deck_6712940-4 Flashcards
(370 cards)
1
Q
What is H2 bacteria a mile down like?
A
-Oxidize Fe^3+ to Fe3SO4 in presence H2 at high temp-Possibly clue to origin of life
2
Q
LEO GER
A
Lose electrons oxidationGain electrons reduction
3
Q
Uses for prokaryotes’ metabolical advantages?
A
-Geochemical cycles-Industrial applications-Environmental decontaminants (BP oil spill)
4
Q
How do prokaryotes reproduce?
A
Not through meiosis or mitosis but through binary fission
5
Q
Four principal time units
A
Eons, Eras, Periods, Epochs (EEPE)
6
Q
Outgroup
A
Outgroup inclusion “completes the tree” by identifying character states presumed ancestral and hence the characteristics of a presumptive common ancestor
7
Q
What does molecular evidence suggest about a whale of a tale?
A
Whales descended from artiodactyls
8
Q
T or F: Many prokaryotes secrete a gel-like extracellular polymeric substance (EPS)
A
True; it traps bacteria and it protects against harmful environmental factors - both physical and biotic
9
Q
What is the support for the theory that dinosaurs were already on their way out in the chicxulub impact during the mesozoic era?
A
Deccan traps when India moved over a hot spot-killed dinosaurs little by little
10
Q
Evolution of Nuclear membrane
A
-Protected archaean’s DNA from increased LGT consequent to symbiont cell lysis-Prevented intron translation (i.e. before their removal of spliceosomes)
11
Q
How does bioluminescence work in Dinoflagellates which are the taxa of aveolates?
A
Enzymes catalyzed production of light which attracts secondary predators and increases predation on dinoflagellate predators. This selects for flashing avoidance in same…this is the burglar alarm theory
12
Q
What does the “dark” reactions of oxygenic photosynthesis entail?
A
- Oxidation of NADPH to NADP+ and ATP to ADP2. Reduction of CO2 to glyceraldehyde 3-phosphate (G3P) -> sugar.BASICALLY: Converts carbon dioxide to carbohydrate
13
Q
Examples of monophyletic taxa
A
Mammals and birds
14
Q
What are the two prokaryotic domains?
A
Archaea and Bacteria
15
Q
The bacterial Flagellum
A
-Icon of Intelligent Design-Related to Type 3 Secretory System - injects toxins into host cells-Materialist-creationist disconnect comprehensible wrt Lakatosian Research
16
Q
What was the precambrian eon lacking?
A
Precambrian eon was lacking both fossils and fossil bearing rocks because the organisms were soft bodied and the rocks were too hard or destroyed the fossils
17
Q
How are Archaea similar to Eukarya?
A
-Histones associates with DNA-Translation initiated by methionine (Met)
18
Q
Terminal nodes
A
Tips
19
Q
Polymerization
A
Peptide formation requires condensation reactions (H2O removed)
20
Q
What are hydrothermal vents home to?
A
Thermophilic Archaea
21
Q
Alveolates (common ancestor of protists) characteristics
A
Name refers to small vesicles (alveoli) that are in or just below the cell membrane. They may regulate ion transport and structural stabilization of the cell membrane and most are unicellular
22
Q
Stromatolites: what are they and what are their contributions
A
-Bacterial mats-Important to the oxidation of earth’s atmosphere-They contain cyanobacteria that produces O2 -byproduct of oxygenic photosynthesis
23
Q
T or F: Water all freezes at once
A
False; It freezes little by little, this is how Miller’s freezer experiment worked
24
Q
List difficulties of the origin of life (4)
A
-Polymerization-Primordial atmosphere insufficiently reducing-Insufficient time-Nucleic acid synthesis impeded by high temp
25
What does the "Pinching off" theory say about nucleus and cytoskeleton?
They arose de novo
26
Oxidation
The loss of electrons
27
What ocean forms during the Cretaceous separating what two modern day countries/continents?
The North Atlantic which separates Europe and NA
28
Placental ungulates =
hoofed mammals
29
General characteristics of protists
-Most live in aqueous environments-Most small; some large-Protists are metabolically less diverse than prokaryotes and more diverse morphologically-Reproduces with/without sex-Some have haploids AND diploids-Primary producers in aquatic habitats-Some cause diseases like malaria and toxoplasmosis-Multicellularity evolved multiple times
30
What can first? Microfossils or biogenic carbon?
1st microfossils date to 3.5 By and biogenic carbon came even earlier
31
What is the Oparin-Haldane Hypothesis?
In the 1920s Oaprin and Haldane independently proposed that life formed spontaneously under pre-biotic conditions.-Both assumed that life evolved from proteins
32
What is the resulting mixture of cells and secretion of the prokaryote gel-like extracellular polymeric substance? (EPS)
Resulting mixture of cells and secretions called a biofilm.Ex. Stromatolites; dental plaque
33
Metabolism and Heterotrophs for both prokaryotes and eukaryotes
-In eukaryotes, principal energy source is glucose-In prokaryotes, diverse energy sources - include glucose, ethanol, acetate, fatty acids, complex carbs, proteins, amino acids, purines, etc.
34
What environment did stromatolites survive in?
They were originally thought to be extinct but they survived in high salinity areas to protect them from grazing invertebrates such as worms and snails
35
What continent forms and drifts during the Cambrian?
Gondwana
36
Two theories of result of insufficient reducing of the atmosphere
Panspermia (microorganisms or chemical precursors of life present in outer space and able to initiate life on reaching a suitable environment)and Early habitable universe
37
Explain the Burglar theory with squids and mosquito fish
Time required by squid to strike mosquito fish in the presence of luminous and non luminous dinoflagellates. Movement by mosquito fish stimulates bioluminescence, thereby increasing fish susceptibility to predation as predicted by burglar alarm hypothesis from the Fleisher Case
38
How were Neanderthals terminated?
Homo sapiens interbred with Neanderthals and terminated them
39
Autogenous models
Prokaryote that basically created a nucleus and then mitochondria and chloroplasts came later.
40
What did Oparin postulate?
