Theoretical considerations of immunogold labeling of cellulose synthesizing terminal complexes

Size: px
Start display at page:

Download "Theoretical considerations of immunogold labeling of cellulose synthesizing terminal complexes"

Transcription

1 ... Cellulose II: , 2004., KlulVer Academic Publishers. Printed in the.velherlands. 385 Theoretical considerations of immunogold labeling of cellulose synthesizing terminal complexes Takao Itoh l,*, Satoshi Kimura 2 and R. Malcolm Brown, Jr. 3 I Wood Research Inslitute, Kyoto University. Uji, Kyoto I, Japan; 2Forestry and Forest Products Research Institute, Tsukuba. Ibaraki Japan; 3Section of _Wolecular Genetics and Microbiology. School of Biological Sciences. University of Texas at Austin, Austin. TX 78712, USA; *Author for correspondence ( _ titoh@rish.kyoto-u.ac.jp; fax: _c ) Received 25 November 2000; accepted in revised form 26 April 2004 Key words: c-di-gmp binding protein, Cellulose synthase, Freeze-fracture labeling, Linear TC, Rosette, Terminal complex Abstract The sodium dodecyl sulfate (SDS)-solubilized freeze fracture replica labeling (SDS-FRL) technique has been successfully applied to a vascular plant, Vigna angularis [Kimura et a!. 1999, Plant Cell II: ] and a bacterium, Acetobaeter xylinum [Kimura et al. 2001, J. Bacteriol. 183: ] for understanding cellulose biosynthesis. However, we do not know yet how many gold particles can be bound with antibodies that label a single rosette or linear TC. We analyzed these techniques from a theoretical background by considering the size of gold particle, primary and secondary antibody, and the rosette and linear TC. The 10 nm gold particles coated with primary and secondary antibodies result in a 30 nm diameter for the gold-conjugated antibody that binds to a rosette TC. Therefore, a rosette TC theoretically could be labeled with, at most, four gold particles and commonly with 1-3 gold particles after the topological consideration of the immunogold labeling of the rosette Te. We interpreted an actual image of freeze-fracture labeling of TCs by comparison with a scale model of the antibody-labeling to a rosette Te. The labeling of linear TCs with the gold-conjugated antibody of c-di-gmp binding protein was quite stable, and 75% of the 277 gold particles were found within 20 nm of the linear row. Labeled TCs with depressions and indistinct particle arrays and non-labeled TCs with distinct particle arrays were observed on the P-fracture face of the outer membrane, suggesting that TCs in A. xylinum are composed of two types of subunits. Introduction More than 20 years have passed since the first demonstration of the existence of cellulose synthesizing terminal complexes in the plasma membrane of a fresh water alga, Ooeystis apiculata, which came to be known as linear terminal complexes (Brown and Montezinos 1976). Traced back to the history of terminal complexes, Roelofsen (1958) first predicted that cellulose could be assembled by a large enzyme complex at the growing tip. Preston (1964) presented a model in which three-layered particle complexes in the plasma membrane are involved in the synthesis of cellulose microfibrils. The deposition of cellulose among a variety of cellulosic organisms is most abundant in higher plant cells. Mueller and Brown (1980) found another type of terminal complex,

2 386 the so-called rosette TC, associated with cellulose microfibril imprints on the P-fracture face of the plasma membrane of corn root cells during the assembly of cellulose microfibrils. Only indirect evidence has been available for the involvement of the TC in cellulose biosynthesis. First, the TC can be observed at the terminus of cellulose microfibril imprints. Second, the linear TCs in O. apiculata can be observed as a pair in different developmental stages of TC growth, suggesting that an individual TC in a pair may move in opposite directions by producing cellulose microfibrils (Brown 1978). Third, the length of linear TCs increases during the transition from primary to secondary walls in Valonia and Boer[<esenia (Hoh and Brown 1988). There has been no direct evidence to prove that cellulose synthesis-related enzymes are localized in the TC on the plasma membrane. Recently, we demonstrated that the rosette TC in a vascular plant and a linear TC in a bacterium are labeled by the antibodies against the CesA cellulose synthase protein (Kimura et al. 1999) and the c-di-gmp binding protein (Kimura et al. 2001) using the SDS-FRL freeze-fracture replica labeling technique first developed by Fujimoto (1995). The dimension of the component membrane particle is approximately 8 nm, while the diameter of the gold particle used in the present experiment is 10 nm. When gold particles are treated with antibodies, the final diameter of the gold-conjugated antibodies should be much larger than 20 nm. Therefore, the labeling of rosette and linear TCs with antibodies must be quite difficult. Thus, we need to know how many gold particles could be labeled to a single rosette TC or a linear TC. Materials and methods Plant materials Cotton plants (Gossypium hirsutum) were grown in the greenhouse under 14 h of light at 32C and 10 h of darkness at 20 C. Vigna radiata seedlings were germinated in darkness for 3-5 days at 25 0c. Isolation of cotton fiber RNA, construction of a cotton cdna library, and cloning of the cotton cellulose synthase are referred to Kimura et al. (1999). Bacterial materials Acetobacter xylinum NQ5 (ATCC 53582) was grown statically in SH medium at 27 cc. The culture and isolation of the cells is referred to Kimura et al. (2001). Antibody production of cotton cellulose synthase The antibody production of cotton cellulose synthase is referred to Kimura et al. (1999). Antibody production of c-di-gmp bindin[< protein The antibody production of c-di-gmp binding protein is referred to Chen and Brown (1999). Freeze-fracture labeling We pioneered the fracture labeling technique, known as the so-called SDS-FRL, with plant cells for the first time. The technique was initially developed by Fujimoto (1995) for animal cells. The application of the technique to plant cells has been difficult because the cell wall is not removed after SDS treatment and obscures evaluation of the replicas of the fractured face of the membrane. This difficulty has been overcome by treating the tissue attached to the replicas with a cellulase mixture. Replicas obtained in this manner appear similar to those obtained by using conventional freeze-fracture techniques, in which harsh acid treatments customarily have been used to remove cell and tissue components. The freeze fracture and immunogold labeling for the rosette TC in V. radiata are referred to Kimura et al. (1999), while those for linear TC in A. xylinum are referred to Kimura et al. (200 I). Results and discussion Localization of the catalytic subunit protein of cellulose synthase in the rosette TC Figure I shows a model of CesA protein redrawn by referring to the report of Pear et al. (1996). We have isolated GhCesA gene, which is one of the

3 386 the so-called rosette TC, associated with cellulose microfibril imprints on the P-fracture face of the plasma membrane of corn root cells during the assembly of cellulose microfibrils. Bacterial materials Acetobacter xylinum NQ5 (ATCC 53582) was grown statically in SH medium at 27 cc. The culture and isolation of the cells is referred to Kimura et al. (2001). Antibody production of cotton cellulose synthase The antibody production of cotton cellulose synthase is referred to Kimura et al. (1999). Antibody production of c-di-gmp bindin[< protein The antibody production of c-di-gmp binding protein is referred to Chen and Brown (1999). Freeze-fracture labeling le is approximately 8 nm, while the diameter of the gold particle used in the present experiment is 10 nm. When gold particles are treated with antibodies, the final diameter of the gold-conjugated antibodies should be much larger than 20 nm. Therefore, the labeling of rosette and linear TCs with antibodies must be quite difficult. Thus, we need to know how many gold particles could be labeled to a single rosette TC or a linear TC. Materials and methods Plant materials Cotton plants (Gossypium hirsutum) were grown in the greenhouse under 14 h of light at 32C and 10 h of darkness at 20 C. Vigna radiata seedlings were germinated in darkness for 3-5 days at 25 0c. Isolation of cotton fiber RNA, construction of a cotton cdna library, and cloning of the cotton cellulose synthase are referred to Kimura et al. (1999). We pioneered the fracture labeling technique, known as the so-called SDS-FRL, with plant cells for the first time. The technique was initially developed by Fujimoto (1995) for animal cells. The application of the technique to plant cells has been difficult because the cell wall is not removed after SDS treatment and obscures evaluation of the replicas of the fractured face of the membrane. This difficulty has been overcome by treating the tissue attached to the replicas with a cellulase mixture. Replicas obtained in this manner appear similar to those obtained by using conventional freeze-fracture techniques, in which harsh acid treatments customarily have been used to remove cell and tissue components. The freeze fracture and immunogold labeling for the rosette TC in V. radiata are referred to Kimura et al. (1999), while those for linear TC in A. xylinum are referred to Kimura et al. (200 I). Results and discussion Localization of the catalytic subunit protein of cellulose synthase in the rosette TC Figure I shows a model of CesA protein redrawn by referring to the report of Pear et al. (1996). We have isolated GhCesA gene, which is one of the

