A. Incorrect! In the binomial naming convention the Kingdom is not part of the name.

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1 Microbiology Problem Drill 08: Classification of Microorganisms No. 1 of In the binomial system of naming which term is always written in lowercase? (A) Kingdom (B) Domain (C) Genus (D) Specific epithet In the binomial naming convention the Kingdom is not part of the name. In the binomial naming convention the Domain is not part of the name. In the binomial naming convention genus is the first part of the name. D. Correct! Yes the second word in the binomial naming system is referred to as the specific epithet. This question is a test of vocabulary. Modern classification uses a two word naming convention called binomial nomenclature. The first word identifies the genus. Second word sometimes describes a characteristic of the organism and is called specific epithet. A scientific name is a combination of the genus + specific epithet.

2 No. 2 of Which of the following statements is not a function of the science of Taxonomy? (A) Bring order out of apparent random information. (B) Make predictions from conclusions based on organization. (C) Identify and name new and unknown organisms. (D) Establish the genotype of an organism. One of the functions of the field of Taxonomy is to organize information. One of the functions of the field of Taxonomy is to draw conclusions from the information once it is organized in comprehensible units. The identification and naming of new organisms is a very important part of Taxonomy. D. Correct! The establishment of an organism s genotype is a function of the Genome Sequencing scientist. Taxonomists sequence DNA s and proteins to be able to classify them not as an end in it self. Answers A, B and C are all goals of the field of Taxonomy. Answer D uses the information from gene and protein sequencing however that is the objective of Taxonomy.

3 No. 3 of Why is Latin used as taxonomic nomenclature? (A) Because Latin is the foundation for all science language. (B) Because Latin was the language of the founder of Taxonomy. (C) Since Latin is no longer spoken it is not changing. (D) Latin uses a familiar alphabet. This answer is somewhat deceptive. Latin is the foundation of written science in general. However that is not the reason it continues to be used. Why did Latin take this prominent position? Linnaeus (born in Sweden) is credited with founding the system we use today to classify organisms. His native language was Swedish. C. Correct! Latin is no longer evolving because it is not spoken. This means that there will be no changes in the language that impacts the naming convention. D. Incorrect! Latin does use the common alphabet. Latin is the basis for scientific names. Latin is used because it is no longer a spoken language and so is not longer evolving and changing. Latin is considered a dead language and is static. The first letter of the genus name is uppercase and the first letter of the specific epithet is lowercase. Latin based scientific names are precise science and can be used to draw conclusions. Unlike common names which can be miss leading. For instance a seahorse is neither a fish nor a horse.

4 No. 4 of The purpose of DNA sequencing of ribosomal RNA with respect to taxonomy is? (A) Used to place microbes in an evolutionary time frame. (B) A measure in the change of an essential trait between microbes. (C) To bring a systematic and measurable parameter to microbe classification. (D) All of the above This answer is partially correct but not the best response. This answer is partially correct but not the best response. This answer is partially correct but not the best response. D. Correct! This is the best answer. All of the responses A-C are only partially correct. rrna sequencing provides a phylogenetic measure of similarities and changes between organisms. The closer two organisms are the fewer changes are in the sequence. Conversely the further apart two organisms are on the taxonomic tree the greater the changes in DNA sequence exist.

5 No. 5 of By understanding the binomial naming convention the name Streptococcus pneumoniae tells us? (A) That this is a Gram-positive organism. (B) That this microbe may cause pneumonia. (C) That this microbe is rod shaped. (D) That this microbe is a bacterium. The name alone does not indicate if this organism is Gram positive or Gram negative. B. Correct! The second word term, the specific epithet, is often used to indicate the disease that this organism causes. The word coccus or cocci would indicate that this organism is round in its shape. D. Incorrect! From the name alone it is not possible to tell if this is a bacterium. The name Streptococcus pneumoniae is a scientific name for a common bacterium that causes pneumonia and can be very serious in the young and old and it also causes middle ear infections. Latin based scientific names can provide a significant amount of information. Even in the absence of any additional information you know a lot about this organism.

6 No. 6 of A cladogram is. (A) The same as a pedigree. (B) The study of evolutionary relatedness. (C) Statistical inferences. (D) A graph that shows the relationship (including genetic) between microbes. Pedigree is similar but does not depict clades. Pedigrees usually show direct parentage. This is phylogenetics which treats a species as a group of lineage-connected individuals over time. Statistical inferences (also known as Bayesian inferences) is a mathematical method that is applied to data to determine the probability of the hypothesis being correct. D. Correct! A cladogram is a diagram that showing relationships between organisms. These can include genetic or other types of relationships. A cladogram is a diagram that shows the relationships between organisms. Order of branching is significant. An example of a clade: vertebrates make up a clade; tetrapods (vertebrates that have four limbs) form their own clade within the vertebrate clade. In the example of vertebrates the primitive clade is Vertebrate and the derived or advanced clade would be the tetrapods. Example cladogram fungus Trichoderma. In these two cases you can see that the difference is based on DNA sequence changes. At the base of each image is a key that shows how many changes are in a given step length. Image:

