LECTURE 2: CHROMOSOMES MITOSIS AND
Before a cell enters mitosis (divides) it undergoes a period of growth called interphase. 90% of a cells time in the
normal cellular cycle may be spent in interphase. The cell may appear to be dormant, however, biochemical activity
is high during interphase.
The genetic material exists as chromatin. The structure of chromatin during interphase is optimised to allow easy
access of transcription and DNA repair factor to the DNA. Not tightly coiled. Different levels of packing on various
regions of the same chromosome.
• Euchromatin: loosely packed region on chromatin, active transcription.
• Heterochromatin: densely packed region on chromatin, inactivated.
Stages of interphase:
• G 1hase (first gap): the period prior to the synthesis of DNA. For many cells, this phase is the major period
of cell growth during its lifespan. New organelles are being synthesised, so the cell requires both structural
proteins and enzymes, resulting in a great amount of protein synthesis and a high rate of metabolism in the
cell. The DNA in a G 1iploid eukaryotic cell is 2n (2 sets of chromosomes present).
• G 0hase: A cell may pause in the G ph1se before entering the S phase and enter a state of dormancy call
the G 0hase. Cells exist in a quiescent (non-dividing) state but can re-enter the cycle at G1. Some cell types
(liver and kidney) enter the G0phase semi-permanently and can be induced to begin dividing again only
under very specific circumstances. Other types of cells, such as epithelial cells, continue to divide throughout
an organism’s life and rarely enter G 0
• Restriction (R) point: present at the end of G 1hase. Depending on levels of nutrients, energy and external
factors, cells must decide to enter the cell cycle or move into G phase.
• S phase: the period during which DNA is synthesised/replicated. The
goal of this phase is to create exactly 2 identical semi-conserved
chromosomes. Damage to DNA is detected and fixed during S-phase.
Each chromosome now consists of 2 sister chromatids. The amount of
DNA in the cell has doubled but the cell is still 2n, there are still 2 sets
• G 2hase: final suphase of interphase in the cell cycle preceding
mitosis. Rapid cell growth and protein synthesis. Microtubules, proteins
required for mitosis, are produced. Although chrmosomes have been replicated they cannot yet be
dstinguished individually because they are still in the form of loosely packed chromatin.
• G 2heckpoint: second checkpoint. Serve to preent the cell from entering mitosis with genomic DNA
damage. If this checkpoint is passed, the cell initates the many molecular processes that signal the beginning
One diploid cell divides to form 2 diploid cells that are identical
to the parent cell. Mitosis is divided into 4 stages:
• Prophase: nucleolus in the nucleus disappears. The
chromatin condenses into double rod-shaped structures
called chromosomes in which the chromatin becomes
visible. The centrosomes move to opposite poles of the cell, forming a bridge of spindle fibres. • Prometaphase: nuclear membrane breaks apart. Microtubules emerging from the centrosomes at the poles
of the spindle reach the chromosomes, now highly condensed. At the centromere region, each sister
chromatid has a protein structure called a kinetochore. Other spindle microtubules make contact with
microtubules coming from opposite pole. Proteins associated with spindle microtubules move the
chromosomes toward the centre of the cell.
• Metaphase: chromosomes align in the middle of the cell. The centromeres of the chromosomes convene
themselves on the metaphase plate. Chromosomes are condensed and highly coiled in metaphase which
makes them most suitable for visual analysis. Used to make karyotypes.
• Spindle checkpoint: This checkpoint monitors the interaction between improperly connected kinetochores
and spindle microtubules, and is maintained until kinetochores are properly attached to the spindle. Another
regulator of checkpoint activation is kinetochore tension. When kinetochores are properly attached to
opposite spindle poles, forces in the mitotic spindle generate tension. If activated, the spindle checkpoint
blocks anaphase entry. Correct orientation of sister chromatids deactivates the checkpoint
• Anaphase: Chromosomes move to opposite poles of the cell. Anaphase is initiated by a protease known as
separase which cleaves cohesin, a protein responsible for holding sister chromatids together. While the
chromosomes are drawn to each side of the cell, the non-kinetochore spindle fibre lengthen and elongate
• Telophase: Two daughter nuclei form in the cell. The nuclear envelopes of the daughter cells are formed
from the fragments of the nuclear envelope of the parent cell. The nucleoli reappear. The chromosomes also
unwind back into loose chromatin
• Cytokinesis: The cleavage furrow is the indentation of the cell's surface that begins the progression of
cleavage. During cellular cleavage, the contractile ring (formed by actin and myosin filaments) tightens
around the cytoplasm of the cell until the cytoplasm is pinched into two daughter cells
Human cells are genetically programmed to divide about 50-80 times. This limit allows growth to adulthood, and
repairs such as wound healing. Replicative exhausted cells undergo senescence, which is a cell cycle arrested state.
They secrete proinflammatory factors to mediate their clearance from the body (macrophages). Alterations in this
program can lead to genetic disorders (premature ageing) or to cancer. Cancer is a disease of the cell cycle.
A form of cell division that produces 4 haploid cells containing only 1 copy (paternal or maternal)
of each chromosome. Meiosis produces 4 haploid cells (n). in humans the haploid number is 23.
• Meiosis I: gametes receive random combinations of maternal and paternal chromosomes
(creates genetic diversity). Result of meiosis 1. Members of a pair of homologous
chromosomes physically associate at this time each chromosome consists of 2 sister
chromatids joined by a common centromere.
