1
Q
What is phylogeny?
A
the evolutionary history of species or group of species
2
Q
What is systematics?
A
classifies organisms and determines their evolutionary relationships
3
Q
what kinds of evidence does systematics use?
A
morphology genes and biochemistry
morphology - the study of form and structure, either of organisms in biology
4
Q
what is a phylogenetic tree?
A
a hypothesis about evolutionary relationships
5
Q
example of independent evolution in reptiles?
A
snakes and legless lizards evolved independently from legged lizards
6
Q
why are phylogenetic trees considered hypotheses?
A
they are based on available data and can change with new evidence
7
Q
what is phylogenetic bracketing?
A
predicting ancestral traits from the traits of descendants
8
Q
example of traits shared by birds and crocodiles ?
A
4-chambered heart, nest-building, brooding behavior
9
Q
who developed binomial nomenclature ?
A
Carl Linnaeus
10
Q
Format of a scientific name?
A
Genus + species epithet (ex; Homo sapiens
11
Q
what is a taxon?
A
a named group at any level of classification
12
Q
order of taxonomic hierarchy?
A
Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species.
“Dear King Phillip Came Over For Good Soup”
13
Q
what is a branch point in a phylogenetic tree?
A
A divergence from a common ancestor
14
Q
Define sister taxa
A
groups that share an immediate common ancestor
15
Q
Define rooted tree
A
a tree that shows the most recent common ancestor of all taxa
16
Q
Define basal taxon
A
a lineage that diverged early in the history of a group
17
Q
what do Phylogenetic trees NOT show?
A
Phenotypic similarity, exact timing of divergence, or direct ancestry.
Looks, when they diverted or direct relatives.
18
Q
Example of Homology
A
the forelimbs of vertebrates (human arm, bat wing, whale flipper, cat leg), which have similar bone structures from a common ancestor but different functions.
19
Q
define Homology
A
similarity due to common ancestry
20
Q
Define analogy
A
a structure or trait with a similar function across different species but that evolved independently from a non-shared common ancestor
looks the same but not the same blood
21
Q
Example of analogy?
A
the wings of a bat and the wings of an insect
22
Q
what is clade?
A
An ancestor and all of its descendants
23
Q
define monophyletic
A
a clade including and ancestor and all descendants
24
Q
Define paraphyletic
A
Ancestor plus some, but not all, descendants
25
Define Polyphyletic
Unrelated species without recent common ancestor grouped as a species
26
define shared ancestral character
trait inherited from ancestor of the clade
27
what is the purpose of an outgrip in cladistics?
to distinguish ancestral vs derived traits
28
what is maximum parsimony?
Simplest explanation (fewest evolutionary changes)
29
what is distance analysis?
calculates sequence similarity to infer evolutionary relationships
30
what can branch lengths in a phylogenetic tree represent ?
number of genetic changes of divergence time
31
Which genes evolve slowly and are useful for deep history?
rRNA genes
32
which DNA evolves rapidly and is useful for recent divergence?
Mitochondrial DNA (mtDNA)
33
Define orthologous genes
genes in different species that originated by speciation
34
Define paralogous genes
genes within a species that arose by duplication
35
what is a molecular clock?
uses mutation rates to estimate divergence times
36
Who Proposed neutral theory?
Motoo Kimura
37
What does neutral theory state?
Most mutations are neutral and accumulate at steady rates
38
problems with molecular clocks?
Mutation rates vary, selection affects rates, uncertainty increases with older divergences
39
Application of DNA analysis in whales ?
detecting illegal whale meat fraud
40
approximate origin of HIV in humans
1930s
41
likely origin of SARS-CoV-1?
bats
42
source of Haiti cholera outbreak ?
strains traced to Nepal
43
why is influenza H3N2 monitored in SE Asia
it circulated there and informs vaccine design
44
Three domains of life ?
Bacteria, Archaea, Eukarya.
45
Which domains are prokaryotic?
Bacteria and Archaea
46
which domain are eukaryotes most closely related to?
Archea
47
what process complicates phylogenetic trees?
Horizontal gene transfer
48
Typical size of prokaryotes?
0.5–5 μm.
49
Prokaryote biomass compared to eukaryotes?
>10x greater.
50
Environments prokaryotes thrive in?
