Biological membranes - Essays in Biochemistry
... Biological membranes are formed by adding to a pre-existing membrane. In prokaryotes this occurs on the inner leaflet of the plasma membrane, facing the cytoplasm. In eukaryotes, membrane synthesis takes place at the ER on the cytoplasmic leaflet of the ER membrane (termed the ‘inside’ of the cell). ...
... Biological membranes are formed by adding to a pre-existing membrane. In prokaryotes this occurs on the inner leaflet of the plasma membrane, facing the cytoplasm. In eukaryotes, membrane synthesis takes place at the ER on the cytoplasmic leaflet of the ER membrane (termed the ‘inside’ of the cell). ...
Document
... Greece, the presentation of the yeast chromosome III and the first 100 kb of the Bacillus subtilis genome revealed that, contrary to expectation (the only cases where this had been observed were phages, for obvious reasons), at least half of the genes uncovered were totally unknown, whether in struc ...
... Greece, the presentation of the yeast chromosome III and the first 100 kb of the Bacillus subtilis genome revealed that, contrary to expectation (the only cases where this had been observed were phages, for obvious reasons), at least half of the genes uncovered were totally unknown, whether in struc ...
The scs Boundary Element: Characterization of Boundary Element
... Band shift and DNase I footprinting assays. Band shift assays were performed as previously described, with empirically determined amounts of protein (39). Binding reactions for DNase I footprinting were similar, except that the probe DNA was labeled on only one end. After treatment with approximatel ...
... Band shift and DNase I footprinting assays. Band shift assays were performed as previously described, with empirically determined amounts of protein (39). Binding reactions for DNase I footprinting were similar, except that the probe DNA was labeled on only one end. After treatment with approximatel ...
Altering the GTP binding site of the DNA/RNA
... hydrolyzed analog of ATP, adenylyl imidophosphate, (data not shown) also does not decrease the RNA binding of TB-RBP (Fig. 2, lane 6). Similar decreases in RNA binding were obtained with endogeneous TB-RBP in mouse testicular extracts in the presence of GTPγS (see below). To investigate the inhibito ...
... hydrolyzed analog of ATP, adenylyl imidophosphate, (data not shown) also does not decrease the RNA binding of TB-RBP (Fig. 2, lane 6). Similar decreases in RNA binding were obtained with endogeneous TB-RBP in mouse testicular extracts in the presence of GTPγS (see below). To investigate the inhibito ...
A Tertiary Plastid Uses Genes from Two Endosymbionts
... and chlorarachniophytes, the nucleus of the primary host was lost. Secondary plastids are situated within the host endomembrane system, so plastidtargeting leaders consist of a signal peptide (SP) followed by a TP. The SP directs the proteins to the endomembrane system via the signal recognition par ...
... and chlorarachniophytes, the nucleus of the primary host was lost. Secondary plastids are situated within the host endomembrane system, so plastidtargeting leaders consist of a signal peptide (SP) followed by a TP. The SP directs the proteins to the endomembrane system via the signal recognition par ...
Mercury, Cadmium, and Arsenite Enhance Heat Shock Protein
... embryo of arsenite (As), cadmium (Cd), or mercury (Hg). Each lane was loaded with 120,000 cpm/lane of a supernatant aliquot from a homogenate of 3 pooled embryos. Enhanced de novo synthesis of stress proteins sp90, sp70, and sp24 was observed after As exposure. Cd and Hg induced de novo expression o ...
... embryo of arsenite (As), cadmium (Cd), or mercury (Hg). Each lane was loaded with 120,000 cpm/lane of a supernatant aliquot from a homogenate of 3 pooled embryos. Enhanced de novo synthesis of stress proteins sp90, sp70, and sp24 was observed after As exposure. Cd and Hg induced de novo expression o ...
Nucleic Acid AptamerssFrom Selection in Vitro to Applications in Vivo
... amino acid, as well as in damage selection experiments. The bases which were conserved among different isolates are shown in uppercase, while variant bases are in lowercase. The three nucleotides critical for amino acid specificity (13, 29, and 31) are indicated by circles (for citrulline) and boxes ...
