CRISPR-Cas9

Introduction to CRISPR-Cas9

  • CRISPR-Cas9 is a gene-editing tool that has transformed biology and has various uses in medicine, farming, and science. This innovative tool allows scientists to modify DNA with great precision, which allows them to target specific genes, edit them, and potentially correct genetic mutations. CRISPR-Cas9 is made up of two key parts: CRISPR, which are like unique genetic codes, and Cas9, which is a strong protein that works like genetic scissors. I have explored CRISPR-Cas9 in class through modelling, visiting simulations online, and making observations with my class.

    What CRISPR-Cas9 Means:

    • CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, which are unique DNA sequences that are found in bacteria and archaea
    • Cas9 is a protein that functions as an enzyme that’s capable of cutting DNA

    The Structure of CRISPR-Cas9

    CRISPR-Cas9
    • CRISPR Sequences: CRISPR consists of repeating DNA patterns that are arranged in a special order. These sequences act like genetic memories, since they’re able to store information from past encounters with viruses
    • Cas9 Protein: Cas9 is a crucial element of the CRISPR system. It’s a protein that acts like a molecular tool for editing the DNA. When Cas9 is directed by a guide RNA, it can precisely locate and cut the DNA at a specific point within the genome

Together, these parts work like a  team to help edit DNA with accuracy. The two can be thought of as a pair of genetic scissors with a set of instructions.

How CRISPR-Cas9 Targets a Specific Gene:

  • CRISPR-Cas9 finds a specific gene using a guide RNA (gRNA), which is like a set of instructions for the gene. The gRNA is made to match the desired gene to change. It guides the Cas9 protein, which is like scissors, to the exact spot in the cell’s DNA where the gene is located. This means CRISPR-Cas9 only changes the gene that’s wanted to be changed and doesn’t meddle with other genes
  • How CRISPR-Cas9 Binds to the Target Area of the Specific Gene:
    • The guide RNA is used to instruct the Cas9 protein, as it directs it to the specific location in the genome where the target gene is in
    • The Cas9 then scans the cell’s DNA until it recognizes and binds to the matching target gene sequence

      How CRISPR-Cas9 Cleaves DNA:

      • Once the Cas9 reaches gene that it’s targetting, it functions like molecular scissors, as it cuts the DNA at the set location
  • The CRISPR-Cas9-induced DNA cut serves as a signal to the cell. The cell starts its internal DNA repair processes when it detects this certain cut. These processes operate as repair tools, fixing the cut or altering the DNA as necessary. Scientists and doctors can take advantage of these natural repair processes, such as by interrupting a gene or adding a specific modification to a DNA sequence.

How CRISPR-Cas9 can repair DNA to “knock out” a gene

  • By purposefully altering the DNA sequence of a gene, CRISPR-Cas9 can “knock” it out or switch it off. The cell’s built-in repair mechanisms kick in when the Cas9 protein snips the DNA at the right spot in the gene. These repairs can occasionally fail, which leads to mutations that prohibit the gene from functioning properly. This basically “knocks out” the gene, making it useless.

How CRISPR-Cas9 can repair a mutation in DNA

  • Alternatively, a DNA mutation can also be fixed using CRISPR-Cas9. Researchers or scientists can direct the repair procedure by introducing a repaired DNA sequence together with the Cas9 protein and guide RNA. The gene’s normal function will be restored when the cell incorporates the proper sequence, replacing the mutant one.

How CRISPR-Cas9 Could Be Used to Our Benefit:

– CRISPR-Cas9 can be used to our benefit in a variety of fields, including medicine, agriculture, science, and biotechnology. In medicine, it has the potential to revolutionize the treatment of genetic diseases through precise gene corrections/repairing mutations, while in agriculture, it can increase crop growth, resilience, and food security for many. The technology also allows for personalized medical treatments for people which allows for more precise treatments which can accommodate a wider variety of conditions and patients . To ensure responsible use, it is essential to approach its application with thorough ethical considerations and strict safety procedures.