Oparin postulated spontaneous appearances of oily droplets (coacervates) that subsequently evolved into cells
41
Convergent evolution
Acquisition of similar traits by distant lineages
42
T or F: Some Ediacaran animals may have persisted into the mid-Cambrian
True
43
Benefits of impacts of comets and meteorites
-They deliver water and gasses-Source of organic and simple
44
Similarity of Anaerobic and Aerobic metabolism
Glucose converted to pyruvate. ATP yield is 2 molecules ATP per molecule of glucose
45
Summarize the nitrogen cycle
Nitrogen fixing bacteria convert atmospheric nitrogen (nitrogen fixation) to compounds that can be used by plants. Ammonia (product of decomposition) is nitrified (oxidized) to NO2^-, and NO3^-, which is then denitrified (reduced to N2
46
Mesozoic Era characterized by
-Mammals and dinosaurs-Mammal-like reptiles dominate-Flowering plants and birds evolve-Chicxulub impact
47
What is unique about Archaea?
-Plasma membrane structure-Cell wall composition-Flagellar structure and development - grow from base (archaea) vs, tip (bacteria)
48
Apical complex
-Complex that facilitates penetration of host cells-An associated structure, the apicoplast, in a non-photosynthetic plastid surrounded by four membranes-By killing the apicoplast does not kill the parasite, but prevents penetration of host cells-Promising target for new anti-malarial drugs because of differing plastid (prokaryote), mammalian cell sensitivities-Malaria caused by various species of Falciparum-Extra-cellular parasite of mosquitoes; an intra-cellular parasite of vertebrate (secondary) host
49
Facts about the earth's formation
-Level of violence was uncertain-If the process was fast or if the moon was created from an enormous impact then the entire surface remelted-If not, only the core melted-The melting vaporized many oceans
50
Main feature of the Permian
"Mammal-like" reptiles
51
Riboswitches
Regulatory segments of messenger RNA that alter/block protein production via translation or transcription
52
What brought on the origin of species?
-Social insects-Vertebrates
53
What occurred in the precambrian eon (4.5-4.6 By a)?
-Origin of Life on Earth-Origin of Prokaryotes-Origin of Eukaryotes-Evolution of sex-Evolution of multicellularity-Formation of the moon-Bombardment phase-Increase in oxygen
54
Example of Pleiotropy
Chimp at London zoo as a young female. In dress and rode bike: when chimp grew older, the jaw grows and teeth get sharper -\> not so cute.-When you select for one thing you select for many things: Pleiotropy (one trait can do a lot of things)
55
Gram positive
Bacteria have more peptidoglycan (Outter layer)
56
Packaging metabolism inside a membrane to avoid the dilution problem is a consequence of...
The 2nd Law
57
Apicoplasts descended from _____ .
chloroplasts which are also free living
58
Periods in Cenozoic era (2)
Tertiary, quaternary (we are in this)
59
What did Haldane imagine regarding the spontaneous origin of life?
Haldane imagined gradual increase in concentration and complexity of pre-biotic molecules in solution-Caused by intense levels of UV radiation reaching earth's surface prior to development of ozone shield
60
T or F: Symbiotic bacteria and protists facilitate digestion of tough vegetation / cellulose
True
61
Who first discussed serial homology for the first time?
Poet J. W. von Goethe when referencing flower parts which he correctly believed were modified leaves - "foliar theory" of the flower
62
Mitochondria phylogeny info.
-Double membranes of mitochondria remnants of engulfing "way back when"-Mitochondrial DNA groups with proteobacteria
63
Dinoflagellates (taxa of aveolates)
-Two (transverse and longitudinal) flagella - permit forward and rotary motion-Some have a theca (protective covering composed of cellulose plates)-Nuclear structure aberrant meaning no histones or nucleosomes and chromosomes condensed during interphase-Important ocean primary producers - coral endosymbionts-Bioluminescence-Red tides
64
What type of evidence suggests that primitive whales had a double pull astragalus?
Fossil evidence
65
Which species of protist is polyphyletic?
Amoebas
66
Theory: Subsurface origins
Theory that life started beneath the surface of the earth; Semi backed up by that fact that we know archaea lived in the earth's surface
67
What solved the "what came first: proteins or DNA?" and what is the answer?
RNA world theory; RNA came first
68
What came out of eukaryotes and the Cambrian explosion?
-Origin of sex-Origin of multicellular life - the latter has occurred multiple times
69
Cladistic relating to relatedness:
-Distinguishes ancestral from derived characters-Infers relatedness from presence of shared derived characters called synapomorphies
70
What continent forms in the Permian and then what does it divide into?
Pangea and then it divides into Laurasia and Gondwana
71
Bombardment Phase
-Ended 4-3.8 Bya-Called bombardment because of colliding objects
72
Metabolism and Autotrophs for both prokaryotes and eukaryotes
-In eukaryotes, carbon source is CO2, which is fixed via Calvin cycle-In prokaryotes, there are multiple carbon sources: CO2 (cyanobacteria and others) CH4 (methanotrophs), CO, CH3OH, etc.
73
What is toxoplasmosis?
A disease from an apicomplexan that is spread by contact with cat feces
74
What is the name Cambria an old name for?
Wales
75
Main feature of the Devonian
Terrestrial vertebrates
76
What did Oparin believe the carbon source was on Earth?
Methane
77
Does sex = reproduction?
NO; Sex without reproduction, e.g. bacterial conjugationReproduction without sex, e.g. mitosis
78
End-Permian characterized by:
Large mass extinction-96% of all species lost-Coincident vulcanism/anoxia: Siberian traps
79
What is rooting the tree?
Including an outgroup
80
Features of silurian
-Jawed fishes-Sea scorpions-First land plants-Terrestrial insects
81
All things carbon isotopes
Carbon has many different isotopes and carbon 12 is the most common. Less common more heavy is carbon 13.-The ratio of C12 to C13 allows us to infer existence of life-The presence of organic matter that are carbon deposits with higher concentration of C12 are said to be the signature of photosynthesis because the enzyme in photosynthesis prefers C12 to C13, the lighter isotope-If you have dark matter, and you find the ratio of C12 to C13 and C12 is higher than C13, this means that there are traces of plant life and animal life in the sample compared to the earth ratio at large
82
Where does the TCA cycle happen in pro- and eukaryotes?
Prokaryotes: CellularEukaryotes: mitochondrial
83
Characteristics of Crenarchaeota
-Most thermophilic and or acidophilic-Sulfolobus lives in hot springs and requires temps greater than 131 F
84
What did the insufficient time difficulty say about the window of opportunity for complex life forms to evolve?
