Chaper 6 Your Inner Fish & Embryology

Embyology

I learned that we are made of 2 trillion cells, but come from one. That one cell forms when the genetic material from the dad's sperm and the mom's egg fuse. Then the cell divides four times and forms 16 cells, which make up a blastocyst. The blastocyst implants into the mother's urethra and the embryo starts to develop. It joins the bloodstream of the mother.

They all look so similar. Different species.

Fertilization of an egg by a sperm, and formation of a blastocyst, which has 16 cells. They all clump together and stay on one side.

The three germ layers are Endoderm (inner), Ectoderm (outer), and Mesoderm (middle).

The Endoderm makes up the inner structures such as the digestive tract and glands. The Ectoderm forms the skin and the nervous system. The Mesoderm forms tissue between gut and skin, such as muscle.

This comes after the blastocyst, and it is known as a tube within a tube structure.

Another tube within a tube picture.

Human Embryo that forms.

These are called the Homeobox genes, and a fly has eight. They are mutated genes that can cause the fly to have extra wings, have a leg on its head, or miss a part of its body.

The DNA control is called the Organizer, and it determines the body plan. I think it is a chemical or something. All species have an organizer.

Unit 4 Test & Unit 5 Project

Last Biology class, on Thursday, I took the Unit 4 Genetics Test. I was pretty nervous before the test because I had spent most of my time working on my Marfan Syndrome prezi and not a whole lot of time studying. However, I a relief when taking the test, because I knew everything on it pretty well. I feel that I probably missed one of the Hardy Weinberg problems. Mr. Weinberg was an evil man. Also, I was unsure about the question with the shark. Other than that, I felt pretty good when taking the test, and felt even better when I saw that I got all 1s on the standards.

As for the Unit 5 project, I have not started it yet. However, I have looked at some pictures of prokaryotic cells (which would be bacteria) and eukaryotic cells (which may be either plant or animal). I have learned only a couple of the organelles, but that is at least a start.


Prokaryotic

Eukaryotic

Similarities and Differences

Marfan Syndrome

For my Unit 4 Project I did Marfan Syndrome. It is a disease that causes a variety of different health problems. People with Marfan always appear to be slender and tall. This is an autosomal dominant trait, and is caused by a mutation of the FBN1 gene. Below I have some pictures of people who have been diagnosed with Marfan Syndrome. If you want to see more, particularly how it relates to our genetics chapter, click on this link to my prezi. http://prezi.com/udoguolukqrr/?utm_campaign=share&utm_medium=copy.

Special Genetics & Pedigrees

In the class before our test, we reviewed some types of special genetics, and we learned about a pedigree. The special genetics that we learned included Codominance, Incomplete Dominiance, and X-linked.

Codominance

Both colors are shown in the F1 generation. Not just one color, and not a mix of the colors. This is because both the gene for red color and the gene for white color are dominant.

People with type AB blood are dominant for both A and B.

The fish shows both colors.

So does the cow.

Incomplete Dominance

The F1 generation is a mix between the two parents. Red x White = Pink. 

Color dominance is incomplete.

White Dog x Brown Dog = Gold Dog

X-linked

Gene is attached to chromosome. Men cannot be heterozygous, the gene is not present on the Y chromosome. Women can be carriers, so have a slimmer chance of actually showing the recessive trait.

Pedigree

Shows the family tree for the trait. Can be a X-linked trait or autosomal. Don't be tricked by Mr. Quick into drawing one of these for no reason. He is sneaky!

Dihybrid Cross

For homework tonight, we are learning about dihybrid crosses, which involve two traits. I have made an example question below.



In this example, the a homozygous dominant father (TTZZ) and a homozygous recessive mother (ttzz) breed and have offspring. All of the offspring, F1 generation, are heterozygous (TtZz). Having a tan (T) is the dominant trait and not having a tan (t) is the recessive trait. Also, having a zigzag tattoo (Z) is the dominant and having no zigzag tattoo (z) is recessive.

The genotype ratio is 1 TTZZ: 2 TTZz : 2 TtZZ : 1 TTzz: 4 TtZz : 1 ttZZ: 2 Ttzz : 2 ttZz : 1 ttzz, and the phenotype ration is 9 tan/zigzag tattoo: 3 tan/no tattoo: 3 no tan/zigzag tattoo: 1 no tan/no tattoo.

Below is a cool example of another dihybrid cross. Four different cats are produced, with the color and the length of tail changing.

Monohybrid Cross

In the last class, we learned about a monohybrid cross. For the most part, I understood how to do it. I got a 5/5 on my quiz, so that should show that I know something. I think that I have cleared up any uncertainties by now.

An example of a monohybrid cross that I will make up right now involves the breeding between a homozygous right handed father (RR) and a heterozygous right handed mother (Rr), with the dominant trait being right handed (R) and the recessive trait being left handed (r).



As shown above, this match results in a genotype ratio of 2 RR: 2 Rr and a phenotype ratio of 4 right handed : 0 left handed.

