Cell and molecular biology                                                                                                                                                                                                        
All human cell types are derived from a single totipotent
stem cell, the zygote (the fertilised ovum). During development,
organs and tissues are formed by the integration
of four closely regulated cellular processes: cell
division, migration, differentiation and programmed
cell death. In many adult tissues such as skin, liver and
the intestine, these processes continue throughout life,
mediated by populations of stem cells that are responsible
for tissue maintenance and repair. Cell biology is the
study of these processes and of intracellular compartments,
called organelles, which maintain cellular homeostasis.
Dysfunction of any of these processes may lead
to disease.
DNA, chromosomes and chromatin                                                                                                                                                                                         
The nucleus is a membrane-bound compartment found
in all cells except erythrocytes and platelets. The human
nucleus contains 46 chromosomes, each a single linear
molecule of deoxyribonucleic acid (DNA) complexed
with proteins to form chromatin. The basic protein unit
of chromatin is the nucleosome, comprising 147 base
pairs (bp) of DNA wound round a core of four different
histone proteins. The vast majority of chromosomal
DNA is double-stranded, with the exception of the ends
of chromosomes, where ‘knotted’ domains of singlestranded
DNA, called telomeres, are found. Telomeres
prevent degradation and accidental fusion of chromosomal
DNA.

fig-3-11

Chromosomal analysis and structural chromosomal disorders. A How chromosome analysis is carried out. Starting with a blood
sample, the white cells are stimulated to divide by adding the mitogen phytohaemagglutinin (PHA), and colchicine is used to trap the cells in metaphase, which allows the chromosomes to be seen using light microscopy following staining with Giemsa, resulting in a banding pattern. B How structural chromosomal anomalies are described. Human chromosomes can be classed as metacentric if the centromere is near the middle, or acrocentric if the
centromere is at the end. The bands of each chromosome are given a number, starting at the centromere and working out along the short (p) arm and long (q) arm. Translocations and inversions are balanced structural chromosome anomalies where no genetic material is missing but it is in the wrong order. Translocations can be divided into reciprocal (direct swap of chromosomal material between non-homologous chromosomes) and Robertsonian (fusion of acrocentric chromosomes). Deletions and duplications can also occur due to non-allelic homologous recombination (illustrated in panel C).
Deletions are classified as interstitial if they lie within a chromosome, and terminal if the terminal region of the chromosome is affected. Duplications can either be in tandem (where the duplicated fragment is orientated in the correct direction) or inverted (where the duplicated fragment is in the wrong direction). (N = normal; A = abnormal) C A common error of meiotic recombination, known as non-allelic homologous recombination, can occur (right panel), resulting in a deletion on one chromosome and a duplication in the homologous chromosome. The error is induced by tandem repeats in the DNA sequences (green), which can misalign and bind to each other, thereby ‘fooling’ the DNA into thinking the pairing prior to recombination is correct.
The genome comprises approximately 3.1 billion bp
of DNA. Humans are diploid organisms, meaning that
each nucleus contains two copies of the genome, visible
microscopically as 22 identical chromosomal pairs – the
autosomes – named 1 to 22 in descending size order (see
Fig. ), and two sex chromosomes (XX in
females and XY in males). Each DNA strand consists of
a linear sequence of four bases – guanine (G), cytosine
(C), adenine (A) and thymine (T) – covalently linked by
phosphate bonds. The sequence of one strand of doublestranded
DNA determines the sequence of the opposite
strand because the helix is held together by hydrogen
bonds between adenine and thymine or guanine and
cytosine nucleotides.