... amino acid, as well as in damage selection experiments. The bases which were conserved among different isolates are shown in uppercase, while variant bases are in lowercase. The three nucleotides critical for amino acid specificity (13, 29, and 31) are indicated by circles (for citrulline) and boxes ...
mbe.oxfordjournals.org - Oxford Academic
... oligonucleotides T-Ag1 and T-Ag2 (table 2) were hybridized giving rise to a double-stranded DNA fragment with a NotI site at the 5# end and an EcoRI site at the 3# end. The SV40 NLS tag was inserted into NotI and EcoRI sites of the plasmid KS-S6DNLS1-3, which contained the S6(3–240) fragment with th ...
... oligonucleotides T-Ag1 and T-Ag2 (table 2) were hybridized giving rise to a double-stranded DNA fragment with a NotI site at the 5# end and an EcoRI site at the 3# end. The SV40 NLS tag was inserted into NotI and EcoRI sites of the plasmid KS-S6DNLS1-3, which contained the S6(3–240) fragment with th ...
Egg Microinjection Technique and Morpholinos
... defects even at low doses. The next best control is to design a second MO, not overlapping with the first. If it elicits the same phenotype as the first, then this provides support that the defect is specific to the gene of interest. 5. For translation blocking morpholinos, an additional control sho ...
... defects even at low doses. The next best control is to design a second MO, not overlapping with the first. If it elicits the same phenotype as the first, then this provides support that the defect is specific to the gene of interest. 5. For translation blocking morpholinos, an additional control sho ...
Instruction Manual, PureZOL RNA Isolation Reagent - Bio-Rad
... total RNA from animal and plant tissues, cultured mammalian cells, and bacterial and yeast cells in under 1 hour. PureZOL can also be used for the simultaneous extraction of RNA, DNA, and proteins from various samples. This reagent allows processing of small amounts of starting material (50 cells or ...
... total RNA from animal and plant tissues, cultured mammalian cells, and bacterial and yeast cells in under 1 hour. PureZOL can also be used for the simultaneous extraction of RNA, DNA, and proteins from various samples. This reagent allows processing of small amounts of starting material (50 cells or ...
Accuracy of protein flexibility predictions
... use a sliding window averaging technique; parameters are summed for a stretch of amino acids within a window which is shifted by one residue at a time. In the KS method residues have coefficients dependent on the location within the window, thus the contribution of a residue to the prediction value ...
... use a sliding window averaging technique; parameters are summed for a stretch of amino acids within a window which is shifted by one residue at a time. In the KS method residues have coefficients dependent on the location within the window, thus the contribution of a residue to the prediction value ...
video slide - Buena Park High School
... Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ...
... Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ...
The Polypeptide Composition of Moving and Stationary
... Mouse neurofilament protein L and M cDNAs were obtained by reverse transcriptase polymerase chain reaction (RT-PCR) using RNA from wild type P24 mouse cerebellum (Genbank Accession Numbers DQ201635 and DQ201636, respectively). For NFM, the forward primer sequence was 50 -AGTAGGATCCGCCTCCAAGATGAGCTACA ...
... Mouse neurofilament protein L and M cDNAs were obtained by reverse transcriptase polymerase chain reaction (RT-PCR) using RNA from wild type P24 mouse cerebellum (Genbank Accession Numbers DQ201635 and DQ201636, respectively). For NFM, the forward primer sequence was 50 -AGTAGGATCCGCCTCCAAGATGAGCTACA ...
Conceptual Questions C1. Answer: The start codon begins at the
... Initiation: The mRNA, initiator tRNA, and initiation factors associate with the small ribosomal subunit; then the large subunit associates. Elongation: The ribosome moves one codon at a time down the mRNA, adding one amino acid at a time to the growing polypeptide chain. Three sites on the ribosome, ...
... Initiation: The mRNA, initiator tRNA, and initiation factors associate with the small ribosomal subunit; then the large subunit associates. Elongation: The ribosome moves one codon at a time down the mRNA, adding one amino acid at a time to the growing polypeptide chain. Three sites on the ribosome, ...
