Protein sequencing
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Protein sequencing is the determination of the amino acid sequence in a protein. There are several methods for protein sequencing including determining the amino acid composition, N-terminal amino acid analysis, C-terminal amino acid analysis, sequencing by proteolytic enzymes, and tandem mass spectrometry. Two important methods for N-terminal amino acid analysis are the Sanger method and Edman degradation method. The Edman degradation method uses phenylisothiocyanate to sequentially remove amino acid residues from the N-terminus to determine the sequence. Proteolytic enzymes can also aid sequencing by cleaving the protein into smaller fragments. Mass spectrometry has also been used to sequence proteins by analyzing the peptide fragments.
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Protein sequencing
Protein sequencing determines the order of amino acids in a protein. The two major methods are Edman degradation and mass spectrometry. Edman degradation involves labeling the N-terminal amino acid, cleaving it off, and identifying it, repeating the process one amino acid at a time to deduce the sequence. Mass spectrometry involves ionizing and separating protein fragments by mass/charge ratio to determine sequence. Protein sequencing is useful for identifying unknown proteins and characterizing modifications.
Protein Sequencing Strategies
Frederick Sanger developed two important methods for protein sequencing: 1) using fluorodinitrobenzene to determine the N-terminal amino acid, and 2) cleaving proteins into fragments and piecing their sequences together. The standard strategy involves separating chains, identifying terminal residues, cleaving the protein, sequencing fragments, and reconstructing the full sequence. The Edman degradation method allows sequential removal of residues from the N-terminus. Mass spectrometry techniques like peptide mass fingerprinting and tandem mass spectrometry now dominate protein sequencing.
Protein sequencing by kk sahu
Introduction
What is Protein Sequencing?
History
Determination of amino acid composition
Sequencing methods
N terminal sequencing
C terminal sequencing
Mass spectrometer
Application
Reference
Sequencing of protein
The document discusses protein sequencing techniques. It begins with an introduction to proteins and protein sequencing. The history of protein sequencing is then outlined, including early work by Edman and Sanger. Methods for determining amino acid composition through hydrolysis, separation, and analysis are described. The mechanisms of Sanger's method using dinitrophenyl reagents and Edman degradation using phenylisothiocyanate are explained. Applications of protein sequencing include determining protein structure and function. The document concludes with locations of protein sequencing institutes in India and abroad.
Protein sequencing
1) The first protein sequencing was achieved in 1953 by Frederic Sanger who determined the amino acid sequence of bovine insulin.
2) Common strategies for protein sequencing include determining the number of subunits, disulfide bonds, amino acid composition, and sequencing fragments using Edman degradation or enzymatic cleavage.
3) Techniques like end-group analysis, solid-phase support, exopeptidases, and mass spectrometry help overcome challenges and complete the protein sequence.
Amino acid sequencing
Amino acid sequencing determines the order of amino acids in a protein. Frederick Sanger determined the first protein sequence in 1953 using N-terminal analysis methods like Edman degradation. Large proteins are sequenced by first breaking them into smaller fragments using enzymes or chemicals, then determining the sequence of individual fragments and combining sequences to deduce the full protein sequence. Modern techniques like mass spectrometry have made sequencing faster and applicable to modified proteins.
Protein sequencing and its application in bioinformatics
Protein sequencing and its applications in bioinformatics. The document discusses the history of protein sequencing including early work by Fred Sanger in 1951. It describes methods of protein sequencing such as N-terminal sequencing using Edman degradation. Mass spectrometry and DNA sequencing are also covered. Bioinformatics tools for sequence alignment are discussed, including BLAST and multiple sequence alignment using CLUSTAL. Protein sequencing provides important information for understanding protein structure and function and has applications in drug development, recombinant protein synthesis, and studying genetic diseases.
Protein dna interactions
Protein-DNA interactions can be either specific or non-specific. Specific interactions involve transcription factors that regulate gene expression by binding to DNA motifs through domains like helix-loop-helix, leucine zipper, or zinc finger motifs. Non-specific interactions involve histones that help structure DNA into nucleosomes within chromatin and can be chemically modified through methylation, demethylation, acetylation, and phosphorylation.
Recommended
Protein sequencing
Protein sequencing determines the order of amino acids in a protein. The two major methods are Edman degradation and mass spectrometry. Edman degradation involves labeling the N-terminal amino acid, cleaving it off, and identifying it, repeating the process one amino acid at a time to deduce the sequence. Mass spectrometry involves ionizing and separating protein fragments by mass/charge ratio to determine sequence. Protein sequencing is useful for identifying unknown proteins and characterizing modifications.
Protein Sequencing Strategies
Frederick Sanger developed two important methods for protein sequencing: 1) using fluorodinitrobenzene to determine the N-terminal amino acid, and 2) cleaving proteins into fragments and piecing their sequences together. The standard strategy involves separating chains, identifying terminal residues, cleaving the protein, sequencing fragments, and reconstructing the full sequence. The Edman degradation method allows sequential removal of residues from the N-terminus. Mass spectrometry techniques like peptide mass fingerprinting and tandem mass spectrometry now dominate protein sequencing.
