Carmen Martínez Genetic

CHAPTER I

All life forms have evolved from a universal common ancestor to adapt to the
environment. They can be classified into two main groups:

Eukaryotes: Complex organisms with organelles and a nuclear membrane

surrounding the genetic material, linear DNA molecules.

Prokaryotes (Bacteria and Archaea): Unicellular organisms without a nuclear

membrane and regularly a single circular molecule.

Viruses are acellular organisms, because they can’t reproduce autonomously, with
a structure of nucleic acid surrounded by protein coat.

Genetics is the study of function, expression, transmission and evolution of genetic

information of organisms. It’s divided in transmission, molecular and population
genetics. The genome is the complete set of genetic instructions and it determines
the genotype; whereas the phenotype is the observable physical traits determined
by the genotype and the environment. The norm of reaction is a set of phenotypes
that come from the same genotype under different conditions. Genes are the
fundamental unit of heredity that carry a specific characteristic. They are formed by
two alleles (homozygote or heterozygote) that vary among a population. Alleles of a
particular gene are found at specific places on the chromosome called locus. The
variation in alleles can be:

Discontinuous: The genotype determines well distinguished phenotypes (one-to-

one relation) rarely affected by the environment.

Continuous: Many genes determine characteristics within a big range of phenotypes

that are affected by the environment.

Most genetic studies use the same organisms (i.e E.coli, drosophila or mus
musculus). Some fields in which genetics is relevant are:

Agriculture: Using selective breeding or genetically modified organisms (GMO).

Medicine: To diagnose, predict or treat genetic disorders and genetic mutations.

They can be monogenic diseases that are rare and not influenced by the
environment; or polygenic diseases that are more common and influenced by the
environment.
Carmen Martínez Genetic

Hereditary theories have evolved throughout the years:

1)Pangenesis stated that each body part contained its corresponding genetic
information, and it travelled to the reproductive organs to be transferred through
gametes. It also included the idea of inheritance of acquired traits.

2)Lamarckism defended the inheritance of acquired traits that appeared or

disappeared following the rule of use vs disuse.

3)Preformationist stated that all traits are inherited from just one parent as
gametes had fully formed adults called homunculus.

4)Blending inheritance stated that the genetic material of both parents mixed
irreversibly so the child resembled both.

5)Cell theory was developed:

The cell is the fundamental unit of structure and function of living organisms.

All life is composed of one or more cells.

All cells come from the division of a preexisting mother cell from which they receive
their genetic information.

7)Germ plasm theory says that reproductive cells have a whole set of
chromosomes passed to gametes that fuse to form the zygote.

8)Chromosomal theory of inheritance followed Mendel’s ideas that traits are

inherited in accord with defined principles.
Carmen Martínez Genetic

CHAPTER II

Mendel experimented with the pea plant (pisum sativum), a self fertilized plant of
rapid growth with many seeds, 7 traits and 2 forms:

1.He made sure the plants were true-breeding by allowing self-fertilization for 2
generations to achieve homozygous traits.

2.He carried monohybrid crosses (differ in 1 trait) between the parental

generation and obtained a first filial generation with individuals with the same
phenotype of one of the parents.

3.He crossed the first filial generation to obtain a second filial generation where
both parental phenotypes reappeared in a 3:1 ratio.

From this, he established Mendel’s first law. Because both phenotypes arise again,
F1 must contain information from both. The two alleles of each parent segregate
randomly in equal proportions in different gametes and one gamete from each
parent is chosen to fuse. Mendel also determined that one allele must be dominant
to the recessive and, for heterozygotes, only the dominant allele is expressed.

However, dominance is not universal, sometimes the heterozygous genotype

expresses as an intermediate or mixed phenotype and we obtain a 1:2:1 ratio in
F2.

In dihybrid crosses for two traits these are independently assorted and inherited
(Mendel’s second law) and all possible phenotypes appear in a 9:3:3:1 ratio, which
can be represented in a Punnett square. This is also true for trihybrid crosses.

Mendelian principles follow laws of probability, so different methods can be used

to predict the inputs and outputs of a cross:

1.Addition rule: Probability of any of two or more mutually exclusive events (OR).

2.Multiplication rule: Probability of two or more independent events taking place

together (AND).
Carmen Martínez Genetic

3.Forked-like method: Determines the possibilities of each lochi independently

and combined in a branching diagram.

4.Binomial expansion: Determines probabilities where there are different ways an

event may occur. We use a Pascal’s triangle

• When n=1 we use 1º row and so on. “p” exponent increases as the “q”
exponent decreases. Where p is the probability of the looked for event
happening and q is the probability of the other event happening. Then then
take the element or elements corresponding to the probability we want to
calculate. And we substitute the p and q with the given probabilities.

