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September 8th, 2023
Delving into the Genome: Unraveling the Intricacies of DNA and Its Influence on Our Genetic Makeup and Inherited Characteristics
Embarking into the intricacies of the genome, exploring the profound role of DNA in shaping our genetic blueprint and inheritance of our traits, and exploring how the structure of DNA molecules encodes the information that dictates both physical and biological attributes.
AUTHOR
Mr. Calvin Musk, Chief executive officer at Calvin Industries Corporation and President of Calvin State University
Image Source : University of Oxford, Time to step inside your DNA
Learning Intention
I understand the fundamental structure of DNA, its role in genetic information storage and transfer, and its significance in the fields of genetics, molecular biology, and biotechnology.
What is DNA?
Imagine having a full book in your cells. This book determines your future. Your genes and inheritance are all inside of this book. A book that consists of 3.2 billion letters. This book is known as DNA. In short, DNA is a long molecule that contains each person's unique genetic code. It holds the critical instructions for building the proteins essential for the body's function. Found in the nucleus of a cell, DNA is a molecule that is found in ALL living organisms, ranging from plants to animals, to microorganisms, to us. DNA serves as the genetic blueprint for the development, functioning, and reproduction of these organisms. DNA consists of hereditary information that gets passed from one generation to the next and is responsible for the diversity we see on our planet.
Source: G.C
Did you know THIS behind the history of DNA?
DNA was 1st discovered in 1869 but little was known about its role 1944
Canadian scientist Oswald Avery confirmed DNA was the material of inheritance.
James Watson and Francis Crick unraveled the structure of DNA and showed how the same chemical building blocks could carry out a wide range of instructions.
Source: The Discovery of DNA - the molecule of life (yourgenome.org).
What makes up our DNA?
Nucleotides are chemical building units that make up DNA. A phosphate group, a sugar group, and one of four different nitrogen bases make up these building components. Nucleotides are joined together into chains, with the phosphate and sugar groups switching places, to create strands of DNA.
Source: National Human Genome Research Institute (genome.gov)
Source : Quora (Basic DNA Structure)
Nucleotides are chemical building units that make up DNA. A phosphate group, a sugar group, and one of four different nitrogen bases make up these building components. Nucleotides are joined together into chains, with the phosphate and sugar groups switching places, to create strands of DNA.
There are 4 different types of Nucleotides as indicated to the left. They are Adenine, Thymine, Cytosine, and Guanine. These four serve as the genetic alphabet. Adenine forms hydrogen bonds with thymine to form an A-T base pair, while cytosine forms hydrogen bonds with guanine to create a G-C base pair. these nitrogenous bases serve as the alphabet of the genetic code. The sequence of these bases along the DNA molecule encodes the information necessary for the synthesis of proteins and the regulation of various cellular processes.
These molecules fit together in specific ways in order to tell a story. The story of you, and your development. The arrangement and order of nitrogen bases forms the ‘letters’ of the DNA molecule that can be arranged into ‘words’ that form instructions for making an organism. These instructions are known as a genome.
Between these hydrogen bonds lies the Double Helix Structure, which consists of two long chains / strands of nucleotides twisted around eachother. These are composed of sugar-phosphates. Sugar-phosphates refer to the components of the DNA molecule's backbone. They consist of deoxyribose sugar molecules bonded to phosphate groups, forming a repeating pattern along the sides of the DNA double helix.
Source: Kurpinski's Class - Biological Diversity (Unit A, Part A)
Source: DNA, Genes, and Chromosomes (Cleveland Clinic)
Source: Human Genomes, National Institute of Health and Wikipedia
Source: Chromosomes (Khan Academy)
Chromosomes in our DNA
DNA is the book. Chromosomes are the chapters.
Chromosomes are a long, thread-like structure found within the nucleus of eukaryotic cells (animals, plants, and humans). It is composed of our DNA and genetic information with associated proteins and carries our genetic information in the form of genes. The DNA in a chromosome contains the instructions (genetic code) necessary for the development, growth, and functioning of an organism. Each chromosome contains numerous genes, which are specific segments of DNA responsible for encoding proteins and determining various traits and characteristics of the organism.
