April 25, NATIONAL DNA DAY.


http://www.genome.gov/dnaday/

60 years today of the publication of “Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid”

http://www.fossilmuseum.net/Biology/WatsonCrickNature.htm

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“Extraordinary Measures” – A Movie about Pompe’s Disease


 

Extraordinary Measures is a 2010 film about parents trying to save their children affected by Pompe Disease, A Glycogen Storage Disease produced by mutations on a gen that makes the enzyme acid alpha Glycosidase (GAA), a lysosomal hydrolase.

 Pompe disease is a rare (estimated at 1 in every 40,000 births), inherited and often fatal disorder that disables the heart and muscles.

The movie is based on the true story of John and Aileen Crowley, whose two youngest children were affected with Pompe Disease.

The real John Crowley

As you know Glycogen storage diseases are genetic enzyme deficiencies that result in excessive glycogen accumulation within cells. Additional symptoms depend on the particular enzyme that is deficient.

There are different forms of Glycogen Storage Diseases (aka Glycogenoses), including the Type Ia GSD or Von Gierke’s disease, caused by hepatic deficiency of Glucose 6 Phosphatase, the Type IV or Andersen’s Disease, caused by deficit of branching enzyme in various organs, including the liver, and the GSD Type V or McArdle’s Disease (caused by muscle deficiency of Glycogen Phosphorylase), among others.

GSD Type II or Pompe’s Disease was described by Pompe in 1932, when he studied a girl who suffered from a cardiopathy caused by glycogen accumulation.

The National Institute of Neurological Disorders and Stroke (NINDS), an Institute of the National Institutes of Health System, describe the disease in these terms:

 

“Early onset (or infantile Pompe disease is the result of complete or near complete deficiency of GAA.  Symptoms begin in the first months of life, with feeding problems, poor weight gain, muscle weakness, floppiness, and head lag. Respiratory difficulties are often complicated by lung infections.  The heart is grossly enlarged. More than half of all infants with Pompe disease also have enlarged tongues.  Most babies with Pompe disease die from cardiac or respiratory complications before their first birthday. 

 

Late onset (or juvenile/adult) Pompe disease is the result of a partial deficiency of GAA.  The onset can be as early as the first decade of childhood or as late as the sixth decade of adulthood.  The primary symptom is muscle weakness progressing to respiratory weakness and death from respiratory failure after a course lasting several years.  The heart may be involved but it will not be grossly enlarged.  A diagnosis of Pompe disease can be confirmed by screening for the common genetic mutations or measuring the level of GAA enzyme activity in a blood sample — a test that has 100 percent accuracy.  Once Pompe disease is diagnosed, testing of all family members and consultation with a professional geneticist is recommended.  Carriers are most reliably identified via genetic mutation analysis.

A diagnosis of Pompe disease can be confirmed by screening for the common genetic mutations or measuring the level of GAA enzyme activity in a blood sample — a test that has 100 percent accuracy.  Once Pompe disease is diagnosed, testing of all family members and consultation with a professional geneticist is recommended.  Carriers are most reliably identified via genetic mutation analysis.”

“…Individuals with Pompe disease are best treated by a team of specialists (such as cardiologist, neurologist, and respiratory therapist) knowledgeable about the disease, who can offer supportive and symptomatic care.  The discovery of the GAA gene has led to rapid progress in understanding the biological mechanisms and properties of the GAA enzyme.  As a result, an enzyme replacement therapy has been developed that has shown, in clinical trials with infantile-onset patients, to decrease heart size, maintain normal heart function, improve muscle function, tone, and strength, and reduce glycogen accumulation.  A drug called alglucosidase alfa (Myozyme©), has received FDA approval for the treatment of infants and children with Pompe disease.  Another alglucosidase alfa drug, Lumizyme©, has been approved for late-onset (non-infantile) Pompe disease. ..”

