Transcript Lecture 4 - University of California, Santa Cruz

Lecture 4
Dominance relationships
1
What is the biochemical explanation for dominance?
The genetic definition of dominance is when an allele expresses its
phenotype in the heterozygous condition.
By saying A is dominant over a, we are saying AA and Aa have the
same phenotype.
Conversely the genetic definition of recessive is when allele does
not express its phenotype in the heterozygous condition.
For example a gene responsible for height in the pea plant has a
dominant allele, T.
T/T= 6ft
T/t= 6ft
t/t=2ft
By definition 6ft is dominant to 2ft. And t is recessive to T.
Now if the short phenotype is observed in the heterozygote, then
T/T= 6ft
T/t= 2ft
t/t=2ft
short is dominant to tall.
Dominant and recessive are operational definitions.
2
Some genes make enzymes
Genes are responsible for the production of specific
proteins/enzymes.
***** Remember enzymes catalyze biochemical reactions.
Substrate
--------->
product
EnzymeA
^
|
GeneA
Wild-type= phenotype observed most of the time in nature
Phenotype characteristic of the majority of individuals of a species
under “natural” conditions
3
For example here is the biochemical reaction responsible for
producing the red pigment in flowers:
Substrate
--------->
Red pigment
EnzymeA
^
|
GeneA
GeneA has two alleles:
A= which is normal and makes functional enzyme
a = which is mutant and produces nonfunctional enzyme
Genotype
Enzyme amount
Phenotype (pigment)
AA
2 enzyme units
Red
Aa
1 enzyme unit
Red
aa
0 enzyme unit
white
So for genes that code for an enzyme,
Dominant = functional enzyme Recessive = nonfunctional
enzyme
4
Incomplete dominanceNow lets look at something different:
Although straightforward dominance/recessive relationships are
the rule, there are a number of variations on this pattern of
inheritance of PHENOTYPES
One of these variations is called Incomplete dominance
Incomplete dominance is the occurrence of an intermediate
phenotype in the heterozygote.
The heterozygote exhibits a phenotype intermediate between the
two homozygotes
A good example of this is in four o'clock plants:
5
Incomplete dominanceAlthough straightforward dominance/recessive relationships are
the rule, there are a number of variations on this pattern of
inheritance.
One of these variations is called Incomplete dominance
Incomplete dominance is the occurrence of an intermediate
phenotype in the heterozygote.
The heterozygote exhibits a phenotype intermediate between the
two homozygotes
A good example of this is in four o'clock plants:
P:
Pure white
F1:
F2:
x
Pure red
All Pink
1/4Red
1/2Pink
1/4White
How are these results explained?
How do we relate genotype to phenotype
6
The following explanation readily explains the phenotypic outcome:
P:
Pure white
F1:
All Pink
F2:
1/4Red
1/2Pink
x
Pure red
1/4White
Do not use C and c to denote the two alleles- Use C1 and C2
C1= white
C2= red
C1/C2= pink
In practice incomplete dominance can lie anywhere on the
phenotypic scale
Height:
A1A1= 2ft
A2A2= 6ft
A1A2= 2ft -6ft
The phenotype of the heterozygous individual is the key
towards determining whether an allele behaves as a recessive,
dominant, or incomplete dominance
In incomplete dominance, Phenotype ratio= Genotype ratio
7
Another classic example of this is the colors of carnations.
R1R2
x
R1
R2
R1
R1R1
R1R2
R2
R1R2
R2R2
R1R2
R1 is the allele for red pigment. R2 is the allele for no pigment.
Thus, R1R1 offspring make a lot of red pigment and appear red.
R2R2 offspring make no red pigment and appear white.
R1R2 and R2R1 offspring make a little bit of red pigment and
therefore appear pink.
Often in biological systems, substrate/product is limiting leading
to incomplete dominance phenotypes.
8
Co-dominance:
Another variation on the classical pattern of inheritance of phenotype
is co-dominance
The biochemical basis of co-dominance is understood for the blood
groups M and N
The surface of a red blood cell carries molecules known as antigens.
More than 20 different blood group antigen systems are recognized.
ABO system
Rh system
……..
The MN blood group system is of little medical importance.
