CHAPTER 2

What determines the fundamental characteristics of different species? (i.e., what causes variation between species)

A species is unique because of the unique set of genes and gene forms that it owns. Many genes may be shared by other species but the total collection and form they take is species-specific

What determines variation within species?

Different forms (alleles) exist for the different genes. Individuals that make up a species have their own specific set of alleles. The set of alleles that an individual possesses is referred to as its genotype. These alleles individually represent messages for specific proteins that generate expressible traits (phenotypes) in organisms.

DNA

DNA is generally the genetic material. The complete set of DNA possessed by an individual represents the individuals genome. Eukaryotes contain most of their DNA in the form of chromosomes found in their nuclei, but they also contain DNA in mitochondria and chloroplasts (plants). Plasmids and viruses also possess their own genomes that may reside in either eukaryotic or prokaryotic host cells.

The structure of DNA was established by Watson and Crick in 1953. It consists of nucleotide monomers bound together into long polymers. Nucleotides consist of a five carbon sugar (deoxyribose), a phosphate and a nitrogenous base. Four different bases are in DNA: Adenine (A), Guanine (G), Cytosine (C), and Thymine (T). The first two are purines, the latter two are pyrimidines. Uracil (U) replaces Thymine in RNA and is a pyrimidine also. A note for memory: CUT PY--C,U,T are pyrimidines. Examine Fig 2-3 and note the size differences between purines (double ring) and pyrimidines (single rings).

Each carbon in the sugar has a reference number, the 5' carbon is where the phosphate attaches and the 1' carbon is where the nitrogenous base attaches. A sugar phosphate backbone is generated by phosphodiester bonds forming between the phosphate of one nucleotide and the 3' carbon belonging to the sugar of an adjacent nucleotide.

Most typically a DNA molecule consists of two sugar phosphate backbones bound to each other due to hydrogen bonds between nitrogenous bases on each backbone. These bonds will form between A and T, as well as C and G. Note it is always a purine complementary with a pyrimidine. Also there are positions for 3 hydrogen bonds between C and G, but only two between A and T. The two sugar phosphate backbones assume an antiparallel orientation. Fig 2-5.

The stable geometry of the DNA molecule is that of a double helix. Fig.2-3. This helix is right handed with major (wide) and minor (narrow) grooves. These grooves differ in size because the ring structures of the nitrogenous bases lie in a plane parallel to the ground if the sugar phosphate backbones are vertical. Since the bases come off carbon 1' at an angle not equal to 90 degrees the one side will be wider than the other side. Fig. 2-4,5

A gene is a region of DNA capable of being transcribed to produce a functional RNA molecule at the correct time and in the correct place. Therefore, a regulatory region must be associated with each gene allowing it to be activated. This region must receive and respond to signals from the rest of the genome or the environment. At the other end of the gene there must be a termination signal.

Most eukaryotic genes contain introns that must be excised from the RNA prior to rejoining the exons and forming a functional message. Fig. 2-6. The average number of exons seems related to the how recently taxa have appeared in the evolutionary record. Despite this, the average length of RNA translated for genes remains relatively constant across taxa. Therefore, introns make up a higher percentage of the gene length in these recently diverged eukaryotes. Figs. 2.7, and Table 2.1.

Introns are very uncommon in prokaryotic organisms.

The genome size seems to be correlated with the complexity of the taxonomic group. Fig. 2.10.

Genome types:

Plasmid: typically circularized DNA found in bacteria, apart from the primary bacterial DNA. Usually have genes and an origin for replication. Multiple copies per cell is common.

Organellar: DNA in mitochondria and chloroplasts. Several copies are typical per organelle. DNA is usually in a circular configuration.

Virus: a protein coat surrounds the genomic core. The genome can consist of single or double stranded RNA or DNA depending on viral type.

Prokaryotic: Usually a single, closed, circular DNA. Functionally related genes are often adjacent to each other forming groups called operons that are turned on or off simultaneously. The DNA is concentrated in the nucleiod, which is not membrane bound. Non-histone proteins are associated with the DNA for packing it.

In all of the above genes are found close together with little intergenic space.

Eukaryotic Nuclear: One continuous double stranded DNA molecule together with associated histone and non-histone proteins forms an individual chromosome. A single set of all the different types of chromosomes in an organism is referred to as the haploid genome. Species typically have a specific number of sets of chromosomes (their ploidy). Those with one set are haploid, two diploid, three triploid, etc.

Diploid organisms have two of each kind of chromosomes or a set of homologous pairs of chromosomes. Homologous chromosomes are the same size and have the same genes in the same relative positions. They may have different alleles for these genes.

A karyotype is a picture of all of the chromosomes of an organism arranged in homologous pairs according to decreasing size. These arrangements are facilitated by the location of the centromeres of the chromosomes. The centromere is a contracted region of the chromosome necessary for attachment of microtubules during Mitosis and Meiosis. Chromosomes can be classified as: telocentric, acrocentric, submetacentric, and metacentric based on the position of the centromere and consequently the length of its arms. Chromosome ends are referred to as telomeres.

Bands may appear when Chromosomes are stained following chemical treatment. Depending on the procedure these bands may reflect regions of high compaction (heterochromatin) or low compaction (euchromatin). Other staining techniques generate region specific bands useful for analyzing karyotypes (G, Q, and R bands) Fig. 2-17.  Prior to the development of these staining technologies bands were only visible in the specialized polytene chromosomes of taxa such as Drosophila.

Two other physical landmarks that exist are nucleolar organizing regions (NOR) and chromomeres. The NOR is the portion of the DNA where the message for rRNA resides and ribosomes are assembled in the surrounding volume Fig 2-16.  Chromomeres are beadlike thickenings that appear along the DNA early during nuclear division.

In eukaryotes, DNA has associated with it histone proteins that organize it into nucleosomes. Nucleosomes are octamers of 4 types of histones (H2A, H2B, H3, and H4). DNA wraps around this octamer 2 times (like thread on a spool) producing the nucleosome that is 10nm in diameter. The length of DNA that wraps about this core is 146bp long. Attached to the each end of the DNA entering and leaving the nucleosome is an additional type of histone H1. Effectively the core histones, and H1 make the nucleosome approximately 200bp long. H3 and H4 are extremely conserved over all eukaryotes, but H2A and H2B are more variable across species. H1 is the most variable across species, but also across tissues within individuals. The histones then assume a higher order structure in which 6 of them form spirals in a series of spirals called a solenoid. Each solenoid has a diameter of 30nm. Fig. 2-19. During interphase chromatin apparently takes this solenoid form. The solenoids then become organized into loops that have attachment points on a nonhistone protein (primarily topoisomerase II) that is referred to as the scaffold. This assemblage has a diameter of approximately 700nm which is the diameter of the chromosomes during nuclear division. Figs 2-22, 2-24, 2-25, 2-26.