• Crossing over: occurs which increases the genetic diversity in the gametes. Occurs
during prophase. Matching regions on matching chromosomes (chromatids) break
and then reconnect to the other chromosome.
• Difference to mitosis: maternal and paternal homologous chromosomes pair
during metaphase in meiosis 1.
• Independent assortment: metaphase homologous chromosomes align in the
middle and then anaphase chromosome pairs independently separate from each other.
• Meiosis II:
• Metaphase II: unpaired chromosomes align at the cell’s middle. There is no synthesis of
chromosomes before meiosis II. Therefore, only the remaining on replicated chromosome.
• Anaphase II: centromeres divide and daughter chromosomes move to opposite poles. STRUCTURE OF CHROMOSOMES
Chromatid: one strand of a duplicated
chromosome. Joined by a centromere to its sister
Sister chromatids: 2 chromatids joined by a
common centromere. Each carries identical genetic
Centromere: region of a chromosome to which
microtubule fibres attach during cell division.
Centromere location gives a chromosome its
Homologous chromosomes: maternal and paternal with identical gene loci
(but often different alleles). They physically pair during meiosis. LECTURE 3: GENE INHERITANCE AND TRANSMISSION
MENDELS BREEDING EXPERIMENTS
1856: performed hybridisation experiments of pea plants. Easy to grow and cross-
breed experimentally. Reproduces well and grows to maturity in a season. Mendel
created “pure breeding” strains for various traits.
A Punnett square shows how the traits are inherited (A=dominant trait, a=recessive
Monohybrid cross: comparing 1 trait. 3:1 ratio between dominant and recessive.
Dihybrid cross: comparing 2 traits. 9:3:3:1
FORKED LINE METHOD
Relies on the simple application of the laws of probability established for the
dihybrid cross. Each gene pair is assumed to behave independently during gamete
A male having genotype AaBBCc mates with a female having genotype aaBbCc.
What are the expected genotype frequencies of their offspring?
P = AaBBCc x aaBbCc
The first step is to decompose the trihybrid cross into its constituent single-gene
(monohybrid) crosses: Aa x aa BB x Bb Cc x Cc
Determine the expected genotype frequencies for these monohybrid crosses. You
can use the Punnett square.
Pair every genotype from the first monohybrid cross with every genotype from the second cross with every genotype
from the third.
Now we traverse each path
through the forked lines, one
path at a time, in order to
determine each trihybrid
genotype and frequency PROBABILITY METHOD
The most flexible and applicable method. A dihybrid cross is a situation in which two monohybrid crosses are
involved and problems can sometimes be more easily solved by considering the two crosses independently (if the
loci are unlinked) and then combining the results. The same principal applies; no matter how many gene loci are
involved. There are two rules of probability you need to understand – Multiplication and Addition. CHI-SQUARED TEST
In experiments, deviations from expected results can be obtained.
The chi-square test converts deviations from expected values into a
measure of the occurrence of the result by chance. A judgement can then
be made as to whether we accept or reject the deviation as being
significant. We therefore have a means of testing the validity of a
hypothesis that formed the basis for an experiment. The point of the Chi-
square test is to either reject or accept our null hypothesis.
1. State the hypothesis being tested and the predicted results
2. Determine the expected numbers for each observational class
3. Calculate chi-squared using the formula
4. Determine degrees of freedom
5. Use the chi-square distribution table to determine
significance of the value. Locate the value closest to your
calculated χ on the degrees of freedom df row. Move
up the column to determine the p value.
6. State your conclusion in terms of your hypothesis. If
p>0.05 accept null hypothesis, if p<005 reject null
Degrees of freedom (df): number of possible outcomes minus 1.
Eg. Flipping a coin df=2-1=1
Probability values (p): 95% sure of accepting or rejecting the null hypothesis. Probability value.
When we assume data will fit a given ratio we establish a null hypothesis (H )0
The null hypothesis assumes there is no real difference between measured values and the predicted values. Any
difference can be attributed purely to chance. WEEK TWO
LECTURE 4: PEDIGREE ANALYSIS
A pedigree analysis follows the inheritance of a trait through a family. Used to establish how a trait is inherited and
to determine the risk of having an affected child. Pedigrees constructed using info from: medical records, interviews,
photographs and family records.
Pedigree: a diagram showing genetic information from a family which uses standardised symbols. Has 2 goals:
• To determine whether the trait has a dominant or a recessive pattern of inheritance.
• To discover whether the gene in question is located on a sex chromosome (X or Y) or on an autosome.
Patterns of inheritance can be se to predict genetic risk for pregnancy outcomes, adult-onset disorders and
recurrence risk of future offspring.
PATTERNS OF INHERITANCE
Genetic disorders can be inherited in a number of different ways.
Males pass an X chromosome to all of their daughters but none of their sons.
Females pass an X chromosome to all of their children. Most genes on the X
chromosome are not on the Y chromosome.
X-linked: pattern of inheritance that results from genes located on the X
Y-linked: pattern of inheritance that results from genes located only on the Y
Hemizygous genes: A gene present on the X chromosome that is expressed
in males in both the recessive and dominant condition. Or a gene present
only in one copy in a diploid organism (most of the X chromosome genes in a
male human). X-linked recessive traits affect males more than females
because males are hemizygous for genes on the X chromosome.
Autosomal recessive inheritance:
• All children of both affected parents are affected
• Most affected individuals have unaffected parent
• About ¼ children in large affected families show the trait
• Both sexes affected in approximately equal numbers
• The risk of an affected child with heterozygous parents is
• For rare traits, most affected individuals have unaffected parents.
