MEDICAL BIOCHEMISTRY

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MEDICAL BIOCHEMISTRY
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• Enzyme Kinetics
• Enzymes are protein catalysts that, like all
  catalysts, speed up the rate of a chemical
  reaction without being used up in the process.
• They achieve their effect by temporarily binding
  to the substrate and, in doing so, lowering the
  activation energy needed to convert it to a
  product.
• The rate at which an enzyme works is influenced
  by several factors, e.g.,
• the concentration of substrate molecules (the
  more of them available, the quicker the enzyme
  molecules collide and bind with them). The
  concentration of substrate is designated S and
  is expressed in units of molarity.
• the temperature. As the temperature rises,
  molecular motion and hence collisions between
  enzyme and substrate speed up. But as enzymes
  are proteins, there is an upper limit beyond
  which the enzyme becomes denatured and
  ineffective.
• the presence of inhibitors.
• competitive inhibitors are molecules that bind to
  the same site as the substrate preventing the
  substrate from binding as they do so but are
  not changed by the enzyme.
• noncompetitive inhibitors are molecules that bind
  to some other site on the enzyme reducing its
  catalytic power.
• pH. The conformation of a protein is influenced
  by pH and as enzyme activity is crucially
  dependent on its conformation, its activity is
  likewise affected.

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• The study of the rate at which an enzyme works is
  called enzyme kinetics. Let us examine enzyme
  kinetics as a function of the concentration of
  substrate available to the enzyme.
• We set up a series of tubes containing graded
  concentrations of substrate, S.
• At time zero, we add a fixed amount of the enzyme
  preparation.
• Over the next few minutes, we measure the
  concentration of product formed. If the product
  absorbs light, we can easily do this in a
  spectrophotometer.
• Early in the run, when the amount of substrate is
  in substantial excess to the amount of enzyme,
  the rate we observe is the initial velocity of
  Vi.

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• Plotting Vi as a function of S, we find that
• At low values of S, the initial velocity,Vi,
  rises almost linearly with increasing S.
• But as S increases, the gains in Vi level off
  (forming a rectangular hyperbola).
• The asymptote represents the maximum velocity of
  the reaction, designated Vmax
• The substrate concentration that produces a Vi
  that is one-half of Vmax is designated the
  Michaelis-Menten constant, Km (named after the
  scientists who developed the study of enzyme
  kinetics).
• Km is (roughly) an inverse measure of the
  affinity or strength of binding between the
  enzyme and its substrate. The lower the Km, the
  greater the affinity (so the lower the
  concentration of substrate needed to achieve a
  given rate).

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• Plotting the reciprocals of the same data points
  yields a "double-reciprocal" or Lineweaver-Burk
  plot. This provides a more precise way to
  determine Vmax and Km.
• Vmax is determined by the point where the line
  crosses the 1/Vi 0 axis (so the S is
  infinite).
• Note that the magnitude represented by the data
  points in this plot decrease from lower left to
  upper right.
• Km equals Vmax times the slope of line. This is
  easily determined from the intercept on the X
  axis.

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• The Effects of Enzyme Inhibitors
• Enzymes can be inhibited
• competitively, when the substrate and inhibitor
  compete for binding to the same active site or
• noncompetitively, when the inhibitor binds
  somewhere else on the enzyme molecule reducing
  its efficiency.
• The distinction can be determined by plotting
  enzyme activity with and without the inhibitor
  present.
• Competitive Inhibition
• In the presence of a competitive inhibitor, it
  takes a higher substrate concentration to achieve
  the same velocities that were reached in its
  absence. So while Vmax can still be reached if
  sufficient substrate is available, one-half Vmax
  requires a higher S than before and thus Km is
  larger.

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• Noncompetitive Inhibition
• With noncompetitive inhibition, enzyme
  molecules that have been bound by the inhibitor
  are taken out of the game so
• enzyme rate (velocity) is reduced for all values
  of S, including
• Vmax and one-half Vmax but
• Km remains unchanged because the active site of
  those enzyme molecules that have not been
  inhibited is unchanged.
• This Lineweaver-Burk plot displays these results.
  

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Amino acids
Each amino acid contains an "amine" group (NH3)
and a "carboxy" group (COOH) (shown in black in
the diagram).The amino acids vary in their side
chains (indicated in blue in the diagram).The
eight amino acids in the orange area are nonpolar
and hydrophobic.The other amino acids are polar
and hydrophilic ("water loving").The two amino
acids in the magenta box are acidic ("carboxy"
group in the side chain).The three amino acids
in the light blue box are basic ("amine" group in
the side chain).
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• ACIDIC AMINOACIDS

BASIC AMINOACIDS
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ESSENTIAL AA
Glucogenic amino acids Their carbon skeletons
are degraded to pyruvate, or to one of the 4- or
5-carbon intermediates of Krebs Cycle that are
precursors for gluconeogenesis. Glucogenic amino
acids are the major carbon source for
gluconeogenesis when glucose levels are low. They
can also be catabolized for energy or converted
to glycogen or fatty acids for energy storage.
Ketogenic amino acids Their carbon skeletons
are degraded to acetyl-CoA or acetoacetate.
Acetyl CoA, and its precursor acetoacetate,
cannot yield net production of oxaloacetate, the
precursor for the gluconeogenesis pathway. For
every 2-C acetyl residue entering Krebs Cycle,
two carbon atoms leave as CO2. (For review, see
notes on Krebs Cycle.) Carbon skeletons of
ketogenic amino acids can be catabolized for
energy in Krebs Cycle, or converted to ketone
bodies or fatty acids. They cannot be converted
to glucose.
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• Glucogenic amino acids Their carbon skeletons
  are degraded to pyruvate, or to one of the 4- or
  5-carbon intermediates of Krebs Cycle that are
  precursors for gluconeogenesis. Glucogenic amino
  acids are the major carbon source for
  gluconeogenesis when glucose levels are low. They
  can also be catabolized for energy or converted
  to glycogen or fatty acids for energy storage.
• Ketogenic amino acids Their carbon skeletons are
  degraded to acetyl-CoA or acetoacetate. Acetyl
  CoA, and its precursor acetoacetate, cannot yield
  net production of oxaloacetate, the precursor for
  the gluconeogenesis pathway. For every 2-C acetyl
  residue entering Krebs Cycle, two carbon atoms
  leave as CO2. (For review, see notes on Krebs
  Cycle.) Carbon skeletons of ketogenic amino acids
  can be catabolized for energy in Krebs Cycle, or
  converted to ketone bodies or fatty acids. They
  cannot be converted to glucose.
• STRICTLY KETOGENIC LEUCINE , LYSINE
• KETO and GLUCOGENIC ISOLEUCINE,
  THREONINE,TRYPTOPHAN, PHENYLALANINE

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The synthesis of serotonin, dopamine,
norepinephrine, and epinephrine from amino acid
precursors.
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• DISORDERS OF AMINO ACID METABOLISM
• This is a group of inherited defects of the
  degradation of amino acids. They include the urea
  cycle disorders, in which the defect involves
  conversion of the amino group to urea, and many
  of the organic acidemias, which are caused by
  defects in the disposal of the carbon skeletons
  of the branched chain amino acids after the
  initial transamination step. With the exception
  of ornithine transcarbamylase deficiency, which
  is X-linked, all amino acid disorders are
  autosomal recessive.