Binomial expansion formula: Determines probabilities where there are different

ways an event may occur. We use the formula:

P = n!/s! · t! p^s q^t Where “s” is the times p occurs and “t” is the times q
occurs

Because probability is based on chance, sometimes there is a deviation, to

calculate the probability that the deviation is in fact due to chance we use the Chi-
square (X2). If the probability is higher than or 0,05 we accept the hypothesis;
otherwise we reject it. We then find the w on the corresponding row of the degree of
freedom (df), which is N-1 where “N” is the different possibilities (phenotypes).

x2 = observed individuals-expected individuals^2/expected individuals = w

Carmen Martínez Genetic

CHAPTER III:

Mendel’s discoveries merely defined an hereditary factor, which were later

discovered to be the genes located on chromosomes. If a cell contains just one set
of chromosomes (gametes) it is called haploid (n); if it has two sets it's called
diploid (2n).

For the DNA to fit in the nucleus it is highly compacted by associating with histone
proteins to form the chromatin. Thanks to cut free DNA, treated with nucleases and
subjected to electrophoresis, we know that the DNA band gives two turns of 146
nucleotide pairs to the histones octamers to form a positively charged
nucleosome of 6-fold compaction. Each nucleosome is separated by a linker DNA
of varying length and formed by 2 H2A, 2 H2B, 2 H3 and 2 H4 proteins. The histones
also contain amino terminals related to posttranslational modifications that
interact to stabilize the structure. There is a H1 as well that joins the outside of the
structure to form a chromatose and helps to join other nucleosomes. This way, it
compacts 40-fold probably following one of the two methods proposed:

• Solenoid model: DNA forms a superhelix of 6 nucleosomes per turn, leaving

a space in the center.

• Zigzag model: Linker DNA passes through the center, which would favor
longer linkers.

For most of the cell cycle, the chromatin stays in a euchromatin relax state with
thin and barely visible fibers. But before nuclear division, the chromatin
condenses, which then it’s called heterochromatin. To form the chromosomes,
the chromatose fiber forms big loops held together by a non-histone
chromosome scaffold. The loops are kept together by condensins and the
chromatids by cohesins.
When the chromatin reaches a 10.000-fold it forms the mitotic chromosome with
two chromatids held by a centromere or primary constriction, an 𝛂-satellite
(repeated DNA) structure. To both sides of the centromere we find the kinetochore,
the region where the microtubules get attached to. Without a centromere there
would be an abnormal distribution of the DNA either randomly segregation for not
having any, or breaking for having more than one. Depending on the position of the
centromere and the size of the p (small) and q (large) arms that form at each side,
a chromosome can be:
Carmen Martínez Genetic

To keep stability, the chromosomes have a telomere, the natural ends that prevent
the chromosome from sticking together or degrading. They are formed by
minisatellites, small repetitive sequences (TTAGGG in humans).The telomere has a
specific T-loop structure to keep stable and a special telomerase enzyme for
replication.

To observe the metaphase chromosome, rapid-grow or isolated white cells are

cultivated, arrested in mitosis, immersed in hypotonic solutions and then stained
by different cytological techniques:

• Quinacrine (Q banding): A fluorescent dye that shows the chromosome

banding, a characteristic pattern that helps identifying.

• Giemsa (G banding): Non-fluorescent dye of popular use. Or R banding, a

reverse Giemsa to study the telomeres

• Chromosome painting (FISH): Treatment of chromosomes with

fluorescently labeled DNA sequences called probes.

After staining, the chromosomes are organized by size and homologous, if they
exist in pairs, to obtain the karyotype, or an idiogram, its schematic
representation. All members of the same species have the same number of
chromosomes, but there is no correlation between the number of chromosomes
and the complexity of the species. The human karyotype, for example, is diploid
and it has 22 pairs of autosomes and 1 pair of sex chromosomes.

For the genetic information to be transmitted it has to be copied, and then the
copies must separate before the cell divides. Unicellular organisms follow a simple
process called binary fission, which is used for asexual reproduction. However,
eukaryotic cells follow a complex cell cycle of 18-24. It is composed of two main
phases:

• Interphase: Composed of a G1 phase of growth and metabolic activity,

followed by a S phase of DNA duplication to obtain chromosomes with two
sister chromatids and ends with a G2 phase of growth and preparation for
division.
Carmen Martínez Genetic

• M phase: It consists of mitosis and cytokinesis. Mitosis is used to produce 2

diploid cells for growth or renewal. It is divided into:

o Prophase: Condensins form chromosomes, the mitotic spindle is formed

and centrosomes migrate to the spindle pole.

o Prometaphase: The nuclear envelope breaks down and the

microtubules (MT) attach to opposite kinetochores.

o Metaphase: Chromosomes align at the equator to form the metaphase

plate.

o Anaphase: The MT drag and break the linkage between sister

chromatids to each pole, becoming daughter chromosomes.

o Telophase: The chromosomes at the poles decondense and the

nuclear envelope reforms to obtain two nuclei.

During the last 2 phases, cytokinesis begins, the separation of the cytoplasm by
a contractile actin ring in the central spindle.

Diploids have another type of cell division called meiosis. It consists of two
successive nuclear divisions to form 4 haploid cells or gametes that then fuse with
another organism's gametes through sexual reproduction:

Meiosis I: There is a reduction of the chromosome numbers and it is composed of:

Prophase I: A long phase with 5 substages

Leptotene: The chromosomes start to condense.

• Zygotene: Homologous chromosomes approach in a process called

synapsis.

• Pachytene: Chromosomes pair to form 2 bivalents or 4 tetrads. And there

is an exchange of material by crossover.

