BIOL 142 Lecture Notes - Lecture 21: Dna Microarray, Fluorescent Tag, Hybridization Probe
30 Apr 2018
School
Department
Course
Professor
1.#You$are$using$a$DNA$microarray$to$test$the$effect$of$a$toxin$on$gene$expression.$To$
perform$this$experiment,$you$administer$the$toxin$to$cells$grown$in$culture$for$several$
days.$As$a$negative$control,$you$culture$cells$without$the$toxin.$
You$generate$cDNA$from$cells$under$each$condition$and$label$the$cDNA$with$
fluorescent$tags$for$use$in$a$microarray—cDNA$from$cells$ exposed$to$the$toxin$was$
labeled$in$green$and$cDNA$from$control$cells$without$the$toxin$was$labeled$in$red.$
To$identify$genes$whose$expression$was$unchanged#by$the$toxin$after$probing$a$DNA$
microarray$with$your$labeled$cDNA,$you$would$search$for$spots$on$the$microarray$
that:$
Either#fluoresced#in#yellow#or#did#not#fluoresce.#
A.
Either$fluoresced$in$red$or$did$not$fluoresce.$
B.
Either$fluoresced$in$red$or$yellow.$
C.
Either$fluoresced$in$green$or$red.$
D.
Fluoresced$in$yellow.$
E.
In$order$to$assess$on$a$large$scale$what$genes$are$being$expressed$in$a$cell$at$a$
particular$time.$
Testing$whether$drug$changes$gene$expression
•
If$toxin$doesn't$change$expression,$they'll$be$on$in$both$conditions
•
Identify$genes$whose$expression$are$unchanged$by$the$drug
•
Have$some$cultured$with$toxin$and$some$without$toxin
•
If$toxin$doesn't$change$expression,$
•
When$you$extract$ mRNA$from$cells$without$the$toxin,$you$make$cDNAs$labeled$
with$red$probe
•
With$toxins,$has$a$green$probe
•
If$it$is$not$changed$by$the$toxin,$then$some$red$probes$will$bind$as$well$as$green
Bind$to$same$spot$in$the$array
○
•
Results$in$yellow
•
If$toxin$doesn't$change$in$expression,$they're$not$expressed$in$the$one$with$the$
toxin
Lack$of$gene$expression$shows$lack$of$a$change
○
•
Toxin$-:$Genes$not$expressed$in$absence$of$a$toxin$have$no$red$probes
•
Toxin$+:$Toxin$didn't$cause$them$to$be$turned$on,$so$there$are$no$green$probes
•
2.#Imagine$you$are$using$a$DNA$microarray$to$test$the$effect$of$a$drug$treatment$on$
gene$expression.$To$perform$this$experiment,$you$administer$the$drug$to$cells$grown$
in$culture$for$several$days.$As$a$negative$control,$you$culture$cells$under$similar$
conditions$without$the$drug.$
You$generate$cDNA$from$cells$under$each$condition,$however,$you$accidentally$label$
both#pools$of$cDNA,$from$drug-treated$and$non-treated$cells,$with$a$green$fluorescent$
tag.$Following$probing$a$DNA$microarray$with$your$labeled$cDNA,$you$would:$
See$every$spot$on$the$DNA$microarray$light$up$in$green.$A.
Be$able$to$detect$differences$in$gene$expression$resulting$from$drug-treatment.$
Can't$see$the$effecta.
B.
See$every$spot$on$the$DNA$microarray$light$up$in$red.$C.
Be$unable$to$determine$what$genes$are$being$expressed.$
Not$completely$accurate
○
If$you$have$a$gene$expressed$without$the$drug,$you$will$make$a$green$DNA$
probe
○
If$the$gene$turns$on$with$the$drug,$you$will$have$a$green$DNA$probe
○
Can't$tell$what$effect$the$drug$had$on$gene$expression$because$they're$all$
green
○
D.
None#of#these#answers#are#correct.#E.