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• Clinical findings.
• Most amino acid disorders present in the neonatal
  period with a severe or fatal metabolic
  encephalopathy, which mimics perinatal asphyxia
  and sepsis. This encephalopathy is caused by the
  toxic effects of the accumulating amino acids and
  their intermediates, hyperammonemia, impairment
  of energy and synthetic pathways, and defective
  synthesis of neurotransmitters. The metabolic
  encephalopathy is often accompanied by
  respiratory depression, seizures, and
  hypoxic-ischemic brain injury. Survivors have
  psychomotor retardation, and suffer from
  recurrent neurotoxic episodes, which are
  triggered by metabolic stress, e.g., infections.
  The clinical picture in older patients resembles
  cerebral palsy. Less severe mutations cause
  milder illness, which presents later in life with
  developmental delay, episodes of metabolic
  decompensation, seizures, and ataxia. A few amino
  acid disorders (phenylketonuria, homocystinuria)
  have an insidious onset and a chronic course.

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The clinical, biochemical, and pathological
findings in the most common amino acid disorders
are summarized below.

• Nonketotic hyperglycinemia (defects of the
  glycine cleavage system)Elevated glycine in
  plasma and CSF Neonatal encephalopathy,
  psychomotor retardationSpongy myelinopathy,
  agenesis of the corpus callosum
• Urea cycle disorders(5 enzymes of the urea
  cycle)HyperammonemiaSeizures Neonatal
  encephalopathyBrain swelling, Alzheimer type II
  astrocytes
• Maple Syrup Urine Disease (defects of
  branched-chain ketoacid dehydrogenase
  complex)Accumulation of branched-chain amino
  acids and their ketoacidsNeonatal
  encephalopathy, psychomotor retardationBrain
  swelling, spongy myelinopathy
• Homocystinuria (cystathionine beta synthase
  deficiency)Elevated homocysteineThrombosis,
  Marfanoid habitus, dislocation of lensVenous and
  arterial thrombosis and cerebral infarcts

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INHERITED METABOLIC DISORDERS

• This section deals with the principles of
  lysosomal, peroxisomal, mitochondrial, and amino
  acid disorders, and highlights some important
  entities in these groups. There are many more
  inherited metabolic diseases that are beyond the
  scope of this web site. Many neurodegenerative
  diseases and muscle diseases are inherited
  metabolic disorders, the molecular and
  biochemical pathways of which we are now
  beginning to understand.

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• The diseases covered in this section are, for the
  most part, childhood disorders. In most of them,
  patients are normal at birth and have progressive
  neurological deterioration beginning at some
  later time. In some of them, the disease is
  manifested in adulthood. The clinical phenotype
  depends on the type and severity of the
  biochemical defect, i.e., what functions are lost
  and whether the loss is total or partial, and on
  structural-functional reserves, i.e., what
  resources are available to replace or cope with
  the loss. Most inherited metabolic disorders are
  autosomal recessive.

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LYSOSOMAL STORAGE DISORDERS-GENERAL PRINCIPLES

• The lysosomal storage disorders (LSDs) are due to
  deficiencies of lysosomal enzymes caused by
  mutations of genes that encode the enzyme
  proteins and related cofactors. Lysosomal enzymes
  degrade most biomolecules. The products of this
  degradation are recycled. This process is crucial
  for the health and growth of cells and tissues.
  LSDs result in accumulation (storage) of
  undegraded products in lysosomes. This causes
  enlargement of cells (ballooning), cellular
  dysfunction, and cell death. On electron
  microscopic examination, the stored products are
  membrane-bound because they are contained within
  lysosomes.

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• LSDs are rare. The most common among them are the
  mucopolysaccharidoses (MPS), which affect one in
  every 100,000 to 200,000 liveborn infants. The
  single most common LSD is Gaucher disease. Most
  LSDs are autosomal recessive. A few are X-linked.
  Patients are normal at birth. Manifestations of
  neurological disease begin in infancy or
  childhood. Initially, there is delay and then
  arrest of psychomotor development, neurological
  regression, blindness, and seizures. Inexorable
  progression leads to a vegetative state.

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CLINICAL MANIFESTATIONS AND PATHOLOGY

• The clinical manifestations of LSDs depend on
  which cells and tissues use the deficient enzyme
  and when is the period of its peak demand. For
  instance, neurons recycle large amounts of
  certain gangliosides which are components of
  their membranes and synapses. Enzymes of
  ganglioside degradation are highly expressed in
  brain tissue and are in great need at all times
  but especially in the first few years of life
  when axons elongate, dendrites branch, and
  synapses develop. Deficiency of these enzymes
  causes neuronal storage of gangliosides. Other
  gangliosides are components of myelin and their
  storage causes white matter disease.

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• LSDs have diverse clinical manifestations. Some
  of them share certain clinical and pathological
  features, on the basis of which four basic
  clinical-pathological phenotypes can be defined
  neuronal lipidosis, leukodystrophy,
  mucopolysaccharidosis, and storage histiocytosis.
  The most prevalent phenotype is neuronal
  lipidosis. A few LSDs have distinct clinical
  features.

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CLINICOPATHLOGICAL LSD PHENOTYPES
PHENOTYPE PATHOLOGY CLINICAL FINDINGS LSDs
NEURONAL LIPIDOSIS Storage in the neuronal body and processes Neurological regression, seizures,blindness Gangliosidoses, mucopolysaccharidoses, neuronal ceroid lipofuscinoses
LEUKODYSTROPHY Storage in oligodendrocytes and Schwann cells Neurological regression, spasticity, peripheral neuropathy Gangliosidoses (metachromatic leukodystrophy, Krabbe's disease)
MUCOPOLYSACCHARIDOSIS Storage in extraneural tissues Visceromegaly, soft tissue swelling, skeletal dysplasia, heart disease Mucopolysaccharidoses, glycoproteinoses, GM1 gangliosidosis
STORAGE HISTIOCYTOSIS Storage in histiocytes Hepatosplenomegaly, hematopoietic abnormalities Gangliosidoses (Gaucher disease, Niemann-Pick disease
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CLASSIFICATION

• The classification of the LSDs is based either on
  the deficient enzyme or on the chemical
  composition of the storage material. Eponymic and
  clinical terms supplement the biochemical
  nomenclature. In terms of the storage material,
  LSDs can be divided into three large groups, the
  sphingolipidoses, mucopolysaccharidoses, and
  glycoproteinoses and several other individual
  entities. Sphingolipids consist of a backbone of
  ceramide with attached oligosaccharide side
  chains. They are major constituents of cell
  membranes. Gangliosides have sialic acid side
  chains and are especially abundant in neuronal
  membranes. Galactosylceramide and sulfatide are
  myelin lipids. Glycosaminoglycans
  (mucopolysaccharides) are long unbranched
  molecules of repeating disaccharides. They are
  attached to core proteins forming proteoglycans.
  They are produced by most cells and are found
  mainly on the surface of cells and in the
  extracellular matrix. They are primarily
  structural molecules. Glycoproteins are also
  stuctural molecules, components of mucinous
  secretions, and have a variety of other
  functions.
• Most LSDs are caused by deficiencies of enzymes
  that degrade carbohydrate side chains and their
  storage materials are carbohydrates or other
  glycocompounds. The table below gives a
  simplified classification of the most common
  LSDs.