Genes and transcription                                                                                                                                                                                                                          
Genes are functional elements on the chromosome that
are capable of transmitting information from the DNA
template via the production of messenger ribonucleic
acid (mRNA) to the production of proteins. The human
genome contains an estimated 21 500 genes, although
many of these are inactive or silenced in different cell
types. For example, although the gene for parathyroid
hormone (PTH) is present in every cell, activation of
gene expression and production of PTH mRNA is virtually
restricted to the parathyroid glands. Genes that
are active in different cells undergo transcription, which
requires binding of an enzyme called RNA polymerase
II to a segment of DNA at the start of the gene termed
the promoter. Once bound, RNA polymerase II moves
along one strand of DNA, producing an RNA molecule
that is complementary to the DNA template. A DNA
sequence close to the end of the gene, called the polyadenylation
signal, acts as a signal for termination of
the RNA transcript (Fig.). The activity of RNA

fig-3-1

RNA synthesis and its translation into protein. Gene
transcription involves binding of RNA polymerase II to the promoter of
genes being transcribed with other proteins (transcription factors) that
regulate the transcription rate. The primary RNA transcript is a copy of
the whole gene and includes both introns and exons, but the introns
are removed within the nucleus by splicing and the exons are joined to
form the messenger RNA (mRNA). Prior to export from the nucleus, a
methylated guanosine nucleotide is added to the 5′ end of the RNA (‘cap’)
and a string of adenine nucleotides is added to the 3′ (‘poly A tail’). This
protects the RNA from degradation and facilitates transport into the
cytoplasm. In the cytoplasm, the mRNA binds to ribosomes and forms a
template for protein production.
polymerase II is regulated by transcription factors.
These proteins bind to specific DNA sequences at the
promoter, or to enhancer elements that may be many
thousands of base pairs away from the promoter. A loop
in the chromosomal DNA brings the enhancer close to
the promoter, enabling the bound proteins to interact.
The human genome encodes approximately 1200 different
transcription factors, and mutations in many of
these can cause genetic diseases (Fig. ). Mutation of

fig-3-2

Examples of genetic diseases caused by mutations in genes encoding either transcription factors or receptors.
the transcription factor binding sites within promoters
or enhancers also causes genetic disease. For example,
the blood disorder alpha-thalassaemia can result from
loss of an enhancer located more than 100 000 bp from
the alpha-globin gene promoter, leading to greatly
reduced transcription. Similarly, variation in the promoter
of the gene encoding intestinal lactase determines
whether or not this is ‘shut off’ in adulthood, producing
lactose intolerance.
The accessibility of promoters to RNA polymerase II
depends on the structural configuration of chromatin.
Transcriptionally active regions have decondensed (or
‘open’) chromatin (euchromatin). Conversely, transcriptionally
silent regions are associated with densely
packed chromatin called heterochromatin. Chemical
modification of both the DNA and core histone proteins
allows heterochromatic regions to be distinguished
from open chromatin. DNA can be modified by addition
of a methyl group to cytosine molecules (methylation).
In promoter regions, this silences transcription, since
methyl cytosines are usually not available for transcription
factor binding or RNA transcription. The
core histones can also be modified via methylation,
phosphorylation, acetylation or sumoylation at specific
amino acid residues in a pattern that reflects the functional
state of the chromatin; this is called the histone
code – reflecting an emerging understanding of the
‘rules’ by which specific modifications mark transcriptionally
activating (trimethylation of lysine 4 on histone
H3; acetylation of many histone residues) or silencing
(methylation of lysine 9 on histone H4; deacetylation of
many histone residues) effects. Such DNA and protein
modifications are termed epigenetic, as they do not
alter the primary sequence of the DNA code but have
biological significance in chromosomal function. Abnormal
epigenetic changes are increasingly recognised as

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important events in the progression of cancer, allowing
expression of genes which are normally silenced during
development to support cancer cell de-differentiation
(see Box). They also afford therapeutic targets.
For instance, the histone deacetylase inhibitor vorinostat
has been successfully used to treat cutaneous T-cell lymphoma,
due to the re-expression of genes that had previously
been silenced in the tumour. These genes encode
transcription factors which promote T-cell cell differentiation
as opposed to proliferation, thereby causing
tumour regression.

