Mitosis and Meiosis

During our last class, we did a lab where we had to look at either an onion cell or an animal cell and find the different phases of mitosis using a microscope. My partner and I had the onion cell. We observed the cell using the microscope we were given and were able to find Interphase, Prophase, Metaphase, Anaphase, and Telophase. We also had to draw what the phase looked like. Later we were given a lecture about mitosis/meiosis. Below is a picture of the cell cycle going through G1 (growth), S (DNA Synthesis), G2 (double check), and mitosis...

Embryology, Gene Layers, and DNA Control

 Embryology...what is it? Well, Embryology is a science (obviously) that is based on the development of an embryo from fertilization. As you can see in the image above, in the very first of all our embryonic stages, we look very similar, almost identical. 

Within this development, there are three germ layers. These layers are known as endoderm, mesoderm, and ectoderm, endoderm being the innermost layer. The endoderm consists at first of flattened cells, and it develops the digestive organs and lungs. 


Mesoderm is the middle germ layer and it is best known for helping develop the muscles, skeleton, and blood system. This layer appears in the third week of embryonic development and is formed through a process called gastrulation. 


The third layer, or the exterior layer, is called ectoderm. It emerges and originates from the outer layer of germ cells. The word "ectoderm" literally means "outside" and "skin" in Greek. Go figure! Anyway, this layer helps form the nervous system. In other words, it forms the spine, peripheral nerves and brain. It also helps form the lining of mouth, anus, nostrils, sweat glands, hair and nails.


In embryology and the development of embryos, DNA interactions help control and show how genes operate. It also opens the information of their network control within the genes.

Animal and Plant cells

We started the class of by getting out Unit 4 tests back...not too bad. Then, because our entire class didn't actually read what we were supposed to for homework (oops!), we discussed with a partner the differences and similarities of a plant and animal cell. We did this by making Venn diagrams. This brought us into discussion about our Unit 5 project and we were then given time to work on it.

After working on the project for a little bit, we learned how to use a new type of microscope. We observed  a dog flea, a cheek cell from our cheek, and a plant cell. We looked so closely that we could actually see the cell walls and chloroplasts in the plant cells. It was so cool! 

TEST DAY

I honestly have no idea what to post on test days. I'm pretty sure I post the same thing on every test day: I have no idea how I did on the test. I studied, I knew my stuff, but I still don't really know how I did on the actual test. You see, tests/quizzes and I don't really work well together. They do this thing to me where they make me second guess myself. For some weird reason, I know and have the right answer, but I end up putting a different answer. I feel like I did that a lot on this last test. Well, I guess I won't really know until I get my test back.

Pedigree

The picture above is an example of a pedigree. A pedigree is kind of like a family tree but for genetics. Pedigrees contain genetic information that can help track and predict certain traits or diseases. There are many symbols that mean certain things. For example, a square that is not filled in is the symbol for a male, and a triangle that is not filled in is the symbol for a female. You can see what the other symbols are and what they mean in the image above.

In a pedigree, one must determine the condition and mode of inheritance...

Condition: sex-linked or autosomal

Mode of inheritance: recessive or dominant

Sex-linked means that the mother is the carrier of a disease and there is a possibility that she will pass it onto her children 

Autosomal refers to any of the chromosomes other than the sex-determining chromosomes (ex: X 
and Y)...in other words, not sex-linked 

More Genetics!

Corn...kernels...so many kernels. I don't think I can look at a corn on the cob the same way ever again. We were given cobs of corn in class and had to determine the corn's parents' genotype and phenotype. This involved the counting of corn kernels. SO MANY KERNELS! I 'm pretty sure I had to start counting over so many times because I kept getting lost in the kernels. But eventually we did it and were able to determine the genotype and phenotype using what we learned from the past two classes.

We reviewed and practiced some genetic problems again. I think I'm starting to understand it a little more. However, I still really need to sit down and practice some genetic problems, because I am seriously slow. Everyone in my class will know the answer way before me while I'm still writing down the trait information. It's a slight problem. We also went over sex chromosomes and worked on some problems about Labradors. The test is coming soon, so I better get studying and perfecting my knowledge on genetics. But now it is time for Thanksgiving break and I can relax! Oh, just kidding, I have a bio project to do...hooray. 