Analyzing the models I used to learn:

1.In what ways did the model accurately reflect the process?
–  When used properly, paper models can correctly represent a variety of processes clearly. My group mates and I were accurately able to reflect the general idea of how the process of CRISPR-Cas9 works with our hands-on visual representation model. It allowed us to grasp a basic idea of CRISPR-Cas9, and the various components of the process like guide RNA, the Cas9 protein, and DNA editing. This activity also made it easier for us to understand the crucial steps involved in this process. However, the paper model may not have been able to accurately capture all of the specific characteristics and components of CRISPR-Cas9. It was difficult to accurately represent every feature through the paper model because of how complicated the actual process is.Although it did a good job of explaining the fundamentals, it might not have gone into great detail about the specifics of how CRISPR-Cas9 works at a higher molecular level. To enhance the accuracy of the paper model, next time we could use or find additional materials and resources to better represent the process. We could also combine our exploration of the topic with other resources such as explanatory guides, animations, or interactions.2. Models are a highly effective tools in communicating scientific concepts and education since they can be used to explain complicated topics simply while providing visual clarity, engaging students, and can break through language barriers as well.  Models make complicated ideas concrete and improve overall comprehension by bridging the gap between scientific language and common understanding. Through these interactive events, models can actively engage students while allowing curiosity to flourish and promote memorable learning. To provide a an updated scientific education, however, in my opinion, models should be combined with real-world applications, case studies, and critical thinking activities since it can stimulate more aspects of the brain. To keep models accurate, models should also be regularly updated. Overall, I believe that models are an effective way to educate students and the public since they break down the complex ideas and processes of science into manageable, relatable forms, which allows for a wider audience to grasp, understand, and appreciate scientific principles all at once.

Work Cited

MedlinePlus. “What Are Genome Editing and CRISPR-Cas9?” Medlineplus.gov, Medlineplus, 22 Mar. 2022, medlineplus.gov/genetics/understanding/genomicresearch/genomeediting/.

Redman, Melody, et al. “What Is CRISPR/Cas9?” Archives of Disease in Childhood – Education & Practice Edition, vol. 101, no. 4, Apr. 2016, pp. 213–15, ep.bmj.com/content/101/4/213.short.

Synthego. “The Ultimate Guide to CRISPR: Mechanism, Applications, Methods & More.” Synthego.com, 2019, www.synthego.com/learn/crispr.

YourGenome. “What Is CRISPR-Cas9?” Yourgenome.org, 8 Feb. 2022, www.yourgenome.org/facts/what-is-crispr-cas9/.

 

EFPH11 – Bento Box

This is my bento box assignment that was inspired by Michelle Good’s captivating novel, “Five Little Indians.” Through this project, I aim to visually represent the novel’s profound themes, compelling characters, and connections to Indigenous culture and history. Each aspect of the bento box contains carefully chosen objects and representations that symbolize resilience, cultural reclamation, trauma, healing, and justice. This visual representation invites viewers to connect with the novel’s emotional journey, fostering understanding, empathy, and appreciation for the power of literature in addressing important issues.

Inquiry Acid Base Lab

Title: Determining the Base of Oxalic Acid Dihydrate

Purpose

  • The purpose of this lab is to accurately determine the base, or the molar concentration, of oxalic acid dihydrate (C2H2O4·2H2O) solution through a titration and flame test. By accurately determining its base, we can understand its chemical behavior and properties and optimize its usage in various processes.
  • In this experiment, we performed a titration using H2O as our base, against a known volume of the oxalic acid dihydrate solution. The reaction between the acid and base will form water and a salt. The balanced chemical equation for the reaction is as follows:

C2H2O4·2H2O + 2Ca(OH)2 → Ca(C2O4) + 4H2O

List of Materials

  • Oxalic acid dihydrate (C2H2O4·2H2O) 0.4g
  • 100ml H2O
  • Analytical balance
  • Burette
  • Burette clamp
  • Funnel
  • Pipette
  • Beaker
  • Volumetric flask
  • Stirring rod
  • Phenolphthalein indicator
  • Bunsen burner
  • Wire loop
  • Lighter/Striker
  • Safety goggles

attire

  • protective clothing
  • closed-toe shoes
  • hair tie

Procedure

  1. Preparations
  • read over the procedure to understand the lab and its purpose
  • ensure that you are wearing proper lab attire, put goggles on, and sanitize hands
  • gather materials and clean/rinse all of them

2. Weighing of Oxalic Acid Dihydrate

  • weight 0.4g of oxalic acid dihydrate (C2H2O4·2H2O)
  • record the weight of the oxalic acid dihydrate