Autosomal dominant inheritance
• 2 affected individuals can have an unaffected child.
• About ½ of children of an affected parent are affected.
• Both sexes equally affected.
• Every affected individual has at least one affected parent
(except in traits with high mutation rates or incomplete
penetrance). • If an affected individual is heterozygous and has an unaffected mate, each child has a 50% chance of being
X-linked dominant inheritance
• Affected males produce all affected daughters and no affected sons.
• A heterozygous affected female will transmit the trait to half of her
children. (sons and daughters equally affects).
• On average, twice as many daughters as sons are affected.
X-linked recessive inheritance
• Affected males receive the mutant allele from their mother and
transmit it to all of their daughters, but not their sons.
• Daughters of affected males are usually heterozygous.
• Sons of heterozygous females have a 50% chance of being affected.
• Hemizygous males are affected and transmit the mutant allele to all
their daughters who become carriers.
• Phenotypic expression much more common in males.
• Only males have Y chromosomes. Males are hemizygous for genes on the Y
• Genes on the Y chromosome are passed directly from father to son. All sons of
affected males are affected.
• All Y-linked genes are expressed.
Non-Mendelian pattern of inheritance observed in traits controlled by mitochondrial genes
Mitochondria: cytoplasmic organelles that convert energy from food into ATP. Carry DNA
for 37 mitochondrial genes. Genetic disorders in mitochondrial DNA are associated with
defects in energy conversion.
The egg provides all the mitochondria to the zygote. The sperm does not pass on any
mitochondria. Hence we have all our mother’s mitochondrial DNA. All siblings in a family
will have the same mitochondrial DNA.
VARIATIONS IN GENE EXPRESSION
Variations in gene expression affect pedigree analysis and assignment of genotypes to members of the pedigree.
Factors can affect gene expression:
• Interactions with other genes in the genotype
• Interaction between genes and the environment.
Huntington disease: an autosomal dominant disorder associated with progressive neural degeneration and
dementia. Adult onset is followed by death in 10 to 15 years.
Porphyria: an autosomal dominant disorder that leads to intermittent attacks of pain and dementia. Symptoms first
appear in adulthood.
Expressivity: the range of phenotypic variation associated with a given phenotype.
Penetrance: the probability that a disease phenotype will appear
when a disease-related genotype is present.
• Incomplete penetrance
• Camptodactyly: a dominant trait (immobile, bent little
fingers) with variable expression and incomplete
ONLINE MENDELIAN INHERITANCE IN MAN (OMIM)
Genetic traits are described, catalogued and numbered in a database. LECTURE 5: EXTENSIONS OF MENDELIAN GENETICS
Mutations occur giving rise to new forms of alleles that may become lethal mutations
Dominant lethal: allele that causes death of the organism, whether homozygous or
heterozygous for the allele. Rarely detected due to their rapid elimination from
populations. Eg. Huntington’s disease but as onset is slow allele can be passed on.
Recessive lethal: allele that is lethal when homozygous. In heterozygous, a lethal allele is
masked by the presence of an allele for “wild type”.
INCOMPLETE DOMINANCE (PARTIAL)
Both alleles blend their effects. The phenotype of the heterozygote lies somewhere
between those of the 2 kinds of homozygotes. The F generation shows only 1 pair of
alleles determines the phenotype. However, phenotype ratio is identical to genotype
ratio and not 3:1 like complete dominance.
Tay-Sachs disease: individuals who are homozygous for this recessive disorder are
severely affected with a lipid storage disease that is fatal within the first 3 years of life.
Neither allele is recessive so different symbols are used.
Both alleles show their effects and do not blend. In codominance, neither allele
is dominant and both are expressed. A cross between organism with 2 different
phenotypes produces offspring which has both phenotypes of the parental traits
The MN blood group: in humans, 2 forms of a glycoprotein exist on the surface
of RBCs (M and N). An individual may exhibit either one or both.
Many genes have more than 2 alternative alleles. This increases
the number of different genotypes and phenotypes that exist
with respect to the particular gene. Multiple alleles can only be
studied in populations. An individual diploid organism will only
have at most 2 alternative forms of the same gene and a
population will show all the alternatives.
ABO blood groups: 3 alternative alleles of one gene, presence of
antigens of the surface of RBCs. 4 phenotypes depending on the
presence or absence of antigens.
Bombay phenotype: Bombay cells can’t be converted to group A or B due to a mutation in the
FUT1 gene which prevents synthesis of H substance, vital for producing functional A and B
antigens. So individual may have I or I alleles
but neither is added to the cell surface and they
are functionally type O.
A form of gene interaction in which one gene
masks the phenotypic expression of another. There are no new
phenotypes produced by this type of gene interaction. The alleles that
are masking the effect are called epistatic alleles. The alleles whose
effect is being altered or suppressed are called the hypostatic alleles. PLEIOTROPY
Occurs when 1 gene influences multiple phenotypic traits. The gene codes for a
product that is used by various cells or has a signalling function on various targets. A
mutation in a pleiotropic gene may have an effect on some or all traits
Phenylketonuria (PKU): symptoms include mental retardation, reduced hair and skin
pigmentation. Caused by any of over 400 mutations in a single gene that codes for the
enzyme phenylalanine hydroxylase, which converts the amino acid phenylalanine to
Antagonistic pleiotropy: the expression of a gene resulting in multiple competing effects, some beneficial but others
detrimental to the organism. Eg. Some genes responsible for increased fitness in younger years contribute to
decreased fitness later in life or the p53 gene which suppresses cancer but also suppresses stem cells which
replenish worn out tissue.