4 Cell Wall Plasma membrane Cytoplasm :'-l-ter... { ~..' / ::;D: : : : :: : ;:::W: "::: n D~:(... '-' (;..' I C-Ier Figure J. Proposed model of plant CesA protein. Cytoplasmic domain of GhCesA protein (dotted area) was used as a specific antigen for the preparation of the CesA antibody. homologs of cotton CesA. The recombinant proteins of the catalytic site (dotted region in Figure 1) exposed to the cytoplasmic side were transformed into Escherichia coli and used as an antigen of CesA antibody. The antigen region includes the D,D,D,QxxRW motif which is the amino acid sequence prerequisite for the activation of CesA. As the antibody is specific for the cytoplasmic region of CesA protein, it was expected that the antibody would specifically recognize the rosette on the P-fracture face of the plasma membrane when subjected to SDS-FRL techniques. The actively elongating region of the seedlings in Azuki bean (V. radiata) was used as the 387 experimental material. The elongating region has some advantages in the present study; first, cellulose is actively synthesized in this region; second, the plasma membrane will be exposed more frequently during the freeze-fracturing because of the small size of the tissue cells; third, the disintegration of cell walls by cellulase treatment is easy because the cell wall is not fully thickened and without lignification. In practice, the cellulase treatment was not effective for disintegrating thickened walls. The remnants of cell walls were often attached to the replica membrane, thus making it difficult to secure a clean replica. Figure 2 shows a rosette TC labeled with CesA antibody. The gold particles indicating the presence of secondary antibodies were observed on the rosette TC or close to the structure. This figure shows rosettes labeled with gold. Nine rosettes among 10 are labeled with gold and one rosette is not labeled in the upper left figure. Eight rosettes among 12 are labeled with gold and four are not labeled in the lower left figure. The figures on the right are a higher magnification of the labeled rosette. The figure on the upper right shows a single rosette labeled with three gold particles. The figure on the middle right shows two rosettes, each labeled with a gold particle. The figure on the lower right shows a single rosette labeled with a gold particle. Most of the rosettes were labeled Figure 2. SDS-FRL image of the P-fractllre face of a Vigna cell. Rosette TCs labeled with gold particles are shown by black solid circles and non-labeled TC is shown by a black dotted circle (upper and lower left). A rosette labeled with three gold particles, two rosettes each labeled with a single particle, and a rosette labeled with a single particle are shown in the upper, middle and lower right of the figure, respectively.

5 </> B" 60 i 50 '- 0 G 40 c: g 30 J: The number of gold particles associated with a single rosette 1 Figure 3. SDS-FRL image of the E-fracture face of a Vigna cell. Two terminal globules surrounded by white dotted circles were never labeled with CesA antibodies. Furthermore, no labeling was detected in the E-fracture face of replicas. with one or two gold particles and often with three gold particles. The terminal globules on the E fracture face complementary to rosettes were not labeled with the antibody (Figure 3). These findings demonstrate that the CesA is indeed a component protein of a rosette TC, and the catalytic site of CesA is localized on the cytoplasmic side, that is, the P-fracture face of a plasma membrane. Examining Figure 2 closer, the distance between any two individual gold particles labeled to rosette TCs is almost the same among the three photos. The individual rosette has a potentiality to produce cellulose microfibrils approximately 4 nm in diameter, calculated to be composed of 36 glucan chains. It is suggested that a single particle subunit among 6 subunits of rosette TC is composed of 6 CesA proteins (Doblin et al. 2002). We predicted that a rosette TC will be labeled with a variable number of particles at the beginning of our experiment. However, this was nol the case. It is valuable, therefore, to analyze how many gold particles can be labeled to a single rosette TC In order to measure the frequency of the number of gold particles per rosette, we re-examined electron micrographs from 17 different cells that include 119 rosettes. Twelve rosettes had no labeling of gold particles. We made a histogram of the number of gold particles labeled to the other 107 rosettes (Figure 4). As shown in the figure, 70 rosettes were labeled with a single gold particle, 28 with two gold particles, and 8 with three gold Figure 4. The histogram shows the frequency of the number of gold particles per rosette. It is based on the re-examination of electron micrographs that cover 17 cells including [19 rosettes. ft should be noted that 12 rosettes were not labeled with gold particles. The other l07 rosettes were labeled with I 4 gold particles. particles. Only one among 107 rosettes was labeled with four gold particles. Figure 5 shows a top view of a rosette TC and a side view of a rosette TC perpendicular to the plasma membrane. The diameter of the rosette TC is approximately 25 nm. At the same time, immunoglobulin G, which is the primary component of CesA, secondary antibody, and 10 nm gold particles are all illustrated at the same scale showing the rosette TC Based on previous research on the analysis of molecular weight and X-ray diffraction for the antibody, the IgG shows an Y shape with 10 nm total length. The gold-labeled IgG which is used as the secondary antibody has a structure attached with a number of IgG molecules surrounding the gold particles, as shown in Figure 5. In short, the gold particles under electron microscopic observation are surrounded by a number of 10 nm antibodies which are not visible. The size of both primary and secondary antibodies is 27.2 nm (Sarma et al. 1971). The actual distance of the gold particle from the antigen, cellulose synthase, could be >27 nm because the proteins in the rosette TC are denatured and extended by SDS treatment. Nevertheless, we selected 20 nm or less as a conservative distance for a 'labeled' rosette TC in our qualitative analyses. Considering these situations, the gold-labeled secondary antibody is approximately 30 nm in diameter, which is larger than the individual rosette TC Figure 6 is a hypothetical illustration showing the labeling of antibody to rosette TC, that is

6 389 Top view ad ~~~ Clue 25 nm ~ ~ Primary -< antibody Secondary antibody =< GO.1e Side view 25 run ~ 10 nm gold-conjugated secondary antibody with 30 nm Figure 5. Scale model of the roselle TC, antibodies and gold particles. The diameter of a roselle is 25 nm. The diameter of the primary antibody, secondary antibody and gold particles is 10 om. The diameter of an antibody conjugated with a gold particle is approximately 30 nm. based on the scale model of Figure 5. A rosette TC labeled with three gold particles is shown. The rosette TC is redrawn by a solid line in the top view model to make the rosette more distinct. The rosette TC is suggested to be roughly covered with gold-conjugated antibodies. Two gold-conjugated antibodies are closely associated with the rosette TC, and one gold-conjugated antibody facing the cytoplasmic side is drawn in the side view model. An alternative positioning of gold particles can be seen for the labeling of antibodies, but it will be easy to understand that there is no room for the labeling of more than four gold particles. The individual gold particle is coated by the antibody, which is 10 nm long. Therefore, it is clear that usually I -3 and at most 4 gold particles can be labeled to a single rosette TC. The antibody labeling to the rosette TC as shown in Figure 3 makes sense from the scale model analysis and, at the same time, supports the successful immunogold labeling experiments. Cellulose synthase is primarily important for the biosynthesis of cellulose in vascular plants. However, Korrigan cellulase and the other types of cellulose synthase are also thought to be involved in the biosynthesis of cellulose and suggested to be components of the rosette TC (Doblin et al. 2002). One of the best ways to prove this concept is to apply SDS-FRL to visualize these proteins localized in the rosette TC. The visualization of Korrigan cellulase could be done by a single labeling of its antibody. However, visualization of different types of cellulose synthases could be done by a double or triple labeling of gold particles. We do not know yet whether there are two or more CesA proteins in a single rosette TC or whether the individual rosette TC is composed of different CesA proteins. Thus, independent immunogold labeling for different CesA antibodies will not solve these questions. We do need double or triple labeling of CesA antibody of the rosette TC. According to our scale model explaining the relation between rosette TC and antibody mentioned above, a rosette TC will be labeled at most with two or three gold particles. We should not expect Original image Top view Side view Figure 6. Scale model for an immunogold-labeled rosette TC. The original image of a TC labeled with three gold particles is shown on the left. The top view in the middle shows a rosette TC redrawn by a solid line. The side view on the right shows two gold-conjugated antibodies closely associated with a rosette and one facing the cytoplasmic side.

