Prokaryotes and eukaryotes' DNA analysis

A gene is a piece of genetic material that is fixedly located on a chromosome. Direct synthesis from proteins is how genes produce their effects. A gene is a functional unit that is inherited that is created by nucleotide sequences in DNA or RNA. Genes control the expression and transmission of features by defining the structure of particular polypeptides (Lawrence, 2002). They are made up of non-coding introns that alternate with promoter regions. Prokaryotes are unicellular organisms' cells that lack membrane-bound organelles like mitochondria and nuclei. The cell wall constituents involved determine how these cells divide. A unicellular or multi-cellular organism with membrane-enclosed organelles are referred to as eukaryotes and contains parts like Golgi apparatus, nucleus, mitochondria and chloroplast in animals.

Eukaryotic cells mainly occur under the four kingdoms: Kingdom Plantae, Kingdom Protoctista, Kingdom Animalia, Kingdom Fungi and Kingdom Animalia. Genes of an organism genome vary from species to species with a human genome containing about 20,000 to 25,000 genes. They are composed of deoxyribonucleic acid (DNA) except for some viruses that have closely related compounds that are known as ribonucleic acid (RNA). A DNA is a structural molecule composed of chains of two strands of nucleotides which makes them look like a twisted ladder with the sides of the ladder made up of sugars and phosphates. In this research paper, we are going to discuss organizational arrangements of genes on the chromosome of prokaryotic and eukaryotic cells including mechanism of DNA repair.

Organizational arrangement of genes on a chromosome in prokaryotic and eukaryotic cells

The genetical material found in the prokaryotes and the eukaryotes is the DNA. Protein coding is associated with DNA sequencing and identification of toxins in higher organisms. Beta goblin genes minimally found in protein-coding have a variable comparison with other vertebrae DNA is little. Gene regulation between the eukaryote and prokaryotes differs in many unique ways that affect the arrangement chromosomes in these two types of cells. Genes can be characterized differently in a bacteria because they get activated or deactivated. Bacteria are composed of three genes types: structural, operator and regulator (Gilbert, 2002). Structural genes coding is necessary for the synthesis of various polypeptides. Operator genes codes are associated with DNA message transcription from one or more genes into mRNA. Therefore, these genes are connected to an operator gene to form a function unit called operon. Operon activity controlling by a regulator gene, through transcription produces tiny molecules referred to as repressor which binds to operator leading to formation or synthesis of proteins.

Eukaryotic genes have no operons, and therefore their regulation is usually independent. Thus, expression of genes in eukaryotes has a vast difference compared to that of prokaryotes though they undergo the same processes. Typically eukaryotic genome is usually larger and multicellular compared to that of the bacterium. Limitation of gene expression occurs in eukaryotic cells due to cell specialization on various cells. Eukaryotic DNA contains large combined amounts of proteins whereby during the interphase the chromatin fibers get highly extended. This extension can be up to 6cm or more. The DNA packing in eukaryotic cells is at levels with the first level with histone proteins which have positively charged amino acids bound to the negatively charged RNA. The specific types of histones are similar from one eukaryote to the other with this presentation even in the bacteria. In the level two of DNA packing, chromosomes get beaded like string coils of about 30-mm chromatin fibers as the process of mitosis is enhanced. Level three shows formed strands of looped domains that are attached to non-histone proteins (Gilbert, 2002). The fourth level shows looped fields that are coiled and folded producing metaphase chromosomes. Interphase chromatin is less condensed than the chromosome of mitosis with about 30-mm fibers, but the looped domains are always intact.

In eukaryotic cells, DNA does not code any protein nor does RNA. The non-coding parts made of regulatory sequences have introns and repetitive DNA which has many copies of this genome. Genetically inherited disorders are associated with the length of the nucleotide which is abnormally elongated leading to some adverse effects on the gene. Fragile X syndrome results from hundreds to thousands of repeated CGG in the fragile X gene. Huntington’s disease occurs from repeated CAG with translated proteins alongside glutamines. Gene families of eukaryotic cells have a single copy of haploid chromosomes, with multi-gene families presenting with identical and similar genes.