Single phenotype or genetic disorder may be caused by any one of a multiple number of alleles or non-allele (locus)
• Allelic heterogeneity: different mutations within a single gene locus (forming multiple alleles of that gene)
cause the same phenotypic expression. Eg. 1000 known mutant alleles of the CFTR gene that cause cystic
• Locus heterogeneity: variations in completely unrelated gene loci cause a single disorder. Ed. Retinitis
pigmentosa has autosomal dominant, autosomal recessive and X-linked origins.
The probability of a gene or genetic trait being expressed.
• Complete penetrance: the gene or genes for a trait are expressed in all the population who have the genes.
• Incomplete penetrance: the genetic trait is expressed in only part of the population
Penetrance can be difficult to determine reliably. Eg. In disease the onset of symptoms could be age related or
affected by environmental codeterminants such as nutrition and smoking, as well as genetic cofactors.
Refers to variations in a phenotype among individuals carrying a particular genotype. Eg. Drosophila flies
homozygous for recessive mutant gene eyeless exhibit range of phenotypes from normal eyes to complete
absence of one or both eyes.
Other genes or environmental factors such as nutrition and temperature may be influencing or modifying
A phenomenon where by the symptoms of a genetic disorder exhibit an earlier age of onset and are more severe as
it is passed on to the next generation. Eg. Huntington’s disease – trinucleotide repeat disease.
Mosaicism: the presence of 2 or more populations of cells with different genotypes in one individual who has
developed from a single fertilized egg.
Germline mosaicism: a special form of mosaicism where some gametes (sperm or oocytes) carry a mutation but the
rest are normal. Cause is usually a mutation that occurred in an early stem cell that gave rise to the gonadal tissue. This can cause only some offspring to be affected, even for a dominant disease.
An individual whose phenotype under a particular
environmental condition, is identical to the one of another
individual whose phenotype is determined by the genotype. The
phenocopy environmental condition mimics the phenotype
produced by a gene.
Occurs when offspring receives 2 copies of a chromosome, or part of a chromosome, from one parent and no copies
from the other parent. Most occurrences result in no phenotypical anomalies. If the event happens during meiosis II,
the genotype may include identical copies of the uniparental chromosome (isodisomy), leading to the manifestation
of rare recessive disorders. Eg. Prader-Willi syndrome and Angelman syndrome
Normally there is no difference of expression of the paternal and maternal alleles.
Genomic imprinting causes selective expression of a gene or genes inherited from 1 parent. Not a mutation or
permanent change. Plays a role in several genetic disorders.
Eg. The same region of chromosome 15 mutated but cases a different disease if inherited from mother or father.
• Prader-Willi syndrome: paternal copy
• Angelman syndrome: maternal copy.
2 or more genes located on the same chromosome that do not show independent assortment and
tend to be inherited together. In a given cross, the outcome depends on how the alleles are arranged
on the chromosome.
Example: a fly that is heterozygous for long wings (Ll) and heterozygous for long aristae (Aa) is
crossed with another fly of the same type. AaLl x AaLl. In both cases the dominant alleles are located
on the same chromosome.
Example: a fly that is heterozygous for long wings (Ll) and heterozygous for long aristae (Aa) is
crossed with another fly of the same type. AaLl x AaLl. In both cases the dominant alleles are located
on separate chromosomes.
The frequency of the genes exchanging during meiosis determines how far apart the alleles are on a
chromosome. Alleles that are close together tend to stick together.
Map units (MU): the distance between alleles. The long wing allele is 13MU from the aristae allele. CONTINUOUS VARIATION
Some traits are controlled by 2 or more genes. Phenotypes can be discontinuous or continuous.
Discontinuous variation: shows distinct (discrete) phenotypes. Eg. Pea plant colour, ABO blood group.
Continuous variation: shows a series of overlapping phenotypic classes. Eg. Height, weight, hand span, milk yield.
HOW ARE TRAITES DEFINED
Polygenic traits: traits controlled by 2 or more genes. Patterns of inheritance that can be measured quantitatively.
• Eg. Human eye colour.
Multifactorial traits: polygenic traits resulting from interactions of 2 or more genes and 1 or more environmental
• Eg. Skin colour controlled by 3 or 4 genes and environmental factors
Complex traits: traits controlled by multiple genes and the interaction of environmental
factors where the contributions of genes and environment are undefined. Many human
diseases are controlled by the action of several genes.
• Eg. Hypertension, obesity, cardiovascular disease, depression, autism. LECTURE 6: SEX DETERMINATION
The mechanisms of sex determination vary from
species to species.
• Primary: gonads, where gametes are
• Secondary: appearance of organism,
including sexual characteristics.
Unisexual, dioecious and gonochroic: individuals
with male or female reproductive organs.
Bisexual, monoecious and hermaphroditic:
individuals with male and female reproductive
organs. Produce eggs and sperm.
Males develop from unfertilised eggs and are
Females develop from fertilised eggs and are
Determines the sex in all members of the insect order (Hymenoptera-bees, ants
and wasps and the Thysanoptera)
Honey bees: drones (males) are entirely derived from the queen, their mother.