7 390 to obtain clear results after the double labeling of the antibodies by the application of present experimental methods. Labeling could be improved with more than double the number of gold particles. This can be successfully accomplished by using antibodies with a lower molecular weight as well as gold particles. The primary and secondary antibodies could be partially hydrolyzed and some parts of hydrolysates necessary for the labeling could be used, thus reducing the diameter of gold particles to a smaller size. It is worth while to note the reason why we used 10 nm gold particles. The reason is that membrane proteins observed by freeze-fracturing are mostly 5-10 nm in diameter, and it is difficult to know the difference between the shadowed membrane proteins and gold particles. However, small gold particles can be differentiated from membrane proteins by controlling the shadowing strength and image processing. It could be beneficial to prepare gold-conjugated primary antibodies for the direct labeling of a rosette TC. An alternative way is to express recombinant CesA with some tag and visualize the tag with fluorescein. For example, the histidine tag often is used. In conclusion, we need to improve a number of techniques and approaches to overcome some of the difficulties in visualizing directly the component proteins of the rosette TC by the application of SDS-FRL. Localization of c-di-gmp binding protein in linear TC We have also applied SDS-FRL to visualize one of the component proteins of cellulose synthases in A. xylinum. The antibody used for the present experiment in Acetobacter is the anti-c-di-gmp binding protein prepared by Chen and Brown (J 999). The antibody is purified against a full length of 93 kda protein by product entrapment. As the c-di-gmp binding protein is suggested to be a transmembrane protein, it was thought that its antibody would recognize TC particles on the P-fracture face of outer membrane or plasma membrane in A. xylinum. When the antibody of c di-gmp binding protein was used for SDS-FRL of A. xylinum, the gold particles specific to the labeling of the antibody were observed in a single row of linear TCs on the P-fracture face of the outer membrane (Figure 7A). It is worthwhile to note that the bacterial cells will be fractured in high frequency at the junction of the outer membrane. When we took electron micrographs of fractured membranes of 300 Acetobacter cells at random, only two showed a fractured plasma membrane. We only selected images that show gold labeled TCs. Usually TC can be observed in every 10 cells. This means that the actual frequency to show the fractured plasma membrane is less than one tenth of the above frequency. Figure 7A D shows all the fractured outer membranes. Figure 7A, B, D shows the P-fracture face of the outer membrane from different bacterial cells after labeling with antibodies against the c-di-gmp binding protein. It should be noted that Figure 7B does not show any reaction of the antibody in spite of the evidence of a distinct row of TC particles. Whenever we had a positive reaction of the antibody to TCs as shown in Figure 7A, there is no distinct row of TC particles but a line of depressions or pits with an indistinct particle array. Thus, the TC structure on the P-fracture face of the outer membrane often showed depressions after freezefracturing. To the contrary, a distinct row of TC particles on the E-fracture face of the outer membrane was often observed as shown in Figure 7C. However, positive labeling of linear TCs was not observed on the E-fracture face. A very rare case of freeze-fracturing showed a distinct row of TC particles and depressions or pits in a single line on the same P-fracture face of the outer membrane (Figure 7D). The TCs in the region of the depressions or pits were exclusively labeled by the antibodies, while the distinct row of TC particles was never labeled by the antibodies. These findings strongly support that two types of TC structures can be seen on the P-fracture face of the outer membrane, depending on the presence or absence of any remaining distinct low of particles after freeze-fracturing of the outer membrane. A scale model showing the close relation between TCs and antibodies on the outer membrane of the bacterium is shown in Figure 8A, B. Compared to the labeling of the rosette TC in Azuki beans (Vigna angularis) with the antibody ofcesa, the number of gold-labeling to the outer membrane of the bacterium was fewer; however, the antibodies against the c-di-gmp binding protein were specifically labeled on and along the row of TCs. The distance between the linear TCs and gold particles was calculated by measuring the vertical

8 391 Figure 7. SDS-FRL images of Ace/abae/er cells. (A) P-fracture face of TC on the outer-membrane with numerous gold particjes (attows) along depressions or pits of the linear TC; (B) P-fracture face of the TC on the ollter-membrane with a distinct row of membrane particles that were never labeled with gold particles; (C) L-fracture face of the TC on the outer-membrane with a distinct row of membrane particles that were never labeled with gold particles; (D) P-fracture face of TC on the outer-membrane with two different particle arrays. Distinct TC particles were not labeled (right half of D), however, a single row of TCs with depressions or pits (left half of D) was labeled with gold particles (arrows). distance between the edge of gold particles and a findings suggested that c-di-gmp binding protein linear row of TC particles. For frequency analysis, is one of the major components of linear TCs in 277 gold particles were randomly sampled from 30 the bacterium, and the principal domain of the different cells that have a single row oftcs. In this protein is localized on the cytoplasmic side. A case, 75% of the 277 gold particles were found number of gold-labeling regions on the outer within 20 nm of the linear row. Most gold particles membrane suggests that the transmembrane rewere found within nm, with a median dis gion of the protein extends not only across the tance of 9.3 nm from the linear row of TCs. These plasma membrane and periplasmic regions, but

9 392 Figure 8. (A) SDS-FRL image showing the distance between gold particles and a linear TC (dotted line). (B) Scale model redrawn from the actual image of (A). Gold particles are all drawn with a coating by the antibodies. also across the outer membrane. It is not realistic to imagine that the c-di-gmp binding protein passes through the outer membrane; however, part of the c-di-gmp binding protein may have extended to the outer membrane. Localization of c di-gmp binding protein in the outer membrane and the methods how we recognize the protein by the labeling of its antibody will be discussed later. The results obtained from the labeling of TCs in the bacterium by antibodies against the c-di-gmp binding protein can be explained as follows: (1) During freeze-fracturing of bacterial cells, almost au fractured planes occurred through the region occupied by c-di-gmp binding protein on the outer membrane. (2) The linear TCs of bacterial cells observed on the outer membrane show depressions or pits on the P-fracture face and distinct membrane particles on the E-fracture face. These are complementary to a single row of TCs on the outer membrane. (3) The TC labeled by antibodies against the c-di GMP binding protein can be observed on the P-fracture face, and the gold particles can be seen only in the depressions or pits. (4) The antibody does not recognize the distinct mem brane particles of TCs on both the P-fracture and E-fracture faces. These findings primarily support the hypothesis that the distinct membrane particles of TCs on both P- and E-fracture faces of the outer membrane are not composed of c-di-gmp binding proteins but rather, other component proteins of TCs. Second, the depressions or pits of TC on the P-fracture face of the outer membrane are caused by a peeling of membrane particles towards the E fracture face due to the complementary structure between the membrane particles of TC on the E fracture face and depressions or pits of TC on the P-fracture face. These membrane particles often are observed on the E-fracture face, but are rarely found on the P-fracture face. Figure 7D shows such a structure found by chance. The c-di-gmp binding protein is held by the replica membrane on the depressions or pits oftc on the P-fracture face of the outer membrane. The membrane particles on TCs not recognized by the antibody are presumed to be 'C' or 'D' proteins of the bacterial cellulose synthase operon as hypothesized by Wong et al. (1990). These proteins are localized in the outer membrane and appear to be involved in the secretion and crystallization of cellulose microfibrils. We summarize the present results using a model illustration (Figure 9). The transmembrane domain of c-di-gmp binding proteins passes through not only the plasma membrane, but also the peripjasmic space and outer membranes (Figure 9A). The 'C' or 'D' proteins in the series of the cellulose synthetic operon are localized in the outer membrane and attached to the c-di-gmp binding proteins. When the outer membrane is fractured, 'C' or 'D' proteins will remain on either the P- (left half of Figure 9B) or the E-fracture face (right half of Figure 9B). In practice, these membrane proteins mostly are fractured away from the FAracture face. When 'C' or 'D' proteins of the TCs in the outer membrane are fractured away, depressions or pits are made in the membrane on the P fracture face, and parts of c-di-gmp binding proteins will be exposed. The c-di-gmp binding proteins will be held by the replica membrane at the Pt-shadowing and carbon-backing (right half of Figure 9C). On the contrary, when 'C' or 'D' proteins remain on top of the c-di-gmp binding proteins, they will not be fixed by the replica membrane (left half of Figure 9C). The plasma membrane and periplasmic space in the bacterium not fixed by replica membrane, and c-di-gmp binding proteins not fixed directly by the replica will be washed away after SDS treatment

