Biochemistry laboratory manual for undergraduates : an inquiry-based approach /

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Biochemistry Laboratory Manual for undergraduates is the first textbook on the market that uses a highly relevant model, antibiotic resistance, to teach seminal topics of biochemistry and molecular biology. Inclusion of a research project does not entail a limitation: this manual includes all classi...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Autores principales: Gerczei, Timea (Autor), Pattison, Scott, 1947- (Autor)
Otros Autores: Rulka, Anna (Editor )
Formato: Electrónico eBook
Idioma:Inglés
Publicado: Warsaw [Poland] ; Berlin [Germany] : De Gruyter Open, 2014.
Temas:
Biochemistry > Laboratory manuals.
Molecular biology > Laboratory manuals.
Drug resistance in microorganisms > Laboratory manuals.
Biochimie > Manuels de laboratoire.
Biologie moléculaire > Manuels de laboratoire.
SCIENCE > Life Sciences > Biochemistry.
Biochemistry
Drug resistance in microorganisms
Molecular biology
Molecular Biology
Laboratory Manual
Laboratory manuals
Laboratory manuals.
Manuels de laboratoire.
Acceso en línea:Texto completo
Tabla de Contenidos:
  • Machine generated contents note: 1. Introducing the Bacterial Antibiotic Sensor Mini Project
  • 1.1. What are Antibiotics?
  • 1.2. What is Bacterial Antibiotic Resistance?
  • 1.3. How Do the Bacteria Detect Antibiotics In Its Environment?
  • 1.4. How Does the ykkCD Sensor Exert Its Function?
  • 1.5. What Do We Do During the Mini Project?
  • 2. Identifying Conserved Elements in the Toxin Sensor and Designing Mutants to Test Whether They are Important for Function
  • 2.1. Learning Objectives
  • 2.2. Mini Project Flowchart
  • 2.3. Why is Sequence Conservation Important for Macromolecule Function, and How Do We Determine This?
  • 2.4. Review of Nucleic Acid Properties
  • 2.5. What is Bioinformatics?
  • 2.6. Identifying Conserved Sequence Elements (Invariable Blocks)
  • 2.7. Identifying Conserved Structural Elements
  • BLAST Prelab
  • Identifying Invariable Blocks in the Toxin Sensor Lab Report Outline and Point Distribution
  • BLAst Problem Set
  • Protein Properties Worksheet.
  • Note continued: 3. Designing Primers for Site-Directed Mutagenesis
  • 3.1. Learning Objectives
  • 3.2. Mini Project Flowchart
  • 3.3. What is PCR? What are polymerases?
  • 3.4. PCR Amplification of a Desired DNA Segment Of The Genome (Conventional Cloning)
  • 3.5. Quickchange Site-Directed Mutagenesis
  • Prelab Questions for Primer Design Lab
  • Introduction to Primer Design Lab Report Outline and Point Distribution
  • 4. Performing Site-Directed Mutagenesis
  • 4.1. Learning Objective
  • 4.2. Mini Project Flowchart
  • 4.3. Review of Nucleic Acid Structure
  • 4.4. How do Polymerases Work?
  • 4.5. Polymerase Chain Reaction (PCR) in Practice
  • 4.6. Why Did PCR Only Become Widely Available in the 1980s?
  • 4.7. Applications of PCR
  • Prelab Questions for Site-Directed Mutagenesis
  • Site-directed Mutagenesis Lab Report Outline and Point Distribution
  • PCR Worksheet.
  • Note continued: 5. Purifying Mutant Toxin Sensor DNA from Bacterial Cells and Evaluating its Quality Using Agarose Gel Electrophoresis and UV Spectroscopy
  • 5.1. Learning Objective
  • 5.2. Mini Project Flowchart
  • 5.3. Purification of Plasmid DNA from Bacterial Cell (Plasmid Prep)
  • 5.4. Transformation
  • 5.5. Cell Growth
  • 5.6. Purification of Plasmid DNA from Bacterial Cells
  • 5.7. Agarose Gel Electrophoresis
  • 5.8. Application of Agarose Gel Electrophoresis
  • 5.9. DNA Quality Control Using UV Spectroscopy
  • Prelab Questions for Plasmid Prep
  • DNA Purification Lab Report Outline and Point Distribution
  • Electrophoresis Problem Set
  • 6. Preparing DNA Template for Mutant RNA Sensor Synthesis Using a Restriction Endonuclease
  • 6.1. Learning Objective
  • 6.2. Mini Project Flowchart
  • 6.3. Synopsis
  • 6.4. How do Restriction Endonucleases Work?
