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What's the difference between Cytoplasmic pool and Granular storage pool?

What's the difference between Cytoplasmic pool and Granular storage pool?


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What's the difference between Cytoplasmic pool and Granular storage pool when speaking about neurotransmitters and synaptic cleft. I encountered this here:

Amphetamine's mechanism of action thus depends on the cytoplasmic, newly synthesized, rapidly metabolized pool of dopamine. Methylphenidate's mechanism of action depends on the granular storage pool (Brust, 2004)

Reference

Brust, J. C. M. (2004). Neurological aspects of substance abuse. Philadelphia, PA, Elsevier.


Neurotransmitters like dopamine are synthesized in the cytoplasm and then imported into synaptic vesicles. When the neurotransmitters are released it is by a fusion of the synaptic vesicle with the neuron's cell membrane, emptying the contents into the synaptic cleft. Re-uptake of the neurotransmitter back into the pre-synaptic neuron's cytoplasm is done by active transporters, in Dopamine's case by DAT. The cytoplasmic pool refers to the dopamine in the cytoplasm, while the granular pool refers to the dopamine stored in the synaptic vesicles.


What is the Difference Between Prokaryotic and Eukaryotic Chromosomes

The main difference between prokaryotic and eukaryotic chromosomes is that the prokaryotic chromosomes are short, circular DNA molecules whereas the eukaryotic chromosomes are long, linear molecules. Furthermore, prokaryotic chromosomes occur in the cytoplasm while eukaryotic chromosomes occur inside the nucleus. Moreover, prokaryotes contain a single chromosome per cell while the number of chromosomes in eukaryotes depends on the species.

Prokaryotic and eukaryotic chromosomes are two organizations of cellular DNA for packing inside the cell. Double-stranded DNA makes up both types of chromosomes.

Key Areas Covered

Key Terms

Chromosome Structure, Eukaryotic Chromosomes, Packaging, Prokaryotic Chromosomes, Quantity, Replication


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The conversion of NAD+ to NADH, and vice versa, are essential reactions in creating ATP during what’s called cellular respiration. The food you consume goes through three phases to become energy: glycolysis, the Krebs Cycle, and the electron transport chain.

In glycolysis and the Krebs cycle, NADH molecules are formed from NAD+. Meanwhile, in the electron transport chain, all of the NADH molecules are subsequently split into NAD+, producing H+ and a couple of electrons, too. The H+ are used to power a sort-of "pump" that sits on the inner membrane of the mitochondria, creating lots of energy in the form of ATP. Once the H+ have cycled through the pump, they subsequently merge with the electrons and a molecule of oxygen to form water. All of the three phases of respiration generate ATP however, the greatest yield of ATP is during the electron transport chain.

The cell uses NAD+ and NADH in other reactions outside of ATP production, too. In liver cells, for instance, the enzymes alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) utilize NAD+ as an oxidizing agent in order to breakdown ethanol from alcoholic drinks into a less toxic compound called acetate. In each of the enzymatic reactions, NAD+ accepts two electrons and a H+ from ethanol to form NADH.


Discussion

The results provide the first direct evidence that synaptic vesicle recycling and resting pools differ in molecular composition. Like VGLUT1 and a number of other synaptic vesicle proteins, VAMP7 undergoes exocytosis in response to stimulation, and with properties very similar to VGLUT1. Conversely, a substantial proportion of VGLUT1 and other vesicle proteins does not respond to stimulation (Fernandez-Alfonso and Ryan, 2008), similar to VAMP7. VGLUT1, VAMP7 and other synaptic vesicle proteins thus target to both recycling and resting pools. However, we now find that the proportions differ dramatically, with higher levels of VGLUT1 and VAMP2 in the recycling pool, and of VAMP7 in the resting pool.

Previous work has suggested that synaptic vesicles undergoing spontaneous release belong to a pool distinct from those responding to stimulation (Chung et al., 2010 Fredj and Burrone, 2009 Sara et al., 2005). Although this hypothesis has proven controversial (Groemer and Klingauf, 2007 Hua et al., 2010 Wilhelm et al., 2010), it predicts that the resting pool, which is largely unresponsive to stimulation, may nonetheless undergo spontaneous release. Indeed, we now find that VAMP7, enriched on resting pool vesicles, undergoes a higher rate of spontaneous release than VGLUT1, which is enriched in the recycling pool. The spontaneous release of VAMP7 thus cannot simply reflect the size of the recycling pool, and may derive in part from the resting pool. Since the response to spontaneous release of a single vesicle (quantal size) has been used to interpret the response to evoked release, a different origin for the two events would have important implications for synaptic physiology. However, the results do not exclude a role for the recycling pool in spontaneous release. Indeed, the sequential analysis of spontaneous and evoked release at the same boutons shows that spontaneous release can occlude the effect of stimulation, indicating that spontaneous release derives from recycling as well as resting pools.

The apparent lack of response to stimulation raises the possibility that VAMP7 + resting pool vesicles may correspond to a population of membranes other than synaptic vesicles, with heterologous expression resulting in mislocalization to the recycling pool. Previous work has indeed suggested that VAMP7 may localize to only a subset of presynaptic terminals such as hippocampal mossy fibers (Coco et al., 1999 Muzerelle et al., 2003). However, recent work has demonstrated the localization of VAMP7 to synaptic vesicles (Newell-Litwa et al., 2009), and a proteomic analysis of purified synaptic vesicles from whole brain also identified VAMP7 (Takamori et al., 2006). In addition, we confirm the localization of endogenous VAMP7 to presynaptic sites by immunofluorescence and to synaptic vesicles by density gradient fractionation and immuno-isolation. Ultrastructural analysis of the VAMP7 + vesicles labeled with lumenal HRP further shows that they exhibit the typical small, round appearance of synaptic vesicles. Morphologically indistinguishable recycling and resting pool vesicles thus exhibit quantitative differences in protein composition.

What is the physiological role of the resting pool? Spontaneous release from this pool may contribute to structural changes such as process extension (Martinez-Arca et al., 2000). Recent work has also implicated spontaneous release in the regulation of synaptic strength (McKinney et al., 1999 Sutton and Schuman, 2006), suggesting additional roles in development and plasticity. Although the relatively small proportion of VGLUT1 (�%) localized to the resting pool might suggest that this pool does not subserve transmitter release, we have recently observed that like VAMP7, the vesicular monoamine transporter VMAT2 which fills synaptic vesicles with monoamines also shows preferential localization to the resting pool (Onoa et al., 2010). The pools may thus be specialized for the release of different transmitters, and the recent evidence for differential release of acetycholine and GABA from retinal starburst amacrine cells is consistent with this possibility (Lee et al., 2010). In addition, spontaneous release of synaptic vesicles may contribute to synapse growth (Huntwork and Littleton, 2007) or the endosomal trafficking of receptors and channels.

Preferential localization of VAMP7 to resting rather than recycling synaptic vesicles presumably reflects differences in the formation of different pools. Recycling pool vesicles are generally considered to form through clathrin- and AP2-dependent endocytosis (Di Paolo and De Camilli, 2006 Granseth et al., 2006 Kim and Ryan, 2009) whereas resting pool vesicles may use a distinct mechanism, perhaps involving AP-3 (Voglmaier and Edwards, 2007) or AP-1 (Glyvuk et al., 2010 Kim and Ryan, 2009). Indeed, we chose VAMP7 for these experiments due to its dependence on AP-3 (Scheuber et al., 2006). Consistent with a distinct endocytic pathway, we find that VAMP7 undergoes endocytosis much more slowly than other synaptic vesicle proteins, and previous work has shown that vesicles internalized after stimulation may respond more slowly to repeat stimulation (Richards et al., 2000 Richards et al., 2003). However, a delay in endocytosis may reflect inefficient targeting to an endocytic pathway as well as an intrinsically slow pathway. On the other hand, deletion of the longin domain, which interacts with AP-3, redistributes VAMP7 toward the recycling pool. The interaction of AP-3 with the longin domain thus targets VAMP7 to the resting pool of synaptic vesicles. We also find that deletion of the polyproline motifs at the C-terminus of VGLUT1 increases spontaneous exocytosis of the transporter, indicating a role for these sequences in targeting to a subset of synaptic vesicles with low rates of spontaneous release. Spontaneous recycling of VAMP7 also depends on actin, in striking contrast to evoked release (Holt et al., 2004 Sankaranarayanan et al., 2003). Different endocytic mechanisms thus appear to account for the targeting of synaptic vesicle proteins to different pools.