The diploid queen has 32 chromosomes and the haploid drones have 16
chromosomes. The queen stores sperm in an internal sac called the
spermatheca. The queen controls the release of stored sperm from within the
organ. If she releases sperm as an egg passes down the oviduct, the egg is
fertilised. So the queen can modify sex ratios within colonies which increases
Relatedness: drones develop from unfertilised eggs and carry 1 copy of
chromosomes (haploid) from their mother only. Females are fertilised and carry
2 copies of chromosomes (diploid). From a queen, all the daughters will share
50% genes from the father (since they are all the same), but 25% of their genes
from the mother. The coefficient of relatedness among the offspring is therefore
0.75 (1 x 0.5 + 0.5 x 0.5). This is much higher than the 0.5 for sister-sister in a diploid
The queen bee is the only fertile female in the hive of domesticated honey bees. If
she dies the worker bees can start to lay eggs. Worker bees are unable to make and
the unfertilised eggs produces only drones (males) which can mate only with a
queen. Eventually all the worker bees die off and the new drones follow. XO SEX-DETEMINATION
There is only 1 sex chromosome, referred to as X.
• Males only have 1 X chromosome (X0) while females have 2 (XX).
Maternal gametes always contain an X chromosome, so the sex of the offspring is decided by the male. Sperm
contains either 1 X chromosome or no sex chromosome at all.
In a variant of this system, some animals are
hermaphroditic with 2 sex chromosomes (XX) and
male with only 1 (X0)
C. elegans: transparent nematode (roundworm)
about 1mm in length that lives in soil. Has 2 sexes:
hermaphrodites and males. Individuals are almost
all hermaphrodite, with males comprising 0.05% of
the total population. Hermaphrodites have a
matched pair of sex chromosomes (XX) with the
males only having 1 sex chromosome (X0). Males
only have testes. Hermaphrodites have testes and
ovaries. Eggs produced in adult stage are self-fertilised. When self-inseminated, the worm will lay approximately 300
eggs. A mating between an adult male and a hermaphrodite produces half male, half hermaphrodite offspring. When
inseminated by a male, the number of offspring can exceed 1000.
ZW SEX DETERMINATION
In the ZW system it is the ovum that determines the sex of the offspring.
• Males are the homogametic sex (ZZ)
• Females are the heterogametic sex (ZW)
The Z chromosome is larger and has more genes. Like the X chromosome in the XY system.
No genes are shared between the avian ZW and mammal XY chromosomes. Comparing
chicken and human, the Z chromosome appeared similar to the autosomal chromosome 9
XY SEX DETERMINATION
Found in humans, most mammals, some insects and some plants.
• Females are homogametic (XX)
• Males are heterogametic (XY)
The presence and absence of a Y chromosome is not the case in all
Drosophila: unlike humans the Y chromosome does not confer
maleness, rather it encodes genes necessary for making sperm. Sex
is determined by the ratio of autosomes to X chromosomes. Each
cell “decides” whether to be male or female independently of the
rest of the organism. Can create gynadromorphs.
• Normal (2X:2A) and triploid (3X:3A) females have a ratio of
1.0. If ratio >1 (more X to A) inviable metafemale produced.
• Males have a ratio of 0.5 (X0:2A males are sterile). If ratio
<0.5 (more A) then infertile metamale produced.
• If ratio in between 0.5 and 1.0 then sterile flies expressing
both sex morphologies produced.
Chromosomal sex: established at
Other aspects of sex depend on
the interaction of genes and
environmental factors, especially hormones.
Humans: the formation of male and female reproductive structures depend on
gene action and the interactions within the embryo, with other embryos in the uterus and the maternal
environment. Sex of an individual is defined at 3 levels:
• Chromosomal sex • Gonadal sex: for the first 7 or 8 weeks, the embryo is neither male nor female due to 2 undifferentiated
gonads. Both male and female reproductive duct systems develop. Genes cause gonads to develop as testes
or ovaries establishing gonadal sex. Alternative pathways can produce intermediates.
• Phenotypic sex: mutations can uncouple chromosomal sex from
phenotypic sex. A mutation in the X-linked androgen receptor gene
(AR) causes XY males to become phenotypic females. Testosterone
is produced, but not testosterone receptors therefore cells develop
The chromosomal sex of an individual (XX or XY) can differ from the
Androgen insensitivity: X-linked genetic trait that causes XY individuals to
develop into phenotypic females.
Pseudohermaphroditism: an autosomal genetic condition that causes XY individuals to develop the phenotype of
females. Caused by mutations in several different genes. Affected individuals have both male and female structures,
but at different times of life. At puberty, females change into males.
Y chromosome and testis development SRY gene.
• Sex-determining region of the Y chromosome. Located near the end of the short arm of the Y chromosome.
Plays a major role in causing the undifferentiated gonad to develop into a testis.
Before sexual differentiation, both male and female embryos have bipotential
gonads. They possess both Wolffian and Mullerian ducts. These ducts can
differentiate into male or female reproductive organs according to the hormonal
status of the foetus.
Female development: requires the absence of the Y chromosome and the presence of 2 X chromosomes. Embryonic
gonad develops as an ovary. In the absence of testosterone, the Wolffian duct system degenerates. In the absence of
MIH, the Mullerian duct system forms female reproductive system.
EXPRESSION OF THE X CHROMOSOMES
Human females have 1 X chromosome inactivated in all somatic cells to balance the expression of X-linked genes in
males and females. Females have 2 X chromosomes; males have 1 yet the amount of gene product is the same.