Protein sequencing by kk sahu
Introduction
What is Protein Sequencing?
History
Determination of amino acid composition
Sequencing methods
N terminal sequencing
C terminal sequencing
Mass spectrometer
Application
Reference
Sequencing of protein
The document discusses protein sequencing techniques. It begins with an introduction to proteins and protein sequencing. The history of protein sequencing is then outlined, including early work by Edman and Sanger. Methods for determining amino acid composition through hydrolysis, separation, and analysis are described. The mechanisms of Sanger's method using dinitrophenyl reagents and Edman degradation using phenylisothiocyanate are explained. Applications of protein sequencing include determining protein structure and function. The document concludes with locations of protein sequencing institutes in India and abroad.
Protein sequencing
1) The first protein sequencing was achieved in 1953 by Frederic Sanger who determined the amino acid sequence of bovine insulin.
2) Common strategies for protein sequencing include determining the number of subunits, disulfide bonds, amino acid composition, and sequencing fragments using Edman degradation or enzymatic cleavage.
3) Techniques like end-group analysis, solid-phase support, exopeptidases, and mass spectrometry help overcome challenges and complete the protein sequence.
Amino acid sequencing
Amino acid sequencing determines the order of amino acids in a protein. Frederick Sanger determined the first protein sequence in 1953 using N-terminal analysis methods like Edman degradation. Large proteins are sequenced by first breaking them into smaller fragments using enzymes or chemicals, then determining the sequence of individual fragments and combining sequences to deduce the full protein sequence. Modern techniques like mass spectrometry have made sequencing faster and applicable to modified proteins.
Protein sequencing and its application in bioinformatics
Protein sequencing and its applications in bioinformatics. The document discusses the history of protein sequencing including early work by Fred Sanger in 1951. It describes methods of protein sequencing such as N-terminal sequencing using Edman degradation. Mass spectrometry and DNA sequencing are also covered. Bioinformatics tools for sequence alignment are discussed, including BLAST and multiple sequence alignment using CLUSTAL. Protein sequencing provides important information for understanding protein structure and function and has applications in drug development, recombinant protein synthesis, and studying genetic diseases.
Protein dna interactions
Protein-DNA interactions can be either specific or non-specific. Specific interactions involve transcription factors that regulate gene expression by binding to DNA motifs through domains like helix-loop-helix, leucine zipper, or zinc finger motifs. Non-specific interactions involve histones that help structure DNA into nucleosomes within chromatin and can be chemically modified through methylation, demethylation, acetylation, and phosphorylation.
Protein seqencing by kk sahu
Introduction.
History of Protein Sequencing.
Determining Amino Acid Composition.
N-terminal amino acid analysis.
C-terminal amino acid analysis
The Edman degradation reaction.
Limitations of the Edman degradation.
Mass spectrometry
Importance
Conclusion
Reference
Protein sequence determinatiom
This document discusses various methods for determining the amino acid sequence of proteins, including:
- Edman degradation, which sequentially removes amino acids from the N-terminus. Up to 60 amino acids can typically be determined.
- Mass spectrometry techniques like MALDI that help determine the mass and sequence of protein fragments.
- Enzymatic cleavage techniques using enzymes like trypsin to break proteins into smaller fragments that can then be sequenced.
Protein sequencing presentation
Protein sequencing involves determining the order of amino acids in a protein chain. [1] Edman degradation is commonly used for N-terminal sequencing and involves labeling the N-terminal amino acid, removing it, and identifying it through chromatography and mass spectrometry. [2] The protein must first be purified and digested before Edman degradation can begin. [3] Mass spectrometry is used to analyze the separated amino acid derivatives and identify the sequence.
protein sequence analysis
The document discusses various methods for protein sequence analysis, including: (1) N-terminal sequencing using Edman degradation, (2) C-terminal sequencing using carboxypeptidases, (3) DNA sequencing to infer protein sequence, and (4) mass spectrometry. It also covers preparing proteins for sequencing by separating chains and cleaving disulfide bridges, as well as bioinformatics tools like BLAST for comparing sequences. The overall goal of protein sequencing is to determine amino acid sequences to understand protein structure, function, and cellular processes.
Polyadenylation
Polyadenylation is the addition of a poly(A) tail to messenger RNA. The poly(A) tail consists of multiple adenosine monophosphates and plays an important role in mRNA stability, nucleocytoplasmic export, and translation. Cleavage and polyadenylation is controlled by cis elements located upstream and downstream of the polyadenylation site and involves endonuclease cleavage of the pre-mRNA followed by poly(A) polymerase addition of adenines in a template-independent manner. Alternative polyadenylation and cytoplasmic polyadenylation allow for regulation of mRNA expression through differing poly(A) tail lengths.
Tryptophan operon
The tryptophan operon regulates the biosynthesis of tryptophan in E. coli through transcriptional attenuation and repression. It contains five genes encoding the enzymes needed to synthesize tryptophan. When tryptophan levels are high, the tryptophan repressor binds to the operator site, preventing transcription. Additionally, a regulatory region can form a terminator stem-loop structure to halt transcription if tryptophan tRNA levels are high during translation of the leader mRNA sequence. However, if tryptophan levels are low, the terminator structure does not form and transcription of the operon proceeds.
