Unit 5 Reflection

In this unit, we learned about walking the dogma - the basics of protein synthesis, the process in which DNA becomes a protein. We did multiple labs that helped us understand the essentials of this unit, including DNA structure and function, DNA replication, and Gene expression and regulation. 

Protein synthesis has many steps. First, a copy of the DNA (deoxyribonucleic acid) is made in a process called transcription, then the copy is used to make a protein, in translation. Proteins are essential to life. The first step of translation is for a section of DNA, known as a gene, to be copied by an enzyme, in the nucleus. The copy is called messenger RNA, often abbreviated as mRNA. RNA has a few main differences form DNA: It is only single stranded, and the base uracil replaces thymine. 

After the copy is made, the mRNA leaves the nucleus and travels to the cytoplasm. Then, translation beings - the mRNA bonds with a ribosome, which will make a protein. The ribosome reads the first three bases called a codon, and determines which amino acid corresponds with that sequence. Each amino acid that is determined by the codon is read by the ribosome. Amino acids are bonded together and when the mRNA is done being translated, the amino acid chain fold up to become a protein. 

The gene expression and regulation lesson was particularly hard for me, but it was the one that I found the most interesting. The basic questions of that unit was: Why do genes appear in the correct places and at the correct times? Why don't we have eyes on our feet and toes on ours heads? And the answer was gene expression and regulation. 

Gene expression is the process of a gene being used to produce a gene product of the phenotype, basically what gene is expressed in the person. Gene regulation is a mechanism used by cells to increase or decrease the expression of a certain gene.

Another essential concept in this unit was Mutations. Although the connotation of the word mutation notes otherwise, mutations are generally very small and can have little to no effect. Is biology a mutation is a change in the DNA code. Mutations are happening almost constantly in our body. There are two main types of mutations - substitution and frameshift mutations. Substitution is when one nucleotide is substituted for another. There are two types of frameshift mutations - insertion and deletion. Insertion is when an extra base is put in and deletion is when a base is taken out.

The effect of the mutation is truly determined by where the mutation is placed. Suppose a harmful mutation to create a STOP amino acid, is placed at the front of the amino acid sequence - then the harms would be devastating. But, if the same mutation is placed near the end, then the amino acid sequence is still changed, but on a much smaller scale, thus it would not be that harmful.

One of my strengths in this unit were the labs - They really helped em visualize and understand the processes. We did a DNA extraction lab as well as a protein synthesis lab, among other things. These labs allowed me to get a full understanding of the concepts. The process of doing the lab, whether the product came out good or not, helps me understand concepts much better than reading or watching a vodcast.

One of my weaknesses in this unit were the vodcasts. Some of the vodcasts were hard to fully understand, but I was able to ask questions to my group and do the labs to make up for it. The vodcasts were especially hard because diagrams were confusing. I was not able to follow some of the diagrams, but when we did them on the board in class, I got the concepts.

Overall my growth as a learner in this unit has become tremendous, mainly because of a VARK questionnaire that I took at the end of my last unit. It told me that I was a better visual learner, and I have always known that I always understanding best when actually doing something. I feel that I have really learned what helps me understand certain concepts and how I should study in the future for science, or for any other subject. This will help me throughout my years of learning, especially as finals week comes nearer.

This unit has also taught me about how to react well to setbacks. During the DNA extraction lab, at first, I was not able to extract DNA properly, due to a mistake in our procedure. But instead of getting mad at myself, I kept my head held high and redid the lab in the correct way. I was able to finish the lab before class ended and thus, I learned how to recover form a small setback in a lab.

This unit also really helped me learn how to collaborate with others in my group. During most of my previous units I understood most of the vodcasts and there was no need, really, to discuss properly with my group about it. But in this unit, since I did not understand the vodcasts completely, I needed to collobarate with my group to make sure I got the concepts down.

Protein Synthesis Lab

In this lab, we asked the questions, "How does the body produce proteins and What kinds of mutations cause the greatest damage to the structure of a protein?" To answer these questions, we followed the steps of protein synthesis, throughout transcription and translation.

Protein production can be sorted into two main steps, with multiple substeps. First, a copy of the DNA (deoxyribonucleic acid) is made in a process called transcription, then the copy is used to make a protein, in translation. Proteins are essential to life. The first step of translation is for a section of DNA, known as a gene, to be copied by an enzyme, in the nucleus. The copy is called messenger RNA, often abbreviated as mRNA. RNA has a few main differences form DNA: It is only single stranded, and the base uracil replaces thymine. After the copy is made, the mRNA leaves the nucleus and travels to the cytoplasm. Then, translation beings - the mRNA bonds with a ribosome, which will make a protein. The ribosome reads the first three bases called a codon, and determines which amino acid corresponds with that sequence. Each amino acid that is determined by the codon is read by the ribosome. Amino acids are bonded together and when the mRNA is done being translated, the amino acid chain fold up to become a protein.

"Protein Biosynthesis." Wikipedia. Wikimedia Foundation, n.d. Web. 12 Dec. 2016. <https://en.wikipedia.org/wiki/Protein_biosynthesis>.

