Unit 5 Reflection

Unit 5 was about protein synthesis, mutations, and how genes are regulated.

For this section, I had to look into my notes, but only to see how to spell some words so that doesn't count! Protein synthesis is how proteins are created from DNA. RNA polymerase makes a copy of the DNA, which is deoxyribose nucleic acid. DNA is made from a sugar, the deoxyribose, a phosphate group, and a nitrogen base, which can be either Adenine, Thymine, Guanine, or Cytosine. DNA has two strands, and twists into a double helix shape, with bases matching together. The bases match with each other, Cytosine with Guanine, and Adenine with Thymine. The copy is called RNA, which is very similar, except Thymine is replaced with Uracil, and it is single stranded instead of double stranded. This is messenger RNA. It goes out of the nucleus and to a ribosome, where it is read. Each codon, which is 3 bases, codes for one amino acid. An amino acid can be coded for by several different codons. Transfer RNA brings the amino acid to the ribosome to build the protein, and matching base pairs for the messenger RNA.


Mutations are changes in DNA. They can be deadly, or do nothing at all, which is called a silent mutation. One type of mutation is a point mutation, where a single base pair is changed. One type of point mutation is a substitution, where one base pair is substituted for another one. This type of mutation causes little to no damage, because some amino acids can be coded for in several ways, and if it does change the amino acid, it only changes one of them, which will have a small effect. The other type of point mutation is a frameshift mutation, where one base pair is added or removed. This has a large effect, and can completely ruin a protein because  in addition to changing the current codon, it shifts over all following codons, which can cause a completely different protein to be made, or cause no protein to be made at all. There are other mutations that aren't point mutations, such as inversions, which cause a piece of DNA to become unattached, and reattach backwards. Translocations are when DNA from one chromosomes attaches to a different chromosome. Mutations are caused by mutagens, such as UV, (checks notes for other mutagens) nuclear radiation, X-rays, and toxins(closes notebook).

Example of a mutation.

Gene regulation was probably the most complex part of the unit, so I will obviously be referring to my notes for this paragraph. All cells have DNA for all genes, but they don't express all genes at all times because cells don't want to waste energy by over expressing genes. A group of genes that work together is called an operon. A good example of gene regulation is the Lac Operon. The RNA attaches to the part of the DNA called the operator, and copies the gene from there. But, in Lac Operon, there is a repressor, which is like a road block, attached to the promoter. The repressor is removed when lactose appears, and attaches to it. Then, the gene can be read to create the enzyme lactase, which breaks down lactose for food. In eukaryotes, the process is more complex, and several proteins can bind before a gene. After RNA copies a gene, sections called introns, which don't code for anything, are cut out, leaving the exons, which are expressed.

1: RNA polymerase. 2: Repressor. 3: Operator. 4: Promoter. 5: Lactose

That's all we covered in unit 5. The only part I really need to study is gene regulation, and the spellings of thymine, adenine, guanine, and cytosine.

Protein Synthesis Conclusion

Proteins are created in the process of protein synthesis. It starts with DNA being copied into RNA by a molecule called RNA polymerase. The RNA then exits the nucleus and goes to a ribosome, where it is read. Each codon, or three base pairs, in RNA codes for one amino acid. An amino acid can be coded for by several codons. Transfer RNA brings the amino acids to the ribosome. At the end of the RNA strand is a STOP codon, which tells the ribosome that the protein is complete.



When DNA bases are changed in a mutation, it affects the RNA, which can either have no effect on the protein, or completely change it, depending on whether the mutation is a substitution, deletion, or insertion. Substitutions substitute one base for another. This type of mutation has very little affect on the protein, if any. It can only change one amino acid, or it may not change it at all, which is called a silent mutation. insertions and deletions have the greatest affect, because they change both the amino acid they are inserted on, and the rest of the DNA sequence. These mutations are most dangerous near the beginning of the gene, because they will affect more codons.

An example of a mutation. The plant produces different colored flowers.

In this lab, we chose a mutation to use on a DNA sequence. I chose to delete the first base, which had a huge affect, as it changed every following codon, causing the protein to have completely different amino acids, and the stop codon to appear early and end the protein before it should have. The effect would have been less if I did this in a later spot in the DNA, because less codons would have been affected.

