How do genes control the phenotype?

• Multiple Alleles…
• Gene Linkage…
• Polygenic Traits…
• Dihybrid Inheritance…
A cross that shows the possible offspring for two traits:
Fur Color: Coat Texture:
B: Black R: Rough
b: White r: Smooth

In this example, we will cross a heterozygous

individual with another heterozygous individual.
Their genotypes will be:
BbRr x BbRr
 BR Br bR br
BbRr x BbRr
BR
Fur Color:
B: Black
b: White Br
Coat Texture:
R: Rough
r: Smooth bR

br
 BR Br bR br
BbRr x BbRr
BR BBRR BBRr BbRR BbRr
Fur Color:
B: Black
b: White Br BBRr BBrr BbRr Bbrr
Coat Texture:
R: Rough
r: Smooth bR BbRR BbRr bbRR bbRr

br BbRr Bbrr bbRr bbrr

 BR Br bR br
How many of the
a BR
BBRR BBRr BbRR BbRr
offspring would have
a. black, rough coat?

b. black, smooth coat? Br BBRr BBrr BbRr Bbrr

c. white, rough coat?

d. white, smooth coat?

bR BbRR BbRr bbRR bbRr

br BbRr Bbrr bbRr bbrr

 BR Br bR br

How many of the offspring would BR BBRR BBRr BbRR BbRr

a. black, rough coat?
b. black, smooth coat?
Br BBRr BBrr BbRr Bbrr
c. white, rough coat?
d. white, smooth coat?
bR BbRR BbRr bbRR bbRr

br BbRr Bbrr bbRr bbrr

Phenotypic Ratio?
Fur Color: Coat Texture:
B: Black R: Rough
b: White r: Smooth
 BR Br bR br

How many of the offspring would BR BBRR BBRr BbRR BbRr

a. black, rough coat?
b. black, smooth coat?
Br BBRr BBrr BbRr Bbrr
c. white, rough coat?
d. white, smooth coat?
bR BbRR BbRr bbRR bbRr

br BbRr Bbrr bbRr bbrr

Phenotypic Ratio?
Fur Color: Coat Texture:
9:3:3:1 B: Black R: Rough
b: White r: Smooth
• Linked genes are inherited to a greater or lesser degree as if they
were a single gene.
• When genes are closely linked, recombination events during
meiosis rarely occurs in the gametes.
• If the genes are more loosely linked, then the number of
recombinant events in meiosis will be higher.
• Therefore, the tightness of the linkage is related to how close
together the linked genes are on the chromosome.
• Tightly linked genes may never split up during meiosis, and so the
gametes formed will always be the parental types.
• If the genes are further apart, crossing over between them is more
likely to occur.
• Although in the majority of cases they will be passed on as a
parental unit, sometimes they will be mixed and recombinant
gametes will be produced, which will in turn be reflected in the
offspring.
Temperature effects on phenotype:
1. Temperature can affect coat
coloration.
2. Siamese cat fur in the extremities is
darker due to cooler temperatures.
3. The enzyme making darker pigment
doesn’t work well at the higher
temperatures in the rest of the body.
• Escherichia coli has the gene to make the enzyme b-
galactocidase (breaks down lactose to glucose and
galactose).
• In it’s normal environment lactose is not present to be used
as a food source.
• So, since enzymes are ‘expensive’ to make (need energy,
amino acids, etc.) the enzyme is not required if no lactose
is present.
• The enzyme gene is regulated by a repressor protein.
• The repressor protein is produced by transcription of
another gene nearby on the chromosome.
1. In normal circumstances when lactose is not present,
the repressor protein binds to the promoter region.
2. So, RNA polymerase cannot bind so the gene is not
transcribed.
1. If lactose is present it gets into the cell and binds with the
repressor protein.
2. This cannot bind to the promoter region so RNA
polymerase can bind.
3. So the gene is transcribed and the enzyme is produced to
break down the lactose as a food source (i.e. lactose is the
signal to switch on the gene).
• The observable characteristics as a result of the
expression of the alleles present is the phenotype.
• Phenotype is the result of the genotype (i.e. the alleles
of the genes) e.g. cystic fibrosis is the result of a
mutation of the CFTR protein gene
• In situations where the phenotype of an organism is
almost entirely due to the genotype, the phenotypes
present in a population fall into discrete groups with no
overlap; this is called discontinuous variation.
• Blood groups are due to the
antigens on the surface of the
red blood cells; these are
controlled by a gene with
three alleles (A,B and O)
which interact to produce only
four blood group phenotypes,
A, B, AB and O.
• The blood group phenotype
depends entirely on the
genotype.
• Phenotype is also the result of the influence of the
environment on the expression of those alleles.
• This type of variation in phenotype is the result of both
genotype – actually the alleles of many genes – and the
effects of the environment.
Phenotype = Genotype + Environment
(i.e. nature and nurture)
• The phenotypes produced
from this interaction do
not fit into discrete groups
so the type of variation
produced is called
continuous variation
and the various
phenotypes often follow a
normal distribution.
Twin studies (using genetically identical individuals) can be
used to try to separate the effects of genes and environment.
These studies use:
1. Identical twins who share the same genetic material
2. Non-identical twins who are like normal siblings but
because they are the same age, are more likely to have a
similar environment.
3. Ordinary siblings, used as a control group.
4. If the result shows greater difference, it suggests that the
environment has a stronger influence on that
characteristic.
 Trait Identical twins Identical twins Non-identical Non-twin
reared apart reared together twins siblings

