Unit 5 Reflection

Unit 5 was about genetic code, DNA replication, making proteins, mutations, and gene expression and regulation. DNA is a double helix made up of two strands twisted around each other like a twisted ladder. DNA is made up of nucleotides. Nucleotides are made up of 3 parts: a nitrogen base (A, T, C, G), a phosphate group, and a sugar (deoxyribose). Phosphate and sugar make up the sides of the ladder and the bases are the steps. DNA is anti-parallel. This means that each nucleotide covalently bonds with another. Nitrogen bases come in two types: double rings called purines(adenine and guanine), and single rings called pyrimidines (thymine and cytosine). Adenine always pairs with thymine, and Cytosine always pairs with guanine. Code is a system of words or symbols that are substituted for other words.

Semi-conservable replication is the process of creating two identical strands of DNA from one original strand. Two strands end up with half of the original strand. First, enzyme unzips DNA by breaking down hydrogen bonds that hold nitrogen bases together. Then, DNA polymerase add matching nucleotides to each strand. The result is two identical strands of DNA molecules that form are identical to the original DNA molecule.

The central dogma of biology is that information flows from DNA to RNA to proteins. Proteins make up out traits (phenotypes). RNA is single-stranded, has a ribose,contains uracil, and is a temporary copy of DNA. RNA delivers a copy to the ribosomes, and the ribosome uses this RNA copy to make proteins. Transcription is a process in the nucleus where RNA polymerase reads and copies the DNA code (gene) for a protein as mRNA. In the process of transcription, DNA unzips, RNA polymerase matches spare nucleotides to make an RNA strand,and mRNA is produced and leaves the nucleus for the cytoplasm. Translation is a process that takes place in the cytoplasm. First mRNA arrives at the ribosome. Then, the ribosome reads mRNA three bases at a time and transcribes the DNA language into amino acids. Each three-base sequence is known as a codon. Each codon codes for one amino acid.

A mutation is a change in DNA code (genes.) The effect can be none and sometimes it can be fatal. Mutagen is anything that causes a mutation. Mutations can happen naturally too. Point mutations are a change in one or two base pairs. These types of mutations are very small and common. A substitution is a change in which one nucleotide is substituted for another. The two types of frameshift mutations are insertion and deletion. Insertion is a mutation where one extra base pair is put in code. Deletion is a mutation in which one base pair is left out of the code. Inversion is a mutation where DNA breaks off and bonds in reverse order. Translocation is the part of a chromosome that breaks off and bonds with another. Mutations cause changes in DNA which cause changes in life. Proteins are essential to life.

This is a picture of an RNA strand being translated to an amino acid.

Gene expression is the process of a gene being used to produce a gene product or phenotype. Gene regulation is a mechanism used by cells to increase or decrease the expression of a gene. Every cell in your body has the same DNA but not all cells look the same. Cells look different because each type of cell expresses or turns on genes specific to those cells. Environment can affect how and when genes are expressed. Gene regulation is the process where cells do not want to waste energy or overexpress genes so they have many steps that are used to control gene expression. A promoter is the location on DNA where RNA polymerase attaches. An operon is a series of genes used to control the expression of a single gene. The operator is a “switch” or segment of DNA at the start of a gene that prevents or allows RNA polymerase from attaching and reading the gene. Eukaryotic regulation is much more complicated than bacterial regulation. EXons are EXpressed and introns are sequences that are cut out. Histones are proteins that allow DNA to coil. Nucleosomes are DNA that is wrapped twice around like a histone. Genes whose promoters are wrapped up in nucleosomes are not expressed. Different enzymes are involved in breaking histones free or binding them up to control gene expression. This is passed to future cells during development.
I really liked learning about making proteins and DNA. I had a difficult time on the protein synthesis lab because I did not understand how to convert a DNA strand to an RNA strand. After going back and watching the vodcast, I understood how to convert DNA to RNA. I also struggled in understanding the last vodcast. The vodcast was about gene expression and requlation. I didn't know the different parts of the operon. After doing the do now in class, I had a better visual understanding of an operon.

This is a picture from the protein synthesis lab that was difficult.

Protein Synthesis Lab

   
    There are many steps required to make a protein. First, RNA polymerase reads and copies the DNA code or gene for a protein as an mRNA copy through the process of transcription. Transcription happens in the nucleus. In the process of transcription, DNA unzips. Then, RNA polymerase matches spare nucleotides to make an RNA strand. mRNA is produced and leaves the nucleus for the cytoplasm. After transcription happens, the mRNA arrives at the ribosome. In the process of translation, the ribosome reads RNA three bases at a time and translates DNA language into protein language. Each three-base sequence is called a codon. Each codon codes for one amino acid.