• Diplotene: The binding between homologous relaxes except at the

chiasmata, the places where crossover happened.
Carmen Martínez Genetic

• Diakinesis: Condensation finishes, still bounded by chiasmata. The nuclear

membrane breaks and the MT attaches.

Metaphase I: The bivalents align at the metaphase plate while the MT attaches to
homologous chromosomes.

Anaphase I: Bivalents separate from each other dragged by the MT in a process

called chromosome disjunction.

Telophase I: The nuclear envelope reforms.

We obtain two haploid cells with chromosomes with chromatids not necessarily
identical. There is a short interphase II or interkinesis without an S phase. The
chromosomes lightly decondense and the spindle dissasemblies.

Meiosis II: This phase is like mitosis and consists of prophase II, metaphase II,
anaphase II, telophase II and the cytokinesis.

The crossing over during prophase I creates a new combination of alleles following
Mendel’s principle of independent assortment of the alleles and the random
separation homologs during anaphase I follows Mendel’s principle of equal
segregation into the gametes. These random processes produce huge genetic
variations between individuals. However, some genes do not assort independently
and therefore travel together during meiosis.
Carmen Martínez Genetic

CHAPTER IV:

Sex determination is the mechanism by which sex is established, the anatomical

and physiological phenotype (male or female). It can be:

Genic determination: The sex is determined by genes found in one or more

autosomal loci, not in specific chromosomes (i.e fungi).

Environmental determination: Sex is determined by factors like temperature

(reptiles), size (marine annelids) or social interaction (clownfish). Found, for
instance, in molluscs with sequential hermaphroditism, where they can be female
o male at different times.

Chromosomal determination: This can be with a heteromorphic sexual pair of

chromosomes that contain sex genes, although these work together with genes
found in autosomes. Or through ploidy, where hymenopters’ sex is determined by
the chromosomal sets, with 2n females and n males. The X chromosome find in all
eggs and some sperms creates different sex-determining systems:

• XX-XO: Females (XX) are the homogametic sex and males (XO) are the
heterogametic sex. Sex is determined by 1X or 2X.

• ZZ-ZW: Females (ZW) are heterogametic and males (ZZ) are homogametic. It
is mostly typical of birds.

• XX-XY: Females (XX) are homogametic and males (XY) are heterogametic. X
and Y are different except for pseudoautosomal regions with the same genes,
which is essential for synapse. Still, it can be determined by different
mechanisms. In drosophila, for example, it depends on the sexual (X) to
autosomal (A) chromosomes ratio (X:A). If 0.5<X:A we obtain metamales and
if X:A>1 we obtain metafemales, because A genes indirectly influence sex by
controlling developmental processes.

Humans have an XX-XY model where maleness is primarily determined by the Y

chromosome. Still, there can be abnormalities like the Turner syndrome (X0), which
leads to sterile women with underdeveloped secondary sex traits; the Klinefelter
syndrome (XXY), which leads to sterile tall men with underdeveloped testes; the
Poly-X females, which leads to generally tall and thin normally fertile women with
and intellectual and physical disability proportional to the amount of X
chromosomes; or XXY males, which leads to tall men sometimes with learning
difficulties. This shows that at least one X is necessary for human development and
two X for fertility in women.
Carmen Martínez Genetic

Maleness occurs because the SRY gene in the p-arm of the Y chromosome contains
a testis-determining factor (TDF), which differentiate the gonads into testes that
later produce testosterone (male traits) and anti-Müllerian hormones (female ducts’
degeneration). However, an XX can produce a male when the SRY gene of the Y is
translocated into the X chromosome. And, similarly, an XY can produce a female
when the Y is missing the SRY gene. But XY females can also happen when there is
a lack of testosterone receptors because of a mutation of the TFM gene in the X
chromosome. This eventually leads to a female appearance with no ovaries, which
is known as testicular feminization syndrome.

The Y chromosome contains little genetic information. The genes of the X have an X-
linkage, with an inheritance that doesn’t follow the Mendelian ratios. When a gene
for another trait has an X-linkage, like green and red color blindness in humans,
there won’t be an homologous allele in the Y, so males can’t be heterozygous nor
homozygous, which makes them hemizygous. This makes X-linkage treat more like
in males, while women tend to be just carriers.

To compensate for the lack of genes, either females reduce the activity of both X or
inhibit the activity of one; or the males increase the activity of the X. In humans, all
X but one is randomly inactivated in each cell. The inactivated X forms a Barr body.
This process is carried out by the X-inactivation center, which is controlled by the
pseudogene Xist that attracts silencing protein complexes PRC2 and PRC1. This
random inactivation makes cells hemizygous and leads to a patchy expression
known as mosaicism. Still, around 15% of X-linkage genes escape inactivation (10%
more in some females), which is why extra X have physiological effects.

Sex can also affect gene expression of autosomal genes that depend on sex
hormones or physiological differences. For example:

• Sex-limited inheritance: Autosomal genes that develop physical traits

present in both sexes both only expressed in one (i.e beard).

• Sex-influenced inheritance: Phenotype influenced but not limited to one sex.

An allele can be recessive for one sex and dominant for the other (i.e
premature balding).