Since VAMP2 and 7 differ in the properties of release and belong to the family of v-SNAREs involved in membrane fusion, we further tested the possibility that like VAMP2, VAMP7 might contribute to the behavior of synaptic vesicles. Although over-expression of wild type VAMP7 has no obvious effect on synaptic vesicle exocytosis, deleting the auto-inhibitory N-terminal longin domain alone increases the spontaneous release of VAMP7 2-3 fold, and this mutation affects the behavior of vesicles containing wild type VAMP7, not simply trafficking of the VAMP7-ND reporter itself. The longin domain deletion also increases spontaneous release of VAMP7 after cleavage of VAMP2 with tetanus toxin, indicating that VAMP7 can support spontaneous release even in the absence of VAMP2. Further, the ND mutant increases evoked release even in the presence of tetanus toxin, indicating that mutant VAMP7 can also mediate the exocytosis of recycling pool vesicles in response to stimulation. When disinhibited by removal of the longin domain, VAMP7 thus has the potential to influence synaptic vesicle exocytosis. Interestingly, mocha mice show changes in asynchronous and spontaneous release, possibly due to the loss of VAMP7 (Scheuber et al., 2006).

Although differences in protein composition presumably contribute to the differences in behavior of synaptic vesicle pools, it seems unlikely that v-SNAREs are alone responsible. The differential targeting of other synaptic vesicle proteins such as the calcium sensor synaptotagmin family (Maximov et al., 2007 Xu et al., 2009) presumably contribute to the difference between pools. Recent work has indeed implicated the related calcium-sensitive C2 domain protein DOC2 specifically in spontaneous rather than evoked release (Groffen et al., 2010), although DOC2 is a soluble protein and its relationship to different vesicle pools remains unclear. By demonstrating that different synaptic vesicle pools contain different proteins, our work now provides a framework for considering their individual contribution to the behavior of these pools, and the role of these pools in synapse development, function and plasticity.


FUNCTIONS FOR CYTOTOXIC GRANULE PROTEINS

Target cell death

The crucial role of pfp became evident when several laboratories created pfp-deficient, gene knock-out mice (pfp −/− ) [ 8 , 9 , 47 ]. These mice have normal T- and NK-cell development [ 8 ], however their cytolytic lymphocytes are compromised, and the mice are highly susceptible to certain intracellular pathogens [ 8 , 9 , 48 ]. In vitro, pfp-deficient CTL and NK cells are defective in their killing of allo-reactive or xeno-reactive tumor cell lines and NK-sensitive target cells, respectively [ 49 , 50 ]. Despite its clear biological importance, little is known about the molecular function of pfp, and only recently have dogmas concerning its mechanism of action been questioned. The inability thus far to assign pfp functions to discrete parts of the molecule represents a major gap in our understanding of effector lymphocyte biology. Pfp shares functional, antigenic, and ultrastructural similarities with complement proteins C6–C9, as described some time ago, and functions such as membrane insertion and polymerization have been tentatively explained on the basis of these similarities [ 51 52 53 54 ]. As already discussed, definitive evidence has emerged that the C-terminal domain of pfp is the site of calcium ion-binding and initiates lipid insertion [ 16 ]. Based on the structure of synaptotagmin and related molecules, it is postulated that after cleavage at the carboxy terminal, multiple aspartate residues of the C2 domain become approximated in three dimensions to bind a calcium ion electrostatically. The refolded pfp molecule becomes highly reactive with lipids as a result of exposure of amphipathic domains elsewhere in the molecule and is able to attach to and be inserted in the plasma membrane.

A pfp receptor?

Although pfp can form transmembrane channels in synthetic, lipid membranes with no protein content, it has long been suspected that, for example, on the basis of markedly differing susceptibility of various cell types to pfp, factors other than lipid composition can regulate the activity of pfp. The recent studies of Berthou et al. [ 55 ] have provided some evidence of this proposition. These investigators have proposed that the lysolipid PAF (known as platelet activating factor because it promotes platelet aggregation) is co-released with pfp when NK cells degranulate and may potentiate pfp lysis by forming a molecular bridge between pfp and the PAF receptor (PAF-R) Thus, ternary complexes containing PAF, PAF-R, and pfp may achieve membrane disruption more efficiently by enhancing the binding of pfp to phosphorylcholine. Furthermore, as PAF-R expression is inducible with interferons (IFNs), local, inflammatory mediators may modulate the sensitivity of cells to pfp at a focus of infection. If verified, the studies by Berthou et al. [ 55 ] may also provide an opportunity to manipulate pfp function for experimental and even therapeutic purposes.

What does pfp actually do?

As with complement, purified pfp can cause cell lysis by forming discrete pores 12–20 nm in diameter but, by itself, cannot account for the morphological changes of apoptosis, such as chromatin condensation and DNA fragmentation [ 56 ]. The nuclear changes occur before cell membrane damage [ 57 , 58 ] and are reproducible in vitro with concentrations of pfp that cause minimal, membrane-permeability changes [ 21 ]. Thus, the proposition that large membrane pores are necessary for grz access to the target cell cytosol has come into question recently. Despite the structural similarities of the pores formed by purified pfp and complement, grzB did not trigger apoptosis of target cells when delivered by complement [ 21 ]. However, listeriolysin (LLO), a virulence factor of Listeria monocytogenes (LM) that causes lysis of endosomes, was able to deliver grzB potently in the absence of measurable plasma-membrane damage [ 21 ]. The pro-apoptotic activity of LLP was inhibited when the pH of endo-lysosomes was raised to neutral with ammonium chloride or bafilomycin [ 21 ]. Direct support for an endosomolytic function of pfp came from the observation that brefeldin A (BFA) inhibited pfp-induced release of grzB from endosomes, blocked its translocation to the nucleus, and inhibited cell death. Consistent with BFA having no effect on receptor-mediated uptake via endocytosis, BFA had no effect in kinetic or absolute terms on grzB uptake into the cell in the absence of pfp [ 21 ].

Because the concentration of pfp delivered to the target cell surface by a CTL has not been determined, a key question is whether endosomolysis is relevant physiologically at pfp concentrations causing appreciable cell-membrane damage. We have found that when target cells are incubated with concentrations of pfp, which caused 100% 51 Cr release, freely diffusible, fluorescent proteins of 9–13 kDa remain excluded for over 1 h, whereas 32-kDa grzB and 65-kDa grzA continued to be delivered to the cytoplasm and nucleus within a few minutes [ 21 ]. This indicates the delivery of apoptotic mediators by pfp is indeed highly selective, and thus, grz entry into cells cannot be ascribed to passive diffusion simply through pfp pores, even if target cells are placed under severe, osmotic stress.