Automated DNA sequencing ; Protein sequencing
This document discusses several methods for DNA and protein sequencing. It describes automated DNA sequencing which is based on the Sanger method but uses fluorescent labels and allows direct computer storage of sequence data. It then discusses various methods for protein sequencing including purification, amino acid composition analysis, N-terminal sequencing using Edman degradation or other methods, C-terminal sequencing, breaking disulfide bonds, cleaving the protein into peptides, ordering peptides by overlap, and locating disulfide bonds. Newer methods discussed are using genomic data and mass spectrometry techniques.
05. Protein Sequencing
There are several key steps to sequencing a protein, including:
1) Separating individual protein chains and breaking disulfide bonds. This can involve reagents like mercaptoethanol or performic acid.
2) Purifying individual protein chains using techniques like electrophoresis or chromatography.
3) Cleaving the purified protein into fragments using enzymes like trypsin or chemicals like cyanogen bromide.
4) Determining the amino acid sequence of each fragment, then combining the overlapping sequences to deduce the full protein sequence.
Protein and nucleic acid sequencing
Protein Sequencing
Introduction
Protein Sequencing
History of Protein Sequencing
Determining Amino Acid Composition
N-terminal amino acid analysis
C-terminal amino acid analysis
Edman degradation
The Edman degradation reaction
Limitations of the Edman degradation
Mass spectrometry
Nucleic Acid Sequencing
Introduction
Nucleic Acid Sequencing
Type of Nucleic Acid Sequencing
DNA Sequencing
Method of DNA Sequencing
Application of DNA Sequencing
DNA Sequencing Institutes
Conclusion
Reference
Gene silencing
Gene silencing is the regulation of gene expression in a cell to prevent the expression of a certain gene. Gene silencing can occur during either transcription or translation and is often used in research.
Protein Folding Mechanism
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
METHODS TO DETERMINE PROTEIN STRUCTURE
This document discusses several methods for determining protein structure: Edman degradation, X-ray crystallography, Western blotting, SDS-PAGE, 2D gel electrophoresis, and isoelectric focusing. Edman degradation involves chemically removing amino acids from the N-terminus of a protein one by one to determine the sequence. X-ray crystallography provides high-resolution 3D structures of proteins. Western blotting identifies specific proteins in a sample using antibodies. SDS-PAGE and 2D gels separate proteins by size and electric charge properties. Isoelectric focusing separates proteins based on their isoelectric points.
Protein protein interaction
Protein-protein interactions are important for many biological processes. There are various types of interactions depending on their composition and duration. Methods to study interactions include yeast two-hybrid, co-immunoprecipitation, affinity chromatography, and chromatin immunoprecipitation. Databases such as IntAct and MINT provide repositories for protein interaction data.
Sequencing of protein ppts
This document discusses protein sequencing techniques. It begins by defining protein sequencing as the technique used to determine the amino acid sequence of a protein. It then provides a brief history of protein sequencing, including that Pehr Edman developed the Edman degradation method in 1947 and Fredrick Sanger determined the complete sequence of insulin in 1955. The document goes on to describe various protein sequencing methods such as Edman degradation, which involves sequential identification of amino acids from the N to C terminus using phenyl isothiocyanate. It notes applications of protein sequencing include understanding protein structure and function, and developing drugs.
Oligonucleotide synthesis - Problems and Challenges
The oligonucleotides are synthesized on solid supports from the 3’-end and the first monomer at this end is normally attached to a CPG(Controlled Pore Glass) or Polystyrene (PS).
Chou fasman algorithm for protein structure prediction
The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time.
A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results.
Chou-Fasman algorithm is an empirical algorithm developed for the prediction of protein secondary structure
Genomics: Organization of Genome, Strategies of Genome Sequencing, Model Plan...
Genomics: Organization of Genome, Strategies of Genome Sequencing, Model Plant Genome Project, Functional Analysis of Genes
Post transcriptional modification ( splicing mechanisms)
Post-transcriptional modifications are important processes that convert primary transcript RNA into mature RNA. These modifications include 5' capping, 3' polyadenylation, and splicing of introns in eukaryotes. The modifications help make RNA molecules recognizable for translation and increase protein synthesis efficiency by removing non-coding regions. Different types of RNA undergo specific processing pathways involving nucleases, snoRNAs and other protein complexes.
Secondary protein structure prediction
Secondary structure prediction tools analyze a protein's amino acid sequence to predict its 3D structure and function. These tools use various methods like Chou-Fasman, GOR, neural networks, and hidden Markov models to identify alpha helices and beta sheets based on characteristics like residue propensity values, sequence homology, and patterns in windows of amino acids. Accurate prediction of secondary structure is important for determining a protein's tertiary structure and biological role.
