In this chapter, we describe thecentral dogmaof genetics, which involves information
flow from DNA to RNA via transcription in the nucleus, followed by RNA transport
into the cytoplasm, where it is translated into protein. Let’s first look at DNA. What
exactly is DNA? DNA, ordeoxyribonucleic acid, is simply a chemical, a double-stranded,
helical polynucleotide, to be specific. However, in the proper biological context, this
chemical determines such traits as the color of a petunia petal, the scent of a citrus
blossom, the sweetness of a corn kernel, the strength of a cotton fiber, and the yield of
a wheat head in the face of biotic and abiotic stress. The majority of a plant’s DNA is
found within the nucleus of each cell. Specific segments of the nuclear DNA, called
genes, contain all the information required for the cell to make proteins (polypeptides)
that are responsible for traits. Each protein-coding gene codes for a particular polypeptide,
which is composed of a unique linear arrangement of amino acids as determined by the
gene sequence.
6.1.2 DNA as a Polynucleotide
Before describing how the DNA of a gene can lead to the production of a protein (gene
expression), the chemical structure of DNA must be understood. DNA is composed of
two strands ofdeoxyribonucleotides[sugar (deoxyribose)þphosphateþa nitrogenous
base—(either adenine (A), guanine (G) (both arepurines), cytosine (C), or thymine (T)
(both are pyrimidines)] (Fig. 6.1). The two strands have a right-handed (clockwise)
helical shape, the so-called double helix (Watson and Crick’s model), with the sugars
and phosphates forming the backbone (or outside), and the bases located in the center of
the molecule (Fig. 6.2). It is important to note here that the phosphates of the DNA back-
bone are negatively charged, and this will allow proteins that have positively charged
domains to bind to the DNA. The importance of such DNA–protein binding will be
discussed later in this chapter in terms of controlling gene expression. The deoxyribo-
nucleotides of each strand are paired through specific hydrogen bonding of their respective
bases: A on one strand always pairs with T on the other via two hydrogen bonds, and G on
one strand always pairs with C on the other via three hydrogen bonds. This hydrogen
bonding keeps the two strands together. Knowing the sequence of only one of the
strands will provide all the information required to make the other strand through this
specific or complementary base-pairing mechanism. It is also sufficient information for
scientists to deduce the sequence of the second strand. It is important to note that the
strands have directionality, each has a 5^0 end and a 3^0 end, and when the DNA strands
pair, they are said to be antiparallel (Fig. 6.1). Since the bases are what distinguish the
nucleotides from one another, a gene sequence conventionally is written by listing the
linear sequence of the bases of one strand (thecodingstrand; see below) starting from
the 5^0 end and proceeding to the 3^0 end.
6.2 DNA Packaging into Eukaryotic Chromosomes
In a cell, the DNA described above is not “naked,” but in association with proteins that
together are packaged as chromosomes that can fit within the nucleus. Specifically, eukary-
otic chromosomes are composed of DNA (2nm in diameter) in association with histone and
nonhistone proteins to form a nucleoprotein structure called chromatin (200 nm in
136 MOLECULAR GENETICS OF GENE EXPRESSION