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88 Cards in this Set
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3 distinct but highly interrelated disciplines of Taxonomy |
- Classification - Nomenclature (naming) - Identification of organisms |
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Provides a consistent means to classify, name and identify organisms |
Taxonomy |
- Consistency allows biologists to use common label for every organism studied - Common language that taxonomy provides minimizes confusion about names |
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Evolutionary history of organisms |
Phylogeny |
Taxonomy is important not only in phylogeny but also in virtually every other biologic discipline, including microbiology |
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This method of classification combines the traditional - genotypic - phenotypic, and - phylogenetic or evolutionary relationships into a general purpose classification system |
Classic/Polyphasic Taxonomy |
At the molecular level this process is multifaceted, using - ribosomal ribonucleic acid (rRNA) sequences - whole genome sequences - epigenetic (variations not caused by nucleic acid sequence similarities or difFerences) factors |
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Provides a more detailed but very complex analysis of the current classification system |
Polyphasic Taxonomic Approach |
- Not all parameters clearly delineate each organism to the species level (some characteristics may strengthen the organization of the genus, and some may be useful at the species level) |
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Have provided means for identifying the historical core genomes used in classification and species identification |
Molecular Methods |
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Happens among organisms, particularly bacteria which creates difficulty in the classification of organisms according to phenotypic traits or biochemical traits and genotypic criteria |
Lateral Gene Transfer |
- The movement of DNA between diverse organisms - Genotypic criteria such as DNA G + C content, which is the hallmark of diagnostic microbiology |
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Expression and classification of organisms will continue to be compounded by the |
Variation in genomes |
Result of lateral gene transfer among organisms |
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Examples of Chemotaxonomic methods |
- Protein studies - Fatty acid analysis - Cell wall composition |
More frequently being applied to the identification and classification of microorganisms |
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Use the separation and analysis of high abundance peptides for the classification and identification of bacterial isolates |
Mass spectrometry and Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) |
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Uses a protein array chip that captures proteins directly without the loss of sample and decreased sensitivity (evident in MALDI-TOF MS) |
Surface-enhanced laser desorption ionization time-of-flight mass spectrometry |
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Method for organizing microorganisms into groups or taxa based on similar morphologic, physiologic, and genetic traits |
Classification |
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Hierarchical Classification |
Domains Kingdom Phylum Class Order Family Genus Species |
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The 3 Domains |
Bacteria Archaea Eukarya |
Bacteria - Contain the environmental prokaryotes (blue green or cyanobacteria) and the heterotrophic medically relevant bacteria Archaea - Environmental isolates that live in extreme environments such as high salt concentrations, jet fuel, or extreme temperatures Eukarya - Eukaryotes (true nucleus), also contains medically relevant organisms, including fungi and parasites
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Encompasses a group of organisms that may contain multiple genera and consists of organisms with a common attribute |
Family |
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The name of a family is formed by adding the suffix |
-aceae |
Added to the root name of one of the group’s genera, called the TYPE GENUS Except: Enterobacteriaceae - Named after enteric group of bacteria rather than the type species E. coli |
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Contains different species that have several important features in common |
Genus |
- Each species within a genus differs sufficiently to maintain its status as an individual species
- Placement of a species within a particular genus is based on various genetic and phenotypic characteristics shared among the species |
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- A collection of bacterial strains that share common physiologic and genetic features - Most basic of the taxonomic groups |
Species |
Differ notably from other microbial species |
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Taxonomic subgroups within a species |
Subspecies |
- Do not display significant enough divergence to be classified as a biotype or a new species
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Designations given to groups below the subspecies level that share specific but relatively minor characteristics |
- Biotype - Serotype - Genotype |
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Is considered the same species with the same genetic makeup but displays differential physiologic characteristics
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Biotype |
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- Naming of microorganisms according to established rules and guidelines
- Provides the accepted labels by which organisms are universally recognized |
Nomenclature |
- Set forth in the International Code of Nomenclature of Bacteria (ICNB) or the Bacteriological Code (BC) |
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Each organism has a scientific “label” consisting of two parts: |
1. Genus Designation 2. Species Designation |
Genus = Always capitalized Species = Always lowercase - Printed in italics - Underlined in script |
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Process by which a microorganism’s key features are delineated |
Identification |
- Once those features have been established, the profile is compared with those of other previously characterized microorganisms - The organism can then be assigned to the most appropriate taxa (classification) and can be given appropriate genus and species names (nomenclature) |
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Role of Taxonomy in Diagnostic Microbiology: |
- Establishes and maintains records of key characteristics of clinically relevant microorganisms - Facilitates communication among technologists, microbiologists, physicians, and scientists by assigning universal names to clinically relevant microorganisms |
