Protein Metabolism PDF

Nutrition and Metabolism Protein Metabolism Protein Metabolism Dr. Almojtaba Abdalkhalig Ahmed Assistant professor of Nutrition and biochemistry  Catabolism of the amino acids => removing amino group => urea synthesis. Carbon skeletons => TCA => CO2 & H2O or gluconeogenesis....

Nutrition and Metabolism Protein Metabolism Protein Metabolism Dr. Almojtaba Abdalkhalig Ahmed Assistant professor of Nutrition and biochemistry  Catabolism of the amino acids => removing amino group => urea synthesis. Carbon skeletons => TCA => CO2 & H2O or gluconeogenesis. Catabolic Pathway of Amino Acids  3 Common Stages: Removal of alpha-amino group => amino acids (amino acid deamination) => amino group => ammonia. ammonia => urea. amino acid’s carbon skeletons => common metabolic intermediate. General Pathway Showing the stages of amino acid Catabolism Amino Acid Deamination involve two types of biochemical reactions:  Transamination and oxidative deamination. Transamination dominant reactions => removing amino acid nitrogen =>transaminations. these reactions => funnel nitrogen of all free amino acids => small no. of compounds => either oxidatively deaminated => ammonia => or their amino groups => urea by urea cycle. Transaminations => moving α-amino group => donor α-amino acid => the keto C of acceptor α-keto acid => α-keto derivatives of amino acid and corresponding amino acid.  All amino acids participate in transamination during catabolism except lysine, threonine and proline. Transamination => readily reversible. catalyzed by aminotransferase (transaminase). Each aminotransferase => specific for one or at most a few amino group donors. named after specific amino group donor, as acceptor is almost always α-ketoglutarate => aminated to glutamate Transamination  Aminotransferases require => aldehyde-containing coenzyme, pyridoxal-5-phosphate, a derivative of pyridoxine (vitamin B6¬). Pyridoxal-5-phosphate => covalently attached to enzyme via a schiff base linkage transferring amino group of an amino acid => pyridoxal part of coenzyme => pyridoxamine phosphate. pyridoxamine reacts => with an α-keto acid => amino acid and => regenerates original aldehyde form of the coenzyme.  glutamate and α- ketoglutarate => most common compounds => as a donor/acceptor pair => transamination reactions => participate in reactions => many different amino transferases. All the amino nitrogen => amino acid that undergo transamination=> concentrated in glutamate => because L- glutamate is the only amino acid that => undergoes oxidative deamination at an appreciable rate. Examination of Transamination Glucose-alanine cycle skeletal muscle => excess amino groups => transferred=> pyruvate=> alanine => enters => liver => undergoes transamination => pyruvate => gluconeogenesis => glucose => returned => muscles => glycolytically degraded => pyruvate. Glucose-alanine cycle Oxidative deamination Transamination => does not result => net deamination. During oxidative deamination, amino acid => keto acid (removal of amine functional group => ammonia and amine functional group => replaced by ketone group) ammonia => urea cycle. glutamate (recipient of amino groups from many sources) => sheds it as => ammonia => excretion  a- ketoglutarate => recycle as nitrogen acceptor => enter TCA cycle or serve as => precursor => gluconeogenesis Deamination occurs through oxidative deamination of glutamate by glutamate dehydrogenase glutamate dehydrogenase is allosterically inhibited by GTP and NADH and activated by ADP and NAD+. The reaction requires an oxidizing agent NAD+ or NADP+. Oxidative deamination of Glutamate  Urea Cycle Living organisms excrete => excess nitrogen ammonia. Where water is less plentiful => processes have evolved => convert ammonia to less toxic waste products => require less water for excretion. one such product is urea and other is uric acid.  Accordingly, living organisms are classified as : ammonotelic (ammonia excreting), ureotelic (urea excreting) or uricotelic (uric acid excreting). Urea is formed cyclic pathway => urea cycle.  Urea cycle => discovered by Krebs and Henseleit So => Krebs Henseleit cycle. Urea synthesis : in the hepatocytes (liver cells) consists of five sequential enzymatic reactions. First two reactions => mitochondria and remaining three reactions => cytosol  Urea cycle => formation of carbamoyl phosphate => mitochondria. Substrates ( NH4+ and HCO3-) => catalyzed by carbamoyl phosphate synthetase I (CPSI). Reaction is essentially irreversible => two molecules of ATP are required : one to activate HCO3- and the second molecule => to phosphorylate carbamate.  Carbamoyl phosphate => with ornithine => citrulline => passes into cytosol. Next three steps => occur in cytosol => formation of argininosuccinate by ATP dependent reaction of citrulline with aspartate. (aspartate provides second nitrogen that is ultimately incorporated into urea). Formation of arginine from argininosuccinate. This reaction => fumarate => critic acid cycle. Formation of urea and regeneration of ornithine. Urea Cycle Net reaction of urea cycle : CO2 + NH4+ + Aspartate + 3ATP + 2H2O  Urea + Fumarate + 2ADP + AMP i.e. four high energy phosphates are consumed in the synthesis of one molecule of urea.  Protein Synthesis Kinds of RNA  The class of RNA found in ribosomes is called ribosomal RNA (rRNA). During polypeptide synthesis, rRNA provides the site where polypeptides are assembled.  