Dosage compensation: is a mechanism that regulates the expression of sex-linked gene products.
Barr bodies and X inactivation:
• Lyon hypothesis: dosage compensation in mammalian females. Random
inactivation of 1 X chromosome in females equalize the activity of X-linked
genes in males and females.
• Barr body: a densely staining mass in the somatic nuclei of mammalian females.
An inactivated X chromosome, tightly coiled. The number of Barr bodies is 1
less than the number of X chromosomes. • Males (46,XY) have no Barr bodies.
• Normal females (46,XX) have one Barr body
• Female with 5 X chromosomes (49,XXXXX) have 4 Barr bodies
In females, some cells express the mothers X chromosome and some cells express the father’s X chromosome.
Inactivated chromosome can come from either mother or father, occur early in development and is permanent (all
descendant of a particular cell have the same X inactivated).
Mosaic expression occurs in female mammals: eg. Calico cats are always female.
X inactivation centre: Inactivation begins and is regulated from the X inactivation centre (Xic) of the X chromosome.
Inactivation begins here. Xic contains the gene XIST which encodes an RNA that coats the inactive X and somehow
Effects of random X chromosome inactivation: random X inactivation can
cause twins with identical genotype to have different phenotypes. The
pedigree shows identical twins who are discordant for the phenotype of
colour blindness. Almost all the active X’s in the colour bind twin carry the
mutant allele, and in the non-colour blind twin, most of the active X’s carry
the normal allele. WEEK THREE
LECTURE 7: KARYOTYPES
Karyology: the study of whole sets of chromosomes
Karyotype: a complete set of chromosomes from a cell that
has been photographed during cell division and arranged in
a standard sequence. The human karyotype includes only
Used to study chromosomal aberrations, cellular function,
taxonomic relationships and to gather info about past
evolutionary events. Karyotypes reveal variations in
chromosomal structure and number. Chromosome banding
and other techniques can identify small changes in
Any nucleus can be used to make karyotype lymphocytes, skin cells, biopsies and tumour cells. Also sampling cells
• Amniocentesis: foetal skin cells come off and float in the amniotic fluid
which can be sampled, grown and analysed for chromosomes, enzymes or
• Chorionic villus sampling (CVS): method of sampling foetal chorionic cells by
inserting a catheter through the vagina or abdominal wall into the uterus.
Used in diagnosing biochemical and cytogenetic defects in the embryo.
Usually performed in the 8 or 9 week of pregnancy. The chorion is the
outermost foetal membrane and the villi are projections from this
membrane that can be sampled without harming the foetus.
PERFORMING A KARYOTYPE FROM BLOOD
• Blood is drawn from the body and treated to stop coagulation.
• Mononuclear cells (lymphocytes and monocytes) are purified from the blood by centrifugation. The purified
cells are cultured for 3-4 days in the presence of a mitogen, which stimulates the lymphocytes to proliferate.
• The cells are treated with a drug such as colcemid which disrupts mitotic spindles and prevents completion
of mitosis (and enriches the population of metaphase cells).
• Cells are harvested and treated briefly with a hypotonic solution which makes the nuclei swell osmotically.
• Swollen cells are fixed, dropped onto a microscope slide
and dried. Slides are stained to induce a banding pattern.
• The slides are scanned to identify a clear chromosome
spread, and then photographed.
• The image is cut up and rearranged in standard format. IDENTIFYING CHROMOSOMES
• Banding pattern: size and location of stained bands on chromosomes make each chromosome pair unique.
• Centromere position: centromeres are regions in chromosomes that appear as a constriction
• Metacentric: centrally places
• Submetacentric: placed closer to one end than the other
• Acrocentric: placed very close to, but not at one end
• Telocentric: placed at one end of the chromatid and hence only one
arm. Not seen in humans.
Diagram of the chromosome banding patterns. Human metaphase chromosomes contain
about 550 bands. More bands can be detected in later prophase chromosomes.
System of naming chromosome bands: allows any region to be identified by a descriptive
address (chromosome number, arm, region and band).
• p: short arm
• q: long arm
• Each arm is divided into regions with bands within the numbered region. Eg. The arrow points
to 1q2.4 (chromosome 1, long arm, region 2 and band 4).
An alpha-numerical karyotype is the designation of the chromosome constitution (46,XX), deletion
(del), duplication (dup), translocation (t), inversion (inv), short arm of chromosome (p),
long arm of chromosome (q), addition or loss of entire chromosome (+/-).
Chromosome-specific DNA probes are labelled with a fluorescent dye. Using
combinations of probes and dyes can produce unique colours for each chromosome. INFORMATION FROM A KARYOTYPE
1. Differences in absolute sizes of chromosomes: chromosomes can vary in absolute size by as much as
twenty-fold between genera of the same family.
2. Differences in the position of centromeres: this can be brought by unequal translocations, pericentric
inversion and centric fusion and fission.
3. Differences in relative size of chromosomes: can be caused by
translocations of unequal lengths.
4. Differences in basic number of chromosomes: number can change due
to a number of reasons.
• Chromosome elimination: during development
• Chromatin diminution: found in some roundworms, portions of
the chromosomes are cast away in particular cells.
• Aneuploidy: where the chromosome number in the cells is not
the typical number for the species.
• Polyploidy: more than 2 sets of chromosomes, this can be normal
for some species.
The number of chromosomes in the karyotype between (relatively) unrelated species is highly variable. Eg.
Pilosula ant males are haploid n=1 or the Ophioglossum fern has an average of 1262 chromosomes.