“…Without enzyme replacement therapy, the hearts of babies with infantile onset Pompe disease progressively thicken and enlarge.  These babies die before the age of one year from either cardiorespiratory failure or respiratory infection.  For individuals with late onset Pompe disease, the prognosis is dependent upon the age of onset.  In general, the later the age of onset, the slower the progression of the disease.  Ultimately, the prognosis is dependent upon the extent of respiratory muscle involvement. …”

 It is interesting that even when the Acid Alpha-glycosidase is only involved in the degradation of about 3 % of the Glycogen, its deficit provokes such important damages. Since this enzyme is not related to the main pathways of degradation of glycogen, its deficit does not produce hypoglycemia or a direct lack of metabolic energy. Cellular damage is caused mainly by accumulation of glycogen in the cytoplasm and the lysosomes.

As describe above, nowadays the treatment is based on the use of a recombinant human acid Glycosidase as a replacement of the normal enzyme.  “Extraordinary Measures” describes, in fact, the events that triggered the development of the enzyme for the treatment of this disease.

My favorite quotes of this movie:

John Crowley (Looking at the college-aged kids hired to work under Dr. Stonehill):

-These guys make me feel old.
Dr. Robert Stonehill:

– Scientists get all sensible & careful when they get old. Young ones like risk, not afraid of new ideas… and you can pay ’em less.

 

John Crowley (talking with Dr. Stonehill after an argument):

–  “Fine, spend the rest of your life dreaming up great ideas that don’t get funded. Draw your diagrams on the wall that cure diseases in theory but never help a single human being in reality.”

 

John Crowley (arguing with a corporate executive about drug research):

–  “This is not about a return on an investment, it’s about kids. Kids with names, dreams, families that love them.”

 

Recommended articles and links:

NINDS Pompe Disease Information Page

Ibrahim, J.; McGovern, M. M.

Glycogen Storage Disease Type II

Some pictures of the Crowley family

How many calories in an Apple Pie?


 

Of course, there are many different apple pies, and many different serving portions  too!!!

So…let’s do the calculations with a “standar” apple pie…certainly not the best but it is standard, so standard that it is the same all around the world!

Of course, I am talking about the MacDonald Apple pie!

Nutrition facts of the Macdonald baked Apple pie (taken from the label):

Proteins 2g

Fat 13 g

Carbohydrates 32 g

Sodium 170 mg

How many calories are obtained when you eat 1 serving size of this pie?

Biochemistry of Platelets: Overview


Platelets or thrombocytes are blood cells which participate in the coagulation of blood.

 

Source of platelets.

 

Platelets are formed from their precursors in the hematopoietic tissue. 

 

Platelets, like other blood cells, are formed from Hemocytoblast that under certain conditions, and mainly under the effects of thrombopoietin, may be converted in a megacarioblast. Megacaryoblast is transformed into Promegacariocyte, and this cell in Megakaryocyte.

 

During Megakaryocyte maturation process,   DNA replication continues, and the nucleus suffers many divisions, but the cell continue undivided. While this process is going on, a large amount of cytoplasm accumulates.

 

Platelets are formed by the development of demarcation membranes in the cytoplasm, with subsequent release of the formed fragments to the venous sinusoids of the marrow bone.

 

A Megakaryocyte can release thousands of platelets, leaving the parenchyma cell with virtually only the nucleus and residual cytoplasma.

 

 

General structure:

 

Platelets are very small (1 to 4 microns in diameter) and circulate between 4 and 10 days, as flattened disks without nucleus. Platelet membrane is very rich in phospholipids and contains various glycoproteins that perform a fundamental role in the reception and transduction of intracellular signals. The cytoplasm of platelets contains a microphylament system and an actin/myosin contractile structure, called thrombosthenin, which, when activated, modify the conformation of the membrane. The cytoplasm also contains microtubules, which together with the microfilaments form an internal cytoskeleton responsible for the platelets conformation, but at the same time flexible enough to allow the conformational changes that occur during the platelet activation.

 

Platelet cytoplasm contains also residual endoplasmic reticulum(forming the so-called dense tubular system), mitochondria, glycogen and three different types of granules: Alpha granules, dense granules and lysosomal granules, containing biologically active substances that are released during the coagulation process The energy for platelet processes (aggregation, secretion and others) derive from the aerobic metabolism  in the mitochondria and anaerobic glycolysis (recall that the cytoplasm contains glycogen granules)

 

Platelet receptors and granules are particularly interesting from the physiological and medical point of view, so they will be discussed in more detail in future posts.