The window of opportunity was very narrow
85
Characteristics of Apicomplexans
-Parasitic (cause malaria)-Name refers to apical complex (apical polar ring) that facilitates penetration of host cells
86
T of F: The moon was originally part of earth?
True
87
What supports the pre-biotic synthesis of biological molecules?
-Existence of carbonaceous chondrites
88
Significance of the first class of organisms that survived the oxygen catastrophe
A few organisms, including ancestors of mitochondria, "learned" to utilize/detoxify oxygen and other products of aerobic metabolism
89
Where were the first fossils found?
Cambria
90
What characteristics do all three domains have in common?
-Genetics (DNA)-Metabolic (utilization of ATP)-Structural (Ribsomes, plasma membranes, and flagella)
91
Traditional RNA world scenario
1.RNA form ribose and nucleotide2.RNA "learns" to self-replicate3.RNA catalyzes protein synthesis4. Proteins facilitate -More efficient RNA self- replication -Double-stranded RNA that evolves into DNA5.DNA assumes role of information storage. RNA relegated to transcription/translation6.Chemistry packaged in a membrane
92
Structural similarities in all Three Domains
Ribosomes, plasma membranes, and flagella
93
Why was the sudden appearance of extensive fossils in the Cambrian concern to Darwin?
-He viewed such an abrupt increase in biotic diversity as contradicting evolutionary gradualism-Imagined abundant Precambrian life, the remains of which were not preserved
94
3 advantages of sex
1. Production of genotypic variability via recombination2. "Hybrid vigor" which is consequent to heterozygous advantage3. Facilitation of DNA repair when homologous chromosomes pair
95
Why are prokaryotes important?
-Abundant and ubiquitous in/on bodies-Essential to proper digestion-Some bacteria pathogenic-Participate in geochemical cycle (nitrogen cycle)-Extremophiles
96
Why was major taxa appearance a problem for Darwin?
It undercut his idea that evolution was gradual
97
Characteristics of Actinobacteria
-Many filamentous-Most free-living in soil - decomposers (chitin, cellulose)-Important source of antibiotics (e.g) streptomycin
98
T or F: Viruses are considered non-life
True, however, that may be starting to crack
99
Difference between convergent and parallel
-At the morphological level, vertebrate and cephalopod eyes are convergent-At genetic level, parallel - the same regulatory genes determine their development
100
Characteristics of Chlamydias
-Extremely small: 0.2-1.5 nanometers. Gram negative cocci-Pathogenic: STDs, eye infections, some forms pneumonia
101
What is the entry of CO2 into the Calvin cycle catalyzed by?
The RuBisCO enzyme
102
What do oxidants do?
They remove electrons from molecules which is called oxidizing the molecules. They are electron acceptors
103
T or F: all three domains have membrane enclosed organelles and sex?
False; only Eukarya has membrane enclosed organelles and sex
104
T or F: High energy compounds (ATP, GTP) are ribonucleoside (nucleobases + sugar) triphosphates
True
105
Nodes
Branching or terminating points
106
Symbiogenesis First Theories (2)
-Ring of Life Hypothesis-Chronocyte Theory
107
Characteristics of eukaryotes
-Lack bacterial wall-DNA organized into chromosomes; DNA wrapped around histones-Possesses cytoskeleton, digestive vesicles, and membrane-encased organelles
108
What are the two carbon sources?
Autotrophs and Heterotrophs
109
Genetic similarities in all Three Domains
-DNA is the hereditary molecule-Semi-conservative DNA replication - daughter molecules consist of one new strand; one old-Transcription and translation: DNA -\> RNA -\> Proteins-"Universal" genetic code
110
The extent to which Precambrian "animals" ancestral to Cambrian assemblages _____ .
uncertain
111
What is the 25 year freezer experiment?
Miller added ammonia and HCN and put it in the freezer for 25 years, it produced amino acids and nucleobases - freezing concentrates impurities- promotes assembly
112
Differences between meiosis and mitosis
in mitosis-Daughter cells identical to each other and parent-Both haploid and diploid cells can reproduce by mitosis
113
T or F: Gram positive eubacteria includes species with gram negative walls
True
114
T or F: Ungulates became prey
False; ungulates became predators
115
Epochs in quaternary (2)
pleistocene, holocene
116
What is 1/4 of earths history?
Phanerozoic Eon
117
What was the oldest microfossils?
3.5 ByaProkaryotes
118
Based on gene sequence of small ribosomal subunit Archaea and Bacteria are
Highly conserved
119
Example of polyphyletic taxa
Flying vertebrates - the MRCA walked
120
Old Theory: A whale of a tale
Whales descended from extinct carnivores
121
RNA world Theory
1.RNA (messenger and ribosomal) manufactures proteins2.RNA can self-replicate in vitro3.RNA can produce DNA via reverse transcriptase4.Single stranded RNA forms 3-D structures that can catalyze reactions, e.g., ribozymes remove introns
122
What do mycobacteria engage in?
-I believe it is a type of proteobacteria-Cooperative "hunting" via chemical mediated aggregation and synthesis of extra-cellular digestive enzymes-Formation of multicellular "fruiting bodies" (reproductive structures) that produce myxospores when resources scarce
123
Biosynthesis
-Requires molecular oxygen-Oxidant protection-Made possible by accumulating oxygen in earth's waters-May also have facilitated evolution of photosynthesis-Approximately coincident with evolution of multicellular cyanobacteria and / or origin of eukaryotes
124
Reduction
The acquisition of electrons
125
What is the consequence of India and Australia drifting north and east during the Cenozoic?
India eventually collides with Asia which then forms the Himalayas
126
Epochs in Tertiary (5)
Paleocene, Eocene, Oligocene, Miocene, Pliocene
127
Difficulty regarding early nucleic acids
Spontaneous synthesis of nucleic acids was impeded by high temperatures
128
T or F: Branch length is arbitrary however order of tip taxa is not
False; both branch length and order of tip taxa are arbitrary
129
T or F: Miller argued that thermophilic is a derived trait
True; He backed up this theory with the fact that high temperatures degrade macromolecule precursors (Sugars and nucleobases) and the results of the 25 year freezer expt.