Post translational modification
This document discusses post-translational modifications (PTMs), which are enzymatic modifications of proteins after translation. It describes various types of PTMs like trimming, covalent attachments through phosphorylation, glycosylation, sulfation, methylation, and hydroxylation. The importance of PTMs in regulating protein function and cellular processes is highlighted. Detection methods for PTMs like mass spectrometry and fluorescent staining are also mentioned.
Enzymology namrata
Protein sequencing is a technique to determine the amino acid sequence of proteins. It involves hydrolyzing proteins into amino acids, separating the amino acids, and using techniques like chromatography to identify the order of the amino acids. There are chemical methods like Edman degradation and physical methods like mass spectrometry to sequentially determine the order of amino acids from the N-terminal to C-terminal end of the protein. Understanding amino acid sequences provides insight into protein structure and function.
Protein sequencing
This document discusses protein sequencing techniques. There are three main methods for determining a protein's amino acid sequence: N-terminal sequencing, C-terminal sequencing, and predicting the sequence from DNA sequencing. N-terminal sequencing involves using methods like Edman degradation to sequentially remove amino acids from the N-terminus and identify them. C-terminal sequencing uses carboxypeptidases to sequentially remove amino acids from the C-terminus over time. DNA sequencing allows predicting the protein sequence by first sequencing the gene that encodes the protein. Protein sequencing is important for understanding cellular processes and developing targeted drugs.
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Protein seqencing by kk sahu
Introduction.
History of Protein Sequencing.
Determining Amino Acid Composition.
N-terminal amino acid analysis.
C-terminal amino acid analysis
The Edman degradation reaction.
Limitations of the Edman degradation.
Mass spectrometry
Importance
Conclusion
Reference
Protein sequence determinatiom
This document discusses various methods for determining the amino acid sequence of proteins, including:
- Edman degradation, which sequentially removes amino acids from the N-terminus. Up to 60 amino acids can typically be determined.
- Mass spectrometry techniques like MALDI that help determine the mass and sequence of protein fragments.
- Enzymatic cleavage techniques using enzymes like trypsin to break proteins into smaller fragments that can then be sequenced.
Protein sequencing presentation
Protein sequencing involves determining the order of amino acids in a protein chain. [1] Edman degradation is commonly used for N-terminal sequencing and involves labeling the N-terminal amino acid, removing it, and identifying it through chromatography and mass spectrometry. [2] The protein must first be purified and digested before Edman degradation can begin. [3] Mass spectrometry is used to analyze the separated amino acid derivatives and identify the sequence.
protein sequence analysis
The document discusses various methods for protein sequence analysis, including: (1) N-terminal sequencing using Edman degradation, (2) C-terminal sequencing using carboxypeptidases, (3) DNA sequencing to infer protein sequence, and (4) mass spectrometry. It also covers preparing proteins for sequencing by separating chains and cleaving disulfide bridges, as well as bioinformatics tools like BLAST for comparing sequences. The overall goal of protein sequencing is to determine amino acid sequences to understand protein structure, function, and cellular processes.
Polyadenylation
Polyadenylation is the addition of a poly(A) tail to messenger RNA. The poly(A) tail consists of multiple adenosine monophosphates and plays an important role in mRNA stability, nucleocytoplasmic export, and translation. Cleavage and polyadenylation is controlled by cis elements located upstream and downstream of the polyadenylation site and involves endonuclease cleavage of the pre-mRNA followed by poly(A) polymerase addition of adenines in a template-independent manner. Alternative polyadenylation and cytoplasmic polyadenylation allow for regulation of mRNA expression through differing poly(A) tail lengths.
Tryptophan operon
The tryptophan operon regulates the biosynthesis of tryptophan in E. coli through transcriptional attenuation and repression. It contains five genes encoding the enzymes needed to synthesize tryptophan. When tryptophan levels are high, the tryptophan repressor binds to the operator site, preventing transcription. Additionally, a regulatory region can form a terminator stem-loop structure to halt transcription if tryptophan tRNA levels are high during translation of the leader mRNA sequence. However, if tryptophan levels are low, the terminator structure does not form and transcription of the operon proceeds.
Automated DNA sequencing ; Protein sequencing
This document discusses several methods for DNA and protein sequencing. It describes automated DNA sequencing which is based on the Sanger method but uses fluorescent labels and allows direct computer storage of sequence data. It then discusses various methods for protein sequencing including purification, amino acid composition analysis, N-terminal sequencing using Edman degradation or other methods, C-terminal sequencing, breaking disulfide bonds, cleaving the protein into peptides, ordering peptides by overlap, and locating disulfide bonds. Newer methods discussed are using genomic data and mass spectrometry techniques.
05. Protein Sequencing
There are several key steps to sequencing a protein, including:
1) Separating individual protein chains and breaking disulfide bonds. This can involve reagents like mercaptoethanol or performic acid.
2) Purifying individual protein chains using techniques like electrophoresis or chromatography.
3) Cleaving the purified protein into fragments using enzymes like trypsin or chemicals like cyanogen bromide.
4) Determining the amino acid sequence of each fragment, then combining the overlapping sequences to deduce the full protein sequence.
