Gene Loci

 Every chromosome consists of a long DNA molecule that contains

several hundred or even thousands of different genes coding for
different proteins
o A length of DNA that codes for a single polypeptide or protein is
called a gene
 The position of a gene on a chromosome is known as its locus (plural:
loci)
o Through experiments and genetic mapping techniques, scientists
have been able to work out the specific physical locations of the
genes on different chromosomes
o 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
 Each gene can exist in two or more different forms called alleles
 Different alleles of a gene have slightly different nucleotide sequences
but they still occupy the same position (locus) on the chromosome

Five different genes found at five different loci

Gene Linkage
 Gene loci are said to be linked if they are on the same chromosome
o Loci (singular: locus) refers to the specific linear positions on the
chromosome that genes occupy
 Linked genes located on human chromosomes 1 to 22 (i.e. any
chromosome that is not a sex chromosome, known as autosomes) are
said to be examples of autosomal linkage
 If genes are located on the same sex chromosome, they are said to
be sex-linked

Autosomal linkage
  As its name implies, autosomal linkage only occurs on the autosomes
(any chromosome that isn’t a sex chromosome)
 Two or more genes on the same autosome do not assort independently
during meiosis
 Instead, these genes are linked and they stay together in the original
parental combination
 These linked genes are passed on to offspring all together (through the
gametes)

Sex linkage

 There are two sex chromosomes: X and Y

 Females have two copies of the X chromosome (XX), whereas males
have one X chromosome and one shorter Y chromosome (XY)
 Some genes are only present on one sex chromosome and not the
other
 As the inheritance of these genes is dependent on the sex of the
individual they are known as sex-linked genes
o Most often sex-linked genes are found on the longer X
chromosome
 If the gene is on the X chromosome, males (XY) will only have one copy
of the gene, whereas females (XX) will have two
o Because males only have one X chromosome, they are much more
likely to show sex-linked recessive conditions (such as red-green
colour blindness and haemophilia)
o Females, having two copies of the X chromosome, are likely to
inherit one dominant allele that masks the effect of the recessive
allele
o A female with one recessive allele masked in this way is known as
a carrier; she doesn’t have the disease, but she has a 50% chance
of passing it on to her offspring
o If that offspring is a male, he will have the disease
 The presence of sex linkage can be identified using pedigree
diagrams and Punnett squares
o When a gene is sex-linked the phenotypes are not spread evenly
across the sexes
o In the case of a gene that causes a sex-linked disease, one sex
will be disproportionately affected
o The results of a cross between a normal male and a female who is
a carrier for colour blindness are shown below. In this cross, there
is a 25% chance of producing a male who is colourblind, a 25%
chance of producing a female carrier, a 25% chance of producing
a normal female and a 25% chance of producing a normal male
 Punnett square showing the inheritance of colourblindness, an X-linked
condition

 Working in the USA in the early 20th century, a scientist called Thomas
Hunt Morgan bred fruit flies (Drosophila melanogaster) over successive
generations
 In his cross-breeding experiments, he came across red-eyed wild types
and white-eyed mutants
 He realised there was a distinct sex bias in the phenotypic distribution of
the offspring:
o All-female offspring of a red-eyed male were red-eyed while all
male offspring of a white-eyed female were also white-eyed
 Morgan hypothesised that this occurred because the gene for eye
colour was located on a sex chromosome (i.e. it was X-linked)

Sex linkage in Drosophila. A cross between a homozygous white-eyed female

and a male with red eyes gives all white-eyed males and red-eyed female
offspring

Independent Assortment
 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)
  During meiosis, the nucleus of the original 'parent' cell undergoes two
rounds of division. These are:
o Meiosis I
o Meiosis II

Meiosis I

 The nucleus of the original 'parent' cell is diploid (2n) i.e. it contains two
sets of chromosomes
 Before meiosis I, these chromosomes replicate
 During meiosis I, the homologous pairs of chromosomes are split up, to
produce two haploid (n) nuclei
o At this point, each chromosome still consists of two chromatids
 Note that the chromosome number halves (from 2n to n) in the first
division of meiosis (meiosis I), not the second division (meiosis II)