 

Recommended articles:

 

Flaumenhaft, R. et al:

The actin cytoskeleton differentially regulates platelet (alpha)granule and dense granule secretions.

 

The Online Metabolic and Molecular Bases of Inhereted Diseases.

The inhereted disorders of platelets

 

Wikipedia:

Platelet.

Biochemistry of the Complement System


 

 

The binding of the antibody and the antigen is not enough sometimes to give an effective protection against the invader agent; that is why it is necessary the complementary action of other components of the immunological system able to neutralize or promote the neutralization of the foreign agent.  

 

Complement system is a set of proteins that form a biochemical cascade which participates in the immunological mechanisms of the body. This system, several times, act complementary (and as result) of the antigen-antibody interaction, but some times can even act independently of the action of antibodies.

 

The proteins that form this system are mainly proteolytic enzymes in form of  zymogens, that when the mechanism is initiated, are activated and trigger defense mechanisms that include a wide range of actions,  from the activation of  phagocytosis to the lysis of foreign cells. Other complement proteins act as cofactors while others act as inhibitors.

 

Most of the proteins that form the complement system are synthesized in the liver. Complement proteins form approximately 5 % -10 % of plasma globulins. They are components of the acute phase response and their concentration in blood is increased during infections, injuries, and traumas. Most of these proteins are named with a C letter and a number that was assigned in the order that they were discovered.

 

The functions of the complement system include:

 

1. – Cell lysis

2. – Stimulation of phagocytosis through opsonization.

3. – Attraction of phagocytic cells through chemotaxis

4. – Contribution to the inflammatory and allergic reactions, by stimulating degranulation and release of intracellular enzymes, histamine, etc.

5. – Facilitation of immune complex elimination.

 

Activation of the complement system can happens through any of the following mechanisms:

 

1. – Classic complement pathway.

2. – Alternative pathway

3. – Mannose-binding Lectine pathway.

 

In the classic activation pathway, the antigen-antibody interaction provokes allosteric changes in the immunoglobulin that exposes, in the constant region 2 the heavy chains (HC2), a binding site for C1q, a protein of the complement system.  The binding (and subsequent activation) of C1q to the constant region of the heavy chains activates two other proteins of the complement system: C1s and C1r.  C1s is a serine protease which acts on C4; when C4 is activated, C4 acts on C2.  The active fragments of C4 and C2 form the complex C3 convertase, which hydrolyzes C3. (C1q can be activated also by mycoplasms, bacterial endotoxins, RNA virus, and some membranes, in the absence of antibodies)

 

When C3 is activated the signal is highly amplified, since C3 is the most abundant protein of the complement system, and it can experiment also self-activation.  The C3 b derived from C3 binds to glycoproteins in the cell surface. Since macrophages and neutrophils have C3b receptors, they recognize the cells covered with C3b and phagocyte them.

 

Another part of C3b binds to C5 forming a complex that is hydrolyzed by C3 convertase (aka C3/C5 convertase).This hydrolysis produce C5a, which attracts neutrophils, and C5b. C5b form a complex in the cellular membrane with C6, C7 and C8. This complex guide the polymerization of around 15 molecules of C9, to form a pore that goes through the membrane lipid bilayer of the foreign cell,  allowing the passage of ions and small molecules, and provoking the cell lysis.  This complement complex is called the Complement Membrane Attack Complex (MAC).