5. Differences in number and position of satellites: small bodies attached to
a chromosome by a thin thread of chromatin. The secondary constrictions
are always constant in their positions and can be used as markers.
6. Differences in degree and distribution of heterochromatic regions:
heterochromatin stains darker than euchromatin, indicating tighter
packing and mainly consists of genetically inactive repetitive DNA
sequences. LECTURE 8: CHROMOSOMAL ABNORMALITIES
CHANGES IN CHROMOSOMAL NUMBER
Polyploidy and aneuploidy are major causes of reproductive failure in humans.
• Polyploidy: chromosomal number that is a multiple of the normal haploid
chromosomal set. Seen only rarely in live births
• Triploidy: chromosomal number that is 3 times the haploid number,
having 3 copies of all autosomes and 3 sex chromosomes.
• Tetraploidy: chromosomal number that is 4 times the haploid number,
having 4 copies of all autosomes and 4 sex chromosomes.
• Aneuploidy: chromosomal number that is not an exact multiple of the haploid
set. The rate of aneuploidy in humans is much higher than in other primates and
mammals. Cause of aneuploidy is nondisjunction which is the failure of
homologous chromosomes to separate properly during meiosis
• Monosomy: condition in which one member of a
chromosomal pair is missing; one less than the
diploid number (2n-1).
▪ Autosomal monosomy: lethal condition
which causes spontaneous abortion.
• Trisomy: condition in which one chromosome is
present in 3 copies, and all others are diploid;
one more than the diploid number (2n+1).
Maternal age is the leading risk factor for
trisomy, by age 42 about 1/3 identified
pregnancies are trisomic.
▪ Autosomal trisomy: relatively common, most result in spontaneous abortion but four types
can result in live births (8, 13, 18, 21)
• Trisomy 13 (Patau syndrome): lethal condition (1/15,000 live births) where half die
within 1 month, average survival is 6 months. Facial malformations, eye defects,
extra digits, malformation of brain and nervous system and congenital heart defects.
• Trisomy 18 (Edwards syndrome): lethal condition (1/11,000 live births) where
survival is 2-4 months and 80% are female. Small size, slow growth, mental
retardation, clenched fists with malformed feet and heart abnormalities.
• Trisomy 21 (down syndrome): first chromosomal abnormality discovered in humans
and the only autosomal trisomy that allows survival into adulthood. 1/800 live
births. Growth and development is retarted, high rate of congenital heart defects,
leukaemia and respiratory infections. 94% of nondisjunctions occur in the mother,
6% in the father. The majority of nondisjunction events occur in meiosis I in oocytes.
▪ Most autosomal trisomy’s are lethal and up to 50% of chromosomal abnormalities in
• Sex chromosomes: involves both X and Y chromosomes. A balance is needed for normal
development with at least one copy of the X chromosome. Increasing numbers of X or Y causes
progressively greater disturbances in phenotype and behaviour. Changes in the number of sex
chromosomes have less impact than changes in the number of autosomes.
▪ Turner syndrome (monosomy of X) resulting in female sterility. Females are short and wide-
chested with rudimentary ovaries.
▪ Klinefelter syndrome: aneuploidy (XXY) 1/1000 live births. Males with some female features
that become apparent after puberty. Some have learning difficulties. Can have more severe
forms such as XXXY and XXXXY
▪ XYY syndrome: males are relatively normal, tend to be taller than average and some have
personality disorders and subnormal intelligence.
Maternal age: Meiosis I is not completed until ovulation, so eggs produced at 40 have been in meiosis I for more
than 40 years. Intracellular events of environmental agents may have damaged the cell so aneuploidy can result
when meiosis resumes at ovulation.
Maternal selection: embryo-uterine interactions that normally abort abnormal embryos become less effective. CHANGES IN CHROMOSOMAL ARRANGEMENT
• Deletions: loss of chromosomal material associated with genetic disorders.
• Cri du chat syndrome (5p-): associated with an array of congenital malformations, with most
characteristic of which is an infant cry that sounds like a cat.
• Prader-Willi syndrome
• Translocations: exchange of chromosome parts with often produces no
overt phenotypic effects and can result in genetically imbalanced and
• Robertsonian translocation: 2 acrocentric chromosomes are
joined at their centromere. Eg. Chromosome 14 and 21
resulting in Down syndrome. Someone carrying the
translocation is phenotypically normal but produces 6 types of
gametes (3-lethal, 1-DS, 1-translocation carrier and 1 normal).
Uniparental disomy (UPD): condition in which both copies of a chromosome are inherited from a single parent.
Associated with several genetic disorders such as X-linked disorders and autosomal recessive disorders (Prader-Willi
syndrome and Angelman syndrome).
Fragile sites: appear as gaps or breaks in chromsomespecific locations. One fragile site on the X chromosome is
associated with a common form of mental retardation in males.
• Fragile X is an X chromosome that carries a nonstaining gap at
band q27. LECTURE 9: DNA AND CHROMOSOME PACKAGING
STRUCTURE OF NUCLEIC ACIDS
Nucleic acids are composed of strings and
nucleotides linked together. Consists of a
phosphate group, pentose sugar (DNA or RNA) and
a nitrogen-containing base (A, G, C, T or U).
Nucleoside: base plus a sugar. Eg. Cytosine +
deoxyribose = deoxycytidine.
