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        Biochemical Genetics
• Early understanding of genetics from
• Study of biochemical pathways led to an
  understanding of mechanisms involved in
• Molecular biology has since been used to track
  mutations responsible for pathology.
• Biochemical processes are catalysed by
• Variants in enzymes affect rate of catalysis.
           Biochemical Genetics
• 1909 Garrod identified Alkaptonuria - caused by inactivity of an
  enzyme in a metabolic pathway; “a metabolic disease”.

• Alkaptonuria (black urine) AKU
   • 1st human disease trait studied at the biochemical level.
   • Shown to fit a Mendelian recessive form of inheritance.
   • Individuals cannot metabolise homogentistic acid (HGA), as a result an
     important metabolic pathway is blocked.
   • Homogentistic acid accumulates in cells and tissues and is excreted in
     urine and can give rise to arthritis.
   • It accumulates in cartilagenous areas resulting in darkening of ears and
   • Rare persistent disease.

• Garrod hypothesised: hereditary information controls chemical
  reactions in the body.
• Now > 350 metabolic diseases described (most are rare).
• Overall they affect ~ 1/2500 births.
       Garrod‟s Original Idea

Normal metabolism
Substrate ---------Product

In-born error of metabolism

Metabolite Metabolite
          Biochemical Genetics
• Many of the enzymes involved in metabolic diseases are
  part of complex cycles.
• Metabolic diseases result from lack of specific functional
  enzyme, this then disrupts whole pathway.
• Most are autosomal recessive.
• Heterozygotes are normally healthy.
• Diagnosis can be challenging
   – E.g.. SIDS and fatty acid metabolism.
• Understanding enzyme involved may help formulate
• Treatments can be as simple as avoidance e.g. lactose
  deficiency, or through reducing, removing or replacing
  the defective enzyme.
           Metabolic diseases
• Major metabolic pathways are those involved in the
  metabolism of nucleic acids, proteins, carbohydrates and
• Glycolysis.
• Citric Acid Cycle.
• Pentose Phosphate Shunt.
• Gluconeogenesis.
• Glycogen and Fatty Acid Synthesis and Storage.
• Degradative Pathways.
• Energy Production.
• Transport systems.
         Metabolic diseases
1. Can be caused by absence of end product of a
   complex reaction, e.g. Albinism.
2. May result from pile up of substrates in a
   pathway, e.g. Galactosaemia.
3. May result from excessive amounts of
   metabolites, e.g. Phenylketonuria.
4. May affect regulatory system, e.g. Adrenal
5. Storage diseases, e.g. Pompe.
6. Transport disorders, e.g. Cystinuria.
7. Vitamins and co-factors, e.g. Wilson Disease.
    1. Absence of an end product of a
            complex reaction
 1 2 3 4

• The end product E may be affected by the absence of any of the
  enzymes in the cycle (1,2,3,4)

•   E.g. Albinism may be caused by one of ten defects in the production of
•   In terms of the genetics of inheritance this is complicated. In a classical
    recessive disease, if both parents have the disease the children are obligate

         Mum rr x Dad rr = offspring rr

BUT if albinism is caused by the absence of enzyme 1 in one parent and
  enzyme 2 in the other the children will all be normal, heterozygotes for each
  mutation but producing functional enzyme

Mum 1,1(albino) x Dad 2,2 (albino) = Offspring 1,2 (normal)
   Metabolic pathway
phenylalanine and tyrosine

•   Recessive.
•   Multi allele.
•   Multi locus (c/s X and c/s15).
•   Broadly described as tyrosine +ve/-ve.
•   Therefore possible for 2 albinos to have 4 normal children.

Tyrosine-------------melanin pigments
      2. Pile up of Substrates in a Pathway


•   If the enzyme (y) that converts A to B is missing then the A substrate will

•   E.g., galactosaemia, the defective enzyme is galactose-1-phosphate uridyl

•   Absence causes a build up of galactose-1-phosphate (rather than conversion to
    glucose-1-phosphate) which accumulates in the blood cells, liver and tissues
    and destroys the kidneys, liver and brain.