In the organization of genes in prokaryotes, small, circular DNA strands are seen presenting in a nucleoid region. The replication in this cell type has a specific single origin of replication. The sizes of the genomes vary with the presence of gene intensity. Almost the whole part of the genome comprising of all genes are polycistronic with multiple transcribed genes through the same cell promoter. Polymerase binding of RNA, (TATAAT sequence at -10bp) involves a regulatory sequence in the promoter part. The recognition part is usually at TIGACA sequence at -35bp. Some characteristic influences from the repressor and activator help in the gene regulation of prokaryotic cells.

In the cytoplasm of these cells is where transcription coupled translation occurs with a single strand of RNA involved in the transcription. N- Formylmethionine happens to be the initiator of t-RNA. Escherichia coli is an example of a prokaryotic cell which has a primary terminal for chromosomal replication. The replication initiation is at the beginning of each cycle leading to the formation of a DNA gene. The distribution of genes between these chromosomes is as per the function of genes, arrangement of genes in the chromosome and non-random chromosome positioning.

Regulation of prokaryote operon

The operon is gene regulators found in bacteria and some of the viruses where gene coding is functionally related to proteins alongside the DNA. Protein synthesis is controlled and coordinated in response to cells needs by the use of an operon. An operon provides the means for a cell to produce proteins only and where they are needed. Conservation of energy is operon related with continuous effects on the DNA. Bacteria arrangement into operons is coregulated with genes. The operon is closely associated to the genome with a physically close characteristic which binds them together. Escherichia coli is an example bacteria operon which involves metabolized enzyme lactose and tryptophan biosynthesis involved in its cell regulation. Lactose operon shares some aspects with other operons which get regulated in a way that they can metabolize lactose. Lactose operon has three genes that encode proteins involved in lactose metabolism. The three genes are, “lactose z, lactose y and lactose a.” All these genes are of importance since they import lactose into cells and break it down for use as a source of food. The genes of lactose operon lie alongside the contiguous stretch of DNA with their expression easily coregulated.

Structural genes of lactose operon have other sequences that join bacterial expression to the machinery. Operon genes have promoter which serves as a recognition site for the transcriptional machinery of the RNA polymerase complex site. Every operon acts as a single messenger RNA which is changed into individual protein gene products. Operator, a unique DNA, is also involved in lactose operon which helps in repression of the whole piece of operon which makes binding in this case very possible. Lactose-metabolizing genes can be turned on and off depending on the efficient way of the genes to adapt to the environment. Terminator regulator is involved which provides information of transcriptional machinery to terminate the available gene transcription. The promoter, in this case, acts as a start spot while terminator serves as a stopping point making the operator to know which transcription will take place.

Operation of eukaryotic signal in transduction pathway

In the cell, messages are relayed from the inside beginning with the cell receptor membrane. Intracellular receptors are involved in this process whereby they bind to the ligands which are inside the cell and directly activates the genes. Cells are highly responsible for specific chemicals released to the environment. Examples of these substances are hormones which signal the cell to respond to many changes occurring in the background. Signal-transduction cascade acts as a mediator that sends and produces stimuli (Jacob and Monod 1962, p.193).Gene expression or gene activity including enzyme detection get regulated by these molecular circuits where they are involved in detection, amplification, and integration of external signal leading to response generation. The transduction pathways association with molecular channels is used in sending messages perceived as stimuli.