A pedigree is a schematic representation of a family genetic history regarding a trait.

It helps to predict and calculate probabilities of inheritance. However, human
analyses are not simple due to the small number of offspring. Some symbols used
in a pedigree tree are:

The types of traits that may be represented in a pedigree tree are:

Carmen Martínez Genetic

• Autosomal recessive traits: Affect both sexes. It skips generations.

Sometimes 1 copy is enough for normal phenotype (i.e albinism).

• Autosomal dominant traits: Rare diseases that don’t skip generations and
affect both sexes (i.e Huntington’s disease).

• X-linked recessive traits: Males are more affected (i.e Haemophilia A or B).

• X-linked dominant traits: Affect both sexes, specially females. Always an

affected parent so they don’t skip generations (i.e Rett).

• Y-linked traits: Only affect males and they don’t skip generations. Most
affect fertility so it's rare (i.e webbed toes).

Genetic counselling is an educational process that helps patients to predict the

risk of disease and transmission, interpret and explain results and psychologically
deal with genetic disorders. Presymptomatic testing in healthy adults, especially
in families with autosomal dominant diseases, is recommended. However, test
results might be difficult to interpret because a disease may be caused by many
muttations, having a mutation does not necessarily imply having a disease and
many diseases don’t have tests. Genetic testing can be:

• Preimplantation genetic diagnosis (PGD): After in vitro fertilization in a Petri

dish, one cell of the 8-16 cell stage embryo is removed and genetically
analyzed. Then, the healthy embryos are implanted.

• Prenatal diagnosis: If non-invasive maternal blood screening,

ultrasonography or cell free foetal DNA analysis are positive, they carry out
invasive amniocentesis (foetal cells from amniotic fluid) or chorionic villus
sampling (chorion cells) tests.

Postnatal: Newborn screening is recommended for early identification, better

treatment and symptom control (i.e heel prick test).
Carmen Martínez Genetic

CHAPTER VI:

MODIFICATION AND EXTENSIONS OF MENDELIAN

1. Phenotypic expression of heterozygotes: incomplete dominance and

codominance.

There are some exceptions to mendelian concept of dominance:

Incomplete dominance: phenotype of the heterozygote is intermediate (falls within

the range) between the phenotypes of the two homozygotes. In this case the
dominant is partially dominant: with a phenotypic ratio of 1:2:1 (1/2 is going to be
the midway) in f2: (red dominant)

Codominance: phenotype of the heterozygote includes the phenotypes of both

homozygotes, both alleles of a gene are expressed fully and simultaneously in the
phenotype of a heterozygous organism.

Complete dominance phenotype of the heterozygote is the same as the phenotype

of one of the homozygotes.

2. Phenotypes concepts.

Level of phenotypes: anatomical, physiological and molecular, and de dominance

depend on the level examined. For example, is possible that an allele express
dominance (in physiological level) but not in other (codominance in molecular level)

Characteristics of dominance:

1. Result of interaction between alleles of genes same locus → Allelic interaction

2. Allelic interaction occurs between product of the genes

3. Dominance does not altered inheritance, only influences phenotype

4. Type of dominance depends on phenotypic level examined.

Multiple alleles: although in an individual only exist genes in two different forms
(both alleles), in the whole population exist multiple alleles for the same gene: ex,
ABO blood types (3 alleles: A B or O). The relationships between these alleles form
an allelic series:

• A and B are dominant over O

• A and B are codominant.
• 0 is recessive.
Carmen Martínez Genetic

Although an individual can only have two alleles for the ABO blood group gene,
multiple alleles can exist within a population. This principle illustrates how
Mendelian genetics applies on a larger population scale, increasing genetic diversity
and observable phenotypes

Recessive lethal alleles: there are some alleles that causes the death of the
individual (mutant of an essential genes), they are tolerated only in
heterozygosis. As the homozygous not survive the phenotype is going to be 2:1.

Incomplete penetrance: the expected phenotype is not always produced by a

given genotype although it was the dominant allele. The penetrance of a
condition refers to the proportion of individuals with a particular genotype that
express the expected phenotype. If penetrance < 100% is incomplete.

EXAMPLE: 42 people with polydactyly allele; only 38 polydactylous

Penetrance → 38/42=0.9=90%.

The expressivity: degree in which the phenotype expresses. There are two main
factors to determine that: the environment and the influence of other genes.

Pleiotropy: one gene can affect phenotype of different traits, for example, it can
be influenced in the metabolism and in mental development.

3.Gene interactions

Most traits are influenced by multiple genes, leading to gene interactions, it means
that phenotypes are often the result of the effects of several genes, the interaction
between the products of genes results in a wide range of phenotypes.

For example, two independent loci interact to produce different phenotypes of a

single trait, it could be observed in a ratio of 9:3:3:1.

Different types:
Carmen Martínez Genetic

Epistasis: one gene (epistatic) masks the effect of another (hypostatic) gene at a
different locus. The epistatic genes could be recessive (are needed two copies) or
dominant (only one copy is needed)

Genotypic frequencies are the same as in classical mendelian crosses. Only

phenotypic ratios change due to gene interactions.

