Option D: EVOLUTION
D1: Origin of life on earth.
D.1.1: Describe four processes needed for the spontaneous origin of life on Earth.
Process 1: producing organic molecules: synthesis of simple organic molecules from environmental
precursors

chemical reactions to produce simple organic molecules, such as:
o amino acids: 20 types
o nucleotides: purines & pyrimidines
o monosaccharides: glucose, ribose
o fatty acids, glycerol
 from inorganic molecules, such as:
o water
o carbon dioxide
o ammonia
Process 2: polymerization: assembly of simple organic molecules into polymers


polypeptides from amino acids
nucleic acids from nucleotides
Process 3: forming a genetic material: formation of polymers that can self-replicate

RNA has two key abilities that make it the likely original genetic material
o genetically: self-replication
 RNA has been experimentally shown to have the ability to self-replicate
 RNA nucleotide sequence is variable,
 allowing for inheritance of information coding for amino acid sequences in
polypeptides
o
enzymatically: catalyzing chemical reactions
 RNA ribozymes are found in modern cell
RNA almost certainly preceded DNA as the genetic material = "RNA world"

Process 4: producing membranes: packaging the above molecules inside membranes creating an
internal chemistry different from their surroundings, including polymers that held the genetic
information


coacervates
o
a spherical aggregation of lipid molecules making up a colloidal inclusion
o
held together by hydrophobic forces
o
form spontaneously from certain dilute organic solutions
o
1 to 100 micrometers in diameter
o
possess osmotic properties
microspheres
o
small spherical aggregations of proteins
o 2 micrometers in diameter
1
o
o

form spontaneously from heated and cooled amino acids
exhibit some properties associated with life:
 basic metabolism
 simple reproduction
liposomes
o
a spherical vesicle composed of a bilayer membrane
o
form spontaneously from phospholipids
Result: "protobionts:" the product of the above four processes is likely to have been cell-like
structures


natural selection is likely to have acted on variants of protobionts competing for resources
selecting for:
o
stability: homeostasis, produced by enzymes controlling metabolic reactions
o
longevity: survivorship
o
fidelity: transmitting genetic information with minimal error
o
fecundity: rate of reproduction
D.1.2 Outline the experiments of Miller and Urey into the origin of organic compounds.
Simulate reducing atmosphere


Miller/Urey: water vapor, hydrogen, methane, ammonia
Others: various mixtures w/ carbon dioxide, carbon monoxide, nitrogen, phosphates,
etc., and even small amounts of oxygen
Simulate high energy sources


Miller/Urey: electric spark simulates lightning
Others: UV radiation, heat, etc.
Products


Miller/Urey: mixture of amino acids
Others: various mixtures including all 20 amino acids, sugars, lipids, purine and
pyrimidine bases of DNA and RNA nucleotides, ATP
2
D.1.3 State that comets may have delivered organic compounds to Earth.
D.1.4 Discuss possible locations where conditions would have allowed the synthesis of organic
compounds.

deep-sea hydrothermal vents
o energy source: heat
o spontaneously produces reduced compounds such as iron sulfide
 which can be oxidized to synthesize organic molecules
o provides a source of energy for assembly of polymers from monomers
 volcanoes
 extraterrestrial sources
o comets
o meteorites
D.1.5 Outline two properties of RNA that would have allowed it to play a role in the origin of life.

RNA has two key abilities that make it the likely original genetic material
o genetic: self-replication

RNA has been experimentally shown to have the ability to selfreplicate

individual RNA nucleotides self-assemble into RNA polymers

RNA polymers attract complementary nucleotide bases
 A=U
 G=C
 transmitting genetic information between genertions

RNA nucleotide sequence is variable,

allowing for inheritance of information coding for amino acid
sequences in polypeptides
o
enzymatic: catalyzing chemical reactions
 RNA can act as an enzyme, catalyzing various reactions, producing
polymers from monomers
 in eukaryotic organisms today, RNA regulates numerous cellular
functions, including protein synthesis and genetic control
 for example, RNA ribozymes are found in modern cell
 Therefore, RNA almost certainly preceded DNA as the genetic material =
"RNA world"
o RNA, like DNA, is a sequence of nucleotides that can carry a genetic
code
o RNA is structurally simpler than DNA
o RNA can self-assemble from nucleotides available from the
environment
3
o
RNA can self-replicate using an existing RNA molecule as a
template, adding free nucleotides available from the environment
o copying mistakes = mutations
o RNA can enzymatically catalyze metabolic reactions
o competition between various RNA varieties selects for most efficient
variety
D.1.6 State that living cells may have been preceded by protobionts, with an internal chemical
environment different from their surroundings.
D.1.7 Outline the contribution of prokaryotes to the creation of an oxygen-rich atmosphere.