Membrane receptor is a molecular circuit that transfers messages from the interior of a cell to the surrounding with a few of non-polar signals such as estrogen used. Other hormones such as steroids can enter the cell membrane where they gain access to the cell interior. When the molecules get inside the cell, they directly bind to the DNA leading to gene transcription. Gene expression follows it. A site on the extracellular domain binds and recognizes the molecule signaling often known to as a ligand. This type of binding sites is responsible for enzyme activation except where a catalyst initiation is required. If the ligand and the receptor interact, the tertiary structure of the receptor alters including the intracellular cell domain. Information may also be relayed by use of multiple receptors which are ligand-dependent (Albert, Johnson and Lewis, 2002). When the concentration of the small molecules changes, the second messenger is produced which initiates the second process of molecular information transmission. The second messenger often diffuses to extended parts of the cell such as the nucleus, influencing gene expression and other processes dependent on it. Enzymes and other membranes are activated in the second messenger with each activated macromolecules leading to the generation of many different second messengers within the cell. Second messengers are i8nvolved in potential problems of the cell due to multiple pathways signals.

Main mechanism of DNA repair

The primary DNA repair mechanisms include; the base excision, nucleotide excision, and mismatch repair. Deamination or alkylation processes recognize bases in the DNA. The method and phase of damage of the base are referred to as “abasic site” or “AP site.” Escherichia coli can detect AP site and removes it bases through its DNA glycosylase. From the adjacent nucleotides, “AP endonuclease” removes the “AP site.” The left gaps are filled with DNA polymerase I and ligase. In the nucleotide excision, Escherichia coli has proteins such as “UvrA, UvrB, and UrvC.”These proteins are involved in the removal of damaged nucleotides such as the dimer that is induced by the UV lights. The left gap gets filled by DNA polymerase I and DNA ligase. The mismatch repair is involved with the bases that are directly mismatched, but the system comes with a way to fix them. Special methylase called the “Dam methylase,” are found in Escherichia coli which helps in mismatch repair. After replication of the DNA, methylated strands production occurs. The repairing process is involved with protein Muts used as a match of the mismatched bases repairs. The MutL is made complicated and activates MutH that binds to GATC sequences (Berg, Tymoczko & Stryer, 2002). The unmethylated strands at GATC site cleave the activation of MutH. The space created at GATC sites is ample as long as 1,000 base repairs are mismatched. Therefore, the mismatch is very expensive and inefficient. Mismatched E.coli are similar to eukaryotes, and the replacement is usually the same in the two. But in eukaryotes templates, strands are no well distinguished.

Conclusion

Living things are divided into either prokaryotes or eukaryotes. Gene transcription controls these cells hence they possess DNA structures. The critical difference between these two types of cells is that prokaryotes lack membrane-bound organelles including the nucleus while eukaryotes consist of cell-bound organelles with membranes with nucleus included. It is essential to understand the organization of chromosomes in prokaryotic and eukaryotic cells. Eukaryotic proteins attachment to the DNA is by use of chromatin with its located in the cell nucleus. The proteins involved are the histone proteins with other critical chromosomal proteins of non-histone type. In prokaryotes, cell regulation is usually by use of operons that contain repressor and regulator genes. Signal-transduction pathways are responsible for chemical production that enables the cells to adapt to various stimulus.



















References

Albert, B, Johnson. A & Lewis J, et al. 2002. Molecular Biology of the Cell. 6th edition. New York: Garland Science. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21054/.

Berg, J.M, Tymoczko J.L and Stryer, L. 2002. Biochemistry. 5th edition. New York: W h Freeman. Chapter 15. Signal-Transduction Pathways: An introduction to Information Metabolism. Available from: http://ww.ncbi.nlm.nih.gov/books/NBK21205/.

Gilbert S.F, 2002. Developmental Biology. 6th edition. Sunderland (MA): Sinauer Associates. Available from: https://www.ncbi.nlm.nih.gov/books/NBK9983/.

Jacob, F. & Monod, J, 1962. On the regulation of gene activity.Cold Spring Harbor Symposia on Quantitative Biology, (26), pp. 193-211.

Lawrence J. G, 2002. Shared strategies for gene organization among prokaryotes and eukaryotes. Cell, (110), pp. 407-413.