Genetics

What is a gene?
• Genetics is the branch of biology concerned with the storage of information in living organisms and how this information can
be passed from parents to progeny
• Genetic information is transmitted from generation to generation to maintain the continuity of life.
• A gene is a heritable factor that consists of a length of DNA and influences a specific trait via the polypeptide production
• A gene is a section or length of DNA that codes for a polypeptide
• DNA is the genetic blueprint which codes for, and determines, the characteristics of an organism
• There are relatively few DNA molecules in a cell – just 46 in a typical human cell for example – yet there are thousands of genes
• This includes the physical, behavioral and physiological features of the organism
• DNA is packaged and organized into discrete structures called chromosomes
 Where are gene located?
• A gene occupies a specific position on a chromosome
• A single chromosome contains several hundred or thousands of genes
• Through experiments and genetic mapping techniques, scientists were able to work out the specific physical location of a
gene on a chromosome
• The location of a gene on a chromosome is known as its locus (the plural of locus is loci)
• Each gene occupies a specific locus so that the gene for a particular characteristic is always found at the same position on a
particular chromosome
 Comparing The Number Of Genes
• Species vary in the number of genes they have
• The number of genes a species has is not related to the size/complexity or even the sophistication of the organism
• Because genes can vary in length, counting the exact number of genes in a species is difficult, so you may see conflicting
numbers in different sources
• Humans have around 20,000 genes
• Dogs have 19,000 genes, which is less than humans
• A water flea has more than a human with 31,000 genes
• E. coli, a bacterium, has only 4,300 genes
• A rice plant has 41,500 genes
 What are alleles?
• Gregor Mendel is usually regarded as the father of genetics discovered after crossing varieties of pea plant that alternative
forms of the same gene can exist, these various specific forms are called alleles
• Note that although alleles are different forms of the same gene, they all still occupy the same locus on the chromosome
• Multiple alleles can exist for a gene that determines a specific trait
• Each allele results in a different variation of that trait
• Eg. blood types A, B, AB and O
• The chromosomes of eukaryotic cells occur in homologous pairs (there are two copies of each chromosome, one copy
inherited from each parent) which means that cells have two copies of every gene
• As a result, a cell possesses two alleles of every gene within its nucleus
• When the two alleles at a locus are the same/identical they are described as homozygous
• When the two alleles at a locus are different, they are described as heterozygous
 Mutation
• A gene mutation is a change in the sequence of base pairs in a DNA molecule; this may result in a new allele
• Mutations occur all the time and at random
• There are certain points in the cell cycle when mutations are more likely to occur, for example, copying errors when DNA is
being replicated (S phase of interphase)
• As the DNA base sequence determines the sequence of amino acids that make up a polypeptide, mutations in a gene can
sometimes lead to a change in the polypeptide that the gene codes for
• Most mutations are harmful or neutral (have no effect) but some can be beneficial
• Inheritance of mutations:
• Almost all mutations are therefore either neutral or harmful. Some mutations are lethal – they cause the death of the cell
in which the mutation occurs. Mutations in body cells are eliminated when the individual dies, but mutations in cells that
develop into gametes can be passed on to offspring and cause genetic disease.
• Substitution Mutations
• A mutation that occurs when a base in the DNA sequence is randomly swapped for a different base is known as a substitution
mutation
• A substitution mutation will only change the amino acid for the triplet (group of three consecutive bases) where the mutation
occurs; it will not have a ripple effect further along the gene/polypeptide
• A small change to a gene can have serious consequences for an organism
• Sickle cell anaemia is a genetic disease caused by a single base substitution mutation within the gene (Hb) that codes for the
alpha-globin polypeptide in haemoglobin
• Most humans have the normal allele HbA
• The Mutation that occurs, within the haemoglobin gene, the base thymine (T) is replaced by the base adenine (A). This causes
the DNA triplet GAG to mutate to GTG
• The mutated DNA codon GTG is transcribed into the mRNA codon GUG, instead of GAG
• During translation, the amino acid valine (VAL) replaces the original amino acid glutamic acid (GLU); this occurs on the sixth
position of the polypeptide
• The slightly different polypeptide results in a new allele, HbS
•The protein haemoglobin S is produced instead of haemoglobin A; this causes a distortion in the shape of the red blood
cells into sickle shapes
•Sickle-shaped red blood cells:
• Have a limited oxygen-carrying capacity
• Block the capillaries limiting the flow of normal red blood cells
•People with sickle cell anaemia suffer from acute pain, fatigue and anaemia
 What is a genome?
• The total of all the genetic information in an organism is called the genome of the organism
• This is a complete set of genes present within every cell of an organism
• This includes all genes as well as non-coding DNA sequences and mitochondrial DNA and chloroplast DNA are included in the
genome
• In a prokaryote cell, plasmid DNA is included in its genome
• The human genome consists of:
• 46 chromosomes
• ~3 billion base pairs
• ~21,000 genes
 The human genome project?
• The Human Genome Project (HGP) was an international, collaborative, research programme to sequence the entire human
genome
• The work began in 1990, was publicly funded, and shared among more than 200 laboratories around the world, avoiding
duplication of effort
• DNA samples were taken from multiple people around the world, sequenced, and used to create a reference genome
• The finished genome was over 3 billion base pairs long but contained only about 25,000 genes
• The HGP discovered new data about non-coding DNA, suggesting that it plays an active role in the cell, and that it isn't just
'junk' DNA
• The sequence of the DNA is stored in databases available to anyone on the Internet
• To sequence a genome:
• The entire genome is broken up into manageable pieces and then the fragments are separated so that they can be
sequenced individually
• Single-stranded copies are made so that the colored nucleotides can bind to the original strand
• Nucleotides are tagged with a differently colored fluorescent marker, one for each base, adenine, cytosine, guanine and
thymine are then added
• Samples are separated according to length, by capillary electrophoresis machine. This procedure is very high
resolution and distinguishes DNA fragments that differ in size
• After separation, a laser beam makes the fluorescent markers fluoresce
• Then an optical detector linked to a computer deduces the base sequence from the sequence of colors detected
 Prokaryotic Chromosomes
• The DNA in prokaryotic cells is significantly different from the DNA found in eukaryotic cells
• Prokaryotes do not possess a nucleus – instead genetic material is found free in the cytoplasm in a region called the nucleoid
• The genetic material of a prokaryote consists of a single chromosome consisting of a circular DNA molecule (genophore)
• The DNA within prokaryotic cells is not associated with any proteins for additional packaging
• Prokaryotic DNA is sometimes referred to as naked
• Eukaryotic DNA associates with histone proteins
• In addition to the genophore, prokaryotic cells may possess additional circular DNA molecules called plasmids
 Plasmids
• Prokaryotes also usually have one or more plasmids, while most eukaryotes do not contain plasmids
• They are usually small, circular and naked, containing a few genes that may be useful to the cell but not those needed for its
basic life processes. For example, genes for antibiotic resistance are often located in plasmids
• Plasmids can sometimes be passed 'sideways' from one cell to another, during cell division
• They can also be used as a vector during genetic engineering to transfer DNA between species
• Bacterial cells may exchange plasmids via their sex pili, in a process known as bacterial conjugation
• This exchange of genetic material allows bacteria to evolve new features within a generation (horizontal gene transfer)
 Autoradiography
• John Cairns was a scientist working in the field of molecular genetics and cancer research in the 1960s
• Autoradiography is a technique used to study DNA by labelling it using radioactive isotopes
• These isotopes were fed to E. coli bacteria which incorporated them into their DNA
• When exposed to a photographic film the radioactive isotopes caused the film to become developed, resulting in
an image of the DNA being produced
• In order to do this scientists, use a radioactive version of the DNA base thymine which is radioactive is because it
contains tritium, a radioactive isotope of hydrogen
• He first kept the E. coli bacteria in a nutrient broth containing a radioactive version of the DNA base
thymine attached to a deoxyribose sugar
• The E. coli bacteria incorporated these bases into their DNA during replication. This meant that after several generations the
DNA was fully radioactive
• He then lysed the cells using an enzyme called lysozyme, breaking apart the cell walls, which allowed the DNA to be accessed
• The DNA was fixed into position onto a membrane
• The membrane was submerged in a photographic emulsion containing silver ions (Ag+) for two months
• When the silver ions were exposed to the radioactive DNA, the ions were reduced to silver metal. The grains of silver metal
caused visible black dots to appear in the photographic emulsion
• Once this emulsion had been developed it could be viewed under an electron microscope and the length and shape of DNA
could be studied

