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BIOL212 SYSTEMATIC BIOLOGY LECTURE > Introduction to Systematics and Taxonomy > Flashcards

Introduction to Systematics and Taxonomy Flashcards

1
Q

systematic biology is a coombination of two major disciplines in biology:

A

taxonomy
systematics

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2
Q

naming, describing, and cllassifying of organisms.
branch of biology concerned with identifying, naming, and classifyying organisms

A

taxonomy

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3
Q

relationship and evolutionary development among organisms

A

systematics

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4
Q

2 things that consist systematics

A

cladistics
phenetics

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5
Q

pathways of evolution (how)

A

cladistics

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6
Q

degree of similarity (how much)

A

phenetics

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7
Q

5 components/principles of systematic biology

A

classification
identification
description
nomenclature
phylogeny

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8
Q

principle - similarities among observed organisms

A

classification

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9
Q

3 components under the principle classification

A

artificial based
natural based
phylogenetic

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10
Q

classification using gross morphological structures

A

artificial based

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11
Q

classification based on developmental and morphological structures

A

natural based

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12
Q

classification based on genetic inheritance, similarity and difference across species

A

phylogenetic

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13
Q

principle - assignment of distinct ecological niche (specific role)

A

identification

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14
Q

principle - unique (diagnostic) characteristics of the organism
statement of characters in taxonomy

A

description

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15
Q

principle - standard naming procedures of new species

A

nomenclature

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16
Q

principle - genealogy (ancestor and descendant analysis)

A

phylogeny

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17
Q

described the idea that organic compounds (C-containing) are capable of self-assembly, self-replication, auto-catalysis of chemicals under the similar conditions in the early period of Earth.

A

Oparin-Haldane Hypothesis

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18
Q

term associated with the Primordial Soup Model

A

abiogenesis

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19
Q

other name for primordial soup model

A

prokaryotic cell evolution

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20
Q

term associated with prokaryotic ingestion model

A

endosymbiosis

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21
Q

other name for prokaryotic ingestion model

A

eukaryotic cell evolution

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22
Q

it describes that certaiin prokaryotes are capable of engulfing and assimilating other prokaryotes to generate double-membrane cells that contains combined functions of both cells.

A

endosymbiosis hypothesis

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23
Q

it describes the idea that the statistical probability of successful evolution cannot occur without a guiding intellectual cause - unlike in the theory of evolution by natural selection

A

intelligent design theory/hypothesis

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24
Q

three hypotheses explaining the origin of life

A

Oparin-Haldane hypothesis
Endosymbiosis hypothesis
Intelligent design hypothesis

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25
Q

5 mechanisms of evolution that generate biodiversity

A

mutation
non-random mating
gene flow (migration)
genetic drift
natural selection

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26
Q

mechanism of evolution - changes in the DNA yields different expressions of traits

A

mutation

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27
Q

mechanism of evolution - reproduction preference and conditions can influence the general characteristic of the population

A

non-random mating

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28
Q

mechanism of evolution - movement oof organisms across different population

A

gene flow (migration)

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29
Q

mechanism of evolution - declining frequency of specific genes is an advantage to others

A

genetic drift

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30
Q

mechanism of evolution - suitability of specific traits to environment is disadvantageous

A

natural selection

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31
Q

application of a correct name to an organism or a taxonomic group

A

nomenclature

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32
Q

standard nomenclature in naming organisms

A

binomical nomenclature (Linnaean)

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33
Q

main proponent of binomial nomenclature.
developed in the mid-eighteenth centure

A

Carl von Lannaeus

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34
Q

4 characteristics of binomial nomenclature

A
  1. binomial (2 epithet)
  2. genus epithet - uppercase first letter
  3. italicized/underline (both epithets). If genus is mentioned already, use a capital letter (G.)
  4. 8 hierarchical classification
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35
Q

8 hierarchical classification

A

domain
king
phylum
class
order
family
genus
species

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36
Q

a group of organisms that fills a particular category of classification

A

taxon

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37
Q

year that the Primordial Soup Theory ws introduced

A

1924

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38
Q

taxonomy word origin

A

taxis - arrangement
nomia - method

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39
Q

science of naming, defining, (circumscribing) and classifying groups of biological organisms on the basis of shared charactristics which includes the bases, rules, and procedures of naming organisms.