Test & Lab Report

To study for my Unit 3 Test, I re-watched all of Mr. Quick's videos, watched some other videos on youtube, and went to Mr. Quick's Sunday review session. When I took the test, I felt pretty confident about my written response, but not to confident about the first ten or so multiple choice questions. I think that I should have spent more time practicing writing DNA sequences, and the replicated or mRNA sequences that came with it. I think that I knew how to do it, I just could not get my brain to work at the time. When taking the test, I was still a little stumped on the 5' to 3' and the 3' to 5'. However, after looking at my mistakes I believe that I understand it clearly now. I also should have practiced finding the amino acids that went with the mRNA codons.


As for the lab report, this one did not take nearly as much time as the last one, but it was still pretty time consuming. I think that the reason that it still took a long time for me was that I was still a bit confused on what my results showed. Our purpose of the experiment became a lot more clear once we talked about operons, but is was still a bit confusing. After reading an explanation, it was all cleared up for me, and I was able to write my report. I think that I wrote too much, but that is because I had to cover a lot more topics than just operons. below is the link to my lab report.

https://sites.google.com/site/blakeshonorsbiologysite/hb-standards/3-dna-structure-and-function/--pglo-lab-report

Operon System

The class before the test, we learned about the Operon System. An operon can come in two different forms. It can be either repressible or inducible.


In a repressible operon, the repressor is initially inactive, and so the RNA Polymerase can go down the DNA strand and create a complementary mRNA strand (transcription). Then, it goes through RNA processing and through transcription and eventually becomes a protein. The protein can then act as the co-repressor, and activate the repressor.




In an inducible operon, the repressor is initially active, so the RNA Polymerase is blocked from going down the strand and eventually creating a protein from that gene. When an inducer, such as arabinose for the pGLO lab, is added, the repressor pops out of the operator and becomes inactive. The RNA Polymerase then goes down the DNA, and through Transcription, RNA Processing, and Translation, the a protein is made. This protein is an enzyme, arabinase, that eats the sugar, arabinose. When all of the sugar, inducer, is eaten up, the repressor becomes active again, and blocks off the RNA Polymerase.

What Do These Photos Mean?

     Using Survival of the Sickest and Your Inner Fish, we have to describe the following two photos.

     This flower has most likely developed its colors for more reasons than one. If I had to take an educated guess, I would say that it developed bright colors to attract bees, so that it can be pollinated. Another possibility is that its colors act as a warning sign, causing less animals to eat this flower for fear of being poisoned. It discussed something like this in Chapter 4 of Survival of the Sickest, when is said that when plants containing phytoestrogens are consumed by animals, the estrogen-like compound affects the reproduction of these animals, reducing the number of animals that eat that plant. 

Rewriting what I wrote in the previous blog post, "Failure of “Sonic hedgehog” to turn on properly can result in extra fingers, paddle hands. Similarly, malfunctioning ZPA results in malformation in hands". This is different than what the scientist in Chapter 3 of Your Inner Fish were doing. What the scientist were doing was moving the ZPA patch from one side of the bud, which in later development is the hand, to the other side, resulting in an exact duplication of the fingers, not like what is seen above, but rather what is seen below.

     Notice that in the experiments done in this chapter, the two ends of the arm where mirror images of each other.

Enzymes Used In DNA Replication

Different Enzymes and their role in DNA replication.

Helicase- an enzyme that unwinds and separates the two strands of DNA double helix in order to
               provide a single-stranded DNA for replication. The helicase moves down the line of DNA        
               and continues to separate the two strands throughout the replication process.

DNA Polymerase III- enzyme involved in prokaryotic DNA replication. For example the replication of
                                   bacteria.

DNA Polymerase I- enzyme that removes RNA primer from the lagging strand and fills the correct
                                necessary nucleotides fragments in the 5' to 3' direction. It proofreads for mistakes.

RNA Primase- an enzyme that synthesizes the RNA primer. It lays down a strand of 8-10 nucleotides
                        that is complimentary to the replicating strand of DNA. DNA polymerase cannot initiate
                        the synthesis of a DNA strand without an initial RNA primer.

Ligase- enzyme that joins the various fragments together into a continuous strand of DNA.

Your Inner Fish Chapter 3 : Handy Gene

In this chapter of Your Inner Fish, I learned that we have hundreds of different cells which gives our tissues and organs their distinct shapes and functions. However, no matter how different all of these cells seem, they all contain the exact same DNA. The reason that the cells are not identical is that each of these cells contains different genes that are actually active. For example, a skin cell is different from neuron cell because different genes are active, so a different protein is made. Our body as a whole is essentially a composition of individual genes that turn on and off inside each cell during our development (The things that control the activity of our genes are known as genetic switches).

Many experiments were done in this chapter to examine organism development. One was done on chicken, and its purpose was to examine limb development. Saunders and Zwilling discovered that there are little patches at the end of a bud, where your fingers would eventually develop, that control the pattern of the bones that make up the limbs. They named this patch of tissue the zone of polarizing activity, or ZPA.