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THE MOST COMMON LSDs
LSD DEFICIENT ENZYME PHENOTYPE
SPHINGOLIPIDOSES SPHINGOLIPIDOSES SPHINGOLIPIDOSES
GM1 gangliosidosis b-galactosidase neuronal lipidosismucopolysaccharidosis
GM2 gangliosidosis(Tay-Sachs disease) hexosaminidase A neuronal lipidosis
Niemann-Pick Disease sphingomyelinase neuronal lipidosisstorage histiocytosis
Globoid cell leukodystrophy(Krabbe dis) galactocerebrosidase leukodystrophy
Metachromatic leukodystrophy arylsulfatase A leukodystrophy
Gaucher disease glucocerebrosidase storage histiocytosis
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THE MOST COMMON LSDs
LSD DEFICIENT ENZYME PHENOTYPE
MUCOPOLYSACCHARIDOSES glycosaminoglycan cleaving enzymes mucopolysacccharidosis
GLYCOPROTEINOSES glycoprotein cleaving enzymes mucopolysacccharidosis
GLYCOGENOSIS TYPE II (POMPE DISEASE) a-glucosidase skeletal and cardiac myopathy
NEURONAL CEROID LIPOFUSCINOSES lysosomal proteases neuronal lipidosis
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LABORATORY DIAGNOSIS OF LSDs

• The gold standard for diagnosis of LSDs is enzyme
  assay. For most LSDs, this can be performed on
  leukocytes with fast turnaround. It is important
  to narrow down the differential diagnosis to help
  decide which assay to order. Cultured fibroblasts
  are required in a few LSDs. Cultured amniocytes
  or chorionic villus cells may be used for
  prenatal diagnosis. Biochemical determination of
  storage products is cumbersome, but has some
  applications. For instance, demonstration of GAGs
  in urine is a useful screening test for GAG
  storage. Storage of abnormal products can be
  detected by light and electron microscopy. In
  addition to neurons, gangliosides and
  ceroid-lipofuscin are stored in somatic cells and
  may be detected by nerve, muscle, skin,
  conjunctival, and other biopsies. Tissue
  diagnosis (detection of specific storage
  materials by electron microscopy) is still the
  standard for some NCLs because no other
  laboratory tests are available. The gene
  mutations of LSDs can be detected by DNA
  analysis. Mutation analysis is used mainly for
  carrier detection.

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GLOBOID CELL LEUKODYSTROPHY (KRABBE'S DISEASE)

• About one third of myelin lipid consists of
  galactocerebroside and its sulfated variant
  sulfatide. Deficiency of galactocerebrosidase
  (GALC) causes a severe infantile leukodystrophy,
  Globoid cell leukodystrophy (GCL) or Krabbe's
  disease. Children with the most common infantile
  form of GCL appear normal at birth but, in a few
  months, develop irritability, spasticity,
  progressive neurological regression, peripheral
  neuropathy and seizures and usually die in one or
  two years, many in a few months. Patients with
  late onset forms have a more protracted course
  eventually leading to severe disability and
  death.

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 globoid cells
Krabbe's disease
In GCL, brain macrophages store
galactocerebroside and are transformed into
globoid cells. Most of the damage, however, is
caused by accumulation in the white matter of a
related metabolite galactosylsphingosine
(psychosine), which is toxic to oligodendrocytes.
The combined effects of lipid imbalance and
toxicity result in early and severe myelin
degeneration. The white matter in GCL is devoid
of myelin and axons (except for the subcortical
fibers), firm because of gliosis, and contains
globoid cells, which tend to accumulate around
vessels. The cortex is normal and there is no
galactocerebroside storage in neurons. There is
neuronal loss in the thalamus, cerebellum and
brainstem. Peripheral nerves show a demyelinative
and axonal neuropathy with accumulation of
galactocerebroside in Schwann cells and
macrophages.
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GAUCHER DISEASE

• Gaucher disease (GD) is due to deficiency of
  glucocerebrosidase (glucosylceramidase) and is
  characterized by storage of glucocerebroside
  (glucosylceramide) in monocyte-macrophage cells.
  Three clinical phenotypes are recognized. The
  most common is type 1 which is especially
  prevalent in Ashkenazi Jews. Type 1 GD presents
  from childhood to early adulthood and causes
  hepatosplenomegaly, bone disease (osteopenia,
  focal lytic or sclerotic lesions, osteonecrosis,
  pathologic fractures, chronic bone pain), anemia
  and thrombocytopenia due to hypersplenism, and
  pulmonary interstitial infiltrates. Spinal cord
  and root compression secondary to bone disease
  may also develop but there is no storage in the
  CNS. Type 2 (acute neuronopathic) GD patients
  have hepatosplenomegaly similar to type 1, but
  develop also neurological manifestations
  (stridor, strabismus and other oculomotor
  abnormalities, swallowing difficulty,
  opisthotonus, spasticity) which cause their death
  by 2 to 4 years of age. There is no special
  ethnic prevalence for type 2 GD. Type 3 (subacute
  neuronopathic) GD is frequent in Northern Sweden
  and has hematological and neurological
  manifestations similar to type 2 but milder and
  more slowly progressive. GD is the first LSD to
  be successfully managed by enzyme replacement.