A

taxonomy

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40
Q

study of the diversification of living forms, both past and present, and the relationships among living things tthrough time.

A

biological systematics
or
systematic biology

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41
Q

used to understand the evolutionary history of life on earth.

A

systematics

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42
Q

studies the pathways of evolution

A

cladistics

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43
Q

the study of relatinoship among a group of organisms on the basis of the degree of similarity between them, be it molecular, phenotypic, or anatomical.

A

phenetics

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44
Q

analytical branch of biology that relies on fossil record data, comparative anatomy and development, and molecular data to determine evolutionary relationship

A

systematics

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45
Q

5 components of systematics

A

classification
identification
description
nomenclature
phylogeny

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46
Q

arrangement of organisms into groups on the basis of similarities

A

classification

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47
Q

3 types of classification

A

artificial
natural
phylogenetic

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48
Q

based on arbitrary, easily observable characters

A

artificial

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49
Q

uses overall simmilarity in grouping

A

natural

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50
Q

based on evolutionary descent of a group of organism
relationship depicted through phylogram

A

phylogenetiic

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51
Q

recognizing unknown specimen with an already known taxon and assigning a correct rank and position in an extant classification.

A

identification

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52
Q

involves listing taxon’s features by recognizing appropriate characters or character states known as diagnostic characters.

A

description

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53
Q

determination of a correct name for a taxonusing rules and recommendations of the CODE which contains rules to obey and has recommendations which is strongly advised to follow.

A

nomenclature

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54
Q

study of the genealogy and evolutionary histoy of a taxonomic group

A

phylogeny

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55
Q

study of ancestral relationships ad lineages; relationships are depicted through a diagram known as a phylogram/cladogram

A

genealogy

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56
Q

theory stating that all life sprouted froma complex RNA world

A

Ribonucleic acid (RNA) Theory

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57
Q

the first self-replicating information-storage molecule
catalyzed the assembly of the first proteins

A

RNA

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58
Q

RNA is older than DNA?

A

true

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59
Q

the first genetic material

A

RNA

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60
Q

RNA is older, and far more sefl-eplicating, if less efficient, than DNA

A

true

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61
Q

___ from the soup model catalyst the formation of ___ in the form of ____ which started as marine photosynthetic bacteria which emerged around 2.5 billion years ago.

A

RNA
prokaryotes
Cyanobacteria

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62
Q

the ___ and __ succeeded the cyanobacteria

A

Archaebacteria
Eubacteria

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63
Q

evolution of prokaryotes (process)

A

inorganic molecules > RNA nucleotides > RNA macromolecules (self-replicating) > RNA molecules catalyze protein synthesis > Proteins

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64
Q

___ were the first eukaryotes andd evolved into ___ the first multicellular organisms around 700 million years ago.

A

protists
algae

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65
Q

the first vertebrates to evolve into amphibians

A

fishes

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65
Q

amphibians > reptiles > birds and mammals (t/f)

A

true

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66
Q

the different genetic traits, species, and ecosystem components of the earth.

A

biodiversity

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67
Q

identified the first principle of the origin o modern biodiversity, namely that all species were linked in a single great phylogeny, or tree of life, and that all could be traced back to a presumed single original species at some distant time in the geological past.

A

Charles Darwin

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68
Q

5 mechanisms of evolution that leads to biodiversity of life

A

mutation
non-random mating
gene flow (migration)
genetic drift
natural selection

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69
Q

the changing of the structure of a
gene, resulting in a variant form that may be
transmitted to subsequent generations, caused
by the alteration of single base units in DNA, or
the deletion, insertion, or rearrangement of
larger sections of genes or chromosomes.
“mutation is, ultimately, the only way in which
new variation enters the species”

A

mutation

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70
Q

organisms choose their
mate with each other, with preference for
particular genotypes. It occurs when the
probability that two individuals in a population
will mate is not the same for all possible pairs of
individuals. Nonrandom mating can take two
forms: Inbreeding - individuals are more likely to mate with close relatives (e.g. their neighbors)
than with distant relatives.