In other way, exists the duplicate recessive epistasis implies that two different loci
can control a single trait and that the presence of recessive alleles (does not matter
in what loci the gene recessive was) at either locus can result in the same
phenotype.

4. Cytoplasmatic inheritance.

Until now we are studying that genes are located on nuclear chromosomes, so the
parental origin not affected inheritance of the genes, but there are some exceptions:
the cytoplasmatic genes (located in mitochondria and chloroplasts).

This cytoplasmatic genes form the cytoplasmatic inheritance, are only maternal
inheritance (sperm does not contribute here) Moreover, this cytoplasmatic genes
are distributed randomly with the organelles, it caused that an extensive
phenotypic variation exhibit.

The mitochondrial diseases are rare disorders caused by mutations in

mitochondrial DNA (mtDNA), which encodes essential genes, especially in the
electron transport chain. These mutations affect ATP synthesis, impacting the
functioning of muscle and nerve cells in the central nervous system, motor
disorders, blindness, deafness and stroke.

Maternal effect: the nuclear genes are inherited from both parents but the
offspring's phenotype is influenced only by the mothers genotype (does not matter
the progeny's phenotype) but is not necessary that both phenotypes are the same,
Progeny’s phenotype is determined by the mother’s genotype, not her phenotype.
Carmen Martínez Genetic

4.Genotipic imprinting

The process by which the expression of an allele depends on whether it has been
inherited from a male or a female parent (parental imprinting), for example in X-
linked genes and cytoplasmatic inheritance, are affected genes related with early
stages of development and foetal growth.
Carmen Martínez Genetic

CHAPTER VII:

1. LINKED GENES

Considering the Mendel's principles:

• Principle of equal segregation → Two alleles at one locus separate

equally in meiosis into each gamete.

• Principle of independent assortment → Alleles at a locus separate

independently of alleles at other loci.

We know that the independent separation of alleles allows the formation of new
combinations of these alleles, a process known as recombination. But thanks to
the Walter Sutton chromosomal theory of heredity that is based on:

• Genes are found on chromosomes

• Chromosomes segregate in meiosis. Each homolog into one gamete.

It could be concluded that many genes are located on the same chromosome
and, therefore, do not assort independently. Because of that we can differ among
linked genes (segregated together) and unliked genes (segregated independently):

Not all the genetic characteristics assort independently if the two loci are close
together on the same chromosome, consequently they inherited together. But in
some cases, these alleles switch from the homologous chromosome (crossing
over creates recombination): to a larger distance more probability.

If in the progeny exist a complete linkage (genes very close) only are going to appear
the parental phenotypes. By the opposite, if it is an incomplete linkage (genes with
more distance that could have crossing over or those that never) there are going to
be new combinations.

2.CROSSING OVER BETWEEN LINKED GENES:

The main consequence is the recombination, it means the alleles rearranged in new
combinations and new traits. There are two types:
Carmen Martínez Genetic

The interchromosomal recombination: it occurs between genes that are

located on different chromosomes. During anaphase I of meiosis, the
chromosomes segregate independently, resulting in new combinations of alleles in
the gametes.

The intrachromosomal recombination: it refers to genes that are located on

the same chromosome. It occurs through crossing over.

Crossing over: (genes not linked), it creates new combinations in prophase

I of meiosis, as a consequence of that is going to appear a exchange of genetic
material between non sister chromatids of homologous: recombinant chromatids
(the two alleles of a locus are always on different homologous chromosomes)=
entre los cromosomas homologos pero no son del mismo padre

The main effect of this process is the recombinant gametes (50%). The number of
gametes that contain new combinations of alleles (recombinant gametes) depends
on how often crossing over occurs during meiosis: each cross over creates 50%
recombinant gametes

TO INCOMPLETELY LINKAGE "% recombinant gametes = % of meiosis with crossing

over/2¨

If the recombination frequency is 50%, the genes behave as if they assort

independently, suggesting that they may be on different chromosomes or very far
apart on the same chromosome.
If the recombination frequency is less than 50%, the genes are linked on the same
chromosome. In these cases, crossing over occurs some of the time, but not
always. If the recombination frequency is 0 are genes with complete linkage: very
close in same chromosome (no crossing over )

A cross between two homozygotes, such as AA BB and aa bb, the result of crossing
over will have no effect on the gametes, as all the gametes produced will be equally
homozygous (AB or ab), and there will be no recombinant gametes.

3. GENE MAPPING AND RECOMBINATION FRECUENCIES

Carmen Martínez Genetic

Thanks to Thomas Morgan hypothesis is possible determine the arrangement and

distances between genes based on recombination frequencies/rates, using that we
can generate maps showing the order and distances: genetic maps

Genetic distance (u.M) = Recombination frequency (%) × 100

Bases on the distance we can determine the gene in the

middle.

If we added and additional gene, we can calculate the relative

distances and determine the position on the others genes in
relation to the additional gene.

A recombination frequency of 50% suggests that there is no

association between the two genes, as they behave as if they
assort independently, which leads to the inability to
distinguish whether they are very far apart on the same
chromosome.

A testcross involving two genes that are very far apart on the
same chromosome may underestimate the true physical
distance between them due to unnoticed double crossovers
between two loci, that are more frequent between distant genes.