130
Two possibilities now that we know the Cambrian explosion is real
1. Most of the major taxa really did originate over 10-15 million years2. Lineages that had previously diverged radiated into new niches and acquired skeletons
131
Overview of meiosis
-Chromosomes number reduced from 2N to N-Recombination =\> new gene combinations-Haploid gametes fuse (fertilization) =\> diploid zygote-Offspring genetically distinct from parents and each other
132
Life cycle of malaria summary
Gametes fuse in mosquito gut, and the mosquito injects the oocyst parasite. Invade liver and infect red cells and trophozoites mature in red cells to become either schizonts of gametocytes and release more and more merozoites. The gametocytes/parasites are removed from female mosquito where they are they fertilized in the female and the gamete forms an ookinete which grows and then bursts and this starts again.
133
What is the mitochondria First Theory?
Nucleus formation in eukaryote ancestors triggered by engulfing mitochondrial ancestors
134
What do methanogens (Archaea) do?
They are a source of methane in cows and people. They basically help with methane in farts
135
T or F: Viruses RNA world relics - originally all used RNA
True
136
What happened when humans arrived on the Bering Straight Land bridge from NA to SA?
Humans caused the extinction of the Pleistocene megafauna in NA including mammoths and lions
137
Why is our earth filled with oxygen?
Oxygen photosynthesis meaning, oxygen came from photosynthesis performing organisms
138
Auxiliary hypothesis
Rescuing the idea you really thought/wanted; being the parent and mediated your experiment
139
What happens when Proteobacteria are pathogenic?
-Can cause gastritis, ulcers, cancer-Survives in stomach by creating - pH neutral micro-environment in the mucosa via urease-mediated conversation of urea to CO2 and NH3 - itself is toxic-Induces inflammatory responses directly and via recruitment of white blood cells that produce so-called reactive oxygen species
140
Two theories that account for Pleistocene megafauna extinction?
-Overkill-Climate Change-Both theories are not mutually exclusive
141
When did the earliest known eukaryote come about?
1750 Mya
142
T or F: mitochondria and chloroplasts have nothing to do with free-living prokaryotes
False; Widely agreed that mitochondria and chloroplasts descended from free-living prokaryotes - have bacteria-like DNA
143
Taxa
Can be species or higher taxonomic groups
144
One problem proposed by May about Darwin's evolution
Calvin's estimations of Earth's age were wrong; evolution can occur because of the very old age of Earth
145
New theory: A whale of a tale
Whales descended that whales descended from artiodactyls - "even-toed" ungulates
146
Paraphyletic taxa
-Includes the MRCA but not all descendants
147
Four monophyletic protist groups
AlveolatesStramenopilesChlorophytesChoanoflahgellates
148
Ring of Life Hypothesis
-Eukaryotes arise vis fusion of an archaebacterium (archaea) and eubacterium (bacteria)-Archaebacterium became the nucleus-Consistent with genomic comparisons of yeast and bacteria: Genes coding for nuclear functions from Archaea; genes coding for cytoplasmic function, from Bacteria
149
Urey-Miller Experiment results
-Stunning confirmation of Oparin-Haldane hypothesis-Interpreted as supporting Haldane's idea that the primordial ocean was a "dilute soup" of organics that precipitated out of the atmosphere
150
Nitrification
Nitrogen fixing bacteria convert atmospheric nitrogen, N2, into compounds that can be used by terrestrial plants. Part of Nitrogen/geochemical cycles
151
Homology
Similarity by virtue of common descent
152
Protists are a ____ group of eukaryotes that are neither plants, not animals, nor fungi
paraphyletic
153
What can strata be used for?
Fossils, matching fossils from different locations, understanding times scales
154
Deriving whales from artiodactyls necessitates an evolutionary reversal: _____ .
DPA gained, then lost
155
T or F: Deoxyribonucleotides (nucleobases + sugar + phosphare) enzymatically synthesized from RNA precursors
True
156
How much oxygen was at the beginning of the Cambrian?
10% oxygen
157
Purpose of the Urey-Miller Experiment
They wanted to test the Oparin-Haldane hypothesis
158
Abiogenesis
Spontaneous generation of living things
159
Where does the glycolytic reactions happen in pro- and eukaryotes?
Cellular in both
160
Characteristics of Euryarchaeota
-Some are methanogens - produce CH4 from CO2-Some halophiles
161
What includes the ancestors of mitochondria?
Proteobacteria
162
Serial homology
Duplication and modification of parts in different ways
163
What is the OOA and what is it supported by?
-"Out of Africa"-Supported by genetics and paleontology -Starts in Africa and humans travel to Asia, Australia, then NA and SA-Recently updated; earlier colonization of Asia
164
What are the three energy sources?
-Light-Organic molecules-Inorganic molecules
165
Which dinosaurs made it out of the Chicxulub impact and which were killed? Avian vs. Non avian
Avian: made it out of chicxulub impact and had radiation from impactNon Avia: Killed from chicxulub impact
166
Four mammalian tooth types
-Incisors-Canines-Premolars-Molars
167
Periods in Mesozoic era (3)
Triassic, Jurassic, Cretaceous
168
What was the earliest life?
Microfossils
169
Multicellular: Bacteria? Archaea? Eukarya?
Bacteria: RarelyArchaea: NoEukarya: Many
170
Characteristics of Firmicutes
-Probably not a monophyletic group-Bacillus, Clostridium, Staphylococcus-Produced long-lived endospores - difficult to remove from environmental (e.g. hospital) surfaces-Recent emergence of antibiotic-resistant strain of C. difficile (causes diarrhea) may be consequent to inclusion of antibiotic in cattle feed.
171
What is ecological homeostasis?
Keeping the environmental conditions stable. Example: microbes eat oil in BP oil spill
172
Creodonts
-Independently evolved carnassial-convergent evolution if reference is to which cheek teeth modified; parallel if to cheek teeth
173
Homoplasy
Similarity by independent acquisition
174
Significance of South America during the Cenozoic Era
-Mammalian fauna consisted of archaic placental ungulates (hoofed mammals) and marsupial carnivores-Home to giant flightless terror birds-Unique biota died out following formation of the Isthmus of Panama and invasion by North American species
175
What brought on the origin of consciousness/self-awareness?
-Primates-Cetaceans-Avian dinosaurs (maybe)
176
Where did the names of the EEPEs came about?