Will$have$spots$where$not$probes$bound
You$know$what$genes$are$turned$on$under$at$least$one$of$the$two$conditions$
and$can$compare$those$to$the$genes$not$being$expressed
•
Know$genes$are$expressed,$don't$know$form$which$condition•
Learning$objectives$
!"#$%&'"()*"()%+,#&)&-,(&,(.*&/-#-.*0(-1($-,#&2"%&,3(4+%&+)&-,(-1()%+&)#(5&)*&,(+(
#."$&"#(+#('"&,3(6,&7.-%)+,)()-('"&,3()*"(8"0()-(6,2"%#)+,2&,3()*"(,+)6%"(-1(
#."$&"#9(
:9
;<./+&,()*"("4&2",$"()*+)(#633"#)#(=>?(#."$&"#($*+,3"(&,()&7"(+,2(=@?(+%"(
&,)"%%"/+)"29(
A9
!"#$%&'"()*"(7"$*+,(-1("4-/6)&-,('0(,+)6%+/(#"$)&-,9(B9
C"#)()*"("11"$)(-1(,+)6%+/(#"/"$)&-,(-,(1%"D6",$0(-1()%+&)#(&,(.-.6/+)&-,#(6#&,3(E9(
)6'"%$6/-#&#(+#(+,("<+7./"9(
F9
NOT$DOING$POPULATION$GENETICS$(p's$&$q's)
:?(;+%/0(G%""8(.*&/-#-.*"%#(2"#$%&'"2()*"(-%3+,&H+)&-,(-1(/&1"(&,(+(typological*7+,,"%9(
Plato#claimed$that$every$organism$was$an$example$of$a$perfect$essence,$or$type.•
These$types$were$unchanging$and$while$individual$organisms$might$deviate$
from$the$perfect$type,$variation#is#unimportant
•
We$know$now$variation$is$vital
If$environment$changes,$in$order$to$not$go$extinct,$some$members$of$the$
species$need$traits$that$allow$it$to$survive
○
•
We$use$typological$thought,$but$not$applied$to$living$thigns•
3.#Draw$a$square$in$LearningCatalytics.$
4.#Does$your$square$precisely$meet$the$following$formal$definition:$“>(1-6%(#&2"2(
.-/03-,($*+%+$)"%&H"2('0(%&3*)(+,3/"#(+,2(#&2"#(-1("D6+/(/",3)*I”$
Yes$A.
No#B.
5.#If$your$answer$to$question$#3$is$“no,”$have$you$drawn$squares?$
Did$not$draw$a$perfect$square•
According$to$typological$thought,$it$is$still$a$square$because$varaition$doesn't$
matter
•
In#mechanism#of#evolution#by#natural#selection,#variety#is#vital
Aristotle ordered these organismal ”types” into a linear scheme called The Great Chain of
Being.
Aristotle's History of Animals classified organisms in relation to a
hierarchical "Ladder of Life" (scala naturae), placing them according to
complexity of structure and function.
•
Implies a progression and direction of progress towards a goal (humans)
•
Implies life proceeds to some perfect form along a scale
•
False
All of these organisms are still modern adapted to live in your
environment
○
All equally evolved, just met the environmental challenges they've
been exposed to in different ways
○
•
In 1809, Jean-Baptiste de Lamarck proposed a formal theory of evolution.
Lamarck proposed a pattern of “inheritance of acquired characters.” His
idea was that individuals change in response to their environment and
then pass on those changes to their offspring.
•
Inheritance of acquired characters
•
Giraffes eat leaves and has to reach high up to get the better leaves
Puts pressure on giraffes so their necks get longer
○
•
What do you predict would happen if...
6. ... to test Lamarck’s idea of the “inheritance of acquired characteristics,” the tails of mice were
cut off, the mice were allowed to mate? In this experiment, the progeny will:
all have tails
A.
all lack tails
B.
have much shorter tails than their parents.
C.
7. ... instead of cropping off the mouse’s tail they had chosen those with the shortest tails for
breeding with others with short tails for several generations? Tail length will _______ from
generation to generation.
decrease
A.
increase What might account for differences in the results of the above two experiments?
B.
remain unchanged
C.
The process outlined in question # 7 is called artificial selection used in the
breeding of domesticated animals.
Charles Darwin was a pigeon breeder and familiar with artificial
selection.
•
He described similarities between artificial selection and natural
selection in The Origin of Species.
•
Had already applied artificial selection for hobbies with pigeons and
agriculture
•
Darwin and Wallace proposed change in species is based on variation among
individuals in populations.
A population consists of individuals of the same species living in the same area at the
same time.
•
Evolution occurs because of natural selection—the$process$by$which$individuals$in$
a$population$with$certain$heritable$traits$tend$to$produce$more$offspring$than$
do$individuals$without$those$traits,$leading$to$changes$in$the$makeup$of$the$
population.$
•
The pattern of evolution.
Darwin described evolution as descent with modification, meaning that change over
time produced modern species from ancestral species.
•
Evolution by natural selection depends upon two facts about the nature of species.
Species:
change through time, and
§
are related by common ancestry
§
○
•
2A. Fossils, any trace of organisms that lived in the past, are evidence for
change through time.
Fossils$are$found$in$sedimentary rocks, which form from layers of sand or mud. •
Layers$of$sedimentary$rock$are$associated$with$different$intervals$in$the$
geologic time scale—a$relative$time$scale$based$upon$fossil$content.$
Found$in$layers
○
Deeper$layers$are$older$than$those$further$up,$allowing$to$see$relative$
change$of$fossils
○
Fossils$more$recent$are$not$identical$to$those$found$in$deeper$
sedimentary$rock
○
•
Geologic$data$show$that$Earth$is$about$4.6$billion$years$old.$The$earliest$ signs$of$
life$are$found$in$rocks$about$3.4$billion$years$old.$
•
Many fossils provide evidence for extinct species, those that are no longer
living.
