Mathematician+Physician=Hardy-Weinberg Equation

To expand on last week's lesson on evolution, this week in AP Biology we learned how to track evolution. There are a few things you have to know before you can actually track evolution though. One of them is a population, which is a local group of interbreeding individuals. Unlike, most previous ideas evolution does not occur through an individual, but a population. Another thing is a gene pool which is the collection of alleles in a population. To add on to that you need to know what allele frequency, which is how common the specific allele is in that population. A big thing to know is a slightly new and updated definition of evolution. Evolution can now be defined as a change in allele frequencies in a population. This leads us into how to measure evolution. 

To measure evolution you need to know the Hardy-Weinberg Equation, and to use this equation the population must be in Hardy-Weinberg Equilibrium. This means there must be a large population, no migration, no mutations, random mating, and no natural selection. Which is pretty much a nonexistent population. So, all of this is hypothetical.  Now to look at the Hardy-Weinberg Equation.
                                                               p+q=1
p= frequency of dominant allele
q= frequency of recessive allele
Both of the frequencies must add together to equal one. To find the frequency of homozygous dominant, heterozygous, and homozygous recessive you need to use this equation:
                                                            p²+2pq+q²=1

p^{2= the frequency of homozygous dominant}

2pq= the frequency of heterozygous

q²= the frequency of homozygous recessive

These two equations serve as a null hypothesis to measure if forces are actually acting on a population. 

From the Ape to Humans... Evolution

This week in AP biology we went over evolution and learned that it's not really about ape to humans and all that. Evolution can be described as genetic changes in a population that happen over time. There are 8 mechanisms of evolution. 

The first one is natural selection. The first thing we think about natural selection is Charles Darwin , the Galápagos Islands, and only the strong survive. While the first two are correct, the third one is incorrect. Instead of only the strong survive it is the most adaptable survive. Three things are really important to natural selection. They are variation of genes in population, the variations to be heritable, and differential reproductive success. An example of natural selection would be a green caterpillar and a blue caterpillar on a green leaf the green caterpillar will blend in while the blue one will be easier for predators to spot. Therefore the green caterpillar will survive to reproduce more than the blue caterpillar will. 

Mutations or any change in the DNA is also a mechanism. Not all mutations are relevant to evolution. Only the mutations that will occur in gamete or sex cells can lead to evolution. 

The third mechanism is recombination. Recombination is mostly about crossing over that occurs during meiosis. The new gene combinations can be helpful and harmful to the organism. 

Gene Flow or migration is the fourth mechanism. Gene flow is one an organism leaves and takes their traits with them. When an organism leaves one population and goes to the other and reproduces their it takes its genes that the population had not been introduced to yet and includes them in the gene pool of the population. 

Genetic drift is chance changes in a population. It is entirely random and doesn't necessarily lead to the best or most adaptable organisms surviving. 

Artificial selection is the sixth mechanism of evolution. It is called this because instead of the organism choosing who to mate with humans do. This is very common in livestock animals. Breeders breed the biggest and best animals to wi the shows. 

Non- Random mating or sexual selection is the fact that not all individuals have the same chance of mating. Not always a good thing as it can lead to organism being more visual sexual selection happens in peacocks, some birds, and flys. 

The last mechanism is reproductive isolation.  Reproductive isolation occurs when a species is separated and then become two different species. This happened on the Galápagos Islands. Most cormorants are able to fly except for a type of cormorant that is found on the Galápagos Islands. 

The Terrorists of Cells

This week in AP Biology we went over viruses. Viruses are made of a protein coat called a capsid that encircles the middle which contains the genetic material and reverse transcriptase. Some viruses have a phospho-lipid bilayer called an envelope encircling them. In the envelope there are glycoproteins that are the key to the lock on plasma membranes. 