The name for the EEPEs came from where the strata, rocks, and fossils were first discovered and dug up
177
Characteristics of Prokaryotes
-Small; mostly unicellular-No nucleus-DNA organized into - Circular chromosomes - Plasmids - exchanged during conjugation or taken up from environment-No mitosis-No meiosis-Reproduces by binary fission-No membrane-enclosed organelles - mitochondria, chloroplasts, etc. but, bacteria do possess - Cytoskeleton proteins - Protein-encased organelles
178
T or F: If atmosphere weakly oxidizing (CO2 and N2), biomolecule yield greatly diminished
True
179
Primordial Sun
Beginnings of the sun
180
T or F: The oldest evidence of living creatures based on the isotopic ratio is a little bit older than the oldest microfossil
True
181
Eras in Phanerozoic eon (3)
Paleozoic, Mesozoic, Cenozoic
182
T or F: If the modern taxa evolved shortly before they appear, molecular data overestimate divergence times
True
183
T or F: Giant viruses have genomes as large as or larger than parasitic prokaryotes
True
184
Main feature of the Ordovician
Jawless fishes abundant
185
Denitrification
Other prokaryotes recycle ammonia (product of decay) back to N2. Part of Nitrogen/geochemical cycles
186
Chronocyte Theory
-Extinct RNA-based eukaryote lineage (chronocyte) evolved cytoskeleton and phagocytosis-Engulfed archaea became DNA based nucleus-Explains eukaryotic signature proteins (ESPs) -membrane systems, ER, cell cycle, etc. unique to Eukaryotes - as chronocyte heritage-Explains spatial separation of transcription (nuclear) and translation (cytoplasmic)
187
Why do morphological evidence conflict with molecular evidence for the whale of a tale?
Morphological evidence claims that whales lack double pulley astragalus (DPA)-DPA (ankle bone) is the synapomorphy that distinguishes artiodactyls from other ungulates-The term "double pulley" refers to the presence of two articular surfaces - one with the tibia (leg bone), the other with the os navicular (another foot bone)
188
Problem of primordial environment
Primordial environment not producing sufficient amount of carbon and oxygen in substances
189
What was rusted in the ocean?
Banded Iron Formations (BIFs)
190
Pterodactyl, bat, and bird wings are homologous or homoplastic?
Depends on point of view-Homologous-viewed as forelimbs - the usual view-Homoplastic-viewed as wings -no winged common ancestor - an alternative, but equally valid view
191
Proteobacteria - purple bacteria
-Metabolically diverse-Primitively photoautotrophic-Some fix nitrogen in legume root nodules-Some pathogenic
192
What period do our ancestors come from?
Permian
193
How are Archaea similar to Bacteria?
Both....-Unicellular-No nuclear envelope-Circular chromosomes-Absence of organelles
194
What are chloroplasts of modern plants descended from?
Cyanobacteria
195
Eons (2)
Precambrian, Phanerozoic
196
Reasons for why the stage was set for the evolution of Metazoa with the evolution of eukaryotic cells?
-Gene based phylogenies: Major groups diverged before the Cambrian-Paleontology: few metazoans at the base of the Cambrian. Dramatic increase in size, numbers and diversity thereafter.-15 my into the Cambrian, 80\_+ skeletal taxa-Trilobites: 530 Mya-Except for bryozoans, all major groups appear in the Cambrian
197
Significance of the second classy of organisms that survived the oxygen catastrophe
Mitochondria is a source of oxidants, against which eukaryotic cells mount enzymatic defenses-This is the reason why we can't get cut with a rusty nail. The oxygen somewhat attacks us.
198
Example of protein-encased organelles
Carboxysomes that increase rate of photosynthesis
199
Story to remember Thylacosmilus
-Thylacosmilus is an extinct South American metatherian carnivore superficially similar to North American saber tooth cats-STORY: Road runners come to Schaffer's backyard and eat the cat kindle by snapping at it with their beaks
200
What gas predominated in the first atmosphere?
Hydrogen which was part of the original nebula
201
T or F: UV light can create and destroy ozone
True; ozone creation and destruction varied over time with the varying development of the sun
202
Why did the ocean take longest to increase the amount of oxygen?
The ocean was too deep to have sunlight reach the plants to begin photosynthesis
203
Significance of when bombardment phase ended
Ended around the same time scientists expected traces of organic life to start being found
204
Paraphyletic taxa example
Reptiles
205
Mnemonic for Paleozoic and Mesozoic periods
Cows Often Sit Down Carefully. Perhaps Their Joints Creak?
206
Polarity of all phospholipids
Nonpolar inside with polar outside
207
T or F: Previously everyone thought that the information being passed on from one generation to the next was nucleic acids but its actually proteins
False; Previously everyone thought that the information being passed on from one generation to the next was proteins but its actually nucleic acids
208
One problem that May proposed about Darwin that has not been resolved
Evolution and the idea of altruism
209
Characteristics of the Cenozoic era
-Post-Chicxulub radiation of surviving Mesozoic mammals and birds-Placental mammals dominate-Man evolved in Africa-Megafauna extinction-OOA-Agricultural Revolution -\> self-domestication
210
What is 3/4 of the earth's history?
Precambrian Eon
211
Parallel evolution
Acquisition of similar traits by closely related lineages
212
Urey-Miller Experiment
Passing an electric spark (simulates lightning) through a reducing atmosphere results in the formation of amino acids - mostly glycine and alanine
213
T or F: Fossils always trump anatomy, genetics, etc. of living organisms
True
214
Types of Archaea (2)
-Crenarchaeota-Euryarchaeota
215
Phylogenetic trees
Represent presumed patters of descent and are analogous to family trees
216
Polyphyletic taxa
-Does not include MRCA, merely just certain branches
217
Examples of homologies
Human arm, cat leg, whale fin, and bad wing all have similar homologies meaning similar structures
218
T or F: All protists are unicellular
False; most but not all
219
What is the problem with polymerization?
In aqueous solutions, rate of polypeptide dissociation far exceeds the rate of condensation
220
Carbonaceous chondrites
-meteorites containing significant concentrations of organic compounds that landed near Murchison, Victoria, Australia-Presence of guanine and adenine the nucleobases
221
What is the signature of photosynthesis?