In$the$early$19th century, researchers discovered fossil bones, leaves, and shells that
were unlike known animal or plant structures. Many$scientists$insisted$that$living$
examples$of$these$species$were$yet$to$be$discovered.$
•
Baron$George$Cuvier$published$a$detailed$analysis$of$an$extinct$ species—the$
“irish$elk,”$that$was$considered$too$large$ to$have$escaped$discovery.$
•
In$1812$most$scientists$accepted$extinction$as$a$reality.$•
The “law of succession:” fossils found in rocks and living species found in
the same geographic areas share striking resemblances.
Used to say that extinction wasn't a thing and that animals may be
in places we haven't seen yet
○
Darwin interpreted this as evidence that extinct forms and living
forms are related, that they represent ancestors and descendants.
○
•
Transitional forms document the changes that occurred as whales
evolved from terrestrial to aquatic mammals.
As the fossil record has become more complete, many transitional forms have
been discovered with traits that are intermediate between earlier and later species.
○
Transitional forms provide strong evidence for change through time.
○
Used to have land-dwelling whales, as seen on fossil record
○
•
Vestigial traits are evidence that the characteristics of species have changed
over time.
A vestigial trait is a reduced or incompletely developed structure in an organism that has
no function or reduced function, but is clearly similar to functioning organs or structures in
closely related species.
•
Traits that have no apparent function an individual, but might have at another time
•
Goosebumps for people who are cold are scared –makes you look bigger, as seen in
chimps
•
Tailbone in humans, even though we have no tails
Help provide balance in other animals
○
•
2. B) Similarities among island species provide evidence of species
relatedness by common ancestry.
Darwin collected mockingbirds from the Galápagos islands. The mockingbirds were superficially
similar, but different islands had distinct species.
Darwin proposed that the mockingbirds were similar because they had descended from a
common ancestor.
Darwin’s phylogenetic explanation for why mockingbirds from different islands
are similar yet distinct.
Shows organisms are interrealated
•The$mockingbird$species$are$part$of$a$phylogeny, a family tree of populations or species.
•The$relationship$between$different$species$can$be$shown$on$a$phylogenetic tree.
Tree represents modern organisms with lines drawn back in time where nodes
show common ancestor shared by current modern living organisms
Homology, “the study of likeness,” provides further evidence for the relatedness
of organisms.
Homology can be recognized and studied at three interacting levels: genetic,
developmental, and structural.
•
Genetic homology is a similarity in the DNA sequences of different species. A main
example is the genetic code itself.
•
Genetic$code$is$the$same$in$humans$and$bacteria$
Why$you$can$express$human$genes$in$bacteria
○
•
Evolution)I
Friday,$April$6,$2018
11:59$AM
1.#You$are$using$a$DNA$microarray$to$test$the$effect$of$a$toxin$on$gene$expression.$To$
perform$this$experiment,$you$administer$the$toxin$to$cells$grown$in$culture$for$several$
days.$As$a$negative$control,$you$culture$cells$without$the$toxin.$
You$generate$cDNA$from$cells$under$each$condition$and$label$the$cDNA$with$
fluorescent$tags$for$use$in$a$microarray—cDNA$from$cells$ exposed$to$the$toxin$was$
labeled$in$green$and$cDNA$from$control$cells$without$the$toxin$was$labeled$in$red.$
To$identify$genes$whose$expression$was$unchanged#by$the$toxin$after$probing$a$DNA$
microarray$with$your$labeled$cDNA,$you$would$search$for$spots$on$the$microarray$
that:$
Either#fluoresced#in#yellow#or#did#not#fluoresce.#A.
Either$fluoresced$in$red$or$did$not$fluoresce.$B.
Either$fluoresced$in$red$or$yellow.$C.
Either$fluoresced$in$green$or$red.$D.
Fluoresced$in$yellow.$E.