The protein used to be:

MET-TYR-LYS-HIS-VAL-ILE-ASN-CYS-ILE

After my mutation, it changed to:

CYS-THR-ASX-MET

Mutations could affect my life because they can happen during mitosis, which means that one can occur at any time. An example of a mutation is Progeria, which causes accelerated aging. People with this disease often die from age related diseases at around age 13, such as heart attacks and strokes.

DNA Extraction Lab

In this lab, we asked how we could extract DNA from cheek cells. We found that removing the cheek cells by scratching the inside of our mouths with Gatorade, which homogenized the cells, which means that the Gatorade and cheek cells formed a colloid, and then mixing the Gatorade with salt, soap, and enzymes in pineapple juice, which  lysed the solution, meaning that the cell membrane and nuclear membrane breaks down. We then put a layer of alcohol which caused the DNA to turn in a precipitate. This worked, because after the process, we were able to see small strings and chunks in the alcohol, which was the DNA, meaning that our process worked.

One error I made was not getting enough cheek cells. When swishing the Gatorade in my mouth, I mistimed how long I was supposed to have the Gatorade in my mouth, so I gathered fewer cheek cells than others. I could fix this error in the future by using a stopwatch. Another error I may have made was using too much Gatorade, so when we poured the Gatorade with the cheek cells into the test tube, I may have poured less cells and more Gatorade, resulting in less DNA. I could fix this error by more carefully measuring any liquids.

The purpose of this lab was to show how every cell in the body has DNA in it, even if they don't use all parts of the DNA. From what I learned in this lab, I could collect cells and use them for other purposes, or collect DNA of other organisms.

Unit 4 Reflection

Unit 4 was about the cell cycle, genetics, and reproduction, and specifically about sexual reproduction.

The cell cycle is the process that divides a cell into two genetically identical cells. The first step is Interphase, which is where a cell spends most of its time. It grow, and duplicates its DNA. Next is Prophase, where the nuclear membrane dissolves and chromosomes form. After that is Metaphase, where the chromosomes line up in the center of the cell. Then, in Anaphase, the sister chromatids are pulled apart into opposite sides of the cell. Then is Telophase, where the nuclear membrane reforms, and the cells start separating. In Cytokinesis, the cells are fully split apart and the organelles duplicate.

Sexual reproduction is the combination of two cells, sperm and egg, from two different organisms to create an organism that is genetically different from the two parents. Some examples of sexual reproduction include broadcast spawning, paired spawning, spores, seeds, and copulation. Asexual reproduction is a single parent creating a genetic clone of itself. Some examples of asexual reproduction are binary fission, regeneration, and budding. Sexual and asexual reproduction both have costs and benefits. Some costs of sexual reproduction are that it takes lots of time and energy, it exposes you to STDs and parasites, not all get to reproduce, and it creates some bad genetic combinations. But its benefits are that it creates new genetic combs which create resistance to change, and it creates competition which results in only the best reproducing. The benefits of asexual reproduction are that it is fast and easy, doesn't require a mate, and you can create a lot of offspring quickly. But the costs are that it creates no genetic variation, which makes it more likely for the species to go extinct.

At this point while summarizing, I had to return to my notes, so this is a reminder to myself to study this part. Chromosomes are DNA that come in a pair, one from each parent. The types of chromosomes are autosomal and sex chromosomes. Sex chromosomes determine the gender of the child. XX is female, and XY is male. Sometimes, there are variations where someone can have extra chromosomes, such as XXY, which results in infertility, and XYY and XXX, which both let the organism have a fairly normal life. Autosomal chromosomes are all the other ones. Chromosomes come in homologous pairs, each coming from a different parent. A cell will a full set of chromosomes is a diploid cell.All cells that make up your body are diploid. Cells with half the number of chromosomes are haploids. Sex cells, or gametes, are haploids. Gametes are produced in a process called meiosis, which is similar to mitosis in the way that it splits apart to create new cells. But in meiosis, 4 cells are created, and they are genetically different haploids gametes. Meiosis happens in 2 phases, each which splits up the cells, meiosis 1 and meiosis 2. Meiosis 1 splits the homologous chromosome pairs apart, and meiosis 2 splits the sister chromatids. During prophase of meiosis 1, the homologous chromosomes cross over to exchange chunks of DNA. This is what makes them genetically different, and leads to many different genetic combinations.

