Basics of Genetics and Evolution - Essay Example

Genetics and Evolution II Q1. Ring Species Ring species is defined by a phenomenon of evolution where two species are apparently present at one place, but these two species are connected by a series of forms, existing in places connected geographically like a ring. The most important feature of ring species is that despite arbitrary similarities, no phenotypic characteristics can be used to divide this ring into two species. This phenomenon is clearly an evolutionary controversy. If phenotypic characters only are taken to be granted for discerning species, there really is no discerning phenotype between these species. This also means there are no clear-cut differentiating phenotypic features between the species of these geographic areas arranged in the form of a ring. Thus in such situations the characters used to recognise the species becomes merely diagnostic, not distinctive. Biologically speaking, these are a connected series of the species in neighbouring areas which interbreed with two end populations which are too phenotypically and geographically separated that they cannot interbreed. These two genetically and phenotypically diverse populations which represent the end populations may exist in the same geographic region, yet due to genetic and phenotypic diversity would not interbreed. As an example, the case of Larus gulls can be taken, the different species of which form a ring around the North Pole. The Lesser Black-beaked Gulls in Siberia form a part of this ring, and although they descend from the same species, adjacent Herring gulls are so different from them that they do not interbreed. Earnst Mayr's Biological species concept tends to recognise species based on defined phenotypic characters. Mayr defined species as groups of interbreeding populations, which do not reproduce across other species. This builds in a concept of reproductive isolation from other such groups. Particular species specific phenotypic characters or attributes prevent interbreeding with other species. Although the biological species concept places the taxonomy of natural species within the concept of population genetics, it fails to explain the ring species. Although there are apparent differences between naturally occurring ring species, the phenotypic distinction within the same or adjacent geographic areas blur, so in actuality, they interbreed. Secondly, the existence of connecting population distinguishes the ring species from two separate species. These features raise questions about the species concept (Liebers et al., 2004). Q2. Neo-Darwinism and Lamarckism The Neo-Darwinism of evolution contends that all life on earth arose from a common ancestor. This was postulated to occur due to random mutations of genes, which survived following the process of natural selection. Where these mutations were beneficial and had survived natural selection, it led to a replicative process leading to more offspring. On the contrary, those with deleterious mutations have fewer or no offspring. Some of these mutations which were beneficial could help new adaptations to altered environments changed or new. These adaptations were incorporated in the genetic traits leading to generation of newer species. It has been postulated that the genetic makeup of the complex organisms is a result of duplication and useful mutation of existing genes of simple organisms. Lamarck's theory of evolution on the other hand posits that when environmental conditions change, an organism goes through the need for changes. With these changes, organs or organ systems may also go through the drives of these changes, which ultimately would need use or disuse of some organs. If used, these organs will develop, and if disused, these organs will demonstrate diminution. In this way a new characteristic or genetic trait is acquired. When acquired traits run in generations, these become hereditary, and the organism demonstrates an evolution. These two theories differ in the concept of causation of mutation. While the neo-Darwinian theory says that natural selection is the initiating process for mutation of the genetic information, according to Lamarck's theory states that natural influences causes change in the genetic information which evolve to be incorporated in the trait, which ultimately become a genetic change induced by the nature. Therefore conceptually, while mutations are naturally selected to become a genetic change in neo-Darwinism, the naturally induced genetic changes are incorporated in the genetic pattern to be known as change hereditary characters which are carried across generations (Aron, 1954). Q3. Molecular Clock The concept of molecular clock states that there is a relatively constant rate of molecular evolution. Although mutations are sudden acute phenomena conceptually, it was assumed in this theory that most genetic changes are effectively neutral, and this may lead to an unexpected constancy in rates of molecular evolution. The concept of molecular clock