In$order$to$assess$on$a$large$scale$what$genes$are$being$expressed$in$a$cell$at$a$
particular$time.$
Testing$whether$drug$changes$gene$expression•
If$toxin$doesn't$change$expression,$they'll$be$on$in$both$conditions•
Identify$genes$whose$expression$are$unchanged$by$the$drug•
Have$some$cultured$with$toxin$and$some$without$toxin•
If$toxin$doesn't$change$expression,$•
When$you$extract$ mRNA$from$cells$without$the$toxin,$you$make$cDNAs$labeled$
with$red$probe
•
With$toxins,$has$a$green$probe•
If$it$is$not$changed$by$the$toxin,$then$some$red$probes$will$bind$as$well$as$green
Bind$to$same$spot$in$the$array
○
•
Results$in$yellow•
If$toxin$doesn't$change$in$expression,$they're$not$expressed$in$the$one$with$the$
toxin
Lack$of$gene$expression$shows$lack$of$a$change
○
•
Toxin$-:$Genes$not$expressed$in$absence$of$a$toxin$have$no$red$probes•
Toxin$+:$Toxin$didn't$cause$them$to$be$turned$on,$so$there$are$no$green$probes
•
2.#Imagine$you$are$using$a$DNA$microarray$to$test$the$effect$of$a$drug$treatment$on$
gene$expression.$To$perform$this$experiment,$you$administer$the$drug$to$cells$grown$
in$culture$for$several$days.$As$a$negative$control,$you$culture$cells$under$similar$
conditions$without$the$drug.$
You$generate$cDNA$from$cells$under$each$condition,$however,$you$accidentally$label$
both#pools$of$cDNA,$from$drug-treated$and$non-treated$cells,$with$a$green$fluorescent$
tag.$Following$probing$a$DNA$microarray$with$your$labeled$cDNA,$you$would:$
See$every$spot$on$the$DNA$microarray$light$up$in$green.$
A.
Be$able$to$detect$differences$in$gene$expression$resulting$from$drug-treatment.$
Can't$see$the$effect
a.
B.
See$every$spot$on$the$DNA$microarray$light$up$in$red.$
C.
Be$unable$to$determine$what$genes$are$being$expressed.$
Not$completely$accurate
○
If$you$have$a$gene$expressed$without$the$drug,$you$will$make$a$green$DNA$
probe
○
If$the$gene$turns$on$with$the$drug,$you$will$have$a$green$DNA$probe
○
Can't$tell$what$effect$the$drug$had$on$gene$expression$because$they're$all$
green
○
D.
None#of#these#answers#are#correct.#
E.
Will$have$spots$where$not$probes$bound
You$know$what$genes$are$turned$on$under$at$least$one$of$the$two$conditions$
and$can$compare$those$to$the$genes$not$being$expressed
•
Know$genes$are$expressed,$don't$know$form$which$condition
•
Learning$objectives$
!"#$%&'"()*"()%+,#&)&-,(&,(.*&/-#-.*0(-1($-,#&2"%&,3(4+%&+)&-,(-1()%+&)#(5&)*&,(+(
#."$&"#(+#('"&,3(6,&7.-%)+,)()-('"&,3()*"(8"0()-(6,2"%#)+,2&,3()*"(,+)6%"(-1(
#."$&"#9(
:9
;<./+&,()*"("4&2",$"()*+)(#633"#)#(=>?(#."$&"#($*+,3"(&,()&7"(+,2(=@?(+%"(
&,)"%%"/+)"29(
A9
!"#$%&'"()*"(7"$*+,(-1("4-/6)&-,('0(,+)6%+/(#"$)&-,9(
B9
C"#)()*"("11"$)(-1(,+)6%+/(#"/"$)&-,(-,(1%"D6",$0(-1()%+&)#(&,(.-.6/+)&-,#(6#&,3(E9(
)6'"%$6/-#&#(+#(+,("<+7./"9(
F9
NOT$DOING$POPULATION$GENETICS$(p's$&$q's)
:?(;+%/0(G%""8(.*&/-#-.*"%#(2"#$%&'"2()*"(-%3+,&H+)&-,(-1(/&1"(&,(+(typological*7+,,"%9(
Plato#claimed$that$every$organism$was$an$example$of$a$perfect$essence,$or$type.
•
These$types$were$unchanging$and$while$individual$organisms$might$deviate$
from$the$perfect$type,$variation#is#unimportant
•
We$know$now$variation$is$vital
If$environment$changes,$in$order$to$not$go$extinct,$some$members$of$the$
species$need$traits$that$allow$it$to$survive
○
•
We$use$typological$thought,$but$not$applied$to$living$thigns•
3.#Draw$a$square$in$LearningCatalytics.$
4.#Does$your$square$precisely$meet$the$following$formal$definition:$“>(1-6%(#&2"2(
.-/03-,($*+%+$)"%&H"2('0(%&3*)(+,3/"#(+,2(#&2"#(-1("D6+/(/",3)*I”$
Yes$A.
No#B.
5.#If$your$answer$to$question$#3$is$“no,”$have$you$drawn$squares?$
Did$not$draw$a$perfect$square•
According$to$typological$thought,$it$is$still$a$square$because$varaition$doesn't$
matter
•
In#mechanism#of#evolution#by#natural#selection,#variety#is#vital
Aristotle ordered these organismal ”types” into a linear scheme called The Great Chain of
Being.