A

non-random mating

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71
Q

is any movement of
individuals, and/or the genetic material they
carry, from one population to another. Gene
flow includes lots of different kinds of events,
such as pollen being blown to a new destination
or people moving to new cities or countries. If
gene versions are carried to a population where
those gene versions previously did not exist,
gene flow can be a very important source of
genetic variation. In the graphic below, the gene
version for brown coloration moves from one
population to another.

A

gene flow/migration

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72
Q

the genes of a strong individual
will persist and may, just by chance, leave
behind a few more descendants or genes than
other individuals. The genes of the next
generation will be the genes of the “lucky”
individuals, not necessarily the healthier or
“better” individuals.

A

genetic drift

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73
Q

the process through which
populations of living organisms adapt and
change. Individuals in a population are naturally
variable, meaning that they are all different in
some ways. This variation means that some
individuals have traits better suited to the
environment than others

A

natural selection

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74
Q

says that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection. (Behe MJ and Meyer SC 2018).

A

intelligent design theory

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75
Q

scientific theory which has its roots in information theory and observations about intelligent action.

A

intelligent design

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76
Q

“global species richness”

A

biodiversity

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77
Q

employs a very slim chance of creating new
species hence it requires a very long period of time.

A

evolution

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77
Q

intelligent design theory makes no statements about the identity
of the intelligent designer(s), but merely says that
intelligent action was involved at some points with the
origins of various aspects of biological life.

A

true

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77
Q

Mutation could not produce
speciation because it violates the two natural laws.

A

true

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78
Q

application of a correct name to an organism or a taxonomic group

A

nomenclature

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79
Q

why are scientific names in Latin?

A

latin is a dead language because it does not change or modify

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80
Q

reasons for using Latin language

A

consistent name of species worldwide
intenational name
make use everybody is using the same Latin name for a speices

81
Q

for plants, ___ is used instead of phylum

A

division

82
Q

need for scientific name instead of vernacular or common name

A

a. Vernacular names are not available for all the
species known to man,
b. Vernacular names are restricted in usage and are
applicable in one or few language only or not
universal,
c. Common names usually do not provide information
indicating family or generic relationship,
d. Many common names may exist for the same
species in the same language in the same or
different localities, and
e. Often two or more unrelated species are known by
the same name.

83
Q

plants

A

ICBN

84
Q

animals

A

ICZN

85
Q

bacteria

A

international code for nomenclature of bacteria

86
Q

cultivated plants

A

international code of nomeclature for cultivated plants, based on ICBN

87
Q
  • Simplest plants
  • No true roots
  • No vascular tissues (no transport system)
  • Simple stems and leaves
  • Have rhizoids for anchorage
  • Spores from capsules (wind-dispersals)
  • Damp terrestrial land
A

mosses

88
Q
  • Roots, feathery leaves, and underground stems
  • Have vascular tissues (transport and support)
  • Spore-producing organ on the underside of leaves
    (reproduction)
  • Damp and shady places
A

ferns

89
Q
  • Tall, evergreen trees
  • Roots, woody stems
  • Needle-shaped leaves
  • Vascular tissues (transport)
  • Cones with reproductive structures
  • Naked seeds in female cones
  • Dry places
A

gymnosperms

90
Q

*One-seed leaf
* Leaves have parallel veins
* Herbaceous plants
* E.g. grass, maize

A

monocotyledon

91
Q
  • Two-seed leaves
  • Leaves have veins in network
  • E.g. trees, sunflower, rose
A

dicotyledons

92
Q
  • Prokaryotic
  • (+) cell membrane
  • Cell wall is made up of pseudomurein
  • extremophiles
  • chemoautotrophs
  • some are heterotrophs
A

Archaea

93
Q

thrive in extreme conditions

A

extremophiles

94
Q

Ability to produce methane (methanogenesis),
utilize alternative energy sources like sulfur or
hydrogen gas, and perform photosynthesis.

