INTRODUCTION TO GENETICS

I. TERMINOLOGY

- Genetics: Science that studies the transmission of hereditary characters (scientific

study of heredity). There is a great number of fields inside human genetics.

- Characters: internal, external or behavioural characteristic of an organism.

• Acquired Characters: the characters that do not come from the parents, they
are not transmitted to the offspring. They are acquired during life e.g.
tanning, acquired disease as trauma or infection
• Intermediate Characters: when a tendency is inherited and it can, more or
less, manifest during life e.g. height, muscular strength, tendency for a
disease as diabetes
• Hereditary Characters: the characters that come from the parents and are
transmitted to the offspring. They are unchangeable, and manifest from birth
(inborn). Hereditary characters can be:

§ Qualitative: characters with discontinuous variability, so individuals

can be grouped into homogenous classes, individuals can be counted
and enumerated e.g. eye colour.

§ Quantitative: characters with continuous variability, so intermediate

values are measured e.g. height

- Genotype: Set of genes in the DNA responsible for a particular trait – genetic
makeup.

- Phenotype: Physical manifestation of the genotype.

The factors that can play a role in defining the phenotype are:

§ Genotype;
§ Action of other genes or their products;
§ Environment – random events during development.

P.S.: Two phenotypes can be the same but caused by different genotypes, as two genotypes
can be the same and cause two different phenotypes.
 MENDELISM

I. HISTORY

i. Mendel –

Gregor Mendel (1822-84) was a Moravian monk and biologist who established the laws
that are the foundation of classical genetics, considered then the ‘father of genetics’. He
performed his studies on pea plants (Pisum sativum) as controlled experiments of
breeding peas.

ii. Pea story –

Pisum sativum was chosen because it was greatly available, easy to grow, reproduce
quickly, it’s hermaphrodite (self-pollinates), the gonads are enclosed in petals and it has
many different variations that are preserved in descendants. Mendel observed seven
traits and 14 variants of these traits in total.

In 1854 Mendel begun his experiments, at this time it was known that both parents
contribute to determine the characters of the offspring and these contributions are
brought through gametes.
 iii. Experiments –

In 1856 begins experimental crossings between true-breeding parents (homozygous), being

a monohybrid cross called the parietal (P) generation. This cross gave rise to the first filial
(F1) generation, which are hybrids.

From all the 7 characters, as a result of the monohybrid cross, he always obtained in F1 only
one variant out of the two, with no mixing.

Therefore, Mendel called dominant the character expressed in F1 and recessive the character
not expressed in F1.

Self-pollinating the plants from F1, Mendel obtained the second filial (F2) generation, which
showed a phenotypic ratio of 3:1 - 75% expressing dominant variant, and 25%
expressing the recessive character. With the F2 Mendel realised that the recessive
character reappeared in defined proportions, which means they were just hidden in the
individuals of F1.
In F2 the genotypic ratio is 1:2:1 being 25% homozygous dominant (double dominant alleles),
25% homozygous recessive, and 50% heterozygous (one dominant and one recessive
allele). So in F2 we have two phenotypes but three genotypes.

Punnet Square Method

According to Mendel, characters were determined by ‘’discrete factors’’, today we know

that discrete factors are genes.

Genes have alleles located on corresponding loci of homologous chromosome pairs, one
from the mother and one from the father, and these alleles will randomly separate during
meiosis of the gametes, in a way that each gamete will have one of the alleles that the
somatic cell carries. Therefore, during fertilization the alleles of the gametes unite randomly
forming a new genotype.
 II. MENDELS LAWS

The laws of inheritance were published in 1865 but only confirmed in 1900 when
technology was advanced enough to do so, since Mendel only worked by observation.
Mendel’s principles are still valid.

- Mendel’s First Law – Principle of (Complete) Dominance

i. Definition –

Recessive alleles will always be masked by dominant alleles. Therefore, a cross

between a homozygous dominant and a homozygous recessive will always
express the dominant phenotype, while still having a heterozygous genotype.

Easily explained with a monohybrid cross experiment, as we see in P generation

cross.

Therefore, a dominant phenotype can have two genotypes, dominant

homozygous or heterozygous.

ii. Experiment – Test Cross

To find out the genotype of a dominant phenotype we can do a Testcross (re-

crossing) which consists in crossing the organism that has the dominant
phenotype with a recessive organism (that you know is homozygous recessive).
This is because recessive alleles do not interfere with the phenotype if we have a
dominant genotype.
- Mendel’s Second Law – Principle of Segregation

i. Definition –

Every individual organism contains two alleles for each trait, and that these
alleles segregate (separate) during meiosis such that each gamete contains only
one of the alleles. An offspring thus receives a pair of alleles for a trait by
inheriting homologous chromosomes from the parent organisms: one allele for
each trait from each parent.

- Mendel’s Third Law – Principle of Independent Assortment

i. Definition –

Alleles for different traits (e.g. colour and seed shape) are passed independently
of one another to the gametes. That is, the biological selection of an allele for
one trait has nothing to do with the selection of an allele for any other trait.

The physical basis of the independent assortment of chromosomes is the random

orientation of each bivalent chromosome along the metaphase plate (in meiosis
l) with respect to the other bivalent chromosomes, along with crossing over (in
pachytene of meiosis l).

ii. Experiment
Mendel found support for this law in his dihybrid cross experiments (involves
two traits - AAbb x aaBB).

In the dihybrid cross below, the gametes from the parents (P) will be YR x yr; The
fusion of the gametes of the parents will originate an offspring (F1) that has
100% of organisms with the genotype YyRr – double heterozygous genotype.
Self-fertilizing F1, we form F2, which has a phenotypic ratio of 9:3:3:1, which
means:

o 9 parts will manifest both dominant traits;

o 6 parts (3+3) will show one dominant trait and one recessive trait;
o 1 part will manifest both recessive traits.
Forked Line Method: Appropriate to be used when there are more than two traits involved,
but it can be also used for only two traits. It shows only the phenotypic ratio.

o Number of gametes an organism produce = 2n; being n the number of heterozygous.

o The phenotypic ratio of a crossing (how many different phenotypes will manifest) is
also 2n.
o The genotypic ratio of a crossing (how many different genotypes in the offspring) is
3n.
Genes exist in alternative forms, called alleles, which can be recessive or dominant.
III. Mendelian Diseases

i. Definition

They are caused by mutations of individual genes and transmitted according to

the classical (Mendelian) principles of inheritance. These diseases are very
numerous (some thousands are known) and affect a total of 1% of those born,
but in most cases the individual diseases are rather rare (incidence less than 1:
10,000 newborns).

ii. Types

There are 3 main ways (first 3) of transmitting Mendelian traits -pattern of

inheritance-, which means transmitting alleles, that can cause diseases -single
gene diseases-:

o Autosomal Dominant: Each affected person has an affected parent. Occurs in

every generation. E.g. Huntington’s disease, neurofibromatosis, achondroplasia,
familial hypercholesterolemia, brachydactyly.
o Autosomal Recessive: Both parents of an affected person are carriers. E.g. sickle
cell anemia, cystic fibrosis, phenylketonuria (PKU), albinism.

o X-Linked:
- X-Linked Dominant: Females are more frequently affected
- X-Linked Recessive: Males are more frequently affected

o Mitochondrial: Can affect both males and females, but it is only passed by
females.
IV. Extensions of Mendelism – Monogenic variation

i. Incomplete Dominance:

Definition –

The heterozygous genotype manifests a different phenotype, which is

intermediate between the complete dominant and the complete recessive
phenotype, so intermediate between the homozygous phenotypes.
Therefore, there are 3 phenotypes for 1 trait, and neither of the alleles is
complete dominant over the other.

Examples -

This is because the complete dominant phenotype will have 2 doses of the gene
product (RR) manifested, while the heterozygous genotype will have only 1 dose
of the gene product (Rr), which is called haploinsufficiency (situation in which the
total level of a gene product, a particular protein, produced by the cell is about
half of the normal level and that is not sufficient to permit the cell to manifest
the dominant expected phenotype, because only one copy of the gene does not
mask completely the recessive gene). The recessive genotype/phenotype has
zero amount of the gene product, so total absence of it.
The phenotypic and genotypic ratio is 1:2:1; 25% homozygous recessive
genotype and recessive phenotype, 50% heterozygous genotype and
 intermediate phenotype, and 25% homozygous dominant genotype and
dominant phenotype.

Alleles are still inherited according to Mendel's basic rules, even when they show
incomplete dominance.
Other examples: plumage in chicken (black, white and grey), palomino horse.

ii. Codominance:

Definition - Both alleles are simultaneously expressed in the heterozygote.

The heterozygous manifests both homozygotic phenotypes instead of
manifesting only the dominant one, only the recessive one, or a mix between
them. We can say that the alleles function independently, without masking each
other. Each genotype has its own phenotype.

Examples-

We can still use Mendel's rules to predict inheritance of codominant alleles.

Examples

- Blood type system in humans – there are more of less 36 different blood
type system in humans, one of this is the MN system, encoded by the L gene.
An LM allele specifies production of an M marker -antigen- displayed on the
surface of red blood cells, while an LN allele specifies production of a slightly
different N antigen.

o Homozygotes LMLM have only M antigen, and therefore only antibody anti-N
 o Homozygotes LNLN have only N antigen, and therefore antibody anti-M
o Heterozygotes LMLN have both types of antigens (M and N), having no antibodies.