originates from the observation that interspecies difference in DNA is a function of time since the time of evolutionary separation. This concept is useful in comprehending the past evolutionary events in time. This has also been used for exploring the mechanisms and processes of evolution. In genetic studies, it was discovered that a given protein has a characteristic rate of evolution, but the genes differ in their characteristic rates of evolution. Thus molecular evolution will differ from morphologic evolution. Over the time of evolution, the amino acid differences between species have a linear rate of accumulation. Proteins have a constant molecular evolution across species, with each protein assuming a characteristic rate. Therefore, there is a relative equality in the rate of evolution for any given protein. Morphologic evolution on the contrary there is usually large variations in interspecies rate of change and over evolutionary time. Therefore, it can be stated that majority of the nucleotide substitutions within a gene have been termed to be selectively neutral and for it to be able to be a fixed morphologic evaluation, it is most often a chance phenomenon. Deriving from this concept, most amino acid changes in a protein being neutral effectively, these do not have any effect on the morphology and function of the organism despite the molecular change or evolution. Therefore, the time sequence of the change was not affected by natural selection (Roger and Hug, 2006). Q4. Genome organisation and accumulation of mutation The eukaryotic genome is nothing but a set of linear DNA molecules, which comprise the chromosome. Chromosomes are much shorter than the DNA molecules. Therefore in a genome, there is a highly organised packaging system. The eukaryotic genome possess more genes and additional control mechanisms to regulate the developmental functions of their genome. There are discontinuous coding regions interrupted by stretches of noncoding DNA. Noncoding DNAs are called introns and the coding segments are known as exons. Introns are abundantly present in eukaryotic genomes. Apart from these, there are enhancer regions and promoter regions. Centromere is used during cell division as the attachment points of the spindle fibres. Telomere is the area at the end of the linear chromosomal thread, where DNA sequences are tandemly repeated. The arrangement of the genes and other DNA sequences are stable. During both mitosis and meiosis, there is a reciprocal crossover of homologous chromosomes. These lead to reshuffling of the genetic information leading to new combination of alleles. Mutation leads to capacity for rearranging genetic information, which may occur at random, leading to deleterious mutations. Mutations leading to breakage, translocation of portions of one chromosome to a nonhomologous chromosome, formation of dicentric and accentric chromosomes structurally lead to changes in the molecular levels, which are manifested as changes in the DNA structure. These will include nonreciprocal and nonallelic homologous crossing over and gene conversion, transposition of DNA segments from one genomic locus to another, formation of additional DNA sequences in tandem or in a dispersed form into new genomic locations or amplification, deletion of specific DNA sequences, and nonhomologous recombinations respectively (Syvanen and Taylor, 2004). 5. Five processes of microevolution Minute and small scale changes in allelic frequencies in a population, below the species level is known as microevolution. Several processes contribute to microevolution. These are mutation, natural selection, genetic drift, artificial selection, and gene flow. Mutation is defined by changes in the genetic material or genome of an organism at the level of nucleotide sequences. There are many causes of mutations, most common of which is copying error or by many other environmental or extraneous reasons. These can be induced by the organisms themselves or by cellular processes. Mutations can be transmitted into the descendents. Mutations cause variances in the gene pool. Microevolution can be effected by natural genetic variation within a population where heritable traits pass through successive generations. This is the most important mechanism of evolution. Natural selection is active on the phenotype of the organism. However, for every phenotype there is a genetic basis which tend to flow down the generations, and over generations, this may lead to adaptation which allows to organism to accommodate with the environment ultimately leading to a new species. Artificial selection can be achieved through selective breeding of certain traits leading to improved survival or enhanced reproductive ability ultimately leading to new organisms. Gene flow is transference of alleles of genes from one particular population to another. This usually occurs due to migration of the population leading to addition of new traits to the preexisting gene pool, which may appear in the progeny as new traits. Genetic