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Phenotypic Criteria for Microbial Identification |
- Macroscopic Morphology - Microscopic Morphology - Staining Characteristics - Environmental Requirements - Nutritional Requirements - Resistance Profiles - Antigenic Properties - Subcellular Properties - Chemotaxonomic Properties |
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Genotypic Criteria for Microbial Identidication |
- Deoxyribonucleic acid (DNA) base composition ratio
- Nucleic acid (DNA and ribonucleic acid [RNA]) base sequence characteristics, including those determined by hybridization assays |
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- The microbial growth patterns on artificial media as observed when inspected with the unaided eye - Examples include the size, texture, and pigmentation of bacterial colonies |
Macroscopic Morphology |
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- The size, shape, intracellular inclusions, cellular appendages, and arrangement of cells |
Microscopic Morphology |
Observed with the aid of microscopic magnification |
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The ability of an organism to reproducibly stain a particular color with the application of specific dyes and reagents |
Staining Characteristics |
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The ability of an organism to grow at various temperatures, in the presence of oxygen and other gases, at various pH levels, or in the presence of other ions and salts, such as NaC |
Environmental Requirements |
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The ability of an organism to utilize various carbon and nitrogen sources as nutritional substrates when grown under specific environmental conditions |
Nutritional Requirements |
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The exhibition of a characteristic inherent resistance to specific antibiotics, heavy metals, or toxins |
Resistance Profiles |
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The profiles of microorganisms established by various serologic and immunologic methods to determine relatedness among various microbial groups |
Antigenic Properties |
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- Molecular constituents of the cell that are typical of a particular taxon, or organism group, as established by various analytic methods - Some examples include cell wall components, components of the cell membrane, and enzymatic content of the microbial cell |
Subcellular Properties |
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The chemical constituents of the cell, such as the structure of teichoic acids, fatty acid analysis, and protein profiles, as determined by analytical methods |
Chemotaxonomic Properties |
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Four bases of the DNA |
- Guanine - Cytosine - Adenine - Thymine |
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Order of bases along a strand of DNA or RNA |
Base sequence |
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Relate to an organism’s genetic makeup, including the nature of the organism’s genes and constituent nucleic acids |
Genotypic Characteristics |
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Are based on features beyond the genetic level, including both readily observable characteristics and features that may require extensive analytic procedures to be detected |
Phenotypic Characteristics |
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Are the keys to microbial viability and survival |
Microbial - Genetics - Metabolism - Structure |
- These processes involve numerous pathways that are widely varied, often complicated, and frequently interactive |
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Bacterial cellular processes that require energy and nutrients |
- Genetic processes - Biosynthesis - Assembly of cell structure - Waste removal - Motion and other responses to the environment
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Where hereditary information resides or is encoded for all living things |
Nucleic Acids |
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The two major classes of nucleic acid |
- Deoxyribonucleic Acid (DNA) - Ribonucleic Acid (RNA) |
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Most common macromolecule that encodes genetic information |
DNA |
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- In some forms, it encodes genetic information for various viruses - In other forms, it plays an essential role in several of the genetic processes in prokaryotic and eukaryotic cells, including the regulation and transfer of information
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RNA |
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Do not have membrane-bound organelles, and the cells’ genetic material is therefore not enclosed in a nucleus |
Prokaryotic/Pre-nuclear organisms |
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Organisms have the genetic material enclosed in a nuclear envelope |
Eukaryotic (True nucleus) |
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DNA consists of _________ and connected by _________ |
Deoxyribose sugars Phosphodiester bonds |
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Are the key to genetic code within the DNA molecule |
The bases that are covalently linked to each deoxyribose sugar |
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The four nitrogenous bases include |
Two Purines: - Adenine - Guanine Two Pyrimidins: - Cytosine - Thymine |
These bases are covalently linked to each of the deoxyribose sugar |
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In RNA the nitrogenous base thymine is replaced by |
Uracil |
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The combined sugar, phosphate, and a base form a single unit referred to as a |
Nucleotide |
- Adenosine Triphosphate [ATP] - Guanine Triphosphate [GTP] - Cytosine Triphosphate [CTP] - Thymine Triphosphate [TTP] - Uridine Triphosphate [UTP] |
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- The order of bases along a DNA or RNA strand - Provides the information that codes for the proteins that will be synthesized by microbial cells |
Base Sequence |
SEQUENCE = GENETIC CODE |
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The intact DNA molecule is composed of |
2 Nucleotide Polymers |
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Each DNA strand has a |
- 5’ (prime) phosphate - 3’ (prime) hydroxyl terminus |
- The two strands run ANTIPARALLEL, with the 5’ of one strand opposed to the 3’ terminal of the other |
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Base pairing which results in a double-stranded DNA (dsDNA) molecule (double helix) |
A-T and G-C |
Complementary Strands |
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The two single strands of DNA are oriented in an |
