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pyrophosphate
In addition to a catalytic center, many enzymes (especially those composed of several subunits) also have a regulatory center where allosteric ligands bind. For example, the second messenger cAMP binds to the tetrameric protein kinase A complex; after binding both regulatory protein subunits dissociate from both catalytic subunits, which results in their activation (Figure 3.9). Enzymes can be inhibited by inhibitors. We distinguish between reversible, irreversible, competitive, and noncompetitive inhibitors.
A further important way to regulate the activity of enzymes or regulatory proteins is that of reversible conformational change. This is achieved by phosphorylation/dephosphorylation with the help of protein kinases or phosphatases, respectively. Most of the protein kinases utilize adenosine triphosphate (ATP); other molecular switches work through the binding of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) (Figure 2.16, Table 2.7). A reversible reduction of disulfide bridges (e.g. through thioredoxin) plays an important role during the regulation of light‐dependent chloroplast enzymes. Biochemists and cell biologists are working extensively to define all cellular proteins that are regulated through phosphorylation and GTP/GDP to gain a better understanding of regulation processes and regulatory pathways or networks inside the cell (see Section 3.1.1.3).
Figure 2.16 Reversible activation and inactivation of enzymes and regulatory proteins. (a) Phosphorylation/dephosphorylation. (b) Binding of GTP/GDP. GEF, guanine nucleotide exchange factor; GAP, GTPase‐activating protein.
Table 2.7 Nomenclature of DNA and RNA building blocks.
| Base | Nucleotide (abbreviation) | Nucleotide (number of phosphate groups) | |||||
|---|---|---|---|---|---|---|---|
| RNA | DNA | ||||||
| 1 | 2 | 3 | 1 | 2 | 3 | ||
| Adenine | Adenosine (A) | AMP | ADP | ATP | dAMP | dADP | dATP |
| Guanine | Guanosine (G) | GMP | GDP | GTP | dGMP | dGDP | dGTP |
| Cytosine | Cytidine (C) | CMP | CDP | CTP | dCMP | dCDP | dCTP |
| Thymine | Thymidine (T) | dTMP | dTDP | dTTP | |||
| Uracil | Uridine (U) | UMP | UDP | UTP |
AMP, adenosine monophosphate; ADP, adenosine diphosphate; ATP, adenosine triphosphate; d, deoxy.
Many pathways have been optimized during evolution to increase the rate and efficacy of them. One way is to organize all proteins of a certain pathway or reaction in form of multienzyme complexes, in which enzymes that share substrates and educts are in close vicinity, thus reducing diffusion rates. Another strategy is to concentrate the pathway enzymes in a particular cellular compartment, e.g. the citric acid cycle in mitochondria.
2.4 Structure of Nucleotides and Nucleic Acids (DNA and RNA)
Nucleotides play important roles in the cell: as energy carriers (ATP, adenosine diphosphate [ADP]); as coenzymes (FAD, NAD+, coenzyme A), during the transfer of sugar moieties (ADP‐glucose); and as building blocks for nucleic acids (Figure 2.17a). Nucleotides consist of the purine bases adenine and guanine and the pyrimidine bases cytosine and thymine or uracil, which form N‐glycosidic bonds with ribose or deoxyribose. The 5′‐hydroxyl group of the pentose is esterified with one, two, or three phosphate residues (Figure 2.17b).
Figure 2.17 Structure of nucleotides. (a) Structures