drift is a process of changing allelic frequencies over time. After certain time, the gene variants may disappear completely leading to reduced genetic variability. It is actually the change in relative frequency with which an allele occurs in a population as a result of random sampling and chance (Hendry and Kinnison, 2001). In the example provided of Chillingham Park of a small herd of white cattle, obviously, there is no genetic drift and gene flow. It is a restricted and small population, so microevolution due to these factors may be ruled out. Since the reproduction is happening within the same population within the same environment, there is no scope for natural selection. However, the specific trait of white cattle is interbred, leading to artificial selection. The role of mutation cannot be overruled, and this may contribute to some changes although occurrences will be less, since over seven centuries, the trait of whiteness may be having identical exchanges, thus mutations are not evident. 6. Restriction endonucleases Two strands of DNA double helix are antiparallel and are complementary to each other. While a gene is the unit of inheritance, it carries the information for polypeptide and also structural RNA molecule. It has a promoter region sequences by a structural gene flanked both upstream and downstream with 5' and 3' regions respectively. Nucleases are enzymes that can break or split nucleic acid chains. When it breaks the frank regions, this is known as exonuclease, however, when it breaks the gene proper, it is known as endonuclease. Restriction endonucleases are specific endonucleases which are capable of recognising specific short sequences of DNA and can cleave the DNA at or near the recognition sequence. These enzymes are isolated from bacteria. These enzymes recognise specific nucleic acid sequences and are able to splice the double stranded RNA. There is a wide variation in recognition sequences. Based on their enzyme cofactor requirements, nature of the target sequence, and the position of the DNA cleavage site, these are classified into three groups, I, II, and III. S-adenosyl methionine acts as the cofactor for this enzyme, and their activities require adenosine triphosphate and magnesium. Type II consists of only one subunit, and their sites of recognition are undivided and 4-8 nucleotide in length. They recognise and break the DNA at the same site. Type III recognises inversely oriented two separate sequences that are nonpalindromic. The spliced segment is usually 20-30 base pairs long following the site of recognition. These are used as manipulation tools of the DNA for scientific applications (Williams, 2003). 7. The Basis of Electrophoresis In biological research, the biomolecules usually occur in mixtures, and they need to be separated for the experiments. Usually in experimental biology, the separation need is small scale, and based on the differences in chemistry, biology, charge, or size of the molecules different separator technologies have been used. Electrophoresis is the method of choice for separation of proteins and nucleic acids. It is widely accepted for its high resolution and sensitivity. This technique involves application of an electric field to a mixture of biological molecules across a chamber of gel. Electrical polarity causes the molecules to migrate through the gel matrix. Based on the size of the molecule in question, separation then takes place across the poles. Evidently, molecules with larger size would have difficulty flowing through the gel. Thus different sized molecules would be separated into bands which would be discretely represented. The smaller molecules would have more mobility, thus molecules of different sizes would create different bands which could be interpreted and recognised. From an individual band, nucleic acids can be purified in this manner. This technique is also applicable for proteins. The proteins are considered to be analogues of repeating units of amino acids. The state of ionization of a protein depends on the chemical environment it is in and the amino acid content. All proteins in basic environment will have a negative charge and during electrophoresis will move towards the positive plate. In an acidic environment, the proteins will have a positive charge and will move towards the negative plate. In this way, with electrophoresis, the proteins may also be separated (Little et al., 2006). 