 

The following video shows a version of this process:

 

 

The alternative pathway occurs in the absence of the antigen:antibody complex.  Usually, a certain quantity of C3 is spontaneously hydrolyzed releasing 3a and 3b. In normal conditions, 3b is inactivated, but in the presence of bacteria, or invader particles or molecules (virus, fungus, bacteria, parasites, snake’s venoms, or Ig A)  3b can bind to the bacteria membrane and interact with other plasma protein, Factor B, forming a C3bB complex. This complex, when hydrolyzed by another protein (Factor D) releases Ba and becomes a C3bBb complex, with C3/C5 convertase activity. This complex triggers ulterior changes that provoke the formation of the Membrane Attack complex and the invader cell lysis. (Some proteins,  Factor H and factor I inhibit C3 convertase, while properdin stabilizes C3 convertase active conformation)

 

 

A third form of complement activation is the Mannose-binding Lectine pathway. In this pathway, the Mannose-Binding Lectine (MBL), a serum protein that is able to link to mannose and other monosaccharides in the glycolipids and glycoproteins of the surface of the invader cells, form a complex with two serine proteases zymogens (Mannose-binding lectin Associated Serine Proteases)  MASP-I and MASP-II. When the MBL binds to the oligosaccharides on the bacteria, virus and fungus surface, the serine proteases result activated and hydrolyze C4 and C2 proteins, triggering the complement cascade.

 

 

It does not matter which activation mechanism is used, the three of them converge in the formation of a complex with C3 convertase activity, formation of C3b and the progression of the cascade that culminates with the foreign cell lysis.

 

 

Even when different textbooks differ in some specific details, the fact is that the complement system main functions include:

 

1.- Opsonization (marking foreign cells for phagocytosis; e.g. C3b)

2.- Chemotaxis (attraction of neutrophils to the invader agent; e.g. C5a)

3.- Lysis of invader cells (Ex C5, C6, C7, C8, and C9)

4.- Contributing to the inflammatory and allergic response,  by stimulating cell degranulation and release of enzymes, histamine, and other substances (Effects of C3a, C4a, C5a)

5.- Promoting the elimination of immune complexes (Ex. C3b )

 

This video summarizes the mechanism of action of the complement system (some small  details are different; do not care about that and pay attention to the big picture):

 

 

 Complement system dysfunction is related to some diseases, like acquired or congenital deficit of individual complement components. In these diseases, the patient shows an increased susceptibility to Neisseria or pyogenic infections.

There is also an important association between the deficiency of complement factors and immunological diseases of the type of Systemic Lupus Erythematosus, and other collagen and vascular diseases, as well as with some cases of chronic nephritis, angioedema, etc.

 

Additional information can be found in the following links:

 

Complement System

 Complement Membrane Attack Complex

 Moore, E.:

Complement Deficiencies.

When the immune system has  inadequate levels of Complement proteins

 

Gupta, R.; Agraharkar, M.:

Complement Related Disorders

 Chaganti, K.R. et al:

Complement Deficiencies

 Glovski, M. et al:

Complement determinations in human disease

Immunoglobulins: structure and functions.


 

Angel of the West (This sculpture represents an IgG molecule)

 

Immunoglobulins are glycoproteins that function as antibodies. In fact, the terms antibodies and immunoglobulins are usually used indistinctly: immunoglobulins highlight structure and antibody highlights function. Immunoglobulins can be found attached to the B-cell membranes, in secretions or circulating in blood.

 

Immunoglobulins are produced as a response to the detection of foreign molecules in our body. These foreign substances that trigger the production of antibodies are called antigens.

 

Circulating immunoglobulins are included in the plasma protein fraction of the gamma globulins.

 

Plasma Electrophoresis

 

 

 

 

 

 There are different types of immunoglobulins: IgG, IgM, IgA, IgD and IgE. All of them have in common that their basic unit is formed by two pairs of peptide chains: a pair of Light chains or L chains (approximately 220 amino acids each) and a pair of Heavy chains or H chains (around 440 amino acids each).

 

These four chains in the basic structure are linked through disulfide bridges between cystein residues in the backbone of the peptide chains. Each Light chain is linked to one Heavy chain and each Heavy chain is associated to a Light chain and to the other Heavy chain.

 

The following graphic shows the Heavy chains in blue, the Light chains in green and the disulfide linkages between the chains in red (there are additional intrachain disulfide bridges that are not shown in this graphic)

 

 

Observe also in the graphic that in the L chains can be distinguished two regions or domains: VL and CL, while in the H chains, 4 regions or domains can be found:  VH, CH1, CH2 and CH3. Each of these regions is composed by 70 to 110 amino acids.

