Unit 5 Reflection

This unit was about genetic code. We talked about what DNA is, a nucleic acid and it's function, to keep the special code of what makes you, you (order of nitrogen bases). It's made of three parts, a phosphate group, deoxyribose, and nitrogen base. There are four nitrogen bases, Adenine, Guanine, which are purnies, meaning they have double rings, Thymine, and Cytosine, which are pyrimidines, meaning they have single rings. Adenine joins with Thymine and Guanine join with Cytosine. We also talked about the process of DNA replication. First, an enzyme, helicase, unzips the DNA by breaking the hydrogen bonds that hold the nitrogen bonds together. Second, another enzyme, DNA Polymerase adds matching nucleotides to each strand. The end result is 2 identical DNA molecules. Then we learned about how proteins are made. It starts with DNA and transcription, which happens in the nucleus. First, DNA unzips. Second, RNA Polymerase match spare nucleotides to make an RNA strand. Third, mRNA is produced and leaves nucleus for cytoplasm. In the cytoplasm, translation occurs. mRNA arrives at a ribosome, which reads the mRNA 3 bases, or one codon, at a time and translates DNA language to protein language (T replaced with U). 3 bases, or one codon, makes one amino acid. The end result is a long chain of amino acids, which twist, fold, and combine with other chains to make a protein. After, we learned about mutations. A point mutation changes one or two bases of DNA. There are two types of this mutation, substitution, in which one nucleotide is substituted for another, and frameshift mutation, where there are two types, insertion, an extra base is put in code, and deletion, a base is cut out of the code. Some other mutations we learned about were inversion, when DNA breaks off and bonds in reverse order, and translocation, when parts of a chromosome breaks off and bonds with another chromosome. The last thing we learned about was gene expression and regulation. Gene expression is the process of a gene being used to produce a gene product or phenotype. Gene regulation is the a mechanism used by cells to increase or decrease the expression of a gene, which is done is a series of steps. Let's use the Lac Operon as an example. Bacteria use lactase to break down lactose. When lactose is absent, the repressor molecule, which stops a gene being made, on the gene blocks RNA Polymerase from transcribing the gene. But if lactose is present, the lactose will bond with the repressor protein and make it detach it from the operator, which is the segment of DNA at the start of a gene that prevents or allows RNA from attaching and reading the gene. A promoter is the location on DNA where RNA Polymers attaches and the operon is the whole series of genes used to control the expression of a single gene. Eukarytoic regualtion is a lot more complicated due to several proteins binding before a gene and required for the gene to be expressed. Exons are the sequences that are expressed and introns are the sequences that are cut out. DNA is highly coiled to pack extra info in a very small space. Histones are proteins that DNA coils around and that forms nuclsomes, which weave together to pack more info more tightly. 

Zephyris. "DNA Structure+Key+Labelled." Wikimedia Commons, 26 Apr. 2011, 
     commons.wikimedia.org/wiki/File:DNA_Structure%2BKey%2BLabelled.pn_NoBB.png. 
     Accessed 15 Dec. 2016. 

"Ending Transciption." Study Blue, www.studyblue.com/notes/note/n/ 
     chapter-16-transcription-and-translation/deck/4811159. Accessed 15 Dec. 
     2016.

Some strengths I had was understanding mutations and DNA replication easily, while having a hard time with gene expression and regulation, but eventually clearing up any questions I had in class. I want to learn more about eukaryotic regulation and the different types of gene regulation examples. An unanswered question I have is how many mutations does an average human have. I wonder about how complex life is and how everything works together to perform tasks like typing up a paper.   

I have grown as a student by being more open to my group members and asking them clarifying questions when I need to. I also learned to be more organized in my lab work and to try to cut down on how many textbook notes I take, since I wrote a lot of unimportant details earlier in the semester. One thing I wish to work on is my time management skills since it always seems I am running about of time.