Genetics! (2 Classes)

Yay! Genetics! For this class we started learning about Mendelian genetics. In the last unit, we read something about how Mendel used pea plants to examine genetics. In this class, we learned how to find genotype and phenotype ratios using a Punnett Square. In other words, we were taught the necessary steps for solving genetics problems. We also practiced some of those problems in class, and then took a quiz on it, which I got a 3 on. I think that means I should retake it, and that I need to practice a few more problems.

The next class consisted was focused entirely on genetic problems. We went over the steps again and did some more problems. Quick even showed us two different ways of finding the phenotype and genotype ratios; the Fitz way and the Quick way. Someone tried explaining to me how to the Fitz way but I just could not grasp it. Especially since this person was basically doing all of the problems in their head. So when it came to take a quiz, I used the Quick way. It took me a little longer than the rest of my class...actually it too me a lot longer than everyone else, but it doesn't matter because i got a 1! So I understand how to solve the problems, it just takes me a really long time to do them. Maybe if I keep practicing, I can get better and faster. 

The Test...DUN DUN DUUUUUUN!

We took our Unit 3 test a couple of weeks ago, and I did a lot better than I thought I would. Perhaps I did better because this unit was on stuff I am genuinely interested in. I have always been fascinated by DNA, genetics, and forensics. This unit was all about DNA and I seemed to get a grasp on all of the concepts pretty easily. I took me a while to understand DNA replication, but I found an animation online that explained the whole process and I think it really helped. Overall, I think I did well. However, there was this one question that had to do with chemistry that I did not get right. I always seem to miss the chemistry questions. Hmmm...I wonder why that is. Oh yeah, because I hate chemistry! I'm sorry, no offense to the subject, but I really don't get it. But no matter what, it seems to always find a way back into my life.

Operons

Today in class, we talked about operons. An operon is a unit made up of a bunch of genes. These genes regulate other genes responsible for protein synthesis. We were shown two examples of operons today. The first one had to do with tryptophan, a type of amino acid. This operon is on, meaning it is repressible. This operon has to be stopped. There is a regulatory gene in the front of this operon, and it has to be read by RNA polymerase. Next, an mRNA is created which then creates a repressor. This repressor is inactive; therefore, the RNA polymerase can go down the system of genes and read them. They create the polypeptides that make up the enzymes for tryptophan synthesis. When there is enough tryptophan, it can go into the repressor and activate it, which can then lock the system of genes. Furthermore, no RNA is made. The repressor is like a wall blocking the RNA from going through, and because of this more tryptophan cannot be made.

We also learned about an inducible operon, meaning it is off. This a lactose operon. Everything is pretty much the same as the tryptophan one. There is a repressor, a promoter, and an operator. One difference, however, is that the represoor starts off active, obviously, because it starts off stopped. So no RNA can be made due to the "wall." This happens when lactose is not present. When lactose is present, it is inducible. Therefore, repressor is inactive, the operon is on, and transcription occurs. In other words, RNA polymerase can pass through and RNA is made. 

All of this connects to a lab we did a few days ago. The lab was on pGLO. In our lab, we had four different containers with bacteria, but only the container containing arabinase was able to glow. This is because of the arabinose (sugar) which turns on the gene, allowing the RNA polymerase passage and causing it the bacteria to glow.

DNA Replication and Protein Synthesis

So DNA replication begins at a specific point in the DNA molecule called the origin of replication. First, the enzyme Helicase separates (or unzips) a portion of the DNA molecule.This causes two single stranded regions of DNA to form. Next, RNA primase comes along on the lagging strand and builds RNA primer. RNA primer is necessary in DNA replication because without it DNA polymrase III cannot not begin a new chain of DNA. And so, the next step is obviously DNA pulymerase III building a new chain of DNA. Then, DNA polymerase I comes in and replaces the RNA primer with DNA nucleotides, leaving fragments know as Okazaki fragments. Lastly, the DNA ligase enzyme swoops in and bonds these fragments together, completing the process of replication. 

It is also important to know that you read the strand from 3' to 5', but it is built from 5' to 3'. 