In this system there are two antigens, M and N.
The L gene in humans codes for a protein present on the surface of
the red blood cells.
There exist two allelic forms of this gene
LM and LN
These two alleles represent two different forms of the protein9on
the cell surface.
So with respect to the red blood cells, the genotype and phenotype
relationships are as follows:
Genotype
Phenotype
LM LM
LN LN
At the protein
level most
phenotypes are
Codominant!!!
LM LN
Both proteins are being expressed in the heterozygote.
We are used to phenotypes as flower color, height, hair length,
shape etc.
The blood group phenotype is at a much finer level- that of the cell
and is harder to observe.
*****
Remember the phenotype chosen is what the geneticists happens
to notice. In this respect it can be somewhat subjective and
depend on how observant the geneticists happens to be.
10
Question: How do you study these phenotypes?
To determine the phenotype of the LM and LN blood cells a very
specific set of antibodies is required. The anti- LM antibodies
specifically recognize the LM blood-cell surface proteins and the anti
LN antibodies specifically recognize the LN surface proteins.
In practice, specific recognition by each antibody results in
precipitation of the red-blood cells.
The antibody allows us to determine if the cell surface markers
are LM or LN
So with the anti- LM and anti- LN antibodies, one can determine
which form of the L gene (LM or LN) is being expressed in each
individual
11
Genotype
LM LM
LN LN
LN LM
Assay
Phenotype
Precipitation by
- LN
- LM
antigen on RBC surface
No
Yes
Yes
No
LM
LN
Yes
Yes
LM and LN
In this case, the heterozygote is expressing both proteins.
Therefore, with regards to expression of LM and LN protein on
the RBC surface these alleles are co-dominant
P:
LM LM
x
LN LN
F1:
LM LN
F2:
LM LM: LM LN : LN LN
1
2
(self cross)
1
Once again phenotype ratios are the same as genotype
ratios.
Co-dominant phenotype is different from incomplete12
phenotype
Paternity issues:
Paternity issues:
The M and N blood typing can be used to disprove that an individual
was the biological father of a child. For example if the mother
expressed only the M antigen, she could be only of one genotypeLMLM.
If the child was of the genotype LMLN, we know the biological
father must possess at least one LN allele.
Mother's genotype
LMLM
x
Father's genotype
LMLN
or
LNLN
This technique only rules out potential fathers (LmLm). It cannot
prove that an individual is the father.
As you will learn later in the course, DNA fingerprints can actually
be used to identify the individual father.
13
Phenotypes
When examining a dominance relationship between two alleles, we
analyze phenotype in a heterozygote.
Genotype
phenotype
Tt
tall? Short? In between?
With respect to blood in a LN LM individual and a LM LM individual
Looking at RBC by the naked eye- the heterozygote will be like the
homozygote.
With regards to the M and N blood groups (by Immunoprecipitation)
the phenotype is different in the two individuals.
We have discussed
pea shape,
flower and eye color,
Morphology
as phenotypes.
These are all properties that are easily visualized.
However with specialized tools, microscopes and specific probes such
as antibodies we can detect less easily visualized phenotypes.
14
Phenotypes
We have discussed
pea shape,
flower and eye color,
Morphology
as phenotypes.
These are all properties that are easily visualized.
However with specialized tools, microscopes and specific probes such
as antibodies we can detect less easily visualized phenotypes.
This indicates that the phenotype has subjective nature to it. It
depends on the way the observer chooses to define it. This in turn
depends on the individual's powers of observation and the tools
available. For example, shown below are a normal and a mutant
Drosophila wing. What is the difference?
Wild-type
Mutant
15
Sickle cell anemia
Sickle cell anemia is a good example of the variance in dominance
relationships.
Sickle cell is an inherited disorder that results from a mutation in the
gene coding for the protein globin.
Hemoglobin is a major constituent of the red blood cells and is
involved in O2 transport.
HbA: an allele that codes for the normal beta globin protein
HbS: an allele that codes for an abnormal form of beta globin
We will examine the phenotype of the two homozygotes and the
heterozygote at three levels:
the individual,
the cell
the protein.
Remember, the phenotype of the heterozygote is the key to
understanding whether a gene behaves as a dominant or recessive.
