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Biochemistry laboratory manual for undergraduates
1 online resource (186 pages) : illustrations (some color)
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 classic biochemistry techniques such as HPLC or enzyme kinetics and is complete with numerous problem sets relating to each topic.
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.
Timea Gerczei, Scott Pattison ; managing editor, Anna Rulka.
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Biochemistry laboratory manual for undergraduates : an inquiry-based approach
Warsaw, [Poland] ; Berlin, [Germany] : De Gruyter Open, ©2014