Nucleotide: nucleoside + phosphate. Eg. Cytidine
Polynucleotides: are directional. Nucleotides are joined together to form a
polynucleotide chain. Polynucleotide chains have slightly different structures at either
end (phosphate group at 5’ end and OH group at 3’ end). DNA is a double helix of 2
polynucleotides held together by hydrogen bonds. The 2 strands run in different
Ratios of bases: C=G and T=A, therefore pyrimidines=purines.
DNA DOUBLE HELIX
Right handed double helix structure. Two polynucleotide chains held together by
hydrogen bonding between the bases and hydrophobic interactions. Repeating substructure every 0.34 nanometers
(base stack). The 2 strands are held together by complementary base pairing. The stability of the helix is due to:
• Large number of hydrogen bonds
• GC rich DNA is more stable than AT rich DNA because the GC pair
has 3 hydrogen bonds compared to 2.
• Hydrophobic bonding (stacking forces) between bases.
There are 3 biologically active double helical structures
DNA can be negatively
supercoiled. The relaxed
form of DNA is twisted into the “biologically active” negatively
coiled structure. This state of supercoiled DNA is maintained within
the cell by a series of enzymes called topoisomerases.
If the DNA of a human cell was stretched out it would span 2
meters. At interphase the DNA is dispersed so that it can be
replicated and expressed but must be condensed into a
chromosome during cell division. CHROMATIN
The combination of DNA and proteins that make up the contents of the nucleus of a
cell. Primary functions:
• Package DNA into a smaller volume to fit in the cell
• Strengthen the DNA to allow mitosis and meiosis and prevent DNA damage
• Control gene expression and DNA replication.
The primary protein components of chromatin are histones that compact the DNA.
Histones: provide the 1 level of packaging for DNA as they compact the DNA by a
factor of approximately 7. Histone protein sequence is highly conserved among
eukaryotes. Rich in lysine and arginine. 5 main types:
• H1: attached to the nucleosome and involved in further compaction of the
DNA (conversion of 10nm chromatin to 30nm chromatin).
2 copies in each nucleosome
• H2B “histone octomer”. DNA wraps
• H4 around this structure 1.75 times.
Non-histone proteins: other proteins that are associated with the chromosomes.
Highly variable in cell types, organisms and at different times in the same cell type.
Amount of non-histone protein varies. May have role in compaction or be involved
in other functions requiring interaction with the DNA. Many are
acidic and negatively charged, bind to the histones, binding may
DNA is further compacted when the DNA nucleosomes associate
with one antoher to produce 30nm chromatin. If H1 is absent
then chromatin cathot be converted from 10 to 30nm. DNA is
condensed to 1/6 its unfolded size.
30nm 300nm: compaction continues by forming looped
domains from the 30nm chromatin which compacts the DNA to
300nm chromatin. Human chromosomes contain about 2000
looped domains. 30nm chromain is looped and attached to a
nonhistone protein scaffolding. DNA in looped domains are
attached to the nuclear matrix via DNA sequences called MARs
(matrix attachment regions).
Level of DNA compaction changes
throughout the cell cycle, most
compact during mitosis and least
compact during synthesis.
2 types of chromatin related to
level of gene expression:
• Euchromatin: areas that
Chromsomes or regions
that exhibit normal
patterns of condensation
and relaxation during the cell cycle. Usually areas where gene expression is
• Heterochromatin: areas that stain darkly. Chromosomes or regions that are condensed throughout the cell
Part of a chromosome that links sister chromatids and acts as the site of assembly of the kinetochore. Two types: • Point centromeres: very small regions of DNA capable
of genetically conferring centromeric function on any
DNA segment into which they are transferred.
• Regional centromeres: more complex. Human and
mammalian regional centromeres contain alpha
satellite DNA. 171bp sequence arranged in tandem
repeats which binds to centromere-associated
proteins. Large centromere bind 30-40 microtubules.
Sequences at the ends of eukaryotic chromosomes
which play critical roles in chromosome replication and
maintenance. Telomeres keep chromosomes protected
and prevent them from fusing into rings or binding with
The telomere DNA sequences of a variety of eukaryotes are similar, consisting of repeats of a
simple sequence DNA containing clusters of G residues on one strand. E.g. the sequence of
telomere repeats in humans and other mammals is AGGGTT, in Tetrahymena (a protozoan) it
is GGGGTT, in Arabidopsis (a plant) it is AGGGTTT.
These sequences are repeated hundreds or thousands of times, Spanning up to several
kilobases and terminate with an overhang of single stranded DNA. Telomere DNA loops back
on itself to form a circular structure that protects the ends of chromosomes.
Maintenance of telomeres appears to
be an important factor in determining
the lifespan and reproductive capacity
of cells. Progerias: accelerated ageing
diseases in humans. Somatic cells from
patients with progerias have shorter
Cancer cells up-regulate telomerase
which can prevent the telomeres from
getting shorter and even elongate
them. Telomerase is activated in
approximately 90% of tumours. WEEK FOUR
LECTURE 10: DNA REPLICATION
To carry the genomic information to daughter cells, the DNA molecule
must replicate using itself as a template.
TRITIATED THYMIDINE EXPERIMENT
Evidence for semiconservative
replication of eukaryotic chromosomes.
Labelling of DNA in bean shoots with
The labelled DNA strands in the
chromosomes is detected by
autoradiography. The second round of
DNA replication was carried out
without the radioactive isotope so the
new strands are not labelled. Note
that only one of each chromatid is
labelled, as predicted from the
semiconservative replication model.