 

The V regions are Variable regions: the amino acid sequence in these regions (the NH2- terminal regions of L and H chains) is highly variable, and within them, in the L and in the C chains, there are hyper variable regions (CDRs of Complementarity-determining regions) that form the specific antigen binding site complementary to the specific antigen.

 

 

This video shows the structure of a typical immunoglobulin IgG:

 

 

As you have seen, there are two binding sites for antigens in each (LH)2 unit. When a (LH)2 unit is hydrolyzed with papain, three fragments are released: two Fab and one Fc fragment.

 

 

The Fab fragments contain the structure that is able to bind to the antigen (Fab = Fragment antigen-binding), while the Fc fragment (c means crystallizable) is not able to bind to the antigen, but contain a complement binding site, that is exposed when the interaction between the Fab fragment and the antigen occurs. This binding occurs through non covalent interactions (Van der Waals forces, Hydrogen bonds, hydrophobic interactions) and triggers conformational changes similar to those observed in the enzyme-substrate inducing fit mechanism. This allosteric effect exposes sites in the constant regions of the heavy chains, related to the binding and activation of complement proteins.

 

This complement system is formed by eleven different proteins that are sequentially activated for associating to the cell membrane to cause lysis and death of the invading bacterial cell.

 

 

Another important role of the complement system is to generate proteins called opsonins, which stimulate phagocytosis by neutrophils and macrophages.

 

(More detailed information about the complement system can be found here)

 

In addition to the activation of the complement system, the constant regions of the Heavy chains define the ability of the (LH)2 basic structure to associate to others (LH)2 units and determine the kind of immunoglobulin.

 

There are four kind of Heavy chains:  g (Gamma),  a (Alpha), d (Delta),  e (Epsilon) and m (Mu).

Gamma chains are similar in their constant regions that are different to the other kind of heavy chain constant regions. The same is valid for each of the different kinds of Heavy chains.

 

Immunoglobulins that contain Gamma chains are called IgG.  IgG molecules are formed by one (LH)2 unit. These are the most abundant immunoglobulins in sera (600-1800 mg/dL). They promote phagocytosis in plasma and activate the complement system. IgG are the only kind of antibodies that can cross the placenta.

 

Observe in the following diagram of an IgG molecule, the two Heavy chains (in red and blue) and the two Light chains (in green and yellow).

 

 

In this diagram can be observed the variable and constant regions of the IgG and the interchain and intrachain disulfide linkages in the structure.

 

 

Immunoglobulins containing alpha chains are called IgA. IgA is found mainly in mucosal secretions, tears, colostrum and milk. These are the initial defense in mucosas against pathogen agents. They appear usually as dimmers of (LH)2 units

 

IgM contain mu heavy chains. IgM antibodies are expressed in the surface of B-cells and are found primarily in plasma. They are the first antibodies produced in significant quantities against an antigen. They promote phagocytosis and activate the complement system. They appear usually as pentamers of (LH)2 units

 

 

Ig E contains Heavy chains type epsilon. IgE, a (LH)2 monomer, plays an important role in allergic reactions and increase in worm infestations.

 

The role of IgD (immunoglobulins with delta heavy chains) is not very well known. This kind if IgG is found in the surface of the B-cells that have not been exposed to antigens. IgD structure correspond also to a (LH)2 monomer,

 

There are also different classes of L chains:  the Lambda (l) and Kappa (k) class. Each immunoglobulin molecule has either lambda or kappa chains, but not both.

Lambda chain are similar in their constant regions, Kappa chains are similar between them in those regions.

 

In summary, immunoglobulins are proteins that function as antibodies. The basic structure of immunoglobulins is a unit formed by two light chains and two heavy chains. These units contain variable domains and constant domains. The variable domains of the L and H chains are responsible of the binding to the antigens, while the constant regions of the H chains are responsible for the activation of the complement system and the ability of some of these (LH)2 units to form polymers.