Previous reviews have described the gene structure, chromosomal loci, and protease specificity of grz family members [ 29 , 30 , 59 , 60 ]. The major, recent advance in terms of grz structure has been the description of a crystal structure for grzB in complex with a macromolecular inhibitor. The primary specificity for Asp residues occurs through a side-on interaction with a “buried” side chain of Arg 226 of granzyme B. A further nine amino acids make contact with the substrate and dictate the extended substrate-specificity profile [ 31 ]. There has also been considerable progress in further elucidating the role of grz in apoptosis [ 60 ]. Early studies unequivocally illustrated that grzA and B could collaborate with pfp to kill target cells [ 57 , 61 , 62 ]. The most potent granzyme in this context is grzB, and grzB-deficient mice have impaired ability to induce rapid DNA fragmentation in the target cell [ 63 ]. Two other grz were purified, which induce target cell DNA fragmentation with much slower kinetics, and these were the tryptases grzA and tryptase-2 [ 57 ]. However, grzA-deficient mice have no generalized defect of target cell DNA fragmentation, indicating that unlike grzB, the absence of grzA can be compensated by other grz [ 64 ]. We and others [ 65 66 67 68 ] have shown that grzB, abundant in cytolytic granules, is the protease largely responsible for eliciting the nuclear changes of apoptosis. We and several other groups [ 67 68 69 ] have shown that grz can enter cells independently of pfp but remain sequestered in endosomes and so do not damage cells unless pfp is also present. Thus, the provision of a membrane pore by pfp is not necessary for grz to enter the target cell cytoplasm. Cell-surface binding of 125 I-grzB is saturable and can be competed by unlabeled grz [ 69 ], suggesting uptake through a specific receptor. Recently, the 270-kDa, cation-independent, mannose 6-phosphate receptor was demonstrated to be a receptor through which grzB can enter the endosomal compartment [ 70 ]. Most surprisingly, it was claimed that expression of the same receptor on H2k-expressing fibroblasts was required for their rejection by allogeneic T cells, suggesting a primary role for grzB in the allogenic-effector response and predicting a further, possible mechanism for immune escape by tumors [ 70 ].

GrzB function in cell death: a crucial role for Bid-cleavage rather than direct caspase activation

Sublytic pfp can induce the redistribution of grzB or dimeric grzA (65 kDa) from endosomes into the cytosol and can amplify greatly cellular uptake of grz [ 67 ]. Apoptotic changes are apparent within only 2 min, and migration of grzB out of endosomes and its appearance in the nucleus are precise predictors of apoptotic death [ 65 ]. In addition to inducing programmed, cell-death pathways operating through caspases, grzB can directly cleave cytoplasmic substrates such as the actin-binding protein, filamin [ 71 ], and nuclear poly(ADPribose) polymerase (PARP) and nuclear matrix antigen at sites different than those preferred by caspases [ 72 ]. Grz entry into the nucleus occurs before apoptotic, nuclear-membrane disruption [ 58 ] and is dependent on an unknown cytosolic carrier protein but does not require expenditure of energy [ 67 ].

Through its unique ability to cleave after aspartate residues, grzB can cleave many pro-caspases in vitro [ 73 74 75 ]. However, in intact cells, there is a requirement for mitochondrial perturbation [ 76 , 77 ], without which direct caspase activation occurs only very slowly [ 78 ] (Fig. 1) We showed recently that a vital part of the apoptotic signal imparted by grzB to mitochondria is through direct cleavage of the pro-apoptotic, BH3-only, Bcl-2 family member Bid, which is specifically cleaved at a site 16 amino acids down-stream of that used by caspases [ 78 ]. Surprisingly, grzB can also induce death through a caspase-independent mechanism that involves damage to non-nuclear structures and is probably mediated by direct, grz-mediated disruption of mitochondria [ 66 , 79 , 80 ]. These caspase-independent pathways may safeguard against viruses that delay programmed cell death by expressing serpins such as the caspase-8 inhibitor of cowpoxvirus, cytokine response modifier A (crmA) [ 81 ].

A simplified scheme for cell death mediated by grzB. Following the entry of grzB into the target cell by endocytosis and its liberation into the cytosol by pfp, the principal role of grzB (thick arrow) is to cleave the pro-apoptotic, Bcl-2-like molecule Bid, specifically at the grzB cleavage site at amino acid 75, which is strongly conserved between mouse and humans. Direct processing of caspases by grzB is inefficient in the absence of mitochondrial perturbation (dotted line). Truncated Bid disrupts mitochondria, resulting in the release of pro-apoptotic mediators, the precise nature of which is unknown at present (dashed arrow). These mediators may include Diablo/Smac and posssibly cytochrome c and induce efficient caspase processing and generic caspase-mediated cell death. Insertion of truncated Bid and release of apoptotic mediators from mitochondria can be negatively regulated by overexpression of Bcl-2. Cell death in response to grzB can also occur without efficient caspase activation through a non-nuclear mechanism, which is poorly understood but may involve cleavage of cytoskeletal elements (dashed arrow for a deeper explanation, see text and ref. [ 76 ]).

GrzA function in cell death

GrzA is a specific tryptase, which becomes concentrated in the nucleus of targeted cells and synergistically enhances DNA fragmentation induced by grzB and pfp [ 58 ]. Little is known about grzA-induced cell death. Using recombinant, mutant, inactive grzA, two grzA-binding proteins, PHAP (putative HLA-associated protein) II and heat shock protein (hsp)27, were isolated [ 82 ], however neither of these has been demonstrated to be important yet in apoptosis mediated by grz. GrzA-induced membrane perturbation, nuclear condensation, and DNA damage are unimpaired by caspase blockade, however entry of grA to the nucleus is totally inhibited by Bcl-2 overexpression [ 83 ]. Recently, grzA was shown to induce single-strand DNA breaks rather than oligonucleosomal fragmentation [ 84 ]. GrzA enhances DNA accessibility to exogenous endonucleases and degrades histone H1in vitro into ∼16-kDa fragments. Histone digestion may provide a mechanism for unfolding compacted chromatin to facilitate endogenous DNase access to DNA [ 85 ]. CTL and NK cells of mice deficient in grzA and grzB (grzAB −/− ) induced 51 Cr-release in target cells at levels and with kinetics similar to those of normal mice [ 86 ]. This contrasts with their inability to induce apoptotic nuclear damage in target cells, suggesting that grzA and -B are critical for CTL/NK granule-mediated nucleolysis, with grzB being the main contributor, and target cell death is pfp-dependent and -independent of both proteases.


Toxoplasma Secretory Proteins and their Roles in Cell Invasion and Intracellular Survival

M. Lebrun , . M.-F. Cesbron-Delauw , in Toxoplasma Gondii , 2007

11.6.2 Biogenesis of dense-granule organelles: dual features of both constitutive and regulated secretory pathways

Dense granules are homogeneous spherical electron-dense vesicles,

200 nm in diameter and enclosed by a unit membrane. The existence of subpopulations of dense granules storing specific GRAs was examined by double or triple labeling with specific antibodies. All dense granules exhibited multiple labeling, showing localization of different GRAs within the same granules ( Sibley et al., 1995 Ferguson et al., 1999a Labruyere et al., 1999 ). The number of DGs varies between the different infectious stages. The largest numbers (

15) have been observed in the tachyzoites and sporozoites, with intermediate numbers (8–10) in the bradyzoites and few (3–6) in the merozoites. This may correlate with the number of GRAs expressed and the type of PV formed (see below).

There are still several unresolved questions regarding both dense-granule formation and the sorting of GRA proteins into these organelles. In particular, whether dense granules are functionally analogous to constitutive versus regulated secretory vesicles is not fully established. In other eukaryotic cells, sorting of proteins to constitutive versus regulated secretory pathways occurs in the trans-Golgi network (TGN). Proteins destined for regulated secretion aggregate and are packaged into immature secretory granules (ISGs). Clathrin-coated vesicles bud from these ISGs and recycle proteins back to the TGN or endosomes, resulting in further concentration of the secretory proteins. The specific coat proteins, identified at the TGN, include both the adaptor proteins, AP1 and AP3, and adaptor-related proteins, GGAs (for review, see Arvan and Castle, 1998 ).