Aristotle's History of Animals classified organisms in relation to a
hierarchical "Ladder of Life" (scala naturae), placing them according to
complexity of structure and function.
•
Implies a progression and direction of progress towards a goal (humans)
•
Implies life proceeds to some perfect form along a scale
•
False
All of these organisms are still modern adapted to live in your
environment
○
All equally evolved, just met the environmental challenges they've
been exposed to in different ways
○
•
In 1809, Jean-Baptiste de Lamarck proposed a formal theory of evolution.
Lamarck proposed a pattern of “inheritance of acquired characters.” His
idea was that individuals change in response to their environment and
then pass on those changes to their offspring.
•
Inheritance of acquired characters
•
Giraffes eat leaves and has to reach high up to get the better leaves
Puts pressure on giraffes so their necks get longer
○
•
What do you predict would happen if...
6. ... to test Lamarck’s idea of the “inheritance of acquired characteristics,” the tails of mice were
cut off, the mice were allowed to mate? In this experiment, the progeny will:
all have tails
A.
all lack tails
B.
have much shorter tails than their parents.
C.
7. ... instead of cropping off the mouse’s tail they had chosen those with the shortest tails for
breeding with others with short tails for several generations? Tail length will _______ from
generation to generation.
decrease
A.
increase What might account for differences in the results of the above two experiments?
B.
remain unchanged
C.
The process outlined in question # 7 is called artificial selection used in the
breeding of domesticated animals.
Charles Darwin was a pigeon breeder and familiar with artificial
selection.
•
He described similarities between artificial selection and natural
selection in The Origin of Species.
•
Had already applied artificial selection for hobbies with pigeons and
agriculture
•
Darwin and Wallace proposed change in species is based on variation among
individuals in populations.
A population consists of individuals of the same species living in the same area at the
same time.
•
Evolution occurs because of natural selection—the$process$by$which$individuals$in$
a$population$with$certain$heritable$traits$tend$to$produce$more$offspring$than$
do$individuals$without$those$traits,$leading$to$changes$in$the$makeup$of$the$
population.$
•
The pattern of evolution.
Darwin described evolution as descent with modification, meaning that change over
time produced modern species from ancestral species.
•
Evolution by natural selection depends upon two facts about the nature of species.
Species:
change through time, and
§
are related by common ancestry
§
○
•
2A. Fossils, any trace of organisms that lived in the past, are evidence for
change through time.
Fossils$are$found$in$sedimentary rocks, which form from layers of sand or mud. •
Layers$of$sedimentary$rock$are$associated$with$different$intervals$in$the$
geologic time scale—a$relative$time$scale$based$upon$fossil$content.$
Found$in$layers
○
Deeper$layers$are$older$than$those$further$up,$allowing$to$see$relative$
change$of$fossils
○
Fossils$more$recent$are$not$identical$to$those$found$in$deeper$
sedimentary$rock
○
•
Geologic$data$show$that$Earth$is$about$4.6$billion$years$old.$The$earliest$ signs$of$
life$are$found$in$rocks$about$3.4$billion$years$old.$
•
Many fossils provide evidence for extinct species, those that are no longer
living.
In$the$early$19th century, researchers discovered fossil bones, leaves, and shells that
were unlike known animal or plant structures. Many$scientists$insisted$that$living$
examples$of$these$species$were$yet$to$be$discovered.$
•
Baron$George$Cuvier$published$a$detailed$analysis$of$an$extinct$ species—the$
“irish$elk,”$that$was$considered$too$large$ to$have$escaped$discovery.$
•
In$1812$most$scientists$accepted$extinction$as$a$reality.$•
The “law of succession:” fossils found in rocks and living species found in
the same geographic areas share striking resemblances.
Used to say that extinction wasn't a thing and that animals may be
in places we haven't seen yet
○
Darwin interpreted this as evidence that extinct forms and living
forms are related, that they represent ancestors and descendants.
○
•
Transitional forms document the changes that occurred as whales
evolved from terrestrial to aquatic mammals.
As the fossil record has become more complete, many transitional forms have
been discovered with traits that are intermediate between earlier and later species.
○
Transitional forms provide strong evidence for change through time.
○
Used to have land-dwelling whales, as seen on fossil record
○
•
Vestigial traits are evidence that the characteristics of species have changed
over time.
A vestigial trait is a reduced or incompletely developed structure in an organism that has
no function or reduced function, but is clearly similar to functioning organs or structures in
closely related species.
•
Traits that have no apparent function an individual, but might have at another time
•
Goosebumps for people who are cold are scared –makes you look bigger, as seen in
chimps
•
Tailbone in humans, even though we have no tails
Help provide balance in other animals
○
•
2. B) Similarities among island species provide evidence of species
relatedness by common ancestry.
