Biology: Taxonomy and Classification

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Questions and Answers

What does taxonomy primarily study?

The metabolic processes of archaea

The classification of organisms into categories (correct)

The evolutionary history of organisms

The structure of ribosomal RNA

Which kingdoms did Carl Linnaeus initially propose?

Plants and Animals (correct)

Fungi and Protista

Eukarya and Prokaryotae

Bacteria and Archaea

In what year did Robert H. Whittaker propose his five-kingdom system?

1969 (correct)

1978

1735

1937

Which domain includes all known pathogenic prokaryotes?

Bacteria Signup and view all the answers

Which of the following is NOT a distinguishing feature between the three domains?

Presence of ribosomes Signup and view all the answers

What characteristic is unique to the Domain Archaea compared to other domains?

Absence of peptidoglycan in cell walls Signup and view all the answers

What did Carl R. Woese propose in 1978 regarding the classification of organisms?

To elevate the three cell types to a domain level Signup and view all the answers

Which of the following groups is NOT included in the Domain Eukarya?

Bacteria Signup and view all the answers

What is the significance of horizontal gene transfer among cell lines?

It shows that gene exchange can occur between different domains. Signup and view all the answers

What does a phylogenetic tree illustrate about organisms?

Grouping indicates a common ancestor and shared characteristics. Signup and view all the answers

In the binomial nomenclature system, how should the genus name be represented?

It is capitalized and italicized. Signup and view all the answers

How are prokaryotes classified according to Bergey’s Manual?

By similarities in rRNA nucleotide sequences. Signup and view all the answers

What does the term 'prokaryotic species' refer to?

A population of cells with a high degree of genomic similarity. Signup and view all the answers

Which level of the taxonomic hierarchy comes after the genus?

Family Signup and view all the answers

What is the primary basis for dividing the domains Bacteria and Archaea?

Differences in rRNA nucleotide sequences. Signup and view all the answers

What major characteristic distinguishes members of a bacterial species?

They exhibit a high degree of genomic similarity. Signup and view all the answers

What is the primary function of antibodies in an animal's immune system?

To specifically bind to and neutralize pathogens Signup and view all the answers

What term is used for different strains with varying antigens within a microbial species?

Serovars Signup and view all the answers

Which of the following methods is NOT used in molecular profiling of microorganisms?

Dichotomous Keys Signup and view all the answers

What technique is used to identify phage susceptibility in bacteria?

Phage Typing Signup and view all the answers

What does a plaque in a phage typing test indicate?

Sensitivity to infection by phages Signup and view all the answers

Which of the following statements about dichotomous keys is true?

They guide identification through successive questions with two possible answers. Signup and view all the answers

What is the primary use of the technique known as ribotyping?

To examine the ribosomal RNA patterns of bacteria Signup and view all the answers

What characteristic is key to bacteriophages in phage typing?

They specifically infect only certain bacterial strains or species. Signup and view all the answers

What is the primary criterion used in Bergey’s Manual of Determinative Bacteriology for classifying bacteria?

Cell wall composition Signup and view all the answers

Which of the following methods is NOT a conventional identification method in microbiology?

Genomic sequencing Signup and view all the answers

What limitation is associated with biochemical testing for microbial identification?

Mutations can lead to incorrect identification Signup and view all the answers

How does a rapid identification system like the EnteroPluri test assign values to test results?

Using a binary system of 0 and 1 Signup and view all the answers

Which of the following is part of the identification process of a bacterial isolate?

Source and habitat of the organism Signup and view all the answers

What is a significant characteristic of transport media used in clinical microbiology?

They prolong the viability of fastidious pathogens Signup and view all the answers

Which factor is NOT considered when identifying microorganisms?

Nutritional preferences Signup and view all the answers

In numerical identification schemes, what is commonly assigned to a positive biochemical test result?

1 Signup and view all the answers

What distinguishes a strain in microbiology?

Strains are populations derived from a single parent cell but may vary in some characteristics. Signup and view all the answers

What is Bergey’s Manual primarily used for?

Providing a reference for identifying bacteria and classifying prokaryotes. Signup and view all the answers

Why are viruses not classified within the three domains of life?

Viruses cannot reproduce independently and must infect host cells. Signup and view all the answers

Which statement accurately represents the nature of a viral species?

A viral species includes viruses with similar characteristics distinguishable by various methods. Signup and view all the answers

Which hypothesis suggests that viruses arose from existing nucleic acids?

Plasmid hypothesis. Signup and view all the answers

What is a major implication of viral genes being incorporated into the host genome?

It provides evidence for viral evolution over millions of years. Signup and view all the answers

Which of these is NOT characteristic of prokaryotes?

They have a defined nucleus. Signup and view all the answers

What role do viruses play in ecosystems despite not being classified as living organisms?