Chromosomes come in pairs in most organisms, with one chromosome in each pair inherited from each parent (your mother and your father). In humans, we have 23 pairs of chromosomes, resulting in 46 total chromosomes. Chromosomes are inherited in pairs, humans cells have 46 chromosomes in total, 23 from mom, 23 from dad. These chromosome pairs include one pair of sex chromosomes (X and Y), which determine an individual's sex, and 22 pairs of autosomes, which carry genetic information related to other traits. There are 4 main types of chromosomes:
We can imagine our DNA as a book consisting of 3.2 billion letters. For reference:
the average novel has 200,000 letters
the bible has 3.12 million letters
all 7 books of the harry potter series have 4 million letters
Source: Kurpinski's Class - Biological Diversity (Unit A, Part A)
Source: DNA, Genes, and Chromosomes (Cleveland Clinic)
Source: Human Genomes, National Institute of Health and Wikipedia
Source: UPMC (Cells become zombies when the ends of their chromosomes are damaged)
DNA Extraction Lab
Delving extensively into the intricate cellular structures of various fruits and conducting an in-depth examination of their genetic makeup, including the analysis of DNA quantities.
September 12th, 2023
Important Key Terms
Deoxyribonucleic Acid
DNA is the Genetic code containing instructions for life's processes, composed of nucleotide pairs in a double helix structure.
Lipids / Fats
Hydrophobic molecules found in the cell wall of plants and fruits, crucial for energy storage, insulation, and cell membranes, including fats, oils, and phospholipids. (basically fats)
Qualitative
Qualitative data relates to evaluating or being evaluated based on the intrinsic qualities or excellence of something, such as taste, smell, appearance, and other qualitative attributes, rather than its quantity.
Filtrate
Filtrates are solid material left after filtering a liquid mixture, often containing impurities or concentrated substances.
Precipitate
Prcipitates are solid substance formed when two solutions react, often falling out of solution due to chemical reactions.
Extraction
Extraction is a separation technique used in laboratories to isolate specific substances from mixtures using solvents or phase differences.
Meet the Test Subjects
Bananas
Bananas, like the Cavendish variety, have three sets of chromosomes (triploid), making them sterile and needing special propagation methods. Genetic studies focus on making them more disease-resistant and tastier.
Straw-berries
Strawberries, unlike bananas, are octoploid, which means they have eight sets of chromosomes. This complex genetic makeup contributes to their unique flavor and characteristics.
Kiwis
Kiwis are typically diploid, which means they have two sets of chromosomes. This genetic makeup influences their growth, development, and fruit production.
Based on this given information..
We can make the hypothesis and safely assume that strawberries likely have the most amount of DNA per given sample. If we have the same quantity of each sample; bananas, strawberries, and kiwis, strawberries will most likely have the most amount of DNA because they have eight sets of chromosomes per pair, compared to three pairs in bananas, and two pairs in kiwis.
Understanding Experimental Variables
Independent
Variable
Independent (manipulated) variables are variables that are being changed by the person that's conducting the experiment.
In this example, we're changing the fruit that we're experimenting with. We're experimenting with bananas, kiwis, and strawberries in different phases of the experiement.
Controlled
Variable
The controlled variable is the variable that remains the same throughout the experiment to ensure and maintain an accurate and reliable test.
The controlled variable within this test is the liquid that is being used to break down the fruit cell wall and the quantity / sample size that is being collected. We're not using one tiny strawberry and one giant banana.
Dependent
Variable
The dependent variable, or the "responding variable", is the variable that we're hoping to find at the end of our experiment to draw a proper conclusion and to answer our initial question.
Here, we are trying to figure out which fruit; bananas, kiwis, or strawberries; has the most amount of DNA in a select, controlled sample size.