• By using this technique Cairns made many important discoveries. He found that E. coli contains a single, circular chromosome
of DNA
• He also measured the length of the circular chromosome to be 1100µm long (550 times bigger than the E. coli cell itself)
 Eukaryote chromosomes
• Eukaryote chromosomes are linear DNA molecules associated with histone proteins.
• The main proteins present are the large, positively charged globular proteins called histones, their role is
to organize and wrap the DNA tightly so that it fits into the nucleus
• The other proteins are enzymes used in copying and repairing the DNA
• The tightly coiled combination of DNA and proteins is called chromatin – this is what chromosomes are made of
• Each chromosome has a constriction point called a centromere, which divides the chromosome into two sections (or ‘arms’)
• Adjacent histones in the chromosome are separated by short stretches of the DNA molecule that are not in contact with
histones. This gives a eukaryotic chromosome the appearance of a string of beads during interphase.
• Organization of eukaryotic chromosomes can be summarized as follows:

• DNA is complexed with eight histone proteins (an octamer) to form a complex called a nucleosome
• Nucleosomes are linked by an additional histone protein (H1 histone) to form a string of chromatosomes
• These fibres then form loops, which are compressed and folded around a protein to form chromatin
• Chromatin will then supercoil during cell division to form chromosomes that are visible (when stained) under microscope
 The Replication Of Chromosomes
• During interphase (the period before mitosis) the DNA replicates to create two identical strands of DNA called chromatids,
joined together by a narrow region called the centromere
• The two chromatids that make up the double structure of a chromosome are known as ‘sister chromatids’
• It is important that the sister chromatids are identical in order to produce genetically identical daughter cells via mitosis
• During anaphase of mitosis one chromatid ends up in one daughter cell while the other chromatid ends up in the other
daughter cell
• After the centromere is split apart at the start of anaphase the chromatids are referred to as
individual chromosomes again
 Chromosomes
• In a eukaryote species, there are different chromosomes that carry different genes
• During mitosis, chromosomes become denser by supercoiling, so are easier to observe than when they are in interphase
• Different types of chromosomes can be seen
• They differ in length and the position of the centromere
• Humans have 23 types of chromosomes
• The largest one is numbered 1
• The smallest is numbered 22
 Homologous Chromosomes
• In diploid cells there are two complete sets of chromosomes in the nucleus (one of maternal origin ; one of paternal origin)
• Homologous chromosomes
• Carry the same genes at the same loci
• Are the same shape, same size, same centromere positions
• Are not usually identical because they may be carrying different alleles to each other
• During fertilization, a diploid zygote is formed
• In a zygote, one chromosome of each homologous pair comes from the female gamete and the other comes from the
male gamete
• Having the same genes in the same loci helps homologous chromosomes line up alongside each other
 Haploid & Diploid
• A diploid cell is a cell that contains two complete sets of chromosomes (2n)
• These chromosomes contain the DNA necessary for protein synthesis and cell function
• Nearly all cells in the human body are diploid with 23 pairs (46) of chromosomes in their nucleus

• Haploid cells contain one complete set of chromosomes (n)

• In other words they have half the number of chromosomes compared to diploid cells
• Humans have haploid cells that contain 23 chromosomes in their nucleus
• These haploid cells are called gametes and they are involved in sexual reproduction
• For humans they are the female egg and the male sperm
 Chromosome number
• The number of chromosomes is a characteristic feature of members of a species.
• One of the most fundamental characteristics of a species is the number of chromosomes.
• Organisms with a different number of chromosomes are unlikely to be able to interbreed so all the interbreeding members of a
species need to have the same number of chromosomes.
 Sex determination in males
Humans have 46 chromosomes in all diploid somatic cells – 22 pairs are autosomes and the 23 rd pair are the sex chromosomes
The remaining chromosomes in the organism are called autosomes (they do not determine sex)

In humans, sex is determined by a pair of chromosomes called the sex chromosomes (or heterosomes)
■ Females possess two copies of the X chromosome (XX), while males possess one X and a shorter Y chromosome (XY)
■ The Y chromosome includes a gene called the SRY gene (Sex Determining Region Y), which leads to male development
■ The SRY gene codes for a testis-determining factor (TDF) that causes embryonic gonads to form into testes (male gonads)
■ In the absence of the TDF protein (i.e. no Y chromosome), the embryonic gonads will develop into ovaries (female gonads)