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early cells competing for energy sources are likely to have provided
a selection pressure favoring the evolution of photosynthesis
o some photosynthetic prokaryotes use sources of electrons
other than water
 photosynthetic prokaryotes that live today in hot
springs use hydrogen sulfide as an electron source
o photosynthetic prokaryotes that use water as an electron
source are highly successful and produce large quantities of
atmospheric oxygen through photolysis of water
 rocks in Greenland dated from 3.7-3.8 billion years
ago, called banded iron formations, provide evidence
of atmospheric oxygen, suggesting the presence of
photosynthetic prokaryotes
o many species of photosynthetic prokaryotes survive today
o cyanobacteria contribute large amounts of oxygen to the
oceans and atmosphere
initially the oxygen produced by photosynthetic prokaryotes would
have been consumed in chemical reactions, or remain dissolved in
the oceans
with additional photosynthesis beyond this level, oxygen would
likely have accumulated in the atmosphere
with the emergence of eukaryotes with chloroplasts, the rate of
oxygen production likely increased
further oxygenating the atmosphere
since oxygen is toxic to some organisms, it is likely to have selected
against some species, leading to their extinction
an abundance of oxygen is likely to have lead to oxidative cellular
respiration
4
D.1.8 Discuss the endosymbiotic theory for the origin of eukaryotes.


eukaryotic cells appear to have evolved from prokaryotic ancestry
as a smaller prokaryote within a larger prokaryote
in other situations besides endosymbiosis, the outcome would be
either:
a. larger host cell digests smaller invader
b. smaller invader multiplies and kills larger host



with endosymbiosis there is a third outcome: coexistence
coexistence is only likely if it is mutually beneficial
a scenario of mutuall beneficial coexistence:
a. larger host cell: Eater consuming other, smaller cells restricted to anaerobic environments
b. smaller invader: Eliminator eliminates oxygen (poison) thus occupying environments where
Eater is absent
c. if Eater consumes eliminator, and eliminator avoids digestion eater benefits from low oxygen
levels & eliminator benefit from predation avoidance
d. the resulting host becomes the eukaryotic cells with eliminator as mitochondria
e. a similar process involves coexistence with an additional consumed cell, photosynthetic
Sunshine
f. sunshine produces oxygen as a byproduct and therefore benefits from coexistence with
mitochondria/eliminator
g. sunshine also benefits from protection within eater, who benefits from the food produced by
sushine/chloroplast

Evidence for endosymbiotic origin of eukaryotic cells
a. mitochondria & chloroplasts both have double membrane
the second outer membrane from the host, eater
b. mitochondria & chloroplasts both have a loop of naked DNA
lacking histone proteins, as do prokaryotes
c. mitochondria & chloroplasts both divide by binary fission
independent of nuclear division
d. mitochondria & chloroplasts both have smaller 70S ribosomes
similar to prokaryotes, & different from 80S eukaryotic ribosomes
5
e. chloroplast thylakoids are similar to cyanobacterial
photosynthetic structures
f. chlorophyll a is the main photosynthetic pigment for both
chloroplasts and prokaryotes
g. mitochondrial cristae are similar to bacterial mesosomes
D2 Species and speciation
D.2.1 Define allele frequency and gene pool.


gene pool = all the genes in an interbreeding population.
allele frequency = the frequency of an allele, as a proportion of all
alleles, in a population.
o allele frequencies range from 0 to 1.0, or as a percentage
o evolution always involves a change in allele frequency in a
population's gene pool, over a number of generations
D.2.2 State that evolution involves a change in allele frequency in a population’s gene pool over a
number of generations.
D.2.3 Discuss the definition of the term species.