In heterozygous the antigens M and N are present in equal numbers on the cell
surface, we can see that there is not a dominant neither recessive allele, they are
both expressed equally.

iii. Multiple Alleles:

Definition –

Mendel's work suggested that just two alleles existed for each gene. Today,
we know that's not always, or even usually, the case. Although individual
humans (for being a diploid organisms) can only carry two alleles for a given
gene, multiple alleles may exist in a population level, and different individuals
in the population may have different pairs of these alleles.

Examples –

Ex 1. Gene that codifies coat colour in rabbits, called C gene, which occurs as 4 different
alleles: c, ch,cch,c+.

The picture shows these alleles behaving in homozygous conditions.

The relationship between the alleles can be seen once we cross homozygous to obtain
heterozygous – Allelic Series.
In heterozygous conditions we see a dominance relation that can be summarized as c+ > cch
> ch > c - no complete dominance of cch on ch-.
A plausible explanation is that the c gene controls a step in the formation of black pigment
in the fur.

c+_ is wild type; cchc shows incomplete dominance; cchch shows codominance

Ex 2. AB0 Blood System

It shows 3 different alleles: IA, IB, and i.

I gene encodes for a glucosyl transferase, enzyme that can transfer a glucosyl group to a
substrate H (or antigen H) in the RBC membrane, enabling the formation of different
antigen groups (A, B or A and B).
- IA encodes for glucosyl transferase A, able to transfer a N-acetyl-galactosamine group to
the substrate H, which when bound to each other form the Antigen A.
- IB encodes for glucosyl transferase B, that adds to the substrate H a galactose group,
forming the Antigen B.
- i does not encode any transferase, so it doesn’t form any antigen, therefore giving rise to
the blood group 0.

In the AB0 system there are 6 different genotypes and 4 different phenotypes. Each
phenotype is a blood type (group):
- Group A has antigen A in the RBC membrane and antibody Anti-B in the plasma.
- Group B has antigen B and antibody Anti- A in plasma.
- Group AB has both antigens A and B -codominance- and no antibodies in the plasma.
- Group 0 has no antigens, therefore antibody Anti-A and Anti-B.
 iv. Essential Genes - Lethal Alleles:

Definition - Some genes have alleles that prevent survival when homozygous
or heterozygous. Lethal alleles are alleles of essential genes that do not allow
the gene to encode mandatory products, which are needed in order to
sustain life. Therefore, if these products are not present the organism dies.

Lethal alleles can be:

■ Recessive Lethal Alleles: The organism needs two copies of this allele for
it to be lethal (aa or AA), therefore a heterozygous organism won’t
present the lethality of the allele, but it can sometimes display a form of
diseased phenotype (unique phenotype), as in the case of Agouti coat
colour in mice.

AA = Agouti Coat
Aa = Yellow Coat
aa = dead
Phenotypic Ratio 1:
2

Another example of recessive lethal allele is the achondroplasia, a form of dwarfism. A

person heterozygous for this allele will have shortened limbs and short stature
(achondroplasia), a condition that is not lethal. However, homozygosity for the same allele
causes death during embryonic development or the first months of life, an example of
recessive lethality.

o Dominant Lethal Alleles: These alleles are going to be lethal when the organism
processes at least one copy of this allele (Aa -more common- or AA -rare-). These
alleles are not commonly found in populations because they usually result in the
death of an organism before its fertile age. An example in humans of a dominant
lethal allele is Huntington's disease, a rare neurodegenerative disorder that
ultimately results in death, but the transmission of this allele can might occur.

o Conditional Lethal Alleles: They are only lethal if triggered by some environmental
factor. One example of a conditional lethal is favism, a sex-linked inherited condition
that causes deficiency of the enzyme glucose-6-phosphate dehydrogenase, resulting
in the carrier to develop hemolytic anemia when they eat fava beans.

P.s.: Favism affected people are more resistant to malaria – one of the causes that justify the
persistence of favism.
- Permissive Environmental Conditions: daily conditions that do not affect the
allele.
- Non-permissive Environmental Conditions: the condition that brings the
lethality of the allele.
 GENE EXPRESSION AND THE ENVIRONMENT

I. Introduction

As we said before, the environment can influence the expression of the genotype, which is the
phenotype.

Internal and external environments interact with the genes by controlling their expression and
interaction with their products.

The development of a multicellular organism from the zygote is a series of phenotypic changes
which result from interaction of the genome and the environment – differentiation of cells, and
arrangement of cells into defined tissues and organs.

II. Penetrance and Expressivity:

These terms quantify the relationship between genotype and phenotype, they both depend on
the genotype and on the environment of the individual.

Both these concepts cause deviation from the usual Mendelian Laws of Inheritance.

i. Penetrance:
Describes how much the presence of an allele correspond with the manifestation
of the trait, which is, the percentage of people with a genotype that manifest the
expected phenotype.

If penetrance is 100% it means that all the people with the genotype in question
express the phenotype expected – complete penetrance.

If the penetrance is 70% it means that only 70% of people with the genotype in
question express the expected phenotype – Individuals with the same genotype
can manifest different phenotypes! - and in this case, we refer to incomplete
penetrance of a trait, and a nonpenetrant allele.

Examples - Polydactyly has incomplete penetrance of 25-30%; osteogenesis

imperfecta has incomplete penetrance (less than 100%); BRCA1 gene involved in
familial breast cancer has penetrance of 80%
 ii. Expressivity:
Describes the variation in expression of the genotype, which is the degree to
which phenotype is expressed. Expressivity regards how much of the phenotype
will be expressed.
Therefore, individuals with the same genotype may manifest different levels of
the phenotype due to variability of gene expression -variable expressivity-, or if
the subjects with the genotype in question express a constant phenotype we
speak about the constant expressivity of a trait.

Ex.: Waardenburg syndrome has a variable expressivity of its symptoms, which are
hearing loss, heterochromia, white hair, and premature greying of hair.
Therefore, a subject with this syndrome may have no symptoms to all symptoms.

We can have in the same trait (gene) incomplete penetrance and variable expressivity,
which means that from all the subject with the genotype in question some will manifest the
phenotype, and from those, the phenotype will vary from subject to subject.

Neurofibromatosis is an example of both incomplete penetrance and variable expressivity; it

is a autosomal dominant disorder with 50-80% penetrance and the individuals with the
disease show a wide range of phenotypes.

III. Pleiotropy:

When one gene influence two or more (seemingly unrelated) phenotypic traits,
called pleiotropic gene. These genes can be influenced by the environment.

Pleiotropy can arise from several distinct but potentially overlapping

mechanisms, such as gene pleiotropy, developmental pleiotropy, and selection
pleiotropy.

- Gene pleiotropy occurs when a gene product interacts with multiple

other proteins or catalyzes multiple reactions.
- Developmental pleiotropy occurs when mutations have multiple effects on
the resulting phenotype.
- Selectional pleiotropy occurs when the resulting phenotype has many effects
on fitness (depending on factors such as age and gender).]
Examples - An example of pleiotropy is phenylketonuria, caused by a defect in a
single gene on chromosome 12 that codes for enzyme phenylalanine
hydroxylase; it affects multiple systems, such as the nervous and integumentary
system.
 Other examples of pleiotropy are albinism, sickle cell anemia (beta globin gene
mutation causes blindness, liver failure, and heart attack -multiple traits), and
certain forms of autism and schizophrenia.

IV. Effects of the Environment

- Internal Environment

Internal environmental factors include age and sex for example.

i. Age can be a crucial factor of the expressivity of a gene. Different genes are expressed at
different times during the life cycle, and programmed activation and inactivation of
genes influences many traits e.g. baldness, Duchenne muscular dystrophy (which
manifests in children aged 2 to 5 years old.

ii. Sex of an individual affects the expression of some autosomal genes.

Sex-limited traits manifest in one sex but not in the other e.g. milk production in dairy
cattle (where both sexes have milk producing genes but only females express them),
horn formation in some sheep species (only males express the genes), facial hair
distribution in humans.

Sex-influenced traits appear in both sexes, but the sexes show either a difference in
frequency of occurrence or an altered relationship between genotype and phenotype
e.g. pattern baldness (controlled by an autosomal gene that is dominant in males and
recessive in females, so the heterozygous phenotype has a different expression in each
sex), cleft lip and palate, rheumatoid arthritis, osteoporosis, etc.
 - External Environment

External environmental factors include temperature and chemicals for example.

i. Temperature
It may alter the activity of enzymes -proteins-, so they can be functional at one
temperature but non-functional at another, which means some alleles are
sensible to temperature e.g. fur colour in Himalayan rabbits (these white rabbits
develop darker fur on the colder parts of their bodies, as ears, nose and paws;
since all body cells have the same genotype, this fur pattern might result from
environmental influences; raising these rabbits under controlled temperature,
the ones that were raised above 30oC were entirely white, the ones raised at 25
o
C had the typical Hymalaian phenotype, and the ones raised at 25 oC with parts
of the body cooled to below 25 oC had dark stops on the experimentally cooled
part); another example is the siamese cat (the ones that live in warm homes tend
to be lighter than outdoor cats).
ii. Chemicals can have significant effects in the expression of a gene e.g.
phenylketonuria (autosomal recessive defect in metabolism of the amino acid
phenylalanine; If not treated by restricting this amino acid in the diet, severe
mental retardation and other symptoms result).