There are two different replication cycles min viruses. One is the lytic cycle this is when the cell is hijacked by the virus and uses the cell's machinery to synthesize more viruses. At the end of the cycle, the cell will burst setting the newly synthesized viruses loose. The other cycle is the lysogenic cycle. This is when the genetic material of the virus has been injected into the cell's DNA. Because the genetic material is in the cell'a DNA whenever the cell replicates the virus's genetic material is replicated too. The genetic material of the virus that is in the cell's DNA is called the prophage. The cell that has been affected by the virus can be in either one of these cycles depending on the circumstance. 

There are also viroids and prions. A viroid is a virus that affects plants. Prions are proteins that affect humans. Prions are associated with mad cow disease. 

Spikes are the glycoproteins. 

How to Make a Protein.

This week in AP Biology we reviewed transcription, RNA processing, and translation. These three processes are what enables helps DNA in the production of proteins. 

Transcription is the first of these processes. The enzyme RNA polymerase attaches to DNA, and starts adding nucleotides. Unlike DNA, in RNA strands adenine bonds with uracil instead of thymine. The strand of RNA then goes through RNA processing. During this process spicesomes cut out the introns in the RNA so that their is only extrinsic left. Next a 5' cap made of guanine is placed at the beginning of the strand and a poly A tail, A standing for adenine, is added to the end. These previous process all deal with mRNA and inside the nucleus. The next process takes place outside of the nucleus and deals with tRNA as well. 

Translation is the reading of mRNA and creating a protein made of amino acids. After RNA processing the smaller subunit of a ribosome will attach to mRNA and the larger subunit will follow. Next, the ribosome will read the mRNA and bring one amino acids per codon. These amino acids are brought by tRNA. The tRNA will dock at the docking site of a ribosome the amino acid it carries will form a peptide bond with amino acids that are already there, and then once getting rid of the amino acid it will leave the ribosome. Once the ribosome is finished with the mRNA the ribosome unattachs and the amino acid chain has formed a protein. From there it will either be used by the cell or a vesicle will transport it out of the cell. 

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DNA Clones and Suitcases

Last week in AP Biology we talked about DNA’s history this week we talked about how those discoveries would inspire future experiments. Once Watson and Crick discovered DNA’s structure the next question is, how does it replicate?

                DNA starts to separate at the origin of replication because of helicase. It then starts to create a replication bubble and fork. Next, single stranded proteins are added to the two parental strands to prevent them from reattaching. DNA polymerase III then starts to add nucleotides to the DNA. The polymerase adds the nucleotides in the direction of 5’ to 3’. Also, there is a leading strand and lagging strand during the replication process. The leading strand is replicated continuously, but the lagging strand is replicated in Okazaki fragments. Pieces of RNA mark the beginnings of the Okazaki fragments. Once pol III is done adding nucleotides pol I start to remove the RNA pieces and replacing them with pieces of DNA. DNA ligase then finishes it all up by connecting all the DNA fragments.

                Next we learned about how the DNA is packaged. In a mixture of DNA and histones we get nucleosomes which are looped in giant supercoils that created chromosomes. The histones have the ability to switch genes on and off and when the DNA spreads out it can be accessible for transcription. 

DNA has a history????

This week in AP biology we covered the history of DNA. There are 11 prominent names that we associate with this subject. The first being T.H. Morgan who worked with fruit flies to find that chromosomes are located on genes. A second name is Freferick Griffith who was working to find a cure for pneumonia by working with Strepococcus pneumonia bacteria. Griffith discovered that there is a "Transforming Factor" that can turn harmless live bacteria into harmful bacteria when combined with heat-killed infectious bacteria. The next three names discovered just what that "Transforming Factor" was. In 1944 scientists Avery, McCarty, and MacLeod purified both proteins and DNA from Strepococcus pneumonia bacteria and injected both into bacteria. It turned out that when protein was injected into bacteria there was no effect, but when DNA was injected into bacteria it transformed the harmless bacteria into virulent bacteria. Hershey and Chase worked with bacteriophage to confirm that DNA was the "Transforming Factor." The next two names are very commonly associated with DNA having won a Novel Prize for their work with DNA. Watson and Crick are two men that discovered the double helix structure of DNA. A controversy surrounds this because it can be believed that they stole Rosalind Franklin's work.Meselson and Stahl worked with transcription, replication, and translation to try and guess where bands would be. These 11 names have forever changed the world because of their wonderful discoveries involving DNA. 

