DNA Extraction Lab Report

Introduction

The extraction of DNA from biological samples stands as a cornerstone process in both molecular biology and biotechnology, facilitating a myriad of research endeavors and practical applications. In the context of this experiment, our primary objective was to extract DNA not only from strawberries but also from an alternative food source, thereby broadening the scope of our investigation and enriching our understanding of DNA extraction techniques. Strawberries were selected as one of the biological samples due to their remarkable abundance of chromosomes, which serve as reservoirs for DNA molecules.

The inherent richness of DNA content in strawberries not only simplifies the extraction process but also ensures a robust yield of genetic material for subsequent analysis. By embarking on this experimental journey, we embarked on a quest to unravel the intricacies of DNA structure and function, delving deep into the molecular landscape to visualize and comprehend the underlying characteristics of this essential biomolecule. Through meticulous experimentation and thoughtful analysis, we sought to illuminate the complex interplay of nucleic acids, proteins, and cellular components involved in DNA extraction, paving the way for new insights and discoveries in the realm of molecular biology.

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Review Pre-Lab Questions

DNA is primarily found in the nucleus of eukaryotic cells, which includes both plant and animal cells. In plant cells, DNA is also present in other organelles such as chloroplasts and mitochondria. Plant cells can be identified by the presence of a cell wall and chloroplasts, which are responsible for photosynthesis. We focus on plant cells in this lab because they offer a rich source of DNA, facilitating the extraction process.

Materials

• Heavy-duty Ziploc bag
• Strawberry
• 10 mL DNA extraction buffer (salt and soap solution)
• Coffee filter
• Funnel
• Beaker
• Glass rod (or finger)
• 20 mL ethanol or isopropyl alcohol

Procedure

1. Strawberry Preparation:
   • Placing a single strawberry in a Ziploc bag marks the initial step in the extraction process. This step serves to contain the biological sample while also providing a conducive environment for subsequent manipulation.
2. Mashing and Grinding:
   • The act of smashing and grinding the strawberry within the Ziploc bag for a duration of 2 minutes is pivotal for disrupting the structural integrity of the plant cells. Careful manipulation with fists and fingers ensures thorough maceration of the tissue, facilitating the release of cellular contents without rupturing the bag's integrity.
3. Addition of Extraction Buffer:
   • Introducing the extraction buffer, a solution containing salts and soap, serves as a critical catalyst for DNA liberation. The buffer aids in breaking down cellular membranes, solubilizing lipids, and facilitating the release of nucleic acids from cellular compartments.
4. Kneading and Mixing:
   • Kneading and mushing the strawberry within the bag post-buffer addition for an additional minute further enhances the disruption of cellular structures and promotes the homogenization of the sample. This mechanical agitation aids in maximizing the yield of DNA extracted from the sample.
5. Assembly of Filtration Apparatus:
   • Assembling the filtration apparatus marks a pivotal transition in the extraction process, where the crude strawberry slurry is subjected to filtration to separate particulate matter from the DNA-containing supernatant. The funnel and coffee filter combination serve as effective means to trap cellular debris while allowing the free flow of liquid.
6. Ethanol Addition and Layer Separation:
   • The gradual addition of cold ethanol to the filtered extract induces the precipitation of DNA from solution. This step capitalizes on the differential solubility of DNA in ethanol compared to the aqueous phase, leading to the formation of a distinct DNA pellet at the interface of the two layers. Observing the separation of layers provides valuable insights into the efficiency of DNA precipitation.
7. Observation of Interface:
   • Dipping a glass rod or finger into the beaker containing the ethanol-strawberry extract mixture allows for the visual inspection of the interface between the DNA precipitate and the ethanol layer. This observation serves to confirm the successful extraction of DNA and provides an opportunity for qualitative assessment of the extracted material.
8. Repeat Procedure for Alternative Food Choice:
   • Replicating the entire extraction procedure with an alternative food source extends the scope of the experiment and enables comparative analysis. This step underscores the versatility of the extraction method and its applicability across diverse biological samples.

Part I: Questions

1. The purpose of mashing up the strawberry is to break open the cells, releasing their contents, including DNA.
2. The extraction buffer, containing salt and soap, helps in breaking up proteins and dissolving cell membranes, aiding in the release of DNA.
3. Soap acts as a surfactant, allowing the removal of dirt and oils by forming micelles that trap these substances, similar to how it removes contaminants when washing hands.
4. The filter separates solid components from the liquid solution, allowing the DNA to pass through while retaining cellular debris.

Part II: Observations

Upon adding ethanol to the strawberry extract, a cloudy layer forms at the interface between the two liquids. This cloudy layer contains DNA precipitates, which become visible as stringy strands. The DNA strands resemble fine threads or fibers, forming clumps within the alcohol layer.

Part III: Conclusions and Analysis

Matching Procedure with Function

• Filter strawberry slurry through coffee filter: To precipitate DNA from solution
• Mush strawberry with salty/soapy solution: Break up the cells
• Initial smashing and grinding of strawberry: Separate components of the cell
• Addition of ethanol to filtered extract: Precipitate DNA from solution

Discussion

When ethanol is added to the filtrate, DNA precipitates out of solution due to its insolubility in alcohol. This forms visible strands or clumps, allowing us to observe the extracted DNA. DNA is a macromolecule that carries genetic information and is present in all living or once-living cells. The successful extraction of DNA from strawberries demonstrates that DNA is present in the foods we eat, highlighting its ubiquity in biological organisms.

Traits expressed in strawberries, controlled by genes found on chromosomes, include fruit color, taste, and size. Scientists extract DNA from organisms for various purposes, including genetic research, forensic analysis, and biotechnological applications. The variability in DNA sequences among individuals means that everyone's DNA is unique, with slight differences in nucleotide sequences.

It is unlikely that all DNA was extracted from the strawberry due to factors such as incomplete cell lysis or loss during filtration. Sources of error include inadequate mixing, incomplete grinding of the strawberry, and variations in ethanol concentration. To improve the experiment, we would ensure thorough mixing and grinding, use standardized procedures, and calibrate ethanol concentrations.

Comparing DNA extraction from strawberries and alternative foods reveals variations in yield and purity. Observations may include differences in DNA strand visibility, clumping, or presence of impurities. These differences reflect variations in cellular structure and DNA content among different food sources.

Conclusion

In conclusion, the DNA extraction experiment stands as a pivotal endeavor that not only offered valuable insights into the intricate structure and properties of DNA but also provided a hands-on learning experience in molecular biology techniques. Through the extraction of DNA from strawberries and alternative food sources, we embarked on a journey of exploration, unraveling the secrets hidden within the genetic blueprint of living organisms.

The practical application of molecular biology methodologies not only broadened our scientific horizons but also fostered a deeper appreciation for the complex processes governing life at the molecular level. As we navigated through each step of the extraction procedure, from macerating strawberries to observing the interface between ethanol and DNA precipitate, we gained firsthand knowledge of the intricacies involved in isolating genetic material. By mastering DNA isolation methods, we equip ourselves with a powerful toolset essential for advancing scientific research, understanding genetic disorders, and engineering novel biotechnological solutions.

References

• Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. Chapter 4, DNA and Chromosomes. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26823/
• Weaver RF. Molecular Biology. 5th edition. Boston: McGraw-Hill Higher Education; 2017. Chapter 5, The Structure and Function of DNA. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21154/