In Toxoplasma, immature dense granules have never been observed. Moreover, transient and stable expression of several soluble reporter proteins in Toxoplasma showed that any soluble protein, provided it possesses a signal peptide, is delivered to dense granules and later secreted into the PV. By contrast, addition of a GPI signal anchor targets the same reporter protein to the plasma membrane through transport vesicles ( Karsten et al., 1998 ). Conversely, the TgSAG1 protein for which the GPI signal anchor domain has been deleted is routed to the PV via the dense granules ( Striepen et al., 1998 ). Thus, dense granules constitute the default constitutive pathway for soluble proteins in Toxoplasma.

However, morphologically, dense granules resemble the dense core granules involved in regulated secretion in mammalian cells, indicating that retention and condensation of secretory products may occur during dense granule formation. The prevailing model of sorting by retention in higher organisms is the selective aggregation of regulated, but not constitutive, secretory proteins, which limits the ability of the former to escape from maturing granules during the process of constitutive vesicle budding ( Arvan and Castle, 1998 ). This condensation may be due to an inherent property of the regulated secretory proteins to aggregate via subtle changes in the forming granule, while trafficking through the different compartments of the secretory pathway. These changes include mild acidification or an increasing concentration of bivalent cations such as calcium ( Chanat and Huttner, 1991 ).

Most of the GRA proteins are not intrinsically soluble, and are predicted as type 1 transmembrane proteins. Indeed, they become membrane associated following their secretion into the PV ( Lecordier et al., 1999 ). Within the dense granules, the GRAs are essentially found as both soluble and aggregated forms ( Labruyere et al., 1999 Lecordier et al., 1999 ). The mechanism by which these proteins remain excluded from the endomembranous system of the parasite is unknown.

Are there signals that mediate GRA targeting and/or aggregation into the dense granules? Since dense granules have never been reported to constitute an acidic compartment, protein condensation is unlikely to result from a substantial decrease in pH. An AP-1 ortholog was localized at the trans-most cisternae of the Golgi apparatus ( Ngo et al., 2003 ) and, despite the fact that YXXϕ motifs were localized in the cytoplasmic tails of two GRA proteins (GRA4 and GRA7), these were not recognized by the Toxoplasma AP-I ( Ngo et al., 2003 ). Whether delivery of the GRAs to dense granules depends on a peculiarity of their transmembrane domain (TMD) ( Karsten et al., 2004 ) or on protein–protein interactions is not yet fully demonstrated (Gendrin, Braun and Cesbron-Delauw, unpublished). Given that GRA1, the most abundant dense-granule product, is a calcium-binding protein ( Cesbron-Delauw et al., 1989 ), a role for Ca 2+ in regulating aggregation remains a possibility.


Nuclear domains

The mammalian cell nucleus is a membrane-bound organelle that contains the machinery essential for gene expression. Although early studies suggested that little organization exists within this compartment, more contemporary studies have identified an increasing number of specialized domains or subnuclear organelles within the nucleus (Lamond and Earnshaw,1998EF7 Spector,1993EF15). In some cases, these domains have been shown to be dynamic structures and, in addition, rapid protein exchange occurs between many of the domains and the nucleoplasm(Misteli, 2001EF10). An extensive effort is currently underway by numerous laboratories to determine the biological function(s) associated with each domain. The accompanying poster presents an overview of commonly observed nuclear domains.FIG1

The nucleus is bounded by a nuclear envelope, a double-membrane structure, of which the outer membrane is contiguous with the rough endoplasmic reticulum and is often studded with ribosomes. The inner and outer nuclear membranes are fused together in places, forming nuclear poresthat serve in the transit of materials between the nucleus and cytoplasm(Stoffler et al., 1999EF16). The nuclear pore complex has been shown to have a remarkable substructure, in which a basket extends into the nucleoplasm. The peripheral nuclear lamina lies inside the nuclear envelope and is composed of lamins A/C and B and is thought to play a role in regulating nuclear envelope structure and anchoring interphase chromatin at the nuclear periphery. Internal patches of lamin protein are also present in the nucleoplasm (Moir et al.,2000EF11). The cartoon depicts much of the nuclear envelope/peripheral lamina as transparent, so that internal structures can be more easily observed.

Within the nucleoplasm, the chromosomes are arranged into chromosome territories, and active genes are thought to reside throughout the surface of the loosely packed territories (Cremer et al.,2000EF1). Homologues do not appear to be paired in interphase mammalian nuclei. In some cell types, a band ofheterochromatin (inactive chromatin) is observed just internal to and associated with the nuclear lamina. In addition, varying amounts of heterochromatin are also observed in more internal nuclear regions. PcG bodies containing polycomb group proteins (i.e. RING1, BMI1 and hPc2) have been observed associated with pericentromeric heterochromatin (Saurin et al.,1998EF13). These domains vary in number (two to several hundred), size (0.2-1.5 μm) and protein composition. It is currently unclear whether these domains are storage compartments or are directly involved in silencing.

Pre-mRNA splicing factors are localized in a pattern of 25-50 nuclear speckles as well as being diffusely distributed throughout the nucleoplasm(Spector, 1993EF15). Many of the larger speckles correspond to interchromatin granule clusters (IGCs). These clusters measure 0.8-1.8 μm in diameter and are composed of 20-25-nm diameter particles that appear connected in places. IGCs have been proposed to be involved in the assembly and/or modification of pre-mRNA splicing factors. Nuclear speckles are dynamic structures, and factors are recruited from them to sites of transcription (perichromatin fibrils). Transcription sitesare observed throughout the nucleoplasm, including on the periphery of IGCs,as several thousand foci. In addition to being diffusely distributed, several transcription factors have also been shown to be concentrated in one to three compartments termed OPT (Oct1/PTF/transcription) domains. These domains are 1.0-1.5 μm in diameter and also contain nascent transcripts as well as other transcription factors, but they contain few, if any, factors involved in RNA processing (Grande et al.,1997EF4 Pombo et al.,1998EF12). The OPT domain appears in G1 phase, when it often resides next to nucleoli, and it disappears during S phase. Its function is unknown.

In many cell types, pre-mRNA splicing factors are also localized in 1-10Cajal bodies, previously called Coiled Bodies (Gall,2000EF3). These dynamic nuclear bodies are 0.2-1.0 μm in diameter and are thought to play a role in snRNP biogenesis and in the trafficking of snRNPs and snoRNPs. Spliceosomal U1, U2,U4/U6 and U5 snRNPs, as well as the U7 snRNP involved in histone 3′-end processing, and U3 and U8 snoRNPs involved in processing of pre-rRNA, all localize to this structure. It has been proposed that these factors move through the Cajal body en route to nuclear speckles (snRNPs) or nucleoli(snoRNPs). In addition, the Cajal body has been shown to associate with histone loci as well as U1, U2 and U3 gene clusters (Matera,1999EF8).

Gems (gemini of Cajal bodies) are found in the nucleoplasm and are coincident with or adjacent to Cajal bodies, depending upon the cell line examined, and they have been characterized by the presence of the survival of motor neurons gene product (SMN) and an associated factor, Gemin2 (Matera,1999EF8). The cytoplasmic pool of SMN and Gemin2 has been implicated in the assembly of snRNPs, and the nuclear pool may play an additional role in snRNP maturation. Interestingly, spinal muscular atrophy, a motor neuron degenerative disease, results from reduced levels of, or a mutation in, the SMN protein.

Several factors specifically involved in the cleavage and polyadenylation steps of pre-mRNA processing (e.g. CstF and CPSF) have a diffuse distribution pattern in the nucleus and in addition are concentrated in 1-4 foci, each 0.3-1.0 μm in diameter, called cleavage bodies (Schul et al.,1996EF14). These structures either overlap with or are localized adjacent to Cajal bodies. The subset of cleavage bodies that do not overlap with Cajal bodies contain newly synthesized RNA.