Phenocopy is a variation in phenotype caused by environmental conditions (external),

mimicking the phenotype of a known gene mutation. Phenocopies are not hereditary,
and the individual does not carry the allele(s) being mimicked e.g. rubella (causes
cataracts, deafness and heart defects in a fetus whose mother is infected during the first
12 weeks of pregnancy; it mimics a rare recessive allele); thalidomide (drug that if taken
on days 35 to 50 of gestation mimics the effects of the genetic disorder phocomelia,
supressing development of long bones); hair bleaching.
 GENE INTERACTIONS

I. Defintion
When two genes placed in different loci (non-allelic genes) interact, determining a single trait, so the
expression of one gene depends on the presence or absence of another gene in an individual -
Interaction of genes at different loci that affect the same character.

Epistasis: defined generally as the interaction between different genes (at different loci), which
describe a masking effect whereby a variant or allele at one locus prevents the variant at another
locus from manifesting its effect.

Types of Gene Interactions:

Gene Interactions can be divided into 2 kinds:

i. Gene Interactions Without Epistasis: We can have or not alteration of mendelian ratio
9:3:3:1 in F2, and we have always a new phenotype - gene interaction that produce new
phenotype.

Examples:

§ No alteration of mendelian ratio: Comb shape in the chicken (allele R and P) - Nonallelic
genes (genes placed in different loci) that affect the same character (trait) may interact to
give a new phenotype and often modified phenotypic ratios. We can assume that the single
comb (since it is double recessive) is a product of other genes, while the other phenotypes
aredue to the activity of R and P alleles.
§ With alteration of mendelian ratio: Fruit shape in summer squash shows a 9:6:1 phenotypic
ratio (modification of mendelian ratio- indicates that two loci are involved). Two genes are
involved, each completely dominant. Interaction between the two loci produces a new
phenotype. In this example if you have one of the locus dominant and in one locus recessive
they encode for the same phenotype (A_bb and aaB_ both encode for sphere-shaped fruits)
that's why the ratio is
changed.

always
P.s. True-breeding organism always pass down the same phenotypic trait to its offspring, which
means that it must be homozygous for both genes.

In the example above, the sphere-shaped fruit is not always true-breeding, because its genotype can
be Aabb/aaBb, but it is true breeding when its genotype is AAbb or aaBB; crossing these true-
breeding genotypes produces a new genotype, disk-shaped (F1), which will result in an F2 with
modified phenotypic ratio (9:6:1).

ii. Gene Interactions With Epistasis : Any time two (or more) different genes (in different
loci) contribute to a single phenotype by masking or modifying the phenotypic
expression of another gene we have epistasis. Epistasis is confined to dihybrid crosses
where two pairs of alleles assort independently.

In epistasis one gene masks the expression of another, but no new phenotype is
produced.
- Epistatic Gene: gene the masks another;
- Hypostatic Gene: gene that gets masked.

Several possibilities for interaction exist, all producing modifications in the mendelian ratio (9:3:3:1
dihybrid ratio).

a) Recessive Epistasis: epistasis caused by recessive alleles, so that recessive homozygous gene
(epistatic) masks the effect of the homozygous dominant/heterozygous gene (hypostatic).
[9:3:4]

Ex.1: Coat colour in rodents where A_cc and aacc encode for the same phenotype, where A gene
determines pigment, and C determines deposit of pigment (it doesn’t matter how much pigment
there is if there is no deposition). C is epistatic when homozygous recessive (cc), whilst A is
hypostatic.
The phenotypic ratio of the F2 is 9:3:4 (4 = 3+1 → mendelian ratio. 4 parts manifest the recessive
trait due to recessive epistasis).
Ex.2: Labrador dog coat color - similar to coat color of rodents. In labradors the B gene is hypostatic,
it codifies black pigment (B_ - black, bb -brown). Whilst the E gene is epistatic, it either allows (E_) or
masks (ee) the expression of the B gene, indeed, genotypes eeB_ and eebb encode the same
phenotype (yellow). The phenotypic ratio in this cases is 9:4:3.
Ex.3: Bombay Phenotype; it is a particular condition in ABO blood type system. In normal conditions
we have one gene that controls our blood type, I gene, and we have 3 alleles (IA, IB, i) of this gene.
Glycosyltransferase A and B are enzymes able to transfer specific groups on antigen H, in the
membrane at the RBC. But the presence of H substrate is regulated by H gene, that encodes a
transferase able to form the antigen H in fucose (H_ we have the H substrate and hh we don't).
If we don't have antigen H we can't have A or B antigen, so we will be type O and we will also be
type O if the genotype is iiHH. Even though is rare to find __hh genotype (bombay phenotype- new
phenotype). So hh is epistatic, whilst the I gene is hypostatic.
For blood transfusion it's important to notify if the phenotype is bombay or not. If you have __hh
phenotype you need to transfer another blood that is also __hh.
b) Dominant Epistasis: happens when epistasis is caused by a dominant allele; so, if the epistatic
gene has one or two dominant alleles, it will mask the effect of the hypostatic gene, regardless if
the hypostatic gene is dominant or recessive. In dominant epistasis A_B_ and aaB_ (considering
gene B is epistatic) have the same phenotype producing an F2 ratio of 12:3:1.

Ex.: Summer Squash colour; have 3 common colors, being yellow recessive to white but dominant to
green. The epistatic dominant gene, W_, is an inhibitor of the pigment coded by the hypostatic gene
Y. So, the phenotype will be white color everytime gene W has at least one dominant allele (Y_W_
or yyW_).
The dominant Y is required to convert green intermediate to yellow.
The dominant W inhibits white to green conversion, resulting in white fruit.

c) Duplicate Recessive Epistasis: When recessive alleles at either of the two loci can mask the
expression of dominant alleles at the two loci, so both genes, if recessive can mask the
dominant, both are epistatic. Both loci produce a identical phenotype. Shows a 9:7 phenotypic
ratio in F2.

Ex.: Colour in sweet pea flower. The purple colour is governed by two dominant genes say C and P.
When these genes are in separate individuals (CCpp or ccPP) or recessive (ccpp) they produce white
flower. Therefore, C_P_ codes for purple phenotype. And C_pp, ccP_ and ccpp code for white
phenotype, resulting in the 9:7 ratio.
d) Duplicate Dominant Epistasis: When at least in one locus there is a least one dominant allele
(or in A or in B or in both - being heterozygous or dominant homozygous) and these alleles can
mask the expression of recessive alleles at the two loci. Phenotypic ratio is 15:1 in F2.

Ex.: Fruit shape in Shepherd's purse plant. There are 2 possible fruit shapes, heart shaped and
narrow. One dominant allele of either duplicate gene will produce heart shaped fruit (A_B_,A_bb
and aaB_) and aabb produce narrow fruit.

The complex relationships of epistasis play a role in many human genetic disorders, further
complicating their analysis.
 CHROMOSOMAL BASIS OF MENDELISM

I. Sex linked traits

A trait whose gene is localized on a sex chromosome is called a sex-linked trait.

From the study of the transmission of these traits Thomas Hunt Morgan has obtained
experimental evidence of the chromosomal theory of herediterity. He discovered two
phenotypes, a normal or wild-type, more common in the population, and a alternative
phenotype (mutant phenotype).

Ex. of sex-linked trait: Eye color in Drosophila. Crossing a wild-type female (red eyes) with a
alternative male (white eyes), the F1 was wild type, F2 had 2 females with wild type, 2 males one
with wild type one with alternative phenotype. So, Thomas Morgan hypothesized that inheritance of
eye color was linked to sex chromosomes. He also said that alternative (white) was recessive to wild-
type (red). The white phenotype manifests itself with only one allele in males that have only one X
chromosome (hemizygote), instead of being a character manifested in homologous chromosomes
as the previous cases. The eye color trait in drosophila is a sex related trait.
To confirm the theory he crossed a heterozygous female (red eyed) and a white eyed male, and also
a white eyed female and a red eyed male.
II. Sex Determination

- Sex Determination in Drosophila: The Y chromosome in drosophila, unlike that in

humans, plays no role in sex determination. Instead the sex of the fly is determined
by the ratio of X chromosomes to autosomes. If the ratio is 0.5 (1 X chromosome
and 2 autosomes) is a male, if the ratio is 1 (2X2) is a female, all the other
combinations generate infertile flies.

- Sex Determination in Other Animals:

We can have males with homogametic genotype (ZZ) and females with
heterogametic genotype (ZW), which is common in butterflies and some reptiles.

We can also have a haplodiplosystem of sex determination where haploid organisms

(unfertilized egg) is male, and diploid organisms (fertilized eggs) are female. It occurs
in bees. where the queen decides the ratio of males and females and she is the only
one not infertile.

Also in species of turtles for example, sex is determined by temperature. Eggs that
have been incubated above 30oC hatch into females, whereas eggs that have been
incubated at a lower temperature result to be male.

- Sex Determination in Humans: Depends on the Y chromosome, which is a little

chromosome, mostly composed of heterochromatin, with only a few genes in it. One
of these genes is called SRY gene, and produces TDF (Testis Determining Factor),
which induces development of testis and consequently production testosterone. In
the absence of the Y chromosome no TDF is produced, and this will allow the
differentiation of the embryonic gonads’s cortex in ovaries, on the other hand, in
males, the TDF will cause the medullary part of the embryonic gonads to
 differentiate into testes. Once testosterone is produced, it has to bind to
testosterone receptors, and this receptors have their gene in the X chromosome (AR
gene), so the testosterone-receptor complex can signal for male differentiation,
causing male secondary sexual characteristics. If there is a problem (mutation) on
the AR gene there will be no testosterone-receptor complex, therefore no signal and
this will produce female secondary sexual characteristics.