Height difference 1.8cm 1.7cm 4.4cm 4.5cm

Mass difference 4.5kg 1.9kg 4.6kg 4.7kg

IQ score 8.2 5.9 9.9 9.8

difference

Conclusion:
1. Height appears to have a strong genetic component and is
influenced relatively little by environmental factors.
2. Mass appears to be affected by external factors such as
the family eating habits.
3. IQ seems to be a combination of both, with environment
playing a distinct and important role.
Transcription Factors

For a gene to be expressed, two things are necessary:

1. The DNA must be accessible, not buried in densely packed
chromatin.
2. Sequence-specific DNA-binding proteins (transcription factors)
must bind to the promoter sequences, upstream of the
sequence to be transcribed, to help recruit RNA polymerase.

These depend on the interactions of sequence elements

(promoters and enhancers), proteins (including transcription
factors, DNA methyltransferases, histone-modifying enzymes and
chromatin remodelling complexes), and various small RNA species.
• Promoter sequences are usually found just above the
starting point for transcription upstream of the gene.
• Some transcription factors stimulate the transcription of a
region of DNA simply by binding to a DNA promoter
sequence, stimulating the start of transcription of that area
of the DNA.
• Other transcription factors bind to regions known as
enhancer sequences and regulate the activity of the DNA
by changing the structure of the chromatin, making it more
open (allowing active gene expression) or less open
(associated with gene inactivation) to RNA polymerase.
• The control of transcription by transcription factors is the most
common form of gene regulation.
• Each gene can be expressed (switched on) and repressed
(switched off) at different stages of development of the
organism, in different cell types and under different
circumstances.
RNA Splicing

• After transcription, the pre-mRNA contains exons and

introns.
• The modifications to the pre-mRNA always involve the
removal of introns.
• Enzyme complexes called spliceosomes join together the
exons that are to be transcribed and produce the mature,
functional mRNA.
• The spliceosomes may join the same exons in a variety
of ways in a process known as RNA splicing.
RNA Splicing

• A single gene may produce several versions of functional

mRNA which is transcribed from the same section of DNA.
• These different versions of mRNA code for different
arrangements of amino acids, producing different proteins.
• These post-transcriptional changes to mRNA lead to more
variety in the phenotype than is coded for directly in the
genotype.
• Epigenetics is the study of heritable changes in gene
expression that do not involve changes to the DNA
sequence — a change in phenotype without a change
in genotype — which in turn affects how cells read the
genes.
• Epigenetic change is a regular and natural occurrence
but can also be influenced by several factors including
age, the environment / lifestyle, and disease state.
• Epigenetic modifications are involved in cell
differentiation.
• Epigenetic change can have more damaging effects that
can result in diseases like cancer.
Three intracellular systems that can interact to control
genes include:
1. DNA methylation
2. Histone modification
3. Non-coding RNA
DNA Methylation
• Addition of a CH3 group at the
5-carbon of the cytosine ring
resulting in 5-methylcytosine
(5-mC).
• Carried out by a family of enzymes called DNA
methyltransferases (DNMTs).
• In somatic cells, 5-mC occurs almost exclusively in the context of
paired symmetrical methylation of a CpG site.
• These methyl groups project into the major groove of DNA and
inhibit transcription.
• Thus methylation modifies the function of the genes and
affects gene expression.
DNA Demethylation

