DNA and Chromosomes

DNA Structure and Replication

DNA Structure

DNA is classified as a type of nucleic acid whose structure consists of a double helix that is composed of two antiparallel strands.

The molecule responsible for hereditary information in cells is deoxyribonucleic acid (DNA), a nucleic acid consisting of deoxyribonucleotides. This means that DNA is made up of nucleotides containing deoxyribose, a ribose sugar that has a missing oxygen. Each nucleotide contains this sugar, which is bound on one side to a phosphate group and on the other to a nucleoside, which is a ring-shaped compound that contains nitrogen. There are four nucleotides that make up DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). The phosphate groups bond on one side to one nucleotide and on the other side to another nucleotide, forming a backbone that can link millions of nucleotides together.

In protein coding DNA, each set of three nucleotides, also known as a codon, specifies a single amino acid (such as methionine placed by the start codon AUG) or the signal to stop, forming the genetic code. The genetic code represents the sets of three bases that encode hereditary information. The unit of heritable material that codes for a particular polypeptide is a gene. Gene expression is the process by which these genes become observable traits. In this way, the DNA strand is a blueprint that encodes the message of heredity. The precise sequence of nucleotides is what makes one organism a crow and another a tree.

Genetic Code

The genetic code lists 64 codons, which are three-base nucleotides. The codons code for one of 20 amino acids, including AUG, with the exception of the codons UAA, UAG, and UGA.
DNA is double-stranded, meaning the strands' nucleotide bases are joined together by hydrogen bonds. The nucleotide bases bind in specific pairs. Adenine and guanine are called purines, which are double-ring nitrogenous bases, and cytosine and thymine are called pyrimidines, or single-ring nitrogenous bases. Adenine always binds to thymine, and cytosine always bonds to guanine. Each set of nucleotides bonded to its complement is called a base pair, which means each strand contains the complementary base pairs of the other. A complementary strand is a strand of DNA that has nitrogenous bases complementary to another strand. The direction of DNA is highly specific. This direction is determined according to how the phosphate and deoxyribose sugar groups are arranged along the entire length of its backbone. The directionality of DNA results in an antiparallel arrangement of the DNA strands. Antiparallel is a condition of DNA in which one strand reads in one direction (3′ to 5′), while the other reads in the opposite direction (5′ to 3′). The two strands also twist, making a double helix, a pair of DNA or polynucleotide strands that wind around a central axis.

Structure of DNA

When nucleotides, which consist of a nitrogenous base, phosphate group, and deoxyribose sugar, bind together, they form the double-helix structure of DNA. This double helix is comprised of two long nucleotide chains that wind together in a helical pattern. During the formation of DNA, adenine bonds with thymine, and cytosine bonds with guanine.
The double-helical structure of DNA was discovered in the 1950s. Rosalind Franklin was an X-ray crystallographer working at King's College in London. She used X-rays to examine a DNA molecule. The famous Photograph 51 shows the diffraction pattern generated by the examination. James Watson and Francis Crick saw the photograph and realized it showed a double-helix structure. Eventually, Franklin's true role in the discovery was revealed.

Diffraction Pattern of DNA

A DNA X-ray diffraction pattern is obtained by bombarding a sample of DNA with X-rays. Regions of repeating units, such as the nitrogenous bases of the DNA helix, will be displayed as dark patterns on the X-ray film , and the central cross pattern indicates a helical structure.

DNA Replication

DNA replicates in a semiconservative manner to generate two daughter DNA molecules, each of which is composed of one strand of the original molecule and one new strand.
Before a cell can divide, it needs to make a copy of its DNA through the process of DNA replication, which happens during the synthesis phase of the cell cycle. Because the strands of the DNA double helix are complementary, when DNA replicates, it creates two new complementary strands: one from each original strand. During replication, the strand that already exists is called the template DNA strand. To begin DNA replication, an enzyme called DNA helicase unwinds the strands so they are no longer a double helix and then partially separates or unwinds them into two strands (sometimes called "unzipping"). As DNA helicase works its way down the DNA molecule, replication occurs. Since one strand is replicated in the direction it reads and is formed continuously during DNA replication from the 3′ end to the 5′ end (named after the carbon number on the deoxyribose sugar that attaches to the backbone of the DNA strand), it is called the leading strand. One strand must be replicated opposite the direction it reads and be synthesized in short segments during DNA replication, so it is called the lagging strand. The replication fork is the location on a replicating DNA molecule, where the new strands will be produced and the DNA molecule comes together.