Ps:. Primary sex characteristics refer to the genotype of the subject, that will cause
the formation of the sexual apparatus. Secondary sex characteristics refer to other
visible changes that mark adult maturation, given by the hormones produced by the
gonads.

III. Y-Linked Inheritance (Holandric Traits)

These traits never occur in female, and occur in all male descendants of an affected male. The
concepts of dominant and recessive do not apply to Y-linked traits, as only one allele (on the Y) is
ever present in any one (male) individual.

P.s.: Males with a single Y or X-linked allele are described as hemizygotes because only one allele is
present.

There are fewer Y-linked then X-linked disorders, since the Y chromosome is smaller and has less
genes than the X chromosome. An example of Y-linked trait is the hair in the ears.

IV. X-Linked Recessive Inheritance: caused by a mutation in the X chromosome. For this reason,
men will never be carrier of the disease, only affected or unaffected (necessarily
hemizygous). Whilst females can be unaffected, carriers, or affected.

What makes possible for females to be carriers and not affected, is that only one X
chromosome is active, it means in this case, that if I’m a carrier several cells will have X with
mutation and others X without mutation.

Ex.1: Hemophilia → people affected can not produce blood clotting factors, they have a deficiency in
either clotting factor VIII or IX.
Ex.2: Daltonism → color blindness.
If we have a father affected and an unaffected mother we will have 50% carrier daughter and 50%
unaffected son. If we cross a unaffected father with a carrier mother we will have 25% UNAFFECTED
SON, 25% affected son, 25% unaffected daughter and 25% carrier daughter.

[In humans, generally men are affected and women are carriers for two reasons. The first is the simple
statistical fact that if the X-chromosomes in a population that carry a particular X-linked mutation at a
frequency of 'f' (for example, 1%) then that will be the frequency that men are likely to express the
mutation (since they have only one X), while women will express it at a frequency of f2 (for example 1% *
1% = 0.01%) since they have two X's and hence two chances to get the normal allele. Thus, X-linked
mutations tend to be rare in women. The second reason for female rarity is that women who express the
mutation must have two X chromosomes that carry the trait and they necessarily got one from their
father, who would have also expressed the trait because he only had one X chromosome in the first
place.]

V. X-Linked Dominant Inheritance: A single copy of the mutation is enough to cause the
disease in both males (who have one X chromosome) and females (who have two X
chromosomes), so, there are no carriers, and do not necessarily affect males more than
females (unlike X-linked recessive traits). The exact pattern of inheritance varies, depending
on whether the father or the mother has the trait of interest. In some conditions, the
absence of a functional gene results in the death of affected males.
 Ex.: Incontinentia pigmenti → is a condition that can affect many body systems particularly
the skin.

If we have an unaffected father and an affected mother (only one X mutated) we will have 25%
unaffected son, 25% affected son, 25% affected daughter and 25% unaffected daughter.
If we have an affected father and an unaffected mother we will have 50% unaffected son and 50%
affected daughter.

[Sex linkage describes the patterns of inheritance and presentation when a mutated gene (an allele)
is present on a sex chromosome (an allosome) rather than a non-sex chromosome (an autosome).
They are characteristically different from the autosomal forms of dominance and recessiveness.
Since humans have several times as many genes on the female X chromosome than on the male Y
chromosome, X-linked traits are much more common than Y-linked traits. Additionally, there are
more X-linked recessive conditions than X-linked dominant, and X-linked recessive conditions affect
males much more commonly, due to males only having the one X chromosome required for the
condition to present.]
- Compensation of X-Linked Gene: for a dominant X-linked disease, if the man is affected XaY and the
woman is affected heterozygous XaX the disease manifests differently, because the female do not
manifest the affected X in all of her cells because of the X inactivation (Barr Body). If the affected
female has both X affected (mutated) XMXM all her cells will manifest a mutated X (same phenotype
as a affected man), but only one anyways, so it does not lead to death, there is not the double of
the genetic material active.
-
 INHERITANCE OF COMPLEX TRAITS

INTRODUCTION
The rules of inheritance discovered by Mendel depended on his wisely choosing traits that varied in
a clear-cut, easily distinguishable, qualitative way. But humans are not either tall or short nor are
they either heavy or light. Many traits differ in a continuous, quantitative way throughout a
population. Quantitative traits are polygenic (many genes) traits.

W. Johannsen (1903) was the first to study quantitative traits. He showed that variation in a
quantitative trait is due to a combination of genetic and environmental factors, he studied the
weight of seeds from the broad bean Phaseolus vulgaris. Among the plants available to him, seed
weight varied from 150 to 900 mg. He established lines from individual seeds across this range and
maintained each line by self-fertilization for several generations. The seeds from each of the ''pure''
lines tended to resemble the seed from which they were founded (this indicated that some variation
in this trait is due to genetic differences). However he observed that seed weight also varied within
each of the pure lines, because of environmental differences.

Nilsson-Ehle (1908) studied color variation in wheat grains. When he crossed a true-breeding red-
grained variety and a true-breeding white-grained variety, he obtained a F1 with an intermediate red
phenotype.

Self fertilization of F1 produced an F2 with seven distinct classes, ranging from white to dark red.
Studying the number of classes of F2 generation he understood that there was 3 classes of genes
which contribute to the color, A B C, and an individual manifests then 6 alleles, so the colour
depends on the number of this alleles that encode for red pigment, which is the number of
dominant alleles. For example, if you have 3 dominant alleles it's gonna be intermediate red, the
genotype can be AABbcc, or AaBbCc etc.
 This is a polygenic inheritance, can also be considered a particular kind of gene interaction but this
time with quantitative genes.

P.s.: The histogram of quantitative traits resembles a bell-shaped curve, a symmetric distribution.

● Corolla length on the tobacco flower by Edward Foist.

● There are several diseases which are ruled by quantitative traits - quantitative diseases.
MULTIFACTORIAL DISEASES

Genetics has found that some traits that do not vary continuously in the population also appear to
be influenced by multiple factors (risk factors). Many factors can predispose an individual to develop
a disease. When the liability exceeds a certain level called threshold the trait is manifested. This type
of trait is therefore called a threshold trait.

This factors are quantitative, but the disease itself is qualitative trait, but in this case called a
multifactorial trait, since it involves many factors, environmental and genetic -predisposition-.

Ex: heart disease, schizophrenia, depression, etc.

I can have a predisposition for these diseases, but if I don’t have risk factors I'm not near the
threshold so, it’s more difficult I’ll manifest my predisposition.

This kind of disease does not have a mendelian inheritance, since there are many factors that can
influence the manifestation of the trait.
 Histogram: Graph that disposes the frequency (y) related to the trait (x). We can see the standard
deviations from the mean, being the mean the central histogram (bar) with higher frequency. Each
histogram (bar) represents a class. Generally we have a normal distribution (symmetric).

● Single gene/monogenic/oligogenic traits and polygenic traits:

 MUTATIONS

INTRODUCTION:

Definition: Mutation is a sudden, random and permanent change in DNA sequence. They are the
main source of genetic variability in some species.

Types:

- gene mutation
- Chromosomal mutation
- Genome mutation.

GENE MUTATIONS

A gene mutation is a permanent alteration in the DNA sequence that makes up a gene, such that the
sequence differs from what is found in most people.

Gene mutations can be:

- Forward Mutation: A→ a or D+ → D ; from the wild type (normal) type to mutant.

- Back Mutation: a → A or D → D+ ; from the mutant to wild type; it's a second mutation
because we need first the forward mutation in order to have back mutation.
FORWARD MUTATIONS

Mutations can be classified by origin, cell type, expression, effect on function, molecular change, or
effect of translation.

i. By Cell Type:

- Germ-Line Mutations: occur in germ cells, and can be passed to the offspring since in meiosis
segregation half of the gametes produced by this organism will be mutated - if only one copy of
the gene carries the mutation-, in this case every cell in the organism will be affected, since they
all come from the zygote and the zygote already has the mutation.
- Somatic Mutations: occurs in a single body cell and cannot be inherited, only tissue derived
from mutated cell are affected, somatic mutations originate in mitosis.
 WEI -516¥

§
ii. By Expression: @ wñ÷÷±% .

- Conditional Mutations: Important because the effect of these mutations can be turned on
and off by the researcher, so, it allows control over gene expression. It produces phenotypic
changes under specific (permissive) conditions but not others (restrictive) conditions. For
example, temperature-sensitive mutation is a conditional mutation whose expression
depends on temperature (temperature is the permissive condition, the lack of it is the
restrictive).
- Unconditional Mutations: Does not need permissive conditions to be expressed.

iii. By Effect on Gene Function:

- Loss of Function: Results in a complete inactivation of gene or completely non-functional

gene product.
- Hypomorphic: Reduction in the level of expression of the gene or reduction in activity of the
product.
- Hypermorphic: Causes a greater than normal level of gene expression because it changes the
regulation of the gene, so the product is overproduced.
- Gain of Function: Causes the expression of a gene that is not normally expressed, so it
qualitatively (yes or no instead of more of less) changes the action of the gene.

iv. By Molecular Change:

a. Base Substitutions: One base pair is replaced with another base pair. It is a single
point mutation - a single nucleotide is changed. Most common. Includes:
b. Transition: substitution of one pyrimidine with another pyrimidine or one purine
with another purine;
c. Transversion: substitution of one pyrimidine to one purine, or vice-versa.
d. Insertion: Addition of one base pair.
e. Deletion: Removal of one base pair.

