Database searching with DNA and protein sequences
... pairs assumed to be the most similar are given the highest total scores. Although, as has already been stated, sequencesearching programs take amino acids or bases simply as characters, biochemical knowledge can be built into the matrix. ...
... pairs assumed to be the most similar are given the highest total scores. Although, as has already been stated, sequencesearching programs take amino acids or bases simply as characters, biochemical knowledge can be built into the matrix. ...
Review Report
... If I understood the paper correctly, the hypothesis is that there were ancestral RNA molecules that both bound amino acids and catalyzed peptide bond formation, but only for what the author calls “bulky” amino acids. Preceding this combined role, the original RNA-AA binding may have been to increase ...
... If I understood the paper correctly, the hypothesis is that there were ancestral RNA molecules that both bound amino acids and catalyzed peptide bond formation, but only for what the author calls “bulky” amino acids. Preceding this combined role, the original RNA-AA binding may have been to increase ...
functional analysis of chromatin assembly genes in tetrahymena
... Renu Jeyapala Bachelor of Science Integrative Biology and Psychology, University of Toronto, 2011 ...
... Renu Jeyapala Bachelor of Science Integrative Biology and Psychology, University of Toronto, 2011 ...
A Mechanistic Analysis of Enzymatic Degradation - J
... The crystal structure of DL-2-haloacid dehalogenase of Pseudomonas putida strain PP3 (DehI), which shares 40% sequence identity with DL-DEX 113, was determined by Schmidberger et al.31) The crystallographic structure of the DehI homodimer was the first reported structure of DL-2-haloacid dehalogenase ...
... The crystal structure of DL-2-haloacid dehalogenase of Pseudomonas putida strain PP3 (DehI), which shares 40% sequence identity with DL-DEX 113, was determined by Schmidberger et al.31) The crystallographic structure of the DehI homodimer was the first reported structure of DL-2-haloacid dehalogenase ...
Assessment by Molecular Dynamics Simulations of the Structural
... structures available for Sp1 are those of individual zinc fingers 2 and 3 in solution.41 Sequence alignment of mammalian Sp1, WT1, and other zinc finger-containing transcription factors such as EGR1 reveals a tandem array of three Cys2-His2 zinc finger domains in their C-terminal regions (Figure 1). ...
... structures available for Sp1 are those of individual zinc fingers 2 and 3 in solution.41 Sequence alignment of mammalian Sp1, WT1, and other zinc finger-containing transcription factors such as EGR1 reveals a tandem array of three Cys2-His2 zinc finger domains in their C-terminal regions (Figure 1). ...
Molecular and Structural Characterization of
... after imbibition (Sue et al., 2000b). Northern-blot analysis showed that the genes are expressed at a high level 36 to 48 h after imbibition and that expression level then gradually decreases as the plant grows (Fig. 2A). This pattern correlated well with that of glucosidase activity. However, north ...
... after imbibition (Sue et al., 2000b). Northern-blot analysis showed that the genes are expressed at a high level 36 to 48 h after imbibition and that expression level then gradually decreases as the plant grows (Fig. 2A). This pattern correlated well with that of glucosidase activity. However, north ...
Dark Reactions
... carbohydrates and fats of the plant. The capacity to accumulate carbon atoms from carbon dioxide for the net synthesis of carbohydrate distinguishes the photoautotrophic from the heterotrophic. The Calvin Cycle takes place in the stroma of the chloroplast. The Calvin cycle is named after Melvin Calv ...
... carbohydrates and fats of the plant. The capacity to accumulate carbon atoms from carbon dioxide for the net synthesis of carbohydrate distinguishes the photoautotrophic from the heterotrophic. The Calvin Cycle takes place in the stroma of the chloroplast. The Calvin cycle is named after Melvin Calv ...
American Scientist
... study selection between genes within a single organism, or upward to study selection between even higher-level entities. The general rule is: Adaptation at level X requires a corresponding process of selection at level X and tends to be undermined by selection at lower levels. This way of thinking a ...
... study selection between genes within a single organism, or upward to study selection between even higher-level entities. The general rule is: Adaptation at level X requires a corresponding process of selection at level X and tends to be undermined by selection at lower levels. This way of thinking a ...
Discovering the Distribution of Palindromic Sequences in the
... and quaternary structures of RNA are important to its function and expression; if an RNA molecule was mutated by a deletion or other mutation (particularly large mutations), RNA expression will be compromised as it may be too susceptible to enzymes or it may be unable to unwind during expression. Sm ...
... and quaternary structures of RNA are important to its function and expression; if an RNA molecule was mutated by a deletion or other mutation (particularly large mutations), RNA expression will be compromised as it may be too susceptible to enzymes or it may be unable to unwind during expression. Sm ...
notes - local.brookings.k12.sd.us
... ACIDS used by cells ____________ to ________________ make proteins ...
... ACIDS used by cells ____________ to ________________ make proteins ...
Stereochemical imperative in enzymic decarboxylations
... for either inversion of retention of configuration. Control Experiments. No evidence was found to suggest that the hydrogens of substrate, precursor, or products underwent any exchange with hydrogens in the medium, under the conditions of the reaction. Consistent with the data of P e d e r ~ o n the ...
... for either inversion of retention of configuration. Control Experiments. No evidence was found to suggest that the hydrogens of substrate, precursor, or products underwent any exchange with hydrogens in the medium, under the conditions of the reaction. Consistent with the data of P e d e r ~ o n the ...
CHAPTER 3 STRUCTURAL ELEMENTS OF
... 1. helix-loop-helix: it is present in many Ca2+ binding proteins (calmodulin, parvalbumin, troponin C ) or DNA binding proteins 2. β hairpin : two antiparallel β-strands are kept together by a short loop of 2-5 residues. 3. greek key: four β strands (minimum), two short loops and one long loop are n ...
