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 of purine and pyrimidine bases, pentoses, and ATP (as an example of a nucleotide). (b) Structures of ATP, AMP, ADP, glucose, FAD+, and coenzyme A.
Our genetic information is stored in the form of deoxyribonucleic acid(DNA). DNA is a macromolecule and is made up of nucleotide subunits bound together linearly (Figure 2.18). DNA contains the bases A, T, G, and C; RNA contains the bases A, U, G, and C. The nomenclature of the bases, nucleosides, and nucleotides is explained in Table 2.7.
Figure 2.18 Linear structure of DNA and RNA. In nucleic acid biosynthesis, the α‐positioned phosphate group of a nucleotide triphosphate (NTPs in RNA, dNTPs in DNA) is linked to the free 3′‐OH group of the available strand.
The nucleotides are the building blocks for DNA and RNA. Nucleotides are esterified into polynucleotide chains via a phosphate backbone. The 5′‐hydroxyl group (“five prime hydroxyl group”) of a pentose is linked via a phosphodiester bond to the 3′‐hydroxyl group of a second pentose (Figure 2.18). During the biosynthesis of the nucleic acids, the respective nucleotide triphosphates are needed whose phosphoric acid anhydride bonds are especially rich in energy. In the completed nucleic acid, only nucleotide monophosphates are present. After cleavage of a diphosphate residue, the α‐phosphate group attacks the free 3′‐end of the already existing nucleic acid strand and forms a new ester bond. The synthesis is said to occur in the 5′ → 3′ direction.
DNA exists as a double helix whereby the bases A and T, and G and T, respectively, face each other in a complementary manner (Figure 2.19). Both DNA strands are arranged antiparallel to each other (i.e. within a helix one of the strands runs in the 5′ → 3′ direction, while the complementary partner strand is oriented in the 3′ → 5′ direction). The DNA double helix has a diameter of 2 nm.
Figure 2.19 Structure of the DNA double helix. The spatial orientation of the base pairs in the double helix and the principle of complementary base pairing between A and T, and G and C, respectively, via the formation of hydrogen bonds. (a) Schematic structure of the double helix. (b) Structural formula.
Complementary base pairing is achieved through the specific formation of two or three hydrogen bonds
