BIO 102 WK 3 SLP: Various Types Of Living Organisms
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Module 3 - Background
PRINCIPLES OF TAXONOMY
Required Material
Characteristics of organisms in the 6 major kingdoms:
DiVenere, Vic (2011) The Diversity of Life. Accessed February 25, 2014
Principles of taxonomy and classification:
Dirnberger, Joseph (n.d.) Phylogeny and Systematics. Accessed February 25, 2014
Variety of plant life forms:
Farabee, MJ (2004) Biological Diversity Nonvascular Plants and Nonseed Vascular Plants. Accessed February 25, 2014
Variety of animal life forms:
Farabee, MJ (2004) Biological Diversity : Animals I. Accessed February 25, 2014
Types of vertebrates and their organ systems:
Kimball, John (2011) The Vertebrates. Accessed February 25, 2014
Guralnick R, Collins A, Waggoner B, Speer B, Whitney C, Smith D. UCMP Exhibit Hall, University of California Museum of Paleontology, UC Berkeley. Accessed on February 20, 2014
SLP
Urakawa, H., Garcia, Juan C., Barreto, Patricia D., Molina, Gabriela A., Barreto, Jose C. (2012). A sensitive crude oil bioassay indicates that oil spills potentially induce a change of major nitrifying prokaryotes from the Archaea to the Bacteria. Environmental Pollution. 164:42-45
Guralnick R, Collins A, Waggoner B, Speer B, Whitney C, Smith D. UCMP Exhibit Hall, University of California Museum of Paleonto
Module 3 - SLP
PRINCIPLES OF TAXONOMY
Overview
As you have learned in Modules 1 and 2, prokaryotes share many common features that differentiate them from eukaryotes, such as:
Lack of nuclear membrane, unicellularity, division by binary-fission and generally small size.
As introduced on the Home page of Module 3, various species differ and can be classified into taxonomic groups based on several characteristics. One characteristic commonly used to differentiate an organism as belonging to one species or another is the potential for the individuals to reproduce sexually and produce viable offspring. However, this characteristic cannot be applied to prokaryotes, and so their identification and classification is often determined based on:
Phylogeny: All bacteria stem from a common ancestor and diversified since, consequently possess different levels of evolutionary relatedness
Metabolism: Different bacteria may have different metabolic abilities
Environment: Different bacteria thrive in different environments, such as high/low temperature and salt
Morphology: There are many structural differences between bacteria, such as cell shape, Gram stain (number of lipid bilayers) or bilayer composition
Pathogenicity: Some bacteria are pathogenic to plants or animals
All microbial metabolisms can be arranged according to three principles:
1. How the organism obtains carbon for synthesizing cell mass:
autotrophic – carbon is obtained from carbon dioxide (CO2)
heterotrophic – carbon is obtained from organic compounds
mixotrophic – carbon is obtained from both organic compounds and by fixing carbon dioxide
2. How the organism obtains reducing equivalents used either in energy conservation or in biosynthetic reactions:
lithotrophic– reducing equivalents are obtained from inorganic compounds
organotrophic – reducing equivalents are obtained from organic compounds
3. How the organism obtains energy for living and growing:
chemotrophic – energy is obtained from external chemical compounds
phototrophic – energy is obtained from light
In practice, these terms are almost freely combined. Typical examples are as follows:
chemolithoautotrophs obtain energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide. ie: Nitrifying bacteria
photolithoautotrophs obtain energy from light and carbon from the fixation of carbon dioxide, using reducing equivalents from inorganic compounds.
For example: Cyanobacteria are photosynthetic autotrophs. Cyanobacteria split water, H2O, molecules and use the electrons to reduce carbon in photosynthesis. Water is the electron donor. However, Chlorobiaceae and Chromatiaceae are also photosynthetic autotrophs, but they use hydrogen sulfide H2S as the electron donor, orreducing equivalent donor.
chemolithoheterotrophs obtain energy from the oxidation of inorganic compounds, but cannot fix carbon dioxide (CO2).