• Removal of a methyl group from DNA.

• Enables genes to become active so they can be transcribed.
• This mechanism is equally as important and coupled with
DNA methylation.
• Necessary for epigenetic reprogramming of genes and is also
directly involved in many important disease mechanisms such
as tumour progression.
Histone Modification
Histone Modification

• DNA that is wrapped up in nucleosomes is not accessible to

RNA polymerase and the other DNA-binding proteins
necessary to initiate transcription.
• In nucleosomes, the histone molecules have protruding N-
terminal ‘tails’ that can interact with other proteins.
• Different proteins bind to the histone tails to stimulate or inhibit
transcription.
• Binding is controlled by covalent modifications to the histone
tails.
• Specific enzymes tag particular amino acid residues in
specific histones with methyl, acetyl and other groups to
allow control of gene expression.
Histone Modification
• Acetylation is performed by histone
acetyltransferases (HATs) which add an
acetyl group to lysine (which are positively
charged) in this histone tail which acts to
mask the positive charge.
• This causes loosening of chromatin to
promote gene activation.
• Methylation can occur on lysine or
arginine catalysed by histone
methyltransferases.
Non-coding RNA (ncRNA)

• ncRNA is transcribed from DNA but not translated into

proteins.
• ncRNAs function to regulate gene expression at the
transcriptional and post-transcriptional level.
• Many long ncRNAs can complex with chromatin-modifying
proteins and recruit their catalytic activity to specific sites in the
genome, thereby modifying chromatin states and influencing
gene expression.
• Long ncRNAs function in chromatin remodeling, transcriptional
regulation, post-transcriptional regulation.
Non-coding RNA

• One widely known example of this is the role of X-inactive

specific transcript gene (Xist), in X-chromosome inactivation
(XCI).
• This process involves two lncRNAs; Xist and its antisense
transcript Tsix, a negative regulator of Xist.
• In this state XCI is a random event.
• Upon differentiation, Xist expression is elevated resulting in
Xist RNA coating the future inactive X chromosome which
triggers extensive histone methylation and chromosome
inactivation.
Non-coding RNA
Chemical stimulus (e.g. demethylation / transcription factor)

some genes activated while others inactivated

only get mRNA from active genes

active mRNA translated to specific protein

proteins modify cell

changes in cell are permanent and/or difficult to reverse

cell differentiated / specialised

 Stem Cells

Embryonic Stem Umbilical Cord Stem

Adult Stem Cells
Cells (ES) Cells

capable of continuing capable of cell divisions

cell divisions and of pluripotent cells which and giving rise to a
developing into almost are indistinguishable limited range of cells
all the cell types – from ES within a tissue type -
pluripotent. multipotent
Embryonic Stem Cells:
Embryonic Stem Cells:
 Embryonic
Stem Cells:

• The zygote begins to divide by mitosis – about 24 hrs after sperm

entry - giving rise to 2, then 4, then 8 cells, and so on
• The cells continue to divide – approx 20 hrs between divisions -
until they eventually produce a cluster of cells resembling a
mulberry, called a morula. Initially the embryo does not grow in
size because successive cell divisions produce smaller cells
• A blastocyst – produced after about 5 days - is a hollow cell ball
containing a cluster of stem cells (the inner cell mass) which will
give rise to the baby itself and the outer cells, which produce the
placenta.
Embryonic Stem Cells:

• After 3 days, embryo = 8 cells

• Each of these cells is TOTIPOTENT
i.e. potentially capable of developing
into a complete human being – ALL
the genes can be transcribed so all 216
types of cell can be produced.
• If the cells get separated these cells
would develop into identical twins.
 Embryonic Stem Cells:

