Midterm 1 Flashcards
1
Q
Scientific Method
A
a deliberate way of asking and answering questions about the natural world
1) observation - asking questions
2) hypothesis - tentative explanation can be tested
3) experiments/more observations
4) Theory or reject hypothesis
2
Q
Fundamental unit of life
A
cell
3
Q
Hypothesis
A
tentative explanation (prediction) that can be tested by observation and experiments
4
Q
Characteristics of Life/Living Organisms
A
1) Complexity, with precise spatial organization on several scales
2) ability to change in response to enviro (adapt)
3) Ability to reproduce
4) capacity to evolve
5
Q
Central Dogma of Molecular Biology
A
DNA –> RNA –> Protein
6
Q
gene
A
the DNA sequence that corresponds to a specific protein product
7
Q
environmental variation
A
differences in the environment that affect the fitness of an organism
ie. plant in sun vs shade, protected from moth etc.
8
Q
genetic variation
A
differences between individuals within nucleotide sequences of their genomes
can lead to physical differences: Granny smith vs. Golden Delicious
source: mutations, recombination
9
Q
ecology
A
the study of how organisms interact with one another and with their physical environment in nature
10
Q
Experiments with Spontaneous Generation
A
1600s Francesco Redi
(maggots) covered and uncovered jars (source: flies)
1800s Louis Pasteur
straight vs swan-necked flasks – boiled and unboiled
(source: dust into straight necks)
11
Q
Evolution
A
the change in the frequency of ales or genotypes over time
12
Q
Non-adaptive mechanisms of evolution
A
migration, mutation, genetic drift
13
Q
phenotype is determined by
A
genotype and environment
14
Q
population genetics
A
study of patterns of genetic variation
15
Q
genetic variation caused by..
A
1) mutations
2) recombination (shuffles mutations)
16
Q
species
A
individuals that can exchange genetic material through interbreeding (can share alleles with another via reproduction)
fundamental evolutionary unit
- can become extinct
- through genetic divergence gives rise to new species
17
Q
gene pool
A
all alleles present in all individuals in a species
18
Q
populations
A
interbreeding groups of organisms of the same species living in the same geographic area
19
Q
somatic mutation
A
occurs in body’s tissues (individual)
20
Q
germ-line mutation
A
occurs in reproductive cells –> passed on to next generation
appears in every cell of offspring
21
Q
3 types of mutations
A
1) deleterious (harmful)
2) neutral
3) advantageous mutations – result in a species that is adapted to its environment (increases survival and reproduction)
22
Q
allele frequency
A
% of that allele in the population x/total * 100%
23
Q
population fixed for an allele means
A
entire population exhibits that one allele at a particular gene
24
Q
gel electrophoresis
A
protein/DNA runs through gel when neg. charge applied – speed determined by charge and size
25
evolution
change in allele/genotype frequency over time
26
Hardy Weinberg equilibrium
conditions in which evolution does not occur --no change in allele/genotype frequency
27
Hardy Weinberg Equilibrium Conditions
1) no natural selection (differences in survival)
2) no gene flow (no migration)
3) no mutations (in germ-line cells)
4) no genetic drift (must have large population)
5) no sexual selection (must have random mating)
28
Hardy Weinberg equations
```
p = allele frequency X
q = allele frequency Y
```
p + q = 1
```
p^2 = genotype frequency XX
2pq = genotype frequency XY
q^2 = genotype frequency YY
```
p^2 + 2pq + q^2 = 1
29
natural selection
filtering process that acts against deleterious alleles and in favor or advantageous ones
30
fitness
measure of the extent to which the individual's genotype is represent in the next generation
higher fitness = more surviving offspring
31
discrete traits
only a few options
| ie. yellow or green? etc.
32
continuous traits
have a spectrum or continuous range
| ie. human heights
33
Mendel's studied..
genetic study of pea plants (discrete traits)
34
Ronald Fisher showed..