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Gaucher cells
GD is the prototype of storage histiocytosis.
Lysosomal storage of glucocerebroside in cells of
the monocyte-macrophage system leads to a
characteristic cellular alteration of these
cells. Gaucher cells (GC) have a large
cytoplasmic mass with a striated appearance that
has been likened to "wrinkled tissue paper" or
"crumpled silk". GCs are present in the bone
marrow, spleen, lymph nodes, hepatic sinusoids,
and other organs and tissues in all forms of GD.
An increased incidence of cancer including
lymphoma, myeloma, and bone tumors has been
reported in GD patients. There is no storage in
neurons or glial cells. In type 2 and 3 GD, there
are numerous GCs in perivascular CNS spaces and
rare GCs in brain parenchyma. No part of the CNS
is spared but the brainstem and deep nuclei are
more severely affected than the cortex and
account for most neurological deficits. Along
with the presence of GCs, type 2 and 3 GD shows
also neuronophagia, neuronal loss, and gliosis.
No neuronal storage is seen. Neuronal
degeneration and loss have been attributed to the
neurotoxic action of glucosyl sphingosine, a
by-product of glucocerebroside not normally
present in the brain.
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MUCOPOLYSACCHARIDOSES (MPS)

• Mucopolysaccharides (now called
  Glycosaminoglycans-GAGs) are synthesized in the
  Golgi apparatus and secreted and assembled in the
  extracellular space. They are produced by all
  cells, and are especially abundant in connective
  tissues. They are an important component of the
  matrix of connective tissue, cartilage and bone.
  For recycling, GAGs are internalized and degraded
  in a stepwise fashion by lysosomal enzymes.
  Deficiency of these enzymes causes lysosomal
  storage of GAGs. There are six clinical groups of
  MPS caused by deficiencies of ten GAG-cleaving
  enzymes.

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• Intracellular storage of GAGs in hepatocytes and
  other cells causes hepatomegaly, cellular
  dysfunction, and cell death. The most severe
  somatic changes in the MPS are due to
  accumulation of GAGs in matrix due to impaired
  recycling and to discharge of GAGs from dying
  mesenchymal cells. Because they are negatively
  charged, GAGs attract a lot of water that causes
  their molecules to swell to tremendous volumes.
  High GAG content of connective tissues affects
  collagen synthesis and causes increased collagen
  deposition.

MPS
MPS thickened cardiac valves
MPS-coronary artery intimal thickening
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• The skin, connective tissues, and cartilage
  become swollen and distorted. The connective
  tissue and cutaneous changes cause facial
  deformity and macroglossia which gave rise to the
  insensitive term gargoylism. Cardiac valves and
  chordae tendineae become thickened and stiff.
  Endocardial and interstitial myocardial fibrosis
  develops. The intima of coronary arteries may be
  thickened to the point of occlusion and the aorta
  develops fibrous intimal plaques without lipid
  deposition. These changes cause a fatal
  cardiomyopathy and ischemic heart disease. GAG
  storage causes joint stiffening and swelling and
  complex skeletal deformities known as dysostosis
  multiplex. Storage in corneal fibroblasts causes
  corneal clouding.

MPS Hydrocephalus
MPS "zebra bodies"
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• GAG deposition in connective tissues of the brain
  and spinal cord causes thickening of the dura
  which along with distortion of vertebraeresults
  in compression myelopathy. Thickening of the
  arachnoid membrane impairs CSF flow, causing
  communicating hydrocephalus. But the most
  devastating neurological effects of MPS are due
  to neuronal storage of gangliosides. The
  mechanism of this storage is poorly understood.
  It is probably due to inhibition of neuraminidase
  and other lysosomal enzymes induced by the
  storage of GAGs. Thus, in addition to the
  skeletal, cardiovascular and other lesions, many
  MPS also cause neuronal lipidosis. Gangliosides
  stored in nerve cells take the form of concentric
  membranes (membranous cytoplasmic bodies) or
  stacks of membranes (zebra bodies).

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NIEMANN-PICK DISEASE TYPE C

• Type A and B Niemann-Pick disease are
  neurovisceral storage diseases caused by
  deficiency of sphingomyelinase. Niemann-Pick type
  C (NPC) is an LSD with protean clinical
  manifestations including neonatal hydrops,
  neonatal hepatitis, storage histiocytosis and
  neuronal lipidosis. The material that is stored
  in lysosomes in NPC is not sphingomyelin but
  cholesterol. Patients with NPC can import LDL
  cholesterol into lysosomes and remove the
  cholesteryl ester generating free cholesterol,
  but they cannot move free cholesterol to its
  normal cellular destinations. Thus, cholesterol
  accumulates in lysosomes. The mutant gene is
  located on 18q and its product, the NPC1 protein,
  is a transmembrane protein which acts as
  "gatekeeper" in the transport of lysosomal
  cholesterol to its other cellular targets. The
  "filipin test", which is used for diagnosis of
  NPC, consists of feeding cultured fibroblasts
  with LDL cholesterol tagged with the fluorescent
  dye filipin. The fibroblasts show bright
  fluorescence due to accumulation of cholesterol.
  NPC is rare but its study has produced some
  important insights into intracellular cholesterol
  homeostasis and trafficking.

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Carbohydrates - Sugars and Polysaccharides
Carbohydrates (also referred to as glycans) have the basic composition                                                                

• Monosaccharides - simple sugars,  with multiple
  hydroxyl groups. Based on the number of carbons
  (e.g., 3, 4, 5, or 6) a monosaccharide is a
  triose, tetrose, pentose, or hexose, etc.
• Disaccharides - two monosaccharides covalently
  linked
• Oligosaccharides - a few monosaccharides
  covalently linked.
• Polysaccharides - polymers consisting of chains
  of monosaccharide or disaccharide units.

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Common monosaccharides found in vertebrates.
N-Acetylneuraminic acid is the most common form
of sialic acid.
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HEZOSE KINASES
These enzymes phosphorylate glucose to
glucose-6-phosphate, which cannot get Out of the
cell. Glucokinase of the liver has a lowe
affinity, removing glucose when Blood
concentrations are high.
Hexokinase glucokinase
Organs Substrate specificity Affinity Vmax (capacity) Inhibited by glucose-6-phosphate Many Many hexoses High Low yes Liver Many hexoses Low High No
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Saccharide disorders
Inborn errors of metabolism that prevent
digestion or carbolism of saccharides. Clinical
symptoms are mostly due to accumulation of
metabolites
Enzyme defect Signs symptoms
Fructosuria Fructokinase Benign asymptomatic
Fructose intolerance Aldolase B Hyperglycemia Liver failure
Galactosemia Uridyltransferase Cataracts Mental retardation
Lactose intolerance Lactase (usually acquired) diarrhea
Diarrhea of any cause can result in temporary
laxtase deficiency
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Hereditary fructose intolerance disease
Hepatic fructose metabolism is quite rapid.  That
is, the initial step, phosphorylation by
fructokinase is rapid.  Further metabolism of
fructose is dependent upon aldolase B. 
Normally, fructose consumption leads to a rapid
flux into glycolysis at the triose phosphate
level, enhancing gluconeogenesis, glycolysis and
triglyceride synthesis . However, individuals who
have reduced levels of aldolase B exhibit
so-called fructose intolerance.   They build up
excessively high hepatic fructose-1-phosphate
levels, trapping inorganic phosphate and reducing
ATP synthesis accordingly.  In these people,
fructose is not a good substrate for glycolysis
or gluconeogenesis.  While the statistics on
this are not clear, it appears that somewhere
between 1 in 10,000 to 1 in 50,000 persons
exhibit fructose intolerance.  Declining ATP
levels interfere with many of the liver's
functions, among these are ureogenesis and
gluconeogenesis. 
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Glycogen storage diseases
The most common glycogen storage disease is
Type I von Gierkes, or hepatorenal glycogen
storage disease which results from a deficiency
of the liver enzyme glucose-6-phosphatase. This
enzyme converts glucose-6-phosphate into free
glucose and is necessary for the release of
stored glycogen and glucose into the
bloodstream, to relieve hypoglycemia. Infants
may die of acidosis before age 2 if they
survive past this age, with proper treatment,
they may grow normally and live to adulthood,
with only minimal hepatomegaly. However, theres
a danger of adenomatous liver nodules, which may
be premalignant. Signs and symptoms Primary
clinical features of the liver glycogen storage
diseases (Types I, III, IV, VI, and VIII) are
hepatomegaly and rapid onset of hypoglycemia and
ketosis when food is withheld. Symptoms of the
muscle glycogen storage diseases (Types II, V,
and VII) include poor muscle tone Type II may
result in death from heart failure. (See Rare
forms of glycogen storage disease.)
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Diagnosis Confirming diagnosis  Liver biopsy
confirms the diagnosis by showing normal glycogen
synthetase and phosphorylase enzyme activities
but reduced or absent glucose-6-phosphatase
activity. Glycogen structure is normal but
amounts are elevated. Spectroscopy may be used to
show abnormal muscle metabolism with the use of
magnetic resonance imaging in specialized
centers. ? Laboratory studies of plasma
demonstrate low glucose levels but high levels of
free fatty acids, triglycerides, cholesterol, and
uric acid. Serum analysis reveals high pyruvic
acid levels and high lactic acid levels. Prenatal
diagnoses are available for Types II, III, and
IV. ? Injection of glucagon or epinephrine
increases pyruvic and lactic acid levels but
doesnt increase blood glucose levels. Glucose
tolerance test curve typically shows depletional
hypoglycemia and reduced insulin output.
Intrauterine diagnosis is possible.
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Mucopolysaccharidoses