Protein and nucleic acid sequencing
Protein Sequencing
Introduction
Protein Sequencing
History of Protein Sequencing
Determining Amino Acid Composition
N-terminal amino acid analysis
C-terminal amino acid analysis
Edman degradation
The Edman degradation reaction
Limitations of the Edman degradation
Mass spectrometry
Nucleic Acid Sequencing
Introduction
Nucleic Acid Sequencing
Type of Nucleic Acid Sequencing
DNA Sequencing
Method of DNA Sequencing
Application of DNA Sequencing
DNA Sequencing Institutes
Conclusion
Reference
Gene silencing
Gene silencing is the regulation of gene expression in a cell to prevent the expression of a certain gene. Gene silencing can occur during either transcription or translation and is often used in research.
Protein Folding Mechanism
Folding depends upon sequence of Amino Acids not the Composition. Folding starts with the secondary structure and ends at quaternary structure.
Denaturation occur at secondary, tertiary & quaternary level but not at primary level.
METHODS TO DETERMINE PROTEIN STRUCTURE
This document discusses several methods for determining protein structure: Edman degradation, X-ray crystallography, Western blotting, SDS-PAGE, 2D gel electrophoresis, and isoelectric focusing. Edman degradation involves chemically removing amino acids from the N-terminus of a protein one by one to determine the sequence. X-ray crystallography provides high-resolution 3D structures of proteins. Western blotting identifies specific proteins in a sample using antibodies. SDS-PAGE and 2D gels separate proteins by size and electric charge properties. Isoelectric focusing separates proteins based on their isoelectric points.
Protein protein interaction
Protein-protein interactions are important for many biological processes. There are various types of interactions depending on their composition and duration. Methods to study interactions include yeast two-hybrid, co-immunoprecipitation, affinity chromatography, and chromatin immunoprecipitation. Databases such as IntAct and MINT provide repositories for protein interaction data.
Sequencing of protein ppts
This document discusses protein sequencing techniques. It begins by defining protein sequencing as the technique used to determine the amino acid sequence of a protein. It then provides a brief history of protein sequencing, including that Pehr Edman developed the Edman degradation method in 1947 and Fredrick Sanger determined the complete sequence of insulin in 1955. The document goes on to describe various protein sequencing methods such as Edman degradation, which involves sequential identification of amino acids from the N to C terminus using phenyl isothiocyanate. It notes applications of protein sequencing include understanding protein structure and function, and developing drugs.
Oligonucleotide synthesis - Problems and Challenges
The oligonucleotides are synthesized on solid supports from the 3’-end and the first monomer at this end is normally attached to a CPG(Controlled Pore Glass) or Polystyrene (PS).
Chou fasman algorithm for protein structure prediction
The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time.
A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results.
Chou-Fasman algorithm is an empirical algorithm developed for the prediction of protein secondary structure
Genomics: Organization of Genome, Strategies of Genome Sequencing, Model Plan...
Genomics: Organization of Genome, Strategies of Genome Sequencing, Model Plant Genome Project, Functional Analysis of Genes
Post transcriptional modification ( splicing mechanisms)
Post-transcriptional modifications are important processes that convert primary transcript RNA into mature RNA. These modifications include 5' capping, 3' polyadenylation, and splicing of introns in eukaryotes. The modifications help make RNA molecules recognizable for translation and increase protein synthesis efficiency by removing non-coding regions. Different types of RNA undergo specific processing pathways involving nucleases, snoRNAs and other protein complexes.
Secondary protein structure prediction
Secondary structure prediction tools analyze a protein's amino acid sequence to predict its 3D structure and function. These tools use various methods like Chou-Fasman, GOR, neural networks, and hidden Markov models to identify alpha helices and beta sheets based on characteristics like residue propensity values, sequence homology, and patterns in windows of amino acids. Accurate prediction of secondary structure is important for determining a protein's tertiary structure and biological role.
Post translational modification
This document discusses post-translational modifications (PTMs), which are enzymatic modifications of proteins after translation. It describes various types of PTMs like trimming, covalent attachments through phosphorylation, glycosylation, sulfation, methylation, and hydroxylation. The importance of PTMs in regulating protein function and cellular processes is highlighted. Detection methods for PTMs like mass spectrometry and fluorescent staining are also mentioned.
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Oligonucleotide synthesis - Problems and Challenges
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Chou fasman algorithm for protein structure prediction
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Genomics: Organization of Genome, Strategies of Genome Sequencing, Model Plan...
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Post transcriptional modification ( splicing mechanisms)
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Similar to Protein sequencing
Enzymology namrata
Protein sequencing is a technique to determine the amino acid sequence of proteins. It involves hydrolyzing proteins into amino acids, separating the amino acids, and using techniques like chromatography to identify the order of the amino acids. There are chemical methods like Edman degradation and physical methods like mass spectrometry to sequentially determine the order of amino acids from the N-terminal to C-terminal end of the protein. Understanding amino acid sequences provides insight into protein structure and function.
