Cytosol-1.ppt

The CytosolThe CytosolMost Intermediary Metabolism Takes Place in the cytosolMost Intermediary Metabolism Takes Place in the cytosol Degrades some small molecules ( ATP, proton gradient)Degrades some small molecules ( ATP, proton gradient) Synthesizes ( for the structure, function, and growth Synthesizes ( for the structure, function, and growth cell)cell)

Cytosol generally represents about 55% of the total Cytosol generally represents about 55% of the total cell volumecell volume

CompartmentCompartment % cell vol% cell vol NumberNumber

CytosolCytosol 54 54 1 1

MitochondriaMitochondria 22 22 1700 1700

Rough ER cisternaeRough ER cisternae 9 9 1 1

Smooth ER cisternae + Golgi Smooth ER cisternae + Golgi 6 6

NucleusNucleus 6 6 1 1

PeroxisomesPeroxisomes 1 1 400 400

LysosomesLysosomes 1 1 300 300

The CytosolThe Cytosol Teeming with thousands of enzyme that Teeming with thousands of enzyme that catalyze the reaction:catalyze the reaction:

Glycolysis & gluconeogenesis ; biosintesa Glycolysis & gluconeogenesis ; biosintesa sugar, fatty acids, sugar, fatty acids,

nucleotides and amino acids.nucleotides and amino acids. Contains a variety of different cytoskeletal Contains a variety of different cytoskeletal proteins proteins

impart shape to cell, impart shape to cell, coherent cytoplasmic movement, andcoherent cytoplasmic movement, and provide a general frame work that is used to help provide a general frame work that is used to help organize the many organize the many

enzyme reaction enzyme reaction About 20% of the weigh of the cytosol is About 20% of the weigh of the cytosol is proteinprotein Cytosol Golgi – not identical the cytosol nuleusCytosol Golgi – not identical the cytosol nuleus

Many Proteins Are Synthesized by Ribosomes in the Many Proteins Are Synthesized by Ribosomes in the CytosolCytosol

mRNAmRNA molecules emerge from the cell nucleus molecules emerge from the cell nucleus and become and become

attached to large ribonucleoprotein particle attached to large ribonucleoprotein particle called called ribosomes.ribosomes. mRNA mRNA sequence is translated into a sequence is translated into a corresponding sequence corresponding sequence

of amino acid.of amino acid. Each ribosome is composed of a large and a Each ribosome is composed of a large and a small subunitsmall subunit Ribosomes are complex structures about 30 nm Ribosomes are complex structures about 30 nm in the largein the large rRNA rRNA molecule form a framework on which molecule form a framework on which dozens of dozens of

species proteins, each present at one copy per species proteins, each present at one copy per ribosome.ribosome. rRNA rRNA and and mRNA mRNA as part of the crucial as part of the crucial

ribosome-mRNA-tRNA recognition process.ribosome-mRNA-tRNA recognition process.

KROMOSOM DAN DNA ……KROMOSOM DAN DNA ……

The Binding of Many Ribosomes to an Individual The Binding of Many Ribosomes to an Individual Messenger RNA Molecule Generates PolysomesMessenger RNA Molecule Generates Polysomes

The initiation codon The initiation codon AUGAUG, which is recognized by a , which is recognized by a special special initiator initiator tRNAtRNA (incorporating methionine) that must (incorporating methionine) that must pair with pair with the AUG codon in order to initiate each new the AUG codon in order to initiate each new polypeptide chain.polypeptide chain. Driven by the energy of GTP hydrolysis, the ribosome Driven by the energy of GTP hydrolysis, the ribosome then moves along then moves along the mRNA in the 5’ – to – 3’ direction to begin the the mRNA in the 5’ – to – 3’ direction to begin the elongation stage.elongation stage. At each step of elongation, the specific aminoacyl tRNA At each step of elongation, the specific aminoacyl tRNA molecule whosemolecule whose anticodon is complementary to the next codon in the anticodon is complementary to the next codon in the mRNA binds to themRNA binds to the ribosome.ribosome. The amino acid linked to that tRNA is then transferred The amino acid linked to that tRNA is then transferred to the carboxyl-to the carboxyl- terminal end of the growing polypeptide chain.terminal end of the growing polypeptide chain. Under physiological conditions, therefore actively Under physiological conditions, therefore actively translated mRNA is translated mRNA is found in found in polyribosomes, or ribosomespolyribosomes, or ribosomes