... 1. helix-loop-helix: it is present in many Ca2+ binding proteins (calmodulin, parvalbumin, troponin C ) or DNA binding proteins 2. β hairpin : two antiparallel β-strands are kept together by a short loop of 2-5 residues. 3. greek key: four β strands (minimum), two short loops and one long loop are n ...
The Genetic Code and RNA-Amino Acid Affinities
... environment is likely to be restrictive to RNA synthesis and survival. Accordingly, the molecules most easily accessed, least sensitive to physical or chemical attack, seem the appropriate targets. That is—it certainly is possible to do selections that optimize a function. Selecting RNAs that slowly ...
... environment is likely to be restrictive to RNA synthesis and survival. Accordingly, the molecules most easily accessed, least sensitive to physical or chemical attack, seem the appropriate targets. That is—it certainly is possible to do selections that optimize a function. Selecting RNAs that slowly ...
Integrated Microfluidic Nucleic Acid Isolation, Isothermal
... proteases for lysis)—and often the sample too—need to be maintained in a cold chain, and the laboratory work area and procedures must minimize cross contamination of samples. The foregoing benchtop procedure can be implemented with a credit-card sized microfluidic cassette “chip”, with total sample ...
... proteases for lysis)—and often the sample too—need to be maintained in a cold chain, and the laboratory work area and procedures must minimize cross contamination of samples. The foregoing benchtop procedure can be implemented with a credit-card sized microfluidic cassette “chip”, with total sample ...
Evolution “for the Good of the Group”
... study selection between genes within a single organism, or upward to study selection between even higher-level entities. The general rule is: Adaptation at level X requires a corresponding process of selection at level X and tends to be undermined by selection at lower levels. This way of thinking a ...
... study selection between genes within a single organism, or upward to study selection between even higher-level entities. The general rule is: Adaptation at level X requires a corresponding process of selection at level X and tends to be undermined by selection at lower levels. This way of thinking a ...
October 15 AP Biology - John D. O`Bryant School of Math & Science
... B) high temperatures make catalysis unnecessary. C) their enzymes have high optimal temperatures. D) their enzymes are completely insensitive to temperature. E) they use molecules other than proteins or RNAs as their main catalysts. ...
... B) high temperatures make catalysis unnecessary. C) their enzymes have high optimal temperatures. D) their enzymes are completely insensitive to temperature. E) they use molecules other than proteins or RNAs as their main catalysts. ...
3 - Milan Area Schools
... 30. The side chain of leucine is a hydrocarbon. In a folded protein, where would you expect to find leucine? a. In the interior of a cytoplasmic enzyme b. On the exterior of a protein embedded in a membrane c. On the exterior of a cytoplasmic enzyme d. Both a and b e. Both a and c Answer: d 31. What ...
... 30. The side chain of leucine is a hydrocarbon. In a folded protein, where would you expect to find leucine? a. In the interior of a cytoplasmic enzyme b. On the exterior of a protein embedded in a membrane c. On the exterior of a cytoplasmic enzyme d. Both a and b e. Both a and c Answer: d 31. What ...
Griffith_155
... weights calculated from the sequences of the enzymes (e.g., 34,466 for the B. cereus PI-PLC). The value is higher than that observed by gel filtration ...
... weights calculated from the sequences of the enzymes (e.g., 34,466 for the B. cereus PI-PLC). The value is higher than that observed by gel filtration ...
Lecture PDF - Carol Eunmi LEE
... Genetic changes that occur because the gene was right next to another gene on a chromosome that was under selection ...
... Genetic changes that occur because the gene was right next to another gene on a chromosome that was under selection ...
Deoxyribozyme
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Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of catalyzing specific chemical reactions, similar to the action of other biological enzymes, such as proteins or ribozymes (enzymes composed of RNA).However, in contrast to the abundance of protein enzymes in biological systems and the discovery of biological ribozymes in the 1980s,there are no known naturally occurring deoxyribozymes.Deoxyribozymes should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but do not catalyze a subsequent chemical reaction.With the exception of ribozymes, nucleic acid molecules within cells primarily serve as storage of genetic information due to its ability to form complementary base pairs, which allows for high-fidelity copying and transfer of genetic information. In contrast, nucleic acid molecules are more limited in their catalytic ability, in comparison to protein enzymes, to just three types of interactions: hydrogen bonding, pi stacking, and metal-ion coordination. This is due to the limited number of functional groups of the nucleic acid monomers: while proteins are built from up to twenty different amino acids with various functional groups, nucleic acids are built from just four chemically similar nucleobases. In addition, DNA lacks the 2'-hydroxyl group found in RNA which limits the catalytic competency of deoxyribozymes even in comparison to ribozymes.In addition to the inherent inferiority of DNA catalytic activity, the apparent lack of naturally occurring deoxyribozymes may also be due to the primarily double-stranded conformation of DNA in biological systems which would limit its physical flexibility and ability to form tertiary structures, and so would drastically limit the ability of double-stranded DNA to act as a catalyst; though there are a few known instances of biological single-stranded DNA such as multicopy single-stranded DNA (msDNA), certain viral genomes, and the replication fork formed during DNA replication. Further structural differences between DNA and RNA may also play a role in the lack of biological deoxyribozymes, such as the additional methyl group of the DNA base thymidine compared to the RNA base uracil or the tendency of DNA to adopt the B-form helix while RNA tends to adopt the A-form helix. However, it has also been shown that DNA can form structures that RNA cannot, which suggests that, though there are differences in structures that each can form, neither is inherently more or less catalytic due to their possible structural motifs.