Extreme heat, cold, salt, acidity, alkalinity
51
are most prokaryotes harmful?
No, most are beneficial
52
Essential roles of prokaryotes?
Nutrient cycling, nitrogen fixation, vitamin production
53
Are prokaryotes unicellular?
yes but can form colonies
54
three shapes of prokaryotes?
Cocci (spheres), bacilli (rods), spirals (helices).
55
Example of a prokaryotic community?
Cyanobacterial mats.
56
function of prokaryotic cell wall?
shape, protection, prevents bursting
57
composition of bacterial cell wall?
peptidoglycan
58
Do arches have peptidoglycan?
No
59
Gram-positive bacteria characteristics?
Thick peptidoglycan, less complex
60
Gram-negative bacteria characteristics?
thin peptidoglycan, outer membrane with lipopolysaccharides, often pathogenic, resistant.
61
Medical relevance of capsules ?
Aid adhesion and protect from immune system
62
function of pili?
DNA transfer in conjugation.
63
Function of fimbriae?
attachment to surfaces
64
Bacterial vs eukaryotic flagella?
Bacterial flagella rotate like a propeller, while eukaryotic flagella move with a wave-like motion
65
define taxis
Movement toward/away from stimulus
66
types of taxis?
Chemotaxis, Phototaxis, Magnetotaxis
67
do prokaryotes have a nucleus?
No
68
Where is DNA found?
Nucleoid region
69
Shape of prokaryotic chromosome ?
circular
70
what are plasmids ?
small, extra DNA circle with resistance or other genes
71
Do prokaryotes have organelles?
No; metabolic functions occur on plasma membrane folds
72
what increases genetic diversity in prokaryotes?
Rapid reproduction, mutation, genetic recombination
73
how do prokaryotes reproduce?
Binary fission
74
why do mutation accumulate quickly ?
short generation times
75
three mechanisms of genetic recombination?
transformation, transduction, conjugation
76
define transformation
Uptake of foreign DNA
77
Define transduction
gene transfer via phages
78
Define conjugation
DNA transfer via pili
79
What is the F factor
Fertility factor for conjugation
80
What are R plasmids?
Plasmids with antibiotic resistance genes
81
How often can binary fission occur?
Every 20 min to 3hrs
82
Why do prokaryotic populations evolve fast ?
high reproduction and mutation rates
83
What are endospores ?
Resistant dormant cells for survival
84
categories based on energy source?
Phototrophs (light) chemotrophs (chemicals).
85
categories based on carbon source?
Autotrophs (CO₂), heterotrophs (organic C).
86
Photoautotrophs use? Example?
Light + CO₂; cyanobacteria.
87
Photoheterotrophs use?
Light + organic molecules.
88
Chemoautotrophs use?
Inorganic chemicals + CO₂.
89
Chemoheterotrophs use?
Organic compounds; majority of prokaryotes.
90
Mnemonic for energy/carbon?
“Photo = light, Chemo = chemicals; Auto = CO₂, Hetero = organic carbon.”
91
Why are prokaryotes crucial in nitrogen cycle?
Make nitrogen bioavailable.
92
Nitrogen fixation?
N₂ → NH₃.
93
Nitrification?
NH₄⁺ → NO₂⁻ → NO₃⁻.
94
Denitrification?
NO₃⁻ → N₂ gas.
95
Example of nitrogen-fixing bacteria?
Rhizobium in legumes.
96
What are heterocyst?
Cyanobacterial cells specialized for N fixation
97
Obligate aerobes?
Require O₂.
98
Facultative anaerobes?
Use O₂ if present but can survive without.
99
Obligate anaerobes?
Poisoned by O₂.
100
Closer relatives of eukaryotes?
Archea
101
Do arches have peptidoglycan?
No
102
special features of archaea?
some have introns, histones
103
Define extremophiles.
Thrive in extreme conditions.
104
Halophiles?
Salt-loving archaea.
105
Thermophiles?
Heat-loving archaea.
106
Methanogens?
Anaerobic archaea that produce methane.
107
Example of methanogen habitat?
Cow rumen.
108
how do pathogens cause disease?
by releasing toxins
109
Exotoxins?
Secreted proteins that cause disease.
110
Endotoxins?