The male and female gametes produce different hormones to promote further development of sex characteristics:
■ The testes produce testosterone to promote the further development of male sex characteristics
■ The ovaries will produce estrogen and progesterone to promote the development of female sex characteristics
 Karyogram
• A karyogram shows the chromosomes of an organism in homologous pairs of decreasing length

• The chromosomes are stained and photographed to generate a visual profile that is known as a karyogram

• The chromosomes of an organism are arranged into homologous pairs according to size (with sex chromosomes shown last)

• Use of karyograms to deduce sex and diagnose Down syndrome in humans

 Two types of nuclear division
• During fertilization the nuclei of gametes fuse together to form the nucleus of the zygote
• For a diploid zygote this means that the gametes must be haploid
• n + n = 2n
• Meiosis produces haploid gametes during sexual reproduction
• The first cell division of meiosis is a reduction division
• This is a nuclear division that reduces the chromosome number of a cell
• In humans the chromosome number is reduced from 46 (diploid) to 23 (haploid)
• The reduction in chromosome number during meiosis ensures the gametes formed are haploid
• When a diploid zygote, which is one cell, grows into an adult with million of cells, the new cells must be genetically identical,
with the same number of chromosomes as the cells that divided to produce them. The type of nuclear division that achieves this
is mitosis.

• Meiosis is not only reductive division, it also introduce genetic variation into the gametes and therefor zygotes that are
produced.
Events that take place during meiosis help to produce genetic variation between daughter cell that are produced:

1. Crossing over, which happens between the chromatids of homologues chromosomes ( between prophase I and metaphase I).
2. Independent assortment of the homologues chromosomes (metaphase I)
3. Random fuse of gametes in fertilization
 Meiosis
• There are two processes by which the nucleus of a eukaryotic cell can divide. These are:
• Mitosis
• Meiosis
• Mitosis gives rise to genetically identical cells and is the type of cell division used for growth, repair of damaged
tissues, replacement of cells and asexual reproduction
• Meiosis gives rise to cells that are genetically different from each other and is the type of cell division used to
produce gametes (sex cells)
• It involves the reduction division of a diploid cell into four genetically distinct haploid nuclei
• The process of meiosis consists of two cellular divisions:
• The first meiotic division separates pairs of homologous chromosomes to halve the chromosome number (diploid → haploid)
Meiosis I
• The second meiotic division separates sister chromatids (created by the replication of DNA during interphase) Meiosis II
• Meiosis involves two divisions of the nucleus, known as meiosis I and meiosis II. meiosis consists of two nuclear divisions
but only one replication of the chromosomes happened in the interphase stage.
• It produces gametes in plants and animals that are used in sexual reproduction
• It has many similarities to mitosis however it has two divisions: meiosis I and meiosis II. As happens in mitosis, chromosomes
are copied, appearing as sister chromatids during interphase, before meiosis occurs.
• Meiosis I is a reduction division, resulting in two daughter nuclei with half the number of chromosomes of the parent nucleus.
• Meiosis II, the chromosomes behave as in mitosis, so that each of the haploid cells divides again resulting in four haploid
nuclei.
 DNA Replication Before Meiosis
• Before meiosis occurs, all the DNA inside the nucleus of the 'parent' cell is replicated
• This occurs during a period of the cell cycle known as interphase
• Once this has occurred, each chromosome now consists of two genetically identical sister chromatids, which are joined together
by a centromere
• The sister chromatids are genetically identical because DNA replication is a very accurate process and only a very small
number of mistakes occur when DNA is being copied
• The two DNA molecules formed by DNA replication prior to meiosis are sister chromatids until the splitting of the
centromere at the start of anaphase
• After this, they are once again considered as individual chromosomes
• We have 46 chromosomes and 23 pairs.
• Chromosomes are counted by the centromere.
• İn interphase stage of both mitosis and meiosis, we double the number of chromosomes.
• We still have 46 chromosomes, 46 centromeres but we have 92 sister chromatids
 Bivalent formation and crossing over
• The early stages of meiosis involve pairing of homologous chromosomes and crossing over followed by condensation.
• Some of the most important events of meiosis happen at the start of meiosis I while the chromosomes are still very elongated
and cannot be seen with a microscope.
• At the start of meiosis, homologous chromosomes pair up with each other
• As DNA replication has already occurred, each chromosome is made up of two sister chromatids
• This means that a pair of homologous chromosomes is made up of four chromatids
• A pair of homologous chromosomes is known as a bivalent and the pairing process resulting in the formation of a bivalent is
called synapsis.
• Soon after synapsis, a process called crossing overtakes place. A junction is created where one chromatid in each of the
homologous chromosomes breaks and rejoins with the other chromatid.
• As these crossover events occur at the same position on the two non-sister chromatids, this allows genes to exchange between
the chromatids
• Non-sister chromatids are homologous but are not genetically identical and this means that some of the alleles of the exchanged
genes will be different

• This process, therefore, produces chromatids with completely new combinations of alleles (that were not previously present in
the DNA of the 'parent' cell)

• As these chromatids will eventually be split up into different gametes, crossing over is of great importance because it is a
significant source of genetic variation between gametes.

• This ensures there is genetic variation in populations of sexually-reproducing species, which is key to a species' ability
to evolve and adapt to changes in its environment over time
 Prophase I
• Each chromosome condense and is visible as a pair of chromatids (sister chromatids) are so-called because they originate from
the same parent.
• Each sister chromatids are joined together by a centromere
• Two homologous chromosomes (four chromatids) move and align side by side to each other. This paring of homologues
chromosomes is called synapsis.
• This is called a bivalent because it is composed of two chromosomes
• It is also called a tetrad because it is composed of four chromatids
• As the homologous chromosomes are very close together the crossing over of non-sister chromatids may occur.

• The point at which the crossing over occurs is called the chiasma (chiasmata; plural), producing genetically recombinant
chromosomes (not identical anymore).

• In this stage centrioles migrate to opposite poles and the spindle is formed.

• The nuclear envelope breaks down and the nucleolus disintegrates

 Metaphase I
The bivalents/tetrad chromosomes line up along the equator of the cell, with the spindle fibers attached to the kinetochore (at
centromeres).
Orientation of paternal and maternal chromosomes on either side of equator is random and independent of other homologous
pairs.

