biology 1620 final exam

gene

a specific, hertiable segment of dna on a chormosome
e.g. eye color

allele

one of two or more alternative versions of a gene located at the same specific position on a chromosome

e.g. blue eyes vs brown eyes

genotype

the genetic composition of an organism

e.g. AA, Aa, aa, etc.

phenotype

observable traits

e.g. hair color, height, blood type, etc.

homology

similarity in characteristics between different organisms due to inheritance from a common ancestor

evolution

the change in alleles of a population over time

natural selection

a fundamental mechanism of evolution where organisms with heritable traits better suited too their environment are more likely to survive and reproduce

what is the mechanism of evolution

nautral selection

what is the result of natural selection

evolution

typological thinking / essentialism

viewed species as fixed types, emphasing an ideal form

population thinking (darwin)

viewing species as diverse populations where variation is crucial and “types” are just the average

the great chain of being

a pre-drawinian hierarchy that orders all existence linearly from inanimate matter to god (humans above animals + plants)

darwin’s four postulates :

1. individuals within a species show variation

2. these variations are heritable

3. more offspring are produced than can survive

4. survival + reproduction are not random (natural selection favors those with advantageous traits)

evidence that species are not unchanging and are all related :

i. fossil record includes transitional species

ii. observed evolution (e.g. antibiotic resistence) shows that species can change over generations

iii. universal genetic code, shared biochemical pathways, homologous structures, molecular similarities, phylogenetic tress, biogeography

adaptation

a genetic change in a population over time

(individuals acclimate, populations adapt)

acclimation

a change in phenotype in an individual to accommodate environmental stress

vestigial trait

structures that have lost most of their function through evolution (e.g. tailbone)

adaptations are constrained by

existing traits

a trait can only evolve from a previously existing one

fitness trade off

a compromise between traits

(e.g. strong immune system → decreased reproduction because of energy allocation)

when does an allele become fixed

when it is the only present variant for a gene (100%)

types of natural selection

• directional selection

• stabilizing selection

• disruptive selection

• balancing selection

directional selection

selects for one extreme, decreases genetic variation

stabilizing selection

selects foor an intermediate of the extremes, decreases genetic variation

disruptive selection

selects for both extremes, increases genetic variation

balancing selection

selects to maintain the prior amount of genetic variation

asexual reproduction

one parent producing genetically identical offspring

sexual reproduction

two parents producing genetically unique offspring

ploidy

the number of complete sets of chromosomes in a cell

ploidy of mitosis

is maintained

ploidy of meiosis

is halved

gametes

reproductive cells (n)

a diplontic life cycle produces gametes by

meiosis

a haplontic life cycle produces gametes by

mitosis

MEMORIZE IMAGE

OKAY?

2-fold cost of sex

sexual reproduction generally taxes twice as much energy/resources as asexual reproduction because only females (50%) can reproduce

sexual reproduction increases

adaptability

sexual reproduction is advantageous in :

• rapidly changing enviornments

  • environments with parasites or pathogens

organisms can reduce the 2-fold cost of sex by :

• sex switching

• having both asexual + sexual life cycles

  • increasing paternal investment

muller’s ratchet

says that asexual populations will over time gain many delterious mutations, leading to a “mutation meltdown” or extinction

how is sexual reproduction beneficial against parasites

parasites adapt at a fast rate to infect hosts

sexual reproduction makes it harder for parasites to adapt because each individual is unique and unpredictable

(aka - there’s no universal trait for the parasite to exploit)

species concepts

• biological species concept

• morphological species concept

• ecological species concept

• phylogenetic species concept

biological species concept

species are groups that can interbreed + produce fertile offspring

pros : works well for most animals

cons : cannot be used for fossils + asexual organisms, difficult to apply to geographically seperated organisms

morphological species concept

species are groups based on their physical traits + structure

pros : can be used for fossils + asexual organisms

cons : subjective, variation of phenotypes may be misleading, allopatric speciation

ecological species concept

species are groups based on their ecological niches

pros : emphasizes adaptation, can be used for asexual organisms

cons : niche boundariesare subjective, niches are occupied by a large array of organisms

phylogenetic species concept

species are the smallest monophyletic group a phylogenetic tree

pro : uses genetic data

cons : can split populations into many small species

prezygotic isolation

prevents organisms from mating or fertilizing

e.g. habitat isolation, behavioral isolation, gametic isolation

postzygotic isolation

issues after fertilization

e.g. offspring dies young, has low fitness, is sterile

allopatric speciation

geographic isolation splits a population

sympatric speciation

reproductive isolations splits a population living in the same area

genetic drift

a random change in allele frequencies within a population due to change events, significantly reduces genetic variation

! includes bottleneck effect + founder effect !

bottleneck effect

large population is reduced to a small population left that become homogenous, reduces genetic variation

founder effect

where a few individuals leave a large population to establish a new population, limiting the gene pool to the small group that left, reduces genetic variation

gene flow (migration)

the transfer of alleles from one population to another

increases genetic variation

hypotheses for origin of life molecules :

i. primordial soup (miller-harold urey experiment)

ii. extraterrestrial

iii. hydrothermal vents

primordial soup theory (miller-harold urey experiment)

a spark in the atmosphere began with gases and water, creating amino acids

extraterrestrial theory

organic molecules were delivered to earth by meteorites

hydrothermal vents theory

earth’s core provided energy near deep sea vents

rna world hypothesis

early life was based on rna because :