10 393 (6) (e) Outer membrane Plasma membrane Freeze fracture ~PoreofPF Knife~--UU~faceon the ~ ~/ outer- 11fiJ.:or-<fffl.l.'lr<(i'JjJ~~Wl:~Bmembrane (D) Lysozyme & SDS-treatment EF-face~ & (E) Antibody labeling EF-face~ Figure 9. Schematic diagram showing c-di-gmp binding proteins revealed in freeze-fractured images. (A) c-di-gmp binding proteins span both the outer membranes and the cytoplasmic membranes. (B) After freeze-fracture, the outer membrane proteins remain attached to the c-di-gmp binding proteins or separate from the latter. (C) After shadowing, the outer membrane proteins are fixed on the P-fraclUre face or the E-fracture face of the outer membrane. In the latter case, the c-di-gmp binding proteins are fixed onto the P fracture face of the outer membrane. (D) After lysozyme and SDS trealment, the c-di-gmp binding proteins will be removed in the case of the left half of the illustration, or they will not be removed in the case of the right half of the illustration. (E) After labeling with antibody, the distinct particle row as shown in 'a' on the P-fraclure face and 'b' on the F-fracture face will not be labeled by the antibody. The depression in the TC structure where c-di-gmp binding proteins are fixed on the P-fraclUre face is labeled by antibodies, as shown in 'c' on the P-fracture face. (Figure 9D). When the replica is labeled by antibodies against the c-di-gmp binding proteins, gold particles are observed on the depressions or pits of the TCs on the outer membrane (inset 'c' in Figure 9E). However, the distinct membrane particles of TC on both the P- (inset 'a' in Figure 9E) and E-fracture faces (inset 'b' in Figure 9E) were not labeled at all. These considerations make reasonable sense to explain the relationship between TC structure and gold-labeling in Acetobacter. We visualized the reaction of a single antibody of a c-di-gmp binding protein; however, the present investigation suggests that a linear TC in Acetobacter could be made of two different membrane proteins. The SDS-FRL appears to be very useful to clarify the component proteins in TCs that are composed of multimeric enzyme complexes, allowing an analysis of the topology of TC structure. Acetobacter xylinum is a relatively easy model system to apply the freeze-fracture technique. It is also a model organism for an understanding of cellulose biosynthesis from the aspects of molecular genetics and biochemistry. A more general understanding of Acetobacter TCs will be clarified in the future through the application of SDS-FRL with the major goal to prepare antibodies against the component proteins of linear TCs such as 'C' or 'D' proteins of cejlulose synthase operon as well as glucanase (Doblin et a ), which is increasingly important for an understanding of cellulose biosynthesis.

11 394 References Sci. USA 73: Brown R.M. Jr Biogenesis of natural polymer systems with special reference to cellulose assembly and deposition. In: The Third Philip Morris Science Symposium, pp Chen H.P. and Brown R.M. Jr Thermal stability of the cellulose synthase complex of AcelObacler xylinwl1. Cellulose 6: Doblin M.S., Hurek I., Jacob-Wilk D. and Delmer D.P Cellulose biosynthesis in plants: from genes to rosettes. Plant Cell Physiol. 43(12): Fujimoto K Freeze-fracture replica electron microscopy combined with SDS digestion for cytochemical labeling of integral membrane proteins. J. Cell Sci. 108: Itoh T. and Brown R.M. Jr Development of cellulose synthesizing complexes in Borgesenia and Valonia. Protoplasma 144: Kimura S., Chen H.P., Saxena I.M., Brown R.M. Jr. and Itoh T Localization of c-di-gmp-binding protein with the linear terminal complexes of Acetobacter xylinul11. J. Bacteriol. 183: Kimura S., Laosinchai W., Itoh T., Cui X., Linder C.R. and Brown R.M. Jr Immunogold labeling of rosette terminal cellulose-synthesizing complexes in the vascular plant, Vigna angularis. Plant Cell II: Mueller S.c. and Brown R.M. Jr Evidence for an intramembranous component associated with a cellulose microfibril synthesizing complex in higher plants. J. Cell BioI. 84: Pear J.R., Kawagoe Y., Schreckengost W.E., Delmer D.P. and Stalker D.M Higher plants contain homologs of the bacterial CesA genes encoding the catalytic subunit of cellulose synthase. Proc. Natl. Acad. Sci. USA 93: Preston R.D Structural and mechanical aspects of plant cell walls with particular reference to synthesis and growth. In: Zimmerman M.H. (ed.), Formation of Wood in Forest Trees. Academic Press, New York, pp Roelofsen A Cell wall structure as related to surface growth. Acta Bot. ~eerl. 7: n 89. Sarma V.R., Silverton E.W., Davies D.R. and Terry W.D. 197/. The three-dimensional structure at 6 Aresolution of a human yg I immunoglobulin molecule. J. BioI. Chern. 216: Wong H.C., Fear A.L., Calhoon R.D., Eichinger G.H., Ylayer R., Amikam D., Benziman M., Gelfand D.H., Meade l.h., Emerick A.W., Bruner R., Ben-Bassat A. and Tal R Genetic organization of the cellulose synthase operon in AcelObacter xylintlm. Proc. Natl. Acad. Sci. USA 87: lll

Immunolabeling as a tool for understanding the spatial distribution of fiber wall components and their biosynthetic enzymes

Immunolabeling as a tool for understanding the spatial distribution of fiber wall components and their biosynthetic enzymes Immunolabeling as a tool for understanding the spatial distribution of fiber wall components and their biosynthetic enzymes Presented by: Candace H. Haigler Professor of Crop Science and Botany candace_haigler

More information

Immunogold Labeling of Rosette Terminal Cellulose-Synthesizing Complexes in the Vascular Plant Vigna angularis

Immunogold Labeling of Rosette Terminal Cellulose-Synthesizing Complexes in the Vascular Plant Vigna angularis The Plant Cell, Vol. 11, 2075 2085, November 1999, www.plantcell.org 1999 American Society of Plant Physiologists RESEARCH ARTICLE Immunogold Labeling of Rosette Terminal Cellulose-Synthesizing Complexes

More information

SCREENING AND PRESERVATION OF DNA LIBRARIES

SCREENING AND PRESERVATION OF DNA LIBRARIES MODULE 4 LECTURE 5 SCREENING AND PRESERVATION OF DNA LIBRARIES 4-5.1. Introduction Library screening is the process of identification of the clones carrying the gene of interest. Screening relies on a

More information

Enhanced production of microbial cellulose

Enhanced production of microbial cellulose Enhanced production of microbial cellulose 2009 International Conference on Nanotechnology for the Forest Products Industry June 23 26, 2009 Jeffrey Catchmark, Kuan Chen Cheng and Ali Demirci Department

More information

CSE : Computational Issues in Molecular Biology. Lecture 19. Spring 2004

CSE : Computational Issues in Molecular Biology. Lecture 19. Spring 2004 CSE 397-497: Computational Issues in Molecular Biology Lecture 19 Spring 2004-1- Protein structure Primary structure of protein is determined by number and order of amino acids within polypeptide chain.