Cell and Molecular Biology
... • What are the A, P, and E sites of a ribosome? What binds at each of these sites? • Does anything beside the ribosome participate in elongation of the amino acid chain? If so, what is it and what does it do? • What signals where translation starts and stops? • What happens to improperly translated ...
... • What are the A, P, and E sites of a ribosome? What binds at each of these sites? • Does anything beside the ribosome participate in elongation of the amino acid chain? If so, what is it and what does it do? • What signals where translation starts and stops? • What happens to improperly translated ...
Expression and purification of proteins using Strep
... to its chemically balanced amino acid composition (8 amino acids, WSHPQFEK) which can be fused to the protein as either N- or C-terminal tag. A two amino acid spacer (SerAla) between the protein and the tag promotes the accessibility of the tag. The further improved Twin-Strep-tag® is a sequential a ...
... to its chemically balanced amino acid composition (8 amino acids, WSHPQFEK) which can be fused to the protein as either N- or C-terminal tag. A two amino acid spacer (SerAla) between the protein and the tag promotes the accessibility of the tag. The further improved Twin-Strep-tag® is a sequential a ...
Full-Text PDF
... acid residues [33]. The small HPCopP is homologous to CopZ, encoded by the E. hirae and B. subtilis cop operons. CopZ proteins have a conserved structure, β-α-β-β-α-β with a similar metal binding region. However, the structure of HPCopP has a β-α-β-β-α fold (Figure 3A). The helices correspond to res ...
... acid residues [33]. The small HPCopP is homologous to CopZ, encoded by the E. hirae and B. subtilis cop operons. CopZ proteins have a conserved structure, β-α-β-β-α-β with a similar metal binding region. However, the structure of HPCopP has a β-α-β-β-α fold (Figure 3A). The helices correspond to res ...
Full-Text PDF
... we are assuming the existence of some form of a very early tRNA amino acid charging system, a proto synthetase. It has been proposed that the tRNA synthetase evolution began with peptides formed in a “Thioester World” preceding those encoded by the earliest RNA based system. The evidence for this ev ...
... we are assuming the existence of some form of a very early tRNA amino acid charging system, a proto synthetase. It has been proposed that the tRNA synthetase evolution began with peptides formed in a “Thioester World” preceding those encoded by the earliest RNA based system. The evidence for this ev ...
AlgPred: prediction of allergenic proteins and mapping of
... WHO 2001 recommendations and recognized the uncertainties associated with different tests. They suggest weight of evidence approach rather than a specific decision tree approach (suggested in FAO/WHO 2001). They recommended various tests for examining allergenic behavior of proteins that includes so ...
... WHO 2001 recommendations and recognized the uncertainties associated with different tests. They suggest weight of evidence approach rather than a specific decision tree approach (suggested in FAO/WHO 2001). They recommended various tests for examining allergenic behavior of proteins that includes so ...
Uncoupling insulin signalling by serine/threonine phosphorylation: a
... beta cells [1]. At the molecular level, insulin binding to its transmembrane receptor (IR) stimulates the intrinsic tyrosine (Tyr) kinase activity of the receptor (IRK), which then phosphorylates selected Tyr residues of target proteins. IR substrates include IRS (IR substrate) proteins (IRS-1–6), S ...
... beta cells [1]. At the molecular level, insulin binding to its transmembrane receptor (IR) stimulates the intrinsic tyrosine (Tyr) kinase activity of the receptor (IRK), which then phosphorylates selected Tyr residues of target proteins. IR substrates include IRS (IR substrate) proteins (IRS-1–6), S ...
Analysis of splice sites in the early region of bovine polyomavirus
... Amplification primers. The location and sequence of the primers used in RT and amplification reactions are presented in Fig. 1(d and e). Each primer contained at least 20 nucleotides complementary to the BPyV genome. The 5' ends of all three primers contained a naturally occurring or an engineered r ...