chemoorganoheterotrophs obtain energy, carbon, and reducing equivalents for biosynthetic reactions by breaking apart organic compounds (made by photoautotrophs). Examples: most bacteria, e. g.Escherichia coli, Bacillus spp., Actinobacteria
photoorganoheterotrophs obtain energy from light, carbon and reducing equivalents for biosynthetic reactions from organic compounds. Some species are strictly heterotrophic, many others can also fix carbon dioxide and are mixotrophic. Examples:Rhodobacter, Rhodopseudomonas,Rhodospirillum, Rhodomicrobium, Rhodocyclus,Heliobacterium, Chloroflexus (alternatively to photolithoautotrophy with hydrogen)
For this SLP assignment, you will continue to analyze the paper by Urakawa et al. (2012) by considering the characteristics that allow us to classify the prokaryotic organisms in this study as belonging to different Domains. You will use the website
UC Berkeley's virtual exhibit hall and resource on taxonomy and phylogeny, to complete this assignment.
SLP Assignment
Review your definitions of Archaea and ammonia-oxidizing bacteria from Module 1
What general characteristics determine whether a prokaryote belongs to the Archaea or Bacteria domain?
Define DNA and RNA. What role do DNA and RNA play in this determination?
What role does the metabolism play in classifying Nitrosococcus oceani and Nitrosopumilus maritimus as Archaea or Bacteria?
Do either of these organisms normally thrive in an environment where crude oil is abundant? What other microbes live in this type of environment?
Bio 102 wk 3 SLP instructions
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Introduction
Life exists on earth, various types of living organisms can be found across different parts of the world. Over the previous 3.8 million years ago, living organisms have evolved, become more variegated and adapted different imaginable environmental settings. Life diversity has been an incredible phenomenon. All organisms have different features, but share certain resemblance. All living organisms are capable of replicating themselves. DNA plays a crucial role for replication process. It is the replicator molecule. According to Farabee (2004), every living organism possesses certain mechanism of transforming information reserved in DNA into significant products utilized to develop cellular organ system from carbohydrates, proteins and fats. In the past, living organisms were classified into Plantea and Animalia kingdoms. During 19th century, enhanced scientific research established that such classification was inadequate. Consequently, living organisms were classified into five kingdoms (Animalia, Prostista, Plantae, Monera and Fungi). This classification coincided with another system of categorizing all living organisms into two major taxonomies: Eukaryotae (protists, fungi, plants and animals) and Prokaryotae (bacteria and others). Nevertheless, recent research indicates that prokaryotes are further classified into two categories: Archaea and Bacteria.
Part 1
Prokaryotic organisms consist of Archaea and Bacteria domains. They are single-celled, simplest and smallest organisms. Prokaryotes are plenty on the moist substances and in the soil, water and air. Prokaryotic organisms are able to live in any form of environment such as very acidic, very cold, very hot or super haline environment (Guralnick, Collins, Waggoner, Speer, Whitney and Smith, 2004). Archaea are organisms, which can survive in extreme environments like inside volcanic sites. Bacteria are prokaryotic organisms, which are common and can live in any environment regardless of the extreme environmental conditions. The cells of these prokaryotic organisms lack nuclei. The organisms are pleomoephic, which means that they do not have constant shapes. Prokaryotes organisms lack membrane organelles such as nucleus, chloroplast, mitochondria and others. Genetic materials are lacking in nucleus, but comprises of a huge DNA molecule consolidated in a cytoplasm known as the nuclide area. Prokaryotes move through flagella. They are asexual organisms and reproduce through budding or binary fission.
Bacteria and Archaea exhibit the features of prokaryotes. They lack organelles or nucleus, and they cannot develop multicell organisms. Moreover, they can live in any kind of environment.
Part 2
DNA means deoxyribonucleic acid. It is a kind of macromolecule, which is identified as a nucleic acid. DNA is constituted of phosphate and sugar units as well as nitrogenous components of cytosine, guanine and adenine. Its structures are organized by chromosomes and located within the nucleus. DNA possesses genetic information essential for the life reproduction as well as production of important cell components (Urakawa, Garcia, Barreto, Molina and Barreto, 2012). On the other hand, RNA stands for ribonucleic acid. It is a type of genetic materials just like DNA. However, RNA is made up of ribose and phosphate groups, with one of these base components: uracil, cytosine, guanine or adenine compacted with ribose molecules. Ribonucleic acid molecules perform important role for protein synthesis and help in the diffusion of genetic information.
Guralnick, Collins, Waggoner, Speer, Whitney and Smith (2004) view that DNA plays a crucial the ...