Protein sequencing
This document discusses protein sequencing techniques. There are three main methods for determining a protein's amino acid sequence: N-terminal sequencing, C-terminal sequencing, and predicting the sequence from DNA sequencing. N-terminal sequencing involves using methods like Edman degradation to sequentially remove amino acids from the N-terminus and identify them. C-terminal sequencing uses carboxypeptidases to sequentially remove amino acids from the C-terminus over time. DNA sequencing allows predicting the protein sequence by first sequencing the gene that encodes the protein. Protein sequencing is important for understanding cellular processes and developing targeted drugs.
sequencingofprotein-151207051238-lva1-app6891.pdf
The document discusses protein sequencing techniques. It begins with an introduction to proteins and protein sequencing. The history of protein sequencing is then outlined, including early work by Edman and Sanger. Methods for determining amino acid composition through hydrolysis, separation, and analysis are described. The mechanisms of Sanger's method using dinitrophenyl reagents and Edman degradation using phenylisothiocyanate are explained. Applications and limitations of protein sequencing are mentioned, along with relevant institutes in India and abroad. The conclusion restates that protein sequencing provides information on structure and function by determining amino acid sequence.
Determination of structure of proteins
A comprehensive presentation on Determination of structure of proteins for MBBS, BDS, B Pharm & Biotechnology students to facilitate self- study.
بروتينات الغذاء
The document discusses the structure of proteins at different levels:
- Primary structure refers to the amino acid sequence in the polypeptide chain. Secondary structure involves hydrogen bonding that forms alpha helices or beta pleated sheets. Tertiary structure describes the overall 3D shape of the folded polypeptide chain. Quaternary structure involves the interactions between multiple polypeptide subunits. The document outlines the forces that stabilize protein structures such as disulfide bonds, hydrogen bonding, and hydrophobic interactions. Proteins are classified based on their composition, which can include modifications like glycoproteins, lipoproteins, or metal-binding groups.
Food proteins
The document discusses the structure of proteins at multiple levels, from primary to quaternary structure. It describes the primary structure as the amino acid sequence linked by peptide bonds. The secondary structure refers to local spatial arrangements, such as alpha helices and beta sheets, formed through hydrogen bonding between peptide bonds. Tertiary structure describes the overall 3D shape of the folded polypeptide chain. Quaternary structure applies to proteins made of multiple polypeptide subunits that assemble into an ordered structure. The document outlines various methods for determining protein structure, including amino acid sequencing and X-ray crystallography.
Peptide Structure Determination by Different Methods
The document describes methods for determining the primary structure of peptides and proteins, including:
1. Classical strategies like amino acid analysis, partial acid hydrolysis to generate fragments, and determining N-terminal/C-terminal residues.
2. The specific example of determining the sequence of bovine insulin B-chain using pepsin and trypsin digestion and identifying overlapping fragments.
3. The Edman degradation method, which sequentially cleaves individual amino acids from the N-terminus, labeling each one for identification to determine the sequence.
Methods for Protein Sequencing.pdf
Edman Degradation is one of the N-terminal amino acid sequence analysis methods for peptide chains/proteins sequencing. The protein is reacted with PTC under weakly basic conditions and then treated with an acid to free the amino-terminal residue of the peptide chain in the form of PTH-AA for subsequent analysis. Peptide Mapping analysis is an effective method for rapidly localizing protein sequences and is a commonly used strategy in protein identification. The method uses mass spectrometry for peptide analysis and compares the obtained spectra with a protein database to obtain amino acid information. De Novo Protein Sequencing is a method based on the enzymatically cleaved peptides that exhibit regular fragmentation in mass spectrometry to obtain amino acid information from the mass differences in regular mass spectral peaks. https://www.creative-proteomics.com/services/proteomics-service.htm
Three Methods for Protein Sequencing
Edman Degradation is one of the N-terminal amino acid sequence analysis methods for peptide chains/proteins sequencing. The protein is reacted with PTC under weakly basic conditions and then treated with an acid to free the amino-terminal residue of the peptide chain in the form of PTH-AA for subsequent analysis. Peptide Mapping analysis is an effective method for rapidly localizing protein sequences and is a commonly used strategy in protein identification. The method uses mass spectrometry for peptide analysis and compares the obtained spectra with a protein database to obtain amino acid information. De Novo Protein Sequencing is a method based on the enzymatically cleaved peptides that exhibit regular fragmentation in mass spectrometry to obtain amino acid information from the mass differences in regular mass spectral peaks. https://www.creative-proteomics.com/services/proteomics-service.htm
peptides proteins ppt
Peptides and proteins are composed of chains of amino acids linked by peptide bonds. Peptides contain 2-50 amino acids while proteins have 50 or more. The primary structure of a peptide or protein refers to the specific sequence of amino acids. This sequence can be determined through amino acid composition analysis and methods like terminal residue analysis and partial hydrolysis, which selectively label and remove amino acids from the termini to reveal the sequence one by one. Determining the primary structure is important as changes in just one amino acid can impact structure and function.
6. aa sequencing site directed application of biotechnology.ppt
Protein sequencing involves an eight step strategy to determine the amino acid sequence of a protein. The steps include separating polypeptide chains, reducing disulfide bonds, determining amino acid composition, identifying terminal residues, cleaving chains into fragments, sequencing the fragments, reconstructing the sequence from overlapping fragments, and determining disulfide bond positions. Frederick Sanger developed the first method for protein sequencing by determining the structure of insulin in 1953. Advances now allow sequencing entire proteins or genomes using techniques like mass spectrometry and determining gene sequences.