Source: - Jessica Pecovsk
External Lab Results
With a difference of 5 to 6 between strawberries, kiwis, and bananas, the overall number of DNA for each fruit varied greatly. Together, kiwis and bananas yielded as much as strawberries did on their own. My prediction that strawberries will produce the most DNA, followed by kiwis, and then bananas last, proved to be accurate.
These results were taken from an external source on Google and in-class results will be updated once they are published.
9-11 Lab Results
The lab findings, obtained by averaging the results from student-conducted experiments, diverge from our initial hypothesis and the data collected from external sources, revealing distinct outcomes.
In these findings, bananas exhibit a notably higher presence of DNA when contrasted with strawberries and kiwis, which stands in stark contrast to the outcomes reported by our external source. Multiple factors and possible explanations might account for why our observed results deviated from what we had initially hypothesized.
What is the procedure for this lab?
Weigh out 10g of strawberry and place in Ziploc bag.
Remove air from the bag and seal tightly. Smash/grind up the fruit using your fist and fingers for 2 minutes. Careful not to break the bag!
Measure 10mL of extraction buffer (salt and soap solution) and add it to the bag.
Kneed/mush the fruit in the bag again for 1 minute.
Assemble your filtration apparatus. Place coffee filter over the opening of the 100 ml beaker, secure with an elastic band.
Carefully pour the fruit slurry into the filter; let sit until no more liquid is dripping through the filter (5-10 minutes). The liquid collected in the breaker is called the filtrate.
Using a pipette, or medicine dropper, slowly add cold rubbing alcohol into the beaker, being careful to tilt the beaker to allow the rubbing alcohol to gently pour into fruit liquid. Do not quickly dump the alcohol straight into the fruit liquid! Record initial observations.
Record the initial weight of the coffee stirrer in the data table. Slowly dip the coffee stirrer into the alcohol layer of the fruit mixture, slowly rotating it to spool out the fruit’s DNA onto the stirrer. This precipitate collected is the fruit’s DNA.
Reweigh the coffee stirrer with the collected DNA. Record weight in the data table.
Repeat steps 1 through 9 using kiwi and then banana.
Why did we need to mash up the fruit before the extraction buffer?
We can access each strawberry's unique cell thanks to the mashing of the strawberries. The lipids (fats) and proteins that makeup cell membranes are dissolved by the detergent, which causes the membranes to degrade. These proteins and lipids precipitate out of the solution after adhering to the detergent.
The plant membranes are composed mainly of lipids, which are composed of fatty substances that can make accessing the nuclei component of the fruit difficult. Mashing up the fruit and adding the extraction buffer, disrupts the plant cell structure (mainly the cell wall and cell membrane) and enables the extraction buffer to penetrate the cells and access the DNA component of the fruit.
What can you conclude about the main differences in extracting DNA from bananas, strawberries, and kiwis?
The main differences can be attributed to the genetic characteristics of these fruits. Strawberries are octoploids, containing eight sets of chromosomes, which typically results in a higher DNA yield per sample (which is why we got this outcome). On the other hand, banans and kiwis are more diploid fruits, meaning they only have two - three sets of chromosomes, leading to a lower DNA content per sample compared to strawberries.
What are 3 possible sources of error in this lab, and what are some possible solutions?
Risk of Contamination from External Sources
Bacteria and other foreign DNA can easily contaminate the purity of the extracted DNA. To ensure that this does not happen, use aseptic techniques, including sterilized equipment and a clean workspace, to minimize the risk of contamination.
Incomplete Cell Lysis
Cell Lysis is the process in which we break down the cell membrane to access its internal components and DNA within the nuclei. Incomplete cell lysis can result in lower DNA yields, as some cells may not be adequately disrupted to release their DNA. To prevent this, ensure thorough mechanical disruption and ensure that we're properly mashing and grinding the fruit tissue to the maximum extent. Monitor the lab and adjust the extraction buffer is needed to enhance the amount of DNA that is released.