The Nucleolus is the site of rRNA synthesis, rRNA processing, and assembly of ribosomal subunits (Spector,1993EF15) and is perhaps the most obvious internal nuclear compartment. Most mamalian cells contain 1-5 nucleoli, each 0.5-5.0 μm in diameter. The nucleolus is differentiated into three clearly identifiable regions. The fibrillar centers (shown as green ovals within the nucleolus) are regions that are thought to be the interphase equivalent of nucleolar-organizing regions (NORs) of chromosomes. Human cells contain approximately 250 copies of rDNA located at NORs on five different pairs of chromosomes. Transcription and processing of rRNA is thought to occur within the dense fibrillar component (shown as a blue reticulum), a region that surrounds and in some cases extends between the fibrillar centers. The granular region (shown as green granules) of the nucleolus is made up of pre-ribosomal particles at different stages of maturation, as well as large and small ribosomal subunits.

The perinucleolar compartment (PNC) and the SAM68 nuclear body (Huang, 2000EF5) have been identified as unique structures that are associated with the surface of nucleoli and are thought to play a role in RNA metabolism. They range in size from 0.25-1.0 μm in diameter, and 1-10 are observed per nucleus. The PNC contains a series of small RNAs transcribed by RNA polymerase III and several RNA-binding proteins, including poly-pyrimidine-tract-binding (PTB) protein. SAM68 nuclear bodies contain members of a group of RNA-binding proteins that contain a GSG domain, also called the STAR (signal transduction and activation of RNA) domain, which is a 100-residue sequence highly homologous to the KH domain found in hnRNP K. Although the functions of the PNC and SAM68 nuclear bodies are unknown, both of these structures are predominantly found in cancer cells, and they are rarely observed in primary cells.

PML bodies (Maul et al.,2000EF9) vary in size from 0.3μm to 1.0 μm in diameter, and a typical mammalian nucleus contains 10-30 of these structures. PML bodies have also been called ND10, PODs (PML oncogenic domains) and Kr bodies. In addition to the PML protein, several other proteins, including Sp100, SUMO1, HAUSP and CBP, have been localized to this nuclear domain in addition to being diffusely distributed in the nucleoplasm. PML bodies have been suggested to play a role in aspects of transcriptional regulation and appear to be targets of viral infection. Interestingly, individuals suffering from acute promyelocytic leukemia (APL)have a t(15,17) translocation, in which the the PML gene is fused to the gene that encodes the α-retinoic acid receptor, which results in the production of a fusion protein. Cells from these individuals exhibit a break-up of PML bodies into a large number of smaller domains, which are scattered throughout the nucleoplasm. Treatment with retinoic acid, which results in these individuals going into remission, also results in a reformation of typical PML bodies.

In addition to the above domains generally observed in mammalian nuclei,other domains that are specific to cell type or physiological state have also been reported. For example, GATA-1 nuclear bodies containing GATA transcription factors have been observed in murine haemopoietic cells(Elefanty et al., 1996EF2). However, these domains are not active in transcription. HSF1 foci containing the transcription factor, heat shock factor 1, have been observed in nuclei of cells that have been subjected to heat shock, however these domains do not coincide with HSP70 or HSP90 transcription sites (Jolly et al., 1997EF6).

The above text provides an expanded legend to the accompanying poster it is not meant to serve as a review of primary research papers, and as such much of the primary literature has not been cited here. Readers are encouraged to access the cited reviews in order to locate the primary research papers on particular nuclear bodies. I thank Jim Duffy for his outstanding artistic skills in developing the cartoon, and the following individuals who provided immunofluorescent images for this poster: Mark Frey and Greg Matera (Cajal body and Gem), Paul Mintz (RNA polymerase II transcription factor, nucleoli,peripheral nuclear lamina, perinucleolar compartment, PML body, nuclear speckles), Ana Pombo (OPT domain), Stéphane Richard (Sam68 nuclear body), Thomas Ried and Evelin Schröck (chromosome territory). In addition, I thank Edith Heard, Greg Matera and members of my laboratory for their insight and useful discussions. Research in my laboratory is funded by NIH/NIGMS 42694-12.


Biomolecules Important Extra Questions Very Short Answer Type

Question 1.
What is hydrolysis?
Answer:
During the digestion of carbohydrates, the glycosidic bond between sugar residues is broken by the addition of water and this is called hydrolysis.

Question 2.
Define fatty acid.
Answer:
Fatty acids are organic acids with a hydrocarbon chain ending in a carboxyl group.

Question 3.
What are iso-enzymes?
Answer:
The enzymes possessing slightly different molecular structures but similar in their bio-catalytic action.

Question 4.
Give the names of 2 non-polar organic solvents that are used for lipid extraction from cells.
Answer:
Chloroform, Ether.

Question 5.
Name one monosaccharide sugar that is found in the blood plasma of human beings.
Answer:
Glucose.

Question 6.
What is the function of calcium in the human body?
Answer:
Calcium in bones and teeth provides strength and rigidity to them.

Question 7.
Name the bonds uniting the monosaccharide subunits.
Answer:
Monosaccharide sub-units are joined together by glycoside bonds.

Question 8.
What are lygases?
Answer:
Lygases are the enzymes that join two substrate molecules.

Question 9.
Name the ending group of fatty acids which are organic acids with a hydrocarbon chain.
Answer:
Carboxyl.

Question 10.
Which is the most common form of sugar in fruits?
Answer:
Fructose.

Question 11.
How can we overcome the deficiency of iodine?
Answer:
By using iodized common salt.

Question 12.
Names the important food storage of carbohydrates.
Answer:
Starch and Glycogen.

Question 13.
Define allosteric modulation.
Answer:
It regulates the activity of some enzymes internally.

Question 14.
Mention two functions of the sodium and potassium ions in the body.
Answer:
Functions of the sodium and potassium ions in the body are:

  1. To maintain the volumes of extracellular and intracellular fluids.
  2. Transmission of nerve impulses.

Question 15.
Name the small molecules of the cell.
Answer:
The small molecules of the cell are:

  1. Minerals
  2. Water
  3. Amino acids
  4. Sugars
  5. Lipids
  6. Nucleotides.

Biomolecules Important Extra Questions Short Answer Type

Question 1.
What are monosaccharides? Give few examples.
Answer:
Monosaccharides are the simplest carbohydrates that cannot be hydrolyzed into still smaller carbohydrates. The general formula is Cn H2n On e.g. Ribose, Glucose, Fructose.

Question 2.
What is a disaccharide?
Answer:
A disaccharide is a sugar molecule composed of two monosaccharide sub-units e.g. a molecule of sucrose is formed from a molecule of glucose and a molecule of fructose by dehydration.

Question 3.
Why do fats release more energy than carbohydrates on oxidation?
Answer:
Like carbohydrates, fats are made up of C, H, and O but they contain fewer oxygen molecules than carbohydrates. On oxidation they consume more oxygen releasing more energy.

Question 4.
What is the function of calcium in our body? In what form is calcium deposited in the middle lamella?
Answer:
Calcium is impregnated in bones and teeth. It provides them with strength and rigidity.
Calcium is deposited in the middle lamella in the form of calcium pectate.

Question 5.
Define cellular pool. What are the characteristics of a small molecule in the cellular pool?
Answer:
The collection of various types of molecules in a cell is termed a cellular pool.

The characteristics of small molecules in the cellular pool are

Question 6.
What are lipids or fats? State their characteristic. What are the functions of subcutaneous fat in our body?
Answer:
Fat or lipids are esters of glycerol and fatty acids. They are made up of C, H, and O but include proportionately less oxygen as compared to carbohydrates. They are insoluble in water and soluble in non-polar organic solvents.

Functions of subcutaneous fat are

Question 7.
How are amino acids linked to form a peptide chain?
Answer:
Amino acids are condensed together to form a peptide chain. The bond is formed between the carboxyl group of one amino acid and the amino group of adjacent amino acid. This is called a peptide bond and it is formed by dehydration.