... Amplification primers. The location and sequence of the primers used in RT and amplification reactions are presented in Fig. 1(d and e). Each primer contained at least 20 nucleotides complementary to the BPyV genome. The 5' ends of all three primers contained a naturally occurring or an engineered r ...
In vitro gastrointestinal digestion study of a novel bio-tofu
... source of soymilk has not satisfied peoples’ nutritional needs, the production of mixed protein matrix is an area of great potential for future development. Composite gels containing casein (the main cow milk proteins) and soy proteins are possible to be obtained according to the previous studies ( ...
... source of soymilk has not satisfied peoples’ nutritional needs, the production of mixed protein matrix is an area of great potential for future development. Composite gels containing casein (the main cow milk proteins) and soy proteins are possible to be obtained according to the previous studies ( ...
Dissecting the protein–RNA interface
... of protein–RNA complexes that had been solved using X-ray crystallography (5). From this data set, 344 complexes were selected based on the following criteria: (i) structural resolution better than 3.0 Å and (ii) polypeptides and polyribonucleotides longer than 20 amino acids and 5 nt, respectively ...
... of protein–RNA complexes that had been solved using X-ray crystallography (5). From this data set, 344 complexes were selected based on the following criteria: (i) structural resolution better than 3.0 Å and (ii) polypeptides and polyribonucleotides longer than 20 amino acids and 5 nt, respectively ...
The nucleolus and herpesviral usurpation
... (HSV-1) infected cell protein 27 (ICP27) is suggested to be a nucleolar targeting protein and contains a relatively short sequence, mapping to residues 110–152, which functions as an NoLS and plays important roles in efficient viral RNA export and regulation of HSV-1 replication (Mears et al., 1995) ...
... (HSV-1) infected cell protein 27 (ICP27) is suggested to be a nucleolar targeting protein and contains a relatively short sequence, mapping to residues 110–152, which functions as an NoLS and plays important roles in efficient viral RNA export and regulation of HSV-1 replication (Mears et al., 1995) ...
Assembly of AO and DHAS - Journal of Cell Science
... were quickly lysed and subjected to a single centrifugation to separate cytosol (and light membranes, the SUP fraction) from peroxisomes (and other organelles, the PEL fraction). Fig. 1B demonstrates that this step results in the release of 94% of a cytosolic marker, formaldehyde dehydrogenase, a me ...
... were quickly lysed and subjected to a single centrifugation to separate cytosol (and light membranes, the SUP fraction) from peroxisomes (and other organelles, the PEL fraction). Fig. 1B demonstrates that this step results in the release of 94% of a cytosolic marker, formaldehyde dehydrogenase, a me ...
SR protein
SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are ""S"" and ""R"" respectively. SR proteins are 50-300 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS binding domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm.SR proteins were discovered in the 1990s in Drosophila and in amphibian oocytes, and later in humans. In general, metazoans appear to have SR proteins and unicellular organisms lack SR proteins.SR proteins are important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, nonsense-mediated decay, and translation. SR proteins alternatively splice pre-mRNA by preferentially selecting different splice sites on the pre-mRNA strands to create multiple mRNA transcripts from one pre-mRNA transcript. Once splicing is complete the SR protein may or may not remain attached to help shuttle the mRNA strand out of the nucleus. As RNA Polymerase II is transcribing DNA into RNA, SR proteins attach to newly made pre-mRNA to prevent the pre-mRNA from binding to the coding DNA strand to increase genome stabilization. Topoisomerase I and SR proteins also interact to increase genome stabilization. SR proteins can control the concentrations of specific mRNA that is successfully translated into protein by selecting for nonsense-mediated decay codons during alternative splicing. SR proteins can alternatively splice NMD codons into its own mRNA transcript to auto-regulate the concentration of SR proteins. Through the mTOR pathway and interactions with polyribosomes, SR proteins can increase translation of mRNA.Ataxia telangiectasia, neurofibromatosis type 1, several cancers, HIV-1, and spinal muscular atrophy have all been linked to alternative splicing by SR proteins.