Leaving my notes, the next SEX-ion (I'm so punny) was on how sex and traits are related. In sex, two gametes join to create a new organism. Gregor Mendel crossed different plants in order to find out how their traits were inherited. The first generation of one of the crosses was with purebred purple and purebred white flowers. The offspring had only purple flowers. After they self fertilized and reproduced, there was a 1:3 ration of white to purple. Mendel discovered that some genes, or pieces of DNA responsible for traits, were dominant, and some were recessive. Genes come in pairs, called alleles. If an organism has a dominant allele, then the organism will get that trait, no matter what the other allele is. But if the organism has 2 recessive alleles, then they will get the recessive trait. In the flowers, purple was dominant, and white was recessive. You can predict the probability of getting a certain phenotype, or physical trait, if you know the genotype, or genes, of the parents. When an organism has 2 of the same allele, it is called homozygous, but if it has 2 different alleles, it is heterozygous.

In sex, you can use a diagram called a punnet square to predict the probability of a phenotype if you know the genotype of the parents. In Meiosis, when crossing over occurs, a copy of an allele could go to any of the four haploid cells. So if an organism had the genotype Aa (capital is dominant, lowercase is recessive) they two of the four possible gametes would have the A gene, and the other two would have the a gene. Punnet squares show the results of crossing all the possible gametes for a given number of genes.

	A	a
A	AA	Aa
a	Aa	aa

In this punnet square, two heterozygotes were crossed, and the probabilty of having a homozygous recessive child is 1/4, because there is only one combination that would result in that.

Returning to my notes again marks another section I should review. You are stuck with whatever genes you get. Some autosomal dominant traits you can get are bipolar disorder, widow's peak, and the ability to curl your tongue. Some autosomal recessive traits include albinism, cystic fibrosis, and sickle cell anemia. Traits can also be X-linked. One X-linked dominant trait is Coffin Lowry Syndrome, which is a physical and mental handicap. Some X-linked recessive traits include colorblindness, and hemophilia.

Once again leaving my notes, the next section is on genetic complications. Genes are not all dominant and recessive. Some traits have incomplete dominance, which means that the two phenotypes from each gene combine to create a new phenotype in heterozygous genotypes. Codominance is when both traits in a heterozygous genotype are expressed completely at the same time. Gene linkage is when two genes are close together on a chromosomes, which makes it more likely for them to be inherited together. Epistasis is when a master gene controls other genes. Multifactorial disorders are when the environment influences how genes affect the phenotype of an organism. And polygenetics is when several genes control a single trait.

The final section is more on punnet squares and the different types of crosses. Monohybrid crosses are crosses where only one gene is crossed. They are done in a 2x2 punnet square. Dihybrid crosses are when 2 genes are being crossed. They are done in a 4x4 punnet square. And finally, test crosses are for finding the genotype for a trait of in an organism with an unknown genotype. To do this, you would cross them with a homozygous recessive organism. If the offspring all have the recessive trait, then the unknown is homozygous recessive. If some have the recessive trait and some have the dominant trait, then the unknown is heterozygous. If all the offspring have the dominant trait, then the unknown is homozygous dominant.

Based off of my experience writing this, I will spend more time studying the different traits found in humans and how chromosomes change in Meiosis.