• The mucopolysaccharidoses are a group of
  inherited metabolic diseases caused by the
  absence or malfunctioning of certain enzymes
  needed to break down molecules called
  glycosaminoglycans - long chains of sugar
  carbohydrates in each of our cells that help
  build bone, cartilage, tendons, corneas, skin,
  and connective tissue. Glycosaminoglycans
  (formerly called mucopolysaccharides) are also
  found in the fluid that lubricates our joints. 
• People with a mucopolysaccharidosis either do not
  produce enough of one of the 11 enzymes required
  to break down these sugar chains into proteins
  and simpler molecules or they produce enzymes
  that do not work properly. Over time, these
  glycosaminoglycans collect in the cells, blood,
  and connective tissues. The result is permanent,
  progressive cellular damage that affects the
  individual's appearance, physical abilities,
  organ and system functioning, and, in most cases,
  mental development. 
• Who is at risk?
• It is estimated that one in every 25,000 babies
  born in the United States will have some form of
  the mucopolysaccharidoses. It is an autosomal
  recessive disorder, meaning that only individuals
  inheriting the defective gene from both parents
  are affected. (The exception is MPS II, or Hunter
  syndrome, in which the mother alone passes along
  the defective gene to a son.) When both people in
  a couple have the defective gene, each pregnancy
  carries with it a one in four chance that the
  child will be affected. The parents and siblings
  of an affected child may have no sign of the
  disorder. Unaffected siblings and select
  relatives of a child with one of the
  mucopolysaccharidoses may carry the recessive
  gene and could pass it to their own children. 

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• In general, the following factors may increase
  the chance of getting or passing on a genetic
  disease
• A family history of a genetic disease.
• Parents who are closely related or part of a
  distinct ethnic or geographic circle.
• Parents who do not show disease symptoms but
  carry a disease gene.
• The mucopolysaccharidoses are classified as
  lysosomal storage diseases. These are conditions
  in which large numbers of molecules that are
  normally broken down or degraded into smaller
  pieces by intracellular units called lysosomes
  accumulate in harmful amounts in the body's cells
  and tissues, particularly in the lysosomes.

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• signs and symptoms?
• The mucopolysaccharidoses share many clinical
  features but have varying degrees of severity.
  These features may not be apparent at birth but
  progress as storage of glycosaminoglycans affects
  bone, skeletal structure, connective tissues, and
  organs. Neurological complications may include
  damage to neurons (which send and receive signals
  throughout the body) as well as pain and impaired
  motor function. This results from compression of
  nerves or nerve roots in the spinal cord or in
  the peripheral nervous system, the part of the
  nervous system that connects the brain and spinal
  cord to sensory organs such as the eyes and to
  other organs, muscles, and tissues throughout the
  body. 
• Depending on the mucopolysaccharidoses subtype,
  affected individuals may have normal intellect or
  may be profoundly retarded, may experience
  developmental delay, or may have severe
  behavioral problems. Many individuals have
  hearing loss, either conductive (in which
  pressure behind the ear drum causes fluid from
  the lining of the middle ear to build up and
  eventually congeal), neurosensitive (in which
  tiny hair cells in the inner ear are damaged), or
  both. Communicating hydrocephalus ¾ in which the
  normal circulation of cerebrospinal fluid becomes
  blocked over time and causes increased pressure
  inside the head ¾ is common in some of the
  mucopolysaccharidoses. Surgically inserting a
  shunt into the brain can drain fluid. The eye's
  cornea often becomes cloudy from intracellular
  storage, and degeneration of the retina and
  glaucoma also may affect the patient's vision. 

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• Physical symptoms generally include coarse or
  rough facial features (including a flat nasal
  bridge, thick lips, and enlarged mouth and
  tongue), short stature with disproportionately
  short trunk (dwarfism), dysplasia (abnormal bone
  size and/or shape) and other skeletal
  irregularities, thickened skin, enlarged organs
  such as liver or spleen, hernias, and excessive
  body hair growth. Short and often claw-like
  hands, progressive joint stiffness, and carpal
  tunnel syndrome can restrict hand mobility and
  function. Recurring respiratory infections are
  common, as are obstructive airway disease and
  obstructive sleep apnea. Many affected
  individuals also have heart disease, often
  involving enlarged or diseased heart valves. 
• Another lysosomal storage disease often confused
  with the mucopolysaccharidoses is mucolipidosis.
  In this disorder, excessive amounts of fatty
  materials known as lipids (another principal
  component of living cells) are stored, in
  addition to sugars. Persons with mucolipidosis
  may share some of the clinical features
  associated with the mucopolysaccharidoses
  (certain facial features, bony structure
  abnormalities, and damage to the brain), and
  increased amounts of the enzymes needed to break
  down the lipids are found in the blood.