In humans, 23 tetrad will align at the equator.

• Random Orientation
• At metaphase, during meiosis I, homologous chromosomes line up at the cell equator as they prepare to separate
• Spindle microtubules grow out from the poles of the cell and attach to the kinetochore of the chromosomes
• Each of the two homologous chromosomes in a bivalent is attached to a different pole
• The orientation of the bivalents when they line up at the cell equator determines which pole each chromosome gets attached
to (and eventually pulled towards)
• The orientation of the bivalents is completely random
• In addition, the bivalents also assort independently of other homologous pairs.
 Anaphase I

• The homologous pairs in the tetrad are separated as microtubules pulling the whole chromosomes to opposite ends of the
spindle

• This process is random, either one can end up on the either side (Independent assortment ).

• The centromeres do not divide, unlike in mitosis. The whole chromosome move toward opposite ends.
 Telophase I
• The chromosomes arrive at opposite poles. Spindle fibers start to break down and Chromosomes decondense
• Reduction of chromosome number from diploid to haploid completed.
• Nuclear envelopes form around the two groups of chromosomes and nucleoli reform
• Cytokinesis occurs
 Meiosis II
• First meiosis was nuclear reduction, second division of meiosis is almost identical to the stages of mitosis of nuclear division
• Prophase II
• The nuclear envelope breaks down and chromosomes condense
• A spindle forms at a right angle to the old one

• Metaphase II
• Chromosomes line up in a single file along the equator of the spindle

• Anaphase II
• Centromeres divide and individual chromatids are pulled to opposite poles
• This creates four groups of chromosomes that have half the number of chromosomes compared to the original parent cell

• Telophase II
• Nuclear membranes form around each group of chromosomes

• Cytokinesis
• Cytoplasm divides as new cell surface membranes are formed creating four haploid cells
Identifying the stages of meiosis
 Genetic Variation & Meiosis
• Crossing Over And Random Orientation Promote Genetic Variation
• Having genetically different offspring can be advantageous for natural selection and therefore increase the survival chances of
a species
• Meiosis has several mechanisms that increase the genetic variation of gametes produced
• Both crossing over and random orientation result in different combinations of alleles in gametes
• Crossing over is the process by which non-sister chromatids exchange alleles:
• During prophase I of meiosis homologous chromosomes pair up and are in very close proximity to each other
• A pair of homologous chromosomes can be referred to as a bivalent
• At this point, there can be an exchange of genetic material (alleles) between non-sister chromatids in the bivalent
• The crossing points are called chiasmata
• This results in a new combination of alleles on the two chromosomes (these can be referred to as recombinant
chromosomes)
• This swapping of alleles is a significant source of genetic variation because it can occur at multiple random positions along the
chromosome
• Crossing over can happen anywhere along the chromosome but is more likely to occur further down the chromosome away
from the centromere
• Random Orientation
• The random orientation of homologous pairs along the equator of the cell during metaphase I result in the production
of different allele combinations in daughter cells
• In prophase I, homologous chromosomes pair up and in metaphase I, they align along the equator of the cell
• Each pair can be arranged with either chromosome on top, this is completely random
• The orientation of each homologous pair is random/independent (unaffected by the orientation of any other pair)
• In anaphase I the homologous chromosomes are separated and pulled apart to different poles
• The combination of alleles that end up in each daughter cell depends on how the pairs of homologous chromosomes were lined
up
• The different combinations of chromosomes in daughter cells increases genetic variation between gametes
• During metaphase I, homologous chromosomes line up at the equator as bivalents in one of two arrangements:
• Maternal copy left / paternal copy right OR paternal copy left / maternal copy right
• Gamete combinations = 2n (where n represents the haploid number)
• The number of possible chromosomal combinations resulting from random assortment is equal to 2n
• n is the number of homologous chromosome pairs or haploid number
• For humans: the number of chromosomes is 46 meaning the number of homologous chromosome pairs is 23 so the
calculation would be:
• 223 = 8,388,608 possible chromosomal combinations
• Calculate how many different chromosomal combinations can result from meiosis in a plant species which has a diploid
number of 16. Assume no crossing over occurs
• Random Fertilization
• The fusion of two haploid gametes results in the formation of a diploid zygote
• As meiosis results in genetically distinct gametes, random fertilization by egg and sperm will always generate different zygotes
• Fusion of gametes from different parents promotes genetic variation.
• the formula to calculate the number of combinations of chromosomes after the random fertilization of two gametes is (2n)2
• n is the haploid number and 2 is the number of gametes
• Therefore, in humans, when the haploid number is 23, the number of combinations following fertilization is (2 23)2­­ =
70,368,744,177,664
• Calculate the number of different possible chromosome combinations after the random fertilization of an ovule and pollen
nuclei from the same plant species (Diploid number = 16)
 Non-disjunction
• Meiosis is sometimes subject to errors. One example of this is when homologous chromosomes fail to separate at anaphase.
• This is termed non-disjunction. This can happen with any of the pairs of homologous chromosomes.
• The result will be a gamete that either has an extra chromosome or is deficient in a chromosome. If the gamete is involved in
human fertilization, the result will be an individual with either 45 or 47 chromosomes.
• An abnormal number of chromosomes will often lead to a person possessing a syndrome
• Conditions that arise from non-disjunction events include:
• Patau’s Syndrome (trisomy 13)
• Edwards Syndrome (trisomy 18)
• Down Syndrome (trisomy 21)
• Klinefelter Syndrome (XXY)
• Turner’s Syndrome (monosomy X)
• Many studies have shown that there is a correlation between age and the incidence of non-disjunction
• It is believed that as the age of the parents increases the incidence of non-disjunction increases
• In particular, the age of the mother has been found to increase the chance of having a child with Down Syndrome
• The impact of age on the risks is represented in the table below

• Karyotyping is typically used to determine the gender of an unborn child and test for chromosomal abnormalities
• Cells are harvested from the fetus before being chemically induced to undertake cell division (so chromosomes are visible)
•Chorionic Villi Sampling
Chorionic villi sampling involves removing a sample of the chorionic villus (placental tissue) via a tube inserted through the cervix
•It can be done at ~11 weeks of pregnancy with a slight risk of inducing miscarriage (~1%)