Protein synthesis is a whole other process. It starts off with Transcription, which is the separation of the double helix. This happens in a eukeryotic cell, a cell with a nucleus. The double helix has to be separated because a full DNA strand is too big to leave the nucleus. Therefore, it must transcribe so that it can fit and change from DNA to mRNA. Before the mRNA can leave the nucleus, the introns on the strand must be cut out (splicesome). The exons are then glued together. A G-cap (Guanine nucleotide) and Poly-A tail (Adenine nucleotides) are put on each end of the strand so that it does not get eaten by enzymes. These two protect the message. Finally, it can leave the nucleus.

Next, Translation occurs. The mRNA will now translate into an amino acid.The mRNA is decode by the ribosome to produce a specific amino acid chain. Met (AUG) is always the first amino acid in the chain. The ribosome reads the codons from 5' to 3'. Translation occurs in the cell's cytoplasm, where the ribosome are located, and they bind to the mRNA. The ribosome makes decoding easier by binding tRNAs with anticodon sequences on the mRNA. tRNA acts as a bus for amino acids and carries them to the mRNA. These amino acids are binded together by peptide bonds into a polypeptide. The amino acids are chained together into polypeptides while the mRNA passes through the ribosome and is read by the ribosome. 

The DNA Structure

So our main topic for this class was DNA. We talked about the double helix DNA structure and even created a paper model of it. The double helix structure was discovered by James D. Watson and Francis Crick. A man, Erwin Chargaff, found that a a composition of DNA varied one species to another, but all organisms had the same bases. These bases are Adenine (A), Cytosine (C), Thymine (T), and Guanine (G). Adenine is equal to Thymine and Cytosine is equal to Guanine. Hydrogen bonds are what hold together the Adenines with the Thymines and the Cytosines with the Guanines. Thymine and Cytosine are Pyrimidines. Adenine and Guanine are Purines. The bonds between the sugar and phosphate in the strucutre are called phosphodiester bonds. We began making a DNA model today and will begin the replication of it next class.

But what does it mean?

This picture is an example of an outcome of plant mutation. You see, mutations can occur when organisms are expose to some type of radiation or chemicals. According to Survival of the Sickest, Chapter 6, before we were able to modify our food on a molecular level with genetic engineering, plant breeders who wanted to grow more efficient crops would irradiate seeds by blasting them with a ray gun. The majority of the time, the seeds were not able to sprout after being irradiated; however, there were rare occasions when this genetic manipulation produced a beneficial trait. This flower could be a survivor of an irradiated seed. The mutation that has occurred in this flower, however, has nothing to do with efficient crops but with color. This flower has streaks of purple and white, which could be the cause of a change in the genes that control flower color.



This photo is an example of a half normal Sonic Hedgehog. Sonic hedgehog is one of dozens of genes that act to sculpt our limbs from shoulder to fingertip by turning on and off at the right time. According to Your Inner Fish, Chapter 3, something had to have gone wrong with Sonic hedgehog. Usually, when something goes wrong, the hands end up looking like a broad paddle with as many as twelve fingers, or eight as shown above, that all look alike.

Your Inner Fish Chapter 3 Summary

Chapter three of "Your Inner Fish" talks a lot about ZPA tissues. The story of our relationship to fossil animals is not just based on anatomy.  It can also be seen in our genes. Genes are a major part of the body and makes each of us who we are. In this chapter, Neil Shubin talks about a lab which is divided into two parts. The first part involves the study of fossils, while the other one focuses on the study of DNA and embryonic development. According to Shubin, the majority of our cells have the same copy of DNA.
So, our limbs exist in three dimensions: a top and a bottom, a pinky side and a thumb side, a base and a tip. Each bone is different from the other, and our body knows to develop in the way that Shubin describes because of chemicals produced by the cells in our our developing body. Researchers found that a certain patch of cells in the body were responsible for all of the limb development going on. If you remove that patch, no limbs develop. If you cut that patch in half, a person would end up with two limbs. All of this was tested on chickens. 

Certain geneticists began to work with flies and found a gene they called hedgehog. This gene determined which end of the fly was which, and this concept is quite similar to that of the patch of cells. Therefore, researchers began looking for something similar to this in humans. The chicken version of the hedgehog is called the Sonic hedgehog. Apparently, every creature on the planet has the Sonic hedgehog gene. This gene can be controlled by a vitamin A injection, resulting in changes in how the limbs develop. 