In normal:                 galactose-1-phosphate uridyl transferase
galactose-1-phosphate ----------------------------------------------> glucose-1-phosphate

In galactosaemia:            defective enzyme
galactose-1-phosphate-----------------------------------------------> galactose-1-phosphate
• Carbohydrate is the most abundant energy source.
• Carbohydrate is metabolised to glucose fructose and galactose.
• The process of glycolysis converts galactose and fructose to glucose.
• In galactosaemia, cannot metabolise galactose.
• 1/55,000 are deficient in the enzyme galactose-1 phosphate
• The disease manifests as hepatomegaly (large liver), excretion of
  albumen and sugar and failure to thrive plus mental retardation.
• If dietary intake is restricted (eliminate galactose from diet), phenotype
  may be ameliorated
• Newborn screening is conducted using a dried blood sample.

• galactose-1-phosphate --------------------> glucose-1-phosphate

     3. Diseases may result from excessive
            amounts of metabolites

1,  2, 3
•   Protein broken down into toxic metabolites instead of correct product.
•   E.g., phenylketonuria, phenylalanine in foodstuff is not converted to tyrosine and breaks
    down to yield toxic metabolites such as phenylpyruvic, phenyllactic and phenylacetic acids.
•   Toxic metabolites affect growth and development. Child may appear normal at birth but then
    deteriorate rapidly.He/she can be treated by avoidance of phenylalanine containing foods.
•   Interestingly, children require the diet only into their teens.
•   However, a sufferer who wishes to become pregnant must also be treated since the toxic
    metabolites may cross the placenta leading to gross malformations in the foetus.

In normal:
              phenylalanine hydroxylase
Phenylalanine--------------------------------------- > tyrosine
In Phenylketonuria:

Phenylalanine > phenylpyruvic, phenyllactic and phenylacetic acids.
• Disorder of amino acid metabolism (proteins).
• Cannot break down phenylalanine to tyrosine.
• Excess phenylalanine disrupts cellular processes in the brain.
• Inactive enzyme: phenylalanine hydroxylase has a 30% level in
• As phenylalanine accumulates, it converts to toxic metabolites such as
  phenylpyrivic acid.
• This enters CSF, resulting in raised brain levels.
• This results in mental retardation.
• The condition is inherited as an autosomal recessive (c/s12).
• It affects about 1/11000 Caucasian and 1/90000 Africans.
• PKU screening of newborns can ameliorate retardation due to a strict diet
• Screening for phenylketonuria (PKU) is part of the screening programme
  for all newborn babies. The UK Newborn Screening Programme Centre
  has been set up to monitor this and screening for other inborn errors of
  metabolism (has been in operation since the early 1980s).
 4. Diseases affecting regulatory systems
A                 B

• Normal regulation relies on feedback, breakdown in regulatory feedback
  results in disease.
• E.g., A block in biosynthesis of cortisol causes Adrenogenital syndrome,
  which is common in the Inuit. This stimulates excessive production of
  ACTH by the pituitary.
• Normally ACTH production is controlled by feedback inhibition involving
  cortisol, which in turn causes production of cortisol precursors.
• Breakdown of the precursors cause the problems seen in this syndrome.
• Cortisol regulates ACTH production through inhibitory feedback.
Adrenogenital syndrome
• Block in production of cortisol therefore excessive ACTH produced as not
  controlled by cortisol.
Adrenal Hyperplasia
         • Deficiency in enzyme of cortisol
         • This leads to increased levels
           of ACTH (adrenocorticotrophic
           hormone - stimulates release of
           hormones from adrenal cortex).
         • These in turn lead to over-
           production and accumulation of
           the steroidal hormone cortisol.
         • Cortisol causes excessive
           production of androgens which
           leads to virilisation.
                 5. Storage disease
A------> b+c+d
• Storage diseases are caused by the build up of products that are usually
  metabolised to small, readily used molecules.
• E.g., glycogen storage diseases. Glycogen is stored in the liver as a
  natural reservoir and is metabolised to the more useful glucose when
  energy is required.
• Lysosomal storage of unmetabolised glycogen is seen in Pompe
  disease, which is caused by the absence of the enzyme 1,4,
• Cells become engorged with glycogen and cease functioning.
              1,4 glucosidase
      Glycogen                      Glucose

