Biochemistry - The Chemical Reactions of Living Cells, Volume 1 - D. Metzler 1980

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Regulation of Chemical Processes in the Cell

Biologists have long been fascinated by the ability of living organisms to maintain a constant internal environment despite drastic fluctuations in external conditions. For example, the pH of human Blood is invariably 7.40±0.05. Although blood glucose concentration may briefly spike after a meal, it generally remains strictly constant at 5 mM. The same holds true for the levels of most other components in Body Fluids and the intracellular milieu. This phenomenon, known as Homeostasis, is governed by a sophisticated network of regulatory mechanisms.

Imagine that a nutrient A enters a Cell. If this substance merely enters and undergoes a series of reactions without any of the reaction products leaving The Cell, an equilibrium state will soon be reached. Such a system has nothing in common with a living cell. Living Cells continuously consume nutrients and excrete Metabolic waste products. Intracellular substance transformations proceed through complex, frequently branched and intersecting reaction pathways. A simple hypothetical reaction sequence with a single branch is illustrated below.

Even in such a simple open system, certain distinctive features of homeostasis are apparent [55]. When the rates of formation and breakdown of intermediate products are equal, a steady state is established (which, however, is not an equilibrium state). Any alteration in The rate of substance A entering the cell, the rate of product removal, or The activity of an enzyme catalyzing an irreversible step in the reaction chain can significantly shift the steady-state concentrations of the system's components.

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Living cells are vastly more complex than the scheme depicted above, primarily because they possess sensitive mechanisms that detect and compensate for concentration shifts that disrupt the steady state. In most cases, these mechanisms operate via feedback loops, functioning in much the same way as a thermostat in a heating system.

The active, or catalytic, site of an enzyme is a relatively small region of the protein molecule. The Amino Acid Composition of the remainder of the molecule, particularly its surface areas, can vary considerably through Mutations without altering the enzyme's catalytic activity. Nevertheless, the binding of other molecules to various surface Regions of the enzyme can indirectly influence catalysis. In concentrated solutions such as the Cytoplasm, molecules may undergo aggregation. The binding of a specific molecule to a particular site on the enzyme's surface can alter its conformation and, consequently, increase or decrease its catalytic activity. For instance, when the end product of a metabolic pathway accumulates in excess, a feedback inhibitor interacts with the Enzymes in this manner and "shuts them down." Interactions of this type constitute a widespread regulatory mechanism.

A strikingly similar mechanism underlies the binding of Hormones to specific receptors located on The cell membrane or within the cytoplasm. Hormones are regulatory compounds secreted by specialized Tissues that modulate METABOLISM in target cells belonging to another tissue. It is hypothesized that hormone binding induces a conformational change in the receptor, which in turn triggers a cascade of reactions leading to the biological response.

Questions and Problems

1. Describe the fundamental structural and organizational differences between prokaryotic and Eukaryotic cells.

2. What are the two primary Functions of Proteins in the cell, one function of DNA, two functions of RNA, and one function of Lipids?

3. Compare The chemical composition of bacterial Ribosomes, cell membranes, and flagella.

4. Consider a set of microorganisms and cells with the following dimensions: a mycoplasma, which is a sphere with a diameter of 0.33 µm; E. coli, a cylinder with a diameter of 0.8 µm and a length of 2 µm; a Liver cell, a sphere with a diameter of 20 µm; and a ROOT Hair, a cylinder with a diameter of 10 µm and a length of 1 mm.

a. Calculate the volume, mass in grams, and mass in Daltons for each of these cells (assuming a specific gravity of 1.0).

b. Assuming bacterial ribosomes are spherical with a diameter of 23 nm, calculate their volume. If the mass of a bacterial ribosome is 2.7∙10⁶ Daltons (Ch. 15, Sec. B.1), what is its apparent density (mass divided by volume)? The density of bacterial ribosomes experimentally determined in a cesium chloride gradient (Ch. 2) is approximately 1.6 g∙cm^-3. How can this discrepancy be explained? If the linear dimensions of eukaryotic ribosomes are 1.17 times greater than those of bacterial ribosomes, What is the volume of a eukaryotic ribosome?

c. What fraction of the E. coli cell volume is occupied by The Cell wall, Plasma Membrane, and ribosomes (assume a total of 15,000 ribosomes)? Given that an E. coli cell is 80% Water, what percentage of the dry cell weight is accounted for by ribosomes? By DNA (assuming one chromosome per cell)?

d. What fraction of a liver cell's volume is made up of ribosomes, The Nucleus, The Plasma Membrane, and Mitochondria (assuming 1,000 mitochondria per cell)?

5. a. What is the molar concentration of an enzyme present in E. coli at a level of only a single molecule per cell?

b. The K⁺ concentration in an E. coli cell is 150 mM. Calculate the number of potassium ions in a single cell.

c. If the intracellular pH is 7.0, how many H⁺ ions are present in the cell?

6. If Chromosomes (and Chromatin) consist of 15% DNA, what is the mass of 23 pairs of chromosomes in a human diploid cell? If the nuclear diameter is 5 µm and its density is 1.1 g∙cm^-3, what fraction of the nuclear weight is contributed by chromatin?

7. Compare the surface-to-volume ratios for E. coli cells, liver cells, eukaryotic nuclei, and root hairs. If 20% of The surface of a cell with a 20 µm diameter is covered with microvilli (0.1 µm in diameter and 1 µm in length), with each microvillus positioned at the center of a 0.2×0.2 µm square, by how much does this increase the surface-to-volume ratio?

8. It is established that each amino acid is encoded by a triplet of NUCLEOTIDES (a codon) in the DNA chain. There are four types of nucleotides in DNA. How many distinct codons can be formed from them? Note that this calculated number of codons exceeds the number of Amino Acids (20) incorporated into proteins, plus three termination codons that halt Polypeptide chain synthesis. (A list of codons is provided in Tables 15-2 and 15-3.)

9. State two similarities and two differences between blue-green Algae and green algae.

10. Compare the Size and Structure of bacterial and eukaryotic flagella.

11. Compare the Chemical composition of extracellular structures—such as outer walls or the extracellular ground substance ("matrix")—secreted by the following cells: Bacteria, fibroblasts, osteoblasts, plant cells, and Fungi.

12. Define THE CONCEPT OF "steady state" for living cells and compare it with the concept of chemical equilibrium.