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

Human Migration

     The last couple of classes we have really started to focus on human migration. After reading The Greatest Journey, reading Traces of Distant Past, and watching The Journey of Man, have learned a lot of things about the world that I did not know before. I would have never before guessed that Native Americans were from Asia.

 


We learned that everyone came out of Africa, and how our migration out of Africa can be determined by genetic markers, either using mitochondria, tracing maternal line, or using the more effective Y-chromosome approach, which gives you a more accurate way to trace the markers because there are tens of million of nucleotides as opposed to just 16,000 in the mitochondria, and they don't get chopped up from generation to generation. These two approaches have given us 'Mitochondrial Eve' and 'Y-chromosome Adam'. This genetic approach of tracing human migration is much more effective than the use of fossils and artifacts, for these are so rare and there are so few that there are huge wholes that would not have been filled without using genetics.

I learned that the San tribe is the first ancestors of mankind. That they are very unique, in that they speak in a clicking language, which is actually very effective in hunting because they can talk without scaring of their food. I learned that humans first migrated to Australia, while the ocean level was low enough for them to walk most of the way, this was due to the Ice Age. One of last cool things that I would like to talk about is the man named Niazov who lived in Central Asia. What was significant about him is that he was a direct descendant of a man who lived there 40,000 years ago, when it was the pit stop to the rest of he world. This man would have been an ancestor to Europeans, Native Americans, Russians, and many more. If you look at his face, you can definitely see a lot of diversity.

Evolution

The last few weeks have been focused on evolution and genetics. We started all of this with Tiktalik, then we worked on our Paleo Projects. Since completing our Paleo Project, we have continued to address these topics.

We read Chapter 8 of Survival of the Fittest, in which we learned about progeria, and how it is caused by a defect in Lamin A, causing cells to deteriorate faster. We learned about how cancer can spread throughout the body with the use of telomerases, and how there is the Hayflick limit, which limits the number of times that a cell can split. Unfortunately, this does not apply to the telomeres, so cancer can grow without limit. We also learned about biological obsolesce, and how humans are like iPods, the defected ones dies and the rest improve.

We leaned about Charles Darwin and his theory of natural selection. We saw examples of how species evolved differently to better survive their specific environment, such as the finches who developed different sized beaks that reflected the food that they ate. We also learned about convergent evolution, which is the development of similar traits bases solely on the fact that species live in similar environments, and selective breeding, in which humans can breed a stronger and better animal, or a better tasting plant, ect. I also learned about speciation, in which two groups of the same species separate and evolve separately.

Evolution

Convergent Evolution

From Atoms to Traits

For this assignment we were asked to answer questions pertaining to the article From Atoms to Traits.

1. Explain the significance of Mendel. 

     The significance of Gregor Mendel is that he showed us that discrete heritable variants are passed down from parents to offspring, even when they may not physically be visible. When I say discrete, I mean that there is no middle ground, they either had tall or short stems, not a blend that would have been medium sized. Mendel conducted many famous breeding experiments, and showed us that variations came from genetics, something that Charles Darwin was unable to discover.

2. Draw the structure of DNA and who discovered this structure. 

     Francis Crick and James D. Watson discovered the DNA structure in 1953. They used Rosalind Franklin's  x-ray pictures to help create this structure.
3. Explain each of the five examples of variations that occur to DNA and give an example of each. 

The five examples of variations that occur in DNA are substitution, deletion, duplication, insertion, and inversion and translocation. Substitution would occur when a single letter is swapped out for another at a particular position in the polymer. This is seen in the whippet dogs. Deletion would occur when a block of letters vanishes. Duplication is when a letter, or even an entire gene, is copied more than once. An example would be that humans have 10 copies of a starch-digesting gene. Insertion is when a new letter is placed in a previously empty spot. Inversion and translocation would occur when existing letters are either inverses, or moved into a different spot.
4. What is evo-devo? 

     Evo-devo is a subspecialty of evolutionary biology that concentrates on studying the effects of changes in important developmental genes, and the role they play in evolution.

5. Make a connection between human migration and the mutation of lactose intolerance.

The mutation of lactose tolerance is a result of human migration to regions where cows, or other milk producing animals, were the primary source of nourishment, as food themselves and as providers of milk. Those with the mutation that allowed them to drink milk would have been able to survive off of this milk, while those without the gene mutation would have died. Some migrators may have attempted to bring cows with them when they traveled, giving them constant access to food and drink.

Response Paper For Traces of Distance Past

Both in the article that I read, titled Traces of Distant Past, and in the video that I watched, called Journey of Man, I learned about how scientists are able to use DNA gathered from different lineages, or groups of people, to construct a “genetic tree”. Geneticists spend a lot of their time traveling around the world, as seen in the video, and they do this in effort to gather as much DNA from as many different lineages as possible. By gathering DNA from multiple different lineages, both in different regions and from different ages, these geneticists can accurately create a “timeline” of human migration. Through this process, scientist has been able to trace the origins of modern humans back to a single African woman who lived close to 200,000 years ago. This woman, the common ancestor of all modern humans, is referred to be scientists as “Mitochondrial Eve”. Later in this article, I learned that Y-chromosomes are now used instead of mitochondria so as to better trace this human migration, since Y-chromosomes have more nucleotides; tens of millions, compared to just the 16,000 nucleotides in mitochondria. This newer approach allows scientists to better distinguish one population from another. As yet another approach, genealogists have used microorganism genes, such as bacteria, viruses, and parasites, to discover patterns in migration. They do this because these microorganisms hitched a ride on humans during their migration, so would have been exposed to the same places. Geneticists also study SNP’s, which stand for single nucleotide polymorphisms, and are swaps of one nucleotide for another. Researchers can use SNP’s to resolve the identities of individual populations. The studies of all of these different genetic variations serves to provide us with a kind of historical “Global Positioning System”.

