Your Inner Fish Chapter 6

3 layers in embryos: 
Ectoderm: outer part of the body and nervous system
Endoderm: the inside layer, inner structures of the body
Mesoderm: our skeleton and our muscles.

What's really interesting is that in fact the same parts in these cells forms the same organs in every animal.

Dihybrid Cross

Once you understand monohybrid cross, dihybrid cross is basically the same thing. However, In contrast to a monohybrid cross, a dihybrid cross is a cross between F₁ offspring (first-generation offspring) of two individuals that differ in two traits of particular interest. For Dihybrid crossing, there are always 2 different traits Represented by different alphabets, for example let R be a dog with Red eyes and r be black eyes while Y be yellow skin and y be white skin. The question might be something like what are the genotype and phenotype ratios if you mate two heterozygous dogs together, which in this case would be RrYy X RrYy. And then basically you simply isolate the Rr X Rr and Yy X Yy and do the punett squares for both of them, then you multiply the results to get the ratios. Not rocket science.

Monohybrid Cross

Monohybrid cross is a really simple idea, simply take a sqaure and label all the sides with letters, which in most cases (A) means dominant trait while (a) refers to the recessive trait then you simply "multiply" them putting the terms together in the respective boxes of the sqaure and there you go, theres your genetic and phenotypic ratios.

Genotypic ratios: 1AA: 2Aa: 1aa
Phenotypic ratios: 3 dominants: 1 recessive

Unit 3 Test/ Lab

This test was pretty hard in my opinion, I forgot the RNA processing part in the free response and the multiple choice was definitely harder and more confusing than the previous tests.
As for the lab report, this is the first lab report that I actually completely did on a word document and it was a rather different yet rewarding experience since I got it done a lot faster than normal.

Operon System

Operon systems can either be inducible or repressible.

Repressible operon:

The repressor is originally inactive and the operon is on. Protein is being synthesized in repressive operons. Tryptophan is created in order for the repressor to be activate.  RNA polymerase reads DNA to create mRNA. Then RNA processing occurs and through transcription it eventually becomes a protein. Then the protein will become the co-repressor, thus activating the repressor to stop the system.

Inducible Operon:

The repressor is initially active and the system is off since RNA polymerase cannot access the gene getting blocked by the repressor. An inducer is needed to inactivate the repressor and allow the system to run again, in the pGLO lab that would be the arabinose. This would allow the RNA polymerase then go down the DNA and through protein synthesis produce the protein. Such protein is an enzyme that eats up the sugar. However, when all the sugar is gone, the repressor plugs back into its original position and activates again, turning the operon system off.

DNA Replication/ Protein Synthesis

DNA Replication is the process of replicating a DNA strand in a semi- conservative sense. First the Helicase comes in and unwind the strands by breaking the hydrogen bond. Then the RNA primase adds short sequences of RNA to both strands (the primer). Thirdly the primer allows DNA polymerase III to bind and start replication. Then DNA polymerase III adds nucleotides to each template strand in a 5'→3' direction. These nucleotides are initially deoxyribonucleoside triphosphates but they lose two phosphate groups during the replication process to release energy. One strand is replicated in a continuous manner in the same direction as the replication fork (leading strand. The other strand is replicated in fragments (Okazaki fragments) in the opposite direction (lagging strand). Then the DNA polymerase I removes the RNA primers and replaces them with DNA. Finally, DNA ligase then joins the Okazaki fragments together to form a continuous strand

Protein synthesis is one of the most fundamental biological processes by which individual cells build their specific proteins. Within the process are involved both DNA (deoxyribonucleic acid) and different in their function ribonucleic acids (RNA). The process is initiated in the cell’s nucleus, where specific enzymes unwind the needed section of DNA, which makes the DNA in this region accessible and a RNA copy can be made. This RNA molecule then moves from the nucleus to the cell cytoplasm, where the actual the process of protein synthesis take place.

DNA Structure

Today in class we discussed the DNA structure as shown below and started cutting out a paper model for it. The structure was discovered by James Waston, and we also learned that there are 4 different bases including Adenine (A), Cytosine (C), Thymine (T) and Guanine (G) and we learn that A is complementary with T while C is complementary with G.