Researchers injected some protein that the Sonic hedgehog makes into a shark embryo. The protein was that of a mouse. Because the mouse gene was similar to the shark gene the limb development was affected the same way as if it were injected with vitamin A injection. This means that the evolution from fish fins to limbs likely involved the use of ancient genes.

"Survival of the Sickest" Chapter 6, Summary

This chapter started off by talking about how the first vaccine was the cowpox infection because it resulted in protection from smallpox. It turns out the word "vaccine" actually comes from the Latin word "vacca," and now suddenly everything makes sense! The chapter went on to talk about "junk DNA," which is 97% of the DNA in your body that, according to early scientists, don't do anything. That means that only 3% of your DNA contains instructions for building cells. We later learn that "junk DNA" isn't so junk after all. The chapter also mentions that a third of your DNA is derived from viruses. It is also brought up that humans have a total of approximately 25,000 genes. A man, Jean-Baptiste Lamark, was also mentioned. He was wrongfully accused of coming up with the theory of inherited acquired traits. This means that whatever traits a parent develops during his life will be passed on to his/her child. This theory, though not exactly right, isn't exactly wrong either. The rest of this chapter mainly talks about Barbara McClintock's evidence for "jumping genes." "Jumping genes," also known as transposons, are whole DNA sequences that move from one place to another when under environmental stress. Transposons act like "copy and paste," inserting themselves into genomes while still remaining in the same location. These "jumping genes" make up a large portion of our "junk DNA." Lastly, this chapter talks about RNA. Retroviruses are made up of RNA, an example being HIV. Using an enzyme called reverse transcriptase, retroviruses can transcribe themselves from RNA to DNA. The retroviruses that are a part of our DNA are called HERVs. They are believed to play a number of roles in human health. 

"From Atoms to Traits"

1. Mendel's experiments changed the view of heritable mutations from ephemeral and blendable to discreet entities passed from parents to offspring, present even if not always visible. His work formed the foundation of genetics. It contributes to everybody's understanding of genes, and all biological advances with genetics. If it weren't for him, genetic advancements would most likely not be possible today. 
2. 
   

This structure was discovered by James D. 

Watson and Francis Crick.

   3.  -Substitution of a single letter for another at a particular position in the polymer :                                        

     ACAAGATGCCATT -  AGAAGATGCCATT        

        -Deletion of a block of letters : ACAAGATGCCATT  -  ACAGCCATT 

        -Duplication of new letters : ACAAGATGCCATTAAA -ACAAGATGCCATTAAAAAA

        -Insertion of new letters : ACAAGATGCCATT -  ACAAGATGCCATTGTC 

        -Inversion and translocation of the letters already present : ACAAGATGCCATT -   

         AACAGAGCTATTC

   4. Evo Devo, short for Evolutionary Developmental Biology, is a field within evolutionar biology         

      that concentrates on studying the effects of changes in important developmental genes and the role 

      they play in evolution. 

  5. If a person migrates from an area where they don't consume lactose products beyond infancy to a       

     region where lactose is consumed through adulthood, it is likely that they will be lactose intolerant         

     because their body is not used to consuming lactose.     

"Does Race Exist?"

Karina Martin

Mr. Quick

A Block

10/22/13

The title of this article asks a very interesting question: “Does Race Exist?” It is interesting because when you think about it, yes, race does exist. Race has existed for years and has caused much conflict throughout the world, especially here in the United States. This article, however, is not talking about the social phenomenon that has existed for years, but the idea of race that has a biological base behind it. A person determines another’s race by looking at his or her physical features. Our features, such as our skin color or hair, are what normally make us a member of a particular race. There are other aspects that also work well in dividing us into groups, like genetically determined propensities for certain diseases.

            In this article, the question of whether genetic information can be used to determine what “group” a person is a “member” of is asked, and the answer to that is yes. As I mentioned before, we determine race by a person’s skin color and hair texture, and these signs are dictated by a handful of genes. However, how some of these “groups” are divided depends on which genes are examined; for example, a person might fit into one group based on their skin color genes, but fit into another based on a different characteristic. An example would be the “African race” in the United States. There are many people that label all Africans as from the same race. However, Africans come from different parts of Africa, which makes them very diverse, especially when it comes to looks. Over the centuries, African-Americans have mixed extensively with different groups originating from different parts of Africa. On the other hand, two people from different “groups or “races” can also share a larger genetic similarity that two from the same “race.”