CONSTRUCTING GENETIC MAPS:

1. Two-point testcross: is a genetic experiment used to study the inheritance of

two different genes located on the same chromosome:the phenotypes of the
offspring can be observed, and the proportion of different allele combinations can
be calculated.

2.Three-point test cross: are more efficient because the gene order is established
in single cross, and the double crossover is detected so the map distance are more
accurate.

We are going to study three loci, among them could occur three types of crossover:
single or double. When the double crossover occurs, the products are two outer
alleles that do not change so are no recombinants and the middle gene are
recombinant.

To map the genes in needed the information where and how often the crossing over
has taken place, in the homozygous recessive parent as the two alelles os the same
locus are the same the crossing over has not consequences, but, in heterozygous
parents as the alleles are different on each chromosome at same loci the cross over
could be detected.
Carmen Martínez Genetic

STEPS

1) Determine the order: identify the middle locus. Focus on

· Non recombinants: most numerous (triple heterozygous or triple

homozygous)

· Double-crossover: least numerous, different genotype of parents.

Because of that you can explain it like this: a simple way tom determine gene order
is to compare nonrecombinants with least frequent progeny that always will be the
double crosser, and the alleles will differ in one that is going to be the middle locus.

2) Rewrite the genotypes in the exact order and determine the points of crossover :

3 classes of progeny • Most abundant → Nonrecombinants

• Least abundant → Double recombinants

• Rest (four classes) → Single crossover.

4)To determine where single crossover takes places: compare alleles in

nonrecombinants vs. alleles single crossover progeny.

5) Calculate map distances, based on recombination frequencies.

To calculate expected proportion of double-recombinants→ Multiplication rule

First add all recombinant progeny (total number of progeny)

-Calculate the frequency of single and double crossovers:

To calculate the single or double crossover, you have to get first two alleles and later
the other two, and in the formula must appear all the combination of these two
alleles that do not be in the non-recombinants.

Is not the same formula to double and single cross over and with that you can also
seen what it the middle locus (it that least distance has with the other alleles). To
calculate the expected proportion of double recombinants: you need the
multiplication rule to the percentages that you have just calculated with the
previous one (frequency formula of single combinants).

But with that you have the EXPECTED not the real number, but you can calculate the
real observed double crossovers with that formula:
Carmen Martínez Genetic

The coefficient of coincidence is the ratio of observed a double crossover into the
expected, but as the double crossovers are not independent and the occurrence of
one influence the other, this `influence´ or how much a crossover interferes in other
is the interference.
Carmen Martínez Genetic

CHAPTER VIII

There are two types of characteristics:

1.Qualitative or discontinuous (has few phenotypes

for each trait). The relation between genotype-
phenotype are straightforward.

2.Quantitative (has a wide range of variability in

phenotypes for each trait.)

In turn quantitative characteristics has two origins:

they could be polygenic; it means that a lot of genes at
different loci influenced for a trait, or environmental
factor, for example that the same genotype in different environments can lead
different phenotypes: MULTIFACTORIAL. Because of that is very complicate know
the relation between phenotypes and genotypes

And, it has three categories:

1) Continuous: any value between two extremes.

2) Meristic: only whole numbers.

3) Threshold: phenotype present or absent depends on the threshold (umbral)

The inheritance of quantitative characteristics could be explained by the

cumulative effects of many genes following Mendel's rules: the additive effect of
alleles at multiple loci determines range of phenotypes of quantitative traits.

For phenotypic proportions is used the addition rule, adding probabilities of

genotypes that produce the same phenotype.

The main difference between inheritance of gene of quantitative and discontinuous

traits is the number of loci that determine the trait, so more genotypes are possible
Carmen Martínez Genetic

to the same number of phenotypes son there is a less obvious phenotype genotype
relation.

To determine the gene number for a polygenic trait: or estimate the number
of loci, we are going to have into account the number of the F2 that has the same
genotype to one of the P ( the proportion on F2 equal to the original homozygous
parents is 1/4 to` n´; n is the number of loci influencing the trait).

To determine the additive effect of each allele we have to focus on the

phenotype that are characterized and compare one recessive homozygous with
other dominant homozygous.

Each additive allele contributes 2 cm to plant height → 2 x 8 = 16 cm.

As we can estimate the number of loci we can determinate the phenotypic classes:

NUMBER OF DISTINCT PHENOTYPE CATEGORIES OBSERVED = (2N+1)

2. Statistical methods for analysing:

To analyse inheritance of quantitative characteristics we use statistical analyses

that have on account the sample, with a random selection that was representative
and with an appropriate size.

The phenotypic variation of sample is showed by a frequency distribution. The

quantitative traits usually follow a normal distribution (bell-shape). We have to
taking into account some several statistical parameters as:

The mean: information about the central point of a range of measurements

arithmetic average of a set of measurements:

The variance: the spread of the distribution, gives information about the
variability of a group of measurements

The standard deviation: square root of variance.

