Cytoplasm, biosynthesis

Figure 17-12 The reactions of cytoplasmic biosynthesis of saturated fatty acids. Compare with pathway of (3 oxidation (Fig. 17-1).

Catecholamine biosynthesis begins with the uptake of the amino acid tyrosine into the sympathetic neuronal cytoplasm, and conversion to DOPA by tyrosine hydroxylase. This enzyme is highly localized to the adrenal medulla, sympathetic nerves, and central adrenergic and dopaminergic nerves. Tyrosine hydroxylase activity is subject to feedback inhibition by its products DOPA, NE, and DA, and is the rate-limiting step in catecholamine synthesis the enzyme can be blocked by the competitive inhibitor a-methyl-/)-tyrosine (31). 

The primary cellular function of mRNA is to direct biosynthesis of the thousands of diverse peptides and proteins required by an organism—perhaps 100,000 in a human. The mechanics of protein biosynthesis take place on ribosomes, small granular particles in the cytoplasm of a cell that consist of about 60% ribosomal RNA and 40% protein. 

Fig. 8.1 Biosynthesis of peptidoglycan. The large circles represent A -acetylglucosamine orN-acetylmuramic acid to the latter is linked initially a pentapeptide chain comprising L-alanine, D-glutamic acid and meso-diaminopiraelic acid (small circles) terminating in two D-alanine residues (small, darker circles). The lipid molecule is undecaprenyl phosphate. In the initial (cytoplasm) stage where inhibition by the antibiotic D-cycloserine is shown, two molecules of Dalanine (small circles) are converted by an isomerase to the D-forms (small, darker circles), alter which a ligase joins the two D-alanines together to produce a D-alanyl-D-alanine dipeptide.

For the sake of study, the biosynthesis of carotenoid plant pigments can be divided into parts involving enzymes and their associated activities as listed in Table 5.3.1 and further detailed in Figure 5.3.1 through Figure 5.3.4. Some of the parts have common enzymatic mechanisms and may also be in distinct subcellular compartments such as cytoplasm, endoplasmic reticulum, or plastid thylakoid. 

The late cannabinoid pathway starts with the alkylation of ohvetolic acid (3.2 in Fig. 4) as polyketide by geranyl diphosphate (3.1) as the terpenoid unit. Terpenoids can be found in all organisms, and in plants two terpenoid pathways are known, the so called mevalonate (MEV) and non-mevalonate (DXP) pathway as described by Eisenrich, lichtenthaler and Rohdich [23,24,29,30]. The mevalonate pathway is located in the cytoplasm of the plant cells [30], whereas the DXP pathway as major pathway is located in the plastids of the plant cells [29] and delivers geranyl diphosphate as one important precursor in the biosynthesis. 

Production of Malonyl-CoA for the Fatty Acid Biosynthesis. Acetyl-CoA serves as a substrate in the production of malonyl-CoA. There are several routes by which acetyl-CoA is supplied to die cytoplasm. One route is the transfer of acetyl residues from the mitochondrial matrix across the mitochondrial membrane into the cyto-plasm. This process resembles a fatty acid transport and is likewise effected with the participation of carnitine and the enzyme acetyl-CoA-camitine transferase. Another route is the production of acetyl-CoA from citrate. Citrate is delivered from the mitochondria and undergoes cleavage in the cytoplasm by the action of the enzyme ATP-citrate lyase ... 

It has, thus, been demonstrated that redirecting the poly(3HB) biosynthetic pathway from the cytoplasm to the plastid resulted in an approximate 100-fold increase in poly(3HB) production [24]. However, it must be kept in mind that the rate of poly(3HB) biosynthesis in A thaliana leaves was relatively low, since poly(3HB) accumulated progressively over 40-60 days to reach 10-14% of the dry weight, whereas synthesis of starch can reach 17% dry weight for a 12 h photoperiod and seed storage lipids can reach 8% dry weight per day. 