Both Insertion and Deletion cause a change in the reading frame, therefore they are called
Frameshift Mutations, so we can say that when classifying mutations by the molecular change we
have single point mutations (which do not alter the reading frame) and frameshift mutations.
v. By Effect on Translation:
- Missense Mutation: when a substitution (change in a single base pair - so also missense
mutation is a single point mutation) causes change in amino acid during translation because
of the replacement of the single nucleotide; this amino acid change may have no effect, it
may result in a more functioning protein (important for evolution) or it can result in a
nonfunctional protein.

For example, missense mutation can cause sickle-cell anemia, which happens when a point
mutation in the beta-globin chain of haemoglobin, causes the hydrophilic amino acid
glutamic acid to be replaced with the hydrophobic amino acid valine at the sixth position;
The association of two wild-type alpha-globin subunits forms hemoglobin S (HbS); Under
low-oxygen conditions like high altitude, for example, the absence of a polar amino acid at
position six of the β-globin chain promotes the non-covalent polymerisation (aggregation) of
hemoglobin, which distorts red blood cells into a sickle shape and decreases their elasticity.
- Nonsense Mutation: when a substitution (change in one nucleotide - single point mutation)
causes the presence of a premature stop codon, so the protein is only partially translated,
therefore it can be either not active, or, if the stop codon is near the original stop codon the
protein can be partially functional.

- Silent Mutation: when the substitution does not cause a change in amino acid -synonymous
substitution-, since the genetic code is redundant/degenerated, so it does not affect the
functioning of the protein.

- Neutral Mutation: substitution causes a change in amino acids, but the new amino acid has
the same chemical properties, so the protein still has the same function.
 - Frameshift Mutation: includes Insertion and Deletion, since they change the reading frame;
the change in the reading frame is due to the triplet nature of gene expression by codons.
Frameshift insertion changes the number of DNA bases in a gene by adding a piece of DNA
(even if it's just one base), as a result the protein coded may not function properly. A
frameshift deletion removes a piece of DNA.

All the mutations above happens in coding sequence, but we can also have

Mutations in Noncoding Regions:

- Mutation at the Promoter Region: it will have as a

consequence no transcription, that’s because the
promoter won’t be recognized by the transcription
factors, for example, and therefore no translation.
These mutations are known to cause important
consequences, since it's not about the function of
protein, but in its expression, quantity. Differs from a
silencer for example, because the silencer is
controlled.

- Splice Mutation: It can happen in donor splice site -

GT- (at the 5’ end of the intron), or in acceptor splice
site -AG- (at the 3’ end of the intron). Can be caused by
substitution, deletion, or insertion.
If the mutation happens at the acceptor site (AG), the splicing machinery does not recognize the
site, so we have the loss of all the sequence from the donor site (GT) of the first intron to the
acceptor site of the next intron, including the exon in between, that will be then lost -exon
skipping-. The exon skipping results in a nonfunctional protein.

If the mutation happens at the donor site (GT) the splicing machinery does not recognize it, so
the splicing will happen in another part of the intron that has a GT, in this way, part of the
intron will be included in the final sequence -intron retention/inclusion-. The intron is just
partially deleted. This situation is similar to alternative splicing but caused by a mutation, it's
not a physiological mechanism.

We can also have Cryptic Splice Site Activation; it happens when a mutation forms a splice site
in the exon sequence, the consequence is the lost of a part of the exon.

Splice mutations can cause pathologies, like Duchenne Muscular Dystrophy (caused by exon
skipping), Neurofibromatosis Type I and Cystic Fibrosis (both by cryptic exon inclusion), Stickler
Syndrome and Hemophilia B (both by exon skipping).
- Repeat Expansion Mutation: It's a repeated trinucleotide (it can also be a tetranucleotide
repetition) mutation. The mutation therefore causes the repetition of a triplet of nucleotides
(codon). The number of repetitions is usually stable (n) and this same number is transmitted
from generation to generation. It can be present in coding or noncoding region. This mutation
can cause the resulting protein to don’t work properly, causing pathologies.

The mutation happens when something becomes unstable and undergo expansion, the causes
of expansion can be slippage in DNA replication, crossing over, or failure in DNA repair
mechanisms.
a) Slippage During Replication: Mutation process which occurs during DNA replication. It
involves denaturation and displacement of the DNA strands, resulting in mispairing of the
complementary bases. Slipped strand mispairing is one explanation for the origin and
evolution of repetitive DNA sequences.

What happens is that, normally nucleotides repeats are present in our genes, so we have
several complementary sequences for the repeat all over the template strand, what can
occur is that during replication of a trinucleotide repeat the 3' end of the growing strand
denaturates, detaches from the template and binds again to the template at a point
upstream from its original location. In this way we will have a loop in the newly synthesized
strand.

Then, continued replication duplicates the nucleotides between the point of detaching and
reannealing. When the repair system acts, it adds nucleotides in the template strand -
expansion-, to correspond to the looped out nucleotides of the new strand, in this way the
mutation is incorporated into the genetic code. If the mismatch correction system fails..
Loop can be cut out?
P.s.: Slippage can happen in the nascent strand but also in the template strand. In the latter slippage
results in deletion of the loop instead of expansion of the strand.

b) Unequal Crossing Over: Instead of

exchanging the same loci (genes)
between homologous
chromosomes, the exchange
happens between different loci. It
happens when the genes loci are
not aligned with their
correspondent. If this happens with
sexual chromosomes, the cells of
the person who possess them will
be fine, but the offspring will
receive only one of the
chromosomes, which is abnormal,
in this case it can cause Daltonism.

c) Failure in DNA repair

There are several diseases caused by

expansion of trinucleotide repetitions, as
Huntington disease (in repeats CAG, that
are normally between 11 to 34, but with
the mutation we will have from 36 to 120
repetitions of CAG), also Fragile X
Syndrome that is an important mental
retardation.

Transposable Elements (‘’Jumping Genes’’): are DNA sequences that can change its position within
the genome. 45% of our genome is derived from TE. These elements contribute for genetic variation,
since it can create a spontaneous mutation (but rarely causes a disease) or reverse a mutation by
changing the cell’s genome size, so, it can cause a rearrangement of the genome.
We can have two kinds of transposable elements:

a) Retrotransposons (Class l): Copy and paste mechanism. This class of transposons first is
copied through transcription into an RNA, then this RNA is converted back into DNA through
reverse transcription using the enzyme reverse transcriptase which is typically encoded by
the transposon. Then this DNA fragment (which is the copied transposon) is inserted back
into the genome in a targeted site. The original transposon therefore, never leaves the DNA.
b) DNA transposons (Class ll): Cut and paste mechanism. In this case there is no RNA
intermediate, instead the class ll transposon remains in DNA form throughout the whole
transposition. Typically DNA transposons code for a multifunctional enzyme called
transposase, which is able to recognize the 3’ and 5’ end of the transposon, cut it and then
reinsert it in another targeted place of the DNA string.
Mutations in the terminal inverted repeats, where transposase binds, or mutations in the gene
encoding the transposase can disrupt the functioning of the transposon, which cannot be excised
from the DNA.
In humans he have three Transposable Elements:
- LINEs: long interspersed nuclear elements. Retrotransposon. 1-5kbp in length. It has an
autonomous transposition (transposon can move without outside help).
- SINEs: short interspersed nuclear elements, it has 100-300bp. Nonautonomous (it means
that it help to move, in this case, the SINE needs LINE to move).

- DNA Transposons: It can be either autonomous (2-3kbp - it means that it has intact inverted
repeats and transposase gene, so the transposon can move without outside help), or
nonautonomous (80-3.000 bp - (it means that it needs help to move, it has intact inverted
repeats but a non-functional transposase gene, so the transposase is provided by an
autonomous transposon).

TE were thought to be the junk of DNA, now we know their importance for variability of DNA. But
the expression of this elements leads to genetic instability, so methylation plays a key role in
silencing TE.

Normally the effects of TE on host genome are little, causing no impact. But we can have diseases
associated to it, in fact 65 diseases caused by TE insertions have been documented.
 Examples of diseases caused by TE:
· Alu & L1 (LINE1): Induces coagulopathies by disruption of coagulation factors VIII/IX;
· Alu& SVA insertions causes immunodeficiency;
· LINE1 insertion results in muscular dystrophies and cardiomyopathies;
· Intronic Alu insertion causes disrupting function of NF1 tumor suppressor causing
neurofibromatosis.
P.s.: ALU element is a short stretch of DNA originally characterized by a bacteria restriction
endonuclease, so it is a recognition site (AGCT) for the restriction enzyme ALU1.

BACK MUTATIONS (mutant to wild-type - point mutations can be reversible!)

- True Back Mutation: when the second mutation it's exactly the contrary of the first mutation, at
the level of the same nucleotide. Restoring the function of the amino acid completely, since it turns
the amino acid back to wild-type.
Ex: UUA (leu) → forward mutation → UUC (phe) → true back mutation → UUA (leu)

- Site Revertants: when the second mutation is at the same codon (mutated by forward mutation)
but not at the level of the same nucleotide, so I can partially or entirely restore the function of the
protein.
Ex: UUA (leu) → forward mutation → UUC (phe) → site revertants → CUC (leu)

& Suppressor Mutation x Back Mutation:

Suppressor Mutation Occurs in a different codon/site from the original mutation, and masks or
compensates for the initial mutation without reversing it. It can be subdivided in:
- Intragenic suppressors: occurs on the same gene, e.g. nearby addition restores a deletion.
- Intergenic suppressors: occurs on a different gene.