RNA splicing, editing and degradation
Transcription produces an RNA molecule that is a copy
of the whole gene, termed the primary or nascent transcript.
RNA differs from DNA in three main ways:
• RNA is single-stranded.
• The sugar residue within the nucleotide is ribose,
rather than deoxyribose.
• Uracil (U) is used in place of thymine (T).
The nascent RNA molecule then undergoes splicing,
to generate the shorter, ‘mature’ mRNA molecule, which
provides the template for protein production. Splicing
removes the regions of the nascent RNA molecule that
are not required to make protein (intronic regions), and
retains and rejoins those segments that are necessary for
protein production (exonic regions). Splicing is a highly
regulated process that is carried out by a multimeric
protein complex called the spliceosome. Following splicing,
the mRNA molecule is exported from the nucleus
and used as a template for protein synthesis. It should
be noted that many genes produce more than one form
of mRNA (and thus protein) by a process termed alternative
splicing. Different proteins from the same gene
can have entirely distinct functions. For example, in
thyroid C cells the calcitonin gene produces mRNA
encoding the osteoclast inhibitor calcitonin ,
but in neurons the same gene produces an mRNA
with a different complement of exons via alternative
splicing, which encodes the neurotransmitter calcitoningene-
related peptide.
The portion of the mRNA molecule that directs synthesis
of a protein product is called the open reading
frame (ORF). This comprises a contiguous series of three
sequential bases (codons), which specify that a particular
amino acid should be incorporated into the protein.
There are 64 different codons; 61 of these specify incorporation
of one of the 20 amino acids, whereas the remaining
three codons – UAA, UAG and UGA (stop codons)
– cause termination of the growing polypeptide chain. In
humans, most ORF start with the amino acid methionine,
which is specified by the codon AUG. All mRNA molecules
have domains before and after the ORF called the
5′ untranslated region (5′UTR) and 3′UTR, respectively.
The start of the 5′UTR contains a cap structure that protects
mRNA from enzymatic degradation, and other
elements within the 5′UTR are required for efficient
translation. The 3′UTR also contains elements that regulate
efficiency of translation and mRNA stability, including
a stretch of adenine bases known as a polyA tail.
However, there are approximately 4500 genes in
humans in which the transcribed RNA molecules do
not code for proteins. There are various categories of

non-coding RNA (ncRNA), including transfer RNA
(tRNA), ribosomal RNA (rRNA), ribozymes and micro-
RNA (miRNA). There are more than 1000 miRNAs that
bind to various target mRNAs, typically in the 3′UTR,
to affect mRNA stability. This usually results in enhanced
degradation of the target mRNA, leading to translational
gene silencing. Together, miRNAs affect over half
of all human genes and have important roles in normal
development, cancer and common degenerative disorders.
This is the subject of considerable research interest
at present.

Translation and protein production
Following splicing and export from the nucleus, mRNAs
associate with ribosomes, which are the sites of protein
production . Each ribosome consists of two
subunits (40S and 60S), which comprise non-coding
rRNA molecules complexed with proteins. During
translation, tRNA binds to the ribosome. The tRNAs
deliver amino acids to the ribosome so that the newly

synthesised protein can be assembled in a stepwise
fashion. Individual tRNA molecules bind a specific
amino acid and ‘read’ the mRNA ORF via an ‘anticodon’
of three nucleotides that is complementary to the
codon in mRNA. A proportion of ribosomes are bound
to the membrane of the endoplasmic reticulum (ER), a
complex tubular structure that surrounds the nucleus.
Proteins synthesised on these ribosomes are translocated
into the lumen of the ER, where they undergo folding
and processing. From here the protein may be transferred
to the Golgi apparatus, where it undergoes
post-translational modifications, such as glycosylation
(covalent attachment of sugar moieties), to form the
mature protein that can be exported into the cytoplasm
or packaged into vesicles for secretion. The clinical
importance of post-translational modification of proteins
is shown by the severe developmental, neurological,
haemostatic and soft-tissue abnormalities that occur
in patients with mutations of the enzymes that catalyse
the addition of chains of sugar moieties to proteins. An
example is phosphomannose isomerase deficiency, in

which there is a defect in the conversion of fructose-6-
phosphate to mannose-6-phosphate. This results in a
defect in supply of D-mannose derivatives for glycosylation
of a variety of proteins, resulting in a multi-system
disorder characterised by protein-losing enteropathy,
hepatic fibrosis, coagulopathy and hypoglycaemia. Posttranslational
modifications can also be disrupted by
the synthesis of proteins with abnormal amino acid
sequences. For example, the most common mutation in
cystic fibrosis (ΔF508) results in an abnormal protein that
cannot be exported from the ER and Golgi.