Darwin collected mockingbirds from the Galápagos islands. The mockingbirds were superficially
similar, but different islands had distinct species.
Darwin proposed that the mockingbirds were similar because they had descended from a
common ancestor.
Darwin’s phylogenetic explanation for why mockingbirds from different islands
are similar yet distinct.
Shows organisms are interrealated
•The$mockingbird$species$are$part$of$a$phylogeny, a family tree of populations or species.
•The$relationship$between$different$species$can$be$shown$on$a$phylogenetic tree.
Tree represents modern organisms with lines drawn back in time where nodes
show common ancestor shared by current modern living organisms
Homology, “the study of likeness,” provides further evidence for the relatedness
of organisms.
Homology can be recognized and studied at three interacting levels: genetic,
developmental, and structural.
•
Genetic homology is a similarity in the DNA sequences of different species. A main
example is the genetic code itself.
•
Genetic$code$is$the$same$in$humans$and$bacteria$
Why$you$can$express$human$genes$in$bacteria
○
•
Evolution)I
Friday,$April$6,$2018 11:59$AM
1.#You$are$using$a$DNA$microarray$to$test$the$effect$of$a$toxin$on$gene$expression.$To$
perform$this$experiment,$you$administer$the$toxin$to$cells$grown$in$culture$for$several$
days.$As$a$negative$control,$you$culture$cells$without$the$toxin.$
You$generate$cDNA$from$cells$under$each$condition$and$label$the$cDNA$with$
fluorescent$tags$for$use$in$a$microarray—cDNA$from$cells$ exposed$to$the$toxin$was$
labeled$in$green$and$cDNA$from$control$cells$without$the$toxin$was$labeled$in$red.$
To$identify$genes$whose$expression$was$unchanged#by$the$toxin$after$probing$a$DNA$
microarray$with$your$labeled$cDNA,$you$would$search$for$spots$on$the$microarray$
that:$
Either#fluoresced#in#yellow#or#did#not#fluoresce.#A.
Either$fluoresced$in$red$or$did$not$fluoresce.$B.
Either$fluoresced$in$red$or$yellow.$C.
Either$fluoresced$in$green$or$red.$D.
Fluoresced$in$yellow.$E.
In$order$to$assess$on$a$large$scale$what$genes$are$being$expressed$in$a$cell$at$a$
particular$time.$
Testing$whether$drug$changes$gene$expression•
If$toxin$doesn't$change$expression,$they'll$be$on$in$both$conditions•
Identify$genes$whose$expression$are$unchanged$by$the$drug•
Have$some$cultured$with$toxin$and$some$without$toxin•
If$toxin$doesn't$change$expression,$•
When$you$extract$ mRNA$from$cells$without$the$toxin,$you$make$cDNAs$labeled$
with$red$probe
•
With$toxins,$has$a$green$probe•
If$it$is$not$changed$by$the$toxin,$then$some$red$probes$will$bind$as$well$as$green
Bind$to$same$spot$in$the$array
○
•
Results$in$yellow•
If$toxin$doesn't$change$in$expression,$they're$not$expressed$in$the$one$with$the$
toxin
Lack$of$gene$expression$shows$lack$of$a$change
○
•
Toxin$-:$Genes$not$expressed$in$absence$of$a$toxin$have$no$red$probes•
Toxin$+:$Toxin$didn't$cause$them$to$be$turned$on,$so$there$are$no$green$probes•
2.#Imagine$you$are$using$a$DNA$microarray$to$test$the$effect$of$a$drug$treatment$on$
gene$expression.$To$perform$this$experiment,$you$administer$the$drug$to$cells$grown$
in$culture$for$several$days.$As$a$negative$control,$you$culture$cells$under$similar$
conditions$without$the$drug.$
You$generate$cDNA$from$cells$under$each$condition,$however,$you$accidentally$label$
both#pools$of$cDNA,$from$drug-treated$and$non-treated$cells,$with$a$green$fluorescent$
tag.$Following$probing$a$DNA$microarray$with$your$labeled$cDNA,$you$would:$
See$every$spot$on$the$DNA$microarray$light$up$in$green.$A.
Be$able$to$detect$differences$in$gene$expression$resulting$from$drug-treatment.$
Can't$see$the$effecta.
B.
See$every$spot$on$the$DNA$microarray$light$up$in$red.$C.
Be$unable$to$determine$what$genes$are$being$expressed.$
Not$completely$accurate
○
If$you$have$a$gene$expressed$without$the$drug,$you$will$make$a$green$DNA$
probe
○
If$the$gene$turns$on$with$the$drug,$you$will$have$a$green$DNA$probe
○
Can't$tell$what$effect$the$drug$had$on$gene$expression$because$they're$all$
green
○
D.
