Principles of Biochemistry Lecture 25 Spring 2024 PDF

Principles of Biochemistry SPRING 2024 Professor: Moncef LADJIMI [email protected] Office: C-169 As faculty of Weill Cornell Medical College in Qatar we are committed to providing transparency for any and all external relationships prior to giving an academic presentation. I, Moncef LADJ...

Principles of Biochemistry SPRING 2024 Professor: Moncef LADJIMI [email protected] Office: C-169 As faculty of Weill Cornell Medical College in Qatar we are committed to providing transparency for any and all external relationships prior to giving an academic presentation. I, Moncef LADJIMI DO NOT have a financial interest in commercial products or services. Lecture 25 Amino Acids degradation and synthesis Additional material for this lecture may be found in: § Lehninger’s Biochemistry (8th ed), chapter 18: p. 639-655 PATHWAYS OF AMINO ACID DEGRADATION END PRODUCTS OF AMINO ACID DEGRADATION Intermediates of the Central Metabolic Pathway Some amino acids result in more than one intermediate Ketogenic amino acids can be converted to ketone bodies Seven to Acetyl-CoA Leu, Ile, Thr, Lys, Phe, Tyr, Trp Glucogenic amino acids can be converted to glucose Six to pyruvate Ala, Cys, Gly, Ser, Thr, Trp Five to a-ketoglutarate Arg, Glu, Gln, His, Pro Four to succinyl-CoA Ile, Met, Thr, Val Two to fumarate Phe, Tyr Two to oxaloacetate Asp, Asn SOME AMINO ACID ARE CONVERTED TO GLUCOSE, OTHERS IN KETONE BODIES Ketogenic amino acids: Seven amino acids are degraded, at least in part, to acetoacetyl-CoA or acetyl-CoA and therefore a source of potential ketone bodies. Their ability to form ketone bodies is particularly important in untreated diabetes in which the liver forms large amounts of ketone bodies. These seven amino acids are: phenylalanine, tyrosine, tryptophan, isoleucine,leucine, lysine and threonine. Glucogenic amino acids: All amino acids that can be degraded, at least in part, to either pyruvate, αketoglutarate, succinyl-CoA, fumarate and/or oxaloacetate can be converted to glucose via the gluconeogenesis pathway. The division between ketogenic and glucogenic is not absolute. Five amino acids are both ketogenic and glucogenic. These are tryptophan, phenylalanine, tyrosine, threonine and isoleucine. Amino acids are grouped according to their major degradative end product. In fact, only two amino acids, leucine and lysine, are entirely ketogenic. Of these two, leucine is very common in proteins and makes a substantial contribution to ketosis under starvation conditions. SEVERAL COFACTORS ARE INVOLVED IN AMINO ACID CATABOLISM Important in one-carbon transfer reactions Tetrahydrafolate (THF): formed from folate, an essential vitamin by dihydrofolate reductase. THF has different forms and transfers 1-carbon in different oxidation states (in the form of CH3, CH2OH, and CHO). Carbon generally comes from serine. Forms interconverted on THF before use S-adenosylmethionine (adoMet): is the preferred cofactor for methyl transfer in biological reactions (methyl from adoMet is 1000 times more reactive than THF methyl group) Synthesized from ATP and methionine Regeneration of adoMet uses N5-methyl THF (the only known use in mammals) Biotin (transfers CO2) TETRAHYDROFOLATE CYCLE Folate trap: Methionine synthase reaction regenerates THF from N5MTHF. If deficient, folates are trapped in the N5-MTHF form (see folates trap, next slides). Methionine synthase (THF) Conversions of one-carbon units on tetrahydrofolate: There are two entry points for one-carbon units into the H4 folate one-carbon pool. - One involves the removal of a hydroxymethyl group from serine, forming glycine and N5,N10-methylene H4folate. - The other involves formic acid, that can be utilized, at the expense of ATP to form initially N10-formyl H4folate and subsequently, N5, N10-methenyl-H4folate. Regardless of the entry point into the one carbon pool, the one carbon units may be oxidized and reduced to three different levels of oxidation state: - In its most reduced form (N5-methyl H4folate), the cofactor carries a methyl group; - in its intermediate state (N5,N10-methylene H4folate) the cofactor carries a methylene group (transferred as –CH2OH); and - in its most oxidized form a methenyl group 5 10 (N ,N -methenyl H4folate) (transferred either as –CHO, or – CH=NH). The primary source of one-carbon units for H4folate is conversion of serine to glycine