Protein Synthesis Is Blocked by Specific InhibitorsProtein Synthesis Is Blocked by Specific Inhibitors

There are many drugs and toxins that specifically affect There are many drugs and toxins that specifically affect each of the each of the major steps of protein synthesis, and these have been major steps of protein synthesis, and these have been very useful for very useful for working out cellular menchanisms, working out cellular menchanisms, Chloramphenicol, Chloramphenicol, Cycloheximide, puromycinCycloheximide, puromycin The first two drugs reversibly inhibit The first two drugs reversibly inhibit peptidyl peptidyl transferasetransferase, the ribosomal , the ribosomal enzyme that forms peptide bonds.enzyme that forms peptide bonds. Chloramphenicol inhibit protein synthesis only on the Chloramphenicol inhibit protein synthesis only on the ribosomes in theribosomes in the mitochondria/chloroplast, cycloheximide affects only mitochondria/chloroplast, cycloheximide affects only cytosolic ribosomecytosolic ribosome Puromycin is a structural analogue of a tRNA molecule Puromycin is a structural analogue of a tRNA molecule linked to an linked to an amino acidd: the ribosome mistakes it for an authentic amino acidd: the ribosome mistakes it for an authentic amino acid andamino acid and covalently incorporates it at the carboxyl terminus of covalently incorporates it at the carboxyl terminus of the growing poly- the growing poly- peptide chain, causing the premature termination and peptide chain, causing the premature termination and release of thisrelease of this polypeptide. polypeptide.

Some Protein Regulate the Rate of Their Own Some Protein Regulate the Rate of Their Own Synthesis by Binding to the Messenger RNA Synthesis by Binding to the Messenger RNA Molecules on Which They Are MadeMolecules on Which They Are Made

The intracellular concentration of a protein must be The intracellular concentration of a protein must be closely regulated closely regulated because an excess would harm the cell. because an excess would harm the cell. Examples: ribosomal protein, many of which will bind Examples: ribosomal protein, many of which will bind to RNA molecule to RNA molecule indiscriminately if more are present than can be bound indiscriminately if more are present than can be bound by the availableby the available rRNA.rRNA. When multiple copies of one of the ribosomal protein When multiple copies of one of the ribosomal protein genes are insertedgenes are inserted into into E. coli, E. coli, the amout of messenger RNA coding for the amout of messenger RNA coding for that protein that protein increase dramatically, but the rate of synthesis of the increase dramatically, but the rate of synthesis of the protein itself protein itself increase only slightly.increase only slightly. Bacterial ribosome synthesis is coordinated by a Bacterial ribosome synthesis is coordinated by a feedback regulation feedback regulation system in which excess proteins bind to specific system in which excess proteins bind to specific sequences.sequences.

In Eucayotes Only One Species of Polypeptide Chain In Eucayotes Only One Species of Polypeptide Chain Can Be Synthesized on Each Messenger RNA Can Be Synthesized on Each Messenger RNA MoleculeMolecule Eucaryotic and procaryotic messenger RNAs ;differ Eucaryotic and procaryotic messenger RNAs ;differ some what in both some what in both structure dan function. structure dan function. Eucaryotic mRNAs are modified in the nucleus Eucaryotic mRNAs are modified in the nucleus immediately after their immediately after their transcription. As a result, they usually carry both a transcription. As a result, they usually carry both a unique unique “cap” “cap” structure, composed of a 7-methylguanosine residu structure, composed of a 7-methylguanosine residu lingked to a lingked to a triphosphate, at their 5’ end and a run of about 200 triphosphate, at their 5’ end and a run of about 200 adenylic residuesadenylic residues ((“poly A”“poly A”) at their 3’ end.) at their 3’ end. Procaryotic mRNAs are quite different from Procaryotic mRNAs are quite different from eucaryoutic mRNAs.eucaryoutic mRNAs. Bacterial mRNAs have no 3’ poly A or 5’ cap Bacterial mRNAs have no 3’ poly A or 5’ cap structure. structure. Bacterial messenger RNAs are commonly Bacterial messenger RNAs are commonly polycistronic, polycistronic, meaning that they meaning that they encode multiple proteins separately translated from encode multiple proteins separately translated from the same mRNA mothe same mRNA mo lecule.lecule. Eucaryotic mRNAs are Eucaryotic mRNAs are monocistronic,monocistronic, only one species only one species of polypeptide of polypeptide chainchain being translated per messenger molecule.being translated per messenger molecule.