Question 8.
What are phospholipids?
Answer:
Phospholipids are lipids containing phosphate groups e.g. phosphoglyceride. They have a hydrophilic polar head and a hydrophobic non-polar tail.

Question 9.
What are macromolecules? Give examples.
Answer:
Simple molecules assemble and form large and complex molecules called macromolecules e.g. proteins, lipids, nucleic acid, and carbohydrates.

Question 10.
Give two examples of storage polysaccharides.
Answer:
Two advantages of storing carbohydrates in the form of polysaccharides:

  1. Food storage polysaccharides are starch and glycogen. Starch is found in rice, wheat, etc. Glycogen is stored in the liver. During their formation, many molecules of water are removed from monosaccharides.
  2. If necessary, polysaccharides are broken down by enzymes for the release of energy.

Question 11.
What is chitin?
Answer:
Chitin: Chitin is similar to cellulose in many ways except its basic units are not glucose, but a similar molecule that contains nitrogen (N-acetyl glucosamine) and is soft as well as leathery.

Question 12.
Explain how glycosidic bonds are formed?
Answer:
Formation of Glycosidic Bonds: The aldehyde or ketone group of a monosaccharide can react and bind with an alcoholic group of another

Glycosidic bond

organic compound to join the two compounds together. This bond is known as a glycosidic bond. This bond may be hydrolyzed to give the original compounds. Monosaccharides by uniting together through glycosidic bonds give rise to compound carbohydrates.

Question 13.
Describe functions of polysaccharides in living organisms.
Answer:
Food storage polysaccharides: As the name suggests saccharides which perform the function of storing food. Examples are starch, glycogen.

Starch: It is formed as a result of photosynthesis. It is found in large quantities in rice, wheat, cereals, legumes, potato, tapioca, and bananas. It is an energy-giving substance as it stores energy.

Glycogen: It is found in the muscles and liver of mammals and stores energy. There are distinct advantages of storing carbohydrates in the form of polysaccharides

  1. During the formation, many molecules of water get removed and bulk reduced
  2. Polysaccharides are relatively easy to store and get broken down easily by enzymes to release energy.

Structural Polysaccharides: Examples of these are cellulose and chitin. These take part in the formation of the organism.

Cellulose: It is a plant product. It is perhaps the most abundant material found in the living world. If forms cell walls. It is a fibrous polysaccharide that has high tensile strength. Wood and cotton have large quantities of cellulose.

Chitin: Chitin is similar to cellulose in many ways except that its basic unit is not glucose, but a similar molecule that contains nitrogen (N-acetyl glucosamine). Chitin is soft and leathery, it becomes hard when it gets impregnated with calcium carbonate or certain proteins. The insolubility of these polysaccharides in water helps in retaining the particular form it also helps in strengthening the structure of organisms.

Question 14.
What is meant by the tertiary structure of proteins?
Answer:
The tertiary structure of proteins: Many amino acid units form polypeptides. The peptide bonds holding the amino acids together in a particular way constitute the primary structure of the protein. A functional protein contains one or more polypeptide chains.

Through the formation of hydrogen bonds, peptide chains assume a secondary structure. Secondary protein may be in the form of a twisted helix or pleated sheet.

When the individual peptide chains of the secondary structure of the protein are further extensively coiled and folded into sphere-like shapes with the hydrogen bonds between the amino and carboxyl group and various other kinds of bonds cross-linking on-chain to another they form tertiary structure.

The ability of proteins to carry out specific reactions is the result of their primary, secondary, and tertiary structure.

The tertiary structure (myoglobin)

Question 15.
Explain the composition of triglycerides.
Answer:
Fat is esters of fatty acids with glycerol. Each molecule of glycerol can react with 3molecules of fatty acid. On the basis of fatty acids that are attached to the glycerol molecule, the esters are called either mono, di, or triglycerides.

Triglyceride-Tripalmitin

Question 16.
Mention the difference between saturated and unsaturated fat?
Answer:
Differences between saturated and unsaturated fat:

Saturated fat Unsaturated fat
(i) They have higher melting points (i) lower melting points
(ii) Carbon align in the chain (ii) Double or triple banded
(iii) Remain in solid form at 20°c but on heating become liquids (iii) Remain in liquid form at 20°c even in water

Question 17.
Describe the structure of phospholipid. How are they arranged in the cell membrane?
Answer:
Structure of phospholipids: Phospholipids are a class of lipids that serve as the structural component of the cell membrane. Phospholipids have only 2 fatty acids attached to the glycerol while the 3rd glycerol binding site holds a phosphate group. This phosphate is bound to alcohol.

These lipids have both hydrophilic and hydrophobic pans due to a charge on the phosphoric acid/alcohol head of a molecule and lack a charge of the long tail of the molecule (made by fatty acids). When exposed to an aqueous solution the charged heads are attracted to the water phase and the non-polar tails are repelled from the water phase.

Phospholipids
When two layers of polar lipids come together to make a double layer, the outer hydrophilic face of every single layer will orient itself towards the solution, and the hydrophobic part will become immersed in the core of the bilayer.

Water acts as a solvent for polar molecules and the arrangement of phospholipids in the lipid bilayer of membranes is dependent on water.

Question 18.
Write short notes on
(i) Steroids
Answer:
Steroids: Steroids are complex compounds mostly found in animal hormones and cell membranes. The best example of steroids is cholesterol. The cell membrane of fungi contains ergosterol. The prostaglandins are fatty acid derivatives. They occur in minute amounts and function in blood clotting, smooth muscle contraction, and allergic reactions, etc.

(ii) Wax.
Answer:
Wax: Waxes are lipids. They are esters formed by the combination of a saturated long-chain fatty acid with long-chain alcohol. They play an important role in protection as tires form a water-proof covering over the root hairs and parts of the body in some organisms. Wax is soft and pliable. The paraffin is hard when cold. Fruits, feathers, leaves, the skin of man, and the exoskeleton of insects are waterproofed by the coating of wax. The bacteria causing TB and leprosy produce wax (Wax D.).

Question 19.
Describe the structure and function of ATP.
Answer:
ATP: It is a primary and universal carrier of chemical energy in the cell. Living cells capture, store and transport energy in a chemical form, largely as ATP and it is the ATP that is the carrier and intermediate source of chemical energy to those reactions in the cell which do not occur simultaneously.

These reactions can take place only if the chemical energy is released. It was Fritze Lipmann in 1941 who postulated this unifying concept and proposed the ATP cycle as given in the figure below.

Adenosine triphosphate

Question 20.
How are amino acids bonded together? Describe how these bonds are formed?
Answer:
Proteins are also formed from amino acids but they have small peptides. The two amino acids are linked by the formation of a peptide bond. Successive amino acids can be linked by peptide bonds to form a linear chain of many amino acids.

When a few amino acids are joined together, the molecule is called a peptide. Proteins are macromolecules formed from a large number of amino acids.

Peptide band

Question 21.
Draw the structure of amino acid.

(A) Acidic amino acid
Answer:
Amino acids: These are small molecules made of carbon, hydrogen, oxygen, and nitrogen, in certain cases sulfur is also found. Amino acids may be monocarboxylic or dicarboxylic acids bearing one or two amino groups.

The a-carbon is next to the carboxyl – C. The four valencies of the a-carbon of an amino acid hold respectively an amino (NH2) group, a carboxyl (COOH) group, a hydrogen atom, and side-chain fig (B) which may be polar or non-polar.

A free amino group is basic, a free carboxyl group is acidic. Lysine and alanine are basic amino acids because they have two amino groups and one carboxyl group. Glutamic acid and aspartic acid contain one amino and two carboxyl groups each is classified as acidic amino acids.

Alanine, glycine, valine, and phenylalanine are neutral amino acids because these contain one carboxyl group. Two amino acids can be linked by the formation Of a bond called a peptide bond. With the help of peptide bonds, many amino acids form a linear chain of many amino acids.