A

archaea

95
Q

derives energy from inorganic compounds

A

chemoautotrophs

96
Q

obtains energy from organic matter

A

heterotrophs

97
Q

ecological significance of Archaea

A
  • Found in diverse environments worldwide
  • Important roles in biogeochemical cycles
  • Involved in nutrient cycling, carbon fixation,
    and the degradation of complex organic
    compounds.
98
Q

symbiotic relationships of Archaea

A
  • Methanogenic archaea can be found in the
    digestive tracts of animals
  • Symbiotic associations with marine animals
99
Q
  • these are not typically associated with human diseases
  • some species can be found in human microbiomes
A

Archaea

100
Q

4 classifications of Archaea

A

euryarchaeota
crenarchaeota
nanoarchaeota
korarchaeota

101
Q

methanogens
halobacteria

A

euryarchaeota

101
Q

produce methane as a metabolic waste product

A

methanogens

102
Q

thrive in extreme saline environments
can form reddish blooms

A

halobacteria

103
Q

the ability of halobacteria to form reddish forms is attributed to the presence of ___

A

bacteriorhodopsin

104
Q
A
104
Q
A
105
Q
  • Play a crucial role in carbon fixation.
  • Many members are extremophiles that are
    sulphur-dependent, thermophilic, or
    hyperthermophilic.
  • Examples include Sulfolobus
A

crenarchaeota

106
Q

grow in volcanic springs at high temperatures and low pH

A

sulfolobus

107
Q
  • Contains a single species,
  • isolated from the bottom of the Atlantic Ocean
    and hydrothermal vents at Yellowstone National
    Park.
  • Forms an obligate symbiotic relationship with
    Ignococcus, another species of archaea
A

nanoarchaeota

108
Q

the only species under nanoarchaeota

A

Nanoarchaeum equitans

109
Q
  • Considered one of the most primitive forms of
    life.
  • Found only in the Obsidian Pool, a hot spring at
    Yellowstone National Park.
A

korarchaeota

110
Q

methanogens and other archaea play a vital role in ____

A

biogeochemical cycle

111
Q

methane produced by methanogens affect the global climate change

A

true

112
Q

some archaea form ____ with other organisms

A

symbiotic associations

113
Q

methanogens aid ____ and ____ in ruminant animals

A

digestion
methane production

114
Q

archaea provide energy through ___ in symbiotic associations in marine animals

A

chemosynthesis

115
Q
  • Archaea represent an early diverging domain of
    life.
  • Studying archaea sheds light on cellular
    processes, genetics, and metabolism.
  • Understanding the archaea enhances our
    knowledge of the tree of life and biological
    origins.
A

importance of the evolutionary insights of Archaea

116
Q

cell wall of archaea is made up of

A

pseudomurein

117
Q
  • Prokaryote
  • (+) cell membrane
  • Cell wall is made up of peptidoglycan
A

eubacteria

118
Q

cell wall of eubacteria is made up of

A

peptidoglycan

119
Q

eubacteria are classified into

A

nutritional categories

120
Q

some bacteria can fix __ for other organisms

A

nitrogen

121
Q

ecological roles of eubacteria

A
  • Participate in nutrient cycling, decomposition,
    and compound recycling.
  • Form symbiotic relationships wit plants,
    animals, and humans.
122
Q

positive impacts of bacteria

A

beneficial bacteria aid in digestion, produce vitamins, and
support the immune system

123
Q

bacteria that can cause diseases

A

pathogenic bacteria

124
Q

industrial and biotechnological appllications of eubacteria

A
  • Antibiotics, enzymes, biofuels, and other
    bioproducts.
  • Wastewater treatment, bioremediation, and
    agriculture.
125
Q

genes are different from eukarya

A

bacteria

126
Q

genes are more similar to eukarya

A

archaea

127
Q

5 classifications of eubacteria

A

proteobacteria
chlamydiae
spirochetes
cyanobacteria
gram-positive bacteria

128
Q

proteobacteria that is photoautotrophic, symbionts, or pathogens

A

alpha proteobacteria

129
Q

proteobacteria - human gut symbionts and pathogens

A

beta proteobacteria

130
Q

proteobacteria - generate spore-forming fruiting bodies or reduce sulfur

A

delta proteobacteria

131
Q

proteobacteria - in animal digestive tracts and hydrothermal vents

A

epsilon proteobacteria

132
Q
  • Obligate intracellular parasites of animal cells.
  • (-) peptidoglycan
  • STDs and other infections
A

chlamydiae

133
Q
  • Spiral-shaped cells with flagella running
    lengthwise.
  • May be harmless or pathogenic.
  • Species causing syphilis and Lyme disease
A