Colored flower/ Extra fingers

According to the book Survival of the sickest, the flowers appears to be this way because of an inherited mutation in its cells. Since scientists found that mutations are inherited when they are beneficial or neutral, therefore this mutation most probably increase the chances of its survival, for example a camouflage while at the same time it may also have no effects on the survival of this species. 

As Your Inner Fish mentioned, hands with extra fingers is due to the ZPA (very similar to the sonic hedgehog genes), specifically too much skin concentrated in a ZPA zone. These genes contains the instructions for a body to construct fingers, and most probably there's extra ZPA gene thus causing more fingers to grow from the baby's hand.

Your Inner Fish Chapter 3

Why do we all look different? Scientists try to solve these questions by looking into embryos and messed around with our DNA to see what would  change. Later they discovered the zone of polarizing activity (ZPA), something that instructs cells to produce different things, such as limbs. They named a gene Sonic hedgehog gene, one relating to flying and hypothesized that these genes are capable of making bodies look different. They found a supplier of shark eggs and started performing experiments on shark embryos since they are very distant from humans. And the results matched with the chicken experiments. That was how scientists solved the answer to what makes us look different

Survival of Sickest Chapter 6 review

The Chapter begins with the history of cowpox and how Edward Jenner invented vaccines as he found out that people who caught cowpox were resistant to small pox. Every human starts of from being 1 bacteria and duplicates millions of times to get to our form and shape now. Our DNA consists of 3 billions different nucleotides and every human has 23 chromosomes from each one of their parents, these are called the sex chromosomes adding up to a total of 46. These chromosomes determine our characteristics.

Scientists originally believed that only accidental mutations can possibly cause genetic changes. They thought pandemics followed a trend with sun spots, but they later realized it was because of the antigenic drift that caused our body to be vulnerable. Babara McClintock discovers the "jumping genes" and proposes that genetic changes does not necessarily have to be accidental. She puts an example of how corn's DNA migrates. John Cairns also did an experiment to prove that digestive bacteria can mutate to be not lactose tolerant when only fed lactose. Proving that genetic changes can happen intentionally.

Finally, only 3% of our DNA are used for coding sequences.And scientists found out that the rest are actually a lot of "jumping genes" instead of "junk sequences". Moreover, the Weissmann barrier distinguishes germ cells and somatic cells as changes of somatic cells cannot be passed on.

From Atoms to Traits

1. Explain the significance of Mendel. 

Mendel observed that the pea plants' traits were often similar to those of their parents. Sometimes, however, the pea plants had different traits than their parents. Mendel experimented with thousands of pea plants to understand the process of heredity. Mendel's work formed the foundation of genetics, the scientific study of heredity. Mendel's experiments changed the general
perception of heritable variants from ephemeral
and blendable to discreet entities passed from
parents to offspring, present even though they
are not always visible.

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


James Watson, Francis Crick, Maurice Wilkins


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

Gene copy number - chimpanzees
point mutation - whipped dogs
insertion - pea plants
Inversion - flipping of large segments of DNA within a chromosome
Repitition - repetitions like those that underlie forensic DNA tests


4. What is evo-devo?  A subspecialty ithin
evolutionary biology that has come to be known
as evo-devo 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.

Lactose-tolerant population started with a little population then later  the populations have differ-
ent mutations in the key region-a striking ex-
ample of the repeated evolution of a similar trait
by independent changes affecting one gene.

Unit Test 2

Today we took the second unit test, I thought it was slightly harder than the first one that we did because of the enzyme part that I wasn't really sure about and there were some questions that I didn't really understand very well. But overall I am confident that I did okay.