Chi Squared... and not its not the straightener.

This week in AP Biology we went over chi² (sounds like ky). Chi² is used to test a null hypothesis, in other words it can be used to see if there is a significant difference in what is observed and what is expected. The formula for chi squared is:

The X²_c  represents chi²

The ∑ is a symbol for a summation.

O_i is the observed data, the data you have collected

E_i  is the expected data, what you would get in a perfect world.

To determine if the discrepancies between the numbers are to large you look at the critical value and degrees of freedom chart.

The chart gives you the number that your answer from the chi² formula must be under for you to accept the null hypothesis.

Chi² is commonly used in genetics to determine phenotypes.

Genetic... chromosomes, chromosomes, and chromosomes!!!

This week in AP Biology we further travelled through genetics. We learned about sex-linked traits, co-dominance, incomplete dominance among other things. From there we went even deeper into the chromosomal basis of inheritance.

                Sex-linked traits are genes that are located on the x or y chromosome.  These genes on the chromosomes bring forth diseases such as hemophilia and color blindness. Co-dominance in genetics is when both alleles are expressed. This is exemplified in the blood type AB and calico cats. Calico cats are also always female which makes it a sex-linked trait. Incomplete dominance is when the dominant allele doesn’t completely mask the other such creating a sort of blending. This can be seen in blending a red and white snapdragon together and it producing a pink.

                The chromosomal basis of inheritance is connected with Thomas Hunt and the, Chromosome Theory of Inheritance which states that Mendelian genes have specific loci on chromosomes that undergo segregation and independent assortment. Thomas Hunt Morgan contributed a lot to his specific subject. He produced a lot of research with fruit flies that had to do with linked genes. Link genes are genes that tend to be inherited together because they are so close on the chromosomes.  He also helped with recombinant offspring. These are offspring that have features from both parents.

                We also looked at genetic disorders such as Huntington’s and Down Syndrome. The fertilization of these gametes cells that produce these disorders is called aneuploidy.

Genetics

This week for AP Biology we reviewed and studied genetics. On Tuesday we went to Sam Ryan's genetic conference at Lubbock High. At the conference we went over genetics and the recent discoveries in the field. 

An interesting thing I learned about was Barr bodies. Barr bodies are little black dots in female cells. They're only in females because the bodies are a disabled X chromosome. When a cell begins to form it randomly picks an X to follow and then disables the other one. This lead to questions about fixing Down syndrome by taking the third chromosome at 21 and disabling it so that it would turn into a Barr body. 

A fun fact I learned was that our phenotype which is the physical representation of our genotype is actually expressed in all of our cells.  

Another concept that I was enlightened about was that you can take skin cells and turn them into stem cells by reprogramming the cell. This can lead to many things. Such as growing new organs and allowing blind people to see again. The stem cells that have been reprogrammed can form new organs by using scaffolds of organs. If an organ cannot be replicated perfectly they use a dead organ and drain the cells out of it. The stem cells can also be used to replace corneas that have become too cloudy for people to see out of and thus making it possible for the replacement of their vision. This procedure has already been done in a young boy. The procedure requires no stiches or blood and the patient is under local anesthesia and last around thirty minutes. 

I also learned about alternative splicing which allows our genes to code for different proteins and telomerase. 

 Telomerase is an enzyme that builds up the telomeres which are caps at the end of chromosomes. Every time a cell divides the telomeres get shorter and shorter until eventually there is next nothing there. At that point the chromosome stops dividing, unless it has telomerase. The shortening of the telomeres is a major component in age. Unfortunately telomerase is only found in testis, ovaries, and cancer cells. If researchers can discover a way to put telomerase in all areas there might be a chance to postpone aging. 