Proteinse quencing
This document discusses methods for separating, detecting, and sequencing amino acids and proteins. It describes how chromatography techniques like ion exchange chromatography, HPLC, and gas chromatography can be used to separate amino acids based on their ionic character, affinity to matrices, or volatility. Electrophoresis can also separate amino acids and proteins based on their charge and size. The document then outlines the steps involved in conventional protein sequencing, including separating polypeptide chains, cleaving disulfide bridges, determining chain composition, and fragmenting the chains enzymatically or chemically to determine overlapping sequences.
PRIMARY STRUCTURE OF PEPTIDES
This presentation shows how primary structure of polypeptides can be determined by "End-Group Analysis".
When you digest a sample of your protein with Chymotrypsin you get a.pdf
When you digest a sample of your protein with Chymotrypsin you get a different set of
fragments:
MNY
LMRNF
CDEKICY
LVSKMQL
IGRASTF
HPPRGATW
a) How does the Edman Degradation method work?
b) What is the correct sequence of your protein?
c) What are alternate ways you could have determined the sequence of your protein?
Solution
Edman degradation is a chemical method used for the sequencing of amino acids in a peptide.
This method is developed by Pehr Edman in 1960. In this method, N-terminal is labeled or
cleaved form the peptide and number of residues are identified
The Edman degradation is a very important reaction for protein sequencing, because it allows the
ordered amino acid composition of a protein to be discovered.
Automated Edman sequencers are now in widespread use, and are able to sequence peptides up
to approximately 50 amino acids long. A reaction scheme for sequencing a protein by the Edman
degradation follows:
1.Break anydisulfide bridgesin the protein with areducing agentlike2-mercaptoethanol.
Aprotecting groupsuch asiodoacetic acidmay be necessary to prevent the bonds from re-forming.
2.Separate and purify the individual chains of the protein complex, if there are more than one.
3.Determine the amino acid composition of each chain.
4.Determine the terminal amino acids of each chain.
5.Break each chain into fragments under 50 amino acids long.
6.Separate and purify the fragments.
7.Determine the sequence of each fragment.
8.Repeat with a different pattern of cleavage.
9.Construct the sequence of the overall protein.
Step – 1: The phenyl isothiocyanate reagent attacks and removes the N-terminal amino acid unit
in the form of a substituted thiohydantoin heterocycle. Characteristic hydantoin derivatives of all
the amino acids have been made and catalogued, so identification of the terminal unit is
accomplished easily by comparison.
Step – 2: The terminal amino group adds to the reactive isothiocyanate function to give a
substituted thiourea. This moiety is conformationally mobile, and the sulfur atom may approach
the carboxyl carbonyl of the N-terminal amino acid.
Step – 3: Anhydrous HCl protonates the amide oxygen atom, activating it to nucleophilic attack
by sulfur. Next, a thiazolinone heterocycle incorporating the N-terminal unit is cleaved, leaving
behind a shorter peptide chain. This heterocyclic ring is unstable and undergoes acid-catalyzed
rearrangement to the isomeric thiohydantoin (in the green shaded box).
Digestion into peptide fragments
Peptides longer than about 50-70 amino acids long cannot be sequenced reliably by the Edman
degradation. Because of this, long protein chains need to be broken up into small fragments that
can then be sequenced individually. Digestion is done either by endopeptidases such as trypsin or
pepsin or by chemical reagents such as cyanogen bromide. Different enzymes give different
cleavage patterns, and the overlap between fragments can be used to construct an overall
sequence.
Reaction
The pe.
Q3 W3 Ppt 4.1 Protein Synthesis-1.pdf
The document discusses protein synthesis, which involves transcription and translation. Transcription occurs in the nucleus and involves RNA polymerase making an mRNA copy of a gene from DNA. The mRNA then undergoes processing and modification before being exported to the cytoplasm. Translation happens in the cytoplasm using ribosomes, where the mRNA sequence is read to create a polypeptide chain according to the genetic code. The genetic code is carried by DNA to RNA to proteins, which give organisms their unique traits.
Metabomeeting2008_rev230408-Jack-parag-final1
1. The document describes using both 1H-NMR spectroscopy and GC-MS to profile metabolites in human serum and cell extract samples. This combined approach identified over 90 metabolites in a single sample.
2. NMR could identify 53 metabolites in cell extract and 51 in serum, while GC-MS identified 62 metabolites in cell extract and 67 in serum. Some metabolites were uniquely identified by each technique, with 19 identified in both cell extract samples and 24 in both serum samples.
3. The results demonstrate the complementary nature and advantages of NMR and GC-MS for comprehensive metabolite coverage, though NMR has advantages for simultaneous identification and quantification.
