يتم فصل بروتينات العينة باستخدام الفصل الكهربائي
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protein stability
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2) Protein stability refers to a protein maintaining its native folded conformation rather than becoming denatured. Stability depends on a balance of forces and is important for protein function.
3) Factors that influence protein stability include pH, ligand binding, disulfide bonds, and interactions within the protein and between the protein and solvent. Chaperone proteins and proteases also help maintain stability in cells.
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swiss-prot<bioinformatics>
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EMBL
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- Protein Data Bank (PDB) which contains 3D protein structures determined via X-ray crystallography or NMR.
- Swiss-Prot which contains manually annotated protein sequences and functions.
- TrEMBL which supplements Swiss-Prot with automatically annotated translations of DNA sequences.
Protein databases are important for comparing proteins, understanding relationships between proteins, and aiding the study of new proteins. Searching databases is often the first step in protein research.
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protein data bank
The Protein Data Bank (PDB) is a single worldwide database that stores 3D structural data of proteins and nucleic acids. It is operated by Rutgers University, the San Diego Supercomputer Center, and the Research Collaboratory for Structural Bioinformatics. The PDB is freely accessible online and contains over 76,000 biomolecular structure entries as of 2011. It uses a common file format to represent structural data and is updated weekly as new entries are submitted by researchers.
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This document discusses various enzymes used for genetic engineering and DNA manipulation. It describes restriction endonucleases and DNA ligase which cut and join DNA fragments. It also discusses other DNA modifying enzymes like nucleases which degrade DNA, and polymerases which synthesize DNA copies. Specific enzymes covered in detail include DNA polymerase I, T4 DNA polymerase, T7 DNA polymerase, terminal transferase, T4 DNA ligase, and T4 RNA ligase.
Flow cytometry and fluorescence activated cell sorting (FACS)
Flow cytometry is a technology that analyzes physical and chemical characteristics of particles in fluid as they pass through a laser. It is used for cell counting, sorting, biomarker detection, and protein engineering. The basic principle is passing cells in single file past a laser for detection, counting, and sorting. It has applications in leukocyte analysis, DNA analysis, detecting enzymatic deficiencies, minimal residual disease, detecting autoantibodies, fetal-maternal hemorrhage quantification, and reticulocyte analysis.
Genomic in situ Hybridization
Genomic in situ hybridization (GISH) is a cytogenetic technique that allows radiolabeling of genomic DNA within cells, allowing visualization under a fluorescence microscope. GISH was developed in 1986 for animal hybrid cell lines and 1987 for plant studies. It involves extracting and radiolabeling genomic DNA from one organism as a probe to target and hybridize to similar genomic regions of another organism. Unhybridized regions can then be stained, allowing visualization of probe-target complexes and unlabeled regions. GISH provides quick, sensitive, and informative results for establishing phylogenetic relationships and identifying hybridized genomes.
Protein data bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
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TrEMBL is a computer-annotated protein sequence database created by Rolf Apweiler that contains translations of coding sequences from nucleotide databases like EMBL and GenBank as well as protein sequences from literature or submitted directly. The database provides automated classification and annotation to enrich the protein sequences.
Nucleic acid sequencing- introduction,DNA sequencing
DNA sequencing is a fundamental process in biotechnology that determines the order of nucleotides in a DNA molecule. There are two main methods: the chemical method developed by Maxam and Gilbert, and the enzymatic method developed by Sanger and Coulson. DNA sequencing involves degrading DNA fragments into smaller pieces, sequencing the individual fragments, and ordering the fragments to determine the full DNA sequence.
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protein stability
1) G.N. Ramachandran created the Ramachandran plot in 1963, which is an essential tool for understanding protein structure. The plot analyzes allowed regions of phi and psi dihedral angles in peptide units.
2) Protein stability refers to a protein maintaining its native folded conformation rather than becoming denatured. Stability depends on a balance of forces and is important for protein function.
3) Factors that influence protein stability include pH, ligand binding, disulfide bonds, and interactions within the protein and between the protein and solvent. Chaperone proteins and proteases also help maintain stability in cells.
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Cyclic systems are ubiquitous, in nature and synthetic chemistry. Establishing an understanding of the shape preferences (e.g., strain and energetics) regarding representative cyclic models is a powerful tool in conformational analysis. The expanded review of fundamental cycloalkanes can further assist in preferential conformational analysis of associated derivatives.
Contributed by: Roland Jones, Dane Brankle, and Peter Stevenson, University of Utah, 2015
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Nucleosomes are the fundamental repeating subunits of eukaryotic chromatin that package DNA into a compact structure. They are composed of 146 base pairs of DNA wrapped around an octamer of histone proteins, resembling beads on a string. This represents the first order of DNA compaction. Higher orders of compaction involve the nucleosomes winding further to form solenoid fibers, scaffold loops, chromatids, and finally full chromosomes. Nucleosomes allow the long DNA molecules to fit within cell nuclei while also regulating genetic expression.