• After 5 days the cells of the inner cell mass of the

blastocyst are PLURIPOTENT i.e. can differentiate into
most but not all of the different cell types (some genes
have already been ‘switched off’).
• Cannot form extra-embryonic tissues (placenta & umbilical
cord).
 Embryonic Stem Cells:
...undifferentiated cells from the embryo which are able to divide
continuously and develop into other types of cell.
...removed from the inner cell mass of the blastocyst, transferred to special
culture conditions to divide further to form stem cells lines which can be
encouraged to differentiate into different types of cell.
Sources of Embryonic Stem Cells:

1. Isolation of ES cells from surplus blastocysts

created during IVF (which would otherwise be
destroyed).
Sources of Embryonic Stem Cells:

1. Isolation of ES cells from surplus blastocysts

created during IVF (which would otherwise be
destroyed).
2. Production of tailor-made ES cells from
blastocysts derived from patients own
differentiated adult cells (therapeutic cloning or
somatic cell nuclear transfer).
1. Egg cell with nucleus removed fused with cell (or nucleus)
from person  diploid cell
2. Cells lines derived from these stem cells will be genetically
identical to the donor which would overcome the problem
of rejection.
3. These could be used or stored for future use
Stem cell therapy potentially for the treatment of:
1. Serious burns which normally need skin grafts
2. Neurodegenerative diseases e.g. Parkinson’s,
Alzheimer’s.
3. Diabetes (to replace insulin-producing cells)
4. Osteoporosis (to replace bone cells)
5. Paralysis from spinal cord injuries
6. Sickle-cell anaemia
7. Degenerative diseases of other tissues e.g. heart
disease, muscular dystrophy .
1. Stem cells come from human embryos. This amounts

to killing unborn an child/potential human being;

analogous to abortion or murder.
2. Parents of the ‘spare’ embryos which would be used

may object.
3. May have unforseen consequences in recipients (in

patients cells may get out of control  cancer),

differentiate into unwanted cell types, e.g. teratomas
4. Women may be put under (financial) pressure to provide
eggs purely for medical research.
5. Money may be better used for funding other (less
controversial? more widely beneficial?) types of
research.
6. Technology may be used for uncontrolled (unregulated)
eugenics – private rather than state sector, i.e. genetic
choices available to parents (based of fads, whim) may
have serious consequences for future generations who
have no choice.
7. It would soon be possible to use non-stem cells so
research into use of embryonic stem cells is
unnecessary.
1. ‘Spare’ embryos from IVF would have been destroyed
anyway.

2. The potential to relieve human suffering is too great to

ignore; it would be unethical not to allow the development
of stem cell technology.

3. Do not accept that embryos should be regarded as

humans (that it is murder to kill them).

4. Do not consider embryos at early stage as human beings

(since only very young embryos are used).
5. Organs for transplantation are in woefully short supply.

6. Its going to happen anyway and you cannot ‘undiscover’

something.

7. Better that the research stays in the UK/US/Europe/in the

public domain where it can be subject to scrutiny/regulation.

8. Can be regulated to prevent excesses.

• Human iPS that are similar but not identical to human embryonic
stem cells in their behaviour.
• This overcomes the problems of cell rejection and address ethical
concerns with the use of embryonic stem cells.
• They are being used for research into both human development and
disease.
• May help us to understand how cancer cells develop and how certain
birth defects occur.
• Could provide a source of normal human cells of virtually any tissue
type for use in screening new drugs.
• The biggest problem is that these cells are not so easy to grow and
manipulate as natural pluripotent stem cells.
E.g. Curing sickle cell anemia…
Skin cells are modified employing
retroviruses customized to insert genes
into the cell's DNA:
1. The inserted genes keep cells in an
embryonic-stem-cell-like state (iPS
cells).
2. The defective blood-production
gene is replaced with a normal gene.
3. The iPS cells are differentiated into
precursors of bone marrow adult
stem cells, which can be
transplanted into mice to generate
normal blood cells.
Sir John Gurdon & Shinya Yamanaka