Released when Gram− bacteria die.
111
% of infectious diseases caused by prokaryotes?
~50%.
112
Example diseases?
Tuberculosis, Lyme disease.
113
What proportion of human cells are microbial?
~90%.
114
Human microbiome roles?
Digestion, vitamin production, immune development.
115
Medical use: fecal transplants treat?
Clostridium difficile infections.
116
What is bioremediation?
Use of microbes to clean pollutants.
117
Example of bioremediation?
Pseudomonas cleaning oil spills.
118
Role of prokaryotes in decomposition?
Recycling organic matter.
119
Global cycles influenced by prokaryotes?
Carbon and nitrogen cycles.
120
Example of biotechnological use of archaea?
Taq polymerase from Thermus aquaticus used in PCR.
121
What are stromatolites?
Fossilized cyanobacterial mats, evidence of early life.
122
who is considered the "father of microbiology?
Anton van Leeuwenhoek (1632–1723); observed microorganisms using 288× microscopes.
123
What was the former kingdom that included unicellular eukaryotes?
Kingdom Protista — now obsolete but still used as a general term.
124
What are protists?
Eukaryotes that are not plants, animals, or fungi.
125
Are most eukaryotes single-celled or multicellular?
Single-celled.
126
How do unicellular protists handle all life functions?
Through organelles within a single cell.
127
How are protists more complex than prokaryotes?
They have organelles that compartmentalize functions.
128
What are sub-cellular organelles responsible for in protists?
Carrying out processes such as movement, energy production, and reproduction.
129
What are the three main nutritional modes of protists?
Photoautotrophs, heterotrophs, and mixotrophs.
130
What do photoautotrophic protists use for nutrition?
Chloroplasts for photosynthesis.
131
How do heterotrophic protists obtain nutrients?
By absorption or ingestion.
132
What is a mixotroph?
A protist that combines photosynthesis and heterotrophy.
133
What is endosymbiosis?
A process where one cell engulfs another that becomes an organelle.
134
Mitochondria originated from what type of bacterium?
Aerobic α-proteobacterium.
135
Plastids originated from what type of organism?
Photosynthetic cyanobacterium.
135
What is secondary endosymbiosis?
When a eukaryote engulfs another eukaryotic alga.
136
What is a nucleomorph?
Vestigial nucleus in some plastids (e.g., in Chlorarachniophytes).
137
What are the four major eukaryotic supergroups?
Excavata, SAR, Archaeplastida, Unikonta.
138
What are the three main Excavata groups?
Diplomonads, Parabasalids, Euglenozoans.
139
What environments do Diplomonads and Parabasalids live in?
Anaerobic.
140
What are mitosomes?
Modified mitochondria in Diplomonads.
140
What disease does Giardia intestinalis cause?
“Beaver fever” (severe diarrhea).
141
What are hydrogenosomes?
Reduced mitochondria in Parabasalids that generate energy anaerobically.
142
What disease does Trichomonas vaginalis cause?
Vaginitis.
143
What feature unites Euglenozoans?
Spiral or crystalline rod in their flagella.
144
What are kinetoplastids?
Protists with a single large mitochondrion (kinetoplast DNA).
145
What disease is caused by Trypanosoma?
Sleeping sickness.
146
What is “antigenic variation”?
Ability of Trypanosoma to change surface proteins and evade immunity.
147
What are Euglenids known for?
Mixotrophy and light-sensitive eyespot for photosynthesis.
148
What does SAR stand for?
Stramenopiles, Alveolates, Rhizarians.
149
What are Stramenopiles characterized by?
A “hairy” flagellum paired with a “smooth” one.
150
What are the main Stramenopile groups?
Diatoms, golden algae, brown algae, oomycetes.
151
What are diatom shells made of?
Silica (hydrated).
152
What is diatomaceous earth?
Fossilized remains of diatoms.
153
What ecological role do diatoms play?
Major component of phytoplankton, key in carbon cycling.
154
What is the biological carbon pump?
The process where CO₂ is captured by phytoplankton and sequestered in the ocean floor.
155
Who proposed the Iron Hypothesis?
John Martin — suggested ocean fertilization with iron to reduce CO₂
156
What toxin does Pseudo-Nitzschia produce?
