Cell Lysis and Chromatography Techniques

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Questions and Answers

What is the main role of the neutralization solution in DNA extraction?

  • To introduce high salt concentrations
  • To enhance the solubility of genomic DNA
  • To degrade plasmid DNA into smaller fragments
  • To promote re-annealing of denatured DNA (correct)

Why is the washing step with an ethanol-rich solution necessary in the DNA isolation process?

  • To remove contaminants and excess salts (correct)
  • To enhance the binding of DNA to the silica membrane
  • To adjust the pH of the solution
  • To increase the yield of plasmid DNA

What would happen if you mix the lysis solution with E. coli vigorously?

  • It would cause the DNA to remain in the pellet
  • It would enhance the yield of DNA
  • It could shear the chromosomal DNA (correct)
  • It would facilitate the separation of plasmid DNA

During the separation of plasmid and genomic DNA, what is primarily responsible for capturing plasmid DNA on the silica membrane?

<p>Formation of salt bridges (A)</p> Signup and view all the answers

How was spinach DNA lysed in the mentioned experiment?

<p>By grinding into a fine powder with liquid nitrogen (C)</p> Signup and view all the answers

What is a lysate?

<p>Fluid containing lysed cells (B)</p> Signup and view all the answers

Which method is NOT commonly used for lysing cells?

<p>Chemical reaction with acids (C)</p> Signup and view all the answers

Why is it possible to purify nucleic acids at room temperature?

<p>It minimizes the deterioration of proteins (C)</p> Signup and view all the answers

What are proteases?

<p>Enzymes that cut proteins into smaller pieces (B)</p> Signup and view all the answers

What is the purpose of centrifugation in nucleic acid extraction?

<p>To separate nucleic acids from lysed cellular components (A)</p> Signup and view all the answers

What is the common drawback of purifying nucleic acids by electrophoresis?

<p>Different nucleic acids cannot be separated effectively (B)</p> Signup and view all the answers

Which of the following is NOT a method of chromatographic separation?

<p>Sonication chromatography (B)</p> Signup and view all the answers

How can agarose gel electrophoresis aid in nucleic acid purification?

<p>It allows for physical extraction of desired nucleic acid fragments (D)</p> Signup and view all the answers

What does specific activity measure in an enzyme sample?

<p>The ratio of enzyme activity to protein amount (B)</p> Signup and view all the answers

What is the primary method used to evaluate the purity of a protein preparation?

<p>Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (D)</p> Signup and view all the answers

What happens to the gel when a pure sample of protein is run through SDS-PAGE?

<p>A single band will appear (C)</p> Signup and view all the answers

What are plasmids primarily known for?

<p>Carrying genetic information that can confer advantages like antibiotic resistance (D)</p> Signup and view all the answers

Which component in the resuspension step is responsible for maintaining the pH?

<p>TRIS (C)</p> Signup and view all the answers

What is the main purpose of EDTA in the resuspension process?

<p>Sequestering cations to protect DNA (A)</p> Signup and view all the answers

What occurs during the lysis step of plasmid purification?

<p>Cells are ruptured using NaOH and SDS (B)</p> Signup and view all the answers

Which method allows plasmids to spread to daughter cells?

<p>Conjugation, transduction, or transformation (D)</p> Signup and view all the answers

Flashcards

Cell Lysis

The process of breaking down cells and releasing their internal components like organelles, cytosol, and dissolved salts into a liquid mixture.

Lysate

A fluid containing lysed cells, essentially a mixture of cellular components.

Proteases

Enzymes that break down proteins into smaller pieces.

Size Exclusion Chromatography

A technique used to separate molecules based on their size, with larger molecules moving slower through a porous gel matrix.

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Ion-Exchange Chromatography

A technique used to separate molecules based on their charge, using an electric field to attract or repel charged molecules.

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Electrophoresis

A technique for separating molecules based on their size and charge, using an electric field to move them through a gel matrix.

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Agarose Gel Electrophoresis

A type of gel electrophoresis commonly used for separating DNA and RNA fragments based on their size.

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Nucleic Acid Extraction

A technique for purifying DNA and RNA by selectively degrading and removing non-nucleic acid components.

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Lysis Solution

A solution used in cell lysis that contains detergents (like SDS) and a strong base (like NaOH) to break down the cell membrane and disrupt proteins.

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Neutralization Solution

A solution that neutralizes the strong base in the lysis solution, allowing DNA to re-form its double helix structure.

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Centrifugation

A technique used to separate components based on their density, with denser components settling at the bottom.

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Plasmid DNA

A small, circular piece of DNA found in bacteria, often used for genetic engineering.

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SDS-PAGE

A method used to evaluate the purity of a protein preparation by separating proteins based on their size using an electric field and a porous gel.

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Specific Activity

The ratio of enzyme activity to the amount of protein in a sample. Higher specific activity indicates a purer enzyme preparation.

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Plasmids

Small, circular, non-genomic DNA molecules found in many bacteria. They can carry genes that provide benefits to the host, such as antibiotic resistance, and can transfer between bacteria.

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TRIS

A chemical that helps maintain the correct pH of a solution, preventing unwanted changes in the pH during experiments.

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EDTA

A chemical that binds to and chelates (removes) metal ions, often used to prevent DNA degradation by enzymes that require metal ions for activity.

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Glucose

A chemical that maintains the osmotic pressure of a solution, preventing cell damage due to changes in water concentration.

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RNAase

An enzyme that breaks down RNA molecules. Used in plasmid purification to remove any RNA contamination.

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Study Notes

Cell Lysis and Lysate

  • Lysate is a fluid containing lysed cells
  • Cell lysis releases cellular components (organelles, cytosol, dissolved salts)
  • Methods of cell lysis include: grinding in a mortar and pestle, freeze/thaw in liquid nitrogen, sonification (high-frequency waves), membrane solubilization by detergents.
  • Enzymatic degradation of the cell wall (using lysozyme) can lyse bacterial cells like E. coli
  • Lysis can be performed at room temperature or 4°C
  • Nucleic acid purification can be done at room temperature because harsh cell lysis conditions don't damage nucleic acids as much.

Chromatography

  • Size exclusion chromatography
  • Ion-exchange chromatography
  • High-performance liquid chromatography
  • Capillary electrophoresis are methods used for chromatographic separation

Nucleic Acid Extraction

  • Kits extract and purify nucleic acids by selectively degrading/precipitating non-nucleic acid molecules, then removing these molecules by centrifugation or washing.

Electrophoresis

  • Electrophoresis separates charged molecules (like nucleic acids) in an electric field based on size.
  • Agarose gel electrophoresis is a common method for partially purifying nucleic acids.

Protein Purification

  • Specific activity measures enzyme activity relative to protein amount.
  • SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) is used to evaluate protein purity. Proteins are separated by mass on a porous gel in an electric field. Pure samples will only show one band.

Plasmids

  • Plasmids are small, non-genomic, double-stranded nucleic acids (usually DNA) found in microorganisms.
  • Plasmids contain genes desirable for the host cell (e.g., antibiotic resistance)
  • Plasmids can directly transfer genetic information between different microorganisms through mechanisms like conjugation, transduction, or transformation.

Plasmid Purification

  • Mini/maxi prep are common procedures for plasmid purification from E. coli via procedures like resuspension, lysis, neutralization, binding, washing and elution.

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