Coin Sex Lab

In this lab, we flipped coins to simulate the randomness of alleles crossing over and recombination in sex. The coins represented the two copies of a gene, and flipping them simulated the randomness of which gene the gamete would get in meiosis, also known as the law of independent assortment. The results we got for simulating getting a male or female were the same as the expected result, 1/2 probability either way, because the females are homozygous, and don't get to determine the gender, while males are heterozygous, so they determine the gender with the one Y chromosome they have which has a 50% chance of being inherited. We then we simulated a monohybrid cross where we tested the probability of inheritance for an autosomal gene that causes bipolar disorder. Bipolar disorder is caused by a dominant gene, and we crossed a homozygous recessive person with a heterozygous person. We predicted that 50% of the children would have bipolar disorder, but we were wrong when our simulation resulted in 8 normal children and 2 children with bipolar disorder. This shows that the probability of getting a trait is not the same as the ratio of people with the trait, because getting a certain allele is completely random, so it doesn't necessarily follow the probability. The third trait that we tested was colorblindness, an X-linked recessive trait. Males are more likely to inherit X-linked traits because they only have one X chromosome. We crossed a heterozygous female and a male with normal vision. We predicted that 25% of the children will be colorblind males. We found that 3 out of 10 were colorblind males, which is about 25%. Our final cross was a dihybrid cross where we tested hair and eye color. We predicted that there was a 1 out of 16 chance of getting a double homozygous child from 2 double heterozygous parents. Our prediction was correct, and we got that result. All these crosses show how you can predict the probability of having a certain child, but you can't predict what the child will be.

Genetics Infographic

https://magic.piktochart.com/output/9061358-reproduction-infograph

This is the link the the full size image, which is actually legible.

Unit 3 Reflection

In Unit 3, we studied the different types and parts of cells, and their functions, and we focused specifically on cellular respiration and photosynthesis.

The different types of cells are eukaryotes and prokaryotes. Prokaryotes are cells that don't have a nucleus or most organelles. Some examples of prokaryotes include bacteria. Eukaryotes are cells with most organelles, including a nucleus. It is theorized that mitochondria and chloroplasts are prokaryotic cells that continued to live after being eaten by a eukaryotic cell.

Membranes of cells are made of 2 layers of lipids. Different membranes include in nuclear membrane, which holds the DNA in the nucleus. The lysosome digests old organelles that don't work any more, or old cells that don't work. There are 2 types of Endoplasmic Reticulum (ER), rough ER, which has ribisomes on the surface, and it helps finish making proteins. Smooth ER has no ribisomes on the surface, and detoxifies drugs. Vesicles take things out of cells. the Golgi Apparatus packages finished proteins, lipids, and hormones. Chloroplasts go through the process of photosynthesis to make glucose, and mitochondria break down glucose to create ATP for energy. And the cell membrane holds everything in the cell, and selects what enters and leaves. Other organelles are the nucleolus, which is the center of the nucleus, which starts ribisome production. In the nucleus, DNA is stored. Vacuoles store things sch as water, salts, proteins, and carbs, but not all cells have vacuoles.

Cellular Respiration and Photosynthesis were the most complicated processes we learned about, so we learned a simpler and less detailed version of both processes. Even so, they are both still somewhat difficult to understand.

A Simple Diagram of  Chloroplast

Photosynthesis occurs in the chloroplasts of cells that contain them. It consists of 2 parts, light dependent reactions, and light independent reactions. The light dependent reactions start with energy from light going through the electron transport chain inside the thykaloid. In this process, ATP and NADPH, an electron carrier, are produced. The ATP is produced when H+ ions from water go into the thykaloid, and escape through the ATP Synthase molecules, which spin to turn ADP into ATP. Then, the ATP, NADHP, and CO2 go through the Calvin Cycle in the stroma to create glucose. After going through the cycle 6 times, 1 glucose molecule is created.

Cellular respiration is the opposite of Photosynthesis. Instead of energy water, and CO2 being used to create glucose and oxygen, glucose and oxygen are used to create CO2, water, and ATP (energy). Cellular respiration goes through 3 steps. The first step is glycolysis, which takes place in the cytoplasm. It turns glucose into 2 ATP molecules, and creates Pyruvic acid, which goes to the next step, the Krebs cycle. The Krebs cycle converts the Pyruvic acid into 2 ATP, CO2, and electron carrying molecules called NADH and FADH2. Then, those electron carrying molecules and oxygen go to the electron transport chain, which uses all of those molecules to convert ADP into ATP, and creates 32 ATP, making a total of 36 for all of cellular respiration.

A much more detailed diagram of Cellular Respiration

Overall, this unit contained lots of information regarding the different organelles of eukaryotes, and focused a lot on photosynthesis and cellular respiration, the most complex topics of the unit. My only remaining questions are how prokaryotes function, since they have no organelles or nucleus.