prior to Darwin, each species was regarded as a fixed entity, morphologically distinct
from other species
o Darwin recognized that the reason individuals within a species are
morphologically similar is because they interbreed
o the ability to interbreed is more important than morphological characteristics
after Darwin, recognizing that species change over time, the biological species
definition has become widely accepted
o biological species definition: a group of a potentially interbreeding
populations, with a common gene pool, which are reproductively isolated
from other such groups
difficulties with the biological species definition:
o sibling species are populations that cannot interbreed, but are
morphologically indistinct
o some pairs of species are morphologically different, but do interbreed
o many plant species form hybrids
o some species always reproduce asexually
o fossil species cannot be classified according to the biological species
definition
6
D.2.4 Describe three examples of barriers between gene pools.
Geographic isolation:



When two populations of a species are segregated by a geographic
barrier such that they cannot reproduce, they are considered
allopatric.
Dispersal mechanisms cause some individuals of a population to
migrate to new locations, separating the parental, sympatric
population, into two or more allopatric populations
allopatric populations that are reproductively isolated will diverge
due to:
o differing natural selection pressures due to slightly differing
environments
o differing mutation pressures due to the random nature of
mutation
o genetic drift, as chance is likely to produce slightly different
allelic frequencies in the allopatric populations, especially if
the number of founding members of the population is few.
Ecological isolation:





Sympatric populations overlap in geographic distribution
a portion of a population may become fixed on resources not used
by the parent population
differences in resource use can lead to a balance between two
different adaptations, a balanced polymorphism
if the balanced polymorphism leads to assortive mating, sympatric
speciation can result
example: North American apple maggot fly, Rhagoletis pomonella
o used to lay eggs only on hawthorn fruits, the food of its
larvae
o now one population also infests apple trees, the food of its
larvae
o because the fruits ripen at different times, the adults emerge
and mate at different times
o thus, there are behavioral and temporal barriers between the
gene pools
7
o
o
there are allelic frequency differences between the two
populations
they are in the process of sympatric population
Reproductive isolation of gene pools





Habitat isolation: populations live in different habitats and do not
meet
Temporal isolation: mating or flowering occurs at different seasons
or different times of day
Behavioral isolation: little or no attraction between males and
females
Mechanical isolation: structural differences in genitalia or flowers
prevent copulation or pollen transfer
Gametic isolation: female and male gametes fail to attract each other
or are not viable
Genetic isolation of gene pools:



Reduced hybrid viability: hybrid zygotes fail to develop or fail to
reach maturity
Reduced hybrid fertility: hybrids fail to produce functional gametes
Hybrid breakdown: offspring of hybrids have reduced viability or
fertility
D.2.5 Explain how polyploidy can contribute to speciation.


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polyploidy is a form of sympatric speciation that does not require
geographic isolation
polyploidy means having more than two sets of homologous
chromosomes
polyploidy occurs most commonly in plant as a result of errors
during meiosis
the formation of even a single polyploid individual, if fertile, could
be a speciation event if the plant reproduces:
8
o
o


asexually (vegetatively)
by self-fertilization
the ability to reproduce on their own enables such polyploid parents
to produce a breeding population
example: modern wheat
D. 2.6 Compare allopatric and sympatric speciation. (DRAW A TABLE)
Allopatric speciation occurs as a result of geographic isolation:



When two populations of a species are segregated by a geographic
barrier such that they cannot interbreed, they are considered
allopatric.
Dispersal mechanisms cause some individuals of a population to
migrate to new locations, separating the parental, sympatric
population, into two or more allopatric populations
allopatric populations that are reproductively isolated will diverge
due to:
o differing natural selection pressures due to slightly differing
environments
o differing mutation pressures due to the random nature of
mutation
o genetic drift, as chance is likely to produce slightly different
allelic frequencies in the allopatric populations, especially if
the number of founding members of the population is few.
Sympatric speciation usually requires ecological/niche isolation:




Sympatric populations overlap in geographic distribution
a portion of a population may become fixed on resources not used
by the parent population
differences in resource use can lead to a balance between two
different adaptations, a balanced polymorphism
if the balanced polymorphism leads to assortive mating, sympatric
speciation can result
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Any type of speciation requires reproductive isolation of gene pools