None#of#these#answers#are#correct.#E.
Will$have$spots$where$not$probes$bound
You$know$what$genes$are$turned$on$under$at$least$one$of$the$two$conditions$
and$can$compare$those$to$the$genes$not$being$expressed
•
Know$genes$are$expressed,$don't$know$form$which$condition•
Learning$objectives$
!"#$%&'"()*"()%+,#&)&-,(&,(.*&/-#-.*0(-1($-,#&2"%&,3(4+%&+)&-,(-1()%+&)#(5&)*&,(+(
#."$&"#(+#('"&,3(6,&7.-%)+,)()-('"&,3()*"(8"0()-(6,2"%#)+,2&,3()*"(,+)6%"(-1(
#."$&"#9(
:9
;<./+&,()*"("4&2",$"()*+)(#633"#)#(=>?(#."$&"#($*+,3"(&,()&7"(+,2(=@?(+%"(
&,)"%%"/+)"29(
A9
!"#$%&'"()*"(7"$*+,(-1("4-/6)&-,('0(,+)6%+/(#"$)&-,9(B9
C"#)()*"("11"$)(-1(,+)6%+/(#"/"$)&-,(-,(1%"D6",$0(-1()%+&)#(&,(.-.6/+)&-,#(6#&,3(E9(
)6'"%$6/-#&#(+#(+,("<+7./"9(
F9
NOT$DOING$POPULATION$GENETICS$(p's$&$q's)
:?(;+%/0(G%""8(.*&/-#-.*"%#(2"#$%&'"2()*"(-%3+,&H+)&-,(-1(/&1"(&,(+(typological*7+,,"%9(
Plato#claimed$that$every$organism$was$an$example$of$a$perfect$essence,$or$type.
•
These$types$were$unchanging$and$while$individual$organisms$might$deviate$
from$the$perfect$type,$variation#is#unimportant
•
We$know$now$variation$is$vital
If$environment$changes,$in$order$to$not$go$extinct,$some$members$of$the$
species$need$traits$that$allow$it$to$survive
○
•
We$use$typological$thought,$but$not$applied$to$living$thigns
•
3.#Draw$a$square$in$LearningCatalytics.$
4.#Does$your$square$precisely$meet$the$following$formal$definition:$“>(1-6%(#&2"2(
.-/03-,($*+%+$)"%&H"2('0(%&3*)(+,3/"#(+,2(#&2"#(-1("D6+/(/",3)*I”$
Yes$
A.
No#
B.
5.#If$your$answer$to$question$#3$is$“no,”$have$you$drawn$squares?$
Did$not$draw$a$perfect$square
•
According$to$typological$thought,$it$is$still$a$square$because$varaition$doesn't$
matter
•
In#mechanism#of#evolution#by#natural#selection,#variety#is#vital
Aristotle ordered these organismal ”types” into a linear scheme called The Great Chain of
Being.
Aristotle's History of Animals classified organisms in relation to a
hierarchical "Ladder of Life" (scala naturae), placing them according to
complexity of structure and function.
•
Implies a progression and direction of progress towards a goal (humans)
•
Implies life proceeds to some perfect form along a scale
•
False
All of these organisms are still modern adapted to live in your
environment
○
All equally evolved, just met the environmental challenges they've
been exposed to in different ways
○
•
In 1809, Jean-Baptiste de Lamarck proposed a formal theory of evolution.
Lamarck proposed a pattern of “inheritance of acquired characters.” His
idea was that individuals change in response to their environment and
then pass on those changes to their offspring.
•
Inheritance of acquired characters
•
Giraffes eat leaves and has to reach high up to get the better leaves
Puts pressure on giraffes so their necks get longer
○
•
What do you predict would happen if...
6. ... to test Lamarck’s idea of the “inheritance of acquired characteristics,” the tails of mice were
cut off, the mice were allowed to mate? In this experiment, the progeny will:
all have tails
A.
all lack tails
B.
have much shorter tails than their parents.
C.
7. ... instead of cropping off the mouse’s tail they had chosen those with the shortest tails for
breeding with others with short tails for several generations? Tail length will _______ from
generation to generation.
decrease
A.
increase What might account for differences in the results of the above two experiments?
B.
remain unchanged
C.
The process outlined in question # 7 is called artificial selection used in the
breeding of domesticated animals.
Charles Darwin was a pigeon breeder and familiar with artificial
selection.
•
He described similarities between artificial selection and natural
selection in The Origin of Species.
•
Had already applied artificial selection for hobbies with pigeons and
agriculture
•
Darwin and Wallace proposed change in species is based on variation among
individuals in populations.
A population consists of individuals of the same species living in the same area at the
same time.