Mitochondria and energy production
The mitochondrion is the main site of energy production
within the cell. Mitochondria arose during
evolution via the symbiotic association with an intracellular
bacterium. They have a distinctive structure
with functionally distinct inner and outer membranes.
Mitochondria produce energy in the form of adenosine
triphosphate (ATP). ATP is mostly derived from the
metabolism of glucose and fat (Fig. ). Glucose cannot

fig-3-3

Mitochondria. A Mitochondrial structure. There is a smooth outer membrane surrounding a convoluted inner membrane, which has inward
projections called cristae. The membranes create two compartments: the inter-membrane compartment, which plays a crucial role in the electron transport
chain, and the inner compartment (or matrix), which contains mitochondrial DNA and the enzymes responsible for the citric acid (Krebs) cycle and the fatty
acid β-oxidation cycle. B Mitochondrial DNA. The mitochondrion contains several copies of a circular double-stranded DNA molecule, which has a
non-coding region, and a coding region which encodes the genes responsible for energy production, mitochondrial tRNA molecules and mitochondrial rRNA
molecules. ATP = adenosine triphosphate; NADH = nicotinamide adenine dinucleotide. C Mitochondrial energy production. Fatty acids enter the
mitochondrion conjugated to carnitine by carnitine-palmityl transferase type 1 (CPT I) and, once inside the matrix, are unconjugated by CPT II to release
free fatty acids (FFA). These are broken down by the β-oxidation cycle to produce acetyl-CoA. Pyruvate can enter the mitochondrion directly and is
metabolised by pyruvate dehydrogenase (PDH) to produce acetyl-CoA. The acetyl-CoA enters the Krebs cycle, leading to the production of NADH and
flavine adenine dinucleotide (reduced form) (FADH2), which are used by proteins in the electron transport chain to generate a hydrogen ion gradient across
the inter-membrane compartment. Reduction of NADH and FADH2 by proteins I and II respectively releases electrons (e), and the energy released is used to
pump protons into the inter-membrane compartment. As these electrons are exchanged between proteins in the chain, more protons are pumped across
the membrane, until the electrons reach complex IV (cytochrome oxidase), which uses the energy to reduce oxygen to water. The hydrogen ion gradient is
used to produce ATP by the enzyme ATP synthase, which consists of a proton channel and catalytic sites for the synthesis of ATP from ADP. When the
channel opens, hydrogen ions enter the matrix down the concentration gradient, and energy is released that is used to make ATP.

enter mitochondria directly but is first metabolised
to pyruvate via glycolysis. Pyruvate is then imported
into the mitochondrion and metabolised to acetylcoenzyme
A (CoA). Fatty acids are transported into
the mitochondria following conjugation with carnitine
and are sequentially catabolised by a process called
β-oxidation to produce acetyl-CoA. The acetyl-CoA
from both pyruvate and fatty acid oxidation is used in
the citric acid (Krebs) cycle – a series of enzymatic reactions
that produces CO2, NADH and FADH2. Both
NADH and FADH2 then donate electrons to the respiratory
chain. Here these electrons are transferred via a
complex series of reactions resulting in the formation of
a proton gradient across the inner mitochondrial membrane.
The gradient is used by an inner mitochondrial
membrane protein, ATP synthase, to produce ATP,
which is then transported to other parts of the cell.
Dephosphorylation of ATP is used to produce the
energy required for many cellular processes.
Each mitochondrion contains 2–10 copies of a 16 kilobase
(kB) double-stranded circular DNA molecule
(mtRNA). mtDNA contains 13 protein-coding genes, all
involved in the respiratory chain, and the ncRNA genes
required for protein synthesis within the mitochondria
(see Fig. 3.3). The mutational rate of mtDNA is relatively
high due to the lack of protection by chromatin. Several
mtDNA diseases characterised by defects in ATP production
have been described. mtDNA diseases are
inherited exclusively via the maternal line (see Fig. ).