7 No. 7 of The two domain system: Prokaryote and Eukaryote was changed to the three domain system: Bacteria, Archaea and Eukarya. What was the main basis for this change in Domain assignment? (A) The sequencing of the 16S rrna gene. (B) The discovery that bacteria live in extreme environments. (C) The differences in cell membranes between bacteria and Archaea. (D) All of the above. This information was important in establishing the differences between bacteria and Archaea but was not the sole fact for creation of a new division. This discovery was important however there is some overlap in niches of bacteria and Archaea so this alone is not correct. There are differences in some membrane linkages and components such as imbedded proteins. However significant differences are seen within bacteria as well, e.g. Gram Negative versus Gram Positive. D. Correct! All of the observations made on the differences between bacteria and extremeophiles were necessary to determine that the requirement for a new division of Archaea. The three-domain system was created by Carl Woese in the 1970 s. Based on many observations including the most significant which was the sequence of the 16S rrna gene. He split the Prokaryota domain into Eubacteria and Archaebacteria. Their genetic sequences indicated that each of these Domains arose separately from an ancestor. The Domains were renamed: Bacteria, Archaea and Eukarya. While the majority of taxonomists concur with this new assignment of domains it is not universally accepted. Kingdoms fall within three Domains: Bacteria, Archaea and Eucarya

8 No. 8 of Which of the statements below best describe why ribosomal RNA is considered a chronometer of change? (A) It is easy to sequence. (B) The genetic changes correspond to a measurable time frame. (C) It is only in organisms of branching interest. (D) Can perform many and different biochemical roles depending on the class it is in. The ease or lack of ease in sequencing a gene is not related to how good a genetic marker it is for a specific trait. B. Correct! Genetic change that is consistent over time is important if it is to be used as a measure. Random changes over time would not make it a good measure. One of the important properties of a good chronometer is that it be widely distributed over all divisions. D. Incorrect! In order to be useful measure the target protein, or enzyme must perform the same or nearly the same function in all cells. If this were not the case it is possible that changes are based on selective advantages generated by the difference in function. Ribosomal RNA is considered a good chronometer of change because: it is widely distributed, has the same functions in all organisms and the rate of change corresponds to measurable time.

9 No. 9 of RNA polymerase is an enzyme that makes trna, mrna and rrna from DNA. Which of the following statements is most accurate? (A) Bacteria and Archaea both have one RNA polymerase and they are nearly the same. (B) Bacteria and Archaea both have one RNA polymerase but they are not the same. (C) Eukarya has three RNA polymerases, one from each of bacteria, eukarya and its own novel one. (D) RNA polymerase is a change chronometer. Eukarya, bacteria and Archaea have nearly the same RNA polymerases. The first half of the statement is true. Archaea and Bacteria both have one RNA polymerase. But they are not the same. That of Archaea is more closely related to Eukarya. B. Correct! Both Archaea and bacteria have one RNA polymerase with the same function. But genetically they are very different from each other. There is a similarity between the one RNA polymerase that Arachaea has and that of eukarya but that is the only correct aspect of this statement. D. Incorrect! RNA polymerase is used to measure the change over time. However the structure does not need to be identical rather the function needs to be similar, which is the case with the RNA polymerases in all three divisions. RNA polymerase is an enzyme that is absolutely essential for the survival of the organism. And the function is maintained between organisms in the different Division. Because of the essential nature of the RNA polymerase tracking any changes in its structure or function is a useful tool to tracking evolutionary processes.

10 No. 10 of Definition of species in asexually reproducing organisms. (A) Produce viable and fertile offspring. (B) Organisms having >97% identical sequences and 70% DNA:DNA homology. (C) Microbes that inhabit and function virtually identically. (D) Belong on the same branch of a phylogenetic tree. (E) None of the above This is the definition for sexually reproducing organisms. B. Correct! In asexual organisms it can be difficult to define species. However those individuals having more then 97% identical gene sequences and a DNA to DNA hybridization homology of 70% are considered to be of the same species. Organisms with a great deal of genetic diversity can inhabit the identical or nearly identical niches yet be substantially different on the genetic level. D. Incorrect! The branches on the trees are further broken down into more refined groups. As such you may have more then one species on any given branch. In asexual organisms it can be difficult to define species because the definition was originally coined to apply to only sexually reproducing species. That is a species in sexually reproducing organisms are said to belong to the same species if their offspring are viable and fertile. In organisms that are asexual individuals having more then 97% identical gene sequences and a DNA to DNA hybridization homology of 70% are considered to be of the same species.

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