3. Dissolution of Oxalic Acid Dihydrate

  • transfer the weighed oxalic acid dehydrate to a clean and dry beaker
  • add 100ml of H2O to the beaker
  • stir the mixture using a stirring rod until all the solid has been dissolved which will form a clear solution
  • add a few drops (we used 3)  of phenolphthalein indicator to the solution to help the ending visual results

4. Titration

  • set up a burette, making sure that it is clean and free of any air bubbles
  • fill the burette with the prepared base solution
  • record the initial volume (V1) of the base solution in the burette
  • slowly add the base solution from the burette into the oxalic acid solution int he beaker, while stirring with a stirring constantly
  • continue the addition until a permanent colour change is observed, which indicates its neutralization
  • using the phenolphthalein indicator, the solution should turn from colourless to a pale pink
  • record the final volume (V2) of the base solution in the burette
trial #1 of titration
process of trial #2 of titration
trial #3 for titration

5. Repeating titration procedure

  • perform titration 2 more times using fresh samples of the oxalic acid dihydrate
  • calculate the average volume of H2O used in the titrations

6. Flame Test

  • Safety precautions: ensure that your work environment is a well-ventilated area and has appropriate safety equipment
  • Clean wire by dipping it in water and holding it in the flame until it burns off any impurities, repeat until clean
  • Light the bunsen burner
  • Soak the wire in the unknown solution
  • hold it above the bunsen burner
  • watch as the flame changes colour and write down any observations and its final colour
  • compare the observed flame colour with a reference flame colour chart or a table that indicates the characteristic colours associated with different metal ions
  • Identify the metal ion present in the compound based on the observed flame colour

photo of flame colour chart indicating the different colours associated with different metal ions

  • our flame burned a bright orange colour, which led us to believe that our base was Calcium (Ca)

7. Calculation of concentration

  • to calculate the volume of the base solution used in the titration, start off by calculating our V by doing: V=V2-V1
  • then, calculate the concentration of the base solution using the volume of the base used (V) and the known concentration

Work:

V: V2-V1 = 25.7 – 15.7 = 10.0

concentration of the base solution:

find mol of Ca(OH)2: M(L)

0.03M (0.0157L)

mol of Ca(OH)2 = 0.000471

concentration of base solution: mol/L

0.000471/0.01567 L

M = 0.03

Data Table for Titration Data

molarity of H2O trial 1 trial 2 trial 3
initial reading of burette 10. 10. 10.
final reading of burette 25.5 25.8 25.7
mL base used 15.5 15.8 15.7
average mL of base 15.67

Conclusion

The purpose of this experiment was to determine the concentration of a base solution by using a titration method to initially ascertain the concentration of the acid, as well as identify the base used. It was determined that the base solution used was calcium hydroxide Ca(OH)2 with a concentration of 0.03 M.

This procedure was chosen because titration allows for the determination of an unknown substance’s concentration by comparing it to a known concentration. By measuring volumes and utilizing the stoichiometry of the reaction, the concentration of the substance under analysis can be calculated. Hence, the concentration of the solution was successfully determined. Additionally, the identity of the base was established through a flame test, confirming it to be calcium hydroxide. Overall, we chose to do a titration for the first portion of this experiment and procedure since it is a highly accurate and versatile method for determining the concentration of a substance. Its simplicity, speed, and effectiveness make it widely used in various fields especially in solution chemistry.

During the experiment, the volume of the base solution used in three trials was measured, resulting in values of 15.5 mL, 15.8 mL, and 15.7 mL. The average volume of the base used was calculated to be 15.7 mL.

By utilizing the known concentration of the base and the volume of the base solution employed, the concentration of the base solution was determined to be 0.03 M.

This finding indicates that the concentration of the base solution remained consistent throughout the experiment, as the calculated concentration closely matched the known concentration. Moreover, it affirms the accuracy and reliability of the titration method employed to ascertain the concentration of the base solution.

Identification and Resolution of Errors:

  1. Instrumental errors can arise from inaccuracies or limitations in the laboratory equipment utilized, such as potential inaccuracies in the burette readings.

Resolution:

  • Ensure proper cleaning of the burette prior to the experiment and periodically check its accuracy.
  • Utilize a burette with a clear and precise scale to facilitate accurate readings and reduce parallax errors.
  • Take multiple readings and calculate their average to enhance accuracy and compensate for individual errors.