spirochetes

134
Q
  • Obtain energy through photosynthesis.
  • In various environments and produce oxygen.
  • Eukaryotic chloroplasts
A

cyanobacteria

135
Q
  • (+) thick cell wall
  • (-) outer membrane
  • May decompose organic matter, others causing
    disease.
  • Species causing anthrax, botulism, and
    antibiotic-resistant infections
A

gram-positive bacteria

136
Q

classifications of bacteria based on shape

A

cocci
bacilli
spirilla
coccobacilli
vibrios

137
Q
  • Spherical-shaped bacteria
  • Staphylococcus and Streptococcus
A

cocci

138
Q
  • Rod-shaped bacteria
  • Escherichia coli and Bacillus anthracis
A

bacilli

139
Q
  • Spiral-shaped bacteria
  • Treponema pallidum and Spirillum volutans
A

spirilla

140
Q

classification of bacteria on the compostion of the cell wall

A

gram-positive
gram-negative

141
Q
  • Thick peptidoglycan layer in cell wall.
  • Retain crystal violet stain in Gram staining.
  • Staphylococcus aureus, Streptococcus pyogenes
A

gram-positive

142
Q
  • Thinner peptidoglycan layer and outer
    membrane.
  • Contain lipopolysaccharides.
  • Do not retain crystal violet stain in Gram
    staining.
  • Escherichia coli, Pseudomonas aeruginosa
A

gram-negative

143
Q

classification based on the mode of nutrition (source of carbon)

A

autotrophs
heterotrophs

144
Q
  • Principal source of carbon utilization is CO2
  • Purple and green sulfur bacteria
A

atutotrophs

145
Q
  • Depend on the others’ organic compounds
  • Escherichia coli, Salmonella Typhi, Proteus
    spp., Staphylococcus aureus, Lactobacillus
    acidophilus
A

heterotrophs

146
Q

classification of bacteria based on the mode of nutrition (source of energy)

A

phototrophs
chemotrophs

147
Q
  • Utilize light as their source of energy
  • Chromatium okenii, Rhodospirillum rubrum,
    etc.
A

phototrophs

148
Q
  • Energy from the oxidation of organic or
    inorganic compounds.
  • Nitrosomonas, Pseudomonas pseudoflava
A

chemotrophs

149
Q

classification of bacteria baed on mode of nutrition (source of electrons)

A

lithotrophs
organotrophs

150
Q
  • Use inorganic compounds as the electron
    source
  • Nitrobacter, Thiobacillus denitrificans,
    Nitrosomonas, etc.
A

lithotrophs

151
Q
  • Use organic compounds as electron source
  • Pseudomonas pseudoflava
A

organotrophs

152
Q

classification of bacteria based on the type of flagella

A

monotrichous
lophotrichous
amphitrichous
peritrichoous

153
Q
  • Flagellum is present only at one end of bacteria,
    polar.
  • Pseudomonas aeruginosa
A

monotrichous

154
Q
  • A cluster of flagella is present only at one end of
    bacteria.
  • Pseudomonas fluorescens
A

lophotrichous

155
Q
  • Flagella are present in both ends of the bacteria
    in single or clusters.
  • Aquaspirillum serpens
A

amphitrichous

156
Q
  • Flagella are present all around the body.
  • Salmonella Typhi
A

peritrichous

157
Q

classification of bacteria based on the ability to form spores

A

non-spore formers
spore formers

158
Q
  • Do not form spores
  • E. coli, Staphylococcus aureus
A

non-spore formers

159
Q
  • produce spores
    8 exospores
  • endospores
A

spore formers

160
Q
  • spores roduced outside of the cell
  • Methylosinus
A

exospores

161
Q

spores produced inside but at different locations

A

endospores

162
Q

3 types of endospores

A

terminal spore
central spore
subterminal spore

163
Q

classification of bacteria based on the optimal growth pH

A

acidophiles
neutrophiles
alkalophiles

164
Q
  • Grow at low pH with the pH optimum of pH 0 to
    5.5.
  • Sulfolobus, Picrophilus, Ferroplasma, Cyanidium
    caldarium
A