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Until now we have described the phenotypic distribution of an individual trait, but is
also interested the relation between two or more traits, the correlation, it means that
when one changes the other changes, to measure the strength of the association
we are going to use the correlation coefficients (r)

But first, we have to calculate the covariance (measures the tendency of pairs of
traits to vary together)

Once we have this:

R is the correlation coefficient, if it is

• Positive value → Increase in X accompanied by increase in Y

• Negative value → Increase in X accompanied by decrease in Y.

r =−1 or +1 → Perfect correlation. A change in X is always accompanied by a

proportional change in Y.

r close to −1 or close to +1 → Strong association. Change in x is almost always

associated with a proportional change in y

Values of 0 or closer to 0 → Weak or no association

3.Heritability

Is the proportion of the variation due to genetic factor, the more was the heritability
less is the environmental impact. Heritability values must be calculated for specific
population in a particular environment because for example, heritability for the
same trait in different population and environments might be different.

CALCULATED: different steps:

Determine the total variation: variance: the phenotypic variance of the trait in the
population.

Phenotypic variance (Vp) can be partitioned into several components:

Carmen Martínez Genetic

• Genetic variance (Vg): proportion of phenotypic variance due to differences

in the genotypes
• Environmental variance (Ve): differences in the phenotype due to
environmental differences

Also it has a third component of Vp, the genic environmental interaction

variance: it means that the effect of a gene depends on a specific
environment

The genetic variance is also subdivided into components:

1. Additive genetic variance (VA ) → Additive

effects of alleles of different genes on the
phenotype • Main determinant resemblance
between parents and progeny. 2. Dominance
genetic variance (VD ) → When alleles have a dominance effects.3. Gene
interaction variance (VI ) → Interaction between gene at different loci .

This equation describes potential causes of differences among individual

phenotypes.

SEVERAL WAYS TO ESTIMATE HERITABILITY:

1. By elimination of variance components, if Ve= 0, Vge=0 and Vp=Vg we can

estimate heritability with that. ( get Ve=0 is very difficult so we prefer to get Vg=0) in
this case Vp=Ve in pure breeding varieties in a specific environment.

1. Generate pure-breeding varieties

2. Raise them in specific environment Vp=Ve

3. Measure phenotypic variance (VP)

4. Raise a group of genetically variable individuals in the previous

environment Vg= Vp-Ve

5. Measure the phenotypic variance (VP )

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6. Using previously calculated VE (assume is the same)→ Obtain the VG.

2.By measuring the responses to artificial selection: narrow-sense heritability is

used to predict response to selection:

The process of choosing specific individuals with preferred phenotypes from a

population and crossing them. If repeated over multiple generations, it increases
the frequency of individuals with desired characteristics. This process has been
carried out by humans for thousands of years, producing domesticated plants and
animals, such as dogs.

Bases of artificial selection: It is based on narrow-sense heritability, which is the

proportion of phenotypic variance due to additive genetic variance. This heritability
is used to predict the response to selection, where additive alleles are responsible
for the resemblance between relatives.

TYPES OF HERITABILITY:

Broad-sense heritability → Proportion of the phenotypic variance due to the total

genetic variance

Narrow sense heritability → Proportion of the phenotypic variance due to additive

genotypic variance alone.
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CHAPTER IX

The nature of the genetic material and the eukaryotic

PART 1:

The nature of the genetic material: the central dogma of biology.

Also, there are some exceptions that for example, in retrovirus the organism can do
the retrotranscription. Despite that the dogma is universal. Concepts:

-Genome: is the complete set of genetic material in an organism. It consists of DNA.

-Transcriptome: is the total pool of RNA molecules. It includes messenger RNA

which carries the genetic code from DNA to the ribosomes for protein production,
and non-coding RNAs.

-Proteome: the cell´s repertoire of proteins.

The differences between eukaryotic and prokaryotic protein coding gene could be
seen:
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ADN, nucleic acids:

1.Components.

The nucleic acids are formed by nucleotides: that consist in a base, a phosphate
and a sugar.

But the nucleotides apart from be nucleic acids as other functions as storage of
chemical energy (ATP), form coenzymes and signalling molecules (cyclic AMP)

The sugar always is a pentose:

The base is a nitrogenous base:

2.Structure of the DNA:

Primary:

The nucleotides are linked in polynucleotide chains: with phosphodiester chains:

-3OH group the growing chain and 5PO

gr group of the new nucleotide.

-Direction of synthesis: 5end to 3end.

( (with this chemical polarity)

- -Regular DNA characterize (backbone)

-The one letter code is given:base

Secondary:
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1.Thanks to the X-ray diffraction DNA images of Franklin: X-ray diffraction is a

method for 3D structure analysis where crystallized molecules are exposed to X-
rays. The rays hit the crystal and are diffracted in specific patterns, revealing the
arrangement of atoms

2.The most important rule is Chargaff´s rules: that considered that the ratios of
DNA bases were not random the purines = pyrimidines (A/T=1) (G/C=1) [(A + G)/(T +
C)=1]

This allows Watson and Crick to determine the secondary structure: double helix:

• Two complementary strands

• Run in opposite direction → Antiparallel

• Winded around each other → Double helix weaker than phosphodiester bonds

• Stands linked by hydrogen bonds between A and T → 2 Hb // G and C → 3 Hb

Different energy to separate strands

• Right-handed helix → clockwise and 10 bp per turn

• Base pairs are 0.34 nm apart so in one complete turn → 3.4 nm: diameter 2 nm

• Spiralling of the strands create two grooves → expression regulation

If we melt the temperature the DNA to the tª required, the DNA pass to the native
state to the single-stranded denatured state. The inverse process is called
denaturation/renaturation and is crucial multiple physiological processes and
molecular biology techniques.