A mutation is a change in DNA code. An insertion is a mutation in which an extra base pair is put in code. A deletion is a mutation where a base pair is left out of the code. The mutation substitution happens when one nucleotide is substituted for another. In my opinion, substitution affected the protein the least because it only changed one nucleotide. A deletion affected the protein the most when it was added in the beginning because it changed every nucleotide after it was added. It does matter where the mutation occurs when it is a deletion or insertion because all the code after the added or deleted nucleotide is affected.

   

 In step 7, I chose to do a deletion. I think that a deletion affects the DNA code the most. It does matter where the mutation occurs. I put my deletion in the beginning, so all my code was affected.

http://bit.ly/2hnDHVv
This is a picture of a child with Progeria.
Mutations can have a big impact on a person's life. They can create genetic disorders. Progeria causes accelerated aging. Most children who have progeria die at the age of 13. Their death is causes by a stroke or heart attack. Progeria is caused by a mutation that is located on the LMNA gene which is a protein. This protein gives support to the cell nucleus. 

   

Human DNA Extraction Lab

In this lab, we asked the question how can DNA be separated from cheek cells in order to study it? We found that it is possible to separate DNA from cheek cells. My hypothesis stated that if DNA can be seoarated fromm cheek cells, then DNA would be visible after precipitation. First, we swished Gatorade in our mouth for 30 seconds. Then, we added enzymes to speed up the process. The enzymes that were added were: salt and dishwasher soap to the solution. Since the DNA was still insoluble, we added rubbing alcohol to the solution. When we added the rubbing alcohol, the DNA percipitated from the Gatorade. In this lab, the rubbing alcohol was a protease because it catalyzed the splitting of the interior peptide bonds in a protein. The DNA rising from the gatorade was a catabolic process, which gave rise to substances of decreasing complexity. I could see the DNA after the DNA was percipitated. This data supports our claim because we could extract DNA from cheek cells, and I predicted that the DNA would be visible after precipitation.
     While our hypothesis was supported by our data, because there was no procedure in this lab, there could have been errors. In the beginning of the lab, we were given a piece of paper with the procedure. However, this paper did not have the steps of the lab in the right order. We had a tough time putting the procedure in order, and we had a big discussion at our table about which step was first. Another error was that someone at our table poured too much Gatorade into my cup. Because of this, I had a hard time swishing all the Gatorade in my mouth. If I had less Gatorade, I probably could have gotten more cheek cells. Due to these errors, I would recommend having an accurate procedure.
     This lab was done to demonstrate DNA replication and extraction. From this lab, I learned that DNA can be extracted from cheek cells, which helps me understand the concept of DNA extraction. Based on my experience from this lab, I now know how complicated DNA is and I was able to see what my DNA looks like.

Coin Sex Lab and Unit 4 Reflection

     In the coin sex lab, we flipped coins to show the probability of the phenotype of an offspring. The coins demonstrated the probability of a child inheriting their parents' genes. In the dihybrid cross, two individuals were both double heterozygous. The dominant alleles were brown hair (B) and brown eyes (E). The recessive alleles were blonde hair (b) and blue eyes (e). Meiosis is the process of making gametes in testes or ovaries. There were two different possibilities for meiosis. By completing the Punnett Square, I found that the expected outcome was 9 offspring with brown hair and brown eyes, 3 offspring with brown hair and blue eyes, 3 offspring with blonde hair and brown eyes, and 1 offspring with blonde hair and blue eyes. After flipping the coins and collecting my data, I found that Punnett Square is an accurate representation in predicting the phenotype of an offspring. I got 9 offspring with brown hair and brown eyes, 3 offspring with brown hair and blue eyes, 3 offspring with blonde hair and brown eyes, and 1 offspring with blonde hair and blue eyes when flipping the coins.
     The autosomal dominance lab determined the probability of having a bipolar offspring if one parent is heterozygous for the trait and the other parent is homozygous and does not have the trait. The Punnett Square was a monohybrid of Bb x bb, where B is the bipolar allele and b is the normal allele. I predicted that 50% of the offspring would have the bipolar disorder. After flipping the coins and collecting the data, I came to the conclusion that 4 offspring had bipolar disorder, and 6 were normal. Although the Punnett Square was not a completely accurate representation of my results, the Punnett Square was pretty close to accurate.
     In the X-Linked Recessive part of the lab, the female was a carrier of colorblindness, and the male had normal color vision. The Punnett Square was a monohybrid of X^B X^b by X^B Y. Through  recombination, the alleles from each parent combined. One offspring was colorblind, and the other nine offspring were normal. When using probability to predict an offspring's traits, a person cannot assume what traits an offspring can have. Instead, they can predict the likelihood of a trait being dominant.

