Ap biology plasmid essay rubric


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Appropriate heading college paper. Ap biology essay rubrics College paper Service clearbiology com. Ap bio evolution essay rubric. Related Post of ap biology essay scoring. Ultimate Social Widgets. Essay sample help - Essay sample help. Ap biology essay rubrics Ap bio essay https www albert io blog mitosis meiosis ap biology crash course Pleasant River Garden Club Ap. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms.

These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes.

Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter — from chemical systems to ecosystems — might be usefully understood as living entities.

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We shall instead address it by describing a spectrum of biological entities that illustrates why no sharp dividing line between living and non-living things is likely to be useful. The more positive goal of these reflections will be to offer a flexible view of life that does in fact make good sense of why particular organizations of matter can be described as living.

In this paper we shall highlight a tension in standard discussions of characteristics of life, which tend to prioritize one or other of two fundamental but very different features of living things: the capacity to form lineages by replication and the capacity to exist as metabolically self-sustaining wholes. We suggest that this tension can best be resolved by seeing life as something that arises only at the intersection of these two features: matter is living when lineages are involved — directly or indirectly — in metabolic processes.


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But also crucial to our argument and, we suggest, to many of the difficulties that have confronted attempts to comprehend life, is the observation that the entities that form lineages are not always, or even usually, the same as those that form metabolic wholes. Metabolism, the transformative biochemical reactions that sustain life processes, we shall argue to be a collaborative affair.

Life, we claim, is typically found at the collaborative intersections of many lineages, and we even suggest that collaboration should be seen as a central characteristic of living matter — a claim that also has implications for how we understand the origins of life. The collaborative nature of living entities and processes is our essential starting point. This focus, however, has had the less salutary consequence of diverting attention from the equally important topic of cooperation and has culminated in the assumption that altruism, understood as the conferral of a benefit by one biological entity on another, is a profound theoretical problem.

Although this is generally seen as a problem pertaining to organisms, a similar argument has notoriously been applied to the topic of genes. Richard Dawkins made famous the idea that genes are fundamentally selfish entities in competition with one another. In this paper we place selfishness in a wider context and emphasize the broader perspective of life as a collaborative enterprise. We are not arguing that interpretations of selfishness are invalid but that, at best, they can only provide a limited perspective on life and evolution.

Rather than reducing cooperation to selfishness, we suggest selfishness and cooperation might better be understood within a framework of collaboration.

AP Biology Lab 6: Molecular Biology

By collaboration, we mean interactions between components of a system that lead to different degrees of stability, maintenance or transformation of that system. As in scientific collaborations, there may be some strongly selfish interests involved in such interactions Hull but these selfish activities can only operate in a collaborative context.

Defecting from collaboration is only possible if collaboration is the general default. In every domain of organismal life, there are extensive sets of organisms that are problematic for standard evolutionary understandings of selfish individuals Roughgarden Evolutionary payoffs for such team members may not be equal, but are distributed across the whole team. Collaboration from this point of view covers a range of interactive processes that may include both cooperative and competitive activities. At one end of this continuum the goals of participants may be completely aligned, while at the other end of the continuum, relationships may be largely or wholly hostile.

One aspect of collaboration is merely interactive combination.


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Thus atoms combine to produce molecules, and the latter have properties that are not found in any of the atoms of which they are composed. But certainly more than this is required to count as collaboration in the sense we are elaborating. In common with most who have considered the question of how living entities are constituted, we assume that there is one necessary condition for being a living thing that most combinations of atoms and molecules lack: the ability to reproduce.

Though we take this to be a necessary condition, it is less obvious that it is sufficient. Living entities have also to be understood in relation to their capacity to sustain themselves through biochemical transformations. Metabolism in our account can be engaged in autonomously this is the usual understanding or collaboratively, through interactions with other biological entities. At any rate, as the microbial and microbe-like entities that we shall describe below illustrate, a very diverse group of things both reproduce and participate in metabolic systems.

Our empirically informed investigation of living matter will not be based on the animal, fungi or plant life that has been the main concern of philosophers and scientists concerned with these issues; nobody questions the status of these as living things, and the problem is only one of deciding which of their characteristics confer the status of living on them.

We shall focus instead on the realm loosely referred to as microbial, which includes some entities only contentiously afforded living status. Viruses are the biological objects that are the pivot of our discussion because many biologists deny that they are living organisms. In fact, they are frequently considered to be test cases for the boundary between life and non-life, organism and non-organism, and biology and chemistry e.