Of the mutations that we tested in this lab, I was able to conclude that each mutation could be nearly as harmful as every other mutation, depending on of the situation, the code, and when the mutations occur. We tested three types of mutations - substitution, insertion and deletion. The effect that substitution caused varied - only being extremely harmful when placed in a certain position. Otherwise, substitution is generally harmless. Insertion and deletion followed a similar pattern. When put near the start of the sequence, the change did quite a bit of damage, but when placed at the end, not much damage occurred.

"What Types of Mutation Are There?" Facts. The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016. Web. 12 Dec. 2016. <http://www.yourgenome.org/facts/what-types-of-mutation-are-there>.

When I chose my mutation I chose to replace the first G with the First T, as I wanted to see what happened if one of the early letters was changed. What ended up happening was that, the stop codon (UAA) was the second amino acid in the sequence, after MET, the start codon. This would have a devastating effect, especially if the protein was important, as it would not be able to make the protein. This shows why the place that the mutation is located can have a really big effect. Earlier in the lab we did a mutation at a different place in the same sequence and there was not a single effect on the amino acid sequence.

"What Types of Mutation Are There?" Facts. The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016. Web. 12 Dec. 2016. <http://www.yourgenome.org/facts/what-types-of-mutation-are-there>.

Because proteins are so essential to life as they play a part in almost every activity we do, mutations can sometimes be extremely harmful, especially if it greatly alters the amino acid sequence formed by the mRNA sequence. But it is also important to note that mutations happen often on a daily basis, and that most mutations are not as harmful. One example of a disease caused by mutations is phenylketonuria, abbreviate PKU. PKU is an incurable, chronic disease, that although rare, can cause great damage to the body. It is a birth defect that causes an amino acid called phenylalaline to build up in the body, which can lead to brain damage, intellectual disabilities, behavioral symptoms or seizures. PKU is an autosomal recessive disease caused by a mutated gene for the enzyme phenylalanine hydroxylase (PAH), which converts the amino acid phenylalanineto other essential compounds in the body.

"Phenylketonuria." U.S. National Library of Medicine. National Institutes of Health, n.d. Web. 12 Dec. 2016. <https://ghr.nlm.nih.gov/condition/phenylketonuria>.

DNA Extraction Lab

In this lab, we asked the question, "How can DNA be separated from cheek cells in order to study it?" We collected information about the three main steps of DNA extraction. Homogenization, lysis, and precipitation. We found that DNA from cheek cells could be extracted and studied if the correct steps are used in the correct order. The correct steps the proper order are as follows:

1.  Measure 2.5mL of Gatorade into a paper cup
2.  Scrape both sides of the inside of your checks using your teeth.
3.  Vigorously swish in your mouth for 30 seconds.
4.  Spit solution back into cup
5.  Add a tiny punch of salt
6.  Carefully poor solution into a test tube about 1/3 to 1/2 of the way up
7.  Add 10 drops of detergent/soap.
8.  Add 5-10 drops of your enzyme (pineapple juice)
9.  Let sit for 5 minutes and record observations.
10.  Tilt the tube at an angle and slowly add cold alcohol along the side of the test tube. You do not want the two layers to mix. The amount added should be about the same as the Gatorade mixture.
11.  Collect the DNA and alcohol and carefully, with a transfer pipette, and place in a microcentrifuge tube. Do your best to only transfer DNA and Alcohol to your tube.
12. Cover the tube with your thumb. Carefully invert 6 times. Be careful not to shake too much. You do not want soapy bubbles to form.
13. Wait for another 5 minutes and record observations. 

Evidence from Experiment: During our first trial we switched steps 11 and 12, and thus we were not able to extract DNA, but when we did these steps in the correct order, we were able to extract DNA.

Reasoning: This evidence supports our claim, because during the first trial, which failed, the two layers, of alcohol and Gatorade, mixed and thus we were not able to separate DNA. However during the second trial which succeed we only inverted the tube after separating DNA, and thus was able to get the DNA.

Possible Error 1: The first error that we made was switching the order of the steps. Part of our lab was to put random steps in the correct order. We ended up switching steps 11 and 12, thus inverting the tube 6 times (and mixing the alcohol and Gatorade solutions), before separating the DNA. The effect of this error on the overall results was the fact that we were not able to get the DNA separate and the end of the experiment.

Possible Error 2: That was the only error we made in the experiment, but a hypothetical error could have been not adding the alcohol while the test tube was tilted. The effect of this would have been the same as the effect in PE 1, as the DNA would not separate at the end of the experiment.

This lab was done to help us understand the process of DNA Extraction, including the 3 main steps - homogenization, lysis and precipitation. I can relate this lab to the vodcast about "Your Genetic Code." The concepts from that vodcast, really helped me to do this lab, and my overall understanding of DNA was solidified through this lab process. The fact that we first messed up and then fixed our mistakes, really helped me understand some of the important concepts, like the enzymes breaking down the DNA.

From this lab, I learned the correct process of DNA extraction, and now I could extract DNA from any cell. This would be helpful if I wanted to study DNA, especially discrepancies in genetic variation, in the future as a scientist. Another outcome I learned from this lab is to slow down. At first, I though for sure that the first procedure we came up with was correct, but in hindsight, I feel like if I thought about it a bit more, I would have been able to see the mistake and correct it before we started the experiment. This teaches me to double check everything I do, and most importantly, slow down.