Transfer RNA (tRNA) molecules both transport the amino acids to the ribosome for use in building the polypeptides and position each amino acid at the correct place on the elongating polypeptide chain. Human cells contain about 45 different kinds of tRNA molecules.  Messenger RNA (mRNA) molecules are long strands of RNA that are transcribed from DNA and that travel to the ribosomes to direct precisely which amino acids are assembled into polypeptides. The Central Dogma Information passes from the genes (DNA) to an RNA copy of the gene, and the RNA copy directs the sequential assembly of a chain of amino acids The Genetic Code  The essential question of gene expression is, “How does the order of nucleotides in a DNA molecule encode the information that specifies the order of amino acids in a polypeptide?”  The answer came in 1961, through an experiment led by Francis Crick.  That experiment was so elegant and the result so critical to understanding the genetic code that we will describe it in detail. Proving code words have only three letters  Crick and his colleagues reasoned that the genetic code most likely consisted of a series of blocks of information called codons.  They further hypothesized that the information within one codon was probably a sequence of three nucleotides specifying a particular amino acid.  They arrived at the number three, because a two-nucleotide codon would not yield enough combinations to code for the 20 different amino acids that commonly occur in proteins.  With four DNA nucleotides (G, C, T, and A), only 42, or 16, different pairs of nucleotides could be formed.  However, these same nucleotides can be arranged in 43, or 64, different combinations of three, more than enough to code for the 20 amino acids.  When they made a single deletion or two deletions near each other, the reading frame of the genetic message shifted, and the downstream gene was transcribed as nonsense.  However, when they made three deletions, the correct reading frame was restored, and the sequences downstream were transcribed correctly.  They obtained the same results when they made additions to the DNA consisting of one, two, or three nucleotides. The code is practically universal  For example, the codon AGA specifies the amino acid arginine in bacteria, in humans, and in all other organisms whose genetic code has been studied.  Because the code is universal, genes transcribed from one organism can be translated in another; the mRNA is fully able to dictate a functionally active protein.  Similarly, genes can be transferred from one organism to another and be successfully transcribed and translated in their new host.  Many commercial products such as the insulin used to treat diabetes are now manufactured by placing human genes into bacteria, which then serve as tiny factories to turn out prodigious quantities of insulin. But Not Quite  In 1979, investigators began to determine the complete nucleotide sequences of the mitochondrial genomes in humans, cattle, and mice.  It came as something of a shock when these investigators learned that the genetic code used by these mammalian mitochondria was not quite the same as the “universal code” that has become so familiar to biologists.  In the mitochondrial genomes, what should have been a “stop” codon, UGA, was instead read as the amino acid tryptophan; AUA was read as methionine rather than isoleucine; and AGA and AGG were read as “stop” rather than arginine.  Thus, it appears that the genetic code is not quite universal.  Genes are first transcribed, and then translated. Transcription  The first step in gene expression is the production of an RNA copy of the DNA sequence encoding the gene, a process called transcription.  To understand the mechanism behind the transcription process, it is useful to focus first on RNA polymerase, the remarkable enzyme responsible for carrying it out. RNA Polymerase  RNA polymerase is best understood in bacteria.  Bacterial RNA polymerase is very large and complex, consisting of five subunits: 1. Two α subunits bind regulatory proteins. 2. β′ subunit binds the DNA template 3. β subunit binds RNA nucleoside subunits. 4. σ subunit recognizes the promoter and initiates synthesis.  Only one of the two strands of DNA, called the template strand, is transcribed.  The strand of DNA that is not transcribed is called the coding strand.  The polymerase adds ribonucleotides to the growing 3′ end of an RNA chain.  Bacteria contain only one RNA polymerase enzyme, while eukaryotes have three different RNA polymerases: 1. RNA polymerase I: synthesizes rRNA in the nucleolus. 2. RNA polymerase II: synthesizes mRNA. 3. RNA polymerase III: synthesizes tRNA. Promoter  Transcription starts at RNA polymerase binding sites called promoters on the DNA template strand.  A promoter is a short sequence that is not itself transcribed by the polymerase that binds to it.  Promoters differ widely in efficiency.  Strong promoters cause frequent initiations of transcription, as often as every 2 seconds in some bacteria.  Weak promoters may transcribe only once every 10 minutes. Initiation  In bacteria, a subunit of RNA polymerase called σ (sigma) recognizes the –10 sequence in the promoter and binds RNA polymerase there.  Importantly, this subunit can detect the –10 sequence without unwinding the DNA double helix.  In eukaryotes, the –25 sequence plays a similar role in initiating transcription, as it is the binding site for a key protein factor.  Other eukaryotic factors then bind one after another, assembling a large and complicated transcription complex.  