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LS 1 > Midterm 1 > Flashcards

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

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2
Q

Fundamental unit of life

A

cell

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3
Q

Hypothesis

A

tentative explanation (prediction) that can be tested by observation and experiments

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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

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5
Q

Central Dogma of Molecular Biology

A

DNA –> RNA –> Protein

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6
Q

gene

A

the DNA sequence that corresponds to a specific protein product

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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.

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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

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9
Q

ecology

A

the study of how organisms interact with one another and with their physical environment in nature

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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)

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11
Q

Evolution

A

the change in the frequency of ales or genotypes over time

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12
Q

Non-adaptive mechanisms of evolution

A

migration, mutation, genetic drift

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13
Q

phenotype is determined by

A

genotype and environment

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14
Q

population genetics

A

study of patterns of genetic variation

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15
Q

genetic variation caused by..

A

1) mutations

2) recombination (shuffles mutations)

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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
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17
Q

gene pool

A

all alleles present in all individuals in a species

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18
Q

populations

A

interbreeding groups of organisms of the same species living in the same geographic area

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19
Q

somatic mutation

A

occurs in body’s tissues (individual)

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20
Q

germ-line mutation

A

occurs in reproductive cells –> passed on to next generation
appears in every cell of offspring

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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)

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22
Q

allele frequency

A

% of that allele in the population x/total * 100%

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23
Q

population fixed for an allele means

A

entire population exhibits that one allele at a particular gene

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24
Q

gel electrophoresis

A

protein/DNA runs through gel when neg. charge applied – speed determined by charge and size

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25
Q

evolution

A

change in allele/genotype frequency over time

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26
Q

Hardy Weinberg equilibrium

A

conditions in which evolution does not occur –no change in allele/genotype frequency

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27
Q

Hardy Weinberg Equilibrium Conditions

A

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)

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28
Q

Hardy Weinberg equations

A 
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

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29
Q

natural selection

A

filtering process that acts against deleterious alleles and in favor or advantageous ones

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30
Q

fitness

A

measure of the extent to which the individual’s genotype is represent in the next generation
higher fitness = more surviving offspring

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31
Q

discrete traits

A

only a few options

ie. yellow or green? etc.

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32
Q

continuous traits

A

have a spectrum or continuous range

ie. human heights

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33
Q

Mendel’s studied..

A

genetic study of pea plants (discrete traits)

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34
Q

Ronald Fisher showed..

A

multiple genes can control a trait

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35
Q

Modern Synthesis

A

Mendelian Genetics + Darwin’s Theory of Evolution

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36
Q

positive selection

A

natural selection that increases the frequency of a favorable allele
–> promotes fixation of an allele (p = 1)

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37
Q

negative selection

A

natural selection that decreases the frequency of a harmful allele
–> difficult to remove recessive deleterious alleles

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38
Q

balancing selection

A

maintains 2+ alleles in a population so that species as a whole maintains intermediate frequency (heterozygote advantage)

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39
Q

heterozygote advantage

A

Example: malaria

SS - sickle cell w/ malaria protection
AA - healthy and no malaria protection
SA - no sickle cell + malaria protection

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40
Q

artificial selection

A

form of directional selection carefully controlled by breeders – no competition

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41
Q

corn selection experiment

A

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

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42
Q

sexual selection

A

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

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43
Q

migration (not adaptive)

A

the movement of individuals from one population to another resulting in gene flow

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44
Q

gene flow (not adaptive)

A

movement of allele from one population to another

results in homogenizing of populations

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45
Q

mutation (not adaptive)

A

rare but the source of genetic variation

produces new alleles and raw material for natural selection

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46
Q

genetic drift (not adaptive)

A

random change in allele frequencies from generation to generation – really affects small populations

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47
Q

Bottleneck (extreme case of genetic drift)

A

population down to just a few individuals –> drastic change in frequency for recessive alleles

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48
Q

founder event (extreme case of genetic drift)

A

few individuals arrive to colonize island

can result in peripatric speciation

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49
Q

molecular evolution

A

change in DNA sequence over time

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50
Q

molecular clock

A

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

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51
Q

pseudogenes

A

genes that are no longer function

all mutations are neutral –> fast molecular clock

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52
Q

microevolution

A

a change in the relative frequencies of alleles in a gene pool over time

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53
Q

genetic variation in sexual reproduction

A

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

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54
Q

antibiotic resistance

A

quite fast – mutation and selection for resistance

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55
Q

speciation

A

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

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56
Q

Ernst Mayr - Biological Species Concept (BSC)

