BCH3004 Principles in Biochemistry PDF

BCH3004 PRINCIPLES IN BIOCHEMISTRY 4(3+1) TS. DR. AZZREENA MOHAMAD AZZEME DEPARTMENT OF BIOCHEMISTRY, FACULTY OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES, UPM Students are able to explain: ▪ Protein and amino acid oxidation ▪ Pathways involved in producing Krebs cycle...

BCH3004 PRINCIPLES IN BIOCHEMISTRY 4(3+1) TS. DR. AZZREENA MOHAMAD AZZEME DEPARTMENT OF BIOCHEMISTRY, FACULTY OF BIOTECHNOLOGY AND BIOMOLECULAR SCIENCES, UPM Students are able to explain: ▪ Protein and amino acid oxidation ▪ Pathways involved in producing Krebs cycle intermediates ▪ Metabolism of ammonia and urea ▪ Biosynthesis and the role of amino acid metabolism The Nitrogen Cycle Nitrogen atoms appear in many different types of inorganic and organic compounds in the atmosphere and biosphere. Inorganic nitrogen: Name Structure Nitrate ion NO3- Nitrite ion NO2- Hyponitrite ion N2O2- Nitrogen gas N2 Hydroxylamine NH2OH Ammonia NH3  Nitrogen is also found in organic compounds: - amino acids - proteins - purines - pyrimidines - porphyrins Nitrogen gas (N2) is the most abundant natural from of nitrogen → makes up almost 80% od the atmosphere The Nitrogen Cycle  Nitrogen from plants and animals is recycled to the soil by two processes: 1. Excretion of nitrogen in the form of urea or uric acid, which is converted to ammonium by microorganism 2. The proteins and other nitrogenous components from dead and decaying plants and animals are hydrolyzed to amino acids and other compounds, which releases ammonia upon microbial degradation. Amino Acid Anabolism Nitrogen from plants and animals is recycled to the soil by two processes: 1. Excretion of nitrogen in the form of urea or uric acid, which is converted to ammonium by microorganism 2. The proteins and other nitrogenous components from dead and decaying plants and animals are hydrolyzed to amino acids and other compounds, which releases ammonia upon microbial degradation.  Utilization of Ammonia: Biogenesis of Organic Nitrogen Ammonia in high concentrations is quite toxic, but lower levels it is a central metabolite, serving as substrates for four enzymes that convert it to various organic nitrogen compounds. Glutamate dehydrogenase Glutamine synthetase Carbamoyl phosphate synthetase Either ammonia or glutamine can serve as the nitrogen donor Amino Acid Anabolism  Essential Amino Nonessential Biosynthesis of Acids Amino Acids Amino Acids Arginine Alanine Histidine Asparagine *Tyrosine is not an Isoleucine Aspartate essential amino acid in humans because it is Leucine Cysteine normally synthesized Lysine Glutamate from phenylalanine Methionine Glutamine Phenylalanine Glycine Threonine Proline Tryptophan Serine Valine *Tyrosine  Essential amino acids: Amino acids that cannot be synthesized and must be supplied in the diet of humans Nonessential amino acids: Amino acids that are synthesized by humans  Nonessential Amino acid biosynthesis Derived from intermediates compounds from glycolysis, citric acids cycle and pentose phosphate pathway. The aromatic amino acids biosynthesis in plants fungi and bacteria 1. Tyrosine 2. Phenylalanine 3. Tryptophan Amino Acid Catabolism  Under normal dietary circumstances, amino acids are not important fuel molecules. They provide the metabolic energy under some conditions: 1. When dietary amino acids are in excess of those needed for synthesis of proteins and other molecules. 2. When the normal process of protein turnover (recycling) releases free amino acids that may be available for catabolism. 3. During times of starvation or untreated diabetes, structural and catalytic proteins are degraded and the amnio acids are used for energy metabolism. General pathway of amino acid catabolism  Intracellular Protein Turnover Continuous process of synthesis and degradation of proteins within a cell or an organism It involves the balance between the creation of new proteins through protein synthesis and the removal of old or damaged proteins through protein degradation Key aspects of protein turnover: 1. Protein Synthesis 2. Protein Degradation Protein Synthesis Synthesized proteins contribute to various cellular functions, including structural support, enzymatic activity, signaling, and regulation. Protein Degradation Protein degradation involves the breakdown of existing proteins. There are two main pathways for protein degradation: 1. Ubiquitin-proteasome system 2. Autophagy Ubiquitin-Proteosome System The pathway targets specific proteins for degradation by marking them with a small protein called ubiquitin. The ubiquitin-tagged proteins are then recognized and degraded by the proteasome, a cellular structure with proteolytic activity. E1 ubiquitin–activating enzyme E2 ubiquitin–conjugating enzyme E3 ubiquitin ligase Autophagy Peptide This process involves the engulfment of cellular components, including proteins, into vesicles called autophagosomes. These autophagosomes fuse with lysosomes, where the enclosed material is degraded by lysosomal enzymes.  