fig-3-7

Drawing a pedigree and patterns of inheritance. A The main symbols used to represent pedigrees in diagrammatic form. B The main
modes of disease inheritance (see text for details).   

 

This unusual inheritance pattern exists because
all mtDNA in an individual is derived from that person’s
mother via the egg cell, as sperm contribute no
mitochondria to the zygote. Mitochondria are most
numerous in cells with high metabolic demands, such as
muscle, retina and the basal ganglia, and these tissues
tend to be the ones most severely affected in mitochondrial
diseases (Box ). There are many other mitochondrial
diseases that are caused by mutations in nuclear
genes, which encode proteins that are then imported
into the mitochondrion and are critical for energy production:
for example, Leigh’s syndrome and complex I
deficiency.

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Protein degradation
The cell uses several different systems to degrade proteins
and other molecules that are damaged, are potentially
toxic or have simply served their purpose. The
proteasome is the main site of protein degradation
within the cell. The first step in proteasomal degradation
is ubiquitination – the covalent attachment of a protein
called ubiquitin as a side chain to the target protein.
Ubiquitination is carried out by a large group of enzymes
called E3 ligases, whose function is to recognise specific
proteins that should be targeted for degradation by the
proteasome. The E3 ligases ubiquitinate their target
protein, which is then transported to a large multiprotein
complex called the 26S proteasome, where it
is degraded. There is mounting evidence that defects
in the proteasome contribute to the pathogenesis of
many diseases, particularly degenerative diseases of the
nervous system like Parkinson’s disease and some types
of dementia that are characterised by formation of
abnormal protein aggregates (inclusion bodies) within
neurons. At least one inherited disease, termed Angelman’s
syndrome, is due to a mutation affecting the UBE3
E3 ligase.
Proteins with complex post-translational modifications
are degraded in membrane-bound structures
called lysosomes, which have an acidic pH and contain
proteolytic enzymes that degrade proteins. There are
many inherited defects in lysosomal enzymes that result
in failure to degrade intracellular toxic substances. For
instance, in Gaucher’s disease, mutations of the gene
encoding lysosomal (acid) β-glucosidase lead to undigested
lipid accumulating in macrophages, producing
hepatosplenomegaly and, if severe, deposition in the
brain and mental retardation.
Lysosomes are also crucial for the process of autophagy,
a process of self-cannibalisation that allows the
cell to adapt to periods of starvation by recycling cellular
components. Autophagy is triggered by metabolic stress
and begins with the formation of a membrane-bound
vesicle called the autophagosome, which contains targeted
cellular components such as long-lived proteins

and organelles. The autophagosome then fuses with
the lysosome to start the degradation and recycling
process. Mutations in proteins that are crucial for formation
of the autophagosome lead to neurodegenerative
diseases in humans, such as juvenile neuronal ceroid
lipofuscinosis (Batten’s disease), caused by autosomal
recessive mutations in CLN3.
Peroxisomes are small, single membrane-bound
cytoplasmic organelles containing many different oxidative
enzymes such as catalase. Peroxisomes degrade
hydrogen peroxide, bile acids and amino acids.
However, the β-oxidation of very long-chain fatty acids
appears to be their most important function, since
mutations in the peroxisomal β-oxidation enzymes
(or the proteins that import these enzymes into the
peroxisome) result in the same severe congenital disorder
as mutations that cause complete failure of peroxisomal
biogenesis. This group of disorders is called
Zellweger’s syndrome (cerebrohepatorenal syndrome)
and is characterised by severe developmental delay, seizures,
hepatomegaly and renal cysts; the biochemical

diagnosis is made on the basis of elevated plasma levels
of very long-chain fatty acids.
The cell membrane and cytoskeleton
The cell membrane is a phospholipid bilayer, with
hydrophilic surfaces and a hydrophobic core (Fig. ).