More information

Supplemental Data. Farmer et al. (2010) Plant Cell /tpc

Supplemental Data. Farmer et al. (2010) Plant Cell /tpc Supplemental Figure 1. Amino acid sequence comparison of RAD23 proteins. Identical and similar residues are shown in the black and gray boxes, respectively. Dots denote gaps. The sequence of plant Ub is

More information

Chapter 8 Lecture Outline. Transcription, Translation, and Bioinformatics

Chapter 8 Lecture Outline. Transcription, Translation, and Bioinformatics Chapter 8 Lecture Outline Transcription, Translation, and Bioinformatics Replication, Transcription, Translation n Repetitive processes Build polymers of nucleotides or amino acids n All have 3 major steps

More information

2012 GENERAL [5 points]

2012 GENERAL [5 points] GENERAL [5 points] 2012 Mark all processes that are part of the 'standard dogma of molecular' [ ] DNA replication [ ] transcription [ ] translation [ ] reverse transposition [ ] DNA restriction [ ] DNA

More information

Chapter 14 Regulation of Transcription

Chapter 14 Regulation of Transcription Chapter 14 Regulation of Transcription Cis-acting sequences Distance-independent cis-acting elements Dissecting regulatory elements Transcription factors Overview transcriptional regulation Transcription

More information

Extracting Pure Proteins from Cells

Extracting Pure Proteins from Cells Extracting Pure Proteins from Cells 0 Purification techniques focus mainly on size & charge 0 The first step is homogenization (grinding, Potter Elvejhem homogenizer, sonication, freezing and thawing,

More information

Bacteriophages get a foothold on their prey

Bacteriophages get a foothold on their prey Bacteriophages get a foothold on their prey Long and thin, the receptor-binding needle of bacteriophage T4 Bacterial viruses, bacteriophages or phages, have served as a tool to decipher principles of molecular

More information

Biotechnology and DNA Technology

Biotechnology and DNA Technology 11/27/2017 PowerPoint Lecture Presentations prepared by Bradley W. Christian, McLennan Community College CHAPTER 9 Biotechnology and DNA Technology Introduction to Biotechnology Learning Objectives Compare

More information

Fatchiyah

Fatchiyah Fatchiyah Email: fatchiya@yahoo.co.id RNAs: mrna trna rrna RNAi DNAs: Protein: genome DNA cdna mikro-makro mono-poly single-multi Analysis: Identification human and animal disease Finger printing Sexing

More information

CHAPTER 2A HOW DO YOU BEGIN TO CLONE A GENE? CHAPTER 2A STUDENT GUIDE 2013 Amgen Foundation. All rights reserved.

CHAPTER 2A HOW DO YOU BEGIN TO CLONE A GENE? CHAPTER 2A STUDENT GUIDE 2013 Amgen Foundation. All rights reserved. CHAPTER 2A HOW DO YOU BEGIN TO CLONE A GENE? 35 INTRODUCTION In the Program Introduction, you learned that the increase in diabetes in the United States has resulted in a great demand for its treatment,

More information

Proteomics 6/4/2009 WESTERN BLOT ANALYSIS

Proteomics 6/4/2009 WESTERN BLOT ANALYSIS SDS-PAGE (PolyAcrylamide Gel Electrophoresis) Proteomics WESTERN BLOT ANALYSIS Presented by: Nuvee Prapasarakul Veterinary Microbiology Chulalongkorn University Proteomics has been said to be the next

More information

Biochemistry 111. Carl Parker x A Braun

Biochemistry 111. Carl Parker x A Braun Biochemistry 111 Carl Parker x6368 101A Braun csp@caltech.edu Central Dogma of Molecular Biology DNA-Dependent RNA Polymerase Requires a DNA Template Synthesizes RNA in a 5 to 3 direction Requires ribonucleoside

More information

Storage and Expression of Genetic Information

Storage and Expression of Genetic Information Storage and Expression of Genetic Information 29. DNA structure, Replication and Repair ->Ch 25. DNA metabolism 30. RNA Structure, Synthesis and Processing ->Ch 26. RNA metabolism 31. Protein Synthesis

More information

Lecture Four. Molecular Approaches I: Nucleic Acids

Lecture Four. Molecular Approaches I: Nucleic Acids Lecture Four. Molecular Approaches I: Nucleic Acids I. Recombinant DNA and Gene Cloning Recombinant DNA is DNA that has been created artificially. DNA from two or more sources is incorporated into a single

More information

Relationship between nucleotide sequence and 3D protein structure of six genes in Escherichia coli, by analysis of DNA sequence using a Markov model

Relationship between nucleotide sequence and 3D protein structure of six genes in Escherichia coli, by analysis of DNA sequence using a Markov model Relationship between nucleotide sequence and 3D protein structure of six genes in Escherichia coli, by analysis of DNA sequence using a Markov model Yuko Ohfuku 1,, 3*, Hideo Tanaka and Masami Uebayasi

More information

Bi 8 Lecture 10. Ellen Rothenberg 4 February 2016

Bi 8 Lecture 10. Ellen Rothenberg 4 February 2016 Bi 8 Lecture 10 Bacterial regulation, II Ellen Rothenberg 4 February 2016 Not all bacterial promoters use the same σ factors, and this provides added regulation capability Most sigma factors are related

More information

Enhancers mutations that make the original mutant phenotype more extreme. Suppressors mutations that make the original mutant phenotype less extreme

Enhancers mutations that make the original mutant phenotype more extreme. Suppressors mutations that make the original mutant phenotype less extreme Interactomics and Proteomics 1. Interactomics The field of interactomics is concerned with interactions between genes or proteins. They can be genetic interactions, in which two genes are involved in the

More information

5. the transformation of the host cell. 2. reject the virus. 4. initiate an attack on the virus.

5. the transformation of the host cell. 2. reject the virus. 4. initiate an attack on the virus. Version 001 Bacterial/Viral Genetics mahon (26) 1 This print-out should have 28 questions. Multiple-choice questions may continue on the next column or page find all choices before answering. Holt Bio

More information

PLNT2530 (2018) Unit 6b Sequence Libraries

PLNT2530 (2018) Unit 6b Sequence Libraries PLNT2530 (2018) Unit 6b Sequence Libraries Molecular Biotechnology (Ch 4) Analysis of Genes and Genomes (Ch 5) Unless otherwise cited or referenced, all content of this presenataion is licensed under the

More information

INTEGRATED PROTEIN SERVICES

INTEGRATED PROTEIN SERVICES iba INTEGRATED PROTEIN SERVICES Customer-specific protein expression, purification and analysis Please fill out the following and fax to Europe +49 (0) 551-50672-181 US 1-888-531-6813 Or send the scanned

More information

Supplementary Material (ESI) for Chemical Society Reviews This journal is The Royal Society of Chemistry 2011

Supplementary Material (ESI) for Chemical Society Reviews This journal is The Royal Society of Chemistry 2011 Supplementary material: From macro to micro - a comparative study Systematic comparison between different types of peptide arrays (macro vs. microarrays) was not described so far in the literature, probably

More information

Pre-Lab: Molecular Biology

Pre-Lab: Molecular Biology Pre-Lab: Molecular Biology Name 1. What are the three chemical parts of a nucleotide. Draw a simple sketch to show how the three parts are arranged. 2. What are the rules of base pairing? 3. In double

More information

Lecture 7: Affinity Chromatography-II

Lecture 7: Affinity Chromatography-II Lecture 7: Affinity Chromatography-II We have studied basics of affinity purification during last lecture. The current lecture is continuation of last lecture and we will cover following: 1. Few specific

More information

Chapter 5: Proteins: Primary Structure

Chapter 5: Proteins: Primary Structure Instant download and all chapters Test Bank Fundamentals of Biochemistry Life at the Molecular Level 4th Edition Donald Voet https://testbanklab.com/download/test-bank-fundamentals-biochemistry-life-molecular-level-

More information

Supporting Information

Supporting Information Supporting Information DNA Crystals as Vehicles for Biocatalysis. Chun Geng and Paul J. Paukstelis* *Email: paukstel@umd.edu Recombinant MBP-tagged RNase inhibitor expression and purification. The porcine

More information

However, only a fraction of these genes are transcribed in an individual cell at any given time.

