Nucleic Acid Structure and Organization
CENTRAL DOGMA OF MOLECULAR BIOLOGYAn organism must be able to store and preserve its genetic information, pass that information along to future generations, and express that information as it carries out all the processes of life. The major steps involved in handling genetic information are illustrated by the central dogma of molecular biology .
Genetic information is stored in the base sequence of DNA molecules. Ultimately, during the process of gene expression, this information is used to synthesize all the proteins made by an organism. Classically, a gene is a unit of the DNA that encodes a particular protein or RNA molecule
Gene Expression and DNA Replication
Gene expression and DNA replication are compared. Transcription, the first stage in gene expression, involves transfer of information found in a double-stranded DNA molecule to the base sequence of a single-stranded RNA molecule.
Comparison of Gene Expression and DNA Replication
DNA replication is the process in which each chromosome is duplicated before cell division.The Eukaryotic Cell Cycle
The M phase (mitosis) is the time in which the cell divides to form two daughter cells. Interphase is the term used to describe the time between two cell divisions or mitoses. Gene expression occurs throughout all stages of interphase. Interphase is subdivided as follows:• G1 phase (gap 1 ) is a period of cellular growth preceding DNA synthesis.
Cells that have stopped cycling, such as muscle and nerve cells, are said to be in a special state called G0•
• S phase (DNA synthesis) is the period of time during which DNA replication
occurs. At the end of S phase, each chromosome has doubled its
DNA content and is composed of two identical sister chromatids linked at the centromere.
• G2 phase (gap 2) is a period of cellular growth after DNA synthesis but
preceding mitosis. Replicated DNA is checked for any errors before cell division.
Bases
There are two types of nitrogen-containing bases commonly found in nucleotides: purines and pyrimidines
• Purines contain two rings in their structure. The two purines commonly found in nucleic acids are adenine (A) and guanine (G); both are found in DNA and RNA.
• Pyrimidines have only one ring. Cytosine (C) is present in both DNA and RNA. Thymine (T) is usually found only in DNA, whereas uracil (U) is found only in RNA.
Nucleosides and Nucleotides
Nucleosides are formed by covalently linking a base to the number 1 carbon of a
sugar. The numbers identifying the carbons of the sugar are labeled with "primes" in nucleosides and nucleotides to distinguish them from the carbons of the purine or pyrimidine base.Nucleotides are formed when one or more phosphate groups is attached to the 5'carbon of a nucleoside .
NUCLEIC ACIDS
Nucleic acids are polymers of nucleotides joined by 3', 5'-phosphodiester bonds; that is, a phosphate group links the 3' carbon of a sugar to the 5' carbon of the next sugar in the chain. Each strand has a distinct 5' end and 3' end, and thus has polarity. A phosphate group is often found at the 5' end, and a hydroxyl group is often found at the 3' end. The base sequence of a nucleic acid strand is written by convention, in the 5'→3' direction (left to right). According to this convention, the sequence of the strand must be written 5'-TCAG-3' or TCAG:• If written backward, the ends must be labeled: 3'-GACT-5'
• The positions of phosphates may be shown: pTpCpApG
• In DNA, a "d" (deoxy) may be included: dTdCdAdG In eukaryotes, DNA is generally double-stranded (dsDNA) and RNA is generally single-stranded ssRNA
DNA Structure
Some of the features of double-stranded DNA include:• The two strands are antiparallel (opposite in direction).
• The two strands are complementary. A always pairs with T (two hydrogen
bonds), and G always pairs with C (three hydrogen bonds). Thus, the base sequence on one strand defines the base sequence on the other strand.
• Because of the specific base pairing, the amount of A equals the amount
of T, and the amount of G equals the amount of C. Thus, total purines
equals total pyrimidines.
With minor modification (substitution ofU for T) these rules also apply to dsRNA.
Most DNA occurs in nature as a right-handed double-helical molecule known as
Watson-Crick DNA or B-DNA .The hydrophilic sugar-phosphate backbone of each strand is on the outside of the double helix. The hydrogen- bonded base pairs are stacked in the center of the molecule. There are about 10 base pairs per complete turn of the helix.
The B-DNA Double Helix
Denaturation and Renaturation of DNADouble-helical DNA can be denatured by conditions that disrupt hydrogen bonding and base stacking, resulting in the "melting" of the double helix into two
single strands that separate from each other. No covalent bonds are broken in this process. Heat, alkaline pH, and chemicals such as formamide and urea are commonly used to denature DNA.
Denatured single-stranded DNA can be renatured (annealed) if the denaturing
condition is slowly removed. For example, if a solution containing heat-denatured DNA is slowly cooled, the two complementary strands can become basepaired again.
Such renaturation or annealing of complementary DNA strands is an important step the polymerase chain reaction. In these techniques, a well-characterized probe DNA is added to a mixture of target DNA molecules. The mixed sample is denatured and then renatured. When probe DNA binds to target DNA sequences of sufficient complementarity, the process is called hybridization
ORGANIZATION OF DNA
Large DNA molecules must be packaged in such a way that they can fit inside the cell and still be functional.Supercoiling
Mitochondrial DNA and the DNA of most prokaryotes are closed circular structures. These molecules may exist as relaxed circles or as supercoiled structures in which the helix is twisted around itself in three-dimensional space. Supercoiling results from strain on the molecule caused by under- or overwinding the double helix:
• Negatively supercoiled DNA is formed if the DNA is wound more loosely than in
Watson-Crick DNA. This form is required for most biologic reactions.
• Positively supercoiled DNA is formed if the DNA is wound more tightly than in
Watson-Crick DNA.
• Topoisomerases are enzymes that can change the amount of supercoiling in
DNA molecules. They make transient breaks in DNA strands by alternately
breaking and resealing the sugar-phosphate backbone. For example, in
Escherichia coli, DNA gyrase (DNA topoisomerase II) can introduce negative
supercoiling into DNA.
Nucleosome and Nucleofilament Structure in Eukaryotic DNA
Nuclear DNA in eukaryotes is found in chromatin associated with histones and
nonhistone proteins. The basic packaging unit of chromatin is the nucleosome• Histones are rich in lysine and arginine, which confer a positive charge on the proteins.
• Two copies each of histones H2A, H2B, H3, and H4 aggregate to form the histone octamer.
• DNA is wound around the outside of this octamer to form a nucleosome (a series of nucleosomes is sometimes called "beads on a string", but is more properly referred to as a 10 nm chromatin fiber).
• Histone Hl is associated with the linker DNA found between nucleosomes to help package them into a solenoid-like structure, which is a thick 30-nm fiber.
• Further condensation occurs to eventually form the chromosome. Each eukaryotic chromosome in Go or G 1 contains one linear molecule of double-stranded DNA.
Cells in interphase contain two types of chromatin: euchromatin (more opened
and available for gene expression) and heterochromatin (much more highly condensed and associated with areas of the chromosomes that are not expressed.)
Euchromatin generally corresponds to the nucleosomes ( 10-nm fibers) loosely associated with each other (looped 30-nm fibers). Heterochromatin is more highly condensed, producing interphase heterochromatin as well as chromatin characteristic of mitotic chromosomes.
During mitosis, all the DNA is highly condensed to allow separation of the sister chromatids. This is the only time in the cell cycle when the chromosome structure is visible. Chromosome abnormalities may be assessed on mitotic chromosomes by karyotype analysis (metaphase chromosomes) and by banding techniques (prophase or prometaphase), which identify translocations, deletions, inversions, and duplications.