16
Normal O2 levels
Sealevel
Low O2 levels
High altitude
HbA/HbA
Normal
Normal
HbA/HbS
Normal
Anemic
HbS/HbS
Anemic
Anemic
Depending on the O2 levels, the HBS allele (and the HBA allele)
behaves as a dominant or recessive.
17
Genes and their products
What is the cellular phenotype with respect to these genotypes
The HBS allelic form of the protein causes the red blood cells to
sickle.
Cell shape
HbA/HbA
HbS/HbS
HBS/HbA
Normal shape
Sickled
Partially sickled
***
At this level the alleles HbA and HBs are incompletely dominant
18
Phenotype at the level of the protein.
With respect to the presence or absence of the proteins
-
+
HbA/HbS
HbS/HbS
HbA/HbA
HbS and HbA are co-dominant
So the HbS allele is classified differently depending on the level the
phenotype is analyzed:
Individual
Cell
Protein
Recessive &/or
Dominant
incomplete
dominant
co-dominant
19
Fitness
Individuals homozygous for HbS/HbS often die in childhood.
Yet, the frequency of the HbS allele is quite high in some regions
of the world. In parts of Africa frequencies of 20% to 40% are
often found for the HbS allele.
It was found however that in areas in which there was a high HbS
allelic frequency, that there was also a corresponding high
frequency of mosquitoes infected with the protozoan parasite,
plasmodium. This parasite causes Malaria in humans.
It was proposed and later proven that heterozygous HbA/HbS
individuals are more resistant to the mosquito born parasite.
Consequently this allele in maintained in the population in spite of
its deleterious consequences in the homozygous state.
This condition in which the heterozygote is more fit than either of
the two homozygotes is known as a balanced polymorphism (over
dominance, heterozygote advantage)
Malaria
HbA/HbA
HbA/HbS
HbS/HbS
sensitive
resistant
dead
resistance
20
Lethal allelesMost of the mutations that we have discussed do not affect
the viability of the individual.
For example the mutations that produce white eyes in
Drosophila or wrinkled yellow cotyledons in the plant do not
disrupt viability. This means that the mutated gene is
specifically involved in determining eye color and is not involved
in processes central to viability of the fly.
What would be the genetic consequences if we isolated a mutation
that disrupted an enzyme that was critical for the viability of the
organism?
In a plant
RPN1/rpn1
x
RPN1/rpn1
seeds produced
You Plant seeds
75% produce plants
25% do not produce plants (lethal)
RPN1 is a essential enzyme (proteosome)
21
In animals lethal mutations are difficult to follow
You detect them by a distortion in the normal segregation ratio
For example in Drosophila, Cy
Cy+/Cy+ is normal wings (flies are alive)
Cy+/Cy is curly wings (flies are alive)
Cy/Cy is (curly wings) (flies are dead)
WHEN YOU LOOK AT WING SHAPE- The Curly mutation is a
dominant mutation that produces Cy wings in the heterozygous
condition
Flat wings (wild type) is recessive
WHEN YOU LOOK AT LIFE, The curly mutation behaves as a
recessiverecessive lethal.
22
Curly
When a heterozygous Cy male is crossed to a heterozygous Cy
female,
look at LIVE PROGENY
Cy to non-Cy progeny are produced in a 2:1 rather than the
Mendelian 3:1 ratio
+ = normal or wild type gene
cy= dominant Cy mutation
23
Curly
When a heterozygous Cy male is crossed to a heterozygous Cy
female, Cy to non-Cy progeny are produced in a 2:1___ rather than
the Mendelian 3:1___ ratio
+ = normal or wild type gene
cy= dominant Cy mutation
cy/+
x
cy/cy
All Flies Lethal
1
Live Flies
Phenotype of survival
Phenotype of curly
cy/+
cy/+
Curly
2
+/+
Normal
1
Curly: Non curly
2
: 1
3alive (75%) : 1 dead (25%)
2 curly (66%) : 1 not curly (33%)
The explanation for the _2:1__ rather than the expected
_3:1__ ratio is that Cy behaves as a recessive lethal mutation
and cy/cy individuals die prior to reaching adulthood. So you
cannot score the wing phenotype.
