Holly Jossart

9-26-17
Stem biology

Alu PCR Lab

Purpose: The labs purpose was to teach us about genotypes and which Allele goes

with each one. An allele is a description for different forms of a gene and and an Alu is a

repeat that can show up on both, one, or neither of our number 16 chromosomes. We

used PCR(polymerase chain reaction; a method used by scientists to rapidly copy, in

vitro, specific segments of DNA) to find out where our own Alu is on our number 16

Chromosomes.

Hypothesis: If we do the lab correctly, step by step, then we will figure out where our

Alu insert in on our number 16 chromosomes.

Procedure: We performed this lab in accordance with the BABEC Alu PV92 PCR lab.

BABEC link: http://babec.org/wp-content/uploads/2016/12/Alu_Student_Guide_2017.pdf

Data/Observation:

-2% agarose gel ran at 1500 for 20 minutes. Agarose Gel for the class

-Loading dye gel was dyed using red dye

-lane 1A has a full ladder

-lane 2C has a thin ladder

-lane 1E has a vague ladder

-lane 1C has dots, but no ladder

-lane 1B (mine) had no results (Outlined in Red)

Analysis/Discussion:

The below data was used by finding how many positive and negative alleles our class

had. We analyzed the data to find what we would expect to find verse our actual results.

-(used other given results because we did not have enough successful results in our

class to find useful data from)

Genotype # of Students Having Genes

+/+ 15

+/- 10

-/- 12

Two Alleles per students: 37 students x2= 74 alleles

Genotype # Of Students # of + alleles # of - alleles

+/+ 15 30 0

+/- 10 10 10

-/- 12 0 24

Total: 37 40 34

Found the expected Genotypes with these equations:

First know p=positive q=negative

Second found: allele freq.; total + alleles (40) divided by total alleles (74) equals .541

Same for - alleles and got allele freq.= .459

Used below equations and plugged in the allele freq. We got into either p or q to solve.

Expected +/+ genotype freq. = p^2

Expected +/- genotype freq. = 2pq
Expected -/- genotype freq. = q^2

Results in below Table:

Genotype Expected Genotype Total # of Students Expected # of

Frequency in Class Students w/
Specific Genotype

+/+ .293 37 10.841

+/- .497 37 18.389

-/- .211 37 7.807

I did not find results as successfully as I would have liked because of errors throughout

the procedure. Some of the few things that could have gone wrong were; imprecise

micropipetting, incorrect time for DNA on ice, inaccurate centrifuge time, shaking after

centrifugation, picking up Chelex beads, and inaccurate loading into gel. My hypothesis

was correct because I did not due the lab correctly, meaning I did not find my Alu insert

in my number 16 chromosome.

For future reference, we could learn how to use a pipet more accurately as this was a

big struggle to hit success. We also could try and see what happens when we mess up

one part of the experiment, but nothing other. We could possibly get results we were not

expecting.

Conclusion:

During the PCR lab, I learned a lot of skills for biology, while also trying to find out some

cool things about myself. The PCR experiment was a lab to try and find out if we had

any Alu inserts in our number 16 chromosomes and if they are negative or positive. We
did this using technology like micro pipetting, centrifuge, and Agarose gel, which helped

us learn many biotechnology skills. Although I improved my skills, I did not find the data

I was hoping for. For example, there was not a full ladder in my Agarose gel, showing

that something went wrong in the lab. I specifically remember one part in the lab where I

accidently shook my DNA after I centrifuged. Although I re-centrifuged, this could be a

big reason why I didnt find results. With the DNA everywhere, it was harder to pick up

with the micropipet, possibly meaning I got a very small amount of DNA. This happening

shows a perfect example of the Scientific Method. Something went wrong and now I

must refine it and try again. Science is a matter of patience, because it is very likely that

the first few times, things dont go as planned. One thing I noticed from my data was

that the +/+ genotype frequency was higher than the -/- frequency. Even though they

are opposites of each other, they will not have the same expected Genotype frequency

because of mutations. A small mutation can cause different sets of genotypes than

expected. This happens in all organisms and it is how we evolve to our surroundings.

For example, it is why brown mice become more common in an area with a lot of brown

coloring. One mouse will have a mutation and be black, and soon all the white mice will

die off because they dont have the mutations. A small mutation in a gene changes a lot.

This lab was a very good learning experience and a good way to first learn how to use

many biotechnology tools.