Founder Mutation

Founder mutations are a special class of genetic mutations embedded in DNA and are identical in people who have the same mutation. Moreover, the length of the stretch allows us to determine the age of the founder mutation. These founder mutations are not necessarily bad, they can be beneficial as they may be recessive on carriers and thus helping them in different ways, for example, a mutation of sickle cell can allow a carrier to survive malaria better. Also, finding out the origins of the mutations helps us have a better understanding in how our ancestors migrated when they moved out of Africa as we can trace the founder mutation and see a pattern of mutations in different locations. As the PTC mutation confirms the anthropological and archaeological evidence that the original population of modern humans lived in Africa since all non- tasters of the PTC supposed have the same ancestor and it seven of those genes exist in sub- Saharan Africa. It also confirms that every human are indeed members of a single family as we share the inheritance of our genome. Overall, founder mutations is a great way for us to reveal the truth of where we came from and how we arrived at our modern locations.

GENESS

Today in class we did another activity in which we run around and pretend to mate with each other to see whether the trend that Hardy Weinberg proposed was correct,that p and q should both be around 0.5. Hardy Weinberg suggested that the amount of recessive and dominant genes can be represented by p^2+2pq+q^2 = . So we were assigned with AaAa genes from the beginning with A as the dominant gene and a as recessive, and we pick off random cards from another classmate when "mating". In the end we got answers pretty close to 0.5 and 0.5 we got something like 0.6 and 0.4 but then again we didnt have a large enough population as Hardy would suggest, so I guess it was good enough.

WANNA LOOK HOT?

I've always wondered why do people look attractive, what is it about their face. Today is parents day and before the class we had readings that explain studies that basically say the more symmetrical your face is the more attractive you are, and it also brings up other theories such as being more average is more attractive. And one of the most important ideas is that no matter male or female, we as human beings are attracted to faces that are more feminized because unlike other creatures we bring in emotions when it comes to mating and studies have found that masculine faces are more intimidating and scares other humans away. So in class we had an activity which we are given slides of different pictures of a same person, one feminized and the other masculinized and we had to record the ones that we thought were more attractive. And what I got was 18/20 feminized faces, I guess I really do like girls.

Mating TIGERS !!!

Today in class we did an activity in which we pretend tigers are mating randomly in a dark forest. We put different color beads in two different paper bags and have on color represent the dominant gene and the other represent the recessive gene, and in our specific lab having both genes as recessive will cause the organism to die because of a disease. Slowly, we take out most of the recessive gene, but then we realize that there will always be 1 recessive gene in the pool of tigers in the end. Then if these group of tigers go mate with other tigers from other places that probably has the same recessive gene, then the recessive gene will reproduce again.

Quiz- Evidence for Evolution

Name: Calvin Li

Block: A Block

Honors Biology

Evidence of Evolution Quiz

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

The picture shows the evolution of whales from being a land living animal to a sea living animal. We can see that the Mesonychids from 55 mya had four limbs and it is obvious that they walked on land. However after 3 my at 52 mya, we have the Ambulocetus that still had limbs, but that were a lot shorter compared to those that the Mesonychids had, they most likely lived both on land and water, they would've swam by paddling their hind limbs. Later at 46 mya, the rodhocetus had already reduced their limb size so that they couldn't walk therefore live on land anymore, and they started swimming by moving up and down like modern whales. The Basilosarus were very similar to modern whales except that modern whales dont have their rear limbs sticking out anymore even though they still have the bone inside their body.

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.

Birds and bats' wings have the same structure, also known as homologous structures. Their wings have very similar structures because they inherited it from a common ancestor. However they are not completely the same because they "tweeked" their wings to enable different functions. On the other hand although birds bats and dragonflies all have wings and they look very similar, however the underlying structure of dragonflies' wings is completely different compared to those of birds and bats. That is because they evolved from different ancestral groups, yet they both evolved so that they have wings, that is called a 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 took the hemoglobin strand of DNA of humans, chimpanzees, gorillas and their common ancestor and compared the similarities. We found out that humans and chimpanzees have the most in common and have the least in common with their common ancestor, that is because humans are the most evolved species out of the whole family. DNA evidence and ancestry serves as evidences for evolution because they allow us to compare the similarity(common sequences) of two different species, thus determining how closely related they are.

5. Explain homology using some examples from your readings.

Homology relates to similar structures in different species because of their common ancestry. However, gradually, the structure develops differently in different species because they have to have different functions. Examples would be that the structure of a human's is the same as the wings of birds, they both consist of 2 big bones linking to a bunch of small bones. And also humans' hands have the same structure as the front limbs of sea creatures like whales.