A

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

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57
Q

morphospecies concept

A

members of the same species look alike

shortcomings - polymorphisms – many forms of the same species, colors, male/female
or similar looking different species

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58
Q

ring species

A

indirect gene flow

reproductively isolated but not genetically isolated because of the gene flow around the ring

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59
Q

hybridization

A

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

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60
Q

ecological niche

A

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

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61
Q

Ecological Species Concept

A

one-to-one correlation between a species and its niche (can work for asexual)
characterization of a species based on ecological niche

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62
Q

Evolutionary Species Concept

A

members of a species all share common ancestry and common fate
“phylogenetic species concept”

63
Q

reproductive isolation

A

inability to produce viable, fertile offspring

64
Q

pre-zygotic factors

A

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
Q

post-zygotic factors

A

genetic incompatibility – genome differences can inhibit development

horse +donkey = sterile mule

66
Q

process of speciation

A

1) population split
2) mutations, reproduction, multiple generations
3) 2 populations cannot interbreed

67
Q

allopatric speciation

A

geographical separation of populations

–> partial reproductive isolation – creates subspecies with population-specific traits

68
Q

mechanisms of allopatric speciation

A

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
Q

peripatric speciation

A

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
Q

adaptive radiation

A

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
Q

co-speciation

A

host and parasite evolve together

–occurs in response to speciation in another species

72
Q

sympatric speciation

A

“same-place”
disruptive selection –> sympatric speciation
natural selection ensues that middle population cannot survive

73
Q

instantaneous speciation

A

most common in plants via hybridization

polyploidy, autopolyploidy, allopolyploidy

74
Q

polyploidy

A

multiple chromosomes

tetraploid - double diploid

75
Q

autopolyploidy

A

multiple chromosome sets from the same species

76
Q

allopolyploidy

A

chromosomes from different species

** often spikes in even numbers

77
Q

phylogenetic tree

A

reasoned hypothesis model of evolutionary relationships of organisms

78
Q

phylogeny

A

evolutionary development and history of a species or higher taxonomic grouping of organisms – history of descent w/ modification

79
Q

taxonomy

A

classification of organisms: naming groups and grouping them

80
Q

phylogenetics

A

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
Q

sister groups

A

groups that are more closely related to each other than either of them is to any other group

82
Q

taxon

A

all the species in some taxonomic entity under discussion

-one or more populations

83
Q

monophyletic

A

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
Q

paraphyletic

A

includes some but not all of the descendants of a common ancestor

85
Q

polyphyletic

A

groupings that do not include the last common ancestor of all members

86
Q

homology

A

similarity by common descent

87
Q

characters

A

anatomical, physiological, or molecular features that make up organisms

88
Q

character states

A

a form of a character observed conditions – ie. lungs/no lungs
Character = eye color
Character state = blue, green, brown

89
Q

homologous

A

similar characters from common ancestors

90
Q

analagous

A

similarities due to independent adaptation

result of convergent evolution

91
Q

synapomorphies

A

shared derived characters (homologies) shared by some but not all members of the group
* help construct trees by identifying sisters groups

92
Q

cladistics

A

phylogenetic reconstruction on the basis of synapomorphies

93
Q

parsimony

A

choosing the simpler of two or more hypotheses to account for a given set of observations

94
Q

molecular data

A

complements comparative morphology in reconstructing phylogenetic history – it is not better but provides more details

95
Q

fossils

A

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
Q

trace fossils

A

tracks and trails, feeding marks

97
Q

molecular fossils

A

protein, DNA (bones), lipids, cholesterol
pigment molecules document non-conventional fossils
line bacterial and single celled eukaryotes

98
Q

Burgess Shale 505 mya

A

mud swept into basin sealing animals including bacterial decay
-preserved remarkable sampling of marine life during diversification of animals

99
Q

Messel Shale 50 mya

A

decrease in oxygen, animals bodies rested into mud

-preserved fish, birds, mammals, reptiles complete with skeletons – fur and color patterning

100
Q

geologic timescale

A

series of time divisions that mark Earth’s history (deeper layers = older)

101
Q

Carbon-14 dating

A

5370 yrs = half life

carbon-14 –> nitrogen-14

102
Q

mass extinctions

A

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
Q

biology + fossil relationship

A

biology provides phylogenetic framework for interpretation of fossils while fossils record life’s history (add context)

104
Q

Keeling curve

A

record of atmospheric carbon dioxide concentrations

105
Q

carbon cycle

A

intricately linked network of biological and physical processes that shuttles carbon among rocks, soil, oceans, air, and organisms