Many types of reproductive isolating mechanisms accelerate
divergence between two populations undergoing speciation
o Habitat isolation: populations live in different habitats and
do not meet
o Temporal isolation: mating or flowering occurs at different
seasons or different times of day
o Behavioral isolation: little or no attraction between males
and females
o Mechanical isolation: structural differences in genitalia or
flowers prevent copulation or pollen transfer
o Gametic isolation: female and male gametes fail to attract
each other or are not viable
o Reduced hybrid viability: hybrid zygotes fail to develop or
fail to reach maturity
o Reduced hybrid fertility: hybrids fail to produce functional
gametes
o Hybrid breakdown: offspring of hybrids have reduced
viability or fertility
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D.2.7: Outline the process of adaptive radiation




speciation involves a process of divergence where initially similar
populations become genetically different from each other
when a population disperses into separate geographic locations, or
ecological niches within a geographic range, the dispersed
populations are exposed to unique sets of selective pressures
o as each population adapts to it local conditions, it population
diverges from the other populations, eventually undergoing
speciation as it becomes reproductivley isolated from related
species
o differentiation between species can lead to success
 reducing competition between related species
 specializing species within ecological roles
the cumulative effect of repeated speciation events produces a
branching process called adaptive radiation
o each new species adapts to its unique environment
o radiating away from other species genetically (expressed as
ecological, behavioral, physiological and morphological
differences)
some groups of species have been tremendously successful,
adaptively radiating into a broad range of related species
o 22% of all known species are beetles
o 59% of all known species are insects
D.2.8 Compare convergent and divergent evolution. (DRAW A TABLE)



divergent evolution: increases the morphological differences
between species, as each species adapts to different ecological
niches
convergent evolution: decreases morphological differences between
species, as each species adapts to similar ecological niches
certain marsupial mammals of Australia show highly similar
morphologies to certain North American placental mammals
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o
o
marsupial and placental mammals diverged from each other
at least 90 million years ago
similarities in the environments of Australia and North
America have selected for similar morphological traits in the
two sets of mammals
D.2.9 Discuss ideas on the pace of evolution, including gradualism and punctuated equilibrium.
Gradualism:



Species descended from a common ancestor gradually diverge more
and more in morphology
as they acquire unique adaptations
through the slow but relentless effects of natural selection.
Punctuated equilibrium:


A new species changes most when it first diverges from a parent
species
then changes little for the rest of its existence.
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D.2.10 Describe one example of transient polymorphism.

Year
1959
1969
1979
1989
1994
Transient polymorphism: industrial melanism in Biston betularia,
the peppered moth, where allelic frequencies continue to change
over time:
Frequency
a
of dark moths (allele for light) (allele for dark)
94%
.24
90%
.32
79%
.46
40%
.77
19%
.9


A
.76
.68
.54
.23
.1
as forests became soot-covered, previously rare dark morphs
became more frequent as they were selected for over light morphs
as forests became less soot-covered with pollution controls, the dark
moths once again decreased in frequency to low levels as light
morphs were selected for over dark morphs
D.2.11 Describe sickle-cell anemia as an example of balanced polymorphism.

Balanced polymorphism: where malarial infestation is prevalent,
both the normal (HBa) and sickle-cell (HBs) hemoglobin alleles are
present is stable frequencies
p = 0.84 = frequency of HBa
q = 0.16 = frequency of HBs
q2 = .03 (= 0.16 x 0.16) thus, 3% of individuals with sickle-cell anemia (HBsHBs)
p2 = .70 (p2 = 0.84 x 0.84) thus, 71% of population = HBaHBa (homozygous) with normal
hemoglobin
2pq = 0.27 (2pq = 2 x 0.84 x 0.16) thus, 27% of population = HBaHBs (heterozygous) with
sickle-cell trait
13



HBaHBs (heterozygous) with sickle-cell trait provides resistance to
malaria, and is thus selected for, increasing the frequency of HBs
alleles
sickle-cell anemia (HBsHBs) is a lethal trait, and is thus strongly
selected against, decreasing the frequency of HBs alleles
the selection both for and against HBs alleles leads to balanced
polymorphism, with three phenotypes coexisting in stable
frequencies
D3 Human evolution
D.3.1 Outline the method for dating rocks and fossils using radioisotopes, with reference to 14C
and 40K.
Accurate dating of fossils allows accurate sequencing of fossils
Select appropriate radioisotope:


14C for young samples, from 1,000 to 100,000 years old
40K for older samples, over 100,000 years old
Extract isotopes from sample:




some fossils contain radioisotopes
many igneous rocks contain radioisotopes
may be in the same strata as fossils
may be in younger or older strata than fossils, allowing age
bracketing
Measure isotopes in sample: proportion of 14C, or 40K, relative to breakdown products, 14N or
40Ar