Glycogen storage disorder
       No enzyme
       Glycogen                 still Glycogen
Glycogen storage disorder
         •   Pompe
         •   Progressive muscle weakness of all muscles
             in the body develops as a result of glycogen
             accumulation or storage in cell vesicles,
             named lysosomes.
         •   Lysosomal Storage Disease or LSD.
         •   Normal: glycogen in the lysosomes is broken
             down by acid alpha-glucosidase (GAA), an
             important and unique lysosomal enzyme that
             reduces large molecules of glycogen to
         •   Pompe : very little or no activity of this enzyme
             because of defects or mutations in the GAA
         •   Autosomal recessive (c/s 17)
         •   1,4 glucosidase absent.
         •   Infantile form: (see opposite) cardiomyopathy -
             disease of heart muscle, lung deficiency, liver
             deficiency & muscular hypotonia.
         •   Juvenile/adult form; skeletal muscle.
         •   Heavy glycogen deposits.
 6. Some errors are involved in transport
• Range of effects, depending on whether barrier integrity altered or
  whether an accumulation of substrate has an impact on physiology.
• Abnormal cysteine transport can manifest as cystinuria or cystinosis
• Cystinuria
   • Renal disease and hypertension resulting in yellow bladder
    • Abnormal cysteine transport between cells and extra-cellular
    •   Autosomal Recessive with at least 3 forms.
    –   Mutation in amino acid transporter gene on c/s 2.
    –   Results in excretion of large amounts of cysteine.
    –   Stones form because of limited solubility of cysteine.
• Cystinosis
   • Inability to transport cysteine across lysosomal membrane.
   • This leads to accumulation of cysteine crystals which cause
     severe disabilities, kidney failure and death if untreated.
• Glucosuria
    – Recessive.
    – Defect in sodium/glucose co-transporter SLC5A2.
    – Low renal threshold for glucose.
7. Problems with vitamins and cofactors

• Vitamins may act as hormones (vitamin D); anti-oxidants
  (vitamin E); neurotransmitters (vitamin A) and co-
  enzymes (vitamin B complex).
• In the past most vitamin deficiencies were the product of
  bad diet but some are due to defects in vitamin
• Co-factors include trace elements and metals.
• Adequate supply of trace elements are critical for
  normal metabolism while excessive amounts or stored
  amounts are highly toxic.
• Examples are :
• Cu (Wilson Disease - autosomal rec and Menkes – X
• Fe (Haemochromatosis).
               Wilson Disease
• Autosomal recessive
• Build up of intracellular
  hepatic copper, resulting in
  subsequent hepatic and
  neurologic abnormalities.
• Disturbance of copper
• Kayser-Fleischer copper
  coloured ring round periphery
  of cornea- copper deposit.
• Have hypercalciuria,
  nephocalcinosis > stones.
     Diagnosis of human disease
• Biochemical analysis gives a better idea of the severity of the disease
  and the symptoms likely to be encountered by the patient.
• The protein is the end product of a reaction that begins with the DNA,
  which transfers its data to mRNA that in turn is translated to yield the
  active product.
• Analysis of protein expression yields information on whether a protein is
  made in its location within a cell, its degradation, the amount present and
  its activity.
• Protein electrophoresis is used to analyse blood of sickle cell patients, A
  single amino acid change, Glu>Val, alters the mobility of the protein in an
  electric field and thus allows determination of the genotype.
• In CF there are more than 1,000 mutations, so screening is difficult.
• In neonatal testing, homozygotes are detected by the sweat test, which
  allows analysis of chloride ion secretion (affected by CFTR mutations).
• DNA neonatal testing is currently conducted throughout Scottish & Welsh
  health authorities but in only a subset of those in England.
• Clotting times in biochemical assays of haemophilia patients give a more
  useful idea of patients‟ condition than analysis of the gene defect.
Understanding can allow treatment