    This unit was about the cell cycle, asexual vs. sexual reproduction, meiosis, Punnett Squares, Mendel's Sex Laws, and genetic exceptions and complications. The cell cycle has three steps: interphase, mitosis, and cytokinesis. In interphase, DNA is copied. Mitosis is the process in which DNA and organelles are split up. Cells divide into two cells during cytokinesis. 
     Asexual reproduction requires one parent. The offspring is genetically identical. Asexual reproduction is easy, takes a short amount of time, does not need a mate, and can make a lot of offspring. Asexual reproduction has no genetic variation, is not resistant to change. The offspring of asexual reproduction are more likely to go extinct if their environment changes. Sexual reproduction requires two parents, and each parent contributes half of offspring's DNA through sperm or egg. Sexual reproduction creates genetic variation, and new traits arise in the population. The costs of sexual reproduction requires a lot of time.
     Sex is determined by a pair of sex chromosomes. Homologus chromosomes are chromosomes that come in pairs, in which one there is one copy from each parent. Sex cells are called gametes. Males produce sperm, while females produce egg. Haploid cells are sex cells that have half of the chromosomes. All body cells are diploid, meaning that cells have two copies of every chromosome. Asexual reproduction always produces diploid cells. 
     Meiosis is the process of making gametes in testes or ovaries. There are four stages in meiosis, but the cell divides twice, meaning that a cell goes through the four stages two times. The four stages are: prophase, metaphase, anaphase, and telophase. The process of meiosis 1 splits homologus chromosomes. Meiosis 2 splits sister chromatids. 
     A trait is a characteristic. A gene is a piece of DNA that gives an organism its trait. Gregor Mendel experimented with pea plants and mated peas to observe their traits. He discovered that traits are determined by two copies of a gene. Some versions of a gene are dominant over the others. A genotype is the alleles that an organism has. A phenotype is the physical trait that results due to an organism's traits. Individuals that have the same two alleles are called homozygous. Individuals with two different alleles are heterozygous. 
    The Law of Segregation, a principle introduced by Mendel, states that the gene pairs of a trait separate where gametes are formed because of meiosis. The Law of Independent Assortment states that gene pairs separate independently, or randomly, from each other during meiosis. The Punnett Square predicts possible genotypes of gametes. 
     Autosomal inheritance is the process in which an organism inherits the gene responsible for a trait from all the 22 autosomes. X-Linked inheritance is when an organism inherits the gene responsible for a trait from the x-chromosome. 
     Incomplete dominance happens when neither allele is dominant nor completely recessive. Both alleles will both be completely expressed in codominance. In other words, codominance has both phenotypes. Codominant alleles are neither dominant nor recessive. 
     Because chromosomes have many genes, the closer they are together, the more likely they are to be inherited together through gene linkage. In epistasis, one gene alters the phenotype of another gene. Multifunctional disorders are disorders where an environment affects genetics. Most humans are polygenic because they have two or more genes to determine their phenotype. 

     http://bit.ly/2fvBp72

     This unit was very fun because I really liked learning about Punnett Squares and how they can determine the probability of an offspring having a specific genotype. I struggled to understand the difference between meiosis and mitosis so I did some extra research. I understood how some versions of alleles could be dominant over others, but I had a difficult time figuring out how codominance works. In my opinion, the infographic helped me get a better understanding of the main concepts from this unit. I definitely feel that I am a better student than I was yesterday because I have expanded my knowledge in biology. I would like to know more about the works that Mendel did to influence the world of biology today.  

Picture of my infographic: https://magic.piktochart.com/output/17955851-genetics

Sexual vs. Asexual Benifits

Is sexual reproduction important?

     Sexual reproduction is necessary for life. "[Sex] prevents parasites from becoming too well adapted to their hosts" (Judson 228). Sexual reproductions remove harmful mutations from the population. Sexual reproduction has a slower production rate. "Sex is an advantage because it breaks up gene combinations" (Judson 229).
     Asexual reproduction does not require fertilization, but there is very little variation, which can cause extinction. "...mammals clone once in a while, when an embryo splits early in development" (Judson 215).
     Some animals reproduce sexually and asexually. "Armadillos... engage in both sexual and asexual reproduction"(Judson 229).
     I learned that many species reproduce in different ways. Some reproduce more than others, and some reproduce sexually, while others reproduce asexually. I understood the text and all my questions were answered in the text.