14C/14N decreases over time at a predictable rate (half-life = 5730
years)
40K/40Ar decreases over time at a predictable rate (half-life =
1,250,000 years)
compare 14C/14N and 40K/40Ar ratios with decay curve to
determine age of sample
14
D.3.2 Define half-life.
the time during which the radioactivity falls to half its original level
D.3.3 Deduce the approximate age of materials based on a simple decay curve for a radioisotope
D.3.4 Describe the major anatomical features that define humans as primates.
Primata = an order of mammals, including apes, monkeys, tarsiers and lemurs
Humans share the following characteristics with other Primates
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grasping limbs, with long fingers and a separated opposable thumb;
mobile arms, with shoulder joints allowing movement in three
planes and the bones of the shoulder girdle allowing weight to be
transferred via the arms;
stereoscopic vision, with forward facing eyes on a flattened face,
giving overlapping fields of view;
skull modified for upright posture;
Thus, it is clear that all primates share a common ancestry
15
D.3.5 Outline the trends illustrated by the fossils of Ardipithecus ramidus, Australopithecus
including A. afarensis and A. africanus, and Homo including H. habilis, H. erectus, H.
neanderthalensis and H. sapiens.
Hominidae is a family within the order Primata which is defined by bipedal locomotion
Trends in hominid evolution:




increasing adaptation to bipedalism, especially forward movement
of foramen magnum
increasing brain size in relation to body size
hominids originated in Africa and spread to other continents
o Ardipithecus fossils found in Ethiopia
o Australopithecus and Homo habilis fossils found in Southern
and Eastern Africa
o Homo erectus fossils found in Eastern Africa and in Asia
o Homo neanderthalensis fossils found in Europe
o Homo sapiens fossils found in all continents except
Antarctica
decreasing relative size of: face, jaw, teeth, esp. canines; increasing
relative size of brain case, forehead
D.3.6: State that, at various stages in hominid evolution, several species may have co-existed
16
D.3.7 Discuss the incompleteness of the fossil record and the resulting uncertainties about human
evolution.


because the hominid fossil record is incomplete, it is unclear how
the various hominid species are related
the fossil record for hominids is incomplete because it is difficult for
remains of animals living in arid or semi-arid habitats to fossilize
o fossils only form when buried under sediment before
decomposition occurs;
o animal bodies are usually easten by detritivores, decomposed
by bacteria, or broken down chemically
 for example, organic acids react with alkali in bones
and teeth
o therefore, few fossils found of savanna-dwelling hominids;
o of remains fossilized, most remain buried in sediment/
remain unfound;
o hominid fossils that have been found may or may not be
representative of hominid history;
o hominid fossils that have been found are usually partial, and
the remainder of the organism must be inferred/ inferences
may or may not be correct;
o only hard parts of individuals fossilize, leaving many
questions concerning the rest of the individual’s phenotype;
D.3.8 Discuss the correlation between the change in diet and increase in brain size during
hominid evolution.

Early hominids (Australopithecus)
o brain sizes were similar in size to those of apes
o powerful jaws and teeth indicate mainly vegetarian diet

About 2.5 million years ago Africa became much cooler and drier
o savannah grassland replaced forest
o may have prompted evolution of Homo
 increasingly sophisticated tools
 change to hunting and killing large animals,
increasing meat in diet

change in diet corresponds to the start of increase in hominid brain
size
o in apes and early hominids, brain growth slows after birth
o but Homo has rapid brain growth after birth

possible explanation
o eating meat increases supply of protein, fat and energy,
making larger brain growth possible
17
o


hunting and killing prey on savannas is more difficult than
gathering plant foods, so natural selection might have
favored larger brains with greater intelligence
bipedalism is characteristic of Australopithecus genus;
dating to at least 3.6 million years ago;
D.3.9 Distinguish between genetic and cultural evolution.
genetic evolution: product of selection for genes producing large brains capable of learning



genes produce the abilities to learn language
genes produce the abilities to learn about natural history
genese produce the abilities to learn complex social information
cultural evolution: the specific learning done by groups of people sharing similarly selected large
brains



culture produces specific languages
culture produces specific natural history information
culture produces specific complex social information