Polyprotein Are Often Made in EucaryotesPolyprotein Are Often Made in Eucaryotes

Related enzymatic activities can be encoded by the Related enzymatic activities can be encoded by the same messenger RNA same messenger RNA molecule in eucaryotes. molecule in eucaryotes. mRNA is translated into a single, large multifunctional mRNA is translated into a single, large multifunctional protein. protein. PolyproteinPolyprotein is cleaved by specific proteases to yield is cleaved by specific proteases to yield distinct enzymes.distinct enzymes. In other cases, however, it remains intact as a single In other cases, however, it remains intact as a single multifunctionalmultifunctional polypeptide.polypeptide. A series of related enzymatic activities can be linked A series of related enzymatic activities can be linked together in a together in a polyprotein in eucaryotes, while in procaryotes the polyprotein in eucaryotes, while in procaryotes the same enzymatic same enzymatic activities often involve the noncovalent complexing of activities often involve the noncovalent complexing of separate enzymeseparate enzyme subunit.subunit. This difference may reflect the greater dificult;y of This difference may reflect the greater dificult;y of bringing together bringing together subunits in the eucayotic cell, approximately 1000-subunits in the eucayotic cell, approximately 1000-fold increase volume.fold increase volume.

Many Proteins Undergo Covalent Modification After Many Proteins Undergo Covalent Modification After Their SynthesisTheir Synthesis Protein undergo some type of covalent modification Protein undergo some type of covalent modification after being released after being released from the ribosome. from the ribosome. More than 100 different such modifications of the More than 100 different such modifications of the amino acid side chainamino acid side chain are known. are known. Example: phosphorylation of a selected free OH group Example: phosphorylation of a selected free OH group of the amino of the amino acid side chain of a serine, a threonine, or a tyrosine acid side chain of a serine, a threonine, or a tyrosine residue in a protein.residue in a protein. Enzyme called Enzyme called protein kinases protein kinases utilize ATP to utilize ATP to phosphorylate proteins in phosphorylate proteins in this way. this way. Protein phosphorylation is reversible because of the Protein phosphorylation is reversible because of the abundant abundant phosphatase present in the cytosol.phosphatase present in the cytosol. Other covalent modifications of proteins that occur in Other covalent modifications of proteins that occur in the cytosol are the cytosol are permanent and requred for activity. Exp: many permanent and requred for activity. Exp: many enzymes have a enzymes have a covalently attached coenzyme (such as biotin, lipoic covalently attached coenzyme (such as biotin, lipoic acid, or pyridoxalacid, or pyridoxal phosphate) that plays an essential part in their phosphate) that plays an essential part in their reaction mechanism.reaction mechanism.

Many Proteins Undergo Covalent Modification Many Proteins Undergo Covalent Modification After Their SynthesisAfter Their Synthesis There are numerous other irreversible modifications There are numerous other irreversible modifications whose exact func- whose exact func- tion are less clear. Exp: the amino terminus of many tion are less clear. Exp: the amino terminus of many proteins in the cytoproteins in the cyto sol is modified (“blocked”) by acetylation, and the sol is modified (“blocked”) by acetylation, and the amino group on a fewamino group on a few selected lysines can be metylated.selected lysines can be metylated. Many other permanent permanent covalent Many other permanent permanent covalent modifications occur only to modifications occur only to those proteins that leave the cytosol for other those proteins that leave the cytosol for other intracellular destinations.intracellular destinations. Exp.: Exp.:

In the ER, almost half of the proline residues in the In the ER, almost half of the proline residues in the secrete protein collagen are secrete protein collagen are hyddroxylated to hydroxyproline.hyddroxylated to hydroxyproline. Addition of a second carboxyl group to glutamic acid Addition of a second carboxyl group to glutamic acid residues in proteins to formresidues in proteins to form γγ-carboxyglutamete, a dicarxylic acid with a high affinity for -carboxyglutamete, a dicarxylic acid with a high affinity for Ca Ca 2++2++

Numerous proteins are secreted by specialized Numerous proteins are secreted by specialized secretory cells: secretory cells: Exp.: Exp.:

Some endocrine cells secrete polypeptide hormones,Some endocrine cells secrete polypeptide hormones, Pancreatic acinar cells secrete digestive enzymes.Pancreatic acinar cells secrete digestive enzymes. If synthesized in an actife form inside a cell are syntehsized If synthesized in an actife form inside a cell are syntehsized and secreted as inactiveand secreted as inactive precursors called precursors called Zymogen.Zymogen.