They contribute to genetic diversity among organisms. Signup and view all the answers

Study Notes

Classification of Organisms

Taxonomy is the study of classifying organisms into categories (taxa).
Systematics (or phylogeny) studies the evolutionary history of organisms.
A hierarchy of taxa reflects evolutionary/phylogenetic relationships.
Historically, organisms were categorized as either plants or animals.
In 1735, Carl Linnaeus introduced a formal system of classification with two kingdoms (Plantae and Animalia).
The term "prokaryote" was introduced in 1937 to distinguish cells without a nucleus from nucleated cells.
In 1968, Robert G. E. Murray proposed the Kingdom Prokaryotae.
In 1969, Robert H. Whittaker established the five-kingdom system, placing prokaryotes in the Kingdom Prokaryotae (or Monera) and eukaryotes in the other four kingdoms.
The Kingdom Prokaryotae was based on microscopic observations.
In 1978, Carl Woese proposed the three domains (Archaea, Bacteria, and Eukarya).

The Three Domains

Ribosomes are present in all cells.
Comparing ribosomal RNA sequences reveals three distinct groups: eukaryotes, bacteria, and archaea.
Domains differ in membrane lipid structure, tRNA molecules, and antibiotic sensitivity.
Eukarya encompasses the kingdoms of animals, plants, and fungi.
Bacteria include both pathogenic and non-pathogenic prokaryotes, as well as photoautotrophs in soil and water.
Archaea comprises prokaryotes lacking peptidoglycan in their cell walls, often found in extreme environments.

The Three Domains (continued)

Based on rRNA analysis, three separate lineages emerged 3.5 billion years ago: archaea, bacteria, and the precursors to the nucleoplasm of eukaryotes.
Horizontal gene transfer occurs among these lineages.
Analysis of complete genomes shows that genes are shared among all three domains.
Gene transfer has been observed between eukaryotic hosts and their prokaryotic symbionts.

Scientific Nomenclature and the Taxonomic Hierarchy

Every organism is assigned two names: genus and species (specific epithet).
Genus names are capitalized, and species names are lowercase.
Both are italicized or underlined.
The system is called binomial nomenclature (e.g., Homo sapiens).
Organisms group into subdivisions that comprise the taxonomic hierarchy.

Classification of Prokaryotes

Bergey's Manual is a widely used reference for prokaryotic classification.
Prokaryotes are divided into two domains: Bacteria and Archaea.
Each domain is then subdivided into phyla, classes, orders, families, genera, and species.
Classification based on similarities in rRNA nucleotide sequences.
Prokaryotic species is defined as a population of cells with high genomic similarity.
Identification based on morphology, differential staining, oxygen requirements, and biochemical testing.
The majority of prokaryotes haven't been cultured.
Methods to identify prokaryotes involve culturing, use of Bergey's Manual, and utilizing biochemical tests (e.g. the EnteroPluri test).
Strains of bacteria are identified by numbers, letters, or names that follow the specific epithet.

Classification of Viruses

Viruses are not part of the three domains.
They are not composed of cells and require host cells to multiply.
Viral classification is determined via multiple methods including morphology, genes, enzymes, and ecological niche.
Some viruses, like bornaviruses and retroviruses, have integrated their genes into mammalian genomes for at least 40 million years.
There are three hypotheses regarding the origin of viruses: independent replicating nucleic acid strands; degeneration of cells and loss of independent survival ability; or coevolution with host cells.
Viruses are obligatory intracellular parasites.

Molecular Profiles

Methods to study organisms at a molecular level for identification.
Flow cytometry, whole genome sequencing, nucleic acid hybridization, nucleic acid amplification tests (NAATs), Southern blotting, DNA chips, ribotyping, and fluorescent in situ hybridization are included.

Putting Classification Methods Together

Dichotomous keys are used for organism identification via successive questions with two-part answers, directing to another question until the organism is identified, though typically without much phylogenetic relationship context.
Cladograms illustrate evolutionary relationships using branching points (nodes) defined by features shared among their respective groups, often employing rRNA sequences as a primary method.

Seriology

Serology studies serum and immune responses.
Microorganisms trigger the production of antibodies, which bind specifically to the bacteria causing the response.
Strains with distinct antigens (serotypes, serovars, or biovars) can be differentiated.
Phage typing tests bacterial susceptibility to bacteriophages, revealing species or strain-specific susceptibility.

Methods of Identifying Microorganisms

Bergey's Manual is a standard reference for identifying bacteria.
Identification schemes are often based on criteria like cell wall composition, morphology, differential staining, oxygen needs, and biochemical testing.
99% of the existing microbial species remain uncultured.
Often, swabs, inserted into transport media, are used for collecting samples from clinical sources.
Transport media help prolong viability of sensitive, fastidious pathogens for easier and more accurate identification processing.

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Description

Test your knowledge on taxonomy and biological classification systems in this quiz. Explore the contributions of scientists like Carl Linnaeus and Robert H. Whittaker, and understand the distinctions between domains and kingdoms. Perfect for biology students looking to reinforce their understanding of organism classification.