Meiosis II

 During meiosis II, the chromatids that make up each chromosome

separate to produce four haploid (n) nuclei
o At this point, each chromosome now consists of a single
chromatid

During meiosis, one diploid nucleus divides by meiosis to produce four haploid
nuclei

 Having genetically different offspring can be advantageous for natural

selection
 Meiosis has several mechanisms that increase the genetic diversity of
gametes produced. The two main mechanisms are:
o Independent assortment
o Crossing over
 Both independent assortment and crossing over result in different
combinations of alleles in gametes
Independent assortment

 Independent assortment is the production of different combinations of

alleles in daughter cells due to the random alignment of homologous
pairs along the equator of the spindle during metaphase I of meiosis I
 The different combinations of chromosomes in daughter cells generate
an increase in the genetic variation between gametes
 In meiosis I, homologous chromosomes pair up and are pulled towards
the equator of the spindle
o Each pair can be arranged with either chromosome on top, this
is completely random
o The orientation of one homologous pair
is independent/unaffected by the orientation of any other pair
 The homologous chromosomes are then 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
 To work out the number of different possible chromosome combinations
the formula 2n can be used, where n corresponds to the number of
chromosomes in a haploid cell
 For humans, this is 223 which calculates as 8,324,608 different
combinations
Independent assortment of homologous chromosomes leads to different
genetic combinations in daughter cells

Crossing Over
 Crossing over is the process by which non-sister chromatids exchange
alleles
 Process:
o During prophase I of meiosis I homologous chromosomes pair
up and are in very close proximity to each other
o The paired chromosomes are known as bivalents
o The non-sister chromatids can cross over and get entangled
o These crossing points are called chiasmata
o The entanglement places stress on the DNA molecules
o As a result of this, a section of chromatid from one chromosome
may break and rejoin with the chromatid from the other
chromosome
  This swapping of alleles is significant as it can result in a new
combination of alleles on the two chromosomes
 There is usually at least one, if not more, chiasmata present in
each bivalent during meiosis
 Crossing over is more likely to occur further down the chromosome away
from the centromere

Crossing over of non-sister chromatids leads to the exchange of genetic

material

Gamete Specialisation
Gametes

 Gametes are the sex cells of an organism

o For example, the sperm and egg (ovum) cells in humans
 Gametes fuse during fertilisation to form a zygote
o Fertilisation is the fusion of the nuclei from a male gamete (sperm
cell) and a female gamete (egg cell)
 These sex cells are formed during meiosis and only have one copy of each
chromosome, so they are haploid cells
o For humans, that means the sperm and egg cells contain 23 single
chromosomes in their nucleus
Sexual reproduction involves the fusing of two gametes to form a zygote that
contains DNA from both parents

Mammalian gametes are specialised for their functions

 Mammalian gametes have adaptations to increase the chances of

fertilisation and successful development of an embryo
 Sperm cells:
o Have a flagellum (tail) that allows them to swim towards the egg cell
o Contain many mitochondria that provide energy for movement of
the flagellum (swimming)
o An acrosome that contains digestive enzymes to break down the
protective glycoprotein layer (a jelly-like coating known as the zona
pellucida) surrounding the egg cell - sperm cells must penetrate this
layer in order to fertilise the egg
 Egg cells:
o Are much larger than sperm cells as most of their internal space
contains food to nourish a growing embryo
o Have follicle cells that form a protective coating
o Have a jelly-like glycoprotein layer, known as the zona pellucida,
that forms an impenetrable barrier after fertilisation by a sperm cell
has occurred, to prevent other sperm nuclei from entering the egg
 These features are summarised in the diagrams and tables below
 Structure of a mammalian sperm cell