fig-3-4

An archetypal human cell. The basic cell components required for function within a tissue: (1) cell-to-cell communication taking place via gap junctions and the various types of receptor that receive signals from the extracellular environment and transduce these into intracellular messengers; (2) the nucleus containing the chromosomal DNA; (3) intracellular organelles, including the mechanisms for proteins and lipid catabolism; (4) the cellular mechanisms for import and export of molecules across the cell membrane. (ABC = ATP-binding cassette transporters; ATP = adenosine triphosphate: cAMP = cyclic adenosine monophosphate; CFTR = cystic fibrosis transmembrane regulator; CREB = cAMP response element-binding protein; GDP/GTP = guanine diphosphate/triphosphate; LDL = low-density lipoproteins; LH/FSH = luteinising hormone/follicle-stimulating hormone; PTH = parathyroid hormone; TSH = thyroid-stimulating hormone)
The cell membrane is, however, much more than a
simple wall. Cholesterol-rich ‘rafts’ float within the
membrane, and proteins are anchored to them via the
post-translational addition of complex lipid moieties.
The membrane also hosts a series of transmembrane
proteins that function as receptors, pores, ion channels,
pumps and associated energy suppliers. These proteins
allow the cell to monitor the extracellular milieu, import
crucial molecules for function, and exclude or exchange
unwanted substances. Many protein–protein interactions
within the cell membrane are highly dynamic, and
individual peptides will associate and disassociate to
effect specific roles.

The cell membrane is permeable to hydrophobic substances,
such as anaesthetic gases. Water is able to pass
through the membrane via a pore formed by aquaporin
proteins; mutations of an aquaporin gene cause congenital
nephrogenic diabetes insipidus . Most other
molecules must be actively transported using either
channels or pumps. Channels are responsible for the
transport of ions and other small molecules across the
cell membrane. They open and close in a highly regulated
manner. The cystic fibrosis transmembrane conductance
regulator (CFTR) is an example of an ion
channel that is responsible for transport of chloride ions
across epithelial cell membranes. Mutation of the CFTR
chloride channel, highly expressed in the lung and gut,
leads to defective chloride transport, producing cystic
fibrosis. Pumps are highly specific for their substrate
and often use energy (ATP) to drive transport against a
concentration gradient.
Endocytosis is a cellular process that allows internalisation
of larger complexes and molecules by invagination
of plasma membrane to create intracellular vesicles.
This process is typically mediated by specific binding
of the particle to surface receptors. An important
example is the binding of low-density lipoprotein (LDL)
cholesterol-rich particles to the LDL receptor (LDLR) in
a specialised region of the membrane called a clathrin
pit. In some cases of familial hypercholesterolaemia
, LDLR mutations cause failure of this binding
and thus reduce cellular uptake of LDL. Other LDLR
mutations change a specific tyrosine in the intracellular
tail of the receptor, preventing LDLR from concentrating
in clathrin-coated pits and hence impairing uptake of
LDL, even though LDLR bound to LDL is present elsewhere
in the cell membrane.
The shape and structure of the cell are maintained by
the cytoskeleton, which consists of a series of proteins
which form microfilaments (actin), microtubules (tubulins)
and intermediate filaments (keratins, desmin,
vimentin, laminins) that facilitate cellular movement
and provide pathways for intracellular transport. Dysfunction
of the cytoskeleton may result in a variety of
human disorders. For instance, some keratin genes
encode intermediate filaments in epithelia. In epidermolysis
bullosa simplex , mutations in keratin
genes (KRT5, KRT14) lead to cell fragility, producing the
characteristic blistering on mild trauma.