(B) Non-polar-side chain

Question 22.
Describe the primary structure of the protein.
Answer:
Primary Structure of Protein: Proteins are made of amino acids which have carboxyl group (COOH) and amino (group) (-NH2). The COOH end of an amino acid is joined to the -NH2 end of the other amino acid. Many amino acids are joined by peptide bonds which held them together in a particular sequence and constitute the primary structure of proteins. The structure does not make a protein functional.

It is a linear sequence of amino acids.

Question 23.
Name different types of RNA.
Answer:
There are three types of RNA.

Question 24.
List the differences between DNA and RNA.
Answer:
Differences between DNA and RNA:

DNA RNA
(1) It consists of double-helical two polynucleotide chains. (1) It consists of only one helical of a single polynucleotide chain.
(2) Deoxyribose sugar is present in the nucleotides. (2) Rihose sugar is present in the nucleotides.
(3) Pyrimidine bases are thymine and cytosine. (3) Uracil base is present instead of thymine-Cytosine is the second pyrimidine base.
(4) DNA synthesizes RNA to regulate cell metabolism. (4) RNA is synthesized by DNA and carries information from DNA to regulate cell metabolism.
(5) DNA from the main genetic material of eukaryotes. (5) It is the genetic material of plant viruses.
(6) DNA occurs in one form only. (6) It is the genetic material of plant viruses.
(7) It controls the transmission of hereditary characters. (7) It controls the synthesis of proteins in the cell.

Question 25.
Distinguish between prosthetic group and co-factors.
Answer:
Differences between coenzyme, cofactor, and prosthetic groups:

Cofactor Coenzyme Prosthetic group
1. It is a non-protein substance or group that gets attached to an enzyme. 1. It is a non-protein group that is loosely attached to the open enzyme in a functional enzyme. 1. It is a non-protein part or group which gets attached to an open enzyme.
2. It is essential for functioning. It may be organic or inorganic or metallic co-factor 2. NAD is a coenzyme for dehydrogenases. 2. Some prosthetic groups have metals e.g. iron porphyrin of the cytochromes.

Question 26.
Explain the structure of an enzyme.
Answer:
Structure of an Enzyme: The enzymes are chemical substances. They catalyze the chemical reactions in the cells. They are secreted and synthesized by living cells. Most all the enzymes are proteinous in nature. Some enzymes contain a nonprotein part called the prosthetic group. Some p esthetic groups are metal compounds. NAD is a coenzyme. All enzymes have active sites.

1. the First carbon forms a part of the aldehyde group. 1. Second carbon forms a part of the keto group.
2. Aldoses are most commonly found in nature i.e. glucose, ribose. 2. Ketoses are less common in nature, e.g., ribulose, fructose.

Question 27.
Distinguish between Unsaturated fatty acids and Saturated fatty acid
Answer:

Unsaturated fatty acid Saturated fatty acid
(i) Don’t have a double band between the carbon atoms. (i) Have one or more double bonds.
(ii) High melting points (ii) Low melting points
(iii) Can’t be synthesized in an animal body. (iii) Can be synthesized in the animal body
(iv) Don’t cause cardiovascular diseases. (iv) Can cause cardiovascular disease

Question 28.
Distinguish between aldose sugar and Ketose sugar
Answer:

Aldose sugar Ketose sugar
(i) First carbon forms a part of the aldehyde group (i) Second carbon forms a part of the Keto group
(ii) Commonly found in nature e.g. glucose, ribose. (ii) Less common in nature, eg. ribulose, fructose.

Question 29.
Distinguish between Oil and Fat.
Answer:

Oils Fats
1. Rich in unsaturated fats. 1. Rich in saturated fats.
2. Liquid at ordinary temperature. 2. Solid or semisolid at ordinary temperature.
3. Contains essential fatty acids. 3. Do not contain essential fatty acids.
4. Do not cause cardiovascular disorders e.g., vegetable oils. 4. Can cause cardio-vascular disorders e.g., Ghee, hydrogenated vegetable oils like Dalda.

Biomolecules Important Extra Questions Long Answer Type

Question 1.
Enlist the functions of small carbohydrates?
Answer:

  1. Monosaccharides are formed during the photosynthetic pathway. They are stored in plants and are utilized by other living organisms depending on them.
  2. Glucose is the blood sugar of many animals and on oxidation, it provides energy for all vital activities.
  3. Nucleotides and nucleosides contain pentose sugar in the form of ribose and deoxyribose sugars. They form a part of nucleic acids.
  4. Lactose of milk is formed from glucose and galactose and mammary glands of mammals.
  5. Glucose is used for the synthesis of fats and amino acids.
  6. Structural polysaccharides like cellulose and oligosaccharides are derived from mono-saccharides.
  7. Food storage polysaccharides like starch and glycogen are derived from monosaccharides.

Question 2.
Enumerate the functions of Lipids.
Answer:

  1. Lipids are storage products in plants as well as animals.
    (a) In plants, fats are stored in cotyledons or endosperm to provide nourishment to the developing embryo.
    (b) In animals fats are stored in adipocytes to be used whenever required by the body.
  2. In animals, subcutaneous fats act as an insulation layer and shock absorber.
  3. They form structural components of membranes, phospholipids, glycolipids, and sterols.
  4. They take part in the synthesis of steroid hormones, vitamin D, and bile salts.
  5. Act as a solvent for fat-soluble vitamins i.e., vitamin A, D, E, and K.
  6. The neutral fats form a concentrated fuel producing more than twice as much energy per gram as do the carbohydrates. They thus, represent an economical food reserve in the body.
  7. The wax lipids form a waterproof protective coating on animal furs, plant stem, leaves, and fruits.

Question 3.
How does water help in maintaining the constancy of the internal environment of an organism?
Answer:
Some substances, capable of neutralizing acids or bases, remain in solution in the cytoplasm as extracellular fluids, e.g., bicarbonate (HCO3), carbonic acid, dibasic phosphate (HPO4 -2 ). Acids and bases mix in the body fluids with these substances and are neutralized by them. Because of its solvent action water aids in keeping a constant pH.

Water also helps in maintaining constant body temperature by eliminating excess heat through the evaporation of sweat. Elimination of waste products through urine also helps in maintaining the constancy of the internal environment of an organism.

Question 4.
What are peroxisomes and phagosomes?
Answer:
Peroxisomes: These were for the first time observed in the kidney of rodents. They are found both in plants and animals. Their size varies from 0.5 to lp in diameter. They are delimited by a single membrane and contain a finely granular matrix. They often possess a central core called nucleoid which may consist of parallel tubules or twisted with strands. Peroxisomes are generally observed in close association with the endoplas¬mic reticulum.

Peroxisomes in different plant and animal cells differ con¬siderably in their enzymatic make-up, but they contain some peroxide-producing enzymes like urate, oxidase, D-amino acid oxidase, B-hydroxy acid oxidase, and catalase. Peroxisomes are somehow associated with some metabolic processes like photorespiration and lipid metabolism in animal cells.

Sphaerosomes: There are cell organelles bounded by a single membrane. They contain enzymes and are visible under the light microscope. These show some affinities for fat stains, including Sudan stain and sodium tetroxide.

These organelles originate from E.R. by budding. They contain enzymatic proteins which help in synthesizing oils and fats. Further devel¬opment of phagosomes takes place through an increase in the lipid content with a concomitant decrease in protein.

Question 5.
Enumerate the importance of Energy carriers.
Answer:
Energy carriers consist of nucleotides having one or two additional phosphate groups linked up at their phosphate end forming diphosphates and triphosphates. Linkage of additional phosphate groups occurs at the cost of a large amount of energy. This energy is provided by the oxidation of food mainly glucose and by photosynthesis.

Separation of the additional phosphate groups from the nucleotides by enzymatic hydrolysis releases a correspondingly large amount of energy.

Thus, ADP and ATP provide ready energy for biological activities.