8. Phenylketonuria is an autosomal recessive disorder The classic PKU occurs when mutations on PAH gene allow severely reduced phenylalanine hydroxylase activity leading to pheylketonuria. The genetic analysis suggests that mutations of PAH gene is probably the main cause of PKU. For analysis of the pedigree, the first important information to note is, there must be presence of two defective alleles that produces an affected phenotype. These conditions in general have four different characteristics. On the average 25% of the offspring from a mating between two unaffected heterozygotes will be affected with the disease. Among the offspring, 25% will be affected, 50% will be unaffected carriers, and 25% will be unaffected noncarriers. Vertical transmission of the trait will be characteristic of the pedigree, meaning the phenotype will manifest itself in siblings. Males and females are equally affected. Both parents must carry the defective allele. Autosomal recessive inheritance means the mutated gene is located on one of the autosomes and hence males and females are equally affected. Recessive also means that both copies of genes must have a mutation in order for the person to have a trait, with one copy inherited from father and the other from the mother. It is evident from the analysis that individual 3 who has a disease has a recessive faulty gene copy located on an autosome. Conditions with autosomal recessive pattern of inheritance usually affect men and women equally. In this analysis, however, both the parents are unaffected carriers of the autosomal faulty gene for PKU. Thus there is 25% chance in every pregnancy of having the inheritance pattern of PKU. Here individual 3 is already affected. The HPLC genotype suggests the individual 6 to have the trait, but it is not manifested, and hence she would not be affected and will be a heterozygote carrier. (Okano and Isshiki, 1995). 9. Practical Class: pGLO-GFP expression vector transformation reaction The pGLO plasmid that contains the GFP gene also contains the gene for beta-lactamase that causes resistance to the antibiotic ampicillin. The beta lactamase is produces and secreted by bacteria containing the plasmid. Beta-lactamase will inactivate ampicillin since this is a beta-lactam ring containing antibiotic. Therefore beta-lactamase would inactivate ampicillin present in the LB nutrient agar allowing bacterial growth, and only the plasmid containing transformed bacteria will be able to survive on plates containing ampicillin. In this experiment, the bacterial transformation with a gene that codes GFP is studied. Following transformation, the bacteria express the newly acquired glowing gene from GFP to produce fluorescent green colour under ultraviolet light. Bacteria naturally contain circular pieces of DNA called plasmids, which usually contains genes for traits that may help their survival. In this question the plasmid confers bacterial resistance to ampicillin antibiotic. The pGLO plasmid in this experiment contains gene for GFP and the gene for resistance to antibiotic ampicillin. pGLO also has a special gene regulation system controlling expression of fluorescence in the transformed cells. The gene for GFP can be switched on in transformed cells by adding arabinose to the nutrient medium. Selection for cells transformed with pGLO DNA is accomplished by growth in antibiotic plates. Transformed cells on plates not containing arabinose will appear white. When arabinose is included in the nutrient agar, the transformed cells will appear fluorescent green. Thus a will appear white, b will show growth of the bacteria, and c will demonstrate fluorescence. 10. Phage Lysis Diagram of agarose gel with undigested and digested separation of DNA The viral DNA is linear, double-stranded molecule of 48,502 base pairs (bp) [48.5 Kbp] with a molecular weight of about 3 x 107 and codes for approximately 50 different phage proteins. The first 12 bases at both 5' ends are single stranded and can be hybridized to each other to form circular molecules. The DNA of phage lambda may be divided into three regions. The left-hand region includes all the genes (A-J) whose products are necessary to produce phage head and tail proteins and to package the DNA into the virus. The remaining portion of the viral genome includes the major control region for transcription and replication as well as the genes for cell lysis. Predictions With X 20130; 28372; 8242 With Y 5600, 5252, 37650, 43250 With X and Y 5600, 42902, 5000, 22772, 20130 Reference List Aron, J, (1954). The Problem of Evolution. Diogenes; 2: 90 - 103. Hendry, AP and Kinnison, MT., (2001). An introduction to microevolution: rate, pattern, process. Genetica; 112-113: 1-8 Liebers, D., de Knijff, P., and Helbig, AJ., (2004). The herring gull complex is not a ring species. Proc R Soc B; 271: 893 - 901. Little, MJ., Paquette, DM., and Roos, PK., (2006). Electrophoresis of pharmaceutical proteins: status quo. Electrophoresis; 27(12): 2477-85. Okano, Y and Isshiki, G., (1995). Newborn mass screening and molecular genetics of phenylketonuria in east Asia. Southeast Asian J Trop Med Public Health; 26 Suppl 1: 123-9. Roger, AJ and Hug, LA., (2006). The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Phil Trans R Soc B; 361: 1039 - 1054. Syvanen, AC and Taylor, GR., (2004). Approaches for analyzing human mutations and nucleotide sequence variation: a report from the Seventh International Mutation Detection meeting, 2003. Hum Mutat; 23(5): 401-5. Williams, RJ., (2003). Restriction endonucleases: classification, properties, and applications. Mol Biotechnol; 23(3): 225-43. Read More