Structure of a mammalian egg cell

Adaptations of Mammalian Gametes Table

 Fertilisation in Mammals
 During sexual intercourse, semen is ejaculated high up into the vagina of the
female, near the cervix
 The sperm cells then follow a chemical trail released by the egg cell and
travel up through the cervix to reach the uterus (the womb)
 The sperm cells then travel into the oviduct containing the egg cell
 If a sperm cell meets the egg cell in the oviduct, fertilisation can occur
o This is most likely to occur 1-2 days after the female has ovulated (i.e.
released an egg cell from one of her ovaries into an oviduct)
 Fertilisation is the fusion of the nuclei from a male gamete (sperm cell) and
a female gamete (egg cell)
o During fertilisation, the head of a sperm cell
releases enzymes that digest a path through the protective outer layer
of the egg cell (the zona pellucida), allowing the sperm to pass
through the egg cell membrane
 This process is known as the acrosome reaction
o Once this occurs, the egg cell immediately releases the contents
of vesicles known as cortical granules into the space between the
egg cell membrane and the zona pellucida
o The chemicals contained within the cortical granules cause the zona
pellucida to rapidly thicken and harden, preventing any more sperm
cells from entering, ensuring only one sperm cell can fertilise the
egg cell
 This process is known as the cortical reaction
 The nucleus of the sperm cell then enters the egg and fuses with the nucleus
of the egg cell
 When the male and female gamete nuclei fuse, they become
a zygote (fertilised egg cell)
 This zygote contains the full 46 chromosomes (23 pairs of chromosomes),
half of which came from the father and half from the mother
 The zygote divides by mitosis to form two new cells, which then continue to
divide like this until an embryo is formed after a few days
 Cell division continues and eventually many of the new cells produced
become specialised to perform particular functions and form all the body
tissues of the offspring
 The process of fertilisation in mammals

Fertilisation in Flowering Plants

 Sexual reproduction in flowering plants requires the transfer of
pollen between male and female parts of flowers
 The development of flowers occurs in the reproductive stage of the plant life
cycle
 Flowers contain all the necessary organs and tissues required for sexual
reproduction by pollination
 Key structures of the flower include
o The anther - where pollen is produced
o The stigma - part of the female reproductive organ which receives the
pollen
o The ovary - where the female gametes are located
 Flowers usually contain both male and female reproductive parts
 The male reproductive parts produce pollen
 The transferal of pollen from the anther to the stigma is known
as pollination

Double fertilisation

 After pollination has occurred, the pollen grain begins to 'grow' or 'germinate'
and a pollen tube grows from the pollen grain down the style to
the ovary of the plant
 As the pollen tube grows towards the ovary, two haploid male nuclei move
down the tube
o These are known as the pollen tube nucleus and the generative
nucleus
 At some point, as it travels down the pollen tube, the generative
nucleus divides by mitosis to form a further two haploid male nuclei
o These are the male gametes
o The two haploid male nuclei travel down the pollen tube towards the
female ovule
 As the pollen tube reaches the ovule, the pollen tube nucleus breaks
down and the two haploid male nuclei pass into the ovule so
that fertilisation can occur
 In fact, a process known as double fertilisation occurs:
o One haploid male nucleus fuses with the nucleus of the egg cell to form
a diploid zygote
o The other haploid male nucleus fuses with two polar nuclei present in
the ovule to form a triploid endosperm nucleus, which will form
the endosperm (the food supply for the embryo plant when it begins to
germinate)
The process of double fertilisation in plants, in which one male nucleus fuses
with the two polar nuclei to form the triploid endosperm nucleus and the other
fuses with the egg cell to form the diploid zygote

Stem Cells
 A stem cell is a cell that can divide (by mitosis) an unlimited number of
times
 Each new cell (produced when a stem cell divides) has the potential to
remain a stem cell or to develop into a specialised cell such as a blood
cell or a muscle cell (by a process known as differentiation)
 This ability of stem cells to differentiate into more specialised cell types
is known as potency
 There are three main types of potency:
o Totipotency – totipotent stem cells are embryonic stem cells that
can differentiate into any cell type found in an embryo, as well
as extra-embryonic cells (the cells that make up
the placenta and umbilical cord)
o Pluripotency – pluripotent stem cells are embryonic stem cells that
can differentiate into any cell type found in an embryo but are not
able to differentiate into cells forming the placenta and umbilical
cord
o Multipotency – multipotent stem cells are adult stem cells that
have lost some of the potency associated with embryonic stem
cells and are no longer pluripotent