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inherited vertically between generations;
physically inherited as genes coded within DNA;
change is random, through mutation;
natural selection determines likelihood of inheritance;
acquired characteristics are not inherited;
occurs slowly as gene pools alter gradually;
genetic evolution = nature:
cultural evolution = nurture:
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




inherited vertically, horizontally, or saltationally between any group,
across any time or distance;
inherited physically or non-physically, independent of DNA;
change can be random or directed by intelligence;
selection determines likelihood of inheritance;
acquired characteristics can be inherited;
can occur at any rate, typically much more rapidly than genetic
evolution, and even instantaneously
18
D.3.10 Discuss the relative importance of genetic and cultural evolution in the recent evolution of
humans.


cultural evolution has played an increasingly greater role in the lives of humans over time;
especially over the past few thousand years, during which human characteristics have
changed hugely

genetic change happens too slowly to produce the huge changes in human culture;

some cultural changes have, such as medical advances, have reduced natural selection
pressures between phenotypes
D4 The Hardy–Weinberg principle
D.4.1 Explain how the Hardy–Weinberg equation is derived.




p (A)
frequency of dominant allele, A = p
frequency of recessive allele, a = q
total of both alleles, p + q = 1.0 (1.0 = 100% of the population;
therefore, p and q must be values between 0 and 1.0; e.g. 0.5 means
50% of the population)
calculate the frequency of each genotype through Punnett square
q (a)
p2
(AA)
pq
(Aa)
pq
(Aa)
q2
(aa)
frequency of AA = p2
frequency of Aa = 2 pq
frequency of aa = q2
determine the frequencies of alleles in the first filial generation
p + q = 1.0
(p + q)2 = 1.0
p2 + 2pq + q2 = 1.0

the Hardy-Weinberg principle allows us to see that, allelic
frequencies will remain constant from one generation to the next,
under certain conditions
AA : Aa : aa = p2 : 2pq : q2
D.4.2 Calculate allele, genotype and phenotype frequencies for two alleles of a gene, using the
Hardy–Weinberg equation.

given that red eyes are dominant and white eyes recessive in
Drosophila, and that 64% of individuals are normal winged, 36%
vestigial-winged, determine the genotypic and phenotypic
19
frequencies of the two alleles, assuming that all Hardy-Weinberg
conditions are met
vg+ = allele for normal wings; p = frequency of vg+
vg = allele for vestigial wings; q = frequency of vg; q2 = frequency of vg/vg

given that q2 = .36
q = 0.6 ( q = √0.36)
p = 0.4 (p = 1 - q; 0.4 = 1 - 0.6)
p2 = .16 (p2 = 0.4 x 0.4) thus, 16% of population = vg+vg+ (homozygous)
with normal wings
2pq = 0.48 (2pq = 2 x 0.4 x 0.6) thus, 48% of population = vg+vg
(heterozygous) with normal wings
D.4.3 State the assumptions made when the Hardy–Weinberg equation is used.







If the frequency of alleles A and a in a parental generation are p and
q, then p + q = 1 and in future generations AA : Aa : aa = p2 : 2pq :
q2
Hardy-Weinberg conditions:
population is large (reducing effects of genetic drift, i.e. chance)
mating must be random
no mutation
no selection
no emigration or immigration (no gene flow)
D5 Phylogeny and systematics
D.5.1 Outline the value of classifying organisms.
Taxonomy = the science of classification: arranging organisms into groups, which provides several
advantages:




species identification: members of a species share nearly all the
same characteristics
predictive value: groups of related taxa share many common
characteristics
evolutionary links: shared derived characteristics are inherited from
common ancestors
effective communication: all scientists use the same terminology for
taxonomy
Taxonomy uses both morphological and biochemical methods to distinguish homologous structures
from analogous structures
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

avoids the problem of convergence, in which unrelated organisms
have similar morphologies, called analogous structures
emphasizes homologous structures which are those derived from a
common ancestor
D.5.2 Explain the biochemical evidence provided by the universality of DNA and protein
structures for the common ancestry of living organisms.
DNA structure is universal, i.e., the same in all organisms, composed of polymers of the same four
nucleotides: adenine, guanine, cytosine, and thymine
mRNA, rRNA, and tRNA are universally used in protein synthesis, RNA is composed of the same
four nucleotide: adenine, guanine, cytosine, and uracil
Ribosome structure is universal, composed of large and small subunits, each composed of proteins
and rRNA, and providing a site for mRNA attachment and two sites for tRNA attachment
Protein structure is universal, composed of polymers made of the same 20 amino acids
Genetic code is universal: The genetic code whereby DNA is transcribed into RNA and then
translated into proteins is universal, so that all organisms use the same codons for determining amino
acid sequence
ATP is the universal energy molecule: commonly used to provide energy for chemical reactions in
all organisms
Amino acids are L-form isomers in all organisms