Receptors, cellular communication and intracellular signalling
Several mechanisms exist that allow cells to communicate
with one another. Direct communication between
adjacent cells occurs through gap junctions. These are
pores formed by the interaction of ‘hemichannels’ in
the membrane of adjacent cells. Many diseases are due
to mutations in gap junction proteins, including the
most common form of autosomal recessive hearing loss
(GJB2) and the X-linked form of Charcot–Marie–Tooth
disease (GJB1).
Communication between cells that are not directly in
contact with each other occurs through hormones,
cytokines and growth factors, which bind to and activate
receptors on the target cell. Receptors then bind to
various other proteins within the cell termed signalling
molecules, which directly or indirectly activate gene
expression to produce a cellular response.

box-3-2

There are many different signalling pathways; for
example, in nuclear steroid hormone signalling, the
ligands (steroid hormones or thyroid hormone) bind
to their cognate receptor in the cytoplasm of target
cells and the receptor/ligand complex then enters the
nucleus, where it acts as a transcription factor to regulate
the expression of target genes (Box ). However, the
most diverse and abundant types of receptor are located
at the cell surface, and these activate gene expression
and cellular responses indirectly. Activation of a cell
surface receptor by its ligand results in a series of intracellular
events, involving a cascade of phosphorylation
of specific residues in target proteins by an important
group of enzymes called kinases. This cascade typically
culminates in phosphorylation and activation of transcription
factors, which bind DNA and modulate gene
expression.
Figure depicts some of the signalling molecules
downstream of the tumour necrosis factor (TNF) receptor.
On activation of the receptor by the ligand (in this
case, TNF), other molecules, including TNF-receptorassociated
proteins (TRAFs), are recruited to the intracellular
domain of the receptor. These regulate the
activity of a kinase termed IKKγ, which in turn regulates
activity of two further kinases termed IKKα and
IKKβ. These regulate degradation of an inhibitory
protein called IκB, which normally binds to the effector
protein NFκB, holding it in the cytoplasm. On receptor
activation, a signal is transmitted through TRAFs
and the IKK proteins to cause phosphorylation and

fig-3-5

The tumour necrosis factor (TNF) signalling pathway.
TNF binds to its receptor, forming a trimeric complex in the cell
membrane. Various receptor-associated factors are attracted to the
intracellular domain of the receptor, including TNF-receptor-associated
protein 6 (TRAF6) and tumour necrosis factor receptor type 1-associated
death domain protein (TRADD). These proteins modulate activity of
downstream signalling proteins, the most important of which are IKKγ
(which in turn modulates activity of IKKα and IKKβ). These proteins cause
phosphorylation of IκB, which is targeted for degradation by the
proteasome, releasing NFκB, which translocates to the nucleus to activate
gene expression. The signalling pathway is further regulated in a negative
manner by cylindromatosis (CYLD), which de-ubiquitinates TRAF6, thereby
impairing its ability to activate downstream signalling.

degradation of IκB, allowing NFκB to translocate to the
nucleus and activate gene expression. The system also
has negative regulators, including the cylindromatosis
(CYLD) enzyme, which regulates the activity of TRAFs
by de-ubiquitination. Other transmembrane receptors
can be grouped into:
• ion channel-linked receptors (glutamate and the
nicotinic acetylcholine receptor)
• G protein-coupled receptors (GnRH, rhodopsin,
olfactory receptors, parathyroid hormone receptor)
• receptors with kinase activity (insulin receptor,
erythropoietin receptor, growth factor receptors)
• receptors which have no kinase activity, but interact
with kinases via their intracellular domain when
activated by ligand (TNF receptor) (see Box).
Many receptors can signal only when they assemble
as a multimeric complex. Mutations which interfere
with assembly of the functional receptor multimer can
result in disease. For example, mutations of the insulin
receptor that inhibit dimerisation lead to childhood
insulin resistance and growth failure. Conversely, some
fibroblast growth factor receptor 2 (FGFR2) gene mutations
cause dimerisation in the absence of ligand binding,
leading to bone overgrowth and an autosomal dominant
form of craniosynostosis called Crouzon’s syndrome.
It is becoming clear that specialised projections on
the cell surface known as cilia are essential for normal
signalling in many tissues. Cilia can be motile or nonmotile.
Motile cilia are crucial for normal respiratory
tract function, with primary ciliary dyskinesia (PCD)
resulting in early-onset bronchiectasis due to failure to
clear lung secretions. PCD is commonly associated with