They are most often assigned to the second of each of these pairs of categories. Viruses are often deemed not to be alive on the grounds that they cannot reproduce themselves autonomously, and nor can they metabolize. They can, however, carry out such biologically impressive activities as entering cells, co-opting the transcription and translation machinery of the cell, and picking up and moving about DNA from the organisms with which they interact.

And by exploiting or collaborating with cellular organisms in these ways, they very effectively reproduce themselves and have no need of autonomous metabolism. Thinking about viruses and their relegation to the realms of non-living and non-organismal entities necessitates a consideration of whether organism and living entity are identical categories, and whether a minimal account of life has to begin with cells.

Such thoughts then invite further reflection on other biological entities that seem to have some autonomy but are almost never described as living organisms. We will take our cue from Lederberg and start our examination of life with a discussion of some of the biological entities that inhabit this grey area between living and non-living, specifically prions, plasmids, organelles, endosymbionts and reduced extracellular symbionts.

As we move along this continuum of biological organization to entities whose living status is never questioned micro- and macroorganisms , we will investigate whether these instances of entities possess some of the most frequently cited life-endowing characteristics, such as spatial boundedness, reproduction, metabolism and evolvability, and how our criterion, collaborativity, relates to these characteristics.

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We will also argue that our account of cellular and sub-cellular entities fits very well with origin-of-life scenarios that stress chemical collaboration and community. Our bottom-up perspective, starting at the microscopic level of biology, rather than top-down from its most complex and undisputed exemplars, will suggest that much standard thinking is based on quite restricted and even covertly normative conceptions of what life is.

This perspective will ultimately challenge the view that entities such as viruses are not alive and that the minimal definition of life must be cellular. Prions are very robust and persisting entities, because their conformation makes them highly resistant to inactivation by chemical, heat and irradiation treatments. The central oddity of prions is that they propagate autocatalytically in a protein-only form, without DNA involvement. Although best known as non-Mendelian hereditary elements [5] in diseased sheep, cattle and humans, prions exist in unicellular organisms too. Yeast and other fungal prions share no amino acid sequence similarities with mammal prions, and they function and are transmitted very differently Bousset and Melki ; Uptain and Lindquist ; Weissmann et al.

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Nevertheless, experimental work on yeast prions has provided deep insights into conformational change in proteins and their transmission Wickner et al. The Modern Synthesis does not cope well with prions, and this has led some commentators to propose that a more comprehensive theory of inheritance is needed for prions to be properly understood evolutionarily Jablonka and Lamb ; Chernoff The prion-forming potential of the implicated yeast proteins is evolutionarily conserved, implying that it is adaptive Chernoff et al.

Diverse functions have been identified or proposed for prions in a range of taxa. There is some evidence that prions are associated with epigenetically enabling yeast cells to cope with fluctuating environments, and that they play a role in memory formation in sea slugs Shorter and Lindquist These capabilities and characteristics do not give a ready answer to the question of whether the self-propagational status of prions gives them the status of being alive.

Prions exhibit collaborative behaviors that benefit themselves, as a class of protein isoforms, as well as their hosts. When low amounts of the non-pathogenic isoform are produced, the prion conversion process halts, and when high amounts of the former are produced, it may stimulate spontaneous prion formation in the previously prion-free cell Chernoff et al. Prion propagation in yeast requires the involvement of chaperon proteins.

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Plasmids are small, stably inherited and self-replicating molecules of DNA sometimes RNA that are independent of the chromosomal DNA in bacterial, archaeal and eukaryotic cells. Plasmids are prolific and diverse; they may be larger than some prokaryote genomes del Solar et al. They are then transmitted vertically, from mother to daughter cells. Plasmids have a two-stage life cycle of establishment and proliferation followed by a steady state that matches the cell cycle del Solar and Espinosa Neighbouring plasmid-free cells are often killed by plasmids, and this leads to a very high rate of successful infection Gerdes et al.

Because of their many talents, plasmids have become a mainstay of laboratory genetic manipulation as vectors of gene transfer. Plasmids are often described as selfish in the same way that other genetic elements are because they encode genes that are not essential for the host and may impose fitness costs Kado Importantly, however, they also play more cooperative roles in cells Wegrzyn Plasmids often encode and express genes of a variety of functions apart from those for their own mobility and replication, such as antibiotic resistance, virulence, environmental protection including biofilm formation , DNA repair and supplementary metabolic pathways Barton et al.