DNA Directionality

DNA is replicated in a specific direction. Beginning at the replication fork, the template DNA strand is read in the 3' to 5' direction whereas the new strand is synthesized in the 5' to 3' direction. The resultant new strands of the double helix are antiparallel to each other, with one being 5′ to 3′ and the opposite strand 3′ to 5′.
To begin DNA replication, RNA primase, an enzyme that generates a primer, binds to the replication origin, a sequence of nucleotide bases that signals for the initiation of replication. A primer is a short sequence of RNA that binds to the template to initiate the new strand of DNA. Once the primer has bound, DNA polymerase, an enzyme in DNA replication that assembles the new strands of DNA from the template strands, binds to the site and begins recruiting free nucleotides to bind. DNA polymerase works its way along the template strand, adding new bases as it goes. This specific DNA polymerase is called DNA polymerase III. On the leading strand, it simply moves forward until the strand is finished. On the lagging strand, however, it makes the new strand in short segments of DNA. Each segment is called an Okazaki fragment, which is the short segment of DNA being made on the lagging strand. Once reaching the end of an Okazaki fragment, DNA polymerase, specifically DNA polymerase I, must replace the RNA primer with DNA before the Okazaki fragments are joined via DNA ligase. Once the primer has been removed, the enzyme DNA ligase joins the fragment with the next fragment. When this occurs, DNA polymerase then moves back to the replication fork and begins again. Replication continues until DNA polymerase reaches the telomere, a repeating nucleotide sequence at each end of a chromosome.

DNA Replication

In DNA replication, the parent DNA is unzipped by DNA helicase. RNA primase creates a primer that binds at the replication origin. Starting at the RNA primer, the leading strand is constructed by DNA polymerase III using free nucleotides (dNTPs). On the lagging strand, DNA polymerase I creates Okazaki fragments that are joined together by DNA ligase.
At the end of DNA replication, two new strands are formed, each containing one strand of the original molecule and one newly synthesized strand. This is known as semiconservative replication and was demonstrated in an experiment called the Meselson-Stahl experiment. The semiconservative hypothesis was shown to be true, while the conservative and dispersive hypotheses were shown to be false. The conservative hypothesis suggested that a new molecule was formed from the original molecule without the original being split apart. The dispersive hypothesis suggested that the original molecule was broken into small pieces, each of which attached to the newly formed molecule, creating a chain of alternating new and old strands. By tagging strands with a heavy isotope of nitrogen and then measuring the density of the strands formed after several replication events, Matthew Meselson and Franklin Stahl showed that the semiconservative hypothesis was correct. During DNA replication, it is possible for errors to be introduced. Such errors are called mutations. A mutation is a permanent change in the nucleotide sequence of DNA. Mutations can be detrimental, so the cell employs mechanisms to check for and repair errors. The first of these mechanisms is DNA proofreading, which is performed by certain forms of DNA polymerase. A portion of the enzyme "proofreads" the base that has just been added, to ensure it matches the complementary base on the template strand. If the base is correct, DNA polymerase continues adding bases. If the base is incorrect, DNA polymerase cuts out the incorrect base, backs up, and adds the correct one. However, not all mistakes are caught this way. After replication is completed, other enzymes check the new strands for mismatched bases. They cut out incorrect bases and replace them with correct ones. This process is known as mismatch repair. A third mechanism, called excision repair, cuts the DNA strand at both the 3′ and 5′ ends, removes damaged bases, and replaces them with new ones. The excision repair mechanism is used when the bases are the correct ones but have bonded to each other instead of their complements, an occurrence called a dimer.

DNA Repair

DNA repair may occur as the strand is being synthesized, in proofreading, or it may occur after the new strand is made, in mismatch repair and excision repair.