 The Genetics Conference was super interesting and I advise everyone to take the opportunity to go to it if they can. 

What time is it? LAB TIME!

 This week in AP Biology we did the mitosis and meiosis lab. As I previously discussed in my last blogs, mitosis which is when two genetically identical diploid daughter cells are produced and meiosis is the process which produces four genetically different haploid daughter cells. To began this lab we modeled mitosis and meiosis. We then prepared garlic for another activity. After following that we looked at onion root and fish egg cells to locate cells in the various stages of mitosis. We then proceeded to prepare the garlic root tip squash lab. In this part of the lab we took the garlic we had previously prepared by putting it into a sand and water mixture and placing it into a dark drawer, and cut off around 2 mm of the root tip. After that we put the root tip and hydrochloric acid on a slide  and passed it through an open flame for five seconds. Then we put a chemical that was bright pink and fuchsia in the name on the slide and passed it over an open flame for 2 minutes. We then squished the root tip and put it under a microscope to see if we could locate cells in the various stage of mitosis, but unfortunately we were unable to. That then concluded the lab.


(I will publish pictures separately.)

Meiosis

 This week in AP Biology we went over meiosis. Meiosis is divided into 2 different parts, meiosis 1 and meiosis 2. Meiosis 2 is the most similar to mitosis. In meiosis 1 there are four stages prophase 1, metaphase 1, anaphase 1, and telophase 1. In prophase 1 chromosomes condense, homologous chromosomes attach, crossing over between chromosomes, and centrioles move to opposite ends. In metaphase 1 the tetras line up at the metaphase plate. During anaphase 1 the homologous chromosomes are separated and taken to opposite poles. After anaphase 1, telophase occurs and the sister chromosomes continued to be pulled. Cytokinesis then takes place. After that meiosis 2 takes place which is very similar to mitosis. 

 Mitosis and meiosis differ greatly in their end products; mitosis results in 2 genetically identical diploid cell and meiosis results in 4 genetically different haploid cells. 

Message Passing and Reproducing in Cells

 This week in AP Biology we reviewed cell to cell communication and the cell cycle. 

 There are three types of cell to cell communication no distance, short distance, and long distance. In no distance communication the cells are touching and can send messages to one another. Plants have holes in there cell wall that allows the message to pass. When there is a short distance in cell to cell communication a local regulator is used to pass on the message, neurotransmitters are an example. When there is a long distance to pass on a message a hormone is used. The hormone is sent all around but only passes the message on to the right cells. 

After we went over cell to cell communication we then went to the cell cycle. The cell cycle is made up of the G1 phase, S phase, G2 phase, mitosis, and cytokinesis. There is also a G0 phase that some cells go into. G1, S, and G2 phase all make up interphase. In G1 phase the cell is working normally as the cell progresses into G2 it starts copying its DNA. When the cell starts S phase it again goes through its normal process. Then the cell gets to mitosis.  When mitosis and cytokinesis are combined it is called the mitosis (m) cycle the first phase is prophase. In prophase the chromatin becomes more clear and thicker and the centrioles become visible. Metaphase follows prophase in which the chromatin which has turned into sister chromatids are lined up in the middle of the cells with the centrioles at opposite ends and the mitotic spindle is forming. Anaphase which is the third phase is when the sister chromatids are pulled apart by kinectchores and nonkinectchores elongate the cell. The fourth and finall stage of mitosis (m) cycle is telophase and cytokinesis which is when the nucleus splits apart and start to reform the nuclear wall. And the cytoplasm splits thus creating another cell identical to its self. 

 To help control mitosis and prevent uncontrollable division there are checkpoints that the cell must pass before it can proceed into different phases. The are also internal and external  mechanisms that help to control uncontrollable division which can lead to cancer.