12c enriched organic matter
222
Characteristics of Spriochaetes
-Gram-negative (thicker middle)-Axial filaments produce corkscrew-like motion-Some pathogenic: causes syphilis, Lyme disease
223
Summarize the biofilm life cycle
1. Single cells colonize a surface2. Extracellular polymeric substances (EPS) produced; attachment becomes irreversible3. Biofilm develops4. Single cells are released colonizing new surfaces and starting the life cycle over
224
Summarize cellular respiration in anaerobic organisms
Glycolysis produces high energy compounds (ATP and NADH) and pyruvate, which is converted to lactic acid (vertebrate muscle) or ethanol (yeast). High energy compounds other than ATP then enter the electron transport chain where they converted to ATP
225
T or F: Three such viruses independently converted (reverse transcription) different RNA hosts to DNA
True; The descendants of the converted checks ancestral to the three domains
226
T or F: The original atmosphere on earth had oxygen
False; it didn't have any oxygen
227
How did the sun come about?
A nebular cloud condensed to become the sun and the gravity was sufficiently large so the atoms became sufficiently close and one day the sun turned on and there was an enormous explosion
228
Why is the viruses = non-life consensus going away?
Giant (double stranded DNA) viruses produce proteins normally associated with cellular physiology including enzymes that synthesize tRNA
229
A pair of taxa that have a common ancestor not shared by any other taxon are called _______ .
Sister taxa
230
Gram negative
Bacteria have less peptidoglycan (middle layer)
231
Accretion:
Stuff coming together
232
What is the principal component of cell membranes?
Phospholipids
233
Evolutionary reversal
The re-acquistion of an ancestral trait or the loss of a derived trait
234
What do reductants do?
They reduce other molecules to which they donate electrons. They are electron donors
235
Chloroplasts phylogeny info
-DNA groups chloroplasts with cyanobacteria-Multiple membranes in some photosynthetic protists reveal history of multiple engulfing in some species
236
Why do species alternate between sexual and asexual reproduction?
-Asexual reproduction in favorable environmental conditions-Sexual reproduction in unfavorable conditions-Sexual reproduction entails production of Hardy which are spores that simultaneously constitute a dispersal stage
237
Autotrophs
Synthesize biomolecules from simple compounds such as CO2
238
How was the Earth formed?
The Earth was formed from accretion over a period of uncertain duration
239
What are the three steps of the "Pinching off" Theory?
1. Loss of cell wall2. Invagination of cell membrane 3. Nucleus pinches off
240
Types of Bacteria (5)
-Proteobacteria-Cyanobacteria-Spirochetes-Chlamydias-Firmicutes
241
Amniotes
Reptiles, birds, and mammals that lay eggs or have amniotic membranes
242
Summarize cellular respiration in aerobic organisms
Pyruvate enters the TCA cycle (Citric acid cycle) which results in the production of additional high energy compounds (ATP, GTP, NADH, and FADH2).High energy compounds other than ATP then enter the electron transport chain where they converted to ATP
243
When did mammals arise?
Triassic period in the Mesozoic era in the Phanerozoic eon
244
What biological activities are the cause of present day oxygen-rich atmosphere?
-The great rusting-Oxidation of bacteria-produced CH4-"Snowball earth" consequent to reduced greenhouse effect a possible result
245
Emergent properties
Thinks: The brain thinks but neurons don't
246
Theories for connecting metabolism and information storage
-Mineral cells-Coacervates (egg and oil idea)
247
Major transitions in the history of life
Origin of life and the origin of eukaryotes
248
Chicxulub impact
-65 Mya-Most likely killed off the dinosaurs-Confusion because scientists aren't sure if dinosaurs were killed off from this one event or if they were on their way out
249
T or F: The orbit of the earth is elliptical and changes on time scales?
True
250
Monophyletic taxa
-Includes most recent common ancestor and ALL its descendants-Monophyletic taxa called clades
251
T or F: Bipedalism precede large brains
True
252
The Three Domain Theory requires that...
...observations consistent with symbiogenic origin of Eukarya is the result of lateral gene transfer
253
Aside from the RNA world theory, what are more recent studies suggesting?
-rRNA and proteins may have evolved in parallel before formation of first ribosome-Early protein synthesis independent of RNA-In either case, packaging may have come first- or not.
254
What does it mean that some prokaryotes are extremophiles?
Some prokaryotes live in extreme environments - high temperature, acidity, salinity - that may be similar to those in which life evolved
255
Spliceosomes
Molecular machines formed of proteins and small nuclear RNA molecules that remove introns from messenger RNA before translation
256
Big question about the origin of life?
Was the origin of life a wildly improbable event (frozen accident) or an inevitable consequence of changing conditions (emergent property)?
257
T or F: If the molecular evidence regarding Cambrian taxa, absent distinguishing skeletal features, is true, then Cambrian taxa evolved long before the end of the Precambrian
True
258
Principle of Parsimony
The most plausible phylogeny is that which necessitates-The fewest evolutionary reversals-Fewest independent character acquisitions
259
When did the platypus arise?
Late jurassic where protherians (platypus, echidna) and therians came about
260
What was the formation of the moon like?
Creation disk that has a lot of rocky stuff in it that condensed into sun or planets. The moon was formed because the earth was hit with a very large object and the moon was shot off into space.
261
What did the Earth look like during the bombardment phase?
The earth wasn't covered in molten lava. it was apparently cool enough to walk on but the earth did have occasional sterilzing periods where it would become incredibly hot
262
How do the phospholipids of archaea and bacteria/eukaryotes differ?
-Archaea phospholipids are composed of branched isoprene chains bound to phosphate group by ether linkages-Bacterial AND eukaryote phospholipids consist of straight chain fatty acids bonded by ester linkages
263
Carnassials
In living carnivores, P4 and M1 (certain teeth) specialized for slicing-A synapomorphy defining order Carnivora
264
Characteristics of the Phanerozoic eon
-Fossils Abundant-Evolution of higher plants and animals with major taxa appearing at or near base of the Cambrian
265
What is similar for both the Chronocyte Theory and the Ring of Life Hypothesis?
They both agree that mitochondria and chloroplasts acquired later
266
What are Sterols and what do they do?