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• Types of the mucopolysaccharidoses?
• Seven distinct clinical types and numerous
  subtypes of the mucopolysaccharidoses have been
  identified. Although each mucopolysaccharidosis
  (MPS) differs clinically, most patients generally
  experience a period of normal development
  followed by a decline in physical and/or mental
  function.  
• MPS I is divided into three subtypes based on
  severity of symptoms. All three types result from
  an absence of, or insufficient levels of, the
  enzyme alpha-L-iduronidase. Children born to an
  MPS I parent carry the defective gene. 
• MPS I H, Hurler syndrome, is the most severe of
  the MPS I subtypes. Developmental delay is
  evident by the end of the first year, and
  patients usually stop developing between ages 2
  and 4. This is followed by progressive mental
  decline and loss of physical skills. Language may
  be limited due to hearing loss and an enlarged
  tongue. In time, the clear layers of the cornea
  become clouded and retinas may begin to
  degenerate. Carpal tunnel syndrome (or similar
  compression of nerves elsewhere in the body) and
  restricted joint movement are common. 
• Affected children may be quite large at birth and
  appear normal but may have inguinal (in the
  groin) or umbilical (where the umbilical cord
  passes through the abdomen) hernias. Growth in
  height may be faster than normal but begins to
  slow before the end of the first year and often
  ends around age 3. Many children develop a short
  body trunk and a maximum stature of less than 4
  feet. Distinct facial features (including flat
  face, depressed nasal bridge, and bulging
  forehead) become more evident in the second year.
  By age 2, the ribs have widened and are
  oar-shaped. The liver, spleen, and heart are
  often enlarged. Children may experience noisy
  breathing and recurring upper respiratory tract
  and ear infections. Feeding may be difficult for
  some children, and many experience periodic bowel
  problems. Children with Hurler syndrome often die
  before age 10 from obstructive airway disease,
  respiratory infections, or cardiac complications. 

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• MPS I S, Scheie syndrome, is the mildest form of
  MPS I. Symptoms generally begin to appear after
  age 5, with diagnosis most commonly made after
  age 10. Children with Scheie syndrome have normal
  intelligence or may have mild learning
  disabilities some may have psychiatric problems.
  Glaucoma, retinal degeneration, and clouded
  corneas may significantly impair vision. Other
  problems include carpal tunnel syndrome or other
  nerve compression, stiff joints, claw hands and
  deformed feet, a short neck, and aortic valve
  disease. Some affected individuals also have
  obstructive airway disease and sleep apnea.
  Persons with Scheie syndrome can live into
  adulthood.
• MPS I H-S, Hurler-Scheie syndrome, is less severe
  than Hurler syndrome alone. Symptoms generally
  begin between ages 3 and 8. Children may have
  moderate mental retardation and learning
  difficulties. Skeletal and systemic
  irregularities include short stature, marked
  smallness in the jaws, progressive joint
  stiffness, compressed spinal cord, clouded
  corneas, hearing loss, heart disease, coarse
  facial features, and umbilical hernia.
  Respiratory problems, sleep apnea, and heart
  disease may develop in adolescence. Some persons
  with MPS I H-S need continuous positive airway
  pressure during sleep to ease breathing. Life
  expectancy is generally into the late teens or
  early twenties. 

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• MPS II, Hunter syndrome, is caused by lack of the
  enzyme iduronate sulfatase. Hunter syndrome has
  two clinical subtypes and is the only one of the
  mucopolysaccharidoses in which the mother alone
  can pass the defective gene to a son. The
  incidence of Hunter syndrome is estimated to be
  one in every 100,000 to 150,000 male births. 
• Children with MPS II A, the more severe form of
  Hunter syndrome, share many of the same clinical
  features associated with Hurler syndrome (MPS I
  H) but with milder symptoms. Onset of the disease
  is usually between ages 2 and 4. Developmental
  decline is usually noticed between the ages of 18
  and 36 months, followed by progressive loss of
  skills. Other clinical features include coarse
  facial features, skeletal irregularities,
  obstructive airway and respiratory complications,
  short stature, joint stiffness, retinal
  degeneration (but no corneal clouding),
  communicating hydrocephalus (see "What are the
  signs and symptoms?"), chronic diarrhea, enlarged
  liver and spleen, and progressive hearing loss.
  Whitish skin lesions may be found on the upper
  arms, back, and upper legs. Death from upper
  airway disease or cardiovascular failure usually
  occurs by age 15.
• Physical characteristics of MPS II B are less
  obvious and progress at a much slower rate.
  Diagnosis is often made in the second decade of
  life. Intellect and social development are not
  affected. Skeletal problems may be less severe,
  but carpal tunnel syndrome and joint stiffness
  can restrict movement and height is somewhat less
  than normal. Other clinical symptoms include
  hearing loss, poor peripheral vision, diarrhea,
  and sleep apnea, although respiratory and cardiac
  complications can contribute to premature death.
  Persons with MPS II B may live into their 50s or
  beyond.

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• BILE ACIDS
• Bile acids are amphipathic (have both polar and
  unipolar parts) allowing them to emulsify
  otherwise insoluble lipids. If bile contains more
  cholesterol than what can be solubilized by bile
  acids and phospholipids , it will crystallize and
  form stones.95 of bile salts are reabsorbed in
  the ileum.

BILE ACIDS FEATURES
PRIMARY Cholic acid Chenodeoxycholic acid Derived from cholesterol
SECONDARY Deoxycholic acid Lithocholic acid Produced by primary conjugated bile salts by intestinal bacteria Less soluble - excreted
CONJUGATE Glycocholic acid (cholic acid glycine) Turocholic acid (cholic acid taurine) Ionized at physiologic ph Form micelles with dietary fats)
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• Glycero-phospholipids
• Spontaneously form lipid bilayers- cell membranes)

Phosphatidyl choline (lecithin) Phosphatidic acid choline
Phosphatidyl ethanolamine Phosphatidic acid ethanolamine
Phosphatidyl serine Phosphatidic acid serine
Phosphatidyl inositol Phosphatidic acid inositol
Cardiolipin 2 x Phosphatidic acid glycerine
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• Sphingo-phospholipids

Ceramide Sphingosine fatty acid
Sphingomyelin Ceramide choline

• Glycolipids

Cerebroside Ceramide mono saccharide
Globoside Ceramide oligosaccharide
Ganglioside Ceramide oligosaccharide NANA
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• SPHINGOLIPIDOSES
• Inborn errors of metabolism that prevent
  catabolism of sphingolipids. Clinical symptoms
  are due to accumulation of metabolites

Accumulate/enzyme Signs symptoms
Niemann-Pick A Sphingomyelin/ sphingomyelinase Liver and spleen enlargement foamy cells
Gaucher A Glucocerebrosidades/ beta glucosidase Liver spleen enlargement osteoporosis Ashkenazi Jews
Krabbe A Galactocerebrosides/ beta glucosidase Blindness, deafness convulsions globoid cells
Metachromatic leukodystrophy A Sulfatides/ beta galactosidase Progressive paralysis
Fabry X Globosides/ alpha galactosidase Reddish purple skin rash kidney heart failure angiokeratoma
Tay-Sachs A Gangliosides/hexosaminidase Blindness cherry red macula Ashkenazi Jews
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• PORPHYRIAS
• Heme is an iron containing derivative of
  porphyrin. Porphyrias are due to defects in heme
  synthesis and as a result precursors of heme
  accumulate.