Normal development of a limb.

Development when ZPA is moved to other side of the bud.

In another experiment, scientist found a gene that made one end of a body segment of a fly look different from the other. They called this gene a “hedgehog”. When the same gene was later found in chickens, it was called the “Sonic hedgehog”.

"Sonic hedgehog"

The "Sonic hedgehog" gene was named after the video game character.

Briefly summarizing as much as I can for the rest of the chapter, the following is the main points. Scientists found that injecting Vitamin A at the right stage in development resulted in a mirror duplication of digits. Scientist attached dye to the “Sonic hedgehog” and found that only cells in a tiny patch at the end of the bud had gene activity, similar to the ZPA. Sonic hedgehog is active in ZPA tissue in every animal with limbs. Failure of “Sonic hedgehog” to turn on properly can result in extra fingers, paddle hands. Similarly, malfunctioning ZPA results in malformation in hands. Randy Dahn experimented on skates (very different structure and cartilage rather than bone) and found the “Sonic hedgehog” gene. Skate reacted the same way as a chicken did for everything, and when Vitamin A was injected in the skate, it produced a patch of tissue on the opposite side that contained the “Sonic hedgehog”, causing a duplication of bones. When a mouse “Sonic hedgehog” was placed in between the rods in a skate embryo, these rods developed differently, and depending on how close they were to the “Sonic hedgehog”.

Examples of malformation of the hands or feet.

 

            Conclusions drawn from all of the experiments were that the “Sonic hedgehog” makes fingers distinct from one another, and the finger formed depended on how close this “Sonic hedgehog” was to it. The author concludes that all appendages, whether fins or limbs, are built by the same genes. Building off of this, he argues that evolutionary transformation of fish fins into limbs did not involve the origin of new DNA, but rather just a shift of ancient genes into new ones. Lastly, Shubin, the author, states that the connection between living creatures is deep, leaving us to wonder what other things we may share with other species.

Survival of the Sickest Chapter 6 Summary

     In chapter 6, Dr. Edward Jenner discovers that the people infected with cowpox are immune to smallpox. To test his findings, he infected a bunch of young men with the cowpox disease, and the results led to the eventual creation of vaccines. The chapter built off of this and began talking about how genes are able to change, and how they can form antibodies to fight against infections. It mentioned that humans have 23 pairs of chromosomes, and that the 23rd one is the sex chromosome which determines whether you will be a boy or a girl. When the sperm from the dad and the egg from the mom are brought together, the form a single cell known as a zygote. 

Zygote Cell

X and Y Chromosomes

     Interestingly, only 3% of our DNA is actually used for coding, and the rest is "junk DNA", which would later be called non-coding DNA. Regarding mitochondria, this chapter mentioned that it produces energy that is needed for the cells to run, and the chapter talked about how mitochondria was likely a separate bacteria, but now lives in our cells. Surprisingly, scientist believe that 1/3 of our DNA may be from viruses.

Previous view of Noncoding DNA 

"Junk DNA" later is discovered to
act as "jumping genes".

     We reviewed that a mutation occurs when the DNA is copied incorrectly, but in this chapter, we learned about mutations caused by radiation, chemicals, or the Sun. Speaking of the sun, we learned that outbreaks of diseases are likely related with the Solar Flares/Sunspot Peaks that occur every 11 years. 

Mutations caused from radiation

 

     We learned how Lamarch was thought to be the man responsible for the creating the theory of inherited acquired traits, which would mean that traits gained throughout one's lifetime would be found in in the future generations. In some support of this theory, Barbara McClintock discovered "jumping genes", or transposons, which are genes that will move from one place to another under stressed conditions. She believed that they jumped to specific locations, toward the genes that would cause the most beneficial possible mutation. Cairns, another scientist, believed that the conditions just caused the mutations to go faster, not jump around. This increase in mutation speed is known today as hypermutation, and it occurs at up to 100,000,000 x faster than the regular mutation.

"Jumping Genes"

Environmental Affect

     Chapter 6 taught us about the Weismann barrier, which prevents mutations, and any information at all, from passing from somatic cells to germ cells. However, it does allow some viruses to pass through. We learned that some cancer is hereditary, and some is by external triggers such as smoking and radiation. 

External cause of cancer

     Connecting everything in the end, we found that "jumping genes" are involved in the producing of antibodies, a large part of Junk DNA is made of "jumping genes" and viruses, and building up anything in your body involves going from DNA to RNA to protein. 

Antibodies

     We also learned that retroviruses are made of RNA, and they can change your DNA, because they go from RNA to DNA. Retroviruses that have written themselves into DNA compose 8% of human the genome, These retroviruses in our DNA are known as HERVs, which stands for human endogenous retroviruses. Lastly, the chapter reminds us again that viruses played a key role in the evolution of mankind.

Not Really