2.Imprecision may arise in the experiment due to contamination or impurities present in the reagents or equipment. If the base solution or burette is contaminated with foreign substances, it could have altered our volume measurements or react with the solution, potentially resulting in inaccurate outcomes.

Resolution:

  • Exercise proper handling techniques to prevent contamination from external sources.
  • Thoroughly clean and rinse the equipment to eliminate any residual substances from prior usage.
  • Ensure the purity of chemicals utilized in the experiment to minimize the risk of impurities affecting the accuracy of the results.

3. Decomposition: We found out that calcium hydroxide can decompose over time, especially when exposed to heat or light. This decomposition can result in the formation of calcium oxide or water loss, which ultimately could have affected the accuracy of our titration

Resolution:

  • Minimize the exposure of calcium hydroxide solutions to the atmosphere during the titration
  • Work efficiently and avoid unnecessary delays between preparation and use
  • Prepare the calcium hydroxide solution as close to the time of use as possible

4. Carbon dioxide absorption: Calcium hydroxide also reacts with carbon dioxide in the air to form calcium carbonate. This reaction is also known as carbonation and it reduces the concentration of calcium hydroxide in the solution which could have lead to an underestimation of its actual concentration.

Resolution:

  • If possible, perform the titration in an environment protected from atmospheric carbon dioxide, such as a glove box or under an inert gas, such as nitrogen or argon
  • Begin the titration promptly after the calcium hydroxide solution is prepared in order to reduce the exposure time to carbon dioxide and ensures more accurate concentration determination

Core Competency Reflection

Neuron Communication Summary

Biology of Psychology

  • the biology of psychology includes all parts of our anatomy that is involved with our thoughts, feelings, behaviour, and emotions

Nerve Cells

  • also called neurone, they transmit electrochemical impulses in order to talk
  • all neutrons have the same basic body parts: (cell body, dendrites, nucleus, axon, node of ranvier, myelin sheath, axon terminals, and Schwann’s cells)

functions of the body parts

  1. Cell body/soma: contains genetic information, maintains the neuron’s structure, and provides energy to drive activities
  2. Dendrites: receives input/signals from many other neuron’s to cell body
  3. Nucleus: acts as the cell’s brain by telling it what to do, how to grow, and reproduce
  4. Axon: carries the electrical impulse that are the means of communication within the brain and the rest of the body
  5. Node of Ranvier: serves to facilitate the rapid conduction of nerve impulses
  6. Myelin Sheath: allows electrical impulses to transmit quickly and efficiently along the nerve cells
  7. Axon Terminals: provides synapses between neutrons, they also release neurotransmitters when stimulated by an electrical signal carried by the axon
  8. Schwann’s Cells: plays an essential role in the development, maintenance, function, regeneration of peripheral nerves
  • there are several types of neurons, and there are 3 involved with our reflexes: the sensory neuron, the interneuron, and the motor neuron

Neuron Structure

Interneuron Play Doh Figure
  • For my play doh figure, I decided to work on the Interneuron which is one of the several types of neurons
  • The Interneuron is found within the centre of the nervous system
  • It’s main function is to send signals between the sensory neuron and the motor neuron or other interneurons
  • they play a crucial role in interpreting and processing information within the nervous system
  • they are also responsible for various other functions, such as motor coordination, reflexes, and higher cognitive processes

 

 

 

Here is a picture of a labelled sensory neuron for reference since I did not do a play doh figure of it:

Neuron Function

  • An action potential is a brief electrical signal that travels along the length of a neuron fiber, also known as an axon, which is a result of the movement of (+) ions into and out of the axon.
  • Action potential has 3 parts: depolarization, repolarization, and refractory period
  1. Resting potential: is when the membrane is polarized, and when there are large negative ions inside the axon, giving it an overall negative charge. The voltage is -70 and Na+ ions are located outside the axon
  2. Depolarization: when the incoming message stimulates a section of the axon, hence, the channels within the membrane become activated which then enables the flow of Na+ions into the axon. Because of this occurrence, the voltage rises up to +30mV
  3. Repolarization: more channels become active and are open, which allows K+ to exit the axon. Since the K+ ions exit, the axon, the voltage decreases back to normal (-70mV). Although the voltage is back to normal, the repolarization causes the next section of the axon to begin depolarization
  4. Refractory period: after repolarization, K+ ions are outside the axon and Na+ are inside. In order for the cycle to “fire again”, the neuron has to be in resting potential, and during this period, pumps in the membrane push Na+ to the outside and K+ back inside, bringing them back into their starting positions.
  5. Overall, the repolarization in one section stimulates depolarization in the next section, and the impulses/cycle does not travel backwards due to the refractory period
  • The action potential, like an electrical signal, can quickly move along the neuron fiber. It repeats this process over and over, making the signal travel rapidly throughout the neuron. This fast movement helps the nervous system communicate efficiently.