However, only a fraction of these genes are transcribed in an individual cell at any given time. All cells in an organism contain the same set of genes. However, only a fraction of these genes are transcribed in an individual cell at any given time. It is the pattern of gene expression that determines

More information

Electrophoresis and transfer

Electrophoresis and transfer Electrophoresis and transfer Electrophoresis Cation = positively charged ion, it moves toward the cathode (-) Anion = negatively charged ion, it moves toward the anode (+) Amphoteric substance = can have

More information

Analysis of the AcrB binding domain of the membrane fusion protein AcrA. Introduction

Analysis of the AcrB binding domain of the membrane fusion protein AcrA. Introduction Analysis of the AcrB binding domain of the membrane fusion protein AcrA Introduction Antibiotic resistance in bacteria is due in large part to multidrug efflux complexes like the TolC-AcrAB complex in

More information

7.012 Problem Set 5. Question 1

7.012 Problem Set 5. Question 1 Name Section 7.012 Problem Set 5 Question 1 While studying the problem of infertility, you attempt to isolate a hypothetical rabbit gene that accounts for the prolific reproduction of rabbits. After much

More information

Motivation From Protein to Gene

Motivation From Protein to Gene MOLECULAR BIOLOGY 2003-4 Topic B Recombinant DNA -principles and tools Construct a library - what for, how Major techniques +principles Bioinformatics - in brief Chapter 7 (MCB) 1 Motivation From Protein

More information

CHAPTER 20 DNA TECHNOLOGY AND GENOMICS. Section A: DNA Cloning

CHAPTER 20 DNA TECHNOLOGY AND GENOMICS. Section A: DNA Cloning Section A: DNA Cloning 1. DNA technology makes it possible to clone genes for basic research and commercial applications: an overview 2. Restriction enzymes are used to make recombinant DNA 3. Genes can

More information

Designer Genes Tryout Test Carmel Science Olympiad

Designer Genes Tryout Test Carmel Science Olympiad Designer Genes Tryout Test 2018-2019 Carmel Science Olympiad Name: Score: / 105 Rank: (Do NOT complete score and rank, for officer use only) Directions: You will have 40 minutes to individually complete

More information

Site directed mutagenesis, Insertional and Deletion Mutagenesis. Mitesh Shrestha

Site directed mutagenesis, Insertional and Deletion Mutagenesis. Mitesh Shrestha Site directed mutagenesis, Insertional and Deletion Mutagenesis Mitesh Shrestha Mutagenesis Mutagenesis (the creation or formation of a mutation) can be used as a powerful genetic tool. By inducing mutations

More information

Recitation CHAPTER 9 DNA Technologies

Recitation CHAPTER 9 DNA Technologies Recitation CHAPTER 9 DNA Technologies DNA Cloning: General Scheme A cloning vector and eukaryotic chromosomes are separately cleaved with the same restriction endonuclease. (A single chromosome is shown

More information

Lecture 8: Affinity Chromatography-III

Lecture 8: Affinity Chromatography-III Lecture 8: Affinity Chromatography-III Key words: Chromatography; Affinity chromatography; Protein Purification During this lecture, we shall be studying few more examples of affinity chromatography. The

More information

Solutions for Your Research

Solutions for Your Research Solutions for Your Research Custom Antibody Services Polyclonal Monoclonal The service we offer is very complete starting from rabbits, mice and rats. The different formats provided by Primm depend on

More information

BIOMAN 2015 IMMUNOASSAYS. Barbara Bielska Northampton Community College Tannersville, PA

BIOMAN 2015 IMMUNOASSAYS. Barbara Bielska Northampton Community College Tannersville, PA BIOMAN 2015 IMMUNOASSAYS Barbara Bielska Northampton Community College Tannersville, PA 1 Immunoassays An immunoassay is a biochemical test that measures the presence or concentration of a molecules (typically

More information

Module 3. Lecture 5. Regulation of Gene Expression in Prokaryotes

Module 3. Lecture 5. Regulation of Gene Expression in Prokaryotes Module 3 Lecture 5 Regulation of Gene Expression in Prokaryotes Recap So far, we have looked at prokaryotic gene regulation using 3 operon models. lac: a catabolic operon which displays induction via negative

More information

Chapter 13A: Viral Basics

Chapter 13A: Viral Basics Chapter 13A: Viral Basics 1. Viral Structure 2. The Viral Life Cycle 3. Bacteriophages 1. Viral Structure What exactly is a Virus? Viruses are extremely small entities that are obligate intracellular parasites

More information

Find this material useful? You can help our team to keep this site up and bring you even more content consider donating via the link on our site.

Find this material useful? You can help our team to keep this site up and bring you even more content consider donating via the link on our site. Find this material useful? You can help our team to keep this site up and bring you even more content consider donating via the link on our site. Still having trouble understanding the material? Check

More information

3. Translation. 2. Transcription. 1. Replication. and functioning through their expression in. Genes are units perpetuating themselves

3. Translation. 2. Transcription. 1. Replication. and functioning through their expression in. Genes are units perpetuating themselves Central Dogma Genes are units perpetuating themselves and functioning through their expression in the form of proteins 1 DNA RNA Protein 2 3 1. Replication 2. Transcription 3. Translation Spring 2002 21

More information

Chem 465 Biochemistry II

Chem 465 Biochemistry II Chem 465 Biochemistry II Name: 2 points Multiple choice (4 points apiece): 1. Which of the following is not true of trna molecules? A) The 3'-terminal sequence is -CCA. B) Their anticodons are complementary

More information

Solutions to Quiz II

Solutions to Quiz II MIT Department of Biology 7.014 Introductory Biology, Spring 2005 Solutions to 7.014 Quiz II Class Average = 79 Median = 82 Grade Range % A 90-100 27 B 75-89 37 C 59 74 25 D 41 58 7 F 0 40 2 Question 1

More information

p Kinesin light chain Kinesin heavy chain Kinesin heavy chain Kinesin light chain + - BCMA

p Kinesin light chain Kinesin heavy chain Kinesin heavy chain Kinesin light chain + - BCMA p.959-970 Kinesin light chain Kinesin heavy chain Kinesin heavy chain Kinesin light chain + - BCMA - 2011-05 1 tetratricopeptide repeat Zona di possibile interazione con cargo BCMA - 2011-05 2 Verhey et

More information

Self-test Quiz for Chapter 12 (From DNA to Protein: Genotype to Phenotype)

Self-test Quiz for Chapter 12 (From DNA to Protein: Genotype to Phenotype) Self-test Quiz for Chapter 12 (From DNA to Protein: Genotype to Phenotype) Question#1: One-Gene, One-Polypeptide The figure below shows the results of feeding trials with one auxotroph strain of Neurospora

More information

Design. Construction. Characterization

Design. Construction. Characterization Design Construction Characterization DNA mrna (messenger) A C C transcription translation C A C protein His A T G C T A C G Plasmids replicon copy number incompatibility selection marker origin of replication

More information

Prokaryotic Transcription

Prokaryotic Transcription Prokaryotic Transcription Transcription Basics DNA is the genetic material Nucleic acid Capable of self-replication and synthesis of RNA RNA is the middle man Nucleic acid Structure and base sequence are

More information

Immunoglobulins. (1 of 2)

Immunoglobulins. (1 of 2) Immunoglobulins (1 of 2) Immunoglobulins (Igs) = antibodies Each B cell synthesizes Igs of single specificity for a specific epitope B cell receptors (BCRs) are the Igs on B cell surface Humoral immunity

More information

The Structure of Proteins The Structure of Proteins. How Proteins are Made: Genetic Transcription, Translation, and Regulation

The Structure of Proteins The Structure of Proteins. How Proteins are Made: Genetic Transcription, Translation, and Regulation How Proteins are Made: Genetic, Translation, and Regulation PLAY The Structure of Proteins 14.1 The Structure of Proteins Proteins - polymer amino acids - monomers Linked together with peptide bonds A

More information

EXPERIMENT 2 Cell Fractionation and DNA Isolation

EXPERIMENT 2 Cell Fractionation and DNA Isolation EXPERIMENT 2 Cell Fractionation and DNA Isolation Background Information A. The Eukaryotic Cell Cells are frequently classified into two basic types: prokaryotic and eukar yotic. The prokaryotic cell,

More information

Click here to read the case study about protein synthesis.