Prabhakar singh ii sem-paper-dna sequencing
Prabhakar singh ii sem-paper-dna sequencingDepartment of Biochemistry, Veer Bahadur Singh Purvanchal Univarsity, Jaunpur
1. Pyrosequencing is a DNA sequencing technique based on detecting pyrophosphate release upon nucleotide incorporation, unlike Sanger sequencing which uses chain termination.
2. In pyrosequencing, only one of the four possible nucleotides is added at a time so light emission determines which nucleotide is incorporated on the template.
3. Next generation sequencing includes 454 pyrosequencing which was the first commercially successful technique and works by parallelizing pyrosequencing on many DNA fragments attached to beads in a picotiter plate.Dna sequencing AND ANALYSIS
Compare and contrast the chemical (Maxam/Gilbert) and chain termination (Sanger) sequencing methods.
List the components and molecular reactions that occur in chain termination sequencing.
Discuss the advantages of dye primer and dye terminator sequencing.
Derive a text DNA sequence from raw sequencing data.
Describe examples of alternative sequencing methods, such as bisulfite sequencing and pyrosequencing.
Maxam/Gilbert chemical sequencing
Sanger chain termination sequencing
Pyrosequencing
Array sequencing
With addition of enzyme (DNA polymerase), the primer is extended until a ddNTP is encountered.
The chain will end with the incorporation of the ddNTP.
With the proper dNTP:ddNTP ratio, the chain will terminate throughout the length of the template.
All terminated chains will end in the ddNTP added to that reaction.
The collection of fragments is a sequencing ladder.
The resulting terminated chains are resolved by electrophoresis.
Fragments from each of the four tubes are placed in four separate gel lanes.
Cycle sequencing is chain termination sequencing performed in a thermal cycler.
Cycle sequencing requires a heat-stable DNA polymerase.
Fluorescent dyes are multicyclic molecules that absorb and emit fluorescent light at specific wavelengths.
Examples are fluorescein and rhodamine derivatives.
For sequencing applications, these molecules can be covalently attached to nucleotides.
In dye primer sequencing, the primer contains fluorescent dye–conjugated nucleotides, labeling the sequencing ladder at the 5′ ends of the chains.
In dye terminator sequencing, the fluorescent dye molecules are covalently attached to the dideoxynucleotides, labeling the sequencing ladder at the 3′ ends of the chains.
Protein sequencing
Protein sequencing determines the order of amino acids in a protein. There are two main methods: Sanger's method uses chemical reagents to degrade the protein into fragments for analysis, while Edman degradation sequentially removes amino acids from the N-terminus. Key steps involve breaking disulfide bonds linking cysteine residues, cleaving the polypeptide chain using proteases or chemicals, then analyzing the fragments by chromatography to determine the amino acid sequence. Protein sequencing is important for understanding protein function and cellular processes, and can provide insights into the evolution of life.
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Peptide Structure Determination by Different Methods
Peptide Structure Determination by Different Methods
6. aa sequencing site directed application of biotechnology.ppt
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When you digest a sample of your protein with Chymotrypsin you get a.pdf
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carbohydrate anabolish
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Basic concept of chromatography
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- 1. Protein sequencing {AMINO ACID SEQUENCING}
- 2. INTRODUCTION Protein sequencing is “the technique for determination of amino acid sequence in a protein”.
- 3. TYPESOF METHODSFORPROTEINSEQUENCING Determination of amino acid composition. N-terminal amino acid analysis C-terminal amino acid analysis Sequencing by proteolytic enzymes Tandem mass spectrometry
- 4. DeterminationofaminoacidCOMPOSITION It gives the information about no. of amino acids present in a polypeptide chain
- 6. N-terminalaminoacidanalysis In this method the amino acid which forms the N-terminal is determined. Methods for amino acid analysis -: 1) Sanger's method 2) Edman degradation method
- 7. Sanger’s method for protein sequencing This method of protein sequencing was developed by “Fred Sanger” in 1958. He determined the sequence of protein insulin. In this method Sanger’s reagent is used i.e. FDNB { 1-fluoro 2,4-dinitro benzene} which reacts with free amino group of N-terminal amino acid.
- 10. Edman degradation method for protein sequencing This method was developed by “Pher Edman” . This chemical method uses Phenylisothiocyanate {k/as Edman reagent} for sequential removal of amino acid residues from the N-terminus of a polypeptide chain.
- 14. Sequencingofproteinsby specificproteolyticenzymes Proteolytic enzymes {proteases} cleaves protein into smaller fragments. Types of proteolytic enzymes -: Endopeptidase Exopeptidase Breaks internal peptide bonds. Breaks terminal peptide bonds Examples Examples Trypsin Chymotrypsin elastin Carboxypeptidase Pepsin Aminopeptidase
- 16. Example-
- 18. A typical spectrum with peaks representing the peptide fragments generated from the sample
- 19. Significanceofproteinsequencing To find out evolutionary history of the protein. To understand the function related to protein Identification of the protein family in which a particular protein belongs to. Prediction of the sequence of the gene encoding the particular protein.
- 20. Submitted to -: Dr.Monika Asthana Dept.of Biotechnology school of life science, DBRAU Agra. Submitted by-: Prashant sharma biotechnologist Thank you