Poly(3HB) synthesis in various subcellular compartments could be used to study how plants adjust their metabolism and gene expression to accommodate the production of a new sink, and how carbon flux through one pathway can affect carbon flux through another. For example, one could study how modifying the flux of carbon to starch or lipid biosynthesis in the plastid affects the flux of carbon to acetyl-CoA and poly(3HB). Alternatively, one could study how plants adjust the activity of genes and proteins involved in isoprenoid and flavonoid biosynthesis to the creation of the poly(3HB) biosynthetic pathway in the cytoplasm, since these three pathways compete for the same building block, i. e., acetyl-CoA. 

Flavonoid biosynthesis is linked to primary metabolism through both plastid- and mitochondria-derived intermediates, each requiring export to the cytoplasm where they are incorporated into separate halves of the molecule. 

Because membranes components participate in nearly every cell activity their structures are also dynamic and far from the equilibrium states that are most readily understood in biophysical terms. Newly synthesized bilayer lipids are initially associated with endoplasmic reticulum (Ch.3) whereas phospholipids initially insert into the cytoplasmic leaflet while cholesterol and sphingolipids insert into the luminal endoplasmic reticulum (ER) leaflet. Glycosylation of ceramides occurs as they transit the Golgi compartments, forming cerebrosides and gangliosides in the luminal leaflet. Thus, unlike model systems, the leaflets of ER membranes are asymmetric by virtue of their mode of biosynthesis. 

Whereas DNA is mostly located in the nucleus of cells in higher organisms (with some also in mitochondria and in plant chloroplasts), RNA comes in three major and distinct forms, each of which plays a crucial role in protein biosynthesis in the cytoplasm. These are, respectively, ribosomal RNA (rRNA), which represents two-thirds of the mass of the ribosome, messenger RNA (mRNA), which encodes the information for the sequence of proteins, and transfer RNAs (tRNAs) which serve as adaptor molecules, allowing the 4-letter code of nucleic acids to be translated into the 20-letter code of proteins. These latter molecules contain a substantial number of modified bases, which are introduced enzymatically. 

Microscopic examination of the mature neutrophils reveals two striking features a single multilobed nucleus and a dense, granular appearance of the cytoplasm (see Fig. 1.1a). The nucleus typically comprises two to four segments, and within this organelle the chromatin is coarsely clumped. Until recently, this abnormal chromatin structure was taken as evidence that the nucleus was transcriptionally inactive however, it is now appreciated that the mature neutrophil does perform active transcription ( 7.3), although rates of biosynthesis are somewhat lower than those observed in cells such as monocytes. There is no detectable nucleolus, so there can be only limited synthesis of ribosomal RNA in these cells. 

Phospholipid turnover also takes place in an asymmetric manner. The enzymes responsible for phospholipid turnover in response to receptor-mediated phospholipase c activation are active from the cytoplasmic surface of the membrane. Likewise, diacylglycerol kinases converting the product of phospholipase c back into the key intermediate of phospholipid biosynthesis, phosphatidic acid, are also located on the cytoplasmic smface of the membrane (Sanjuan et al., 2001). 

Once synthesized several factors influence the particular leaflet of the membrane lipid bilayer where the lipids reside. One is static interactions with intrinsic and extrinsic membrane proteins which, by virtue of their mechanism of biosynthesis, are also asymmetric with respect to the membrane. The interaction of the cytoplasmic protein, spectrin with the erythrocye membrane has been the subject of a number of studies. Coupling of spectrin to the transmembrane proteins, band 3 and glycophorin 3 via ankyrin and protein 4.1, respectively, has been well documented (van Doit et al, 1998). Interaction of spectrin with membrane lipids is still somewhat conjectural but recent studies have characterized such interactions more precisely. O Toole et al. (2000) have used a fluorescine derivative of phosphatidylethanolamine to investigate the binding affinity of specttin to lipid bilayers comprised of phosphatidylcholine or a binary mixture of phosphatidylcholine and phosphatidylserine. They concluded on the basis... 