Peptidase Site of Catalytic Hydrolysis Dietary Protein Pepsin Amino acid siede of Phe, Tyr, Trp Trypsin Carboxyl side of Lys and Arg Chymotrypsin Carboxyl site of Phe, Tyr, Trp Carboxypeptidase Sequential removal of amino acids beginning at C-terminus Aminopeptidase Sequential removal of amino acids beginning at N-terminus Elastase Cleaves peptide bonds in elastin Carboxyl site of alanine, glycine, and serine Combined action of the enzymes result in a mixture of free amino acids, which are transported 3. SMALL INTESTINE across the epithelial cell lining of small intestine into Enzymatic digestion (chymotrypsin, trypsin, the blood. aminopeptidase, carboxypeptidase, and elastase) Absorption of amino acids, di- The amino acids are distributed to peripheral tissue and tripeptides for biosynthetic use and to liver for catabolism.  The general hydrolysis reaction for the breakdown of a peptide bond in a protein or peptide substrate can be represented as follows: Protein or Peptide + H2O → Products Transamination The initial phase for most amino acids is the removal of the amino group by a process common to the amino acids, the transamination. Enzyme: aminotransferase E.g. Purpose of transamination: To remove amino groups from the various α-amino acids and collect them in a single type of molecule, glutamate. Glutamate then acts as a single source of amino groups for continuing nitrogen metabolism (biosynthesis or excretion). Aminotransferases Most of aminotransferases present in mitochondria. These enzymes contribute to processes such as the tricarboxylic acid (TCA) cycle, urea cycle, and the metabolism of specific amino acids. There are also aminotransferases localized in other cellular compartments, such as the cytoplasm. The distribution of these enzymes is tailored to the specific metabolic needs of the cell. All of aminotransferases have the same type of prosthetic group, the pyridoxal phosphate (PLP), which derived from the vitamin pyridoxine (B6) Fate of each carbon skeleton in amino acid catabolism Yellow: Glucogenic amino acids Blue: Ketogenic amino acids Purple: Amino acids that can be both glucogenic and ketogenic Asterisk: Amino acids with more than one route of entry to central pathways Elimination of NH4+  Amino group from amino acid catabolism are collected by glutamate through transamination process. Combination of transamination and deamination leads to an amino group removal.  - High [NH4+] may lower [α-ketoglutarate], thus lowering concentration of α- ketoglutarate available for citric acid cycle. This condition may give detrimental effect for developing brain cells, which depends on aerobic metabolism of glucose.  NH4+ above physiological needs is a waste product and is excreted in different chemical forms depending on species. Terrestrial vertebrate including mammals, excrete excess NH4+ → urea (Urea Cycle) Birds, primates, insect and reptilian → uric acid Marine invertebrates → NH4+ The Urea Cycle  An enzyme arginase present only in vertebrates, catalyzes the hydrolysis of: arginine → urea and ornithine The pathway to arginine (reactions 1 to 4) is present in all organisms for synthesizing arginine Reaction 5 – only in those organisms that excrete urea  Net reaction of urea cycle: CO2 + NH4+ + 3 ATP + aspartate + 2 H2O Urea + 2 ADP + 2 Pi + AMP + PPi + fumarate  The formation of one molecule of urea requires the energy from the cleavage of 4 phosphoanhydrous bond First reaction (Carbamoyl-1-phosphate synthase): 2 ATP → 2 ADP + Pi Third reaction (Argininosuccinate synthetase): ATP → AMP + PPi PPi + H2O → 2 Pi (Enzyme: phosphorylase)  The two nitrogen atoms in urea come directly from two diverse molecules NH4+ and amino acid aspartate However, the original source of both nitrogen is glutamate  A complete block of any reactions of the urea cycle can give negative effects on human. Clinical symptoms caused by partial deficiency of these enzymes include: i. Elevated levels of NH4+ in blood and urine (hyperammonemia) ii. Nausea and illness after ingestion of proteins iii. Gradual mental retardation  Patients are fed low-protein diets supplemented with mixture α-keto acids. The purposes of α-keto acids are: i. The α-keto acids pick up excess NH4+ by combined reactions of glutamate dehydrogenase and transamination. ii. If the proper α-keto acids are chosen, they can be converted to essential amino amino acids that may lack in the low-protein diet. - α-ketoisovalerate + NH4+ Valine - α-ketoisocaproate + NH4+ Leucine