Protein Synthesis Lab

To make a protein, mRNA is made from DNA and is transferred to the cytoplasm. The mRNA bonds with a ribosome, which will make the protein. The ribsome reads three bases, or codons, at a time to make an amino acid. The type of amino acid is determined by the codon's sequence of bases. The amino acids are bonded together as more are made and once the ribosome has finished translating the mRNA into amino acids, the amino acids folds up to form a protein. 

Boumphreyfr. "Peptide Syn." Wikimedia Commons, 1 Mar. 2009, 
     commons.wikimedia.org/wiki/File:Peptide_syn.png. Accessed 13 Dec. 2016. 

The deletion mutation seemed to have the biggest effect. If the mutation deletes a base and makes the new codon a stop codon, the protein produced will be too short. If it deletes a base in the beginning of the mRNA, then it will affect the whole sequence. Where as if it happens at the end of the mRNA, then it will only effect the last couple bases or none, which is a smaller area that is effected. The substitution mutation seemed to have the smallest effect.  if the mutation changes a codon into a stop codon, it will make the whole amino acid chain shorter. If it changes a C to a G but the same amino acid is produced, then nothing will change. If it changes a C to a G and a diffrent amino acid is produced, several things way change.

Institute, National Human Genome Research. "Missense Mutation Example." 
     Wikimedia Commons, 25 Mar. 2013, commons.wikimedia.org/wiki/ 
     File:Missense_Mutation_Example.jpg. Accessed 13 Dec. 2016. 

I choose the deletion mutation to show that the translation process can be stopped very early. This mutation had the biggest effect out of all of them because the translation stopped after the start codon. It does matter where the mutation occurs because it will effect the bases after them and can stop the process of translation early on.

Before:

After:

A mutation can cause an important boldly function to stop working properly or stop working at all. This can lead to having a difficult life that may end earlier than most. Tay-Sachs disease causes fatty liquids to build up in the brain, damaging brain cells and the spinal cord. Tay-Sachs diseas comes from a defect in a gene on chromosome 15. 

Source:
"Tay-Sachs Disease." PudMed Health, www.ncbi.nlm.nih.gov/pubmedhealth/
     PMHT0024672/. Accessed 13 Dec. 2016.

"Human Male Karyotpe High Resolution." Wikimedia Commons, 4 July 2015,
     commons.wikimedia.org/wiki/
     File:Human_male_karyotpe_high_resolution_-_Chromosome_15.png. Accessed 13
     Dec. 2016.

Human DNA Extraction Lab Conclusion

In this lab we asked the question, how can DNA be separated from cheek cells in order to study it. We found that we could if we followed a series of steps. A qualitative observation that proves this is the chuck of DNA that was formed when I followed the procedure correctly. Some evidence from current scientific concepts say that if cheek cells are taken from someone, add a pinch of salt, which protects the negative phosphate of DNA, making them move closer to each other, 10 drops of detergent, which is used to lyse o disintegrate the cell membrane and causes all the contents of the cell to be released into the mixture, and 5-10 drops of enzymes, which breaks down the proteins called histones that causes DNA to wrap itself around them, shake the tube 6 times, let the solution sit for 5 minutes, add the same amount of alcohol as the mixture, making sure not to mix them, and since alcohol is polar and DNA is nonpolar, the DNA becomes a precipitate, let it sit again for 5 minutes, DNA would become visible.

While our hypothesis, if we are able to see DNA, then we will see it after we add the alcohol to the solution, was supported by our data, there could have been mistakes of how much of a certain solution we added, so some of us were not able to see our DNA or only a certain amount of it, and how long it took to make part of the solution, so if some of us took 5 minutes making a part of the solution, while others took 10, maybe the people who took longer were not able to see their DNA or only a certain amount of it. Due to these errors, in future experiments I would recommend being more precise with measurements and to time everything as closely as possible.

This lab was done to demonstrate how DNA could be extracted. From this lab I learned that certain items, like pineapple juice, salt, and detergent, have certain items in them like pineapple juice has catabolic proteases which break up certain proteins, which helps me understand the concept of what a cell and DNA molecule is made of more clearly. Based on my experience from this lab, I have a better understanding of the chemical properties of cells and DNA and will be able to understand more difficult concepts later.