CRISPR-Cas9 Assignment

CRISPR – Cas9

For the past week in Anatomy and Physiology 12, we’ve been exploring CRISPR-Cas9, a biotechnological tool that allows us to edit an organism’s DNA. In this unit, we’ve learned about mutations—changes in DNA sequences—and how our DNA replicates itself during cell division. Understanding this process is crucial because errors can occur during DNA replication. For example, bases can become mismatched, and if the repair enzyme that checks the DNA fails to recognize this error, it can lead to a mutation. CRISPR is closely related to these mutations because it is a powerful gene-editing tool that can potentially correct errors in the DNA sequence. Since CRISPR is a relatively new concept in the scientific community, we’re focusing on presenting our understanding of this technology. One of our first activities as a group was to create a paper model of the CRISPR system and how it functions. This hands-on project allowed us to visualize the tool’s role in editing DNA, making the concept much easier to understand. To deepen our understanding of CRISPR and its capabilities, we also used an interactive online resource featuring animations explaining each process step. My goal in writing this edublog post is to examine the CRISPR process and its application.

 

DNA editing using CRISPR-Cas9

CRISPR stands for clustered, regularly interspaced short palindromic repeats, which are repeating sequences found in the DNA genome of bacteria. Cas9 stands for CRISPR-associated protein 9. It is an endonuclease, meaning it’s an enzyme that cuts nucleic acids. CRISPR was first founded to be used as a natural defence mechanism for bacteria when a virus invaded them. When a virus invades a bacterium, the bacterium will capture a small piece of the virus’s DNA and store it so if the same virus invades again bacterium can recognize and target the virus, leading the Cas9 enzyme to cut and destroy the viral DNA.

The process will start with CRISPR targeting specific genes through its interactions with guide RNA. Scientists synthesize the guide RNA and consists of about 20 nucleotides that match a particular sequence in cell DNA that they want to target. When introduced into a cell, the guide RNA actively seeks out and attaches to the precise region within the target gene, helped by the presence of PAM. PAM stands for Protospacer Adjacent Motif, and it is a certain type of nucleotide sequence that is usually 5’-NGG-3’ where N represents any nucleotide (A, C, T, G). PAM sequences occur every 50 bases or less, which is why scientists can target nearly every human gene. Once guide RNA successfully guides Cas9 to the target gene, it will bind there. After binding, the Cas9 will “unzip” the DNA double helix, if the unzipped DNA strand is not an exact match to the guide RNA, the Cas9 will disengage and zip back up the DNA. If the DNA is a perfect match, the guide RNA will bind with the single DNA strand and form a DNA-RNA helix.

Cleaving DNA “cutting DNA” begins with the 3 nucleotides upstream from the PAM site. Cas9 unwinds the DNA and uses its nuclease domains to cut both strands, creating a double-strand break.

Cas9 will repair DNA to “knock out a gene”. There are two ways that DNA can be repaired: non-homologous end joining (NHEJ) – more frequently used – or homology-directed repair (HDR). During NHEJ, specific enzymes within the cell quickly repair the double-stranded DNA break by inserting or deleting nucleotides at the site of the cut. When using CRISPR-Cas9, the Cas9 enzyme cleaves the DNA at a targeted sequence, and NHEJ attempts to repair it. However, the repair is often imperfect, and after several rounds of repair and re-cleaving by Cas9, this process can result in a mutation. If the mutation happens at the target site, it may inactivate or “knock out” the gene, preventing it from functioning. Another way that DNA can be repaired is HDR. Through the process of HDR, scientists introduce a DNA template (also called donor DNA) to “trick” the cell into using this template to repair the DNA break. The template is designed to introduce specific changes to the target DNA sequence, allowing scientists to either replace a faulty gene with a correct version or insert entirely new sequences.

Overall, between these two ways that DNA repairs itself, NHEJ is faster, but HDR is more precise.

 

Benefits of CRISPR – Cas9

This relatively new biotechnological DNA editing tool can be used to human advantage in many ways. In the medical field, CRISPR can be used as a treatment for cancer by addressing particular genetic mutations. It can also improve resistance to diseases and lower health risks associated with genetic factors like heart disease. In the agriculture field, CRISPR can used for crop improvement and edit crop genes to be resistant to pests. In conclusion, because CRISPR allows us to make precise, targeted changes to DNA quickly, and affordably it can be used in many different fields.

Models used to understand CRISPR-Cas9

To understand how CRISPR–Cas9 effectively edits DNA, we used two different ways to understand the process: digital simulation and paper cutouts with instructions. I believe that the easiest way of understanding how this tool works was by the digital simulation. With the digital simulation, I got to see the process in 3D and interactively explore the website. It provided simple definitions of key terms and went into depth when explaining the four main steps in a CRISPR-Cas9 process. A disadvantage of the digital simulation was that I couldn’t get hands-on experience and learn from investigating and collaborating with my group members. The paper cutout activity that we participated in with our group members gave us a chance to get hands-on experience and learn from mistakes and steps. It was also detailed and stated the functions of each tool. A disadvantage that the paper cutout activity had was that it was hard to follow and prone to errors. The paper cutout didn’t give us a chance to see everything in 3D.