Some Proteins Are Degraded Soon After They Have Some Proteins Are Degraded Soon After They Have Been SynthesizedBeen Synthesized Concentration of protein in a cell is determined by the Concentration of protein in a cell is determined by the balance between balance between the rate of its synthesis and the rate of its degradation. the rate of its synthesis and the rate of its degradation. As a result, thereAs a result, there is a constantis a constant Protein turnover. Protein turnover. The rate of synthesis of a protein is usually controlled The rate of synthesis of a protein is usually controlled by regulating the by regulating the amount of its mRNA available for translation.amount of its mRNA available for translation. In addition, a cell can contorol the concentration of a In addition, a cell can contorol the concentration of a protein by regulaprotein by regula ting the rate at which the protein is destroyed. ting the rate at which the protein is destroyed. Most proteins are compact structures, inherntly Most proteins are compact structures, inherntly somewhat resistant to somewhat resistant to roteolytic attack and, therefore, to degradation. roteolytic attack and, therefore, to degradation. Many of the “normal” proteins that are subject to rapid Many of the “normal” proteins that are subject to rapid degradation degradation within a cell are enzymes that catalyze a rate-within a cell are enzymes that catalyze a rate-determining step in a metadetermining step in a meta bolic pathway.bolic pathway.

Not All Proteins Synthesized in the Cytosol Remain Not All Proteins Synthesized in the Cytosol Remain ThereThere Many of the proteins destined for a variety of Many of the proteins destined for a variety of intracellular organelles intracellular organelles and their membranes, as well as all known proteins and their membranes, as well as all known proteins destined for secretiondestined for secretion are synthesized by suchare synthesized by such ribosomes. ribosomes. But some of the proteins translated by free ribosomes But some of the proteins translated by free ribosomes in the cytosol also in the cytosol also leave the cytosol.leave the cytosol. Example :Example :

Histones, as well as many other chromatin proteins, rapidly Histones, as well as many other chromatin proteins, rapidly diffuse through largediffuse through large nuclear pores and bind to structures in the nucleus followinng nuclear pores and bind to structures in the nucleus followinng their synthesistheir synthesis in the cytoplasm.in the cytoplasm.

Most of the proteins in chloroplasts and mitochondria, Most of the proteins in chloroplasts and mitochondria, and at least and at least some of those in peroxisomes, are translated by free some of those in peroxisomes, are translated by free ribosomes in the ribosomes in the cytosol and then are transported across membranes cytosol and then are transported across membranes surrounding their surrounding their respective organelles.respective organelles.

The CytosolThe Cytosol The cytosol sonsists of all of the space outside the The cytosol sonsists of all of the space outside the cellular organelles and cellular organelles and generally represents 50%-60% of the total cell vol.generally represents 50%-60% of the total cell vol. Most intermediary metabolism and the protein Most intermediary metabolism and the protein synthesis required for cell synthesis required for cell growth and maintenance occur in the cytosol.growth and maintenance occur in the cytosol. The amount of any jparticular protein in a cell depends The amount of any jparticular protein in a cell depends on the balance on the balance between the rate at which its mRNA is synthesizedin between the rate at which its mRNA is synthesizedin the nucleus and the the nucleus and the rate rate at which it is degraded.rate rate at which it is degraded. Some protein are degraded rapidly and continuously in Some protein are degraded rapidly and continuously in cells, presumably cells, presumably to allow rapid changes in their concentrations in to allow rapid changes in their concentrations in response to regulatory response to regulatory signals.signals. The reversible covalent modification of proteins The reversible covalent modification of proteins provides an important provides an important mechanism for regulating the activity of specific mechanism for regulating the activity of specific proteins in cells.proteins in cells. For example, the activities of many cellular proteins are For example, the activities of many cellular proteins are controlled by controlled by cycles of phosphorylation and dephosphorylation.cycles of phosphorylation and dephosphorylation.