24
How would you test this hypothesis?
Take the progeny of the previous cross and perform a test cross with
the homozygous recessive parent
(+/+ wild-type fly)- Test cross
+/+
x
+/+
all normal flies
cy/+
x
+/+
1:1 curly:normal
cy/cy
x
+/+
all curly (not found)
All curly flies from the previous cross only give a 1:1
ratio.
There are no cy/cy flies!!!
25
Lethal mutations arise in many different genes.
These mutations remain “silent” except in rare cases of
homozygosity.
A mutation produces an allele that prevents production of a
crucial molecule
Homozygous individuals would not make any of this molecule
and would not survive.
Heterozygotes with one normal allele and one mutant allele
would produce 50% of wild-type molecule which is sufficient to
sustain normal cellular processes- life goes on.
Unlike cy, most recessive lethal alleles do not have an additional
dominant visible phenotype.
Mutations in enzymes required for DNA replication are lethal.
Cells lacking this enzyme cannot replicate their DNA and die.
For example let say a gene codes for an essential enzyme.
GeneA (normal enzyme)
Genea (mutant enzyme)
The expected genotypes and phenotypes are as follows:
genotype:
phenotype:
A/A
alive
A/a
alive
Phenotype of survival is 3:1
a/A
alive
a/a
die
26
Side bar-Lethal stocks
It is difficult to keep a stock that is a recessive lethal and has
no other phenotype. In each generation some of the lethal
alleles are eliminated
Gene A
·
·
enzyme
encodes an essential enzyme:
A = normal allele that encodes functional enzyme
a = mutant allele that encodes a non-functional
and is recessive lethal (lethal when homozygous)
Genetics helps solve this:
In order to maintain a lethal allele geneticists use "marker"
mutations such as cy
27
Lethal stocks
It is difficult to keep a stock that is a recessive lethal and has
no other phenotype. In each generation some of the lethal
alleles are eliminated
Gene A
·
·
enzyme
A/a
encodes an essential enzyme:
A = normal allele that encodes functional enzyme
a = mutant allele that encodes a non-functional
and is recessive lethal (lethal when homozygous)
x
A/a
You get a/a A/a and A/A
a/a die (some of the lethal alleles are eliminated)
A/a and A/A cannot be distinguished!!!!
Genetics helps solve this:
In order to maintain a lethal allele geneticists use "marker"
mutations such as cy
cy+ wild-type allele
cy is an allele that is dominant for curly wings and recessive for
lethality.
28
Take a heterozygous fly for both the A gene and curly
P:
29
Take a heterozygous fly for both the lethal A gene and the
lethal curly gene
P:
a-CY+
A-cy
X
a-CY+
a-CY+
A-cy
A-cy
a-CY+
a-CY+
a-CY+
dead
a-CY+
A-cy
Alive
A-cy
a-cy
A-CY+
Alive
A-cy
A-cy
dead
Notice only those classes identical to the parents survive and
therefore the lethal allele can be kept in the heterozygous
condition indefinitely
30
Multiple alleles
We have described a gene as exiting in one of two states:
normal or mutant.
Each of these states is called an allele of that gene.
Normal (wild-type)
-----> Mutant
Red eye
white eye
Smooth peas
wrinkled peas
However it is possible and common for a gene to have more
than two forms.
Many genes exist in three or more forms
(we say there exists three or more alleles of that gene)
Such a gene is said to have multiple alleles
******
It is important to remember that even though a given gene may
have many forms, each individual possesses only two forms of
that gene. Diploids contain two copies of each gene.
31
For example in Drosophila, many alleles exist for the white gene:
1) The normal (wild-type) allele W or w+ gives red eyes
2) white allele w has white eyes
3) white apricot wa gives apricot colored eyes
As of 1996, there exist over 150 alleles of the white gene
But in an individual fly there are only two alleles- e.g. W & wa
or w & wa
How many genotypes are possible given three alleles at the white
gene?