 

I believe that models are a great way to teach students about scientific (or any other subject) ideas. Many individuals take advantage of visual learning. Models are visual, which makes it easier to paint the picture in the student’s minds. Models are also interactive, allowing for hands-on engagement and active learning. Interactive models encourage students to experiment, explore, and observe outcomes in real-time.

 

https://www.youtube.com/watch?v=jb4xRMyKEz4

https://www.biointeractive.org/classroom-resources/crispr-cas9-mechanism-applications

https://innovativegenomics.org/crisprpedia/crispr-in-agriculture/

Week 18 – my top 5 things from PC 11

With this being the last blog post of Precalculus 11, I want to talk about 5 things I learned in this class that have been enjoyable or eye-opening.

Sine law & cosine law

  • these 2 laws have to be one of the most interesting things I learned this year because they took everything that I learned in Math 10 and summed it up into formulas. This is way easier to use than SOH CAH TOA or anything similar.
  • here are the formulas

  • Sine Law: Useful for finding unknown sides or angles in non-right triangles when we know either:
    • Two angles and one side
    • Two sides and a non-included angle
  • Cosine Law: Useful for solving triangles when we know:
    • Two sides and the included angle
    • All three sides to find any angle

Quadratic formula

  • this formula is another example of a formula that I could’ve used in math 10 to make math a little easier. once you have the formula memorized it becomes a straightforward process to apply it to any quadratic equation and compared to other factoring methods like completing the square or grouping, this is way more straight forward.
  • here is the formula 
  • once you have identified your values and put them in the formula you start solving for x
  • by only solving the discriminant you can find the nature of the roots
  • if discriminant = 0 —- there is 1 solution
  • if discriminant = negative —– no solution
  • if discriminant = positive —– 2 solutions

Radicals as powers (flower power)

  • viewing radicals as fractional exponents makes working with them a lot easier. once you apply the radical as a power you can easily apply all the exponent rules to the expression.
  • the denominator is the root.
  • the numerator is the power 

Graphing quadratic functions

  • graphing quadratic functions provides a visual representation of the relationships between variables. it shows how many units the parent functions needs to move around.
  • The graph of a quadratic function is a parabola, which is a U-shaped curve. The direction and openness of the parabola depend on the sign of the coefficients. If a > 0, the parabola opens upwards, and if 0>a the parabola opens downwards.

  • Vertical Translations: Adding a number moves the graph up. Subtracting a number moves the graph down.
  • Horizontal Translations: Adding a number inside the function shifts the graph left. Subtracting a number inside the function shifts the graph right.
  • Vertical Stretching/Compression: Multiplying the function by a number: If the number is greater than 1, it stretches the graph vertically. If the number is between 0 and 1, it compresses the graph vertically

 

Restrictions with radical

  • the last thing is the restrictions that come with radicals and even fractions. restrictions ensure that we have real number solutions and that the solution is not undefined/no solution.
  • Even-Root Radicals (e.g., Square Roots):
    • The radicand (the number under the root) must be non-negative. This is because the square root of a negative number is not defined in the real number system (it belongs to the complex number system).
    • For example, square root of x, .
  • Odd-Root Radicals (e.g., Cube Roots):
    • The radicand can be any real number (positive, negative, or zero). This is because the cube root of a negative number is a negative number, and the cube root of a positive number is a positive number.
    • For example, cube root of x, all real x. 

 

Week 17 in PreCalc 11 – Sine Law

This week in precalc 11 we learned about sine law. I chose this topic to cover for this week because you can use sine law for any type of triangle (acute, obtuse, right, non-right etc.) you can also use this formula to find angles AND sides. 

If you would like to find an angle, have SIN be on top. If you want to find a side flip it the other way (small letter goes on top)

  • once you have the formula fill it out with the given information.
  • Sin A, B, C are the angles
  • a, b, c are the sides
  • Select one of the ratios from the law of sines based on the given parts of the triangle.
  • Use the chosen ratio to set up an equation involving the known and unknown parts of the triangle.
  • isolate and solve.
  • make sure to add brackets when putting the numbers in the calculator.

Week 16 in Pre calc 11 –

In trigonometry, special angles have exact trigonometric values, which are useful for simplifying calculations and solving problems. The special angles are 30°, 45°, and 60°.

30°/60°Angle

Reference Triangle: The 30° angle is often found in a 30°-60° triangle, which is half of an equilateral triangle.

45° Angle

Reference Triangle: The 45° angle is found in a 45° triangle, which is an isosceles right triangle.

  • In a 45° triangle, both legs are equal in length.

Use this concept whenever you get a reference angle of 30,60 or 45. make sure to draw the triangles and refer to them throughout the question. use the x,y and r values given by the triangles.