Click here to read the case study about protein synthesis. Click here to read the case study about protein synthesis. Big Question: How do cells use the genetic information stored in DNA to make millions of different proteins the body needs? Key Concept: Genetics

More information

Introduction to Plant Genomics and Online Resources. Manish Raizada University of Guelph

Introduction to Plant Genomics and Online Resources. Manish Raizada University of Guelph Introduction to Plant Genomics and Online Resources Manish Raizada University of Guelph Genomics Glossary http://www.genomenewsnetwork.org/articles/06_00/sequence_primer.shtml Annotation Adding pertinent

More information

Bi 8 Lecture 4. Ellen Rothenberg 14 January Reading: from Alberts Ch. 8

Bi 8 Lecture 4. Ellen Rothenberg 14 January Reading: from Alberts Ch. 8 Bi 8 Lecture 4 DNA approaches: How we know what we know Ellen Rothenberg 14 January 2016 Reading: from Alberts Ch. 8 Central concept: DNA or RNA polymer length as an identifying feature RNA has intrinsically

More information

Lesson 8. DNA: The Molecule of Heredity. Gene Expression and Regulation. Introduction to Life Processes - SCI 102 1

Lesson 8. DNA: The Molecule of Heredity. Gene Expression and Regulation. Introduction to Life Processes - SCI 102 1 Lesson 8 DNA: The Molecule of Heredity Gene Expression and Regulation Introduction to Life Processes - SCI 102 1 Genes and DNA Hereditary information is found in discrete units called genes Genes are segments

More information

Chapter 15 Recombinant DNA and Genetic Engineering. Restriction Enzymes Function as Nature s Pinking Shears

Chapter 15 Recombinant DNA and Genetic Engineering. Restriction Enzymes Function as Nature s Pinking Shears Chapter 15 Recombinant DNA and Genetic Engineering In this chapter you will learn How restriction enzyme work and why they are essential to DNA technology. About various procedures such as cloning and

More information

Microbial Genetics. Chapter 8

Microbial Genetics. Chapter 8 Microbial Genetics Chapter 8 Structure and Function of Genetic Material Genome A cell s genetic information Chromosome Structures containing DNA that physically carry hereditary information Gene Segments

More information

BIOLOGY REVISION SHEET FINAL EXAM TERM-III Session: CCS: 10.BIO.4 a, 5 a, 5 b.

BIOLOGY REVISION SHEET FINAL EXAM TERM-III Session: CCS: 10.BIO.4 a, 5 a, 5 b. BIOLOGY REVISION SHEET FINAL EXAM TERM-III Session: 2017-18 CCS: 10.BIO.4 a, 5 a, 5 b. Name: Grade: 10 CHAPTER.8: SECTION 8.1, SECTION 8.2, SECTION 8.3, SECTION 8.4 & SECTION 8.5. NOTE: THE STUDENTS SHOULD

More information

Lecture 25 (11/15/17)

Lecture 25 (11/15/17) Lecture 25 (11/15/17) Reading: Ch9; 328-332 Ch25; 990-995, 1005-1012 Problems: Ch9 (study-guide: applying); 1,2 Ch9 (study-guide: facts); 7,8 Ch25 (text); 1-3,5-7,9,10,13-15 Ch25 (study-guide: applying);

More information

Bi 8 Lecture 5. Ellen Rothenberg 19 January 2016

Bi 8 Lecture 5. Ellen Rothenberg 19 January 2016 Bi 8 Lecture 5 MORE ON HOW WE KNOW WHAT WE KNOW and intro to the protein code Ellen Rothenberg 19 January 2016 SIZE AND PURIFICATION BY SYNTHESIS: BASIS OF EARLY SEQUENCING complex mixture of aborted DNA

More information

Supporting Information

Supporting Information Title Structure of bacterial cellulose synthase subunit D Hu, Song-Qing; Gao, Yong-Gui; Tajima, Kenji; Sunagaw Author(s) Yoda, Takanori; Shimura, Daisuke; Satoh, Yasuharu; M CitationProceedings of the

More information

THE USE OF PIT APERTURES AS WINDOWS TO MEASURE MICROFIBRIL ANGLE IN CHEMICAL PULP FIBERS1. L. A. Donaldson

THE USE OF PIT APERTURES AS WINDOWS TO MEASURE MICROFIBRIL ANGLE IN CHEMICAL PULP FIBERS1. L. A. Donaldson THE USE OF PIT APERTURES AS WINDOWS TO MEASURE MICROFIBRIL ANGLE IN CHEMICAL PULP FIBERS1 L. A. Donaldson Scientist Ministry of Forestry, Forest Research Institute Private Bag, Rotorua, New Zealand (Received

More information

Q2 (1 point). How many carbon atoms does a glucose molecule contain?

Q2 (1 point). How many carbon atoms does a glucose molecule contain? Q1 (1 point). Name three amino acids that are typically found at the surface of integrated membrane proteins.. Q2 (1 point). How many carbon atoms does a glucose molecule contain? Q3 (1 point). What do

More information

AMINO ACIDS, POLYPEPTIDES AND PROTEINS

AMINO ACIDS, POLYPEPTIDES AND PROTEINS AMINO ACIDS, POLYPEPTIDES AND PROTEINS As mentioned above, some of the simplest and most stable forms of nucleic acid to be produced were the transfer RNA molecules - probably at random at first but later

More information

Chapter 17. PCR the polymerase chain reaction and its many uses. Prepared by Woojoo Choi

Chapter 17. PCR the polymerase chain reaction and its many uses. Prepared by Woojoo Choi Chapter 17. PCR the polymerase chain reaction and its many uses Prepared by Woojoo Choi Polymerase chain reaction 1) Polymerase chain reaction (PCR): artificial amplification of a DNA sequence by repeated

More information

Nature Methods: doi: /nmeth Supplementary Figure 1. Construction of a sensitive TetR mediated auxotrophic off-switch.

Nature Methods: doi: /nmeth Supplementary Figure 1. Construction of a sensitive TetR mediated auxotrophic off-switch. Supplementary Figure 1 Construction of a sensitive TetR mediated auxotrophic off-switch. A Production of the Tet repressor in yeast when conjugated to either the LexA4 or LexA8 promoter DNA binding sequences.

More information

Applicazioni biotecnologiche

Applicazioni biotecnologiche Applicazioni biotecnologiche Analisi forense Sintesi di proteine ricombinanti Restriction Fragment Length Polymorphism (RFLP) Polymorphism (more fully genetic polymorphism) refers to the simultaneous occurrence

More information

Biological consequences of site specific recombination: integration, excision, deletion

Biological consequences of site specific recombination: integration, excision, deletion Biological consequences of site specific recombination: integration, excision, deletion The types of DNA rearrangements promoted by a large number of site specific recombination systems and their physiological

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi: 10.1038/nature06147 SUPPLEMENTARY INFORMATION Figure S1 The genomic and domain structure of Dscam. The Dscam gene comprises 24 exons, encoding a signal peptide (SP), 10 IgSF domains, 6 fibronectin

More information

All This For Four Letters!?! DNA and Its Role in Heredity

All This For Four Letters!?! DNA and Its Role in Heredity All This For Four Letters!?! DNA and Its Role in Heredity What Is the Evidence that the Gene Is DNA? By the 1920s, it was known that chromosomes consisted of DNA and proteins. A new dye stained DNA and

More information

Supplementary information

Supplementary information Supplementary information Supplementary figures Figure S1 Level of mycdet1 protein in DET1 OE-1, OE-2 and OE-3 transgenic lines. Total protein extract from wild type Col0, det1-1 mutant and DET1 OE lines

More information

OpenStax-CNX module: m Antibodies * OpenStax. Abstract

OpenStax-CNX module: m Antibodies * OpenStax. Abstract OpenStax-CNX module: m44823 1 Antibodies * OpenStax This work is produced by OpenStax-CNX and licensed under the Creative Commons Attribution License 3.0 By the end of this section, you will be able to:

More information

Supplemental Data. Benstein et al. (2013). Plant Cell /tpc

Supplemental Data. Benstein et al. (2013). Plant Cell /tpc Supplemental Figure 1. Purification of the heterologously expressed PGDH1, PGDH2 and PGDH3 enzymes by Ni-NTA affinity chromatography. Protein extracts (2 µl) of different fractions (lane 1 = total extract,

More information

Vectors for Gene Cloning: Plasmids and Bacteriophages

Vectors for Gene Cloning: Plasmids and Bacteriophages Vectors for Gene Cloning: Plasmids and Bacteriophages DNA molecule must be able to replicate within the host cell to be able to act as a vector for gene cloning, so that numerous copies of the recombinant

More information

BIOTECHNOLOGY. Sticky & blunt ends. Restriction endonucleases. Gene cloning an overview. DNA isolation & restriction

BIOTECHNOLOGY. Sticky & blunt ends. Restriction endonucleases. Gene cloning an overview. DNA isolation & restriction BIOTECHNOLOGY RECOMBINANT DNA TECHNOLOGY Recombinant DNA technology involves sticking together bits of DNA from different sources. Made possible because DNA & the genetic code are universal. 2004 Biology

More information

Key Area 1.3: Gene Expression

Key Area 1.3: Gene Expression Key Area 1.3: Gene Expression RNA There is a second type of nucleic acid in the cell, called RNA. RNA plays a vital role in the production of protein from the code in the DNA. What is gene expression?