Antiparallel Configuration/ Twisted Ladder Structure |
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Provide the essential format for consistent replication and expression of the genetic code |
Base Pairs |
Dedicated base pairs |
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Rarely exists as double-stranded molecule |
RNA |
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Four major types of RNA |
- Messenger RNA [mRNA] - Transfer RNA [tRNA] - Ribosomal RNA [rRNA] - Noncoding RNA [ncRNA] |
ncRNA - Molecules that play key roles in gene expression |
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- DNA sequence that encodes for a specific product (RNA or protein) - Encode messages or blueprints for the production of one or more proteins and RNA products that play essential metabolic roles in the cell |
Gene |
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All the genes in an organism comprise the organism’s |
Genome |
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The size of a gene and an entire genome is usually expressed in the |
Number of base pairs present |
- kilobases [10^3 bases] - megabases [10^6 bases] |
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Basis for the development of molecular methods used to detect, identify, and characterize clinically relevant microorganisms |
Similarities and differences in gene content and sequences |
Base pair sequence for individual genes may be highly conserved (show limited sequence differences among different organisms) or be widely variable |
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The genome is organized into discrete elements known as |
Chromosome |
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The set of genes within a given chromosome are arranged in a |
Linear Fashion |
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Contains the genes essential for viability and exists as a double-stranded, closed, circular macromolecule |
Bacterial Chromosome |
- The molecule is extensively folded and twisted (supercoiled) to fit within the confined space of the bacterial cell |
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The chromosomes of ___________ number more than one per cell, are linear, and are housed within a membrane-bound organelle (the nucleus) of the cell |
Parasites and Fungi |
This difference is a major criterion for classifying - Bacteria as Prokaryotes - Fungi and Parasites as Eukaryotes |
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The genetic makeup of a virus may consist of DNA or RNA contained within a ________ rather than a cell |
Protein Coat |
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Human cells contain ______ pairs of chromosome |
23 |
DIPLOID |
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Bacteria contain a ________ chromose |
Single |
UNPAIRED/HAPLOID |
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Bacterial elements capable of replication independently of the host chromosome |
Episomes |
- Not as stable as the chromosome and may be lost during cellular replication, often without any detrimental effects on the viability of the cell |
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Not all genes are confined to the chromosome, many genes may also be located on the |
- Plasmids - Transposable elements |
- Both of these extrachromosomal elements are able to replicate and encode information for the production of various cellular products |
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- Exist as double-stranded, closed, circular, autonomously replicating extrachromosomal genetic elements - Do not usually encode for products essential for viability |
Plasmids |
Ranging in size from 1 to 2 kilobases up to 1 megabase or more |
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- Pieces of DNA that move from one genetic element to another, from plasmid to chromosome or vice versa - Many are unable to replicate independently and do not exist as separate entities in the bacterial cell |
Transposable elements |
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2 types of transposable elements |
- Simple Transposon/Insertion Sequence (IS)
- Composite Transposon |
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Transposable elements that are limited to containing the genes that encode information required for movement from one site in the genome to another |
Simple Transposon/Insertion Sequence (IS) |
- Internal gene embedded in the insertion sequence encodes for an accessory function, such as antimicrobial resistance |
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Transposable elements that are cassettes (grouping of genes) flanked by insertion sequences |
Composite Transposon |
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Bacteria multiple by |
Binary Fission |
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Four stages of Replication |
1. Unwinding or relaxation of the chromosome’s super-coiled DNA 2. Separation of the complementary strands of the parental DNA 3. Synthesis of the new (daughter) DNA strands 4. Termination of replication |
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Required so that enzymes and cofactors involved in replication can access the DNA molecule at the site where the replication process will originate |
Relaxation of supercoiled chromosomal DNA |
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A specific sequence of approximately 300 base pairs recognized by several initiation proteins |
Origin of Replication |
- Followed by the separation of the complementary strands of parental DNA - Where the replication process will originate |
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Site of active replication |
Replication Fork |
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Each replication fork moves through the parent DNA molecule in opposite directions as a |
Bidirectional process |
- Two bidirectional forks are involved in the replication process |
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- Must occur so that there will be a template (pattern) for synthesis of new DNA strands
- Referred to as Semi-conservative Replication |
Separation of the complementary strands of the parental DNA |
- Each parental strand serves as a template for the synthesis of a new complementary daughter strand |
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Adds nucleotide bases to each growing daughter strand in a sequence that is complementary to the base sequence of the template (parent) strand |
DNA Polymerase |
- Plays a central role in the activity at each replication fork together with different cofactors and enzymes |
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The complementary bases of each strand are then held together by |
- Hydrogen bonding between nucleotides - Hydrophobic nature of the nitrogenous bases |
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