Amniocentesis
Amniocentesis involves the extraction of a small amount of amniotic fluid (contains fetal cells) with a needle
•It is usually conducted later than CVS (~16 weeks of pregnancy) with a slightly lower risk of miscarriage (~0.5%)
 Gametes
• Gametes are the sex cells of an organism
• For example, the sperm and egg (ovum) cells in humans
• The egg is larger than the sperm as most of its space contains food to nourish a growing embryo
• The sperm cell contains many mitochondria to release energy for its motion
• Gametes fuse during fertilization to form a zygote
• These sex cells are formed during meiosis and only have one copy of each chromosome and so are haploid cells
• For humans, that means the sperm and egg cells contain 23 single chromosomes in their nucleus
• As there is only one chromosome from each homologous pair there is only one allele of each gene present
• This allele may be dominant, recessive or co-dominant
 Diploid Zygotes
• Fusion of gametes results in diploid zygotes with two alleles of each gene that may be the same allele or different alleles
• Fertilization is defined as the fusion of gamete nuclei, and as each gamete comes from a different parent, there is variation in
the offspring
• When a male and female gamete fuse their chromosomes are combined
• This means the resulting zygote is diploid
• The zygote contains two chromosomes of each type
• It will therefore also have two alleles of each gene
• If the two alleles for a particular gene are the same then the genotype is described as homozygous
• If the two alleles for a particular gene are different then the genotype is described as heterozygous
 Alleles
• Alleles are variations of the same gene
• As we have two copies of each chromosome, we have two copies of each gene and therefore two alleles for each
gene. One of the alleles is inherited from the mother and the other from the father
• This means that the alleles may not be the same
• The observable characteristics of an organism is called the phenotype
• The combination of alleles that control each characteristic is called the genotype
• Alleles can be dominant or recessive
• A dominant allele only needs to be inherited from one parent for the characteristic to be expressed in the
phenotype
• A recessive allele needs to be inherited from both parents for the characteristic to be expressed in the phenotype.
• If there is only one recessive allele, it will remain hidden, and the dominant characteristic will show
• If the two alleles of a gene are the same, we describe the individual as being homozygous (homo = same)
• An individual could be homozygous dominant (having two copies of the dominant allele), or homozygous
recessive (having two copies of the recessive allele)
• If the two alleles of a gene are different, we describe the individual as being heterozygous (hetero = different)
 How did Mendel discover genes?
• Gregor Mendel was an Austrian monk. He was trained in mathematics and natural history at the University of Vienna, he
studied how characteristics were passed on between generations of plants. Due to his extensive work on the understanding of
inheritance, he is sometimes called the father of genetics
• Mendel was working at a time when DNA hadn’t been discovered and it was generally believed that we show a mixture of the
characteristics of our parents. This theory is called blending inheritance.
• If blending inheritance happens, over the course of many generations it will lead to less and less variation in a population. For
example, a human population starting with blue and brown eye colors and a mixture of heights would change to one where
everyone had an intermediate eye color and the same height.
• Mendel used a large number of pea plants in his studies, for example in one investigation he recorded the characteristics for
over 7,000 pea seeds
• Mendel did his experiments on purebred variety; all the plants and their progeny (offspring) have the same characteristics.

• Purebred varieties can be developed quite easily by growing many plants of one variety together, so pollen is unlikely to be
spread to them from other varieties and by saving seed only from plants with the desired characteristics. In peas it is particularly
easy because the flowers tend to self‐pollinate.
• Mendel chose varieties of pea that differed in distinctive ways, for example, the colour of the flowers (purple or white) and the
height of the plant (tall or dwarf).
• He performed simple hybridization experiments by transferring pollen from the anthers of one variety to the stigmas in
flowers of another variety. These experiments are called crosses, and the progeny are called first filial or F1 hybrids.
• The results of all of Mendel’s crosses were the same—all the F1 hybrid plants were like one of the parental types. The other
type disappeared.
• Mendel allowed the F1 hybrid plants to self‐pollinate, to find what type of progeny they produced. Again, the results were
always the same. Both of the original parental types appeared in this F2 generation, in a 3:1 ratio.
• Using the purple/white example again, 75% were purple ‐flowered and 25% were white. Despite apparently disappearing in the
F1 generation, white‐flowered peas had reappeared and they were just as white as the original parents.
• Again, this showed that the theory of blending inheritance was false. Mendel had revealed that discrete factors which determine
our characteristics are passed unchanged from parent to offspring.
• Mendel found that characteristics were inherited in a predictable pattern. All pea plants in the first generation had the same
characteristic as one of the parental plants
• The offspring plants in the second generation had characteristics of both parent plants in a 3:1 ratio
• Without knowing it, Mendel had discovered genes, he referred to them as 'units of inheritance’. He also discovered that some
genes are dominant and some genes are recessive. Different forms of the same gene are called alleles
• From these findings, Mendel drew the following conclusions:
• Organisms have discrete factors that determine its features (these ‘factors’ are now recognised as genes)
• Furthermore, organisms possess two versions of each factor (these ‘versions’ are now recognised as alleles)
• Each gamete contains only one version of each factor (sex cells are now recognised to be haploid)
• Parents contribute equally to the inheritance of offspring as a result of the fusion between randomly selected egg and sperm
• For each factor, one version is dominant over another and will be completely expressed if present

• While there are limitations to Mendel’s conclusions, certain rules can be established:
1. Law of Segregation: When gametes form, alleles are separated so that each gamete carries only one allele for each gene
2. Law of Independent Assortment: The segregation of alleles for one gene occurs independently to that of any other gene
3. Principle of Dominance: Recessive alleles will be masked by dominant alleles
 F1 and F2 generations
• When a homozygous dominant individual is crossed with a homozygous recessive individual the offspring are called
the F1 generation
• All of the F1 generation are heterozygous

• If two individuals from the F1 generation are then crossed, the offspring they produce are called the F 2 generation
 Dominance
• Sometimes, neither of a pair of alleles is completely dominant or completely recessive. They both influence the phenotype.

• In the normal alleles we have three genotype and only two phenotype. In co-dominant allele we have three genotype and
three phenotypes.

• Co-dominant alleles have a combined effect on the phenotype. The alleles are both expressed to an equal extent in the
phenotype

• Co-dominant alleles both influence the phenotype of a heterozygous organism.

In each of Mendel’s crosses one of the alleles was dominant and the other was recessive. However, some genes have pairs of
alleles where both have an effect when they are present together. They are called co-dominant alleles. A well-known example is
the flower color of Mirabilis jalapa. If a red-flowered plant is crossed with a white-flowered plant, the offspring have pink flowers.

