Supplemental Reading for Bio220 Module 1 PDF

Life Requires the transfer and Transformation of energy and matter moving, growing, reproducing, and the various cellular activities of life are work, and work requires energy. The input of energy, primarily from the sun, and the transformation of energy from one form to another make life possible P...

Life Requires the transfer and Transformation of energy and matter moving, growing, reproducing, and the various cellular activities of life are work, and work requires energy. The input of energy, primarily from the sun, and the transformation of energy from one form to another make life possible Producers: photosynthetic organisms Consumers: organisms that feed on other organisms. Decomposers: break down waste products and the bodies of dead organisms (fungi, bacteria). From Molecules to Ecosystems interactions are important in Biological systems. At any level of the biological hierarchy, interactions between the components of the system ensure smooth integration of all the parts, they function as a whole. Molecules; interactions within organisms: at lower levels of organization, the interaction between components that make up living organisms-organs, tissues, cells, and molecules-are crucial to their smooth operation. The key is the ability of many biological processes to self-regulate by a mechanism called feedback. In feedback regulation, the output or product of a process regulates that very process Ecosystems: An organism’s interactions with other organisms and the physical environment At the ecosystem level, every organism interacts with other organisms. Interactions between organisms include those that are mutually beneEcial, and those in which one species beneEts and the other is harmed. In some interactions between species, both are harmed. Interactions among organisms help regulate the functioning of the ecosystem as a whole. Each organism also interacts continuously with physical factors in its environment. We humans interact with our environment. Our interactions sometimes have dire consequences; global warming is a major aspect of climate change Evolution accounts for the unity and diversity of life. A process of biological change in which species accumulate diJerences from their ancestors as they adapt to diJerent environments over time. The human Genome Project Upon sequencing the genome of any species, scientists can study whole sets of genes and their interactions, an approach called genomics Bioinformatics, the application of computational methods to store and analyze biological data. Reference genome, a full sequence that best represents the genome of a species. The whole-genome shotgun approach; starts with the cloning and sequencing of DNA fragments from randomly cut DNA, computer programs assemble the resulting very large number of overlapping short sequences into a single continuous sequence Metagenomics; in which DNA from an entire community of species is collected from an environmental sample and sequenced Understanding Genes and Gene Expression at the systems level. The tools of bioinformatics allow the study of whole sets of genes and their interactions, as well as the comparison of genomes from diJerent species. Genomics is a rich source of new insights into fundamental questions about genome organization, regulation of gene expression, embryonic development, and evolution Duplication, rearrangement, and mutation of DNA contribute to genome evolution - Errors in cell division can lead to extra copies of all or part of entire chromosome set, which may then diverge if one set accumulates sequence changes. Polyploidy occurs more often among plants than animals and contributes to speciation. - The chromosomal organization of genomes can be compared among species, providing information about evolutionary relationships. Within a given species, rearrangements of chromosomes are thought to contribute to the emergence of new species. - Rearrangement of exons within and between genes during evolution has led to genes containing multiple copies of similar exons and/or several diJerent exons derived from other genes. - Movement of transposable elements or recombination between copies of the same element can generate new sequence combinations that are beneEcial to the organism. These may alter the functions of genes or their patterns of expression and regulation. - Comparison of genomes from widely divergent and closely related species provide valuable information about ancients and more recent evolutionary history, respectively. ArtiMcial Selection, Natural Selection, and Adaptation; Darwin, Erst discussed familiar examples of selective breeding of domestic plants and animals. Humans have modiEed other species over many generations by selecting and breeding individuals that possess desired traits, a process called artiEcial selection. Darwin then argued that a similar process occurs in nature. He based his argument on two observations, from which he drew two inferences; - observation 1: Members of a population often vary in their inherited traits. - Observation 2: All species can produce more oJspring than their environment can support, and of these oJspring fail to survive and reproduce. - Inference1: individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more oJspring than do other individuals. - Inference 2: this unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations. Key Features of Natural Selection: - Natural selection is a process in which individuals that have certain heritable traits survive and reproduce at a higher rate than do other individuals because of those traits. - Over time, natural selection can increase the frequency of adaptations that are favorable in a given environment. - If an environment changes, or if individuals move to a new environment, natural selection may result in adaptation to these new conditions, sometimes giving rise to new species. One important point; is that although natural selection occurs through interactions between individual organisms and their environment, individuals do not evolve. Rather, it is the population that evolves over time. A second point is that natural selection can amplify or diminish only those heritable traits that diJer among the individuals in a population. Thus, even if a trait is heritable, if all the individuals in a population are genetically identical for that trait, evolution by natural selection cannot occur. Third point, environmental factors vary from place to place and over time. A trait that is favorable in one place or time may be useless-or even detrimental- in other places or times. Natural selection is always operating, but which traits are favored depends on the context in which a species lives and mates. Direct observation of evolutionary change: - example of the Soapberry bug in southern Florida feeds on the seeds of a native plant, the balloon vine, when the plant becomes rare, the bugs feed on the seeds of the golden rain tree (introduce from Asia) - The evolution of drug-resistant bacteria; methicillin-resistant S. Aureus (MRSA) resistant to multiple antibiotics and highly contagious, this strain can cause lethal infections of the skin, lungs, and blood. - Homology; is the similarity resulting from common ancestry; example the genetic code, shared by all species because they date to the deep ancestral past. Also consider the tetrapods, the vertebrate group that consists of amphibians, mammals, and reptiles. Like all vertebrates, tetrapods have a backbone. But unlike other vertebrates, tetrapods also have limbs with digits. - The fossil record; the fossil record documents the pattern of evolution, showing that past organisms diJered from present-day organisms and that many species have become extinct. Fossils also show the evolutionary changes that have occurred in various groups of organisms. The Evolution of Populations; Sources of Genetic Variation It originates when mutation (new alleles can arise by mutation), gene duplication, or other processes produce new alleles and new genes. Genetic variants can be produced rapidly in organisms with short generation times. Sexual reproduction can also result in genetic variation as existing genes are arranged in new ways. The Hardy-Weinberg equation can be used to test whether a population is evolving; The presence of genetic variation in a population does not guarantee that the population will evolve. For evolution to occur, one or more factors must be at work. One way to assess whether natural selection or other factors are causing evolution at a particular locus is to determine what the genetic makeup of a population would be if it were not evolving at that locus. We can then compare that with the data we actually observed for the population. No diJerence suggests not evolving, if there are diJerences this suggests that the population is evolving. Conditions for Hardy-Weinberg equilibrium; 1) no mutations 2) random mating 3) no natural selection 4) extremely large population size 5) no gene ^ow. Natural selection, genetic drift, and gene Wow can alter allele frequencies in a population; A deviation from any of these conditions is a potential cause of evolution - New mutations can alter allele frequencies, but because mutations are rare, the change from one generation to the next is likely to be very small. - Nonrandom mating can aJect the frequencies homozygous and heterozygous genotypes but by itself has no eJect on allele frequencies in the gene pool - Chance events can also cause allele frequencies to ^uctuate unpredictably from one generation to the next, especially in small populations, a process called genetic drift. Certain circumstances can result in genetic drift having a signiEcant impact on a population. Two examples are the founder eXect (a few individuals become isolated from a larger population). And the bottleneck eXect (A sudden change in the environment, such as Ere or ^ood, may drastically reduce the size of a population) - Allele frequencies can also change by gene Wow, the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes. Natural selection is the only mechanism that consistently causes adaptive evolution.