More information

Bi 8 Lecture 7. Ellen Rothenberg 26 January Reading: Ch. 3, pp ; panel 3-1

Bi 8 Lecture 7. Ellen Rothenberg 26 January Reading: Ch. 3, pp ; panel 3-1 Bi 8 Lecture 7 PROTEIN STRUCTURE, Functional analysis, and evolution Ellen Rothenberg 26 January 2016 Reading: Ch. 3, pp. 109-134; panel 3-1 (end with free amine) aromatic, hydrophobic small, hydrophilic

More information

CHAPTER 17 FROM GENE TO PROTEIN. Section C: The Synthesis of Protein

CHAPTER 17 FROM GENE TO PROTEIN. Section C: The Synthesis of Protein CHAPTER 17 FROM GENE TO PROTEIN Section C: The Synthesis of Protein 1. Translation is the RNA-directed synthesis of a polypeptide: a closer look 2. Signal peptides target some eukaryotic polypeptides to

More information

National 5 Unit 1: Cell Biology Topic 1.1 Cell Structure. Which part of the cell is composed of cellulose? 1

National 5 Unit 1: Cell Biology Topic 1.1 Cell Structure. Which part of the cell is composed of cellulose? 1 National 5 Unit 1: Cell Biology Topic 1.1 Cell Structure 1. The diagram below shows parts of a plant cell. Which part of the cell is composed of cellulose? 1 2. Which structural feature is found in a plant

More information

Protein analysis. Dr. Mamoun Ahram Summer semester, Resources This lecture Campbell and Farrell s Biochemistry, Chapters 5

Protein analysis. Dr. Mamoun Ahram Summer semester, Resources This lecture Campbell and Farrell s Biochemistry, Chapters 5 Protein analysis Dr. Mamoun Ahram Summer semester, 2015-2016 Resources This lecture Campbell and Farrell s Biochemistry, Chapters 5 Bases of protein separation Proteins can be purified on the basis Solubility

More information

Chapter 4. Antigen Recognition by B-cell and T-cell Receptors

Chapter 4. Antigen Recognition by B-cell and T-cell Receptors Chapter 4 Antigen Recognition by B-cell and T-cell Receptors Antigen recognition by BCR and TCR B cells 2 separate functions of immunoglobulin (Ig) bind pathogen & induce immune responses recruit cells

More information

Which diagram represents a DNA nucleotide? A) B) C) D)

Which diagram represents a DNA nucleotide? A) B) C) D) 3594-1 - Page 1 Name: 1) What is a definition of the term "gene"? A) a transfer-rna nucleotide sequence specific for a particular amino acid B) three messenger-rna nucleotides coded for a specific amino

More information

Problem Set 8. Answer Key

Problem Set 8. Answer Key MCB 102 University of California, Berkeley August 11, 2009 Isabelle Philipp Online Document Problem Set 8 Answer Key 1. The Genetic Code (a) Are all amino acids encoded by the same number of codons? no

More information

Enzyme that uses RNA as a template to synthesize a complementary DNA

Enzyme that uses RNA as a template to synthesize a complementary DNA Biology 105: Introduction to Genetics PRACTICE FINAL EXAM 2006 Part I: Definitions Homology: Comparison of two or more protein or DNA sequence to ascertain similarities in sequences. If two genes have

More information

4/3/2013. DNA Synthesis Replication of Bacterial DNA Replication of Bacterial DNA

4/3/2013. DNA Synthesis Replication of Bacterial DNA Replication of Bacterial DNA 4/3/03 3 4 5 6 7 8 9 0 Chapter 8 Microbial Genetics Terminology Genetics: The study of what genes are, how they carry information, how information is expressed, and how genes are replicated Gene: A segment

More information

Microarray. Key components Array Probes Detection system. Normalisation. Data-analysis - ratio generation

Microarray. Key components Array Probes Detection system. Normalisation. Data-analysis - ratio generation Microarray Key components Array Probes Detection system Normalisation Data-analysis - ratio generation MICROARRAY Measures Gene Expression Global - Genome wide scale Why Measure Gene Expression? What information

More information

Selected Techniques Part I

Selected Techniques Part I 1 Selected Techniques Part I Gel Electrophoresis Can be both qualitative and quantitative Qualitative About what size is the fragment? How many fragments are present? Is there in insert or not? Quantitative

More information

Chapter 17. From Gene to Protein

Chapter 17. From Gene to Protein Chapter 17 From Gene to Protein Overview: The Flow of Genetic Information The information content of DNA is in the form of specific sequences of nucleotides The DNA inherited by an organism leads to specific

More information

Multiple Cellulose Synthase Catalytic Subunits Are Required for Cellulose Synthesis in Arabidopsis

Multiple Cellulose Synthase Catalytic Subunits Are Required for Cellulose Synthesis in Arabidopsis The Plant Cell, Vol. 12, 2529 2539, December 2000, www.plantcell.org 2000 American Society of Plant Physiologists Multiple Cellulose Synthase Catalytic Subunits Are Required for Cellulose Synthesis in

More information

Optically Controlled Reversible Protein Hydrogels Based on Photoswitchable Fluorescent Protein Dronpa. Electronic Supplementary Information

Optically Controlled Reversible Protein Hydrogels Based on Photoswitchable Fluorescent Protein Dronpa. Electronic Supplementary Information Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2017 Optically Controlled Reversible Protein Hydrogels Based on Photoswitchable Fluorescent Protein

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION doi:10.1038/nature12119 SUPPLEMENTARY FIGURES AND LEGENDS pre-let-7a- 1 +14U pre-let-7a- 1 Ddx3x Dhx30 Dis3l2 Elavl1 Ggt5 Hnrnph 2 Osbpl5 Puf60 Rnpc3 Rpl7 Sf3b3 Sf3b4 Tia1 Triobp U2af1 U2af2 1 6 2 4 3

More information

Introduction to Bioinformatics

Introduction to Bioinformatics Introduction to Bioinformatics Contents Cell biology Organisms and cells Building blocks of cells How genes encode proteins? Bioinformatics What is bioinformatics? Practical applications Tools and databases

More information

COPYRIGHTED MATERIAL. Tissue Preparation and Microscopy. General Concepts. Chemical Fixation CHAPTER 1

COPYRIGHTED MATERIAL. Tissue Preparation and Microscopy. General Concepts. Chemical Fixation CHAPTER 1 CHAPTER 1 Tissue Preparation and Microscopy General Concepts I. Biological tissues must undergo a series of treatments to be observed with light and electron microscopes. The process begins by stabilization

More information

SCIENTIFIC REPORT. regarding the implementation of the project between December December 2014

SCIENTIFIC REPORT. regarding the implementation of the project between December December 2014 SCIENTIFIC REPORT regarding the implementation of the project between December 013 - December 014 Title of the project: DETECTION AND IDENTIFICATION OF BIOMOLECULES OF MEDICAL INTEREST BY USING MAGNETIC

More information

Integrated Protein Services

Integrated Protein Services Integrated Protein Services Customer-specific protein expression, purification and analysis - - Last date of revision December 2015 Version DC04-0014 www.iba-lifesciences.com Please fill out the following

More information

The Size and Packaging of Genomes

The Size and Packaging of Genomes DNA Replication The Size and Packaging of Genomes Vary greatly in size Ø Smallest viruses- 4 or 5 genes Ø Escherichia coli- 4,288 genes Ø Human cell- 20,000 to 25,000 genes E. coli 4 million base pairs

More information