When studying co-dominance, upper and lower letters are not used to represent alleles, instead a letter is chosen to represent the
gene, in this example C for colour of flower. The different alleles are then represented using second letter shown as a superscript.
 Blood Type
• Human blood type is determined by co-dominant alleles. There are three different alleles for human blood type, known as I A, IB,
and i. We can call these alleles A (for IA), B (for IB), and O (for i).

• Each of us has two ABO blood type alleles, because we each inherit one blood type allele from our mother and one from our
father.

• Since there are three different alleles, there are a total of six different genotypes at the human ABO. The different possible
genotypes are AA, AO, BB, BO, AB, and OO
IA and IB are co-dominant whereas Io is recessive to both of the other alleles. Different combination of these alleles
result in the four blood groups.
• IA results in the production of antigen A on the surface of red blood cells
• IB results in the production of antigen B on the surface of red blood cells
• IO results in no antigens being produced on the surface of red blood cells
 Punnett grid
1. Write down the parental phenotypes and genotypes
2. Write down all the possible gamete genotypes that each parent could produce for sexual reproduction
3. Place each parental genotype against one axis of a Punnett grid (2 x 2 table)
4. In the boxes of the Punnett grid, combine the gametes into the possible genotypes of the offspring. This gives the offspring of
the F1 generation (1st filial generation)
5. List the phenotype and genotype ratios for the offspring

• Sweet peas grow pods that are either green or yellow. The allele for green, G, is dominant to the allele for yellow, g. Construct
a Punnett grid to predict the outcome when crossing green and yellow pure-bred plants to show the F1 generation offspring.
Using plants from the F1 generation, construct a second Punnett grid to show the outcomes of the F2 generation.
• The height of pea plants is controlled by a single gene that has two alleles: tall and short
• The tall allele is dominant and is shown as T
• The small allele is recessive and is shown as t
• A pure breeding short plant is bred with a pure breeding tall plant
• The term pure breeding indicates that the individual is homozygous for that characteristic
 Pedigree Charts
• Family pedigree diagrams are usually used to trace the pattern of inheritance of a specific characteristic
(usually a disease) through generations of a family
• This can be used to work out the probability that someone in the family will inherit the genetic disorder
• Below is a pedigree chart which traces the inheritance of albinism across several generations. Albinism affects the production
of the pigment melanin leading to lighter hair, skin and eyes.

• Using the pedigree chart, deduce and explain the following:

• What type of allele causes albinism
• The genotype of individuals named 9 and 7
• The possible genotypes of 10 and 11
 Inheritance Of Genetic Diseases
• Many genetic diseases in humans are due to recessive alleles of autosomal genes.
• If a person has one recessive allele for the genetic disease and one dominant allele, they will not show symptoms of the
disease, but they can pass on the recessive allele to their offspring. These individuals are called carriers.
• This means that an individual would need two copies of the recessive allele to develop the disease
• A disease determined by a recessive allele includes cystic fibrosis
• Some diseases are caused by dominant allele includes Huntington's disease
• This means that only one copy of the allele is required to develop the disease and this one copy can also be passed on to
the next generation
• Individuals that are homozygous dominant, will suffer from the disease and will also pass the allele on to the next
generation with 100% probability
• It is also possible, but rare, for a disease to be caused by codominant alleles. A disease determined by codominant alleles
includes sickle cell anaemia
• Cystic Fibrosis
• Cystic fibrosis is a genetic disorder of cell membranes caused by a recessive allele (f) of the CFTR gene located on chromosome
7
• This gene codes to produce chloride ion channels required for secretion of sweat, mucus and digestive juices
• A fault in the CFTR gene leads to production of non-functional channels. This leads to reduced levels of sodium chloride in
secretions which subsequently reduces the movement of water by osmosis into the secretions
• Ultimately resulting in the body producing large amounts of thick, sticky mucus in the air passages
• Over time, the mucus builds up in the lungs leading to infections and blocks narrow passageways
• Huntington's Disease
• Huntington’s disease is a genetic condition that develops as a person ages. Usually, a person with the disease will not show
symptoms until they are 30 plus years old
• An individual with the condition experiences neurological degeneration; they lose their ability to walk, talk and think. The
disease is ultimately fatal
• It has been found that individuals with Huntington's disease have abnormal alleles of the HTT gene
• The HTT gene codes for the protein huntingtin which is involved in neuronal development
• The abnormal allele is dominant over the normal allele
• If an individual has one abnormal allele present, they will suffer from the disease
• If only one parent is a carrier of the dominant allele, there is still a 1 in 2 or 50% chance of producing a child with the
disease
 Linked genes
There are two types of linkage in genetics: sex linkage and autosomal linkage
Autosomal gene linkage is when the gene are on the same autosome, and sex linkage when the gene are located on the X
chromosome.
Some characteristics are determined by genes carried on the sex chromosomes-these genes are called sex linked.
• The Y chromosome is much shorter than the X chromosome and contains only a few genes (50 million bp; 78 genes)
• The X chromosome is longer and contains many genes not present on the Y chromosomes (153 million bp ; ~ 2,000 genes)
• Hence, sex-linked conditions are usually X-linked - as very few genes exist on the shorter Y chromosome

Haemophilia is well known example of a sex-linked disease, patients with haemophilia have blood which clots extremely slow due
to the absence of a protein blood-clotting factor (VII).
As a result, injury can result in prolonged bleeding which, if left untreated, is potentially fatal.
• There is a gene found on the X chromosome that codes for a protein called factor VIII. Factor VIII is needed to make blood clot

• There are two alleles for factor VIII, the dominant F allele which codes for normal factor VIII and the recessive f allele which
results in a lack of factor VIII

• When a person possesses only the recessive allele f, they don’t produce factor VIII and their blood can’t clot normally