106
Q

short-term carbon cycle

A

geologic:
volcanoes, mid-ocean ridges vs chemical weathering of rocks

biological:
respiration vs photosynthesis

human activities: only add
deforestation, burning fossil fuels

107
Q

reasons for carbon dioxide fluctuation

A

respiration is constant but photosynthesis is not
summer = lots of photosynthesis = carbon dioxide low
winter = low photosynthesis = high carbon dioxide level

108
Q

correlation

A

indicates that two events or processes occur together

**NEVER indicates causation

109
Q

causation

A

a relationship in which one event leads to another

110
Q

carbon sinks (long-term carbon cycle)

A

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
Q

biomass

A

all carbon contained in the total mass of organisms living on land (organic matter that can be used for energy)

112
Q

nitrogen fixation

A

atmospheric nitrogen –> ammonia

occurs in soil, water (not in air)

113
Q

physical carbon fluxes

A

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
Q

anthropoegenic

A

made by humans

115
Q

anthropoegenic carbon sources

A

fossil fuels, deforestation

116
Q

laws of thermodynamics

A

1) energy is conserved, never created nor destroyed
2) all things have a tendency toward disorder

input –> output + heat

117
Q

biomineralization

A

skeleton formation = precipitation of minerals by organisms

118
Q

greenhouse gas

A

carbon dioxide. retains heat so that global temp increases as CO2 levels increase

119
Q

primary producers

A

organisms that reduce CO2 to form carbohydrates

plants, algae, photosynthetic bacteria

120
Q

consumers

A

heterotrophs ducks, insects eat the plants

121
Q

decomposers

A

decompose at all trophic levels, obtain carbon from other sources

122
Q

trophic pyramid

A

energy transfer through communities (trophs)

–show the inefficiency in energy transfer ~10%

123
Q

denitrification

A

nitrate –> atmospheric nitrogen

124
Q

gram-positive/neg bacteria

A

amount of peptidoglycan

gram-positive - stain darker = thicker peptidoglycan cell wall

125
Q

domains of life

A

Eukarya, Bacteria, Archaea

  • -Bacteria and Archaea earliest forms of life
  • -Eukarya and Archaea more closely related
126
Q

plasmids

A

small circles of DNA that replicate independently of the cell’s circular chromosome
–non essential but can give adaptive value

127
Q

cell membrane

A

stie of photosynthesis for bacteria

128
Q

cell wall

A

made up of peptidoglycan, sugar, and AAs

129
Q

bacterial size limitations

A

diffusion and surface area : volume ratio

130
Q

horizontal gene transfer

A

process by which bacteria exchange genetic info, increasing genetic diversity

131
Q

horizontal gene transfer methods:

A

conjugation, transformation, transduction

132
Q

conjugation

A

pilus creates cell-to-cell contact, generally transfers plasmids

133
Q

transformation

A

DNA in environment picked up by bacteria into the genome

134
Q

transduction

A

DNA transfer by virus

135
Q

autotroph

A

plants, algae, cyanobacteria

136
Q

chemoheterotrophs

A

animals, fungi, many prokaryotes

137
Q

cyanobacteria

A

all bacteria capable of oxygenic photosynthesis

138
Q

Proteobacteria

A

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
Q

anammox

A

anaerobic ammonia oxidation

used in low-oxygen areas

140
Q

periodic selection

A

diversity up then down when one variant outcompetes the rest

141
Q

Archaea divisions

A

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
Q

stromatolites

A

layered structures that record sediment accumulation by microbial communities in limestone

143
Q

symbiosis

A

the living together in more or less intimate association or close union of two dissimilar organisms as in parasitism or commensalism; especially : mutualism

144
Q

Theory

A

a general explanation of the world supported by a large body of experiments and observations

145
Q

tree of life

A

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
Q

assimilation

A

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
Q

nitrification

A

ammonia –> nitrate

148
Q

denitrification

A

nitrate –> atmospheric Nitrogen

149
Q

prokaryotes

A

domains Bacteria and Archaea

  • circular DNA + plasmids
  • cell wall of peptidoglycan
  • small size (uses diffusion)
  • horizontal gene transfer for genetic diversity
150
Q

photoheterotroph

A

obtain energy from light but obtain carbon from preformed organic molecules

151
Q

chemoautotrophs

A

fix carbon –> organic carbon
obtain energy from chemical reactions

live between oxygen rich and oxygen poor layers

152
Q

fermentation

A

alternative to cellular respiration

enviro: oxygen poor, rich in organic molecules (often many fermenters together)

153
Q

shotgun sequencing

A

molecular sequencing techniques that allow for whole genome sequences of bacteria to classify them (bacterial diversity)

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