Totipotent cells

 Totipotent cells can divide and produce any type of body cell
 Totipotent cells exist for a limited time in early mammalian embryos
 The zygote formed when a sperm cell fertilises an egg cell is totipotent
 The embryonic cells up to the 16-cell stage of human embryo
development (around the fourth day after fertilisation) are also totipotent
o These cells are still in the form of a solid ball of cells known as
a morula
 Initially, the totipotent cells in the embryo are unspecialised
 During development, totipotent cells begin to translate only part of their
DNA, which results in cell specialisation
 There are no totipotent cells present in the later stages of development
as cells lose their ability to differentiate into any cell type

Pluripotent cells

 By around the fifth day after fertilization, the embryonic cells have
divided further and formed a structure known as a blastocyst, which has
 an outer layer of cells and an inner mass of cells (that are located
inside the outer layer)
 The outer layer of cells will later form the placenta
 The inner mass cells are no longer totipotent (they have lost some of
their ability to differentiate)
o They can still differentiate into any cell type found in an embryo
but are not able to differentiate into cells forming the placenta and
umbilical cord
o These cells are known as pluripotent embryonic stem cells

Multipotent cells

 Stem cells are also found in some adult tissues but they are much less
potent than embryonic stem cells (i.e. they can only specialise
into certain types of cells)
o For example, intestinal stem cells specialise into intestinal
epithelial cells to replace those that are constantly being lost
 This form of potency is known as multipotency – multipotent stem cells
are adult stem cells that have lost some of the potency associated with
embryonic stem cells and are no longer pluripotent
 Plants also contain stem cell in areas of growth, such as their shoots and
roots

Stem cells can be totipotent, pluripotent or multipotent

Use of Stem Cells in Medicine

 As stem cells have the ability to differentiate into other specialised cell
types, they are very valuable in medical research and treatments as they
have the potential to replace damaged tissues and cells (that result from
certain diseases)
 o For example, many stem cell therapies already exist, including the
treatment for leukaemia (bone marrow cancer), in which the
existing stem cells in the bone marrow are killed, before being
replaced using a bone marrow stem cell transplant, which will
eventually replace all the bone marrow cells
o Other stem cell therapies are being researched, including therapies
that replace damaged nerve tissue to treat spinal cord
injuries and therapies that replace damaged heart tissue to
treat heart disease and tissue damage caused by heart attacks
 There are two sources of human stem cells for use in medicine and
research:
o Embryonic stem cells
o Adult stem cells

Use of embryonic stem cells

 Due to their ability to differentiate into almost any cell type, embryonic
stem cells have huge potential in the therapeutic treatment of many
diseases
 For many countries, such as the USA and some countries within the EU,
the use of embryonic stem cells is banned, even for research
 In other countries, such as the UK, the use of embryonic stem cells is
allowed for research but is very tightly regulated
 Embryonic stem cells can be one of two potencies:
o Totipotent if taken in the first 3-4 days after fertilisation
o Pluripotent if taken on day 5
 The embryos used for research are often the waste (fertilised) embryos
from in vitro fertilisation (IVF) treatment
o This means these embryos have the potential to develop into
human beings
o This is why many people have ethical objections to using them in
research or medicine

Use of adult stem cells

 Adult stem cells can divide (by mitosis) an unlimited number of times but
they are only able to produce a limited range of cell types
 A small number of adult stem cells are found in certain tissues within the
body such as:
o Bone marrow - used to produce different types of blood cell
o Brain - used to produce different types of neural and glial cells
 These small numbers of stem cells remain to produce new cells for the
essential processes of growth, cell replacement and tissue repair
 Research is being carried out on stem cell therapy, which is the
introduction of adult stem cells into damaged tissue to treat diseases
(e.g. leukaemia) and injuries (e.g. skin burns)
 The use of adult stem cells is less controversial than embryonic stem
cells because the donor is able to give permission
 o For example, many people donate bone marrow to help treat
leukaemia patients
 However, if adult stem cells are being donated from one person to
another they need to be a close match in terms of blood type and other
body antigens
o Otherwise, there is a chance that the cells used are rejected by
the patient's immune system (the cells in the stem cell transplant
are recognised as being foreign and are attacked by the patient's
immune system)
o Ideally, the patient's own adult stem cells are used to treat them,
as there is a much lower chance of rejection

