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. 

3-9-14

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.