• The genetic diagram below shows how two parents with normal factor VIII can have offspring with haemophilia
• Parental phenotypes: carrier female x normal male
• Parental genotypes: XFXf XFY
• Parental gametes: XF or Xf XF or Y
• The gene which is responsible for manufacturing the photoreceptor proteins of the eye, are found on the X chromosome
• The photoreceptor proteins are made in the cone cells of the eye and detect the specific wavelengths of light entering the eye
• Red-green color blindness is caused by a recessive allele of this gene
• Males are more likely to be red-green color blind as they only posses 1 allele for the gene, whereas females have 2 alleles and
need to inherit 1 faulty allele from both parents to be color blind
 Genetic Modifcation and biotechnology
• Gel electrophoresis is used to separate proteins or fragments of DNA according to size. Its a technique used widely in the analysis of DNA, RNA,
and proteins
• During electrophoresis, the molecules are separated with an electric current according to their size or mass and their net charge
• This separation occurs because of:
• The electrical charge molecules carry:
• Positively charged molecules will move towards the cathode (negative pole), whereas negatively charged molecules will move
towards the anode (positive pole) e.g. DNA is negatively charged due to the phosphate groups and thus, when placed in an electric
current, the molecules move towards the anode
• The different sizes of the molecules:
• Different sized molecules move through the gel at different rates. The tiny pores in the gel result in smaller
molecules moving quickly, whereas larger molecules move slowly
• The type of gel:
• Different gels have different sized pores that affect the speed at which the molecules can move through the gel mostly they use
agarose (polysaccharide from seaweed and allow DNA fragments travel within it)
• Gel electrophoresis to separate DNA:
1. DNA can be collected from almost anywhere on the body, e.g. the root of a hair or saliva from a cup. After collection, DNA
must be prepared for gel electrophoresis so that the DNA can be sequenced or analyzed for genetic profiling (fingerprinting)
2. To prepare the fragments, scientists must first increase (amplify) the number of DNA molecules by the Polymerase Chain
Reaction (PCR)
3. Then restriction (DNA-cutting) enzymes are used to chop the DNA into fragments (unless the samples are clones, we will get
different sizes of DNA fragments from the 2 samples)
3. Create an agarose gel plate in a tank
4. Submerge the gel in an electrolyte solution (a salt solution that conducts electricity) in the tank
5. Load (insert) the DNA fragments into the wells using a micropipette
6. Apply an electrical current to the tank.
The negative electrode must be connected to the end of the plate with the wells as the DNA fragments will then move towards
the anode (positive pole) due to the attraction between the negatively charged phosphates of DNA and the anode
• DNA fragments with a smaller mass (i.e. shorter DNA fragments) will move faster and further from the wells than the larger
fragments
• The fragments are not visible so we can stain the gel itself and view it under UV light
• Or transfer the tank it onto absorbent paper or nitrocellulose which is then heated to separate the two DNA strands
• Or to develop a visual output, we can either:
• A radioactive label (e.g. a phosphorus isotope), which causes the fragments to emit radiation that makes the X-ray film go
dark, creating a pattern of dark bands
• A fluorescent stain or dye which fluoresces (shines) when exposed to ultraviolet (UV) light, creating a pattern of colored
bands
 Polymerase Chain Reaction (PCR)
• Polymerase Chain Reaction (PCR) is a common molecular biology technique used in most applications of gene technology to amplify small
amount of DNA.
• For example, it is used in DNA profiling (forensic investigations, determining paternity) or genetic engineering
• In the COVID-19 pandemic, PCR has been used in routine diagnostic testing to amplify small amounts of viral RNA
• It can be described as the in vitro method of DNA amplification
• It is used to produce large quantities of specific fragments of DNA or RNA from very small quantities (even just one molecule of DNA or RNA)
• Using PCR, scientists can produce billions of identical copies of the DNA or RNA samples within a few hours, these can then be used for analysis
• PCR is not used to copy the entire set of DNA molecules in a sample such as blood or semen. Instead, PCR is used to copy specific DNA
sequences.
• A sequence is selected for copying by using a primer that binds to the start of the desired sequence. The primer binds by complementary base
pairing ( without a primer, DNA polymerase cannot copy the DNA).
• The Requirements Of PCR
• The target DNA or RNA that is being amplified. It's important that the whole genome is not required to be copied - only
specific sections that vary from one individual to another
• These sections are identified by adding a primer sequence that binds to them
• DNA polymerase - the enzyme used to build the new DNA or RNA strand. The most used polymerase is Taq polymerase as
it comes from a bacteria that lives in hot springs. This means it does not denature at the high temperature involved during
the first stage of the PCR reaction
• Free nucleotides - used in the construction of the DNA or RNA strands
• Buffer solution - to provide the optimum pH for the reactions to occur in
• The Key Stages Of PCR
• The PCR process involves three key stages per cycle
• Denaturation – the double-stranded DNA is heated to 95°C which breaks the hydrogen bonds that bond the two DNA
strands together
• Annealing – the temperature is decreased to between 50 - 60°C so that primers can anneal to the ends of the single
strands of DNA
• Elongation / Extension – the temperature is increased to 72°C for at least a minute, as this is the optimum temperature
for Taq polymerase to build the complementary strands of DNA to produce the new identical double-stranded DNA
molecules
• Each whole cycle takes a few minutes, so 30 cycles can take just a few hours and can generate 231 (over 1 billion) copies of a
gene from a single DNA molecule, by exponential amplification
 DNA profiling
• DNA profiling (genetic fingerprinting) enables scientists to identify suspects for a crime and identify corpses
• To create a DNA profile from the DNA being tested scientists complete the following in sequence:
• Obtain the DNA, which can be extracted from the root of a hair, a spot of blood, semen or saliva
• Increase the quantity of DNA by using PCR to produce large quantities of the required fragment of DNA from very small
samples (even just one molecule of DNA or RNA).
• Use restriction endonucleases to cut the amplified DNA molecules into fragments
• Separate the fragments using gel electrophoresis
• X-ray images are produced, or UV light is used to produce images of the fluorescent labels glowing
• These images contain patterns of bands (the DNA profile) which are then analyses and compared to see which band are
the same and which are different.
 Genetic Modification
• Genetic modification is a term usually used to refer to the transfer of DNA sequences from one species to another
• The key feature of the genetic code that makes this possible is that it is universal, meaning that almost every organism uses the
same four nitrogenous bases – A, T, C & G.
• So, when genes are transferred between species, the amino acid sequence translated from them is unchanged – the same
polypeptide is produced.
• Thus, scientists have been able to change an organism's DNA artificially by combining lengths of nucleotides from different
sources
• DNA that has been introduced into the genome of another organism is called recombinant DNA (rDNA)
• Any organism that has introduced genetic material is a genetically modified organism (GMO)
 Recombinant DNA
• This form of genetic modification involves the transfer of fragments of DNA from one organism/species into
another organism/species
• The resulting genetically modified organism will then contain recombinant DNA and will be a Genetically Modified
Organism (GMO)
• Example
• A gene from the bacterium Bacillus codes for a toxin that has insecticide properties
• This gene has useful properties in commercial maize plants, so has been transferred into maize plants to make them less
susceptible to insect pests, improving agricultural productivity as a result
• Genes can be transferred from one species to another by a variety of techniques. Together
these techniques are known as genetic engineering. Gene transfer to bacteria usually involves
plasmids, restriction enzymes and DNA ligase.