With 3 alleles, there are six possible pair-wise combinations
W+/w
W+/W+ W+/wa
w/w
wa/wa
wa/w
WT
32
WT -- Brown
WT -- Vermilion
WT -- White
Enz V+
Precursor -----Brown pigment
\
Precursor ----- Vermilion pigment /
\ transporter W+
--------- Red
/
Enz B+
33
The C gene in rabbits
·
·
C- full color
cch- chinchilla (light gray)
ch- Himalayan (albino, black extremities)
c- albino
·
·
These represent different alleles of the c locus with the
following dominance relationship:
Dominant
C
--------------->
---> Cch
---> Ch
Recessive
---->c
The dominance relationship is relative to alleles being
tested.
You can only test TWO alleles at a time in a diploid
(because there are only two alleles in any one individual)
CC
Ccch
Cch
cchcch
cchch
cchc
chch
chc
cc
Cc
full color
chinchila
Himalayan
albino
34
The C enzyme is a tyrosinase involved in melanin production
Tyrosinase breaks down tyrosine
Wildtype produces dark brown rabbits
Ch allele has 20% of the activity of normal. Therefore Chinchilla
is light brown
h is a Ts mutant. Therefore Himalayan rabbits have black feet
and ears but white body.
C is albino. No enzyme made.
35
ABO blood groups
The Human A,B,O blood group is the result of multiple allelism
They were discovered in 1900 by Dr. Landsteiner.
The 4 blood types were defined on the basis of a clumping
reaction. Serum (the liquid part of the blood-Ab) from one
individual is mixed with red blood cells (erythrocytes) from
another individual. If they belong to different groups they will
clump. This reaction is similar to the M and N groups discussed
earlier. The clumping is due to the presence of antibodies in the
serum.
Blood group
Genotype
Ant on RBC
A
IAIA
IAi
B
IBIB
IBi
B
AB
IAIB
AB
O
ii
A
Ab in blood
B
A
--
-
A B
36
A
B
The ABO gene has three alleles
IA synthesizes an enzyme that adds sugar A to RBC surface
IB synthesizes an enzyme that adds sugar B to RBC surface
i does not produce an enzyme
The A phenotypes arises from two genotypes
B blood type is due to two genotypes
AB blood type is due to a single genotype
O Blood type is due to a single genotype
Three alleles give you six genotypes but only four phenotypes
Each phenotype is determined by two alleles
37
The ABO gene has three alleles
IA
IB
i
IA synthesizes an enzyme that adds sugar A to RBC surface
IB synthesizes an enzyme that adds sugar B to RBC surface
i does not produce an enzyme
A phenotype arises from two genotypes
IAIA and Iai
B blood type is due to two genotypes
IBIB and Ibi
AB blood type is due to a single genotype
IAIB
O Blood type is due to a single genotype
ii
Three alleles give you six genotypes but only four phenotypes
Each phenotype is determined by two alleles
IA is dominant to i but is co-dominant to IB
38
Blood transfusions
There is a reciprocal relationship between antigens in the RBC
surface and antibodies present in the serum. If an individual
has A antigens in their RBCs, they will have B antibodies in
their sera.
The biological significance of this reciprocal relationship and
the presence of the antibodies are not clear.
This relationship has important implications for blood
transfusions:
B
A
B
B
A
A
A
B
A
B
A
B
A
B
AB
O
Cannot get blood from
anyone except O
individuals but can donate
RBC to anyone
UNIVERSAL DONOR
Can get blood from anybody
UNIVERSAL ACCEPTOR
39
Blood transfusions
If O individuals are transfused with A blood, the anti-A
antibodies will react with the A cells resulting in clumping.
·
If O individuals are transfused with B or AB blood,
clumping also occurs
·
O individuals can only receive O blood, but they can
donate Red blood cells to A,B, AB, and O individuals- they are
universal donors.