They are a moderately flexible and permeable important component of eukaryotic cell membranes
267
Mineral cell theory
Holds that metabolism originated in tiny cavities in minerals such as FeS. Cell membranes came later
268
Numerous hypotheses proposed since Urey-Miller
-RNA world-Lipid world
269
Which of the three domains has circular chromosomes?
Most bacteria and all archaea
270
What was the second atmosphere a product of?
-Outgassing - Volcanic eruptions-Impacts from meteors etc.-No free oxygen-Reducing or weakly oxidizing-H2 (maybe) and H2O
271
Significance of Australia during the Cenozoic Era
-Home to the world's only living monotremes (egg laying mammals)-Marsupials (descended from opossums) dominate to this day
272
Radiometric dating
20th century; used C14 which Is the heaviest isotopes
273
What is malaria?
A disease from an apicomplexan in mosquitoes. Malaria is an extra cellular parasite of mosquitoes and an intra-cellular parasite of secondary, vertebrate host
274
Phenetic relating to relatedness:
Infers relatedness from overall similarity
275
What do the large and small subunits do together?
They collaborate to assemble proteins (translation)
276
What two things does cellular respiration entail?
Cellular respiration (glycolysis, TCA cycle) entails-The oxidation of compounds such as glucose-The reduction of oxidized forms of high energy compounds such as NAD+, ADP to NADH, ATP, etc.
277
What is the waste product of Photosynthesis?
Oxygen
278
What does the "light" reactions of oxygenic photosynthesis entail?
1. Reduction of NADP+ to NADPH and ADP to ATP (source of energy)2. Oxidation of H2O to O2 (source of atmospheric oxygen)
279
T or F: Viruses have not evolved DNA
False; Viruses evolved DNA in a co-evolutionary arms race with their RNA hosts
280
Phagocytosing Archeon Theory (PhAT)
-Now extinct Archaea evolve phagocytosis-Mitochondrial ancestor engulfed-Mitochondria DNA contaminates host cell DNA - source of eukaryotic introns
281
Original age of Earth (later proved false)
3000 years old
282
Characteristics of Agricultural Revolution
-Hunter gatherers become farmers-Rise of kings, armies, and tax collectors-Selection of docility - man becomes a domesticated species-Recall fox farm experiment (correlated characteristics)-In general: Self-domestication
283
T or F: Eukaryotic DNA is wrapped around histones
True
284
What did Haldane believe the carbon source was on Earth?
Carbon dioxide
285
Characteristics of Red Tides
-Consist of trillions of cells-Induced by nutrient upwelling and warm temperatures-Result is massive fish kills consequent to oxygen depletion and or neurotoxin production-Accumulation of dinoflagellate toxins in shellfish causes paralytic shellfish poisoning when eaten by humans
286
Where did RNA and Lipid world come from?
Hydrothermal vents as environments where life may have evolved due to the fact that it provided both energy and chemical building blocks
287
Periods in Paleozoic era (6)
Cambrian, Ordovician, Silurian, Devonian, Carboniferous, Permian
288
What is strata made from?
Fluids like fresh and salt water; not from lava
289
When and where did man first evolve?
In Africa during the Pleistocene period. First Homo Erectus makes its way out of Africa and invades Asia and then H. sapiens do the same
290
3 discoveries that proved Earth was older than originally thought
1) Existence of distinct layers of strata of sedimentary rock2) Law of superposition3) Strata can be correlated based on fossils
291
Law of Superposition
Oldest strata of undeformed sequences at the bottom; youngest at the top
292
T of F: The rise of oxygen was gradual
False; the rise of oxygen was not gradual and occurred in a two step process
293
What has to happen for oxygen to increase in the water and the air?
The oxygen has to first rust all available metals. This is called Great Rusting
294
In what era of the Phanerozoic eon did amniotes come about?
Palaeozoic
295
Changing physical environment
-Increase solar output by 25% over 4.5by-Recurrent changes in earth's orbit and orientation-Drifting continents-Changing climate including periods of extensive glaciation-Changing levels of atmospheric oxygen and CO2 due to geological and biological processes-Cataclysmic impacts
296
Summarize the Calvin Cycle
CO2 enters which is catalyzed by the enzyme RuBisCO, extra G3P molecules are produced, these three carbon sugars are converted into glucose, plants then store glucose as starch
297
Factors to account for explosive morphological change in the Cambrian
-Increasing concentration of oxygen made possible larger size and the secretion of hard parts-Increasing genomic complexity-A co-evolutionary arm's race in which advances in predator "fire power" were countered by advances in victim armor - shells, spines, etc.
298
Internal nodes
Points of lineage splitting
299
T or F: Carnivals closely related to marsupials
True
300
Oxygen vs. Anoxic photosynthesis
Oxygenic: the electron donor (reductant) is H2O, which is oxidized to O2Anoxic: electron donor is something else, for example, H2S, which is oxidized to elemental sulfurBOTH: The carbon source is CO2
301
Metabolic similarities in all Three Domains
-Use of high-energy compounds such as ATP-Production of ATP by glycolysis - anaerobic respiration
302
Inherent Cost
A population of parthenogenetic females will increase twice as fast as comparable populations of males and females - "cost of males"
303
Cambrian Explosion
Major phyla appear at or near the base of the Cambrian 550 Mya. Most of modern phyla appeared at once.
304
Heterotrophs
Utilize biomolecules produced by other organisms
305
T or F: Since Darwin's time a number of late Precambrian (565-543 Mya) fossil assemblages have been discovered
True; These so-called Ediacaran faunas consist of soft-bodied forms and trace fossils. The only modern group represented for sure is Cnidaria (jellyfish)
306
T or F: What is good for primitive Earth also good for outer space
True
307
Characteristics of Cyanobacteria
-Photoautotrophs-Chloroplast ancestors-Some multicellular-Preceded/caused GOE-Many fix oxygen
308
T or F: The synapomorphies that define clades are homologies
True
309
For a whale of a tale, _____ confirms molecular biology's take on the tale.
PaleontologyMolecular biology says: Whales descended from artiodactyls
310
What was rusted on the land?
Red beds
311
What are Giant viruses descendants of?
Early, now extinct, domains of life as they also code for non-virus activities such as sugar metabolism and DNA repair
312
Consequence of increased O2
Most organisms perished
313
How are red tides red?
The reddish color is due to photosynthetic pigment called carotenoids but not all are red - depends on species
314
What do both the archaea and bacteria/eukaryote phospholipids have in common?