multiple genes can control a trait
35
Modern Synthesis
Mendelian Genetics + Darwin's Theory of Evolution
36
positive selection
natural selection that increases the frequency of a favorable allele
--> promotes fixation of an allele (p = 1)
37
negative selection
natural selection that decreases the frequency of a harmful allele
--> difficult to remove recessive deleterious alleles
38
balancing selection
maintains 2+ alleles in a population so that species as a whole maintains intermediate frequency (heterozygote advantage)
39
heterozygote advantage
Example: malaria
SS - sickle cell w/ malaria protection
AA - healthy and no malaria protection
SA - no sickle cell + malaria protection
40
artificial selection
form of directional selection carefully controlled by breeders -- no competition
41
corn selection experiment
U Illinois 1980s selection for high vs low oil contact
| --testing whether populations can respond to continued directional selection or reach stopping pt no response
42
sexual selection
promotes traits that increase individual's access to reproductive opportunities
can act against natural selection
ie. peacock trade-off/compromise
bigger tail = chosen as mate but easier for attack by predator
43
migration (not adaptive)
the movement of individuals from one population to another resulting in gene flow
44
gene flow (not adaptive)
movement of allele from one population to another
| results in homogenizing of populations
45
mutation (not adaptive)
rare but the source of genetic variation
| produces new alleles and raw material for natural selection
46
genetic drift (not adaptive)
random change in allele frequencies from generation to generation -- really affects small populations
47
Bottleneck (extreme case of genetic drift)
population down to just a few individuals --> drastic change in frequency for recessive alleles
48
founder event (extreme case of genetic drift)
few individuals arrive to colonize island
| can result in peripatric speciation
49
molecular evolution
change in DNA sequence over time
50
molecular clock
correlation between the time two species have been apart and the amount of genetic divergence between them
speed:
extremely slow for histones (few changes over long time)
negative selection ensures elimination of mutations
51
pseudogenes
genes that are no longer function
| all mutations are neutral --> fast molecular clock
52
microevolution
a change in the relative frequencies of alleles in a gene pool over time
53
genetic variation in sexual reproduction
1) meiosis -- results in four genetically unique daughter cells
2) law of independent assortment -- each daughter cell gets 1 chromosome --random distribution
3) gamete diversity -- fusion of two different gametes
7*10^12 poss combinations for each couple
54
antibiotic resistance
quite fast -- mutation and selection for resistance
55
speciation
the process that produces new and distinct forms of life
-- process by which two populations of the same species become distinct
-by-product of the genetic divergence of separated populations
56
Ernst Mayr - Biological Species Concept (BSC)
species are groups of actually or potentially interbreeding populations that are reproductively isolated from other such groups
shortcomings - asexual organisms or fossils of extinct species
57
morphospecies concept
members of the same species look alike
shortcomings - polymorphisms -- many forms of the same species, colors, male/female
or similar looking different species
58
ring species
indirect gene flow
| reproductively isolated but not genetically isolated because of the gene flow around the ring
59
hybridization
interbreeding between species
**plants**
plants maintain distinct appearances but can exchange genes w/ other species in genera
according to BSC would be 1 big species but w/ different appearances-- natural selection keeps them different
form of sympatric speciation
60
ecological niche
characterizes a species, describes the role a species plays in its environment
2 species cannot co-habit the same niche due to competition -- one will die out
61
Ecological Species Concept
one-to-one correlation between a species and its niche (can work for asexual)
characterization of a species based on ecological niche
62
Evolutionary Species Concept
members of a species all share common ancestry and common fate
"phylogenetic species concept"
63
reproductive isolation
inability to produce viable, fertile offspring
64
pre-zygotic factors
1) behavioral isolation - courtship rituals -- song, dance, call
2) spatial isolation -- geographic (barrier) and ecological (niche differences)
3) temporal isolation -- different mating times
4) mechanical incompatibility -- lock and key, genitalia do not fit
65
post-zygotic factors
genetic incompatibility -- genome differences can inhibit development
horse +donkey = sterile mule
66
process of speciation
1) population split
2) mutations, reproduction, multiple generations
3) 2 populations cannot interbreed
67
allopatric speciation
geographical separation of populations
--> partial reproductive isolation -- creates subspecies with population-specific traits
68
mechanisms of allopatric speciation