•
Evolution occurs because of natural selection—the$process$by$which$individuals$in$
a$population$with$certain$heritable$traits$tend$to$produce$more$offspring$than$
do$individuals$without$those$traits,$leading$to$changes$in$the$makeup$of$the$
population.$
•
The pattern of evolution.
Darwin described evolution as descent with modification, meaning that change over
time produced modern species from ancestral species.
•
Evolution by natural selection depends upon two facts about the nature of species.
Species:
change through time, and
§
are related by common ancestry
§
○
•
2A. Fossils, any trace of organisms that lived in the past, are evidence for
change through time.
Fossils$are$found$in$sedimentary rocks, which form from layers of sand or mud. •
Layers$of$sedimentary$rock$are$associated$with$different$intervals$in$the$
geologic time scale—a$relative$time$scale$based$upon$fossil$content.$
Found$in$layers
○
Deeper$layers$are$older$than$those$further$up,$allowing$to$see$relative$
change$of$fossils
○
Fossils$more$recent$are$not$identical$to$those$found$in$deeper$
sedimentary$rock
○
•
Geologic$data$show$that$Earth$is$about$4.6$billion$years$old.$The$earliest$ signs$of$
life$are$found$in$rocks$about$3.4$billion$years$old.$
•
Many fossils provide evidence for extinct species, those that are no longer
living.
In$the$early$19th century, researchers discovered fossil bones, leaves, and shells that
were unlike known animal or plant structures. Many$scientists$insisted$that$living$
examples$of$these$species$were$yet$to$be$discovered.$
•
Baron$George$Cuvier$published$a$detailed$analysis$of$an$extinct$ species—the$
“irish$elk,”$that$was$considered$too$large$ to$have$escaped$discovery.$
•
In$1812$most$scientists$accepted$extinction$as$a$reality.$•
The “law of succession:” fossils found in rocks and living species found in
the same geographic areas share striking resemblances.
Used to say that extinction wasn't a thing and that animals may be
in places we haven't seen yet
○
Darwin interpreted this as evidence that extinct forms and living
forms are related, that they represent ancestors and descendants.
○
•
Transitional forms document the changes that occurred as whales
evolved from terrestrial to aquatic mammals.
As the fossil record has become more complete, many transitional forms have
been discovered with traits that are intermediate between earlier and later species.
○
Transitional forms provide strong evidence for change through time.
○
Used to have land-dwelling whales, as seen on fossil record
○
•
Vestigial traits are evidence that the characteristics of species have changed
over time.
A vestigial trait is a reduced or incompletely developed structure in an organism that has
no function or reduced function, but is clearly similar to functioning organs or structures in
closely related species.
•
Traits that have no apparent function an individual, but might have at another time
•
Goosebumps for people who are cold are scared –makes you look bigger, as seen in
chimps
•
Tailbone in humans, even though we have no tails
Help provide balance in other animals
○
•
2. B) Similarities among island species provide evidence of species
relatedness by common ancestry.
Darwin collected mockingbirds from the Galápagos islands. The mockingbirds were superficially
similar, but different islands had distinct species.
Darwin proposed that the mockingbirds were similar because they had descended from a
common ancestor.
Darwin’s phylogenetic explanation for why mockingbirds from different islands
are similar yet distinct.
Shows organisms are interrealated
•The$mockingbird$species$are$part$of$a$phylogeny, a family tree of populations or species.
•The$relationship$between$different$species$can$be$shown$on$a$phylogenetic tree.
Tree represents modern organisms with lines drawn back in time where nodes
show common ancestor shared by current modern living organisms
Homology, “the study of likeness,” provides further evidence for the relatedness
of organisms.
Homology can be recognized and studied at three interacting levels: genetic,
developmental, and structural.
•
Genetic homology is a similarity in the DNA sequences of different species. A main
example is the genetic code itself.
•
Genetic$code$is$the$same$in$humans$and$bacteria$
Why$you$can$express$human$genes$in$bacteria
○
•
Evolution)I
Friday,$April$6,$2018 11:59$AM
Document Summary
11:59 am: you are using a dna microarray to test the effect of a toxin on gene expression. To perform this experiment, you administer the toxin to cells grown in culture for several days. As a negative control, you culture cells without the toxin. To identify genes whose expression was unchanged by the toxin after probing a dna microarray with your labeled cdna, you would search for spots on the microarray that: Either fluoresced in yellow or did not fluoresce. Either fluoresced in red or did not fluoresce. In order to assess on a large scale what genes are being expressed in a cell at a particular time. If toxin doesn"t change expression, they"ll be on in both conditions. Identify genes whose expression are unchanged by the drug. Have some cultured with toxin and some without toxin. When you extract mrna from cells without the toxin, you make cdnas labeled with red probe.