producing N5,N10-methylene H4folate. Although, H4folate can carry a methyl group, its potential for transferring this group in biosynthetic reactions is insufficient for most biological reactions. What is required is a more potent donor of methyl groups in most biosynthetic reactions and that is S-adenosylmethionine. ADOMET IS BETTER THAN THF AT TRANSFERRING CH3 S-adenosylmethionine (adoMet) is the prefered cofactor for methyl transfer in biological reactions – Methyl from adoMet is 1000 times more reactive than THF methyl group Synthesized from ATP and methionine Regeneration uses N5-methyl THF – The only known use in mammals REGENERATION OF ADOMET: THE ACTIVATED METHYL CYCLE Regeneration of different forms of THF Folate trap: if methylcobalamin methylcobalamin (CoEnz B12) is not available, or if methionine synthase is deficient, the folates become trapped as N5-methyl THF and cannot regenerate the other forms of THF: Methyl transfer Synthesis of methionine and S-adenosylmethionine in an activated-methyl cycle. In the methionine synthase reaction (step 4), the methyl group is transferred to cobalamin to form methylcobalamin, which in turn is the methyl donor in the formation of methionine. S-Adenosylmethionine, which has a positively charged sulfur (and is thus a sulfonium ion), is a powerful methylating agent in several biosynthetic reactions. The methyl group acceptor (step 2) is designated R. THE LINK BETWEEN TWO VITAMINS: VITAMIN B12 AND FOLATE Vitamin B12 and folate are closely linked in the pathway to regenerate methionine If vitamin B12 is not available à No methyl-cobalamin for the methionine synthase reaction), à à the folates become trapped as N5-methyl THF (folate trap) and cannot regenerate THF from N5methyl THF. If THF is not regenerated, N5,N10-methylene THF, which is used in DNA synthesis (through thymidylate synthase reaction that makes dTMP), is not formed (see folates cycle) à à Megaloblastic anemia (manifests as a decline in mature erythrocytes which are slowly replaced by smaller numbers of abnormally large erythrocytes called macrocytes, since cells cannot divide). This anemia can be partially treated with folates (THF), since Vitamin B12 deficiency alone will not cause the syndrome in the presence of sufficient folate (the mechanism is loss of B12 -dependent folate recycling needed for DNA synthesis). If vitamin B12 is not available à No methyl-cobalamin for the methionine synthase reaction à à No methionine formation à (no methyl transfer (since no adomet), no cysteine à oxidative stress etc.) Accumulation of homocysteine à homocysteinemia and homocysteinuria (rise in homocysteine in blood and urine) à (heart disease, hypertension and stroke). High levels of homocysteine may be responsible for 10% of all cases of heart disease. If vitamin B12 is not available à No deoxyadenosyl-cobalamin for the methyl malonyl CoA mutase reaction à à no degradation, accumulation of odd carbon numbered fatty acid à neurological disorders Rare defect in intestinal absorption of vitamin B12 (no Intrinsic Factor) or in vegetarians (B12 does not occur in plants) à Pernicious anemia and neurologic disorders: The anemia symptoms of pernicious anemia can be treated by administering either vitamin B12 or folate. However, the neurological symptoms of pernicious anemia cannot be treated by folate alone, because these symptoms result not from a defect in the methionine synthase reaction but from an accumulation of odd-carbon numbered fatty acids in neural membranes (role of deoxyadenosylcobalamin, in the conversion of methylmalonyl-CoA to succinyl-CoA ). BRANCHED CHAIN AMINO ACIDS ARE NOT DEGRADED IN THE LIVER Odd number Fatty acid degradation Propionyl CoA Coenzyme B12 (adenosyl form) Succinyl CoA Absent in the liver Methyl-crotonyl CoA carboxylase (Biotin) Acetyl CoA Most amino acids are catabolized in the liver, however, the three branched amino acids, valine, leucine and isoleucine are oxidized as fuels largely in muscle, adipose tissue, kidney and brain. These tissues contain a branched-chain aminotransferase that is absent in the liver. In a second reaction, a branched-chain α-keto acid dehydrogenase complex catalyzes oxidative decarboxylation of all three α-keto acids releasing the carboxyl group as CO2 and producing the acyl-CoA derivative. This reaction is analogous to the pyruvate dehydrogenase-catalyzed reaction that requires five cofactors (TPP, lipoate, CoASH, FAD, NAD). BRANCHED CHAIN AMINO ACIDS METABOLISM DISEASE In a relatively rare genetic disease, the α-keto acid dehydrogenase complex is defective leading to an accumulation of the precursor amino acids and the three branched-chain α-keto acids in the blood and urine. This condition is called maple syrup urine disease, because of the characteristic odor of the urine because of the branched keto acids. Untreated, this disease results in abnormal development of the brain, mental retardation and death early in infancy. Treatment entails rigid control of diet, limiting the intake of valine, leucine and isoleucine to the minimum required to permit normal growth. GENETIC DEFECTS IN MANY STEPS OF PHE DEGRADATION LEAD TO DISEASE In humans, these amino acids are normally converted to acetoacetyl-CoA and fumarate. Genetic defects in many of these enzymes cause inheritable human diseases (shaded yellow). ALTERNATIVE PATHWAYS FOR CATABOLISM OF PHENYLALANINE IN PHENYLKETONURIA (PKU) In individuals with a defect in phenylalanine hydroxylase, the level of phenylalanine rises, bringing into action a normally little used pathway. In this pathway, phenylalanine undergoes transamination to phenylpyruvate. Phenylalanine and phenylpyruvate accumulate in the blood and tissues and are excreted in the urine – hence the name phenylketonuria. Phenylpyruvate is decarboxylated to phenylacetate or reduced to phenyllactate (may also be found in the urine). The accumulation of phenylalanine or its metabolites early in life causes severe mental retardation. Mental retardation can be prevented by strict dietary control of phenylalanine intake. ANOTHER CAUSE OF PKU Role of tetrahydrobiopterin in the phenylalanine hydroxylase reaction. The H atom shaded pink is transferred directly from C-4 to C-3 in the reaction. Phenlyketonuria is also caused by a defect in the enzyme that regenerates the cofactor tetrahydrobiopterin, dihydrobiopterin reductase. In this case, however, the treatment is more complex than restricting the intake of Phe or Tyr, because tetrahydrobiopterin is required as a cofactor for other reactions that are precursors of the neurotransmitters norepinephrine and serotonin (so precursors such as L-dopa and 5-hydroxy-Trp must be supllied in the diet. Providing the cofactor itself is not effective because it cannot cross the blood-brain barrier. ALKAPTONURIA IS ANOTHER HERITABLE DISEASE OF PHENYLALANINE METABOLISM. In this case the defective enzyme is homogentisate dioxygenase. The effects of this defect are less serious, but individuals with this disease are likely to develop a form of arthritis. The excretion of large concentrations of homogentisate causes urine to turn black when the former is oxidized. JC10: SOME HUMAN GENETIC DISORDERS AFFECTING AMINO ACID CATABOLISM SUMMARY Amino acids from protein are an important energy source in carnivorous animals The first step of amino acid catabolism is transfer of the NH3 via PLP-dependent aminotransferase usually to aketoglutarate to yield L-glutamate In most mammals, toxic ammonia is quickly recaptured into carbamoyl phosphate and passed into the urea cycle Amino acids are degraded to pyruvate, acetyl-CoA, αketoglutarate, succinyl-CoA, and/or oxaloacetate Amino acids yielding acetyl-CoA are ketogenic Amino acids yielding other end products are glucogenic Genetic defects in amino acid degradation pathways result in a number of human diseases PATHWAYS OF AMINO ACID SYNTHESIS NOT ALL AMINO ACIDS CAN BE SYNTHESIZED IN HUMANS Essential amino acids must be obtained from dietary protein (from Pyr) Consumption of a variety of foods supplies all the essential amino acids – including vegetarianonly diets (from Asp) (from Oxalo) (from KetoG) (from 3-P-G) (from urea cycle) (from Ser) (from Glu) (from Ser) (from Arg) (from Phe) Bacteria and most plants can synthesize all 20 AAs BIOSYNTHESIS OF NONESSENTIAL AMINO ACIDS IN HUMANS § Alanine (from pyruvate; transamination from glutamate) § Aspartate (from oxaloacetate; transamination from glutamate) § Asparagine (amidation of Asp; glutamine donates NH4+) § Glutamate (from α-ketoglutarate) § Serine (from 3-phosphoglycerate) MOLECULES DERIVED FROM AMINO ACID porphyrin/heme creatine glutathione neurotransmitters (GABA, serotonin, …) nitric oxide sphingolipids polyamines Remember to prepare for next lecture: Lehninger’s Biochemistry (8th ed), §chapter 22: p. 823-838