The cytoplasmic NAD-reducing hydrogenase (SH) of the bacterium R. eutropha is a heterotetrameric enzyme, which contains several cofactors (Friedrich et al. 1996 Thiemermann et al. 1996). The Ni-containing subunit is called HoxH. This subunit plus the small subunit HoxY form the strictly conserved hydrogenase module with the Ni-Fe centre and a proximal [4Fe-4S] cluster. HoxF and HoxU represents the Fe-S/flavoprotein moiety which is closely related to a similar moiety in NADHrubiquinone oxidoreductase. The SH has been subject to molecular biological techniques in order to study its modular structure, mechanism and biosynthesis. 

It is obvious that the biosynthesis of such a complex structure involves many proteins and steps. In fact, the anchor is synthesized in the ER, requiring a membrane-bound multistep pathway in which more than 20 gene products, mainly polytopic membrane proteins, take part." " The first two steps of the biosynthesis occur on the cytoplasmic site of the ER, and after flipping to the lumen of the ER the biosynthesis is completed. The GPI... 

Acetyl CoA is activated in the cytoplasm for incorporation into fetty adds by acetyl CoA car- boxyiase, the rate Iimiting enzyme of fatty add biosynthesis. Acetyl CoA carboxylase requires biotin, ATP, and COj. Controls include ... 

The Protein Coat. Twenty-four polypeptides assemble into a hollow sphere, of ca. 100-120 X in outer diameter, to form the protein coat of ferritin. The diameter of the interior, which becomes filled with hydrous ferric oxide, is ca. 70-80 A. Subunit assembly appears to be spontaneous the coat remains assembled even without the iron core. Subunit biosynthesis is actually controlled by the amount of iron to be stored by a cell the subunit templates (mRNAs) are stored in the cytoplasm of a cell in a repressed form and are recruited for biosynthesis when the concentration of iron increases (3). 

Although messenger RNA is synthesized in the cell nucleus, it then moves to the cytoplasm and to the ribosomes, where protein biosynthesis occurs. These particles are composed of two subunits, termed 508 and 308, and are combinations of rRNA and protein. The ribosomes are responsible for binding... 

The tricarboxylic acid cycle not only takes up acetyl CoA from fatty acid degradation, but also supplies the material for the biosynthesis of fatty acids and isoprenoids. Acetyl CoA, which is formed in the matrix space of mitochondria by pyruvate dehydrogenase (see p. 134), is not capable of passing through the inner mitochondrial membrane. The acetyl residue is therefore condensed with oxaloacetate by mitochondrial citrate synthase to form citrate. This then leaves the mitochondria by antiport with malate (right see p. 212). In the cytoplasm, it is cleaved again by ATP-dependent citrate lyase [4] into acetyl-CoA and oxaloacetate. The oxaloacetate formed is reduced by a cytoplasmic malate dehydrogenase to malate [2], which then returns to the mitochondrion via the antiport already mentioned. Alternatively, the malate can be oxidized by malic enzyme" [5], with decarboxylation, to pyruvate. The NADPH+H formed in this process is also used for fatty acid biosynthesis. 

The pentose phosphate pathway (PPP, also known as the hexose monophosphate pathway) is an oxidative metabolic pathway located in the cytoplasm, which, like glycolysis, starts from glucose 6-phosphate. It supplies two important precursors for anabolic pathways NADPH+H+, which is required for the biosynthesis of fatty acids and isopren-oids, for example (see p. 168), and ribose 5-phosphate, a precursor in nucleotide biosynthesis (see p. 188). 

Fat synthesis in the liver (right). Fatty acids and fats are mainly synthesized in the liver and in adipose tissue, as well as in the kidneys, lungs, and mammary glands. Fatty acid biosynthesis occurs in the cytoplasm—in contrast to fatty acid degradation. The most important precursor is glucose, but certain amino acids can also be used. 

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