1. Identification of the DNA fragment or gene

2. Isolation of the desired DNA fragment either using restriction endonucleases (cutting
the insulin gene) or using reverse transcriptase ( after extracting the mRNA responsible
to produce insulin)
3. Mark the desired genes that can be tracked (such as green fluorescent protein which
fluoresces under UV light
4. Multiplication of the DNA fragment (using polymerase chain reaction - PCR)
5. Cut the plasmid using restriction endonucleases enzyme
6. Transfer cDNA into the vector (plasmids, viruses)
7. Plasmid and cDNA fuse together using DNA ligase
8. Recombinant plasmid introduced into host cells
9. Multiply in a fermenter and purify the human insulin
• Geneticists need the following 'tools' to modify an organism:
• Enzyme
• Restriction endonucleases - used to cut genes at specific base sequences (restriction sites). Different restriction enzymes
cut at different restriction sites which create sticky ends
• Ligase -used to join the cut ends of DNA by forming covalent bonds ( sugar-phosphate bonds) and sealing up nicks where
fragments have not quite been joined firmly with covalent bonds
• Reverse transcriptase - used to build double-stranded DNA from single-stranded mRNA. This DNA is
called cDNA (complementary DNA)
• Vectors - Plasmids - transfer DNA into bacteria or yeast
• Markers - genes that code for identifiable substances that can be tracked
H.W Risk and benefit of GM crops
 Clones
• The production of genetically identical organisms is called cloning, and a group of genetically identical organisms is called a
clone
• A cloned cell is a cell that is genetically identical to the cell that it originated from
• Sexual reproduction produces a zygote when gametes fuse
• In a single birth, this zygote is not cloned and will itself reproduce sexually as an adult
• Identical twins are clones of each other as they are formed from one zygote splitting into two parts, which each develops
into an embryo.
• Identical twins are not identical in all their characteristics and have, for example, different fingerprints. Better term for
them is monozygotic
• Clones can form naturally and artificially.
• Other organisms are manipulated to form multiple clones when grown commercially eg. large-scale growth of crop plants, to
ensure a uniform crop and good crop yields
 Natural methods of cloning
• Many plant species and some animal species have natural methods of cloning
• Some small animals reproduce asexually by budding like Hydra.
• The other naturally occurring incidence of cloning in animals is identical twins
• Natural Cloning In Plant. Many methods of cloning do not require seeds as it is not sexual reproduction that is occurring, it
is asexual reproduction
• A well as runners, plants can propagate asexually using tubers, rhizomes and bulbs.
• All modes of natural plant cloning contain modified stems that can generate meristem tissue
• Potato tubers are swollen modified roots that form eyes on their surface
• Eyes can sprout new growth
• The starch stored in the tuber fuels the early growth of the new plant
• Ginger forms rhizomes, a modified stem that grows horizontally underground
• New growth stems from nodes in the rhizome, forming new stems and adventitious roots
• The section used in cookery is the rhizome
• Onions and garlic form bulbs that can grow adventitious roots underground and leafy shoots above ground
 Cloning animal embryos
• Animals can be cloned at the embryo stage by breaking up the embryo into more than one group of cells using a glass rod.
• The process of embryo splitting, or fragmentation produces offspring that are clones of each other but not of their parents
• At an early stage of development all cells in an animal embryo are pluripotent (capable of developing into all types of tissue). It
is therefore theoretically possible for the embryo to divide into two or more parts and each part to develop into a separate
individual with all body parts. This process is called splitting or fragmentation.
• Formation of identical twins could be regarded as cloning by splitting, but most animal species do not appear to do this
naturally. However, it is possible to break up animal embryos artificially and, in some cases, the separated parts develop into
multiple embryos.
• In livestock, an egg can be fertilized in vitro and allowed to develop into a multicellular embryo. Individual cells can be
separated from the embryo while they are still pluripotent and transplanted into surrogate mothers.
• Only a limited number of clones can be obtained this way, because after a certain number of divisions the embryo cells are no
longer pluripotent. Splitting of embryos is usually most successful at the eight-cell stage.
• There has been little interest in this method of artificial cloning because at the embryo stage it is not possible to assess
whether a new individual produced by sexual reproduction has desirable characteristics.
 Cloning using differentiated cells
• It is relatively easy to clone animal embryos, but at that stage it is impossible to know whether the embryos will have desirable
characteristics.
• Once the embryos have grown into adults it is easy to assess their characteristics, but it is much more difficult to clone them.
This is because the cells that make up the body of an adult animal are differentiated.
• Pluripotent cells can develop into any specialized cell, but it is difficult to predict whether, once differentiated, they will display
desirable characteristics
• Methods have been developed for cloning adult animals using differentiated cells
• It would be desirable to clone a differentiated cell because by then it would be easy to assess the organism's characteristics
and whether any of its traits were desirable enough to clone
• Differentiated cells are more difficult to clone because certain genes have been permanently switched off (those genes will
never be transcribed again) as the cell has developed its specialized role
• Cloning using differentiated cells proved to be much more difficult in mammals. The first cloned mammal was Dolly the sheep
in 1996
• This is the method made famous by Dolly the sheep, cloned in Edinburgh, UK in 1996
• Its full name is Somatic Cell Nuclear Transfer (SCNT). Dolly made headlines as being the first livestock animal to be created
from a clone
• Three separate animals are required:
• The animal being cloned (by donating a cell)
• The female to donate an egg cell
• The surrogate mother
• How the procedure is carried out:
• The animal to be cloned donates a somatic (body) cell. In Dolly's case, this was an udder cell (mammary gland)
• The egg cell is extracted from the egg donor and enucleated (its nucleus is removed by suction and discarded)
• The nucleus from the udder cell is injected into the enucleated egg cell
• The hybrid zygote cell is now treated to encourage it to divide by mitosis by electrical shocks
• The embryo is implanted into the surrogate mother for gestation and birth