I found it interesting when the author of this article said that there is no race, but rather that there are only geographical gradients, and that there is no sharp difference between people of different regions or continents. This makes me wonder how the world would act today if everyone looked at it with this sort of scientific view. Would there have ever been slavery?

            The biggest controversy brought to light in this article is whether humans came strictly out of Africa, as the Out-of-Africa theory would suggest, or if they came out of Africa, Europe, and Asia, as argued by the Multiregional theory.  So far, almost all of the evidence points toward the Out-of-Africa theory. Another popular controversy brought to light in this article is the argument over whether humans interbreed with archaic species, such as Homo erectus. There has not been any solid evidence to prove that interbreeding occurred yet, however the fact that modern humans have a deep ancestry would support this possibility.

            This article left me with many different questions to ponder. One of the most interesting questions that I would like to find out is whether we will one day be able to find suspects in criminal cases through examining lineages. Particularly, lineages that are connected by a common surname. I would also like to know what impact genetic diversity plays in our ability to survive?  Some more general questions that I would like to find the answer to would be why the Africans left in the first place. Was it because of a change in climate, or was it because of a loss in food? Was there another reason? My last question that builds off of the article is whether the rate of evolution is still accelerating to this day? Could our improvements in medicine, which seem to eliminate natural selection and survival of the fittest, be causing the rate of human evolution to decrease?

Parents Day

     Our homework before parents day was to read three articles all dealing with attractiveness. There was Averageness, Masculinity, and Symmetry.

     We learned that the more average a face is, the more attractive it is. This is because it is easiest to process, and is closest to the faces that we visualize in our mind. Curiously, when the features of the faces were exaggerated, the face was deemed the most attractive, somewhat disproving that the most average is the most attractive.

The Average is More Attractive

     We learned that both men and women typically find feminine facial features in the opposite sex to be more attractive. However, a female will find a more masculine face to be more attractive when seeking offspring.

Masculine Features vs. Feminine Features

     We also learned that the more symmetric the face is, the more attractive it appears to us, for it is the easiest to process. This is also true for objects.

Symmetrical Is Most Attractive

What Makes A Face Attractive

Both my parents and I found feminine facial features to be more attractive in both male and female faces. Feminine facial features are associated with a more caring and parenting person.

Brine Shrimp Lab Continued

   
     On Thursday, October 3rd, we finished up our Brine Shrimp lab. After collecting our final data and calculating the percent survival rates in the different salt-concentrated water, Brian and I calculated that the 0.5% salt-concentrated water had the highest survival rate. This would suggest that the majority of Brine Shrimp are adapted to survive in bodies of water similar to this example.

After finishing this lab, we did another lab, which showed how the animals that were not naturally selected to survive would die out. This could be caused by a gene that changes the animals appearance or features. For example, tigers that genetically have thin fur will die out in cold weather, will tigers with thick fur will survive. We represented this process by using two different colored beads.

We took the last moments of class taking a quiz on mutations, hereditary traits, ect.

Brine Shrimp Lab

Class Day 13

     On Tuesday, October 1st, we started a three day lab. This lab continued into office hours of the next day, and ended during our class on Thursday, October 3rd. Our goal was to find the affect of the concentration of salt in the water on the lives of Brine Shrimp. My prediction is that the Brine Shrimp need at least some salt to survive, for they are found in the ocean. However, I also predict that if the salt concentration is too high, the Brine Shrimp will die. What we must do is set up five different concentrations of salt in water, and recorded how many Brine Shrimp survive, and how many die or fail to hatch. I guess the water with either 1% or 1.5% salt will contain the highest percent of surviving Brine Shrimp.

     We tried to get about 20 eggs into each dish of water, but some of the dishes ended up with twice this amount. But since we recorded how many there were in each one, we should be fine.

Close Up Of Brine Shrimp Eggs

     When we showed back up on Wednesday during office hours, a few of the eggs had already hatched. At this time, the most amount of hatched eggs was found in the 0.5% salt concentrated water. This may suggest that Brine Shrimp live in bodies of water with salt concentrations similar to this.

Hatched Eggs

    The fact that there existed hatched eggs in different bodies of water prove that there were mutations that occurred that allowed some Brine Shrimp to live in higher salt-concentrated water, and some to live in lower salt-concentrated water.

At this point, our data also showed that no Brine Shrimp were able to survive in pure water.

Paleo Project Day

     During our class on Thursday, September 26th, we took a quiz on variables. It was extremely easy, and I got a perfect score on it. We learned a little bit more about the evidence of evolution, and about mutations and stuff. The remaining part of the class, we got to spend some time working on our Paleo Project, and planning out how we will divide the work and stuff like that.

Brian and I chose to research Miacoid, which is an early carnivore. According to what we found, Miacoid looks something like this...

For homework, we just had to watch a video and read a powerpoint on evidence for evolution, work on our Paleo Project, and work on our objective sheet if we wanted to.