Sources of Human Stem Cells Table

Evaluating the use of stem cells in medicine

 The use of stem cells that are collected from embryos created via IVF
is ethically questionable as this results in a viable embryo (an embryo
that could become a foetus if implanted in a uterus) being destroyed
 Although their use raises fewer ethical questions, the disadvantage of
only using adult stem cells is that, unlike embryonic stem cells, they are
unable to differentiate into all of the specialised cell types (some of
which may be required to treat certain diseases)
 This means that society has to use all the available scientific
knowledge to make decisions about the use of stem cells (especially
embryonic stem cells) in medical therapies, considering all
the arguments for and against their use
 Official regulatory authorities are required to help society make these
decisions. They do this by comparing the benefits and ethical issues of
stem cell research and making decisions on the extent to which stem
cells can be used. These regulatory authorities carry out the following
tasks:
 o Reviewing proposals for scientific research that uses stem cells
and deciding if this research should be allowed to go ahead
o Licensing and monitoring of research centres that are involved in
stem cell research
o Providing guidelines and codes of practice for stem cell
researchers to ensure they are working to the same high standards
o Monitoring developments in scientific research into stem cell
therapies
o Providing governments and other professional bodies with correct,
up-to-date advice and information on stem cell research, which in
turn helps society to understand how stem cells are being used
and why this work is important

Evaluating the Use of Stem Cells Table

Differential Gene Expression

 Stem cells become specialised through differential gene expression

o This means that only certain genes in the DNA of the stem cell
are activated and get expressed
 Every nucleus within the stem cells of a multicellular organism contains
the same genes, that is, all stem cells within an organism have an identical
genome
 Despite the stem cells having the same genome, they are able to specialise
into a diverse range of cell types because during differentiation certain
genes are expressed ('switched' on)
 Controlling gene expression is the key to development as stem cells
differentiate due to the different genes being expressed
 This differentiation occurs via the following basic steps:
o Under certain conditions, some genes in a stem cell are activated,
whilst others are inactivated
o mRNA is transcribed from active genes only
o This mRNA is then translated to form proteins
o These proteins are responsible for modifying the cell (e.g. they help
to determine the structure of the cell and the processes that occur
within the cell)
o As these proteins continue to modify the cell, the cell
becomes increasingly specialised
o The process of specialisation is irreversible (once differentiation has
occurred, the cell remains in its specialised form)
 Differential gene expression results in the differentiation of stem cells

Transcription factors control the expression of genes

 Eukaryotes use transcription factors to control gene expression

  A transcription factor is a protein that controls the transcription of genes
by binding to a specific region of DNA
 They ensure that genes are being expressed in the correct cells, at the correct
time and to the right level
 It is estimated that ~10% of human genes code for transcription factors
o There are several types of transcription factors that have varying
effects on gene expression
o This is still a relatively young area of research and scientists are
working hard to understand how all the different transcription factors
function
o Transcription factors allow organisms to respond to their environment
o Some hormones achieve their effect via transcription factors
 Transcription factors that increase the rate of transcription are known
as activators
o Activators work by helping RNA polymerase to bind to the DNA at
the start of a gene and to begin transcription of that gene
 Transcription factors that decrease the rate of transcription are known
as repressors
o Repressors work by stopping RNA polymerase from binding to the
DNA at the start of a gene, inhibiting transcription of that gene
 Some transcription factors bind to the promoter region of a gene
o This binding can either allow or prevent the transcription of the gene
from taking place
o Transcription factors interact with RNA polymerase, either by assisting
RNA polymerase binding to the gene (to stimulate expression of the
gene) or by preventing it from binding (to inhibit gene expression)
o Therefore, the presence of a transcription factor will
either increase or decrease the rate of transcription of a gene

In the example above, the transcription factor is an activator as it stimulates

the transcription of the gene. Transcription factors, known as repressors, can
also inhibit the transcription of genes
Operons

 In prokaryotes, control of gene expression often requires the binding of

transcription factors to operons
 An operon is a section of DNA that includes:
o A cluster of structural genes that are transcribed together (these
code for useful proteins e.g. enzymes)
o Control elements, including a promoter region (a DNA sequence that
RNA polymerase initially binds to) and an operator region (where
transcription factors bind)
o Some operons may include regulatory genes that code
for activators or repressors