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Lab 7 dna fingerprinting and gel electrophoresis fall 2014
يتم فصل بروتينات العينة باستخدام الفصل الكهربائي
- 1. يتم فصل بروتينات العينة باستخدام الفصل الكهربائي . فصل البروتينات قد يكون باستخدام النقطة متوازنة الكهربة Isoelectric point (pI) ، ، الوزن الجزيئي، الشحنة الكهربائية أو مجموعة من هذه العوامل. طبيعة الفصل تعتمد على طريقة .معالجة العينة وطبيعة الهلام إلى حد الآن، الطريقة الأكثر شيوعاً للفصل الكهربائي للهلام توظف هلامات متعدد الأكريلامايد polyacrylamide ومحاليل تحتوي على كبريتات دوديكل الصوديوم Sodium Dodecyl Sulfate (SDS). أي ) الفصل الكهربائي لهلام كبريتات دوديكل الصوديوم متعددالأكريلامايد SDS-Polyacrylamide Gel Electrophoresis) تحافظ على سلسلة البروتيات في حالة مفككة denatured state حالماً يتم معالجتهم مع عوامل إختزال قوية للقضاء على الأشكال الثانوية والثالثية. )مثل تحويل الروابط ثنائية الكبريت S-S إلى SH و SH) و بذلك يسمح لفصل البروتينات حسب وزنهم الجزيئي. يتم تغطية البروتينات في العينة بكبريتات دوديكل الصوديوم السالبة الشحنة ونقلها إلى القطب الكهربائي الموجب الشحنة خلال شبكة الأكريلامايد في الهلام. البروتينات الصغيرة تهاجر أسرع خلال هذه الشبكة وبذلك يتم فصل البروتينات حسب الحجم )عادة ما يتم قياسها بالكيلودالتون، kD ، kiloDaltons). تركيز الأكريلامايد يحدد دقة الهلام - كلما زاد تركيز الأكريلامايد كلما زادت دقة البروتينات ذات الأوزان الجزيئية .العالية. البروتينات تهاجر ببعد واحد خلال الهلام لأغلب اللطخات
- 2. الهلام ويلاحظ فيه الدرج بصورة حزم زرقاء اللون بسبب الصبغة الزرقاء كوماسي بلو Coomassie Blue يتم تحميل العينات في آبار في الهلام. يتم حفظ إحدي الأسطر للـ درج أو العلامات، وهما خليط متوفر تجارياً من عدة بروتينات معروفة الوزن الجزيئي، عادة ما تكون مصبوغة لكي تظُهر حزم ملونة مرئية. أحد الأمثلة على الدرج، هو درج الأوزان الجزيئية الكامل المدى لشركة GE ( كما في الشكل(. عندما يتم تطبيق فرق الجهد على الهلام، تهاجر البروتينات ضمنه بسرع مختلفة. هذه المعدلات الزمنية المختلفة للتقدم )حركات الفصل الكهربائي .المختلفة( تفُصل إلى حُزم ضم كل سطر من الممكن أيضاً استخدام الفصل الكهربائي ثنائي الأبعاد الذي يفصل البروتينات من عينة واحدة في بُعدين. البروتينات تفصل بحسب النقطة متوازنة الكهربة )تركيز أيونات الهيدروجين pH الذي تكون فيه الشحنة متعادلة( في البعد الأول، وبحسب الوزن الجزيئي في .البعد الثاني النقل
- 3. من أجل جعل الوصول للبروتينات أسهل للأكتشاف بالأجسام المضادة، يتم نقلهم من الهلام إلى غشاء مصنوع من النيتروسيليوز أو الـ PVDF. يتم وضع هذا الغشاء فوق الهلام، ووضع مجموعة من طبقات أوراق الترشيح فوق ذلك. ثم يتم وضع الطبقات كلها في محلول يقوم بالتنقل إلى الأعلى عبر الأوراق بالخاصية الشعرية Capillary action .، جالباً البروتينات معه إلى الغشاء ومن الطرق الأخرى لنقل البروتينات تدعى اللطخة الكهربائية .وتستخدم تياراً كهربائي لسحب البروتينات من الهلام إلى الغشاء البروتينات الآن نُقلت من داخل الهلام إلى سطح غشاء من النيتروسيليلوز أو PVDF مع ثباء الترتيب التي كانت البروتينات عليه داخل الهلام. ويكون ناتج هذه العملية، هو عرض البروتينات على سطح رقيق للإكتشاف )أنظر أسفلاً(. كلا نوعي الغشاء نيتروسيليلوز أو ( PVDF) يتم إختيارهم لخاصية الإلتصاق غير المحدد بالبروتيات )أي أنهم يلتصقون بأي بروتين بصورة متساوية(. إلتصاق البروتينات مبني على تفاعلات مصابة بفوبيا الماء hydrophobic interactions) ، بالإضافة إلى التفاعلات المشحونة بين الغشاء والبروتين. إن أغشية النيتروسيليلوز تكون أقل كلفة من الـ PVDF ، ولكنهم هشة أكثر ولا تستطيع الوقوف لتحقيقات مجددة reprobes [كثيرة.] 3 التأثير الكلّي والموحّد لنقل البروتين من الهلام إلى الغشاء يمكن التأكد منه بصبغ الغشاء بصبغة كوماسي Coomassie أو بونسو س Ponceau S. كوماسي هي الصبغة الأكثر حساسية
- 4. من الصبغتين، بالرغم من أن سهولة ذوبان بونسو س في الماء [تجعله أسهل للإزالة لاحقاً والتحقق من الغشاء كما في أدناه.] 4