly neutral pH—in humans, to pH = 7.3, a value often referred to as physiological pH. In what form, then, do carboxylic acids exist inside cells The question is an important one for understanding the acid catalysts so often found in biological reactions. 

What is true for acetic acid is also true for other carboxylic acids at the ph ysiological pH that exists inside cells, carboxylic acids are almost entirely dissociated. To reflect this fact, we always refer to cellular carboxylic acids by the name of their anion—acetate, lactate, citrate, and so forth, rather than acetic acid, lactic acid, and citric acid. 

What about amine bases In what form do they exist at the physiological pH inside cells—as the amine (A- = RNH2), or as the ammonium ion (HA = RNH3+) Let s take a 0.0010 Vf solution of methylamine at pH = 7.3, for example. According to Table 24.1, the pKa of methvlammonium ion is 10.64, so from the Henderson-Hasselbalch equation, we have... 

The first pharmacological agent shown to activate AMPK was 5-aminoimidazole-4-carboxamide (AICA) riboside, also known as acadesine. This adenosine analogue is taken up into cells by adenosine transporters and phosphoiylated by adenosine kinase to the mono-phosphorylated form, AICA ribotide or ZMP. ZMP accumulates inside cells to higher concentrations than the concentration of AICA riboside present in the medium, and it mimics both effects of AMP on AMPK system (allosteric activation and inhibition of... 

A secondary metabolite produced by Tolypocladium inflation. This fungus was initially isolated in a soil sample collected in Norway. Cyclosporin A is a cyclic undecapeptide. Inside cells, cyclosporine A binds its immunophillin receptor known as cyclophillin. Like the FK506-FKBP12 complex, cyclosporin A-cyclophillin binds and inhibits the protein phosphatase calcineurin. 

Inward Rectifier K+ Channels. Figure 2 High [K+] inside cells relative to outside results in normal rectification, whereby outward (positive by convention) potassium currents (/) when cells are depolarized (is positive relative to EK), are biggerthan inward (negative) currents at hyperpolarized (negative) voltages. Inward or anomalous rectifiers show strong or weak inward rectification whereby outward currents are smaller than inward currents. 

Rapamycin is a macrocyclic lactone produced by Streptomyces hygroscopious. This bacterium was originally cultured from a soil sample collected on Easter Island (known locally as Rapa Nui hence the name rapamycin). Parenthetically, rapamycin shares an interesting mode of action with two other antifungal and immunosuppressive compounds, FK506and cyclosporin A. Inside cells, rapamycin first binds to FKBP12, a small protein receptor known as an immunophilin. FKBP12 is not an essential protein but is an important cofactor required for rapamycin to bind and inhibit TOR. 

C. G., Janowski B.A., Corey D. R. Inhibition of gene expression inside cells by peptide nucleic acids effect of mRNA target sequence, mismatched bases, and PNA length. Biochemistry 2001 40 53-64. 

Table 8 5 shows that each of the four common s-block ions is abundant not only in seawater but also in body fluids, where these ions play essential biochemical roles. Sodium is the most abundant cation in fluids that are outside of cells, and proper functioning of body cells requires that sodium concentrations be maintained within a narrow range. One of the main functions of the kidneys is to control the excretion of sodium. Whereas sodium cations are abundant in the fluids outside of cells, potassium cations are the most abundant ions in the fluids inside cells. The difference in ion concentration across cell walls is responsible for the generation of nerve impulses that drive muscle contraction. If the difference in potassium ion concentration across cell walls deteriorates, muscular activity, including the regular muscle contractions of the heart, can be seriously disrupted. 

A biochemical catalyst is called an enzyme. Enzymes are specialized proteins that catalyze specific biochemical reactions. Some enzymes are found in extracellular fluids such as saliva and gastric juices, but most are found inside cells. Each type of cell has a different array of enzymes that act together to determine what role the cell plays in the overall biochemistry of the organism. Enzymes are complicated molecules. Biochemists have determined the molecular structures of some enzymes, but the structures of many enzymes are not yet known. 