The membrane is a bilayer with the hydrophobic ends on the inside
315
Brown algae has _____ as its MRCA
Stramenopiles
316
Characteristics of brown algae
-Multicellular marine forms - giant kelp up to 60m-Stem-like stipes, root-like hold-fasts and leaf-like blades-Phloem-like conducting cells distribute photosynthate from "leaves" to "stem" and "roots"-Alternating generations
317
Explain what alternating generations means
-Haploid gametophyte-Diploid sporophyte -Both multicellular -Grow mitotically -Sporophyte produces haploid cells via meiosis
318
Chlorophytes
-Contain the photosynthetic pigment used by plants to capture protons-Unicellular, colonial, and truly multicellular
319
Which sea plant is two cell layers thick?
Sea lettuce: Ulva lactuca
320
What do stramenopiles, amoebas, and chlorophytes have in common regarding their life cycles?
Both have alternating generations
321
When sporophyte and gametophyte phases are similar they are said to be
isomorphic
322
When sporophyte and gametophyte generations differ they are said to be
heteromorphic
323
Haplontic chlorophytes
Immediate meiosis after fertilization; no sporophyte
324
Diplontic chlorophytes
Gametes produced by sporophyte; no gametophytes
325
What are embryophytes and why are they called that?
They are green/land plants that retain an embryo and protect it by parental tissue
326
Characteristics of embryophytes
-Differentiation of cells/tissues such as xylem, phloem-Differentiation of organs - true roots, stems, leaves
327
Describe the life cycle of embryophytes
They are heteromorphic and the embryophyte evolution marked by progressive gametophyte reduction and sporophyte enlargement
328
What does opisthotonos include?
First, the names means posterior pole meaning the flagellum-Fungi-Choanoflagellates that are filter feeders (heterotrophs), solitary, colonial, similar to the collar cells of sponges and the excretory "flame" cells of flatworms and rotifers-Animalia "higher" animals
329
T or F: Amoebas are monophyletic
False; amoebas are polyphyletic - they are not a clade
330
How do amoebas move and feed?
They move and feed by pseudopods and they generally lack flagella
331
Which group of protists lack flagella?
Amoebas
332
Can amoebas be pathogenic?
Yes! They are Entamoebas which causes amoebic dysentery
333
Foraminifera
Calcareous shells with internal partitions; a type of amoeba
334
Xenophypphores
Giant, multinucleate Deep water benthic deposit feeders. Found in Galapagos island
335
Describe the late precambrian "edicaran" biotas
Dominated by bacterial mats within which enigmatic "quilted" organisms believed by some to have been giant protozoans later exterminated by metazoans that ate them
336
What is the Garden of Edicara
Late precambrian biota in the ocean with giant bacterial mats
337
What did Otti Seilacher conjecture "frond animals" to be?
Giant protozoans
338
Cellular slime molds (social amoebae)
Aggregating amoebae form multicellular fruiting bodies when bacteria on which they feed become scarce
339
2 Recurrent evolutionary trends in protists
-Evolution of complex life cycles-Evolution of multicellularity and cell differentiation
340
T or F: Choanoflagellates, fungi, and Animalia form a clade
True
341
What derived traits do choanoflagellates, fungi, and Animalia share?
1. Chitin2. Glycogen - so-called "animal starch" (storage molecule)3. Receptor tyrosine kinase (RTK) - a single receptor molecule
342
Chitin in choanoflagellates
Component of surrounding lorica - most/mostly siliceous
343
Chitin in fungi
Cell walls
344
Chitin in metazoa
exoskeletons
345
Why do fungi secrete enzymes?
To break down living or dead organisms on which they grow
346
Do multicellular or unicellular fungi consist of branching, thread like hyphae that absorb nutrients?
Multicellular; Hyphae underground = mycelia and above ground = reproductive structures
347
T or F: All fungi are multicellular
False; yeast are unicellular
348
T or F: Most fungi saprobes
True; this means they feed on dead matter like cellulose and ligin
349
Pilobus characteristics
-Lives on dung-Has a light sensitive organ that points the fruiting body toward the light-Hydrostatic pressure propels spores 2-3 meters
350
T or F: Some fungi are predators
True
351
What are the "pioneer" species that colonize bare rock
Lichens: symbiotic associations of fungi and cyanobacteria or photosynthetic eukaryotes (algae)
352
Mycorrhizae
Plant-fungus mutualism
353
Fungal life cycle summary
-Life cycle is haplontic-Mycelial cells haploid-Nuclear fusion followed by meiosis and haploid spores-Spores divide mitotically to form mycelia
354
Most fungal life cycles include a ______ (heterokaryon) stage where cells contain n \>= 2 haploid nuclei
Dikaryon
355
Dikaryon stage in fungal life cycle result of
-Hyphal fusion (mycelium)
356
In septate fungi...
-Hyphae partially divided by septa-if no septa, the structure is called a coenocyte
357
What are other names for 1) nuclear fusion and 2) cell fusion
1)Karyogamy2)PlasmogamyIn most organisms, nuclear fusion (karyogamfy) immediately follows cell fusion (plasmogamy) -e.g. when a sperm fertilizes an egg
358
In fungi, karyogamy is \_\_\_\_\_
delayed which is a derived trait
359
Sex in fungi
Fusion of two nuclei followed by meiosis
360
Recombination in fungi
Involves gene exchange
361
Reproduction in fungi
Can be sexual or asexual
362
Sexual reproduction in fungi entails...
1) Fusion of flagellated gametes in chytrids - the ancestral reproductive mode2) Fusion of hyphae of different mating types except in chytrida3) production of spores by meiosis4) Except in chytrids, karyogamy follows plasmogamy
363
Asexual reproduction in fungi entails
1) Mycelial fragmentation2) spore production by mitosis3) fission (equal sized products( and budding (small cell buds off from large) in yeasts
364
How are spores produced sexually?
Through meiosis
365
How are spores produced asexually?
Through mitosis
366
Meiosis results in...
Haploids
367
Mitosis results in...
Diploids
368
T or F: Spores typically wait to germinate upon exposure to favorable conditions
True
369
T or F: Spores are often long-lived, resistant to heat, cold, desiccation, etc.
True
370
Spores are everywhere
10^4 per meters cubed of air