Problem: Find the exact values of sin⁡(150°), cos⁡(210°), and tan⁡(330°)

  1. Reference Angle: 180°−150°=30
  2. Trigonometric Value: sin 30° = y/r —> square root of 3/2 

  1. Reference Angle: 210°−180°=30 
  2. Trigonometric value: cos 30°= x/r —> 1/2

  1. Reference Angle: 360°−330°=30°
  2. Trigonometric Value: tan⁡(30°)= y/x —-> 2 

Week 15 in Precalc 11 – Word Problems

This week in Pre calc 11 we have been working on rational expressions. I learned how to tackle word problems with rational expressions this is useful because many of these word problems are problems that you would tackle in the real world. I’m going to be talking about distance, speed and time problems. To get started we need to memorize this formula that can help us solve:  Speed Distance Time - GCSE Maths - Steps, Examples & Worksheet if you want to find speed, you cover speed with your finger and see that distance is on top of time, this means that we need to divide distance over time to figure out speed. The same goes for the rest.

World Problem:  Evan drove 308 km at the same time that Meghan drove 329 km. If Meghan drove on average 6km/h faster than Evan, calculate her average speed and the time taken for the journey. 

step 1. Read the questions carefully and figure out what you are trying to find. We are trying to find Meghan’s speed.

step 2. Make a let statement. This word problem doesn’t tell us the time, it only tells us that Meghan was 6km/h faster. Therefore let x be Evans speed.

step 3. Draw your table and plug in numbers

step 3. time. to find the time, we use our triangle. Distance divided by speed. the only information given about time is that Mgehan and Evan drove in the same time. This indicates that our expressions would equal one another.

step 4. solve the equation.

Step 5. add 6 because meghan was 6km/h faster

Week 14 in Precalc 11 – Multiplication of rational expressions

This week in precalc 11 we learned how to add, subtract, multiply and divide rational expressions. In this unit, rational expressions are complex-looking fractions with variables. I will be focusing on how to multiply these rational expressions

Working with rational expressions is no different than working with regular fractions. In regular fractions, we multiply across and simplify where possible.

Example: 

  • simplify
  • multiply across
  • set restrictions (non permissible value)
  • cancel things out

Example:

  • factor if possible
  • cancel things out
  • multiply
  • set restrictions
  • bring down the other expression and do the same

Week 13 in Precalc 11 – simplifying rational expressions

This week in precalc we started working with rational expressions (fractions with variables). We first started with simplifying them which is a key aspect for working with these kinds of questions (adding, subtracting, etc.). It is important to remember after each question you are required to state the non-permissible value because there is a variable in the expression.

Non-permissible value: The value of a variable that makes the denominator of a rational expression equal to zero.

example 1:

  • the first thing should always be observing to see if you can make the expression any simple like factoring out anything or cancelling any numbers or variables.
  • In this case, we can cancel (a-8).
  • The non-permissible value should always be stated before you cancel anything out.

example 2:

  • by observing the expression we can see that both the numerator and the denominator are factorable.
  • write the non-permissible value
  • cancel anything that is left over.

example 3:

  • here we can see that the expressions are similar but they aren’t in the same order.
  • in this case, we can still simplify BUT it does not simplify to a 1. It simplifies to a -1.

Week 12 in PreCalc 11 – Graphing inequalities

This week in Precalculas 11 we went over inequalities and what they mean. We also learned how to graph them. In graphing inequalities, we can use what ve learned from the last unit, like vertex, x-intercept, y-intercept, etc. to help us graph inequalities.

Example : y> – (x+4)^2

  • first I graphed the expression on demos without the inequality sign to see what it would look like. in this example we already have the inequality in vertex form so it is easy to graph but if we dont have to solve it a little bit.

  • now that I plugged in the inequality sign there are some changes we can see so let’s break it down
  1. As you can see the parabola has a dashed line, this is because our inequality does not have the small line under it. This means that y is greater than… If it was greater than or equal we would but a bold line.
  2. Everything outside the graph is shaded. This is because of the inequality sign. Our expression is telling us that our solution has to be greater than – (x+4)^2. So how to we figure out where to shade.
  • take a random point in a graph and plug in the x and y into the original function
  • if you get a true statement then this means that the shading should go in this zone. In this case it is outside the parabola. 

Week 11 in PreCalc 11 – Inequalities

This week in pre-calc 11, we briefly went over inequalities and systems in one lesson. By inequalities, I’m referring to the relationship between two expressions. I like to think about the inequality signs as alligator mouths, they eat whichever number or expression is the biggest.

example: x>7 — x is bigger than 7 that’s why it is getting eaten. X could be any number that is above 7

example: 78 Less Than or Equal Symbol (≤) x —– x is bigger than or equal to 78.

  • during graphing or on number lines if there is a dash line, it means the inequality sign does not have the small line under it

  • if there is a solid line, it means that the small line is on the inequality sign.

Graphing inequalities :

  • When the expression is given to us, we move everything to one side and make sure to isolate y. what we are left with is our slope and y-intercept.

  • graph the expression
  • the inequality sign tells you which side of the line to shade, to figure this out take point (0,0) substitute into the inequality and simplify. If the inequality is false we shade the part that doesn’t contain the point.  if it is true we do shade the point.