Nucleotide pairs

Figure 7.2 Three helical forms of DNA, each containing 22 nucleotide pairs, shown in both side and top views. The sugar-phosphate backbone is dark the paired nucleotide bases are light, (a) B-DNA, which is the most common form in cells, (b) A-DNA, which is obtained under dehydrated nonphysiological conditions. Notice the hole along the helical axis in this form, (c) Z-DNA, which can be formed by certain DNA sequences under special circumstances. (Courtesy of Richard Feldmann.)...

The renaturation rate of DNA is an excellent indicator of the sequence complexity of DNA. For example, bacteriophage T4 DNA contains about 2 X 10 nucleotide pairs, whereas Escherichia coli DNA possesses 4.64 X 10 . E. coli DNA is considerably more complex in that it encodes more information. Expressed another way, for any given amount of DNA (in grams), the sequences represented in an E. coli sample are more heterogeneous, that is, more dissimilar from one another, than those in an equal weight of phage T4 DNA. Therefore, it will take the E. coli DNA strands longer to find their complementary partners and reanneal. This situation can be analyzed quantitatively. 

Rho-dependent transcription termination signals in E coll also appear to have a distinct consensus sequence, as shown in Figure 37—6. The conserved consensus sequence, which is about 40 nucleotide pairs in length, can be seen to contain a hyphenated or interrupted inverted repeat followed by a series of AT base pairs. As transcription proceeds through the hyphenated, inverted repeat, the generated transcript can form the intramolecular hairpin structure, also depicted in Figure 37-6. 

Genotype An unphased 5 to 3 sequence of nucleotide pair(s) found at one or more polymorphic sites in a locus on a pair of homologous chromosomes in an individual. 

The rules of base pairing (or nucleotide pairing) in DNA are adenine (A) always pairs with thymine (T) cytosine (C) always pairs with guanine (G). 

Fig. 1. The three structural levels of DNA-based Immunomodulatory sequence (DIMS). G-rich motifs are shown in blacK, sequences containing unmethylated CpG motifs shown in grey (corresponding to the color of motif background in Table 1) thin grey/mes indicate hydrogen bonds formed by Watson-Crick nucleotide pairs (DNA secondary structure level) or by Floogsteen hydrogen bonding (DNA tertiary structure level).

Aframeshift mutation causes one or more nucleotide pairs to be added or deleted and that can cause more dramatic changes in the amino acid sequences of a protein coded for by the mutated gene, with more dramatic effects on the functioning of the protein. 

DNA, adenine (A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). Therefore, when there is an A in one strand of the double-stranded DNA molecule, there is a T in the other strand. When the genetic code is copied from DNA to RNA, the two strands of DNA molecule separate, and the RNA nucleotides pair with nucleotides on each strand of DNA. In this case, the nucleotide that pairs with adenine (A) on the DNA is uracil (U) because RNA does not contain thymine (T). Because of the exact nature of base pairing, the genetic code can be transmitted accurately at each stage of the process. 

The base pairs are on the inside of the helix, and the sugar-phosphate backbone is on the outside. The pitch of the helix is such that ten successive nucleotide pairs form one complete turn in 34 A (the repeat distance). The exterior width of the spiral is about 20 A, and the internal distance between T-positions of ribose units on opposite chains is about 11 A. 

DNA of the Human Body Calculate the weight in grams of a double-helical DNA molecule stretching from the earth to the moon (-320,000 km). The DNA double helix weighs about 1 X 10 18 g per 1,000 nucleotide pairs each base pair extends 3.4 A. For an interesting comparison, your body contains about 0.5 g of DNA ... 

Figure 5. A DNA molecule whose helix axes have the connectivity of a cube. The molecule shown consists of six cyclic strands that have been catenated together in this particular arrangement. They are labeled by the first letters of their positional designations, Up, Down, Front, Back, Left, and Right. Each edge contains 20 nucleotide pairs of DNA, so we expect that their lengths will be approximately 68 A. All of the twisting has been shown in the middle of the edges for clarity, but the DNA is base-paired from vertex to vertex. From model building, the axis-to-axis distance across a square face seems to be approximately 100 A, with a volume (in a cubic configuration) of approximately 1760 nm3 when the cube is folded as shown.

The genetic instructions for a cell are found in the DNA molecules. All DNA is derived from four different kinds of monomers, which we call nucleotides. DNA molecules are double-stranded two polymer chains are coiled together, their nucleotide units being associated as nucleotide pairs (see Fig. 5-7). The genetic messages in the DNA are in the form of... 

Each nucleotide pair contributes 0.34 nm to the length of the DNA molecule thus, the total length of DNA of an E. coli chromosome is 1.4 mm. This is about 700 times the length of the cell which contains it. Clearly, the molecules of DNA are highly folded, a fact that accounts for their appearance in the electron microscope as dense aggregates called nucleoids, which occupy about one-fifth of the cell volume (Fig. 1-4). 

A puzzle was the fact that structural studies indicate that the editing center is over 3 nm away from the catalytic center in Pol I.267 The proposed solution to the puzzle is illustrated in Fig. 27-14. When the catalytic center "identifies" a nucleotide triphosphate as able to form a proper Watson-Crick nucleotide pair, it catalyzes the formation of the new nucleotide linkage. Then it releases the 3 -chain end, which sometimes "melts" and over a 10- to 100-ms time interval is able to reach over into the exonuclease site where the newly added nucleotide may be hydrolytically removed. However, if the newly formed nucleotide is properly paired, it will be less likely to melt, and the new nucleotide will be more likely to be retained.2593 265 267 DNA polymerase I and other related polymerases utilize processive mechanisms, moving from one site to the next without diffusing away from the DNA. The schematic picture shown in Fig. 27-14 also indicates how the 5-3 exonuclease activity can come into play, when the polymerase reaches the end of a single-stranded gap. 

For the present it is enough to say that a mutation may occur at any point within a gene. Theoretically there should be as many "mutational sites" within a gene as there are nucleotide pairs. 

Because in E. coli there are at least 3000 genes and the chromosome has 4 x I Or nucleotide pairs then the average size of a gene is 4,000,000/300= 1300, or less, nucleotide pairs. The true value is more likely to be 900-1000 pairs per gene. 

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