·
Since AB individuals have no antibodies they can
receive RBC from A,B,AB, or O individuals. They are universal
recipients
·
With respect to dominant relationships we say IA and
IB are dominant to i and that IA and IB are co-dominant
B
A
B
B
A
A
A
B
A
B
O
Cannot get blood from anyone
except O individuals but can
donate RBC to anyone (universal
donor)
A
B
A
B
AB
Can get blood from anybody
(Universal acceptor)
40
Evolutionary significance
The evolutionary significance of these blood groups is obscure as
there is no obvious advantage to possessing one blood group over
another
Blood group frequencies vary dramatically throughout the world
and are invaluable in population genetic and anthropological studies
Study in the Soloman Islands:
One Island was 130 miles long and 40 miles wide. This island is
home to over 17 major languages and most of these distinct
languages are spoken in a range of less than 10 miles. Local
populations appeared to have limited contact with one another
suggesting that the island consisted of 17 socially and culturally
isolated populations. That is there was little inbreeding among
between the individual populations. Genetics were able to confirm
this by identifying 17 distinct frequencies of ABO blood groups.
This indicated that each population has been genetically isolated
for a long time. If there were a significant frequency of
marriages between the populations the frequencies would have
equalized. This provided genetic evidence for the theory that
they were culturally isolated.
41
Multiple alleles at the human HLA loci
The HLA locus is the basis of tissue incompatibility in humans.
That is, when an organ transplant or tissue graft is required,
the success of the procedure depends on host donor
genotypes.
If the two are mismatched, graft rejection occurs. Whether
a tissue is rejected depends primarily on the genotypes at two
important loci known as the HLA loci:
HLA-A------------ 23 recognized alleles
HLA-B------------ 47 recognized alleles
The HLA and HLB genes code for proteins that are located on
the surface of the cells. For a successful transplant, the
donor and recipient must have matching alleles at the HLA-A
and HLA-B genes or risk graft rejection.
If the alleles are different however, graft rejection will occur
in some but not all of the transplant combinations
Why this multiple allele system evolved at the HLA locus in
unclear. It probably involved the tagging of the system as self
or non-self (foreign). Cancer cells often express foreign
antigens and are recognized by the immune system as foreign
and destroyed.
42
Polymorphism
Polymorphism is the existence of two or more allelic forms of a
gene segregating in a population. Often these allelic forms have
different phenotypic consequences.
43
Left-handedness:
The inheritance of left-handedness in humans:
9% of the human population is left-handed
Surprisingly no cultural group has been discovered that deviates
substantially from this 9% value
Population in remote area of Westerns Highlands 21/188 individuals
statistically compatible with an 9 % value.
Handedness and languageMost individuals have language functions located to their left
hemisphere
In 30% of left-handers and less than 5% of right-handers language
functions are localized to right hemisphere
44
Handedness is human
Rats, mice cats, dogs all show handedness- however there is
no population preference 50% left-pawed 50% right-pawed
Chimpanzee are 2/3 right handed and 1/3 left handed
Humans are 90% right handed and 9% left handed
A mutation may have produced a "dextral" (D) allele, strongly
biasing handedness in favor of the right hand and control of
speech toward the left cerebral hemisphere.
Why study handedness?
The laterization in the brain of language and handedness,
indicates that studying handedness should illuminate the biology
of language.
Handedness much easier to measure and study than is
language.
45
Is there a genetic basis for handedness?
Family studies:
Left-handedness runs in families
Adoption studies- In contrast to that of biological children, the
handedness of adapted children showed no relationship to that
of their adoptive parents. The family trends reflect genetic
rather than environmental effects.
Modeling the genetics of handedness has always been difficult
because of twin studies:
The same Handedness is seen in Monozygotic twins (identical)
only 82 % of the time.
46
iv gene in the mouse
An important clue towards developing a model came from studying
the inheritance of situs inversus encoded by the iv gene in the
mouse
Vertebrates are externally bilaterally symmetrical, but internal
there is extensive left/right asymmetry with respect to the
placement of internal organs. Researchers identified a mutation
that caused the placement of the organs to be inverted with
respect to the left/right axis. This mutation was named inversus
viscerum (iv).
Researchers identified a mutation that caused the placement of
the organs to be inverted with respect to the left/right axis.
This mutation was named inversus viscerum (iv).
Heterozygous individuals exhibit normal positioning while
homozygous individuals exhibit randomization: 50% of the
homozygotes show a normal positioning and 50% an inverted
positioning.
The notion that a mutation may result in randomizing a process
was new and readily applied to modeling the genetics of lefthandedness in humans.
The McNanus model- single gene at an autosomal locus has two
alleles segregating in the population showing incomplete dominance
47