Unit 3 Reflection

     Unit 3 was about cells and their functions. Macromolecules serve as the building blocks for life because they make up different parts of the cell and they all serve different purposes. The cell theory states that all things are composed of cells, a cell is the basic unit of life, and new cells generate from existing cells. Prokaryotic cells have no nucleus, while eukaryotic cells have a nucleus.

     Membranes and their unique characteristics are so essential for life because they all have different functions that are necessary for life. The nuclear membrane holds DNA in the nucleus and allows RNA to leave through the pores. The lysosome holds enzymes for recycling proteins. The endoplasmic reticulum (ER) holds proteins as they are finished off and holds lipids as they are made. The vesicles export molecules in and out of the cell. The golgi apparatus packages and releases finished proteins, lipids, and hormones. The membranes in chloroplasts and mitochondria creates carbohydrates through the process of photosynthesis, and breaks down carbohydrates through the process of cellular respiration. The cell membrane holds all cell contents inside and protects from the outside environment. The cell membrane also controls the passage of molecules inside.

       Semipermeable membranes allow some molecules to cross the membrane, while others can not. Passive transports require no effort or energy. Active transports use energy to bring rare but highly needed molecules into the cell. Diffusion is the movement of small molecules from high to low concentration through the lipid bilayer. Proteins that make it possible for large molecules to pass through the membrane through the process of facilitated diffusion. Osmosis is the diffusion of water across selectively permeable membrane. An isotonic solution is when the solute concentration is the same outside and inside the cell. A hypertonic solution is a solute concentration that is greater than that inside the cell. A hypotonic solution is a solute concentration that is less than that inside the cell.
     Cells specialize in making proteins. Mitosis is the process in which one cell reproduces by dividing into two cells. Photosynthesis converts light into chemical energy. A cell creates energy by creating ATP  from glucose to power the cell. The endosymbiotic theory explains how a large cell ingested bacteria and became part of it.
     Photosynthesis is the process in which plants produce glucose and oxygen using sunlight and carbon dioxide. Light dependent reactions occur in the thylakoids of grana. Light independent reactions occur in the stroma.
     Cellular respiration is the process of breaking down glucose into energy. It has 3 stages: glycolysis, krebs cycle, and the electron transport chain. Glycolysis produces two ATP for every one glucose molecule. The Krebs Cycle coverts molecules from glycolysis into two ATP, CO2, Nadh, and FADH2. The electron transport chain uses oxygen, NADH, Fadh2, and converts ATP into ADP. This last stage produces 32 ATP.
     The process of photosynthesis and the process of cellular respiration undo each other. Photosynthesis occurs in the chloroplasts in autotrophs, while cellular respiration occurs in the mitochondria in autotrophs and heterotrophs.
     Overalll, I really enjoyed this unit. I liked learning about photosynthesis and cellular respiration. I had a tough time remembering the function of each organelle in a  cell. I had a fun time looking at cells under a microscope, and I realized how complicated a single cell can be. 

Photosynthesis Virtual Labs

Lab 1: Glencoe Photosynthesis Lab

Analysis Questions

1. Make a hypothesis about which color in the visible spectrum causes the most plant growth and which color in the visible spectrum causes the least plant growth?

If the color in the visible spectrum is blue or red, then the plant will grow bigger.

If the color in the visible spectrum is green, then the plant will grow the smallest.

2. How did you test your hypothesis? Which variables did you control in your experiment and which variable did you change in order to compare your growth results?

I tested my hypothesis by planting spinach in all the different lights for 30 days. Then I did the same for the radish and lettuce.In my experiment, the controlled variable was the type of plant. The variable that I changed to compare the growth was the color of the light.

Results:

Filter Color	Spinach Avg. Height (cm)	Radish Avg. Height (cm)	Lettuce Avg. Height (cm)
Red	18	12	12
Orange	16	7	5
Green	3	2	3
Blue	18	15	12
Violet	15	11	7

3. Analyze the results of your experiment. Did your data support your hypothesis? Explain. If you conducted tests with more than one type of seed, explain any differences or similarities you found among types of seeds.

My data supported my hypothesis. I predicted that the blue light and the red light would show the most plant growth and that green light would show the least amount of plant growth. I found that spinach grew best under the red light and the blue light. The radishes showed the second most amount of plant growth under red and blue light. The lettuce showed the least amount of plant growth under red and blue light compared to the spinach and the radish.

4. What conclusions can you draw about which color in the visible spectrum causes the most plant growth?

I conclude that blue light causes the most plant growth in the visible spectrum.

5. Given that white light contains all colors of the spectrum, what growth results would you expect under white light?

I would expect a normal rate of growth under white light because white light is an average of all light lengths.