Once bound to the promoter, the RNA polymerase begins to unwind the DNA helix. Elongation  Unlike DNA synthesis, a primer is not required.  The region containing the RNA polymerase, DNA, and growing RNA transcript is called the transcription bubble because it contains a locally unwound “bubble” of DNA.  The transcription bubble moves down the DNA at a constant rate, about 50 nucleotides per second, leaving the growing RNA strand protruding from the bubble.  After the transcription bubble passes, the now transcribed DNA is rewound as it leaves the bubble.  Unlike DNA polymerase, RNA polymerase has no proofreading capability.  Transcription thus produces many more copying errors than replication.  Most genes are transcribed many times, so a few faulty copies are not harmful. Termination  At the end of a gene are “stop” sequences that cause the formation of phosphodiester bonds to cease the RNA polymerase to release the DNA, and the DNA within the transcription bubble to rewind.  The simplest stop signal is a series of GC base-pairs followed by a series of AT base-pairs.  The RNA transcript of this stop region forms a GC hairpin followed by four or more U ribonucleotides.  How does this structure terminate transcription? The hairpin causes the RNA polymerase to pause immediately after the polymerase has synthesized it, placing the polymerase directly over the run of four uracils.  The pairing of U with DNA’s A is the weakest of the four hybrid base-pairs and is not strong enough to hold the hybrid strands together during the long pause.  Instead, the RNA strand dissociates from the DNA within the transcription bubble, and transcription stops.  A variety of protein factors aid hairpin loops in terminating transcription of particular genes. Translation  In prokaryotes, translation begins when the initial portion of an mRNA molecule binds to an rRNA molecule in a ribosome.  The mRNA lies on the ribosome in such a way that only one of its codons is exposed at the polypeptidemaking site at any time.  A tRNA molecule possessing the complementary three- nucleotide sequence, or anticodon, binds to the exposed codon on the mRNA.  Because this tRNA molecule carries a particular amino acid, that amino acid and no other is added to the polypeptide in that position.  As the mRNA molecule moves through the ribosome, successive codons on the mRNA are exposed, and a series of tRNA molecules bind one after another to the exposed codons.  Each of these tRNA molecules carries an attached amino acid, which it adds to the end of the growing polypeptide chain.  There are about 45 different kinds of tRNA molecules. Why are there 45 and not 64 tRNAs (one for each codon)?  How do particular amino acids become associated with particular tRNA molecules? The key translation step, which pairs the three-nucleotide sequences with appropriate amino acids, is carried out by a remarkable set of enzymes called activating enzymes. Activating Enzymes  Activating enzymes called aminoacyl-tRNA synthetases, one of which exists for each of the 20 common amino acids.  Therefore, these enzymes must correspond to specific anticodon sequences on a tRNA molecule as well as particular amino acids.  Some activating enzymes correspond to only one anticodon and thus only one tRNA molecule.  Others recognize two, three, four, or six different tRNA molecules, each with a different anticodon but coding for the same amino acid. “Start” and “Stop” Signals  There is no tRNA with an anticodon complementary to three of the 64 codons: UAA, UAG, and UGA.  These codons, called nonsense codons, serve as “stop” signals in the mRNA message, marking the end of a polypeptide.  The “start” signal that marks the beginning of a polypeptide within an mRNA message is the codon AUG, which also encodes the amino acid methionine.  The ribosome will usually use the first AUG that it encounters in the mRNA to signal the start of translation. Initiation  Initiation in eukaryotes and prokaryotes is similar, although it differs in two important ways: 1. First: in eukaryotes, the initiating amino acid is methionine rather than N-formylmethionine. 2. Second: the initiation complex is far more complicated than in bacteria, containing nine or more protein factors, many consisting of several subunits. Elongation  When a tRNA molecule with the appropriate anticodon appears, proteins called elongation factors assist in binding it to the exposed mRNA codon at the A site.  When the second tRNA binds to the ribosome, it places its amino acid directly adjacent to the initial methionine, which is still attached to its tRNA molecule, which in turn is still bound to the ribosome.  The two amino acids undergo a chemical reaction, catalyzed by peptidyl transferase, which releases the initial methionine from its tRNA and attaches it instead by a peptide bond to the second amino acid. Translocation  In a process called translocation the ribosome now moves (translocates) three more nucleotides along the mRNA molecule in the 5´ →3´ direction.  This movement relocates the initial tRNA to the E site and ejects it from the ribosome, repositions the growing polypeptide chain to the P site, and exposes the next codon on the mRNA at the A site. Termination  Elongation continues in this fashion until a chain- terminating nonsense codon is exposed (for example, UAA).  Nonsense codons do not bind to tRNA, but they are recognized by release factors, proteins that release the newly made polypeptide from the ribosome. The End