 •   Avoidance e.g. PKU, Lactase deficiency.
 •   Substrate reduction.
 •   Removal of toxic products.
 •   Product replacement.
 •   Co-factor supplementation.
             Lactase Deficiency
• Recessive, Congenital- lactase absent.
• Adult type- 5-10% enzyme activity.
• Intolerance of the milk sugar lactose.
• Results in diarrhoea, flatulence, abdominal cramps.
• Particularly prevalent in Intuits, Africans, Asians and
  Americans with these heritages.
• Lactose is reduced if one converts milk to cheese,
  butter or yoghurt.
• To avoid problems then avoid dairy products.
• Study of hereditary basis for individual variation
  in drug response.
• Some patients respond well to drugs.
• Others respond poorly to the same medication.
• Drug may be toxic to some patients but not to
• Predict treatment response .
• Future; individualised drug therapy?
• Require greater understanding of complex
  pathways and interactions.
    Example: Genetic polymorphism and
       the modulation of drug action
• Polymorphisms of the Cyp2D6 allele of the cytochrome P450 genes.
• > 70 known polymorphisms.
   • Some alleles are associated with “poor metabolism of drugs” while
     others are associated with “hyper-extensive metabolism”.
   • Drugs that rely on P450, e.g., tri-cyclic antidepressants, are shown to
     be less effective in hyper metabolisers, whereas side effects are
     more common in poor metabolisers.
   • Drugs such as codeine that require P450 to catalyse transformation
     into active metabolites (morphines), are less active in poor
     metabolisers and show excessive effects in hyper-metabolisers.
• G6PD.
   – About 10% of Black servicemen in the USA who were given the anti-
     malarial drug primaquine developed acute, but self limiting, anaemia.
   – A smaller group of white soldiers of Mediterranean descent also
   – This was due to a defect in glucose-6-phosphate dehydrogenase,
     which exhibits about 15% of normal activity.

• P glycoprotein genes (drug pump) affect the way in which certain drugs
  are cleared from the cell.
             Genetic polymorphism and the
               modulation of drug action
                                         MINOR ALLELE
CYP2C9                Warfarin           Reduced anti-coagulation
CYP2C19               Omeprazole         Enhanced cure rate H.Pylori
CYP2D6                Codeine            Decreased analgesia, euphoria, nausea.

P glycoprotein        Digoxin            Altered blood level and effect.
N-acetyltransferase   Isoniazid          Slow acetylator increased liver toxicity.

Thiopurine methyl     6-mercaptopurine   Bone marrow aplasia, Suboptimal
transferase                              response.
Pseudocholine         Succinylcholine    Prolonged apnoea
UDP glucuronosyl      Irinotecan         Enhanced toxicity
• Environmental and genetic factors involved in aetiology.
• Disorder caused by many genes, which render the
  individual susceptible to particular environmental factors;
  so called multifactorial inheritance.
• Unlike unifactorial disorders, multifactorial disorders are
   –    common,
   –    their genetics are complex,
   –    the risks to relatives are usually low (less than 1 in twenty),
   –   cannot be predicted on genetic theory but have to be determined
       empirically for each disorder.
• What are examples of multifactoral inheritance?
Disease                   People Affected in UK
Huntington Disease                   2500
Duchenne Muscular                    3000
Cystic Fibrosis                      7000
Alzheimer's Dementia              400,000
Diabetes                        1,000,000
Ischaemic Heart Disease         1,250,000
Cancer                          1,500,000
Hypertension                    5,000,000
Genetics of Common Diseases in Adults