acidophiles

165
Q
  • Grow at neutral pH with a pH optimum of 5.5.
    to 8.0.
  • Escherichia coli, Salmonella, etc.
A

neutrophiles

166
Q
  • These bacteria grow at high pH with a pH
    optimum of 8.0 to 11.5.
A

alkalophiles

167
Q

classification of bacteria based on the required growth temperature

A

psychrophiles
mesophiles
thermophiles
hyperthermophiles

168
Q

grows at arounf -5 to 20 C

A

psychrophiles

169
Q

grows at 15 C to 45 C

A

mesophiles

170
Q

grows at around 45 C to 80 C

A

thermophiles

171
Q

grows are 65 C to 105 C

A

hyperthermophiles

172
Q

classification based on the mode of respiration

A

obligate aerboes
obligate anaerobes
facultative anaerobes
facultative aerboes
aerotolerant anaerobes
microaerophiles

173
Q

no oxygen level preference

A

aerotolerant

174
Q

grow in the basence and presence of oxygen bt prefers O2 presence

A

facultative aerobes

175
Q

require 2% of atmosphere oxygen for growth

A

microaerophiles

176
Q

killed by normal atmospheric concentrations of oxygen

A

obligate anaerobes

177
Q

need oxygen because they cannot ferment or respire anaerobically

A

obligate aerobes

178
Q

ecological roles of eubacteria

A
  • Involved in nutrient cycling, including nitrogen
    fixation and organic matter decomposition.
179
Q

positive impact of eubacteria to human health

A

digestion, vitamin production, and immune system

180
Q

bacteria that can cause infectious diseases

A

pathogenic bacteria

181
Q

importance of eubacteria to biotechnology and industry

A
  • Economic significance in biotechnology and
    industry.
  • Used in the production of antibiotics, enzymes,
    and bioactive compounds.
  • Model organisms for genetic engineering.
182
Q

importance of eubacteria to food production and fermentation

A
  • Crucial in food production and fermentation
    processes.
  • Contribute to the production of fermented food
    like yogurt and cheese.
  • Bacteria enhance flavor, texture, and
    preservation of food products
183
Q

governs the scientific names for bacteria and archaea

A

international code of nomenclature for prokaryotes

184
Q

ICSP

A

international committee on systematics of prokaryotes

185
Q

International Code of Botanical Nomenclature
included bacteria, but references to bacteria
were removed in ___

A

1975

186
Q

Early code for bacterial nomenclature was
approved in ___ but later discarded.

A

1947

187
Q

2008 revision was published in the

A

international journal of systematics and evolutionary microbiology (IJSEM)

188
Q

Until 1975, most bacteria were covered by the
bacterial code, while cyanobacteria were
covered by the ___

A

botanical code

189
Q

Starting in ___, cyanobacteria were included in
both the botanical and bacteriological codes,
causing nomenclatural problems

A

1999

190
Q

By 2020, three proposals were suggested to
resolve the situation

A

(1) excluding
cyanobacteria from the bacteriological code,
(2)
applying the bacteriological code to all
cyanobacteria, or
(3) considering valid
publication under the botanical code as valid
under the bacteriological code

191
Q

in 2021, the ICSP held a frmal vote and chose the ___ as the resolution

A

third option

192
Q

living culture to which the scientific name of the organism is attached

A

type strain

193
Q

To validly publish a new species name, the type
strain must be deposited in a public culture
collection in at least ___ different countries

A

2

194
Q

since ___ a type strain must be designated when describing a new bacterial or archaeal species

A

2001

195
Q

In cases where a prokaryotic species cannot be
cultivated in the laboratory, it may be given a
________ but is not
considered validly published

A

provisional candidatus name

196
Q

Starting in ____, prokaryotic species and
subspecies can be named and considered validly
published under the ______ using high-quality genome
sequences as type

A

2022
Code of Nomenclature of
Prokaryotes Described from Sequence Data
(SeqCode)

197
Q

spore found near the end of the cell

A

subterminal spore

198
Q

crystal violet serves as the ___ in gram staining

A

primary stain

199
Q

the mordant used in gram staining

A

iodine

200
Q

spore found at the end of the cell

A

terminal spore

201
Q

classification of bacteria with grape-like clustered spherical cells

A

staphylococci

202
Q

95% of ethanol or acetone serves as ____ in gram staining

A

decolorizer

BIOL212 SYSTEMATIC BIOLOGY LECTURE (3 decks)

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