Domoic acid (causes amnesic shellfish poisoning).
157
Are brown algae unicellular or multicellular?
Multicellular.
158
What is the plant-like structure of brown algae called?
Thallus (with blade, stipe, holdfast).
159
What type of life cycle do brown algae exhibit?
Alternation of generations.
160
What is the defining feature of Alveolates?
Membrane sacs (alveoli) beneath the plasma membrane.
161
What are the three groups of Alveolates?
Dinoflagellates, Apicomplexans, Ciliates.
162
What causes “red tides”?
Dinoflagellate blooms.
163
What is bioluminescence in dinoflagellates caused by?
Luciferin-luciferase reaction.
164
Why are harmful algal blooms (HABs) increasing?
Runoff, pollution, and warming waters.
165
What is the role of dinoflagellates in coral reefs?
Symbiotic relationship (zooxanthellae) providing energy to corals.
166
What type of organisms are Apicomplexans?
Animal parasites (e.g., Plasmodium causes malaria).
167
What organelle helps Apicomplexans invade host cells?
Apical complex.
168
What is the apicoplast?
Non-photosynthetic plastid essential for parasite survival.
169
Why is malaria vaccine development difficult?
Large genome, antigenic variation, complex life cycle, low pharma incentive.
170
How do ciliates move and feed?
Using cilia.
171
What are the two types of nuclei in ciliates?
Macronucleus (daily function) and micronucleus (reproduction).
172
What is conjugation in ciliates?
Exchange of micronuclei between two cells for genetic variation.
173
What are Rhizarians known for?
DNA similarities and threadlike pseudopodia.
174
What are Radiolarians made of?
Silica skeletons with radiating pseudopodia.
175
What are Foraminiferans (Forams)?
Protists with calcium carbonate shells (tests).
176
Why are forams important fossils?
Form extensive marine sediment records.
177
What groups are included in Archaeplastida?
Red algae, green algae, and land plants.
178
How did red and green algae evolve?
From a protist that engulfed a cyanobacterium (primary endosymbiosis).
179
What pigment gives red algae their color?
Phycoerythrin
180
What advantage does phycoerythrin provide?
Absorbs blue/green light — allows deep-water photosynthesis.
181
What commercial product is made from red algae?
Nori (Porphyra).
182
What are the two main groups of green algae?
Chlorophytes and Charophytes.
183
Which group is most closely related to land plants?
Charophytes
184
What environments do chlorophytes live in?
Freshwater, marine, or terrestrial.
185
What is Chlamydomonas nivalis known for?
“Watermelon snow” — red carotenoid pigment in ice.
186
How did chlorophytes become multicellular?
By forming colonies, multicellular bodies, or multinucleate filaments.
187
What invasive green alga is known as a “supercell”?
Caulerpa taxifolia — multinucleate thallus, toxic to herbivores.
188
What group are plants closest relatives
green algae called charophytes
189
What polymer protects plant spores from desiccation?
Sporopollenin
190
what structure guides new call wall formation in plants and charophytes?
Phragmoplast
191
what are the main advantages for plants colonizing land?
More Sunlight, CO₂, and nutrients
192
What are the main challenges of terrestrial life?
Desiccation and gravity.
193
What is alternation of generations?
Life cycle alternating between multicellular haploid (gametophyte) and diploid (sporophyte) stages.
194
What is the function of archegonia and antheridia?
Archegonia produce eggs; antheridia produce sperm.
195
What are apical meristems?
Regions of active cell division at shoot and root tips.
196
What do cuticles and stomata do?
Cuticle prevents water loss; stomata regulate gas exchange.
197
What are bryophytes?
Nonvascular plants (mosses, liverworts, hornworts).
198
In bryophytes, which life stage is dominant?
Gametophyte (haploid).
199
What type of tissue allows vascular plants to grow tall?
Lignified xylem and phloem.
200
What are microphylls and megaphylls?
Microphylls = one vein; megaphylls = branched veins.
201
What is the dominant stage in ferns?
Sporophyte (diploid).
202
What are the derived traits of plants ?
– Alternation of generations and
multicellular, dependent embryos
– Walled spores produced in sporangia
– Multicellular gametangia
– Apical meristems
(absent in the charophytes)
203
BISC 120
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