            There are also medical implications of racial genetic differences that have brought many controversies among scientists. Diseases, such as sickle-cell and cystic fibrosis, result from genetic changes have risen in frequency due to being protective against diseases common in Africa and Europe. For certain diseases such as these, physicians may have to rely on background information about a person’s ancestry in order to best treat them. Some investigators say that group membership play a small role in genetic and medical studies, while others suggest that we can only understand how genetic and environmental differences among groups contribute to disease by using group membership. This dispute over the importance of group membership shows us how strongly our view of race is shaped by different social and political perspectives. 

Journey of Man

Today, we finished the video I talked about in my last post. We learned why the Y chromosome is the best place to look for genetic markers. This is because, unlike the X chromosome, the Y chromosome passes unchanged from father to son, making it the genetic marker easier to follow. The narrator of this video goes from Australia to a small Indian village and takes blood samples from them because he is trying to prove that the San Bushmen tribesmen traveled through India to get to Australia. He is taking samples from this small village specifically because the more indigenous a people are, the easier they are to connect to ancestors.

We also learned about why our skin color is different. This is because people living near the equator tend to have dark skin, while light-skinned people live nearer the poles. Also, selection on skin color depends on the UV radiation levels. In the video, we met a man named Niazov who has a genetic marker that has been inherited by 2,000 generations. Next, we met the Chuchki, a nomadic tribe, who are distant cousins of the Native Americans. They live by the Arctic Circle and have grown very accustomed to the freezing temperatures. In fact, they seem to have evolved or adapted in a way to survive int these harsh conditions. They adapted to a smaller sized body to reduce surface area in which heat can be lost. Moreover, their whole body contains body heat. The narrator finally came to the end with the Native Americans. Did you know that the first Americans to arrive on this continent arrived 13,000 years ago? It's crazy! Until next time...

WE ARE FAMILY!

In our last class, we talked about an article that we had to read for homework. The article pretty much talked about how all of us humans today are, in some way, related to each other. Weird, right? For the rest of the class, we began a video called "Journey of Man." This video is a documentary of a man who went on a journey around the world trying to discover how we are all related and where this relation started. What we have learned so far is that we all originate from Africa, from the San Bushmen tribe. The people of this tribe are the first ancestors of mankind, which lived about 50,000 years ago. These people a few major advantages: state of the art hunting technology, advanced language, and excellent tracking skills. We also learned about genetic markers, inherited mutations that write our history and are passed on from generation to generation. At some point in history, a few people of the San Bushmen tribe migrated and ended up in Australia. There is no evidence that can be found that can prove how the tribe made  it to Australia. This is because the sea levels at the time were lower than they are today, therefore, they could walk from one continent to the other. We will be finishing the video next class. Until next time!

My beautiful (not really) poem

So, remember how I said I wrote a poem about Fava Beans? Well, here it is. Think of it as a slam poem. Maybe that will make it seem less ridiculous...

Waka Flaka Fava Bean!

Can you do me a fava?

Tell me, what is a fava bean?

Fava beans are two faced fiends!

For some humans, it can help.

But for others…WELP! DEATH!

Favism, a fatal disease.

Those who have it die with ease.

Fava beans can be so mean.

If you live where they cultivate

You’re sure to feel their hate.

You’d think from spending so much time with them

They’d be your friend.

But nay! They like to slay

Those who spend time with them all day.

Fava beans aren’t the only ones who want to kill

Like Hannibal, who likes his fill.

Because they face fava beans pain

People are resistant to malaria’s reign.

Malarial parasites want to pillage your red blood cells

But G6PD gives them hell!

Evolution doesn’t fava traits

So be careful if you put them on your plates.

Because you might find out that nature

Is one of your biggest haters.

Because of all this strife

There is advancing of human life.

I am so sorry...

Hardy-Weinberg

So we did math in Bio class. It was cool, because, for once, I knew what I was doing. I actually grasped the concept of how to do a Hardy-Weinberg problem pretty quickly. Honestly, I really happy with myself. Hardy-Weinberg problems, by the way, are problems used, in some cases, to figure out the percentage of recessive and dominant individuals in a population. You can also figure out the frequencies of alleles. The equation is