DNA can be LOST
DNA can be lost during the purification steps, such as ethanol precipitation or centrifugation, reducing the final DNA yield, therefore resulting in inaccurate data and comparisons. Ensure that you handle DNA carefully during purification and use proper conditions to avoid DNA loss.
Can we extract DNA cells from human cells the same way we did with fruits?
Extracting DNA both from humans and fruits follows a similar process, but there are obviously differences. The first obvious one is how humans lack a rigid cell wall made of cellulose. Animals and humans instead have a flexible cell membrane which means that the primary barrier to DNA extraction is the cell membrane. This would require a different procedure and different sets of detergents tailored to break down the lipid bilayer of the cell membrane. It is also important to remember that in humans, cells are organized into tissues, organs, and systems, making it important to isolate specific cell types for DNA extraction.
Why does the DNA strand come out as a precipitate (solid) into the alcohol?
DNA comes out as a solid precipitate in cold alcohol during DNA extraction because DNA is soluble in water but less soluble in alcohol. The phosphate backbone of DNA forms hydrogen bonds with water molecules due to its polar nature, making it water-soluble. When alcohol is added, which is less polar than water, DNA molecules aggregate and precipitate as they can no longer form strong hydrogen bonds with the less polar environment. This precipitation is a key step in DNA extraction, separating DNA from other cellular components.
Do you think it would work the same way if the alcohol was at room temperature?
If the alcohol was at room temperature, it may still be effective but it may still require minimal adjustments in the DNA extraction protocol. DNA is less soluble in room-temperature alcohol compared to cold alcohol, but it can still precipitate. You may require a higher concentration of alcohol or allow the solution to sit for a longer period to ensure that the DNA effectively precipitates.
Drawing Conclusions.. What's going on?!
The data presented above highlights disparities between our class results, our initial hypothesis, and data from an external online lab report conducted by a student by the name of "Jessica Pecovsk", which both follow a similar extraction process. Both procedures share the same basic steps for DNA extraction, including the use of an extraction buffer, filtration apparatus, and rubbing alcohol, but they differ in terms of the fruit types specified and the level of detail provided. Our initial hypothesis expected strawberries to have the most amount of DNA per sample due to them having more DNA per pair, and kiwis having the least amount of chromosomes per sample due to them having the least amount of DNA per pair. But both given data above show differences compared to our hypothesis. The external lab did show that strawberries have the most DNA per sample, but it showed that bananas had the least, although hypothetically speaking, they should've been kiwis. In our lab, it showed that bananas had the most amount of DNA per sample, although it should've been strawberries.
Why are we seeing the results that we are seeing?
It's unknown why this is happening without observing the lab directly. There may be a variation in genetic composition amongst the fruit samples, differences in the DNA extraction methods used in our lab compared to our external source, and potential errors or miscalculations in the experimental procedures. Another potential explanation could be mutations within the strawberry. Spontaneous mutations can occur in the DNA of not just strawberries, but other plants, animals, and viruses. Ploidy, a measurement of the amount of a complete set of chromosomes in a cell, can change in certain conditions if these mutations are inherited. Additionally, plant breeders and researchers may intentionally manipulate the ploidy of strawberry plants to develop varieties with desired characteristics. This can involve selecting and breeding plants with specific ploidy levels.
Factors like the ripeness of the fruit, storage conditions, and specific parts of the fruit used for DNA extraction may have also played a role. The amount of size that we sampled as a result of human error, improper handling of samples, inaccurate calibration of instruments, cross-contamination.. they all have a factor to play in what may have gone wrong in either lab. In conclusion, the observed disparities in DNA content among different fruit types in our experiments suggest that multiple factors are at play. To better understand the reasons behind these differences, further investigation, careful control of variables, and replication of experiments may be necessary. Additionally, comparing findings with a larger sample size, cross-referencing between groups and external sources, and taking more precautions to ensure accuracy is needed in not just this, but every lab.
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