DNA Structure
Assessment Statement
7.1.1Describe the structure of DNA, including the anti-parallel strands, 3’ – 5’ linkages and hydrogen bonding between the purines
7.1.2Outline the structure of nucleosome
7.1.3State that nucleosomes help to supercoil chromosomes and help to regulate transcription
7.1.4Distinguish between unique or single-copy genes and highly repetitive sequences in nuclear DNA
7.1.5State that eukaryotic genes can contain exons and introns
DNA Structure
Previously, you learned that DNA (deoxyribonucleic acid) is a double stranded molecule formed in the shape of a double helix. Since deoxyribose is a 5-carbon sugar, the ends are numbered as so.
Each strand is composed of a phosphate backbone, alternating with deoxyribose molecules. The molecules are held together by a covalent bond called a phosphodiester bond or linkage (phosphate --- oxygen --- carbon).
The DNA chain of nucleotides is formed by condensation reactions between the 5’ carbon of the deoxyribose and the phosphate and the hydroxyl group on the 3’ carbon and the next phosphate group. Therefore, the polymer forms in such a way, that there is a free carbon at the 5’ end and 3’ carbon free at the other end. Even with thousands of nucleotides bonded, these ends will be free. As the nucleotides are bonded together, another chain forms on the other side in the opposite, 5’ – 3’ direction. Since the 3’ and 5’ ends are opposite, the two strands are described as antiparallel. The two strands are attached to each other by the nitrogenous bases. The bases form links by hydrogen bonds between the four bases; adenine (A), thymine (T), cytosine (C) and guanine (G). A and G and double ring structures called purines and C and T are single ring structures called pyrimidines. A single ring bonds to a double ring. Therefore, A bonds with T and C bonds with G.
As a result of the nucleotides linked by the phosphodiester bonds, a definite sequence of nitrogenous bases develops. The sequence carries out the genetic code that is essential for the life of the organism. The specific bases are held together by different numbers of hydrogen bonds. A and T are linked by two hydrogen bonds and G and C are linked by three hydrogen bonds. As a result, the hydrogen bonds allow the chains to curl around in the familiar double helix.
Packaging DNA
DNA is packaged with a protein structure called a histone. There are eight histones to help package the DNA. The DNA / histone structure is called a nucleosome. The nucleosome looks like beads on a string. The DNA wraps twice around the eight-histone structure and one more histone (H1) holds the structure together.
The nucleosomes have two functions:
- They help package up the DNA during mitosis and meiosis by the process of supercoiling
- They can be used to mark particular genes, either to promote gene expression by transcription and translation, or to cause silencing of a gene by preventing transcription
In other words, the nucleosomes allow for the entire strand of DNA to fit inside the nucleus. If not, as some DNA strands are 4 cm long, there could be tangling or pieces not enclosed in the nucleus. As the DNA is coiled, enzymes controlling transcription cannot access the strand, and therefore, regulates the process.
DNA Sequences
As we see, the sequence of the chain of deoxyribose sugar and phosphate backbone, with the specific bases, creates a specific sequences or combination of nucleotides. This creates highly repetitive sequences, which code for genes or just structure.
Highly repetitive Sequences
Eukaryote genomes contain large amounts of repetitive sequences (from 5% to 45% of the total genome), usually made up of 5-300 base pairs per repetitive sequence. There may be as many as 100 000 replicates per genome. If the repetitive sequences are clustered in an area, it is referred to as satellite DNA, but may be dispersed throughout the genome. Its function is not known. Satellite DNA is useful in DNA profiling, as massive amounts of DNA can be made from one piece of DNA found, for example, at a crime scene. More on this later.
Unique or Single Copy Genes
Some of the remaining 55% of the genome is structural and parts that have not been labelled for any use, than “other”. The structural DNA is around the centromere and near the ends of the chromosome at the telomeres. It is highly coiled and does not have a coding function. There are also some inactive genes, or pseudogenes, which do not have a function.
A very small portion of our DNA is used to code for genes. These protein coding genes, or unique or single copy genes, make up about 30% of our genome.
These sequences in our DNA, provide the base sequences essential to produce proteins at the ribosomes of cells. We will see later how the cell takes these sequences and translates the code to make a protein.
A gene is not a fixed sequence of bases like letters of a word. Genes of eukaryotes are made of many fragments that code for proteins mixed with non-coding fragments. The coding fragments are called exons and the non-coding fragments are called introns. When the DNA is to be made in to RNA, to code for proteins, the introns are removed to make something called mature messenger RNA or mRNA. More on this later. Prokaryotes do not usually have introns.
DNA Sequences in the Human Genome / %Protein-coding genes (exons) / 1-2
Introns / 24
Highly repetitive sequences / 45
Structural DNA / 20
Inactive genes (pseudogenes) / 2
Other / 7-8