• rna can store genetic information

• rna can act as an enzyme

  • rna can self replicate

darwinian threshold hypothesis

early life exchanged genes freely through horizontal gene transfer

afterwards, cells became complex enough that vertical inheritance became dominant

luca

the most recent organism from which all current life descends (not the first life form)

probably had dna, ribosomes, cell membrane, basic metabolism

evidence life existed 3700 mya :

• stromatolite fossils (date back to 3.7 billion years ago)

• carbon isoptope ratios showing biological compatibility (lighter carbon is preffered)

• universal genetic code across all life

atmospheric conditions of early earth

high co2, almost no o2

bacteria + archaea are both

prokaryotes

prokaryotes

have no nucleus or membrane-bound organelles

bacteria have cell walls made of _____ while archaea have _____ in cell walls

pepitdoglycan, pepitoglycan

bacteria have _____ fatty acids while archaea have _____ fatty acids

ester linked, ether linked

bacteria ribosomes are similar to

other prokaryotes

archaea ribosomes are similar to

eukaryotes

bacteria are sensitive to many ____ that archaea are resitant to

antibiotics

bacteria are found ___ while archaea are found ____

nearly everywhere, in extreme conditions

autotrophs

organisms that use co2 as a carbon source

heterotrophs

organisms that consume other organisms for organic carbon

phototrophs

organisms that use light energy

chemotroph

organisms that use chemical energy

photoautotrophs

use light energy to convert co2 to organic carbon

e.g. plants, cyanobacteria

photoheterotrophs

use light as energy but must get carbon from other organisms

e.g. purple non-sulfur bacteria, heliobacteria, aquatic bacteria

chemoautotrophs

use chemical energy to convert co2 to organic carbon

e.g. archaea

chemoheterotrophs

use chemical energy and gets carbon from other organisms

e.g. animals, many bacteria

prokaryotes are more ____ than eukaryotes

metabolically diverse

prokaryotes can perform (metabolically) :

• oxygenic photosynthesis

• anoxygeneic photosynthesis

• aerobic + anaerobic respiration

• fermentation

• nitrogen fixation

• sulfur reduction

• methanogenesis

the most energy is produced when glucose

is accepted by h2o, producing o2

when o2 is not available

organisms use weaker acceptors and less energy is produced

anoxygenic photosynthesis

• uses electron donors other than water

• does not product oxygen

• uses one photosystem

• cyclic electron flow

found in green sulfur bacteria + purple sulfur bacteria

oxygenic photosynthesis

• uses water as an electron donor

• produces oxygen (o2) as a byproduct

• uses two photosystems

• non-cyclic electron flow

found in cyanobacteria, algae, plants

evolution of photoautotrophs

3.5 bya - first photoautotrophs wwere anoxygenic bacteria → earth dominated by anaerobic, sulfur-based bacteria

2.5 bya - cyanobacteria evolves oxygenic photosynthesis, leadding to the great oxidation event

after the great oxidation event - atmospheric oxygen accumulates → rapid extinction of anerobic organisms + rapid evolution of aerobic organisms

evolutionary innovations of oxygenic photosynthesis

• water splitting (provides electrons + releases o2)

• combining of photosystems

• non-cyclic electron transport (produces ATP + NADPH)

• chlorophyll (pigment) captures light energy

  • calvin cycle (rubisco) for co2 fixation

impacts of oxygenic photosyntehsis

• oxygen increased in the atmosphere + oceans

• aerobic respiration → more energy production

• great oxidation event → extinction + adaptation of anaerobes

geology :

• red beds indicate modern levels of oxygen

• banded iron formations (BIFs) indicate microbial iron oxidation

snowball earth

reduced amounts of greenhouse gases (specifically co2) leading to global cooling

what happened to co2 when cyanobacteria increased

co2 decreased

the cyanobacteria are using it as a reactant of photosynthesis

ozone layer

atmospheric oxygen (o2) formed ozone (o3)

ozone accumulated in the stratosphere and blocked out harmful uv radiation, allowing organisms to colonize land

prokaryote cell traits

• no nucleus (dna is in the nucleoid)

• no membrane bound organielles

• circular dna

• no cytoskeleton

• divides by binary fission

• cell walls

eukaryote cell traits :

• nucleus

• membrane bound organelles

• linear chromosomes

• cytoskeleton

• can perform endocytosis/engulfing (those without cell walls)

  • divides via mitosis + meiosis

ring of life / fusion hypothesis

eukaryotes formed from a fusion of archaea + bacteria

archaeal genes -→ dna processing, bacterial genes → metabolism

woese’s tree of life

eukaryotes are a seperate + ancient lineage, with a long independent evolution

loki’s tree of life

eukaryotes evolved within archaea, implies the eukaryotes are more recent

endosymbiosis theory

eukaryotic cells evolved from prokaryotic organisms when one cell engulfed another, creating the mitochondria + chloroplasts

evidence for endosymbiosis theory :

• mitochondria + chloroplasts have their own circular dna

• microchondria + chloroplasts produce their own ribosomes

• mitochondria + chloroplasts can divide via binary fission

did mitochondria or chloroplast evolve first?

mitochondria

mitochondria ancestor

alpha protobacteria

aerobic → high atp production

chloroplast ancestor

cyanobacteria

introduced oxygenic photosynthesis into eukaryotes