Biochemistry 401 Lecture 34 Today we re going to talk about nucleotide catabolism We re also going to discuss DNA structure including A B and Z DNA and we ll talk about histones and higher order structures So let s get started The breakdown of nucleotides relies on three major classes of enzymes These are nucleotidases nucleoside phosphorylases and phosphoribomutases The nucleotidases breakdown nucleotides to nucleosides by removing the phosphate groups Nucleoside phosphorylase removes the base from the nucleoside to yield a free base plus ribose 1 phosphate Phosphoribomutase isomerizes ribose 1phosphate to ribose 5 phosphate which is an intermediate in the production of PRPP And so ribose 5 phosphate can be recycled to make more nucleotides Once the base is released it can be broken down Now we re going to look at the catabolism of purines The strategy is this First convert both AMP and GMP into a common intermediate xanthine and then convert that into urate for excretion in the urine We re going to start with a nucleotidase that s going to cleave the phosphate group from the nucleotide AMP to form adenosine the nucleoside We re then going to release the amino group We re going to use adenosine deaminase to do this and we end up with free ammonium and inosine And the next thing that we re going to do is we re going to use a nucleoside phosphorylase to remove the base hypoxanthine from ribose 1 phosphate We re then going to use a very important enzyme called xanthine oxidase This is going to introduce another ketone group in hypoxanthine to make xanthine There s one less oxygen in hypoxanthine than there is in xanthine and that s a good way to remember the difference between these two intermediates and so what we re going to do is we re going to add oxygen and water we re going to make peroxide and we re going to make xanthine This is a common intermediate in the breakdown of both GMP and AMP We re going to use xanthine oxidase again and this time we re going to make another ketone group in another position We re going to end up with peroxide again and uric acid This is going to become deprotonated to form urate which is the conjugate base And so for humans this is where it stops with urate Most mammals turn uric acid into allantoin and then this is released in the urine Fish break down allantoin even further and release ammonia into the water But for humans and great apes the catabolism of purines stops at urate This is because we ve lost the uricase gene and so we cannot catabolize urate to form allentoin and for this reason we excrete urate in the urine Now the thing is urate circulates in the bloodstream at fairly high concentrations Humans have an even higher concentration of urate than other primates and this is thought to have given us an evolutionary advantage This is because urate is a very potent antioxidant In fact it s just about as powerful as ascorbate vitamin C and so it s thought that perhaps the loss of uricase counters our loss of the ability to make vitamin C Urate is present in high concentration in the blood and it s really close to saturating concentrations It can actually precipitate out as sodium urate crystals These are shown in polarized light here and they look like little needles You can imagine if these precipitated out of the blood into joints or into the kidneys that it would be very painful and this is true This causes a painful condition called gout and persons who have overly high concentrations of urate can also have kidney stones Treatments for gout are to change the diet to decrease the amount of foods taken in that have high purine concentrations Believe it or not one of the first things to go is beer And shellfish And spinach Gout can also be treated with medicine Now allopurinol is used as a competitive inhibitor of xanthine oxidase It inhibits in two places both in the production of xanthine and in the production of uric acid and so in this way it blocks both the production of uric acid from AMP and also from GMP Another problem that s associated with the catabolism of purines is something that s called severe combined immunodeficiency syndrome and this is caused by a defect in adenosine deaminase and so the deamination of adenosine to make inosine is deficient and for this reason there s a roadblock Adenosine will build up and AMP will build up Because of the ADA deficiency the road from AMP and adenosine to inosine is blocked Therefore these intermediates AMP and adenosine will feed into the production of ATP Now we know that ATP is a positive regulator of ribonucleotide reductase and because we have an overabundance of AMP and adenosine above normal levels these will be used in order to make dATP and because of the rise in levels of dATP this will inhibit ribonucleotide reductase and will inhibit the production of deoxyribonucleotides as a whole and this has a profound effect on one of the organs in our body especially This is the thymus The thymus is an organ that sits in the middle of the chest just beneath the breastbone It encircles part of the trachea This is an organ that is responsible for the maturation of thymic cells T cells which are a primary cell involved in the immune response As you can see from this slide at birth the thymus is about 15 g and it increases in size from birth to puberty more than doubling in fact Then there is a general decrease in size until by 70 years of age it s only about 5 g It just about disappears The mass in fact of the thymus at this point is mostly adipose and connective tissue Now thymic tissue is especially sensitive to decreases in adenosine deaminase activity and this is because the thymus cells generally have a great deal of adenosine deaminase activity In fact if you look at the activity of adenosine deaminase per milligram of protein the levels of adenosine deaminase activity in human tissues taken from surgeries and postmortems on children that were up to and including one year old as you can see the greatest nanomole of adenosine activity per milligram of protein is seen in the thymus By far and away this is true As we saw the thymus should increase in size in children This is why a loss of ADA hits the thymus hard It causes severe combined immunodeficiency syndrome Nearly half of all cases of SCID in fact are caused by ADA deficiency This is because the maturing thymic cells T cells in children are especially sensitive to ADA deficit This is because cell division is decreased because
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