Summary of "Survival of the Sickest" Chapter 6

  The Chapter 6 of "Survival of the Sickest" starts off with the origin of vaccination. The vaccine came from the Latin word of "cowpox" which is an infection that can used against smallpox. Soon after, the author begins to talk about genes. The genes of a person are organized in 23 pairs of chromosomes, one set of 23 chromosomes came from the mother, and the other set came from the father. However, less than 3% of the DNA are about instructions of building cells, and scientists decided to call the other 97% the noncoding DNA instead of "junk DNA" because the fact that they are only not directly involved with creating proteins doesn't make the 97% useless. Also, the author noted an interesting fact that the mitochondria (the power plant of a cell) was once a bacteria that lived along with humans. 
  Later on, the author switches the topic to mutations. The genetic changes occur not only when there are errors in the transport of genetic data between generations, but also when organisms are exposed radiation or powerful chemicals. Outbreaks and pandemics are caused by either antegenic drift (when a mutation occurs in DNA of a virus), or antigenic shift (when a virus acquires new genes from a related strain).
  And finally, another topic the author mentioned was the "jumping gene". When the organisms are under extreme outside conditions, a sequence of DNA "copy and paste" themselves from one place to another, insert themselves into active genes and affect nearby genes by changing the entire sequence. This mutation is called "Jumping genes", and it was discovered by Barbara McClintock. There are two types of "jumping genes"- the first is DNA transposons, which jump through a cut-and-paste process; the second type is called DNA retrotransposons, which goes through a copy-and-paste process. Especially, the transposon is a huge part of our noncoding DNA, or "junk DNA".

- Andy Liu '15

13. Understanding DNA

  Today, to start off Unit 3, we learned about the structure and functions of DNA. DNA is the genetic material that transfers to a cell, and it is composed of nucleotides. Each nucleotide contains a nitrogen base, a 5-carbon sugar, and a phosphate group. 
  According to Chargaff's rule (discovered by Edwin Chargaff in 1947), he found out that the 4 types of bases are A (adenine), C (Cytosine), G (Guanine), and T (Thymine), and A=T, C=G. Also, Chargaff claimed that the composition of DNA is different between species, which add more evidence to prove that the DNA is the genetic material. 
  In early 1950s, Rosalin Franklin made a x-ray diffraction data on the structure of DNA. James D. Watson and Francis Crick indirectly obtained her data, and concluded that the structure of DNA is a double helix. The phosphate group and 5-carbon sugar are the backbones. The nitrogen bases became the "steps"  and they face toward the center of the helix. 
  The finding of Chargaff and the structure of DNA demonstrated the nature of base pair. Adenine always pairs with Thymine, and Cytosine always pairs with Guanine. This explains why the number of Adenine is always equal to that of Thymine, and the number of Cytosine is equal to that of Guanine. Adenine and Guanine are purines, which consist of two ring structures. Thymine and Cytosine are pyramidines which have one ring structures. By combining a purine structure with a pyramidine structure together, the distance between two sugar-phosphate backbones are always constant, thus maintaining a uniform structure. 

A summary of everything above... (just in case if you're bored)

  The activity we did today was to create a double-helical structure of DNA. We were given 4 pieces of paper with the drawing of 10 bases, scissors and tapes. We need to cut the paper in half, and cut along the edges of the nitrogen bases so that the bases can connect to each other, and become 5 base pairs with short pieces of tape attached. Later on, we taped all 4 pieces of paper together from the edges, and twisted the long piece of paper to create a helix shape. Finally we taped both ends of the paper. 

So this is what we got at the end... kindergarten style lol

  Finally we learned about the DNA replication. DNA replication occurs when the eukaryotic cell cycle is in the Synthesis phase. Both strands of the double helix can serve as the template for replication. 
  The process starts as an enzyme, DNA helicase, breaks the hydrogen bonds connecting the two parts of the parental strand and creates a replication fork. the final structure would be two branch strands (leading (5-Carbon) strand and lagging (3-carbon) strand) with exposed nitrogen bases, that allow themselves to be read by DNA polymerase. This enzyme is in charge of building complementary DNA strands. 

- Andy Liu '15

Answers for Article "From Atoms to Traits"

1.  Explain the significance of Mendel. 

  Mendel’s experiments on crossbreeding peas changed the general view in his period on heritable variations from ephemeral and random mixing to traits passed from one generation to another, even though the traits may not be visible.

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

  James D. Watson and Francis Crick discovered the structure (drawing above)

3. Explain each of the five examples of variations that occur to DNA and give an example of each.

 1) Point Mutation: The substitution of a single base pair. 

Example: A slender silhouette and a hulking animal

 2) Insertion: The addition of extra base pairs in the sequence

Example: A smooth pea and a wrinkled pea

 3) Gene Copy Number: Difference in the number of duplication of an entire sequence
Example: the genes for starch digestion in chimpanzees and humans

 4) Duplication: Difference in the number of duplication of a base pair
Example: Signal receptor for pigment cells in pigs

 5) Regulatory changes: the change in the formation of gene sequences during the organism's development
Example: the difference in traits of the bushy teosinte and the tall modern cornstalk

4. What is evo-devo? 

  Evo-devo is the abbreviation of Evolutionary development biology. It is a field of biology that compares the developmental processes of different organism to determine the ancestral relationship between them, and to discover how the processes are influenced by evolutionary forces. 

5. Make a connection between human migration and the mutation of lactose intolerance.
  If a person comes from a population that stop consuming lactose products after infancy, and he goes to a region where the people consume lactose through adulthood, he will be lactose intolerant since his body lacks the mutant form of lactase enzyme that continues to be active in adulthood. 

Response to "Does Race Exist?"

Here is the link to the original article.

  We usually define the race of a person by his geological origin and the culture of his country. However, from this article, I understand this definition is only valid through a biological standpoint, but it is inaccurate to determine the race of a person through his skin color and facial features. Usually, the genetic information we own can be used to distinguish human groups having common heritage and to assign individual to particular ones, and this information can help us find our races.

  There are tiny variations within our genes, and they are called polymorphisms. Polymorphisms contribute to differentiation between individuals. One of the useful classes of polymorphism is called Alu sequence, which is made of short pieces of DNA that are similar in sequence to one another. From research, we found out that the Alu sequence is heritable, which means that it can be passed on to the next generation. If 2 people have Alu sequence at the same spot in genome, they must be descended from a common ancestor. Therefore, the Alu sequence is a genetic marker, which means a inherited mutation in the DNA. According to the documentary “Journey of Man”, a genetic marker in our DNA can help us trace our ancestry, which can also lead to our geological origin.

  However, the skin color and facial features cannot determine the race of a man, since they can be strongly affected by the environment. The aboriginal Australian and sub-Saharan African people may have the same skin colors since both of them are exposed to strong sun, while natural selection can make the people in same group look more dissimilar.  
  And finally, it is important to find out the relationship between races and genetic variations because several polymorphisms different in frequency from group to group may have different effects on health. For example, some of the most common diseases like hypertension or diabetes are the results of polymorphisms in several genes, and each of them has a small influence of its own. Therefore, scientists may have to rely on one's ancestry to find out information for the treatment. 
  In conclusion, the article talked about how the biological explanation of races and ethnicity are related to genes, physical features and health. It is true that one can find out his ancestry through tracing multiple inherited mutations in his genes. Even though ethnic groups may share differences in physical features, but through the study of our DNA, finding out that every ethnic group are interconnected with another certainly brings us one step closer to discovering the dawn of man in the course of history. 

12. Survival of Fittest - Population Genetics

  Today we learned about genetics in a population, and the Hardy-Weinberg equations. We did an activity where everyone was given four cards. Two of the cards has an A in capital, and the other has an a in lowercase. Later on, everyone was put together in a spot, and we're supposed to do a type of mating dance with the music and keep walking to different and random spots. When the music stops, everyone stops moving, and began picking one card with the closest one to him or her. After both persons finished picking twice, the person has to switch the other two cards to the same cards as the two cards he picked (AA, Aa, aa), and the music starts again. The activity stops after 5 times.

   The activity was a demonstration of the Hardy-Weinberg equations. So in a population, each member is either evident in the presence of a dominant allele, with homozygous condition (AA), or heterozygous condition (Aa), or it has a recessive allele, with homozygous recessive genes (aa).
The percentage of all the conditions in the population can be calculated.
If p=the frequency of the dominant allele, q=the frequency of the recessive allele
Then p+q=1, and the population would be p^2+2pq+q^2=1, while p^2=AA, 2pq=Aa, and q^2=aa

Also, if the following conditions are met, the percentage of the conditions within the population will remain constant for all generations:
1. The population is large
2. Mating is random
3. There is no mutation for the alleles
4. No immigration or emigration occurs
5. There is no selection.

- Andy Liu '15

11. The Otis Project

  Click on the link to see more of the Paleo project, created by Karina and I: The Otis Project

- Andy Liu '15

10. The Beauty of Mutations

  Today we learned about the importance of mutations for organisms. We started the class by differentiating the shells in multiple ways (the shells were found in the same area). My partner Karina and I separated the shells by their shapes, patterns on the surface and colors. Later on, I learned that these beautiful shells are different because of mutations. Each of the shells have different genes to help them survive and reproduce in an environment, and pass on to the next generation.
  Looking for further information, we did a lab of breeding brine shrimp in salt water with different concentrations. The purpose of the lab is to see what is the percentage of salt water would be better for the brine shrimps to survive and reproduce.

Question: In what environment can the brine shrimp can survive and reproduce more easily?

Hypothesis: Brine shrimps can survive and reproduce better in water with high concentration of salt.

Design:
1. Get 5 dishes with the same size.
2. Put 50 ml of distilled water in each dish, with a salt concentration of 0%, 0.5%, 1%, 1.5% and 2%
3. Place 20 brine shrimp eggs in each dish, and put the lids on top of the dishes
4. Wait for 24 hours, and open the lids to find out how many brine shrimps hatched in each dish
5. Calculate the percentage and record the results

Analysis: As a result, the dish with 0.5% concentration of salt has the most brine shrimps hatched. There is no brine shrimps hatched in the dish with 0% concentration, and the number of brine shrimps hatched goes down from 0.5% concentration.

Conclusion: From the lab, we can see that the brine shrimps can almost adapt to any type of water with different salt concentrations, which explains why they can survive when the rains fall or the water evaporates.

- Andy Liu '15

9. Hey there... Can you do me a fava?

  Today in class we learned about the fava beans. It's normal if you haven't heard of this plant before, but you would definitely recognize the name if you are a crazy fan of Dr. Hannibal Lecter. It appeared in one of his most famous quotes in the film "Silence of the Lambs", when Dr. Lecter said "A census taker once tried to test me. I ate his liver with some fava beans and a nice Chianti." From this, you can probably imagine what the beans are like. Indeed, they are dangerous, and just lethal enough to make them interesting.
  Fava beans are interesting because they only harm the "chosen ones". The "chosen ones" are the people who have favism. Favism is an inherited enzyme deficiency carried by 400 million people, which makes it the most common enzyme deficiency in the world. The sickness is also closely linked to G6PD deficiency. G6PD (glucose-6phosphate dehydrogenase) is in every cell in the body. It protects cellular integrity, and clears chemical elements that would destroy the cell. The fava beans have 2 sugar-related compounds called vicine and convicine. They produce free radicals like hydrogen peroxide. If the hydrogen peroxide isn't cleared out by G6PD, it will start to attack your red blood cell. This is why fava beans can be deadly.

  There are a lot more examples in nature when plants use chemicals to defend themselves. The Indian vetch in Asia and Africa has a chemical weapon of neurotoxin that can cause paralysis. The jimsonweed, one of the nightshade family, contains a large portion of alkaloids that can be toxic to insects and other herbivores.

-Andy Liu '15

8. Find your Inner Fish

 
  This class is the first class for our 2nd unit, and the topic for this unit is evolution. In the book "Inner Fish", the author mentioned the importance of tiktaalik, a type of species that lived millions of years ago. The tiktaalik is crucial to the course of evolution because it is a key link for us to find out how marine animals evolved into land animals.
  Tiktaalik had features that helps him to survive both in water and on land. For land features, tiktaalik had limbs for doing push-up, and eyes on top of the head for larger vision. For marine features, the tiktaalik has scales and fins for swimming in water.
 

  Today, we also learned that the sedimentary rocks are important for fossil preservation, and the deeper the layer is, the older the rock is. This is also how paleontologists look for fossils in different periods.

- Andy Liu '15

Test #1

  Today we took the first biology test of the year. I think that I didn't do well on it, since I'm still having trouble recollecting what I learned from the chemistry class last year, and I missed a lot of details in the free response section. I believe that I need to put more focus on the course for the next unit. But for this unit I can't anything but hope for the best...

7. Macromolecules + Lab

  Today we learned about macromolecules. The reactions that join molecules with release of water is called a condensation reaction, and the polymerization (monomers join to make polymer) of a molecule is known as a condensation reaction. For water, the OH- comes from one monomer and H+ comes from another. In contrast, a depolymerization is when water molecules react with polymer to release monomers, so it is called a hydrolysis reaction. This is used when cells break down damaged or useless polymers.
  The monosaccharide structure are the basic unit in carbohydrates. A few examples of monosaccharides are glucose, galactose and fructose. The disaccharide formation is when two monosaccharides undergo a condensation reaction. There are two examples:
  Glucose + Fructose = Sucrose
  Glucose + Glucose = Maltose
  Glucose + Galactose = Lactose
  Also, there are polysacchrides, which are long chains of sugar units. Some of the examples are starch, glycogen, cellulose and chitin. The plant storage product is starch, and the animal storage product is glycogen. The plant structural product is cellulose and the animal structural product is chitin.

  We also learned that protein is made of amino acids. Some examples of amino acids are leucine (hydrophobic), serine and cysteine (hydrophilic). Also, we learned that RNA (ribonucleic acid) helps form proteins from DNA (deoxy-nucleic acids).
  Finally, we did a lab today on indicating protein, fat, starch and glucose in different substances.The indicators we used are biurets, benedict's solution, sudan III, and iodine.

-Andy Liu '15

6. HOUSE Case + Cell membrane

  Today we began discussing about our 1st HOUSE case of the semester. This case is about a senior cross-country runner. The athlete suffered from huge headache, confusion and nausea. We asked the patient a few questions concerning his habits and conditions before running, and we had a few hypotheses for the cause of the patient's sickness. The hypotheses include dehydration, over-hydration, gastroenteritis, sleep deprivation and migraine. Personally, I believed that the patient was suffering from over-hydration.
  To see more of my analysis of the patient's condition and diagnosis, click on this link: HOUSE case #1

  Today we also learned about cell membrane's structure and its functions. The cell membrane is the security wall of the cell, and it is selectively permeable. The parts in cell membrane include phospholipid, proteins and cholesterol. The function of cell membrane is communicate in a chemical way through glycolipid and glycoprotein, a result of inbeded proteins interacting with carbohydrate. The functions of proteins include transport, enzymatic activity, signal transduction, and cell-cell recognition.

-Andy Liu '15