•   Heart Disease
•   Cancer
•   Diabetes
•   Obesity
•   Alzheimer‟s
•   Schizophrenia
                         Heart Disease
•   CHD causes over 120,000 deaths a year in the UK: approximately one in
•   four deaths in men and one in six deaths in women.
•   To put in perspective, 34,000 deaths a year result from lung cancer, 16,000
    deaths from colo-rectal cancer and 13,000 deaths from breast cancer.
•   It is the most common cause of premature death in the UK:
•   Nearly all deaths from CHD are because of a heart attack.
•   Death rates for CHD have been falling in the UK since the late 1970s.
•   Whereas mortality from CHD is rapidly falling, morbidity is not falling, and
•   in older age groups it has risen by around a quarter since the late 1980‟s.
•   Deaths from CHD highest in Scotland and the North of England, lowest in the
    South of England and intermediate in Wales and Northern Ireland.
•   It has been estimated that around 5,000 lives are lost each year in men aged 20-
    64 years due to social class differences in CHD death rates.
•   South Asians living in the UK (Indians, Bangladeshis, Pakistanis and Sri
    Lankans), have a higher premature death rate from CHD than average. (46%
    higher for men and 51% higher for women). The difference in the death rates
    between South Asians and the rest of the population is increasing.
•   Stephens JW, Humphries SE.The molecular genetics of cardiovascular disease:
    clinical implications.J Intern Med. 2003 Feb;253(2):120-7. Review.
                   Heart Disease
• Leading killer.
• Coronary artery disease (CAD).
• Risk factors; obesity, smoking, hypertension, high
  cholesterol, +FH (Family History).
• Aggregates in families.
• Specific genes:
   – Familial Hypercholesterolaemia, 5% LDL.
   – Apolipoprotein B defects: 1/1000.
   – Lipoprotein lipase: 6-10% of the population carries one of these
     mutations. Carriers are at a greatly elevated risk of developing
     early heart disease, but only if they are smokers.
• Lifestyle changes:
   – E.g. in US, 60% reduction in mortality due to CAD since 1950.
Familial Hypercholesterolaemia
         • LDL (low density lipoprotein receptor)
             • Mutation (1/500) > cholesterol levels
             • Mutation > reduction in number of
               receptors therefore cellular uptake of
               cholesterol is reduced, circulating
               cholesterol increases.
             • Autosomal dominant, 5% experience a
               myocardial infarction (MI) before the age
               of 60.
             • Xanthomas (cholesterol deposits in skin
               and tendons see opposite).
             • Homozygotes are much more severely
               affected; without treatment most die
               before the age of 30.

• Second leading cause death in the UK.
• Many types cluster in families – due to shared
  environment and genes.
• Also due to infectious agents.

• Rarely is cancer the result of a single gene
  mutation; often it is the result of a number of factors:
   –   Inherited susceptibility,
   –   New mutations,
   –   Environmental interactions,
   –   The 2-hit hypothesis, e.g., Rb: one inherited and one
       environmental induced mutation.
• E.g., hereditary colon cancer, Familial
  Adenomatous Polyposis coli (FAP), involves
  between 4 and 6 different genetic events and no
  one is sure of the original trigger.
                           Colon cancer

        5q                         12p              18q             17p

        Mutation                   Mutation         Loss            Loss

        APC                        K-ras            DCC             p53

Normal Proliferating Benign                         Late         Cancerous     Colon
colon                                               adenoma      adenoma       cancer
          epithelium adenoma adenoma
epithelium                                          with villi

    First step is loss of one allele of the APC gene on c/s 5
    Subsequent mutations in genes on c/s 12, 18 and 17 in the cells of the benign
    adenoma can lead to malignant transformation and cancer.
             Diabetes Mellitus
• Complex aetiology.
• Familial clustering.
• Leading cause of adult blindness, kidney failure
  and lower limb amputation, and major cause of
  heart disease and stroke.
• Heterogeneous group of disorders all characterised
  by elevated blood sugar.
• Type 1 (IDDM) HLA autoimmune.
• Type 2 NIDDM insulin resistance.
           Type 1 (IDDM)

– Usually manifests before 40.
– Patients must receive insulin to survive.
– MZ concordance 30-50%, DZ 5-10%.
– Insulin gene c/s 11, VNTR polymorphism (see
  later lecture) ~10% familial clustering.
– At least 20 other associated loci.
             Type 2 (NIDDM)