  • 6.5. How do Restriction Enzymes Achieve Million-Fold Specificity?
  • Note continued: 6.6. How Do We Judge Whether The Plasmid DNA is Successfully Linearized?
  • 6.7. What are We Going to do in the Lab?
  • Prelab Questions for DNA Linearization
  • DNA Linearization Lab Report Outline and Point Distribution
  • Worksheet
  • Restriction Endonucleases
  • Cloning Experiment Design
  • Worksheet
  • 7. Synthesizing the ykkCD Mutant Toxin Sensor RNA in vitro
  • 7.1. Learning Objective
  • 7.2. Mini Project Flowchart
  • 7.3. How do RNA Polymerases Work?
  • 7.4. How Does Transcription Start?
  • 7.5. How Does Transcription End?
  • 7.6. Transcription in Practice
  • 7.7. What Are We Going To Do Today?
  • Prelab Questions for RNA Transcription
  • RNA Synthesis Lab Report Outline and Point Distribution
  • 8. Purifying the ykkCD Mutant Toxin Sensor RNA and Evaluating its Purity Using Denaturing Page and UV spectrometry
  • 8.1. Learning Objective
  • 8.2. Mini Project Flowchart
  • 8.3. RNA Purification Methods
  • 8.4. Denaturing Page
  • 8.5. Phenol/chloroform Extraction.
  • Note continued: 8.6. Column Purification
  • Prelab Questions for RNA Purification
  • RNA Purification Lab Report Outline and Point Distribution
  • 9. Evaluating the Ability of the ykkCD Toxin Sensor to Recognize the Antibiotic Tetracycline Using Fluorescent Quenching
  • 9.1. Learning Objective
  • 9.2. Mini Project Flowchart
  • 9.3. What is Binding Affinity (KD)?
  • 9.4. What is Fluorescence?
  • 9.5. How Do We Measure Binding Affinity of the Tetracycline-Sensor RNA Complex?
  • 9.6. How do We Evaluate Binding Affinity?
  • 9.7. How do We Analyze Data?
  • Analysis of Binding Experiments
  • Binding Assays Prelab
  • YkkCD sensor RNA
  • Tetracycline Binding Lab Report Outline and Point Distribution
  • 10. Evaluating Antibiotic Binding to Blood Serum Albumin Using Fluorescence Spectroscopy
  • 10.1. Learning Objectives
  • 10.2. Biological Role of Serum Albumin
  • 10.3. Fluoroquinoline Antibiotics
  • 10.4. Protein Structure, Aromatic Amino Acids, and Fluorescence.
  • Note continued: 10.5. Measuring Fluorescence
  • 10.6. Synchronous Spectroscopy
  • 10.7. Data Analysis
  • Albumin
  • Levofloxacin Binding Lab Report Outline and Point Distribution
  • 11. Understanding the Importance of Buffers in Biological Systems
  • 11.1. Learning Objectives
  • 11.2. Introduction
  • 11.3. Buffer Preparation
  • Prelab for the Buffer Lab
  • Buffer Lab Report Outline and Point Distributions
  • Buffer Problem Set
  • 12. Molecular Visualization of an Enzyme, Acetylcholinesterase
  • 12.1. Learning Objectives
  • 12.2. Introduction and Background
  • 12.3. Introduction to Molecular Visualization Using the Program Chimera
  • 12.4. Analysis of Acethylcholinesterase Using the Computer Visualization Program Chimera
  • Molecular Visualization of Acethylcholinesterase Prelab
  • Acetylcholinesterase Characteristics Worksheet
  • 13. Determining the Efficiency of the Enzyme Acetylcholine Esterase Using Steady-State Kinetic Experiment
  • 13.1. Learning Objective.
  • Note continued: 13.2. Measuring the Catalytic Efficiency of Acetylcholinesterase
  • 13.3. Running a Steady-State Enzyme Kinetics Experiment
  • 13.4. Designing a Steady-State Experiment
  • Prelab for AchE Kinetics
  • Lab Report Outline and Point Distribution
  • Enzyme Kinetics Worksheet
  • 14. Separation of the Phosphatidylcholines Using Reverse Phase HPLC
  • 14.1. Learning Objective
  • 14.2. Phosphatidylcholines
  • 14.3. High Performance Liquid Chromatography (HPLC)
  • 14.4. Quantifying Chromatography
  • HPLC of Lipids Prelab
  • HPLC of Phosphatidylcholines Lab Report Outline and Point Distribution
  • HPLC Problem Set.

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