The bonds joining the additional phosphate groups to the nucleotides are called high energy or energy-rich bonds, as they carry a great deal of energy. The nucleotides having more than one phosphate group are called higher nucleotides.

The energy of energy carriers, when set free is utilized for driving energy-dependent reactions in the cell and is biologically useful energy. ATP is the most common energy carrier in cells and is often called the energy currency of the cell.

Question 6.
Explain the functions of amino acids.
Answer:

  1. Amino acids are the building blocks for proteins.
  2. The amino acid Tyrosine takes part in the formation of the skin pigment melanin as well as hormones thyroxine and adrenaline.
  3. Glycine is important for the formation of heme.
  4. Tryptophan takes part in the formation of the vitamin nicotinamide.
  5. In plants, tryptophan forms the growth hormone indole-3- acetic acid.
  6. Amino acids are converted into glucose by deamination.
  7. Histamine and other biogenic amines are formed by the removal of carboxyl groups from amino acids.

Question 7.
Give reasons for following
(i) Salts dissolve in water but oil does not
Answer:
Water molecules are hydrogen-bonded to form short-lived macromolecular aggregates. To dissolve in water, a solute molecule must form hydrogen bonds with water molecules. Salts are polar compounds, their hydrophilic polar groups form hydrogen bonds with water molecules. So they dissolve oils having hydrophobic non-polar groups that cannot join the lattice structure of water. Thus non-polar molecules of oil do not dissolve in water.

(ii) Amino acid can be basic
Answer:
A free amino group is basic and a free carboxyl group is acidic. Amino acids can be basic because they may carry two amino groups and one carboxyl group e.g., Arginine. One free amino group causes amino acids to be basic.

(iii) Phospholipids form a thin layer on the surface of an aqueous medium.
Answer:
Phospholipids form a thin layer on the surface of an aqueous medium due to the simultaneous presence of both polar and non-polar groups in the molecule. As a result, the phospholipid molecules may arrange themselves in a double-layered membrane in aqueous media.

Question 8.
Illustrate lock and key hypothesis of enzyme action?
Answer:
Mechanism of Enzyme action: The working of enzymes is a complex one. All enzymes first of all combine with the reactions they catalyze. In other words, enzymes with substrates form an intermediate complex before decomposition of the substrate can occur.

This two-way reaction can be represented as follows.
1st step: Enzyme substrate complex = Enzyme + Product.
Formation of the enzyme-substrate complex during enzyme action.

From the above, it is clear that the enzymes must combine first with substrate molecules in order to act. In order to explain the mode of action of an enzyme. Fischer proposed a lock and key theory. According to him if the right key fits in the right lock. The lock can be opened, otherwise not.

Model of enzyme activity

To explain the above in context with the enzyme action it is believed that molecules have specific configurations into which other molecules can fit. The molecules which are acted upon by the enzymes are called substrates of the enzymes. Under the above assumption, only those substrate molecules with the proper geometric shape can fit into the active site of the enzymes.

If this happens, the above molecules may compete with the substrate, and the reaction may either slow down or stop. Substances are called competitive inhibitors because they act to prevent the production of a substance.

An induced-fit model of enzyme action was given by Koshland (1959). Buttressing and catalytic are two groups of the active site of the enzyme. Their site when the substrate attaches to its bonds is broken.

Question 9.
What is the structure of DNA?
Answer:
The nucleic acids are among the largest of all molecules found in living beings. They contain three types of molecules (a) 5 carbon sugar, (b) Phosphoric acid (usually called phosphates when in chemical combi¬nation), and nitrogen-containing bases (Purines and Pyrimidines). The three join together to form a nucleotide i.e., sugar+ base + phosphate = Nucleotide. Only a few nucleotides are possible. They differ only in the kind of purines or pyrimidine (nitrogen-containing bases).

In 1953 J.D. Watson and F.H.C. Crick working in Cambridge Uni¬versity, England prepared a model of DNA molecule elucidating the struc¬ture of DNA molecule. They were awarded the Nobel Prize for this outstanding work.

Structure of DNA

Watson and Crick model of DNA: According to Watson and Crick, the DNA molecule consisted of two strands twisted around each other in the form of a helix. Each strand is made of polynucleotides, each polynucleotide consisting of many nucleotides which remain united with its complimentary’ chain with the help of bases.

Adenine always unites with thymine and cytosine with guanine. It means that one polynucleotide chain of DNA molecule is complementary to the other.

The distance between two chains of the helix is about 20 A and the helix turns over every 34 A. Each mm of the chain consists of about 10 nucleotides.

Structure of DNA

Question 10.
How does the substrate concentration affect the velocity of enzyme reaction?
Answer:
Michaelis constant or more appropriately Michaelis-Menten constant (Km) is a mathematical derivation given by Leonor Michaelis and Monde Menten in 1913 with the help of which velocity of reaction can be calculated for any substrate concentration.

Effect of substrate concentration on enzyme action

Km or Michaelis constant is the substrate concentration at which the chemical reaction attains half its maximum velocity. The constant is an inverse measure of the affinity of an enzyme for its substrate, that is the smaller the Km the greater the substrate affinity and vice versa. The value usually lies between 10 4 – 10 5 M


Conclusion and Future Prospects

The past few decades have been exciting in terms of identifying and characterizing a variety of RNP granules induced by stress. RNP granules have received additional attention as broadly conserved examples of phase separation. The preponderance of studies utilize yeast and mammalian cell culture for their ease however, these studies are limited in the insights they can provide regarding the in vivo functions of RNP granules during stress. In particular, the germ line has unique requirements for regulating gene expression, and its adaptive stress responses may differ from those in somatic cells. At a basic level, we still do not know what the visible phase separation of RNP granules means at a molecular level. Many hypotheses exist as to whether stress-induced RNP granules assemble to: maintain the protein or RNA components within them, prime cells for rapid protein synthesis and recovery after stress ceases, reduce the concentration of RNA binding proteins in the bulk cytoplasm surrounding the granules, or whether the granules are just a consequence of more global remodeling occurring throughout the cell (Guzikowski et al., 2019). Creative in vitro studies have identified many types of interactions that promote phase separation outside of cells: protein-protein, RNA-RNA binding protein, roles of intrinsically disordered regions of proteins, RNA-RNA, and electrostatic interactions between RNA and protein. Triggers of phase separation in vitro also include the concentration of proteins and RNA, phosphorylation state, and salt concentration (Kato et al., 2012 Kwon et al., 2013 Su et al., 2016). Because RNP granules in vivo are more complex than those in vitro, the relative contributions of these various triggers are not yet clear. Complementary in vivo studies have also revealed regulators of RNP granule assembly. Chaperone proteins have now been implicated in regulating RNP granule assembly in both somatic cells and in the germ line (Spiess et al., 2004 Tam et al., 2006 Curran et al., 2009 Updike and Strome, 2009 Nadler-Holly et al., 2012 Hubstenberger et al., 2013 Jain et al., 2016 Wood et al., 2016). The role of single transcript RNPs in seeding stress-induced RNP granules is also worth exploring based on Drosophila studies showing germ granule assembly is regulated by recruitment of single transcript RNPs to homotypic clusters (Nielpielko et al., 2018). Autophagy has been implicated in the homeostasis of the chromatoid body, a unique RNP granule in mouse spermatocytes, and in regulating germ granule components in C. elegans (Da Ros et al., 2017 Min et al., 2019) therefore, it may also be worth investigating in the context of stress-induced RNP granules. Much remains to be discovered as to the regulation and function of RNP granules induced by stress in the germ line however, the future is promising with advances in in vitro reconstitution assays, improved single molecule FISH methods, and increased attention on the impact of RNP remodeling on gene expression. Combinations of in vitro and in vivo approaches will likely be important to illuminate the function of stress-induced RNP granules in the germ line.


Watch the video: My white blood count is low: Should I Worry? (May 2022).


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