– >90% all diabetes.
– Can often be treated with dietary intervention and oral
– Insulin resistance.
– Older people, >40yrs and now rising dramatically in
  adolescents (strongly correlated with incidence of
– MZ concordance > 90%.
– +FH and obesity = greatest risk factors, regular
  exercise reduces risk.
– Numerous variable genetic associations, e.g.,
MODY (Maturity Onset of Diabetes in
          the Young)
• Before age 25.
• AD.
• Not associated with obesity.
• 50% cases occur due to a mutation in the glucokinase
  gene – enzyme that converts glucose-6-phosphate in the
• Also involved are 5 other genes involved in pancreatic
  development or insulin regulation:
• HNF1α, HNF1β, HNF4α, IPF1, NEU-ROD1
• Mutations in these genes, all expressed in the pancreatic
  beta cells, lead to beta cell abnormalities and diabetes.
                       Obesity I
• Causes about 30,000 deaths a year in the UK, through
  problems such as heart disease, stroke and diabetes.
• 23% of women and 21% of men were obese in 2001 –
  the figures are already higher.
• Compare these with the same figures for 1980 - 8% and
• Cost to the NHS £500m a year and rising.
• 16% of six to 15 year olds were obese in 2001; in 1990,
  that figure was 5% .
• Obesity in pre-school children was 9% in 1998.
• If current trends continue, at least a third of adults; a fifth
  of boys and a third of girls will be obese by 2020.
                     Obesity II
• Adoption and twin studies indicate that at least half of
  the variation in obesity may be caused by genes.
• Genes are involved in appetite control.
• Leptin is a hormone secreted by fat storage cells and
  binds to hypothalamus- appetite control centre.
• Increased fat stores > elevated leptin > satiety and loss
  of appetite.
• Mice deficient in leptin lead to uncontrolled appetite >
  obesity. When injected with leptin, mice lose weight.
• Leptin mutations in humans with severe obesity lead to a
  BMI (body mass index) >40, – this is v. rare.
• Other genes include neuropeptide Y; α melanocyte-
  stimulating hormone; POMC; TNF α ; MC4R; serotonin;
  serotonin receptor and many more.
Mice without the leptin gene are morbidly obese
(right) compared to normal mice (left).
Image courtesy Sebastien Bouret/University of Oregon (Google image).
     BMI – Body mass index
                           BMI =    Weight (kg)
                                   [Height (m)]2

 Normal                                   Severely   Morbidly
              Overweight      Obese
 Weight                                    Obese      Obese
BMI 20 - 25     25 - 30       30 - 35      35 - 40     > 40
         Alzheimer‟s Disease
• Dementia.
• Physical disease affecting brain.
• Accumulation of amyloid beta protein leads to
  plaques and tangles in the brain and results in
  death of brain cells.
• Progressive disease.
• No cure, survival approx 6yrs.
• Memory loss.
• Confusion.
• Shortage of important neurotransmitter
• Mood swings- Behavioural and psychological
  symptoms associated with dementia (BPSD).
            Alzheimer‟s Disease II
• Dementia currently affects over 750,000 people in the UK.
• Over 18,000 people with dementia are aged under 65 years.
• Dementia affects one person in 20 aged over 65 years and
  one person in five over 80 years of age.
• There is no single gene responsible for all cases of
  Alzheimer‟s disease.
• Genetic factors cause the disease in only a small number of
  families with dementia.
• Amongst cases without a family link, there is a genetic
  component to the disease; however, inherited factors alone do
  not explain why some people develop it and others do not.
What causes Alzheimer‟s disease?
• Age
• Genetic Inheritance
    • Early onset- „Familial Alzheimer‟s disease‟
       – Onset between 35 and 60
       – APP (amyloid precursor protein) C/s 21, PS1 (presenilin 1)
         C/s14, PS2 (presenilin 2) C/s. 1.
       – Autosomal dominant
    • Late onset
       – Majority of cases
       – Onset over 65
       – Apoe E4
• Environmental and other factors
                Amyloid cascade           Microglia

 (APP, PS-1)

Altered APP      Increased
metabolism       Ab 42

                             Amyloid plaques

(Head injury)
• Severe emotional disorder; delusions,
  hallucinations, retreat from reality,
  inappropriate behaviour.
• 47% concordance MZ, 12% DZ.
• Number of c/s regions implicated yet still
  no conclusive schizophrenia gene
 Conclusions: Common diseases
• The more strongly inherited then the
  generally earlier onset.
• Most have a genetic and an environmental
  contribution, therefore „destiny‟ is not purely
  genetically determined.
• Lifestyle modifies risk.
• Identification of contributing genes can help
  early identification for screening, early drug
  treatment and the possibly of gene therapy.