1) dispersal -- some individuals colonize a distant place such as an island far from the main source population
2) vicariance - geographical barrier arises within a single population separating into 2 isolated populations
ie. formation of Isthmus of Panama
69
peripatric speciation
result of dispersal (type of allopatric speciation)
dispersal --> small island population --> natural selection, genetic drift
difference from dispersal = small population on island
suggests faster genetic divergence on island population
70
adaptive radiation
a bout of unusually rapid evolutionary diversification in which natural selection accelerates the rates of speciation and adaptation
** occurs when there are many ecological opportunities available for exploitation
71
co-speciation
host and parasite evolve together
| --occurs in response to speciation in another species
72
sympatric speciation
"same-place"
disruptive selection --> sympatric speciation
natural selection ensues that middle population cannot survive
73
instantaneous speciation
most common in plants via hybridization
| polyploidy, autopolyploidy, allopolyploidy
74
polyploidy
multiple chromosomes
| tetraploid - double diploid
75
autopolyploidy
multiple chromosome sets from the same species
76
allopolyploidy
chromosomes from different species
| ** often spikes in even numbers
77
phylogenetic tree
reasoned hypothesis model of evolutionary relationships of organisms
78
phylogeny
evolutionary development and history of a species or higher taxonomic grouping of organisms -- history of descent w/ modification
79
taxonomy
classification of organisms: naming groups and grouping them
80
phylogenetics
patterns of evolutionary relatedness among groups of species or other groups by comparing their anatomical or molecular features and depict these relationships as a phylogenetic tree
81
sister groups
groups that are more closely related to each other than either of them is to any other group
82
taxon
all the species in some taxonomic entity under discussion
| -one or more populations
83
monophyletic
all members share a single common ancestor not shared with any other species or group of species
*care most about determining monophyletic groups because they let us track the changes from 1 common ancestor and all of its descendants
84
paraphyletic
includes some but not all of the descendants of a common ancestor
85
polyphyletic
groupings that do not include the last common ancestor of all members
86
homology
similarity by common descent
87
characters
anatomical, physiological, or molecular features that make up organisms
88
character states
a form of a character observed conditions -- ie. lungs/no lungs
Character = eye color
Character state = blue, green, brown
89
homologous
similar characters from common ancestors
90
analagous
similarities due to independent adaptation
| result of convergent evolution
91
synapomorphies
shared derived characters (homologies) shared by some but not all members of the group
* help construct trees by identifying sisters groups
92
cladistics
phylogenetic reconstruction on the basis of synapomorphies
93
parsimony
choosing the simpler of two or more hypotheses to account for a given set of observations
94
molecular data
complements comparative morphology in reconstructing phylogenetic history -- it is not better but provides more details
95
fossils
remains of once-living organisms preserved through time in sedimentary rock
- -provide unique information esp with extinct species
- provide evidence of form, function, diversity, changes in geographic distribution - movement of continents
- documents life and response to change (gradual vs catastrophic)
96
trace fossils
tracks and trails, feeding marks
97
molecular fossils
protein, DNA (bones), lipids, cholesterol
pigment molecules document non-conventional fossils
line bacterial and single celled eukaryotes
98
Burgess Shale 505 mya
mud swept into basin sealing animals including bacterial decay
-preserved remarkable sampling of marine life during diversification of animals
99
Messel Shale 50 mya
decrease in oxygen, animals bodies rested into mud
| -preserved fish, birds, mammals, reptiles complete with skeletons -- fur and color patterning
100
geologic timescale
series of time divisions that mark Earth's history (deeper layers = older)
101
Carbon-14 dating
5370 yrs = half life
| carbon-14 --> nitrogen-14
102
mass extinctions
open up possibilities for evolution
Cambrian explosion - 542 diversity of marine life and multicellular organisms with increase in O2 levels
Permian&Triassic 252mya- marine and dinosaur extinction --> increase in mammals
103
biology + fossil relationship
biology provides phylogenetic framework for interpretation of fossils while fossils record life's history (add context)
104
Keeling curve
record of atmospheric carbon dioxide concentrations
105
carbon cycle
intricately linked network of biological and physical processes that shuttles carbon among rocks, soil, oceans, air, and organisms
106
short-term carbon cycle
geologic:
volcanoes, mid-ocean ridges vs chemical weathering of rocks
biological:
respiration vs photosynthesis
human activities: only add
deforestation, burning fossil fuels
107
reasons for carbon dioxide fluctuation