The lac operon

 Structural genes in prokaryotes can form an operon: a group or a cluster of

genes that are controlled by the same promoter
 The lac operon found in some bacteria is one of the most well-known of
these
 The lac operon controls the production of the enzyme lactase (also called β-
galactosidase) and two other structural proteins
 Lactase breaks down the substrate lactose so that it can be used as
an energy source in the bacterial cell
 It is known as an inducible enzyme (this means it is only synthesized when
lactose is present)
 This helps the bacteria avoid wasting energy and materials

Structure of the lac operon

 The components of the lac operon are found in the following order:
o Promoter for structural genes
o Operator
o Structural gene lacZ that codes for lactase
o Structural gene lacY that codes for permease (allows lactose into the
cell)
o Structural gene lacA that codes for transacetylase
 Located to the left (upstream) of the lac operon on the bacterium's DNA there
is also the:
o Promoter for regulatory gene
o Regulatory gene lacI that codes for the lac repressor protein
 The lac repressor protein has two binding sites that allow it to bind to
the operator in the lac operon and also to lactose (the effector molecule)
o When it binds to the operator it prevents the transcription of the
structural genes as RNA polymerase cannot attach to the
promoter
o When it binds to lactose the shape of the repressor
protein distorts and the repressor protein can no longer bind to the
operator
 The components of the lac operon along with the upstream regulatory gene
and its associated promoter

When lactose is absent

 The following processes take place when lactose is absent in the medium
that the bacterium is growing in:
o The regulatory gene is transcribed and translated to
produce lac repressor protein
o The lac repressor protein binds to the operator region upstream
of lacZ
o Due to the presence of the repressor protein RNA polymerase is
unable to bind to the promoter region
o Transcription of the structural genes does not take place
o No lactase enzyme is synthesized

The repressor protein binds to the operator region of the lac operon and
prevents transcription of the structural gene

When lactose is present

 The following processes take place when lactose is present in the medium
that the bacterium is growing in:
o There is an uptake of lactose by the bacterium
o The lactose binds to the second binding site on the repressor
protein, distorting its shape so that the repressor protein cannot bind
to the operator region
o RNA polymerase is then able to bind to the promoter region
and transcription takes place
o The mRNA from all three structural genes is translated
 o The enzyme lactase is produced and lactose can be broken
down and used for energy by the bacterium

The binding of lactose to the repressor protein frees up the operator region of
the lac operon so RNA polymerase can bind and begin transcription of the
structural genes

One Gene Can Code for More Than One Protein

 Gene expression can be regulated after an mRNA transcript has been
produced
 In eukaryotes, transcription and translation occur in separate parts of the
cell, allowing for significant post-transcriptional modification to occur
 Post-transcriptional modification mechanisms include
o Splicing
o Alternative splicing

Splicing

 Polypeptides are made during the process of protein synthesis, during which
the DNA base code is transcribed and translated
 The DNA code within eukaryotic cells contains many non-coding sections
 Non-coding DNA can be found within genes; these sections are
called introns, whilst sections of coding DNA are called exons
 During transcription, eukaryotic cells transcribe both introns and exons to
produce pre-mRNA molecules
 Before the pre-mRNA exits the nucleus, a process called splicing occurs
o The non-coding intron sections are removed
o The coding exon sections are joined together
o The resulting mRNA molecule contains only the coding sequences of
the gene
 Since these modifications are made after transcription occurred, they are
called post-transcriptional modifications
 Pre-mRNA is spliced before it exits the nucleus

Alternative splicing

 The exons (coding regions) of genes can be spliced in many different ways to
produce different mature mRNA molecules through alternative splicing
 A particular exon may or may not be incorporated into the final mature mRNA
 Polypeptides translated from alternatively spliced mRNAs may differ in their
amino acid sequence, structure and function
 This means that a single eukaryotic gene can code for multiple proteins
 This is part of the reason why the proteome is much bigger than the
genome

Alternative splicing of a gene can produce more than one type of protein