They can thus be seen as collaborative elements that enhance the functionality and adaptiveness of their host cells. The fact that these features favour plasmid survival has allowed these phenomena to be interpreted as instances of selfishness Kado , but in our framework they could equally well be interpreted as examples of sometimes mutualistic collaboration.

Organelles are diverse membrane-bound compartments in eukaryote cells. Major organelles include mitochondria and plastids including chloroplasts, the organelles enabling photosynthesis in plants , as well as peroxisomes compartments involved in metabolic activities that include the oxidative metabolism of fatty acids and the breakdown of hydrogen peroxide Golgi complexes and endoplasmic reticula.

Apart from the nucleus, most organelles are primarily involved in energy generation, transport and storage. They are often highly dynamic, mobile structures that react to relevant features of the environment to maintain cell function Cutler and Ehrhardt ; Braun and Schleif ; Collings et al. Organelles reproduce within cells and a complete set is passed on to the daughter cells during cell division. However, because most membranes have to be inherited from pre-existing membranes and are usually not constructed de novo, [8] organelles are templated from pre-existing organelles.

They self-assemble on the basis of the information their membranes carry about membrane polarity, type and location Cavalier-Smith ; Lowe and Barr Two of the most evolutionarily fascinating organelles were once free-living bacteria. Mitochondria and plastids functioned first as intracellular symbionts until most of their DNA migrated to the nucleus of the host over a billion years ago — a process that profoundly shaped the structure and content of the eukaryote genome and cell Timmis et al.

This loss of genetic autonomy is not total, however, because plastids and mitochondria retain genes. They divide and grow independently of the cell cycle, although mitochondria gain some division assistance from the host cell Osteryoung and Nunnari As well as inheriting their membranes directly, both organelles inherit their own organelle-specific DNA. Mitochondria and plastids are not only essential to their cellular hosts, but are defining characteristics of them: there are no eukaryotes without mitochondria or plants without plastids.

Indeed, the eukaryote cell could no more survive without its mitochondrial residents than the latter could survive in natural circumstances outside the cell. Viruses are typically very small packages of single- or double-stranded DNA or RNA [11] often just a few genes , wrapped up in a coating of protein and sometimes an additional lipid envelope. Viruses are generally excluded from organismal status because although they can synthesize some of their own proteins, they do not metabolize or reproduce independently Van Regenmortel They either use their hosts, which probably include every organism past and present, or occasionally work in collaboration with other viruses to make necessary enzymes.

Viruses do not reproduce by division but by self-assembly of the components that they manufacture with the help of the host cell. Some viruses influence host behaviour quite significantly by, for example, conferring either protection against other viruses or virulence properties e. A number of plant viruses move actively from cell to cell, using virus-encoded movement proteins Boevink and Oparka Some viruses have an extra developmental stage in which they remain dormant in the host cell or genome as prophages or proviruses and are inherited Casjens ; Bannert et al.

Endogenous retroviruses, which are viruses that have integrated permanently into the host chromosomes and are inherited vertically, have left their mark on many organismal genomes, including our own Griffiths ; Hamilton Included amongst these viruses are those that are crucial for the development of the placenta in mammals Mallet et al. The diversity and mutability of viruses makes them difficult to classify, although both genome sequence and protein structure analyses are constantly refining viral groupings, which were once based primarily on pathogenic effect Bamford et al. One earlier and another more recent division of life into superkingdoms give viruses a superkingdom domain of their own: the Acytota or Akamara, both of which are categories for acellular organisms possessing genomes Jeffrey ; Hurst ; Weinbauer These domain-level classification schemas have the potential to identify viruses as genuine forms of life but have yet to gain many adherents.

There are three main hypotheses about the origins of viruses: primeval pre-cellular life the virus-first or primordial hypothesis , degenerate intracellular parasites the reduction or regression hypothesis , and as renegade prokaryote genes the escape hypothesis. However, new versions of the primordial. Whatever their origins, viruses have made extraordinary contributions to the evolution of non-viral life through their proclivity for mutation and recombination, and their ability to pick up and move genes from one organism to another transduction and integrate their own and other genetic material into host genomes Weinbauer and Rassoulzadegan ; Lawrence et al.

Moreover, their role as carbon regulators in the global oceans, for example Suttle , shows how a broader conception of collaboration is necessary to understand the evolutionary, biogeochemical and ecosystemic contributions of viruses to all living systems.

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