the chain, the 5′ carbon of the deoxyribose is phosphorylated but otherwise free. This is called the 5′ end of the DNA chain. At the other end is a deoxyribose with a free hydroxyl group on its 3′ carbon. This is the 3′ end.
IN DEPTH 3.1 WE HAVE A SECOND GENOME IN OUR CELLS
The set of 23 chromosomes that we inherit from each parent encodes a complete copy of our nuclear genome that resides in the nucleus of our cells. We have a second genome that resides in our mitochondria – the energy‐producing organelles inside our cells. Unlike our large nuclear genome, which is organized in linear chromosomes, our mitochondrial genome is circular and only 16 569 base pairs in length. The mitochondrial genome contains 37 genes but only 13 of these encode proteins. These proteins are all involved in mitochondrial energy production. While nuclear genomes are inherited from both parents, our mitochondrial genome is always inherited maternally. This has allowed a prediction of “mitochondrial Eve,” the most recent female ancestor from whom all living humans descend in the matrilineal line, estimated to have lived between 165 000 and 190 000 years ago.
The DNA Molecule Is a Double Helix
In 1953 Rosalind Franklin used X‐ray diffraction to show that DNA was a helical (i.e. twisted) polymer. James Watson and Francis Crick demonstrated, by building three‐dimensional models, that the molecule is a double helix (Figure 3.4). Two hydrophilic sugar‐phosphate backbones lie on the outside of the molecule and the purine and pyrimidine bases lie on the inside of the molecule. There is just enough space for one purine and one pyrimidine in the center of the double helix. The Watson–Crick model showed that the purine guanine (G) would fit nicely with the pyrimidine cytosine (C). The purine adenine (A) would fit nicely with the pyrimidine thymine (T). Thus A always base pairs with T and G always base pairs with C.
Hydrogen Bonds Form Between Base Pairs
A hydrogen bond forms when a hydrogen atom is shared. The hydrogen bonds in an A–T and a G–C base pair (Figure 3.4) form when the hydrogen attached to a nitrogen in one base gets close to an electron‐grabbing oxygen or nitrogen in the other base of the pair. The hydrogen bonds formed between the base pairs hold the DNA helix together. The three hydrogen bonds formed between G and C produce a relatively strong base pair. Because only two hydrogen bonds are formed between A and T, this weaker base pair is more easily broken. The difference in strengths between a G–C and an A–T base pair is important in the initiation of DNA replication (page 51) and in the initiation and termination of RNA synthesis (page 69).
DNA Strands Are Antiparallel
The two strands of DNA are said to be antiparallel because they lie in the opposite orientation with respect to one another, with the 3′‐hydroxyl terminus of one strand opposite the 5′‐phosphate terminus of the second strand. The sugar‐phosphate backbones do not completely conceal the bases inside. There are two grooves along the surface of the DNA molecule. One is wide and deep – the major groove – and the other is narrow and shallow – the minor groove (Figure 3.4). DNA‐binding proteins can use the grooves to gain access to the bases and bind to specific sequences. This is important in initiating replication (page 51) and transcription (page 69) and is also used when manipulating DNA in the laboratory.
Example 3.1 Erwin Chargaff's Puzzling Data
In a key discovery of the 1950s, Erwin Chargaff analyzed the purine and pyrimidine content of DNA isolated from many different organisms and found that the amounts of A and T were always the same, as were the amounts of G and C. Such an identity was inexplicable at the time but helped James Watson and Francis Crick build their double‐helix model in which every A on one strand of the DNA helix has a matching T on the other strand and every G on one strand has a matching C on the other.
The Two DNA Strands Are Complementary
A consequence of the base pairing that joins the two strands of DNA is that if the base sequence of one strand is known, then that of its partner can be inferred. A G in one strand will always be paired with a C in the other. Similarly an A will always pair with a T. The two strands are therefore said to be complementary.
Deoxyribonucleic acid carries the genetic information encoded in the sequence of the four bases – guanine, adenine, thymine, and cytosine. The information in DNA is transferred to its daughter molecules through replication (the duplication of DNA molecules) and subsequent cell division. DNA directs the synthesis of proteins through the intermediary molecule messenger RNA( mRNA). The DNA code is transferred to mRNA by a process known as transcription (Chapter 5). The mRNA code is then translated into a sequence of amino acids during protein synthesis (Chapter 6). This is the central dogma of molecular biology: DNA makes RNA makes protein.
Retroviruses