here is an action potential graph which essentially is a visual representation of the electrical activity that occurs in a neuron during the process of generating and transmitting an electrical signal called the action potential. It plots the changes in voltage or membrane potential of a neuron over time.

 

Synapse

A synapse is a specialized connection between two neurons or a neuron and a target cell, where information is transmitted through chemical signals called neurotransmitters.

  • Synapses enable communication and information transfer in the nervous system
  • They transmit signals between neurons or between a neuron and a target cell
  • They also use chemical signals called neurotransmitters to transmit information
  • The presynaptic neuron releases neurotransmitters into the synaptic cleft
  • Neurotransmitters bind to receptors on the postsynaptic neuron or target cell
  • This binding leads to changes in the electrical activity of the postsynaptic neuron or target cell
  • Synapses play an important role in transmitting and integrating information within the nervous system

Synapse Structure

A synapse includes:
1. Axon terminal
  • Site of neurotransmitter release
  • Conversion of electrical to chemical signal
  • Signal transmission between neurons
  • Regulates signal strength
  • Involved in synaptic plasticity
  • Subject to presynaptic modulation

2. Synapse vesicles

  • Store and package neurotransmitters
  • Release neurotransmitters into the synaptic cleft
  • Regulate neurotransmitter release
  • Facilitate recycling of membrane components
  • Subject to presynaptic modulation

3. Synaptic gap

  • Separates the presynaptic neuron from the postsynaptic neuron or target cell.
  • Allows for the scattering of neurotransmitters.
  • Gives a space for the transmission of chemical signals.
  • Helps/facilitates the binding of neurotransmitters to receptors.
  • Enables communication and information transfer between neurons

4. Neurotransmitters

  • Transmits chemical signals between neurons
  • Carry information across the synaptic gap
  • Bind to receptors on the postsynaptic neuron or target cell
  • Influence the electrical activity of the postsynaptic neuron
  • Regulates the communication and signaling in the nervous system

5. Neurotransmitter receptor

  • Receive neurotransmitters
  • Binds to specific neurotransmitters
  • Initiates signaling pathways
  • Influences the postsynaptic neuron’s activity
  • Regulate synaptic transmission and communication

6. Dendrite receiving neuron

  • Receives incoming signals
  • Contains receptor sites for neurotransmitters
  • Detects and responds to neurotransmitter binding
  • Initiates electrical changes in the neuron
  • Integrates signals from multiple synapses
  • Transfers information towards the cell body

7. Postsynaptic membrane

  • Receives neurotransmitters
  • Contains receptors for neurotransmitters
  • Converts chemical signals into electrical signals
  • Initiates changes in membrane potential
  • Integrates signals from multiple synapses
  • Determines whether an action potential is generated

How is a signal sent from the axon of sending neuron to the dendrite of the receiving neuron?

  • When a message travels through a neuron, it starts as an electrical signal called an action potential. This signal travels along a long, thin part of the neuron called the axon. At the end of the axon, it causes special chemicals called neurotransmitters to be released. These neurotransmitters cross a tiny gap called the synapse and attach to the neighboring neuron’s dendrite, which is like a receiving antenna. When enough neurotransmitters attach to the dendrite, it can create a new electrical signal in the receiving neuron, allowing the message to continue on its way

How does the receiving neuron “determine” whether or not to send its own action potential

  • The receiving neuron decides whether to send its own action potential by adding up the effects of the incoming signals. When neurotransmitters attach to the neuron’s dendrites, they cause changes in its electrical activity. Hence, if the overall effect is strong enough, the neuron sends an action potential. But if the effect is not strong enough, it doesn’t send an action potential. So, the receiving neuron makes a decision based on the combined signals it receives.