Accumulate Photo-sensitivity Other signs
Acute intermittent Porphobilinogen No Abdominal pain
Cutanea tardia uroprphyrinogen Yes
Coproporphyria Coproporphyrinogen Yes Abdominal pain
Load poisoning Gamma ALA protoporphyrin No Anemia ( microcytic hyprochrome basophile stippling)
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• Preferred nutrients
• The heart is completely aerobic. In contrast,
  skeletal muscles can function anaerobically for
  some time. After a prolonged fast, metabolism
  adapts to preserve amino acids.

NORMAL PROLONGED FAST
BRAIN Glucose Ketone bodies glucose
Muscle Rest fatty acids Exercise glucose Fatty acids
Heart Fatty acids Ketone bodies Lactate Glucose Fatty acids Ketone bodies Lactate Glucose
Erythrocytes Glucose Glucose
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• The heart is completely aerobic. In contrast
  skeletal muscles can function anaerobically for
  some time.
• DURING FASTING
• The brain and RBC always need glucose
• The liver maintains glucose levels by
  glycogenolysis and gluconeogenesis
• Substrates for liver gluconeogenesis muscle, RBC
  lactate
• fat cells triglycerides- glycerol
• 4. Production of ketones by liver
  triglycerides-fatty acids- ketones

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• VITAMINS
• Vitamins are essential nutrients that cannot be
  synthesized by human cells. Deficiencies are mot
  common in poverty and chronic alcohol abuse.

Vitamin Function Signs of deficiency
A Part of rhodopsin Night blindness Growth retardation
D GI tract Ca absorption Bone supports PTH Rickets, osteomalacia
E Antioxidant Ataxia
K Carboxylation of Glutamate Bleeding disorders (II,VII, IX, X)
C Hydroxylation of Proline and lysine Scurvy
B1 thiamine Decarboxylations beriberi
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B2 riboflavin Flavins (FMN) Glossitis, cheilosis
B6 pyridoxine Transaminations Deaminations Microcytic anemia neuropathy
B12 Methionine synthesis Odd carbon fatty acid Degradation Macrocytic anemia Neuropathy D. latum infestations
NIACIN NAD, NADP Pellagra (Diarrhea, dementia, dermatitis)
Pantothenate Coenzyme A Headache, nauseas
Biotin Carboxylations Seborrheic dermatitis Nervous disorders Raw egg white binds biotin
Folic acid One carbon metabolism Mycrocytic anemia Glossitis, colitis
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ATP EQUIVALENTSFat (9 kcal/g) is more rich in
energy than protein (4 kcal/g) or sugar
(4kcal/g). Here is why
YIELD EXPLANATION
FADH2 NADH 2 3
Acetyl CoA Pyruvate 12 15 Acetyl CoA 2CO2 3NADH FADH3 GTP Pyruvate acetylCoA NADH
Glycolysis (anaerobe) Glycolysis (aerobe) Glucose (complete oxidation) Fatty acid 2 8 38 129 Glucose lactate 4ATP minus 2 ATP Glucose pyruvate (4ATP MINUS 2 ATP) 2NADH Glucose 6 CO2 (8 2X15 PYRUVATE)
Gluconeogenesis Urea synthesis -12 -4
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• 2 ATP are required for hexokinase and
  fructokinase reactions
• Glycerophosphate shuttle (yields 2 ATP per NADH)
  reducing equivalents are transferred from
  cytosolic NADH to mitochondrial FADH2
• Malate shuttle (yields 3 ATP per NADH) reducing
  equivalents are transferred from cytosolic NADH
  to mitochondrial NADH.

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Key enzymes sugarsMost metabolic pathways
are regulated by one or two key enzymes which can
be allosterically activated or inhibited.
Sometime enzyme activity is dependent on
phosphorylation.

• Carbohydrate metabolism

Enzyme Allosteric inhibitors Allosteric activators Effect on phosphorylation
glycolysis Phosphofructokinase 1 ATP Citrate AMP Fructose 2,6dp
Phosphofructokinase 2 inhibits
gluconeogenesis Fructosediphosphotase 1 AMP Fructose 2,6 dp ATP Citrate
Fructosediphosphotase 2 activates
Glycogenolysis Glycogenphosphorylase activates
Glycogen synthesis Glycogen synthetase inhibits
Pentose phosphate path. Glucose-6-phosphate dehydrogenase NADPH
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Key enzymes- fats

• Fat metabolism

Enzyme Allosteric inhibitor Allosteric activators Effect on phosphorylation
Lipolysis Carnitine acyltransferase Malonyl CoA
Fat mobilization Hormone sensitive lipase activates
Lipid synthesis Acetyl-CoA carboxylase Citrate Inhibits
Cholesterol synthesis HMG CoA reductase Cholesterol inhibits
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Key enzymes - others

• Other pathways

Enzyme Allosteric inhibitors Effect on phosphorylation
Ketone body synthesis HMG CoA synthase
Purine synthesis Amidotransferase AMP GMP IMP
Citric acid cycle Pyruvate dehydrogenase Inhibits Acetyl CoA ATP NADH
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Steroids made from cholesterol
CLASS EXAMPLE Number of c-atoms
Sterols Cholesterol 27
Bile acids Glycocholate Taurocholate 24
Glucocortocoids Cortisol 21
Mineralocorticoids Aldosterone 21
Gestagens Progesterone 21
Androgens Testosterone Androstenedione DHEAS 19
Estrogens Estradiol Estriol 18
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• 17 Ketosteroids (dehydroandrosterone and
  androstenedione)
• 11-hydroxylase deficiency
• 21-hydroxylase deficiency
• Cushings syndrome
• Androgen producing adrenal or gonadal tumors
• 17-Hydroxysteroids (cortisol metabolites)
• 11-hydroxylase deficiency
• Cushings syndrome

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Some deficiencies

• 17 alpha-hydroxylase deficiency
• Male ambiguous genitalia
• Female primary amenorrhea at puberty
• 21-alpha-hydroxylase deficiency (most common
  defect of corticoid synthesis, 95)
• Male precocious puberty ( incrs. DHEA)
• Female ambiguous genitalia (incrs. DHEA)
• Salt wasting 50-60 of patients (lack of
  aldosterone)
• 11-BETA-HYDROXYLASE
• Male precocious puberty (incrs. Androgens)
• Female ambiguous genitalia (incrs. androgens)
• Salt retention hypertension, hypokalemia
  (deoxycorticosterone has mineralocoticoid action)