Ex.: if you have a forward nonsense mutation, it means that we will have a premature stop codon,
that will cause a premature protein. But we can have a backward mutation on the level of the tRNA
anticodon, that can then recognize the premature stop codon as a coding codon, and insert an
amino acid. As a consequence we will have a functional protein with one incorrect amino acid.
Classification of Mutations by Origin:

Spontaneous Mutations:
Arise from errors in replication process and base modifications. Due to natural (biological) chemical
process, instead of being caused by mutagens as the induced mutations. Despite its very low
frequency (1 in 10 6 - 8) they are the most important mutations for evolution process.

a) Base Modification (spontaneous lesions) includes:

- Depurination: Loss of a purine base (A and G), occurs spontaneously.

When depurination occurs, the gap left is called apurinic site.
 - Deamination: Cytosine when deaminated becomes Uracil, and 5-methylcytosine (because
of epigenetic in our genome there are a lot of methylated cytosines) when deaminated
becomes thymine (5-methyluracil).

In this case the presence of 5-methylcytosine in our genome identifies a mutation spot,
where the mutation rate is higher than normal, we say this mutation is stabilized in our
genome, and only half of the time the correction happens. When deamination occurs it
only changes the N-base, not the entire nucleotide because the sugar is still a deoxyribose.

b) Errors in DNA replication includes:

- Base substitution
- Base insertion and deletion

Some errors that might occur at replication are immediately corrected by the proofreading
mechanism and some are corrected after replication in the mismatch repair mechanism. The
mistakes that still exist after the mismatch repair will become permanent mutations after the next
cell division.

Possible Errors During DNA Replication - cause insertion, deletion, or substitution:

Error due to strand slippage during replication: when slippage happens a DNA strand may loop out,
resulting in the insertion or deletion of a nucleotide on the newly-synthesized strand. If the template
strand loops out we will have a deletion. If the newly-synthesized strand loops out we will have an
addition.

Error due to tautomeric shift causes substitution: the change of the hydrogen atoms between the

number 3 and number 4 positions of the pyrimidines (C, U, T) and between the number 1 and
number 6 positions of the purines (A, G) changes the base-pairing potential, altering the
complementarity of the bases.

Tautomers are isomers of a compound which differ only in the position of the protons and electrons,
the carbon skeleton of the compound is unchanged.

· The thymine assumes a keto form (canonical), and in rare cases an enol form (tautomeric);
· The cytosine assumes an amino form (canonical) and in rare cases an imino form (tautomeric);
· The adenine assumes an amino form (canonical) and in rare cases an imino form (tautomeric);
· The guanine assumes a keto (canonical) form and in rare cases an enol form (tautomeric).
&

When cytosine and guanine are in their tautomeric imino and enol, they form hydrogen bonds
respectively with adenine and thymine. If the tautomeric forms are incorporated, after DNA
replication we can observe mutations.

Induced Mutations:
Caused by environmental agents called mutagens. We can have chemical mutagens and physical
mutagens. These mutations are more frequent than spontaneous mutations.
A mutagen is an agent or substance that can bring about a permanent alteration to the physical
composition of the DNA gene.
ionizing TTI
→
a) Physical Mutagens: non ionizing
-
E- RAY
- Ultraviolet Radiation: non ionizing radiation, able to react with DNA and other biological
molecules. The most important mutation caused by UV radiation is the formation of thymine
dimers T-T, that bind laterally to each other←
- =
distorting the DNA helix. UV is generated by the
=
sun and also by tanning beds.
-
 - Ionizing Radiation: for example X-rays and Gamma-rays; this kind of radiation can produce
reactive ions that react with biological molecules, causing breaks in one or both strands of
DNA, damaging bases, causing loss of bases, causes crosslinking of DNA on itself or on
proteins, so we can have several kinds of mutation caused by ionizing radiation.

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b) Chemical Mutagens:
- Compounds that can cause modification of a base: cause chemical modification of purine
and pyrimidine bases that alter their hydrogen-bonding properties. Ex: nitrous acid,
nitrosoguanidine. Eventually causes a substitution.
- Base Analogs: These chemicals, structurally resemble purines and pyrimidines and may be
incorporated into DNA instead of the normal base during replication e.g. bromouracil (BU). It
can cause substitution.
- Intercalating Agents: During DNA replication, these compounds can insert or intercalate
between adjacent base pairs. They are all flat, multiple ring molecules which interact with
bases of DNA and insert themselves between the nucleotides. This insertion causes a
stretching of the duplex and the DNA polymerase is ''fooled'' into inserting an extra random
base opposite to the intercalated molecule. In this case it does not cause a substitution, but
a frameshift mutation e.g. ethidium bromide, acridine orange, proflavine
How can we recognize that a substance is a mutagen?

There is a test called AMES test, it uses the frequency of spontaneous and induced mutations since
we will have much more mutation in the presence of a mutagen -induced mutation is more frequent
than spontaneous-. In the control plate you will still have spontaneous back mutations, but in the
experimental plate if the compound is a mutagen it will increase the rate of mutation (back
mutation) so it will have a greater number of bacteria -in the example- . It is important to
understand if an agent is mutagenic or not.

DNA Repair:
a) Base Excision Repair (BER): fixes spontaneous damage in bases.
b) Nucleotide Excision Repair: corresponds to UVR system in eukaryotes.
c) Mismatch Repair: activates in the presence of methylation of the template strand after
replication. MUT system in E.coli.
d) Based on DNA Photolyases: Photolyases are DNA repair enzymes that repair damage caused by
exposure to ultraviolet light, if they fail we can have a pathology called Xeroderma Pigmentosum,
with very high incidence of skin cancer.
POLYMORPHISMS:

A gene is said to be polymorphic if more than one allele occupies that gene’s locus within a
population. In addition to having more than one allele at a specific locus, each allele must also occur
in the population at a rate of at least 1%.
The main difference between mutation and polymorphism is the frequency in population.
Mutation occurs in less than 1% of the population, polymorphism in at least 1%.

A polymorphic variant of a gene can lead to the abnormal expression or to the production of an
abnormal form of the protein; this abnormality may cause or be associated with disease.

A polymorphism can be any difference in the DNA sequence. Therefore, there are many types of
polymorphism, just like mutation. The most important ones include:
a) SNP - Single Nucleotide Polymorphisms: are a single nucleotide changes that happen in the
genome in a particular location. The single nucleotide polymorphism is the most common
form of genetic variation. SNPs are about 5 million in the whole genome, about 100.000 of
them are functional polymorphisms (which means they are able to affect the protein
production). The 0.1% difference between humans genome is due to SNPs.
b) Insertions/Deletions of a variable number of base pairs.
c) VNTR - Variable Number Tandem Repeats
d) CNV - Copy Number Variation
 CHROMOSOMAL MUTATIONS

Definition - variations in the structure or number of chromosomes and they can arise spontaneously
(chromosomal mutations usually occur when there's an error in cellular division, meiosis or mitosis,
as errors in crossing over) or can be induced (by mutagens, radiation, for example).

● Chromosomal mutations can be detected by:

- Genetic Analysis: observing changes in linkage
- Microscope examination: karyotype assay

● Chromosomal variations contribute to miscarriage (about 50% of spontaneous abortions result

from major chromosomal aberrations), stillbirth (death or loss of a baby before or during delivery),
and genetics disorders.

● Structural Mutations → Variations in chromosome structure occurs in four common types, and
always begin with a break in DNA producing sticky ends that may adhere to other ends:

1. Deletions:

When a portion of the chromosome is missing or deleted, so it can not be

reverted.
It can be induced by heat or radiation, chemicals, viruses, TE, errors in
recombinations, etc.
The effect depends on what was deleted; a deletion in one allele of a
homozygous wild type (AA) may give a normal phenotype, whilst the same
deletion but in a heterozygous (Aa) wild-type can give off a mutant type (a).
- Pseudodominance: expression of a recessive trait caused by the absence
of the dominant allele.
Deletions of the centromere results in an acentric chromosome, that is lost,
usually causing serious or lethal consequences.
Large deletions can be present in unpaired loops, which is seen during
karyotype analysis.
Human disorders caused by large chromosomal deletions are usually seen in
heterozygous, since homozygotes usually dies
· Cri-du-chat: Deletion of the short arm of chromosome 5; results in mental retardation and physical
abnormalities.
· Prader-Willi Syndrome: Part of the long arm of the chromosome 15 deleted; results in oor male
sexual development, feeding difficulties, retardation and behaviour problems.
 2. Duplications:

Results of the doubling of a chromosomal segment,

which can occur in a range of size and locations:
- Tandem Duplications: duplication of segments
adjacent to each other.
- Reverse Tandem Duplications: duplication of the
adjacent genes, but arranged in an opposite order
of the original.
- Terminal Tandem Duplication: at the end of the
chromosome.