situs inversus (left–right laterality reversal) as a result
of failure of a specific signalling process in very early
embryogenesis. Mutations in proteins that are essential
for non-motile cilia formation or function are responsible
for a large number of autosomal recessive disorders
known collectively as ciliopathies, which are commonly
associated with intellectual disability, renal cystic dysplasia
and retinal degeneration. For example, in the
Bardet–Biedl syndrome, mutations in a series of genes
encoding ciliary structure cause polydactyly, obesity,
hypogonadism, retinitis pigmentosa and renal failure.

Cell division, differentiation and migration
In normal tissues, molecules such as hormones, growth
factors and cytokines provide the signal to activate the
cell cycle, a controlled programme of biochemical events
that culminates in cell division. During the first phase,
G1, synthesis of the cellular components necessary to
complete cell division occurs. In S phase, the cell produces
an identical copy of each chromosome – which
carries the cell’s genetic information – via a process
called DNA replication. The cell then enters G2, when
any errors in the replicated DNA are repaired before
proceeding to mitosis, in which identical copies of all
chromosomes are segregated to the daughter cells. The
progression from one phase to the next is tightly controlled
by cell cycle checkpoints. For example, the checkpoint
between G2 and mitosis ensures that all damaged
DNA is repaired prior to segregation of the chromosomes.
Failure of these control processes is a crucial
driver in the pathogenesis of cancer

During development, cells must become progressively
less like a stem cell and acquire the morphological
and biochemical configuration of the tissue to which
they will contribute. This process is called differentiation
and it is achieved by activation of tissue-specific genes
and inactivation or silencing of genes that maintain the
cell in a progenitor state. This epigenetic process enables
cells containing the same genetic material to have very
different structures and functions. The programme of
differentiation is often deranged or partially reversed in
cancer cells. A similar mechanism allows adult stem
cells to maintain and repair tissues. Cell migration is a
process that is also necessary for development and
wound healing. Migration also requires the activation of
a specific set of genes, such as the transcription factor
TWIST, that give the cell polarity and enable the leading
edge of the cell to interact with the extracellular environment
to control the speed and direction of travel. Again,
this process can be reactivated in cancer cells and is
thought to facilitate tumour metastasis.
Cell death, apoptosis and
senescence
With the exception of stem cells, human cells have
only a limited capacity for cell division. The Hayflick
limit is the number of divisions a cell population can go
through in culture before division stops and the cell
enters a state known as senescence. This ‘biological
clock’ is of great interest in the study of the normal
ageing process. Rare human diseases associated with
premature ageing, called progeric syndromes, have been
very helpful in identifying the importance of DNA
repair mechanisms in senescence (p. 168). For example,
in Werner syndrome, a DNA helicase (an enzyme that
separates the two DNA strands) is mutated, leading to
failure of DNA repair and premature ageing. A distinct
mechanism of cell death is seen in apoptosis, or programmed
cell death.
Apoptosis is an active process that occurs in normal
tissues and plays an important role in development,
tissue remodelling and the immune response. The signal
that triggers apoptosis is specific to each tissue or cell
type. This signal activates enzymes, called caspases,
which actively destroy cellular components, including
chromosomal DNA. This degradation results in cell
death, but the cellular corpse contains characteristic
vesicles called apoptotic bodies. The corpse is then recognised
and removed by phagocytic cells of the immune
system, such as macrophages, in a manner that does not
provoke an inflammatory response.
A third mechanism of cell death is necrosis. This is a
pathological process in which the cellular environment
loses one or more of the components necessary for cell
viability. Hypoxia is probably the most common cause
of necrosis..