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Endocrine Control of metabolismLliver
Mmuscle Ffat A-anabolic Ccatabolic
Fat Sugar Proteins
Insulin Synthesis (A) Uptake (M, F) (A) Glycolysis ( L, M) Glycogen synthesis ( L, M) Synthesis (A)
glucagon Lysis (C ) Gluconeogenesis (L) (C ) Glycogenolysis (L) Incrs. Uptake of (C ) AA in liver for gluconeogenesis
Growth hormone Lysis (C ) Gluconeogenesis (L) ( C ) Synthesis (A)
Cortisol Lysis (C ) Redistribution Inhibits uptake (M,F) Gluconeogenesis (L) Glycogen synthesis (L) (A) Degradation (C )
epinephrine Lysis (C ) Incrs. Uptake (M) (C ) Glycolysis (M) Gluconeogenesis (L) Glycogenolysis L, M)
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NUCLEOTIDESNucleosides are purines or
pyrimidines linked to a pentose
sugar.Nucleotides are phosphates of the
nucleosides
BASE NUCLEOSIDE NUCLEOTIDE
PURINES Adenine Guanine Adenosine Guanosine Adenylate (AMP) Guanyalate (GMP)
PIRIMIDINES Uracil Cytosine thymine Uridine Cytidine Deoxythymidine Uridylate (UMP) Cytidylate (CMP) Deocythymidylate (dTMP)
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AZT

• THYMIDINE

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• AZT (zidovudine) can be incorporated into DNA by
  viral reverse transcriptase. Lock of the 3 -OH
  group then inhibits further elongation of DNA
• Mammalian polymerase is less likely to mistake
  AZT for thymidine

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PURINESPurines can be either made de novo,
from amino acids or they can be recycled.
Recycling is especially important for tissues
with rapid cell turn over like epithelia or blood
cells.

• De novo synthesis in liver
• Phosphoribosyl pyrophosphate -gt IMP
• Imp -gt AMP or GMP -gt ADP or GDP
• Salvage of purine bases (recycling)
• Hypoxanthine -gt IMP
• Guanine -gt GMP
• Adenine -gt AMP
• Lech-Nyhan Defective phosphoribosyl transferase
  Purine bases cannot be salvaged and are all
  degraded to uric acid leading to gout, sever
  neurologic signs.

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• 3. Degradation of purine bases in liver
• Adenosine -gt inosine -gt hypoxanthine -gt xanthine
• Guanosine -gt guanine -gt xanthine
• Xanthine -gt uric acid
• Allopurinol inhibits conversion of xanthine to
  uric acid used to treatment of gout.

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PyrimidinesLike the purines, pyrimidines can
be made de novo or recycled

• De novo
• Glutamine -gt carbamoylphosphate -gt OMP -gtUMP
• UTP -gt CTP
• dUMP -gtdTMP
• 2. Salvage of pyrimidine bases
• Uracil -gt UMP
• Cytosine -gt CMP
• 3. Degradation of pyrimidine bases Pyrimidine
  rings can be opened and completely degraded.
• Cytosine -gt CO2, NH4 and beta alanine
• Thymine -gt CO2, NH4 and beta amonoisobutyrate
• These degradation products are harmless and
  excreted in urine.

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Gene expressionWhen studying molecular biology
you must pay attention to differences between
prokaryotes and eukaryotes. While he principles
are the same, the details are different.

• Bacteria (prokaryotes)

Operon (DNA) Operational unit that is either on or off Consists of promoter, operator and one or more structural genes
Promoter (DNA) RNA polymerase binds to promoter Located 5 end or operon (upstream)
Operator (DNA) Located between promoter and structural genes Binding site of repressors If repressor binds to operator, the operon is off and polymerase cannot proceed
Repressor (protein) Regulated protein that binds to operator and prevents transcription
Regulator gene ( DNA) Codes for repressor
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• Iac- OPERON
• Metabolite (lactose) binds to repressor
  preventing its interaction with DNA
• Operon freed of repressor is switched on and
  polymerase begins transcription of structural
  genes
• Gene products beta galactosidase plus two other
  proteins

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Humans (eukaryotes)

• No operon. Each structural gene has its own
  promoter containing many different response
  elements (binding sites for regulatory proteins)
• Regulatory proteins can bind to several promoters
  activating a set of structural genes which may be
  located on different chromosomes.
• Transcription is regulated by various
  combinations of regulatory proteins.

Transcription factor Binds to TATA box (art of promoter) RNA polymerase does not recognize promoter in absence of transcription factor
Inducers Ex steroid hormones Bind to nuclear receptor protein Inducer-receptor complex binds to DNA and activates some gene while inactivates others
Enhancers Regulatory DNA sequence Can be upstream or downstream of promoter May be located several thousand base pairs from starting point of transcription Loops in DNA bring enhancers near the promoter region of the gene.
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Transcription DNA -gtRNAmessenger RNA
are the working copies of the DNA. While cells
from different tissues of the body have the same
DNA, they differ in their gene expression and
have different sets of messenger RNA. If you want
to know which genes are active you can make c
DNA LIBRARY COMPLIMENTARY DNA synthesized to all
RNA present in a cell.

• Bacteria ( prokaryotes )

Holoenzyme core enzyme plus delta factor
Delta factors Bind to RNA polymerase Depending on delta factor, RNA polymerase Recognizes certain promoters but not others
Cistron Region of DNA that encodes a single protein
Prokaryotic messenger RNA is polycistronic (
encodes multiple proteins)
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• Human (eukaryotes)

Polymerase I Makes r NRA
Polymerase II Makes m RNA
Polymerase III Makes t RNA

• Eukaryotic m RNA is heavily processed I the
  nucleus.
• 5-cap (methylated GTP) is added
• Poly (A) tail is added to 3 end
• Introns are removed and exons are spliced together

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Replication DNA -gt
RNAReplication of DNA is semi conservative
parental strands separate and each serves as a
template for a newly synthesized one. DNA
polymerase cannot initiate synthesis of a new
strand but require a primer (short
oligonucleotide sequence composed of RNA). The
primer is later replaced by DNA.

• Parental strand is read in 3 to 5 direction
• New strand is produced in 5 to 3 direction

BACTERIA helicase Separates parental DNA
Primase RNA polymerase that copies parental strand and makes RNA primer.
Polymerase III Major DNA polymerase replicates both parental strands has proofreading ability has 3 exonuclease activity to remove wrong nucleotides
Polymerase I Removes primer and fills gap with DNA (5 exonuclease activity)
Polymerase II DNA repair (3 exonuclease activity)
Ligase Jinks Okazaki fragments of lagging strand
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Human (eukaryote)
Delta Major DNA polymerase Produces leading strand Has helicase activity No proofreading No exonuclease activity
Alpha DNA polymerase Produces lagging strand Has primase activity
Beta, epsilon Minor DNA polymerases DNA repair ( 3 exonuclease activity)
Gamma Mitochondrial DNA polymerase
Ligase Joins Okazaki fragments of lagging strand.
Endonuclease Incision of DNA Exonuclease
Removal of nucleotides from incised end