Duplication can give rise to multigene families (evolution

of multiple genes) e.g. globin; each set of gene for alpha
and beta globin comes from a different ancestor by
duplication, which can be caused by:
· Unequal crossing over
· Replication slippage
· Retrotransposition

(Repeat Expansion Mutation at the chromosome level)

3. Inversions:

Happens when a chromosomal segment excises and reintegrates oriented 180o from the original
orientation. Unlike deletions and duplications, inversions do not change the overall amount of the
genetic material, so inversions are generally viable and might not show any particular abnormalities
at the phenotypic level; inversions can be made homozygous if the breakpoint is not within an
essential gene.
There are two types of inversion:
- Pericentric Inversion: centromere included; Two
viable gametes, one with genes in the normal
order, the other with the inversion AND 2 inviable
gametes, each with some genes deleted and
others duplicated.
- Paracentric Inversion: no centromere included,
results in a visible inversion loops between
homologous chromosomes.

Crossover in the inversion region results in unbalanced

sets of genes produced for gametes.

Consequence → Normal amount of DNA, but we can

have an alteration of phenotype.
Different recombinant chromosomes are
produced by crossover in a heterozygote,
depending on the centromere’s
involvement:

- An individual who is
HETEROZYGOUS for the PERICENTRIC
inversion has one chromosome with the
normal order of genes and one
chromosome with the inverted order
constituting a pair of homologues. This pair
will be duplicated prior to meiosis, and
then undergo crossing over at the prophase
l. The homologous pair at meiosis, and this
means the creation of a inversion loop. If
the cross over occurs within the loop the
result is the creation of viable and inviable
gametes.
 - Individual who is HETEROZYGOUS for the
PARACENTRIC inversion. During crossing over an
acentric (with no centromere) fragment will be
produced and therefore, discarded. The
crossing over will generate 2 viable gametes,
one has the normal order of genes and one has
the inverted order -identical to the pair of
homologues before crossing over-, and two not
viable gametes, which have had genes deleted.

P.s.: The viable gametes generated both for

heterozygous paracentric or pericentric are not
recombinant.

4. Translocations

A change in location of a chromosome segment is a

translocation. No DNA is lost or gained.

- Interchromosomal: transfer of the segment to a

nonhomologous chromosome.
- Intrachromosomal: change of position within the same chromosome.
- Reciprocal: transfer involves 2 segments exchange.

Gamete formation is affected, resulting in the altering gene linkage and unbalanced duplication
and/or deletion.
Subjects HOMOZYGOUS for the RECIPROCAL translocation (when translocation happens before
duplication) won’t produce problematic gametes, they will all be balanced.

Subjects HETEROZYGOUS for the RECIPROCAL translocation (when translocation happens after
duplication) must pair a translocated set of chromosomes with a normal set, resulting in the
production of a cross link structure with partial homology to others in the group. The segregation of
these chromosomes during anaphase can be adjacent of alternate. It can generate viable or not
viable gametes.
● Chromosomal Mutations and Human Tumors: Most human malignant tumors have chromosomal
mutations, commonly in the form of a translocation.
· Chronic Myelogenous Leukemia: Reciprocal translocation of chromosomes 9 and 22. It causes
Myeloblasts to replicate uncontrollably
· Burkitt Lymphoma: Reciprocal translocation of chromosomes 8 and 14. Induced by a virus,
causes B-lymphocytes to produce antibodies as they proliferate.

● Position Effect: Sometimes inversions or translocations change the phenotypic expression by the
position effect (change in location of a gene in the chromosome), by moving a gene from
euchromatin area to heterochromatin are or vice-versa. This is an example of an epigenetic effect
since the DNA sequence of the gene is not affected. Ex: eye color in drosophila.

● Fragile Sites and Fragile X-Syndrome:

Chromosome in cultured human cells develop narrowings or unstained areas called fragile sites.
[Fragile site is a specific heritable point on a chromosome that tends to form a gap or constriction
and may tend to break when the cell is exposed to partial replication stress.Based on their
frequency, fragile sites are classified as "common" or "rare". To date, more than 120 fragile sites
have been identified in the human genome.]
A well known example of fragile site is the Fragile X-Syndrome in which a region at position Xq27.3 is
likely to break. It affects 1 in 2500 children. The molecular basis of the X fragile chromosome has
been traced to expansion of a CGG trinucleotide repeat (normally there is from 5 to 50 repeats, but
in FXS more than 200) present at the site where breakage takes place. The FSX follows Mendelian
inheritance patterns, it has a dominant X-linked pattern of inheritance, affecting mostly men.
 - About 80% of males with the condition are mentally retarded. The other 20% of males present a
normal phenotype and are transmitting males → They can pass the X chromosome to his
daughters, where DNA alteration takes place; sons of these daughters frequently show mental
retardation.
- About 30% of female carriers (one X affected is enough to manifest the phenotype in a X
dominant trait) are mentally retarded; sons of carries females have 50% chance of inheriting the
fragile X whilst daughters of carriers females have a 50% chance of being carriers (and
consequently presenting the disorder).

Molecular analysis shows a repeated 3 base pairs CGG in the FMR-1 gene (Fragile-X Mental
Retardation 1), at the fragile X site. The FMR-1 product (FMRP - Fragile X Mental Retardation
Protein) is an RNA-binding protein, which affects expression of certain mRNAs in the brain at
neuronal synapses. An excessive number of copies of the CGG repeat cause loss of function of the
FMR1 gene. So, individuals with the full mutation (more than 200 repeats because from 55 to 200
repeats no symptoms are shown, indicating a threshold) undergo cytosine (at the CGG repeats)
methylation, silencing FMR-1 gene,
resulting in mental retardation.

● Isochromosome: It is a chromosome that presents an unbalanced structural abnormality because

it has two copies of the same arm, mirror image around centromere (it has 2 q arms or 2 p arms,
instead of 1 q and 1 p). They are formed when the centromeres part in wrong plane (transversely
 instead of longitudinally) during metaphase ll (when the sister chromatids are separated), causing
monosomy for one chromosome arm and trisomy for the other arm.

[The most common isochromosome is the X sex chromosome. Acrocentric autosomal chromosomes
13, 14, 15, 21, and 22 are also common candidates for isochromosome formation. Chromosomes
containing smaller arms are more likely to become isochromosomes because the loss of genetic
material in those arms can be tolerated.]

[A more common mechanism in the formation of isochromosomes is through the breakage and
fusion of sister chromatids, most likely occurring in early anaphase of mitosis or meiosis. A double-
stranded break in the pericentric region of the chromosome is repaired when the sister chromatids,
each containing a centromere, are fused together. This is called U-type strand exchange.]

[In 15% of Turner syndrome patients, the structural abnormality is isochromosome X, which is
composed of two copies of the q arm.]

● Ring Chromosome: A ring chromosome is an aberrant chromosome whose ends have fused
together to form a ring. In rare cases the telomeres fuse together without any loss of genetic
material, resulting in a normal phenotype. Ring chromosomes may form in cells following genetic
damage by mutagens like radiation, but they may also arise spontaneously during development.
Human genetic disorders can be caused by ring chromosome formation.

● Numerical Chromosome Mutations → Variation in Chromosome Number:

An organism or cell is euploid when has one complete set of chromosomes or exact multiples of
complete sets; Eukaryotes that are normally diploid or haploid are euploid. Normal number.

Aneuploidy is the
result of variations in
the number of
individual
chromosomes, so that
the chromosome
number is not an
exact multiple of the
haploid number (seja
ele qual for). It occurs
due to nondisjunction
during meiosis I or II.
Wrong number of
chromosomes.
Autosomal
aneuploidy normally
is not supported by
mammals and causes
spontaneous abortion.

There are four main types of aneuploidy:

1. Nullisomy: loss of one homologous chromosomes

pair (2n-2 = 44 chromosomes or 22 pairs)

2. Monosomy: Loss of a single chromosome (2n-1 =

45 chromosomes)
Partial monosomy can occur in unbalanced
translocations or deletions, in which only a
portion of the chromosome is present in a single
copy.

3. Trisomy: One extra chromosome (2n+1 = 47

chromosomes), so that one of the chromosomes
has three copies (one extra).

4. Tetrasomy: The cell has an extra chromosome

pair (2n+2 = 48 chromosomes), which means that
one chromosome has 4 copies (two extra).

Aneuploidy also happens when more than one

chromosome or chromosome pair may be added or lost:

5. Double Monosomic: two separated chromosomes

present in only one copy each (2N-1-1)

6. Double Tetrasomic: Two chromosomes present in

four copies. (2N+2+2)

P.s.: Disomy is the presence of two copies of a chromosome. For organisms such as humans that
have two copies of each chromosome (those that are diploid), it is the normal condition. For
organisms that normally have three or more copies of each chromosome (those that are triploid or
above), disomy is an aneuploid chromosome complement.

➢ Human Examples of Aneuploidy:

- Autosomal trisomies account for half of fetal

deaths, only a few result in live birth, and from
these few, most result in early death. Trisomy
8 (Mosaicism Syndrome or Warkany Syndrome
ll), trisomy 13 (Patau) and trisomy 18
(Edward’s Syndrome) result in early death,
whilst trisomy 21 (Down’s Syndrome) subjects
survive until adulthood.

IMPORTANT

Robertsonian Translocation: Consists in the centric

fusion of non-homologous acrocentric
chromosomes, resulting in production of 3 copies of
the long arm of chromosome 21; it is a reciprocal
translocation between chromosome 21 and usually
chromosome 14, and it accounts for about 4% of all Down
Syndrome cases.
Mating of a heterozygous carrier and a normal individual
has a high risk of Down Syndrome offspring.
 A reciprocal translocation occurs
between for example chromosome 14
with chromosome 21 (in the case of
Down Syndrome). That’s because
chromosome 13, 14, 25, 21 and 22
share a bit of similarity, they’re all
acrocentric, meaning that they have a
small P arm and also contain in the P
arm a repetitive information. The Q
arms of two of these chromosomes
fuse together and the P arms fuse
together (reciprocal translocation).
This non homologous pair of P arms
are so small that can get lost, leaving
as a result one large chromosome,
meaning that you're left with 45
chromosomes.