(Optical isomers are molecules that are mirror images of one
another, known as D- and L- forms)
Carbohydrates in DNA and RNA are D-form isomers in all organisms
Glycolysis is universal, the common biochemical pathway by which glucose is hydrolyzed to
produce ATP
Membranes are universal, fluid mosaics of proteins within a phospholipid bilayer
Summary: because all of the basic biochemistry of genetic information, protein synthesis, cellular
organization and energy transfer is near identical in all organisms, they likely inherited it from a
common ancestry
D.5.3 Explain how variations in specific molecules can indicate phylogeny.
Differences between molecules can be used as part of the evidence to deduce phylogenetic
relationships

phylogeny = the evolutionary history of a taxonomic group, often
shown in a phylogenetic tree
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

mutations in DNA occur with predictable rates
differences can be used as a molecular clock to develop phylogeny
o DNA nucleotide sequences
o protein amino acid sequences
Globins: hemoglobin and myoglobin
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globin genes are present in all animals and some plants
the greater the similarity in the globin genes of two species, the less
time has passed during which mutations could accumulate, and thus,
the degree of similarity can be used as a measure of how closely
related the two species are
the greater the similarity in a protein produced by two species, the
more recently they shared a common ancestor
the greater the difference in a protein produced by two species, the
more distantly they shared a common ancestor
D.5.4 Discuss how biochemical variations can be used as an evolutionary clock.
Differences in nucleotide base sequences in DNA, and therefore amino acid sequences in proteins,
accumulate gradually over long periods of time


differences accumulate at roughly constant and predictable rate
o therefore, the number of differences can be used as a clock
o to measure the time since two divergent groups shared a
common ancestor
however, variations are partly due to mutations
o which are unpredictable chance events
o so there must be caution in interpreting data
Hemoglobin varies between vertebrates: Hemoglobin, a blood protein found in all vertebrates, shows
amino acid differences compared to humans in of a variety of vertebrates:

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horse: 18
mouse: 16
reptile: 35
frog: 62
shark: 79
Calibrate variation to time: Hemoglobin amino acid differences correlate to geological time based
on fossil record:
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
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mammals: originated 70 million years ago
reptile: originated 270 million years ago
frog: originated 350 million years ago
shark: originated 450 million years ago
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Establish a variety of molecular clocks:


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

Hemoglobin changes at a regular rate over hundreds of millions of
years, acting as a molecular clock.
A variety of proteins have been studied, each producing its own
molecular clock.
Histones (organize DNA) hardly change at all.
Cytochrome c (a mitochondrial protein) changes slowly.
Hemoglobin (blood protein) changes moderately.
Fibrinopeptides (clotting proteins) change rapidly.
D.5.5 Define clade and cladistics.
Clade: a group of organisms that evolved from a common ancestor
Cladistics: a method of classification of living organisms based on the construction and analysis of
cladograms
Nodes: branch points indicating the evolution of shared derived characteristics
D.5.6 Distinguish, with examples, between analogous and homologous characteristics.
Analogous characteristics: structures with a common function, but a different evolutionary origin

example: dolphin fins and shark fins
Homologous characteristics: structures that have a common evolutionary origin, even if they have
different functions

example: dolphin forelimbs and human arms
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D.5.7 Outline the methods used to construct cladograms and the conclusions that can be drawn
from them.
[link] Construct a Cladogram
[link] Construct another Cladogram
D.5.8 Construct a simple cladogram.
D.5.9 Analyse cladograms in terms of phylogenetic relationships.
[link] Construct a Cladogram [link] Construct another Cladogram
D.5.10 Discuss the relationship between cladograms and the classification of living organisms.
The classification of many groups has been re-examined using cladograms.

in many cases, cladograms have confirmed existing classifications, as expected, since both
are based on phylogeny
 in some cases, cladograms can be difficult to reconcile with traditional classifications
o nodes can be placed at any point
o making the fit of taxa to the cladogram arbitrary
 insome cases, cladograms radically alter existing classifications
o for example, birds are grouped within a clade including dinosaurs
The strength of cladistics is that the comparisons are objective, relying on morphological and
molecular homologies
The weakness of cladistics is that molecular differences are analysed on the basis of probabilities

improbably events occasionally occur, making the analyses wrong
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