Most cell walls are able to deesteriJfy exogeneous pectin very rapidly but in vivo these cell walls still contain large amounts of methyl-esterified pectins. How can the substrate and the enzymes coexist inside cell walls ... 

Despite the higher selectivity of enzymatic methyl transfer over chemical methylation, where toxic or hazardous reagents are often employed, such as methyl sulfonate and diazomethane, the synthetic applications of these enzymes have been largely ignored primarily as a result of high costs associated with the cofactor SAM. Recent efforts have been directed to in vivo methylation, where SAM may be regenerated inside cells. For example, methyl benzoate production was engineered in recombinant Saccharomyces cerevisiae and in vivo... 

Figure 4.2 Hypothetical plasma membrane (PM)-associated structure of FR02. Four histidine residues (white spots) predicted to coordinate two intramembraneous haem groups (white bars) are indicated, as are the tetrapeptide binding sites for FAD and N AD(P)H. The sites of mutations in the FRO gene are indicated (frdl-l,frdl-3) i, inside cell o, outside cell. Reprinted with permission from Nature (Robinson et al., 1999). Copyright (1999) Macmillan Magazines Limited.

Equilibrium considerations other than those of binding are those of oxidation/reduction potentials to which we drew attention in Section 1.14 considering the elements in the sea. Inside cells certain oxidation/reductions also equilibrate rapidly, especially those of transition metal ions with thiols and -S-S- bonds, while most non-metal oxidation/reduction changes between C/H/N/O compounds are slow and kinetically controlled (see Chapter 2). In the case of fast redox reactions oxidation/reduction potentials are fixed constants. 

Now, most metal ion/organic molecule chemical reactions inside cells also come to equilibrium rapidly. The organic products, made irreversibly available by synthesis under feedback control, contain a broad set of possible binding sites for selected metal ions mainly in soluble proteins (enzymes) and in the pumps for uptake or rejection managed at the cell membrane, as well as in the factors, transcription factors, necessary for controlled production of those organic products under the direction of the coded system. These ion-selective binding sites are common to all cells so that while all cells are based on similar major organic reactions and similar but specific biopolymer products, they also have in common a set of... 

The fluorescence intensity of fluorescent proteins is pH dependent and most fluorescent proteins are less fluorescent at lower pH mainly because of a reduction in absorbance. Since the absorbance of the acceptor determines the FRET efficiency, changes in the acceptor absorbance spectrum due to pH variations can be wrongly interpreted as changes in FRET efficiency. Thus, a pKa well below physiological pH is recommended to prevent artifacts due to pH changes inside cells. This is especially challenging if the fluorescent proteins are to be targeted to acid cellular compartments, for example, endosomes, lysosomes, or plant vacuoles. 

Acrylonitrile can enter your body if you breathe its vapors or eat or drink acrylonitrile-contaminated food or water. Acrylonitrile can pass through your skin, but how much gets through is not known. Inside the body, acrylonitrile is broken down into other chemicals, including cyanide. Most of these breakdown products are removed from the body in the urine. Overall, most acrylonitrile is removed from the body within 24 hours, but approximately 25% of what is taken in becomes attached to materials inside cells of the body. More information on how acrylonitrile enters and leaves the body is given in Chapter 2. 

Nanoparticles such as those of the heavy metals, like cadmium selenide, cadmium sulfide, lead sulfide, and cadmium telluride are potentially toxic [14,15]. The possible mechanisms by which nanoparticles cause toxicity inside cells are schematically shown in Fig. 2. They need to be coated or capped with low toxicity or nontoxic organic molecules or polymers (e.g., PEG) or with inorganic layers (e.g., ZnS and silica) for most of the biomedical applications. In fact, many biomedical imaging and detection applications of QDs encapsulated by complex molecules do not exhibit noticeable toxic effects [16]. One report shows that the tumor cells labeled with QDs survived in circulation and extravasated into tissues... 

Fig. 2 Possible mechanisms by which nanoparticles cause toxicity inside cells. GSH glutathione, GSSG glutathione disulfide, MDA malondialdehyde, NFkB nuclear factor kappa B, Nrf2 nuclear factor-erythroid 2-related factor 2, ROS reactive oxygen species...

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