respiration is constant but photosynthesis is not
summer = lots of photosynthesis = carbon dioxide low
winter = low photosynthesis = high carbon dioxide level
108
correlation
indicates that two events or processes occur together
| **NEVER indicates causation
109
causation
a relationship in which one event leads to another
110
carbon sinks (long-term carbon cycle)
shells of sea animals that take in carbon via the ocean -- calcium carbonate
sedimentary rock -- long term carbon reservoir
sink vs reservoir
sink takes up the carbon -- out of cycle
111
biomass
all carbon contained in the total mass of organisms living on land (organic matter that can be used for energy)
112
nitrogen fixation
atmospheric nitrogen --> ammonia
| occurs in soil, water (not in air)
113
physical carbon fluxes
plate tectonics -- takes in sediments then recycles to the surface as CO2 from volcanoes and mid-ocean ridges
glacial melting -- CO2 levels increase from ocean churning
114
anthropoegenic
made by humans
115
anthropoegenic carbon sources
fossil fuels, deforestation
116
laws of thermodynamics
1) energy is conserved, never created nor destroyed
2) all things have a tendency toward disorder
input --> output + heat
117
biomineralization
skeleton formation = precipitation of minerals by organisms
118
greenhouse gas
carbon dioxide. retains heat so that global temp increases as CO2 levels increase
119
primary producers
organisms that reduce CO2 to form carbohydrates
| plants, algae, photosynthetic bacteria
120
consumers
heterotrophs ducks, insects eat the plants
121
decomposers
decompose at all trophic levels, obtain carbon from other sources
122
trophic pyramid
energy transfer through communities (trophs)
| --show the inefficiency in energy transfer ~10%
123
denitrification
nitrate --> atmospheric nitrogen
124
gram-positive/neg bacteria
amount of peptidoglycan
| gram-positive - stain darker = thicker peptidoglycan cell wall
125
domains of life
Eukarya, Bacteria, Archaea
- -Bacteria and Archaea earliest forms of life
- -Eukarya and Archaea more closely related
126
plasmids
small circles of DNA that replicate independently of the cell's circular chromosome
--non essential but can give adaptive value
127
cell membrane
stie of photosynthesis for bacteria
128
cell wall
made up of peptidoglycan, sugar, and AAs
129
bacterial size limitations
diffusion and surface area : volume ratio
130
horizontal gene transfer
process by which bacteria exchange genetic info, increasing genetic diversity
131
horizontal gene transfer methods:
conjugation, transformation, transduction
132
conjugation
pilus creates cell-to-cell contact, generally transfers plasmids
133
transformation
DNA in environment picked up by bacteria into the genome
134
transduction
DNA transfer by virus
135
autotroph
plants, algae, cyanobacteria
136
chemoheterotrophs
animals, fungi, many prokaryotes
137
cyanobacteria
all bacteria capable of oxygenic photosynthesis
138
Proteobacteria
the most diverse of all bacterial groups
includes anoxygenic photosynthetic bacteria and chemoautotrophs that oxidize NH3, H2S, and Fe2+, as well as bacteria able to respire using SO42−, NO3−, or Fe3+
Many Proteobacteria have evolved intimate ecological relationships with eukaryotic organisms
139
anammox
anaerobic ammonia oxidation
| used in low-oxygen areas
140
periodic selection
diversity up then down when one variant outcompetes the rest
141
Archaea divisions
Crenarchaeota, Euryarchaeota, Thaumarchaeota
Cren + Eury include acid-loving microorganisms
Eury include thermophiles, methanogenic archaeons, halophiles
Thaumarchaeota - may be most abundant cells in ocean oxidize ammonia to NO2
142
stromatolites
layered structures that record sediment accumulation by microbial communities in limestone
143
symbiosis
the living together in more or less intimate association or close union of two dissimilar organisms as in parasitism or commensalism; especially : mutualism
144
Theory
a general explanation of the world supported by a large body of experiments and observations
145
tree of life
the full set of evolutionary relationships among all organisms
root - last common ancestor of all living organisms between branch to Bacteria and branch to Archaea and Eukarya
146
assimilation
On land, plants take up sulfate (SO42−) ions from the soil and reduce them within their cells to hydrogen sulfide (H2S) that can be incorporated into cysteine and other biomolecules
147
nitrification
ammonia --> nitrate
148
denitrification
nitrate --> atmospheric Nitrogen
149
prokaryotes
domains Bacteria and Archaea
- circular DNA + plasmids
- cell wall of peptidoglycan
- small size (uses diffusion)
- horizontal gene transfer for genetic diversity
150
photoheterotroph
obtain energy from light but obtain carbon from preformed organic molecules
151
chemoautotrophs
fix carbon --> organic carbon
obtain energy from chemical reactions
live between oxygen rich and oxygen poor layers
152
fermentation
alternative to cellular respiration
| enviro: oxygen poor, rich in organic molecules (often many fermenters together)
153
shotgun sequencing
molecular sequencing techniques that allow for whole genome sequences of bacteria to classify them (bacterial diversity)