In Down Syndrome: Chromosome 21 fuses with chromosome 14. Its P arm disappears and we’re left
with a huge chromosome 14q-21q. So, down syndrome can be caused by nondisjunction (95% of
cases) during meiosis 1 or 2, but can also be caused by a Robertsonian translocation (4% - fusion
between chromosomes 14, 21).

For a Robertsonian translocation carrier there are six possible combinations for a gamete: 14q21q,
14-14q21q, 21-14q21q, 14-21, 14, 21.

Familial Down Syndrome: robertsonian translocation in one of the two parents.

14-21-14q21q = carrier, but normal; 14-21-21= 14 monosomy (death);
14-14-21= 21 monosomy (death); 14-14-14q21q-21= trisomy of chromosome 14q (Mosaicism
Syndrome -rare); 14-14q21q-21-21: Trisomy of chromosome 21(Down's Syndrome)

Monoploidy and Poliploidy are changes in the complete set of chromosomes, therefore, both are
cases of euploidy. Monoploidy and poliploidy can be caused when meiosis lacks cytokinesis or when
meiotic nondisjunction occurs for all chromosomes. Even number of polyploid chromosomal sets
(tetraploid, hexaploid) are more likely to be at
least partially fertile, whilst odd number of
polyploid chromosomal sets are usually sterile.
 Quick Review…

- Principle of Dominance: One allele conceal the presence of another (in a heterozygous).
- Principle of Segregation: During formation of gametes, the two alleles responsible for a trait
separate from each other.
- Principle of Independent Assortment: Alleles for different traits are distributed to sex cells
independently of one another.

Today we know that the concepts above are true only for genes mapped on different
chromosomes, due to the independent assortment of the homologues during anaphase l.
The genes that are on the same chromosome can however be separated by crossing over.

Making some points clear:

a) Two characters/traits:
- AABB: Double Dominant Homozygous; Gametes AB
- aabb: Double Recessive Homozygous; Gametes ab
- AaBb: Double Heterozygous Gametes: AB, Ab, aB, ab

b) One character/trait:
- AA: Dominant homozygous; Gametes: A
- aa: Recessive homozygous; Gametes a
- Aa: Heterozygous; Gametes a or A

Remembering Test Cross: In order to understand the genotype of an individual by its phenotype we
realize test cross. For example: A certain phenotype A_B_, what is the genotype? Possible genotype:
AABB, AaBb. We cross the possible genotypes with aabb. If the product is 100% AB, means that we
have a double dominant homozygous.

.
 Linkage, Crossing Over and Chromosome Mapping

I. Definition:
Genes that don't segregate independently (travel through meiosis together) because they are
located in the same chromosome show association – Linkage

These are called association or linked genes and they belong to an association group.

Closer these genes are in the chromosome, harder it is for the crossing over to separate them (less
probable that recombination will happen), closer they are, stronger is the linkage.

How to detect linkage?

- Test Cross

II. Detecting Linkage Through Testcrosses:

The testcross involves the crossing of the individual from who you wish to know the genotype with a
genotypically recessive individual -homozygous recessive-, to determine the zygosity (homozygosity
or heterozygosity) by analyzing proportions of offspring phenotypes.

P.s.: Zygosity is the degree of similarity of the alleles for a trait in an organism. Most eukaryotes have
two matching sets of chromosomes; that is, they are diploid.

● Configuration of linked genes → There are two kinds of dihybrids (double heterozygous) involving
linked genes.

· Cis arrangement/Coupling Heterozygote

· Trans arrangement/Repulsion Heterozygote
 Linked genes are found by looking for deviation from the frequencies expected from independent
assortment. A test cross (one parent is homozygous recessive) works well for analyzing linkage:

- If the alleles are not linked, and the second parent (the one we wish to know the phenotype)
is heterozygous (AaBb), all four possible combinations of traits will be present in equal
numbers in progeny (50% parental and 50% recombinant) due to the independent
segregation.

- If alleles are linked a significant deviation in this ratio will be manifested (more parental and
fewer recombinant types, because the possibility of crossing over is less than 50%, since 50%
is the probability given by independent assortment, but there is no independent assortment if
genes are on the same chromosome) indicates linkage.

Explanation for lack of independent assortment in the data -change in the ratio expected- is that the
genes are on the same chromosome.

Parental and Recombinants → The way of observing if we have a recombinant genotype is to

compare the gametes without crossing over and the ones after crossover. The gametes that are the
same as the parent genotype are parental, the ones that presents a different phenotype are
recombinants.

Example: Sweet pea flowers colours and pollen shape.

There was 1000 progeny scored, from those, 920 resemble one of the parents (parental) and 80 are
recombinant.

The frequency of recombinants produced by the heterozygous F1 plants is 0.08 (8%) because 0,08 is
also the frequency of recombinant gametes produced by the heterozygous F1 plant, which is the
frequency of crossing over.

Crossing over is the physical basis of recombination.

We can use the recombination frequency to know the intensity of the linkage between genes; genes
that are tightly linked rarely recombine, and the opposite is true. The recombination frequency is
never 50% or more, because this limit is only obtained when genes are in different chromosomes.
 CHROMOSOME MAPPING
Linked genes can be mapped in a chromosome by studying how often their alleles recombine.

Statistically speaking, linked genes that are farther from each other should have more crossover
between them then points that are close together.

The quantity that we really need to measure is the average number of crossing overs in a particular
chromosome region (that involves the genes we are interested), which corresponds to the distance
between two points on the genetic map of a chromosome.

A chromosome in which the alleles have recombined must have arisen by crossing over.
Two Point Testcross: A two-point testcross is done to determine the recombination frequency
between two linked genes. The method to map our genes use recombination frequencies between
alleles in order to determine the relative distances between them.

In the example above with the flies, we see that the frequency of crossover is 0,18 (18%), in this way
we can say that alleles vg and b are separated by 18 units of the genetic map, or 18 cM
(centiMorgan).

Hypothesis → 1% crossover rate (genes are close) is a genetic distance of 1 map unit = 1 cM.

Geneticists use recombination frequency as a way to estimate crossover frequency, and it is also
used to map genes, since closer the genes are less recombination will be seen.

% recombinants = no. of recombinants/total no. of test cross progeny x100

We can have a max of 50% recombinants otherwise it would mean that the genes are found in
different chromosomes (independent assortment), which means that we also consider the whole
distance of the chromosome 50 map units.

Limitation of Two Point test cross: It underestimates the recombinant events as it cannot take into
consideration multiple crossing over that can randomly occur between loci that have a distance
greater than 10-15 cM.
Three-point Testcross: We can also use the recombination mapping procedure with data from test
crosses involving more than two genes. Three point cross refers using 3 genes to determine the
order and distance between genes.

In the example above we can see that in the progeny, class1 and class 2 are parental; Class 3 to class
6 have had one crossover; Class 7 and class 8 have had two crossovers.

We can see that a double crossover switches the gene in the middle with respect to the genetic
markers on either side of it.
With three point mapping, we can:

a) Establish the order of the genes: simple because by comparing the classes which have
undergone two crossovers with the parental classes we can see each gene was switched,
and we know that this gene must be in the middle of the other two.
b) Determine the distance (in map units) between each pair of genes. We do this by calculating
the crossover frequency between each two genes
c) Three must be a sufficient number of offspring produced to give a representative sample, its
large enough to get accurate results.

Rearrangement of three genes → Take into consideration two genes at time

Example above: How to calculate the distance between p and j?

- We calculate all the recombinations in the first region including those involved in double
crossing over → no. of recombinant progeny (class 3 + class 4 + class 7 + class 8) / total
number of progeny x 100 = 20,8%

The distance between p and j is 20.8 cM so the probability of crossing over is 0.208.

Then, we calculate the distance between j and r → we calculate all the recombinants in the second
region including those involved in double crossing over (class 5,6,7,8). The result will be 0,1 or 10%,
which means the distance between those genes is 10cM.

- Double crossover probability: product of probabilities of a single event. In the example it

would be

(4 + 2/500)x100 = 1,2 %
 INTERFERENCE AND COEFFICIENT OF COINCIDENCE:
A three-point testcross has an important advantage over a two-point cross, since it allows the
detection of double crossover permitting us to determine if exchanges in adjacent regions are
independent of each other.

For example, in the example with drosophila: does a crossover in the region between sc and ec occur
independently of a crossover in region ll? Or does one crossover inhibits the other?

To find out...

1. We must calculate the expected frequency of double crossover based on the idea of
independency → in region l = 0.091 ; region ll = 0.105. If we assume independency the the
frequency of double crossover would be 0.091x0.105=0.0095
2. But comparing the results with the observed frequency (which was 2/3248= 0.0006) we see
that there were much less frequent crossovers than expected

This means that one crossover inhibits the occurrence of a second crossover nearby, and this
phenomenon is known as interference.

The extent of the interference is measured by the coefficient of coincidence

When the C.o.C is close to zero, interference is very strong → one crossover strongly inhibits
another.

When the C.o.C is one, interference is zero → crossovers occur independently from each other.

Interference is strong over map distances smaller than 20cM, so double crossover rarely happens in
short chromosome regions; strength of interference is therefore a function of map distance