The tª required to denature the DNA depends on the length, on the GC content
(bound with 3 hydrogen bonds) and Ionic strength (cations shield negative charge of
phosphate groups)

The B DNA car vary depends on the

environment and the base sequence:

-BDNA: water-rich environment and most

stable under physiological conditions.

-ADNA: water-poor environment, more

compact (11 bp/turn), right-handed and
dsRNA/ RNA-DNA

-ZDNA: Zig-Zag appearance (12 bp/turn)

left-handed, high salt concentration and
uncertain physiological significance.
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ARN:

1.Structure

Primary:

1) Hydroxyl group on 2’C of the pentose.

2) Uracil instead of thymine.

3) Single stranded

Secondary:

Depends on the RNA specific functions and the structure of RNA is not the typical
double helix due to the presence of nucleotides that do not pair correctly, which can
have implications for the stability of DNA and its biological function.

Tertiary:

High rotational freedom. Interaction of secondary elements and distant

complementary sequences, pseudoknot, base pairing between non-contiguous
complementary sequences, D-loop, the T-loop and the acceptor arm fold upon
each other.

The tertiary structures provide RNA ability to perform catalytic functions with
ribozymes that eliminate the pre-rna and it became mature-RNA.
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PART II: EUKARIOTIC GENOME

The C-VALUE:

Is the total amount of DNA in the haploids genome(gametes). In relation with this
concept there are two key points:

Paradox: the C-value is not always related to the complexity of the

organism. For example, some "less complex" species can have a higher C-value
than "more complex" species. Moreover, the number of genes is neither relational
with biological complexity.

Non-coding DNA: The C-value paradox is partly explained by the presence

of large amounts of non-coding DNA in many organisms. This DNA does not contain
genes that code for proteins.

Also, the density of the genes has a inverse correlation with the complexity, because
a low gene density means that the DNA between genes is intergenic and a big size
of genes means introns.

Type sequences in eukaryotic genomes:

The repeated sequence is dispersed along the genomes and the shorter are
repeated in specific regions of the genome.

Interspersed repeats.
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45% of the genome is generated by transposition: a process by which a DNA

segment can move from one region of the genome to another. It creates three types
of genes:

1.LINE: 21%

They are long interspersed nuclear elements with a length of 1000-7000 of bp (pairs
of bases).

2.SINE: 13%

They are short interspersed nuclear elements with a length of 100-500 bp.

3.LTR: 8%

They are retroviral but without infectious capacity with a length of 1000 bp.

Tandem repeats:

There are sequences of different lengths repeated one after other, they could be
classified in:

1.SATELITE DNA:

They have a repetition unit of 100-400 nt and we could find them in centromeres.

2.MINISATELLITES:

They have a repletion unit lower than 25 bp, and their specific region is the telomeric
(or sub telomeric)

3.MICROSATELLITES OR STR:

They have a repetition of unit lower 6 bp, but they are repeated from 5 to 100 times
so exist almost 600000 copies, but the number of repeats is highly variable between
individuals, we can se if with the DNA profiling.

Genes and gene related sequences:

The coding regions are the exons.

The non-coding regions:

1. Introns: These are DNA sequences within genes that do not code for
proteins. However, they contribute to protein diversity through a process
called alternative splicing, where different combinations of exons can form
multiple proteins from a single gene, so increases the biological complexity
with this number of genes.

2. UTR (Untranslated Regions): These are sequences at the ends of mRNA that
are not translated into proteins. UTRs are important for functions like
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ribosome recruitment (to initiate translation) and RNA stability, influencing

how long the mRNA lasts in the cell.

3. Promoter: This is a DNA region where transcription begins. It contains

sequences recognized by transcription factors (TF) and RNA polymerase;
the enzyme responsible for synthesizing RNA from DNA.

4. Enhancers: These are sequences that regulate transcription, but they don’t
need to be close to the gene they control. Enhancers can be located far from
the gene they regulate and still increase its transcription levels.

DNA direction conventions:

• Upstream: Refers to the direction toward the 5' end of the DNA strand,
meaning it is before the transcription start site.

• Downstream: Refers to the direction toward the 3' end of the DNA strand,
meaning it is after the transcription start site.

The sense strand of DNA is always drawn from left (5' end) to right (3' end).

The introns are excised from pre-mRNA, that becomes in mature RNA.

The evolution: genome sequences constantly changing by random process or

several mechanisms, for example:

1)Mutation in a gene on in a regulatory DNA.

2)Duplication of gene and divergence.

3)Exon shuffling: it involves the rearrangement or recombination of exons (the

coding regions of genes) between different genes, either through recombination
events, transposable elements, or errors in splicing.

4)Transposition: changes on the DNA sequence location.

5) Horizonal transfer: between two different organisms. It could be by two ways: