My Cell Tour Project

Click on the link to see my unit 5 project I made for the standards. :)

16. Intro to Genetics

  Today we started learning about genetics. This unit is very similar to the Hardy Weinberg principle we learned. For every inherited trait (features) of an organism (all traits are inherited through meiosis or mitosis), there must be an unique type of gene in the DNA to provide instruction to determine the features, and those genes are called "alleles". If one allele overrides another in the organism, the allele is called dominant allele, and the other allele is called recessive allele. For example, if the allele for black hair for human is dominant, and allele for blond hair is recessive, a man with heterozygous alleles will have black hair, but the allele for blond hair is in the man as well. Therefore we say that the genes shown on the surface is phenotype, and the genes inside the organism is genotype.

 
    This diagram shows an example of monohybrid cross. In the diagram, T is the dominant allele and t is the recessive allele. If the father and mother are both heterozygous, the ratio of genotypes would be 1 homozygous dominant: 2 heterozygous: 1 homozygous recessive. The ratio of phenotypes would be 3 dominant: 1 recessive.

  This diagram shows an example of dihybrid cross with 2 traits. In the diagram, A & B are the dominant alleles and a & b are the recessive alleles. If the parents are AABB and aabb, all the F1 generation are heterozygous for both traits. Through self-pollination, the F1 generation will breed the next generation (F2), which has a phenotypic ratio of 9 dominant/dominant: 3 dominant/recessive: 3 recessive/dominant: 1 recessive/recessive.

- Andy Liu '15

15. Operon System

  Today in class we learned about the operon system. The operon system only exists in the prokaryotic cells (bacteria), and there are only two types of operons - repressible (on to off) and inducible (off to on).
  One example of the repressible type of operon systems is tryptophan. A regulatory gene is synthesized into an inactive repressor protein while the RNA polymerase transcribes the rest of the genes to create tryptophan. Once enough tryptophan is created, the tryptophan will connect to the repressor protein and switch it to be active. the active repressor will bond with the operator that started the transcription, and eventually RNA polymerase stops creating more tryptophan.
  The second type of operon system is inducible, and one example for that would be lactose. The repressor protein synthesized in this system is active at the beginning. And once enough lactose is created, the lactose will connect enter the repressor protein and triggers to be inactive. The repressor protein will leave the operator and allow lactase to be synthesized to reduce the amount of lactose in the body.

- Andy Liu '15

14. Protein Synthesis

  Today we talked about protein synthesis in class. Since DNA is double-stranded and has a large size, it cannot leave the nucleus to synthesize protein. So in order to convert the order of DNA bases to protein, the first step would be the process of translating DNA language to mRNA language, that is also known as "transcription". To start this process, the DNA would first have to break apart to allow access for RNA polymerase to begin translation. After this step is done, the introns in the mRNA are cut out and only exons are left in mRNA because introns are useless codes, also known as "junk DNA". Also, a cap made of Guanine (G-cap) and a tail made of multiple Adenine bases (poly-A tail) are added to the mRNA strand as well, to protect it from being eaten away by enzymes in cytoplasm.
  After the mRNA leaves the nucleus and enters the cytoplasm, the process of converting mRNA language to amino acids starts. This process, also known as "translation" begins with mRNA bonding with ribosome. The ribosome will read each codon (3-letter message) on mRNA, and match it with an anti-codon, carrying an amino acid. The message always begins with AUG (Met) and ends with UAG, UGA or UAA. After each codon is processed, the amino acid will connect to other amino acids and create a long string. When the translation is finished, the long string of amino acids will leave the ribosome, and will become protein.

- Andy Liu '15

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

5. Diffusion & Osmosis - Don't Stop Movin' (Part 2)

  Today we did another lab about the concept of diffusion and osmosis. We put three cubes of "cells" in the solution of NaOH after we measured their surface areas, and as you can see in the picture above, the cube's reaction with the solution involves color change. We took the cubes out after 3 minutes. 

  As you can see, the purple part on the outer layer of the cube was the part involved in the reaction, and the white part in the center of cube wasn't involved. In order to see the difference in color more clearly, we cut all the cubes in half. 

  We calculated the thickness of the purple part in order to find out the amount of reaction involved. Finally, we discovered that the smaller the volume of the cube is, the faster it reacts with the solution. 

- Andy Liu '15

4. Diffusion & Osmosis - Don't Stop Movin' (Part 1)

  DIFFUSION: Molecules are always in constant motion, and tend to move from a place of higher concentration to another with lower concentration. And the net movement of those molecules are called diffusion. The diffusion can occur in gas, liquid, or through solids. One example of diffusion is that when a bottle of perfume is opened, within minutes people in further distance can smell the perfume.

  OSMOSIS: Osmosis is a type of diffusion. However, it is special as well since it involves a selectively permeable membrane in the transport. The membrane allows certain molecules to pass through to the place with lower concentration, while it restricts the movement of others.

  TYPES OF SOLUTION BASED ON SOLUTE CONCENTRATION:
  If the solution in the bag has lower concentration than the solution in the beaker, the solution in the bag is hypotonic to the solution in beaker.
  If the solution in the bag has higher concentration than the solution in the beaker, the solution in the bag is hypertonic to the solution in beaker.
  If the solution in the bag has same concentration as the solution in the beaker, the solution in the bag is isotonic to the solution in beaker.

  WATER POTENTIAL: Water potential is the tendency of water to move from the place of higher concentration to another with lower concentration. It is affected by the pressure and the amount of solute.
 
  According the 1st lab we did today on diffusion and osmosis, we made 6 small packs ("cells") of 7 ml of solutions in different molarities.

  After we dried and massed all the 6 cells, we placed each of them into a labeled cup, which contained 50ml of distilled water.

  We let them stay for 30 minutes. After taking them out of the cups, we re-massed the cells and calculated the percent change in mass to find out the molarities.

  The 2nd lab we did today was based on diffusion and osmosis as well. However, instead of using "cells" of different solutions, we used russet potato. We cut 24 pieces of russet potatoes into roughly same size. We massed every 4 pieces of potatoes before we put them in each labeled cup.

  Later, we put 25ml of each solution into each labeled cup, and after we covered the top of the cups, we let them stay for about 9 hours. Then after we took the potatoes out of each cup, we re-massed them and calculated the percent change in each cup.

-Andy Liu'15

 
 

Answers for Evolution Quiz #1

1. Explain the following picture in terms evidence for evolution.

  This picture demonstrates the evolution of modern whales. The Mesonychid's living condition began switching from terrestrial to aquatic from around 55 million years ago, while its homologous structure changes as well. 3 million years later, the Ambulocetus it evolved to has a more flexible backbone and hind limbs in order to walk on land and swim. 6 million years later,  the Ambulocetus evolved to Rodhocetus, which its limbs could not support it to walk on land, and swam in an up-and-down motion. 4 million years later, Basilosaurus has more reduced limbs than those of Rodhocetus, and its size was bigger than Rodhocetus, which was closer to the sizes of the modern whale today.

2. Which of the following continents did marsupials begin from?

  E, North America

3. Comparing a dragonfly, bird, bats - explain the type of evolution that these organisms show

  Dragonfly, bird and bats have wings for their ability to fly. However, their underlying structures are different since they evolved from different ancestral structures. The bats has fingers on their wings, and the bird only has a single forelimb, while the dragonfly almost has none. This is why they show a type of convergent evolution.

4. Explain how the Common Descent Lab shows DNA evidence and ancestry as evidence for evolution. Include examples of Primates.

  In the Common Descent lab, we were looking for the similarities and differences of the hemoglobin strands in DNA of humans, chimpanzees, gorillas, and their common ancestor. We found out that the human DNA has the least similarity with DNA of the common ancestor, while it share the most similarities with Chimpanzee DNA. comparison of DNA sequences can be a useful tool to find out the similarities between species. Therefore, it can be a strong evidence for evolution.

5. Explain homology using some examples from your readings.

  Homology is the similarities in the structures of organisms of same or different species because of their common ancestor. For example, tiktaalik has same backbone structure as fish, and modern whale has same tail and backbone structure as Basilosaurus.

3. The Water Miracle

  The water has some very important properties, based on its polarity and capacity to create hydrogen bonds to help support Earth's fitness for life, including its ability to moderate temperature, its cohesive behavior, its expansion upon freezing, and its versatility as a solvent.

  One of the "miracles" water performs is that the ice can float on water. This can happen because hydrogen bonds water molecules create between each other can break and re-form through molecular motion. However, the hydrogen bonds will become stable at a certain temperature (0 degree Celsius), and the bonds will form a crystalline structure while the water molecules become farther from each other. Therefore, that's why the ice is less dense than water and, as a result, the ice floats on water.

The Crystalline Structure of Ice

-  Andy Liu '15

2. Covalent + Ionic Bonds

  The covalent bond is usually described as sharing of valence electrons, and this is why the covalent bonds only consist of non-metals. The covalent bonds are strong, and they usually lead to stable compounds. However, the covalent bonds are poor conductors of heat and electricity since they aren't composed of charged ions.

  Examples of covalent bonds: H2, H2O, Cl2, O2, CO2 & CH4

  The ionic bond is made up by a metal element and a non-metal element. To create bonds between each other, the metal donates certain amount of valence electrons to the non-metal. This results with a strong attraction between a positive ion and a negative ion. However, the ionic bonds usually lead to unstable compounds or molecules. 

  Examples of ionic bonds: KCl, MgI2, Na2O, NaCl, CaCl2, AlCl3

-Andy Liu '15