Evolution- Titaalik

We spent most of the class discussing and going over the book "Your Inner Fish" and talked about how humans and all other creatures share a common ancestor. And Neil Shubin decided to look for the intermediate creature between fish and reptiles.

We went to the museum and look at a real life model of the tiktaalik and we observed its differences and similarities with fish and in the end of the class took a quiz on this topic.

Unit Test 1

Today we had our first unit test on chapter 1, that covers everything that we have learnt so far.  That test was reasonably challenging since the free response had quite a lot of writing, however the multiple choice was decently handled I believed. I am looking forward to getting my test grades back!

All Chemistry

Today in class we did a review on all chemistry, about all the topics that were covered previously, including water, basic chemistry, macromolecules and isomers. The quiz was rather easy considering I got 1s on both parts. Also we have to complete our lab reports for next class since that is the most important assignment so far.

Macromolecules and Lab

Today in class, we went through the slides of macromolecules and isomers. We went through basic knowledge such as structural polymers, geometric polymers and how different isomers are formed. For basic structures and functions of macromolecules, we went through dehydration, hydrolysis, DNA, RNA and other basic informations.
For the second part of the class, we finished a lab, and the objective is to identify what is in 16 different substances, whether its protein, starch, glucose and lipid or any combinations of these substances. We use different tests to test the existence of these substances including biuret, benedicts, sudan III and iodine.

House Case

In the beginning of the class, we went through basic concepts of the cell membrane:

We learnt why water and how water goes through a cell, through the protein channels, since the lipid fat layers will repel water away.

For the second half of the class, we did a house case diagnosis on a high school senior runner with symptoms of vomit, headache, cramps etc. Me, Anthony and Blake volunteered to be the three "main doctors" and we had to put the clients' symptoms, tests that we think we should perform, and our hypothesized diagnosis on the board. After our class has asked for the meal history, vitals, medical history and performing some tests on the high school senior. I came up with the conclusion that he is over hydrated, or diagnosed Hypertremia due to different factors, such as his urine having too little amount of Na in it. A detailed lab report will soon be uploaded for this house case, and I will go over the details of the diagnosis. 

After learning about diffusion and osmosis, today inclass we went onto the topic of rate of diffusion, as explained below:

Rate of Diffusion

Since the average kinectic enerygy of different types of molecules (different masses) which are at thermal equilibrium is the same, then their average velocities are different. Their average diffusion rate is expected to depend upon that average velocity, which gives a relative diffusion rate

where the constant K depends upon geometric factors including the area across which the diffusion is occuring. The relative diffusion rate for two different molecular species is then given by
Reference : http://hyperphysics.phy-astr.gsu.edu/hbase/kinetic/diffus.html
We did a lab that was done the first time ever at Webb Schools of california, it was a lab to check the rate of diffusion of something and determine what is the best shape for a cell to acquire maximum performance on rate of diffusion. We were given three cubes of 3% agar-phenolphthalein in different sizes and also some NaOH solute, since phenolphthalein reacts with NaOH and when it does it turns pink, we can determine how fast did the rate of diffusion happened by using three cubes of different sizes and lengths to determine the best shape. So first, we put the blocks into the NaOH solution,

Then after 3 minutes we took the cubes out of the beakers and cut them in halves then measured them:

After the measurements, we realized that the smaller the cube is the faster the rate of diffusion and thus explaining why cell division happens. Because cells needs their nucleus to be in a reaction in order to react therefore having a smaller volume allows other chemicals to penetrate in the cell easier.

Diffusion/ Osmosis

Diffusion

Diffusion refers to a process which molecules intermingle because of their kinetic energy that goes in all directions. They tend to move from places with higher concentration of the molecule to lower concentrated area. It is defined by Pearson as the net movement of molecules down their concentration gradient.
e.g. perfume spreading across room

Osmosis

Osmosis is a special case of diffusion that only happens in water. Where there is a semi- permeable membrane once again from higher concentration to lower concentration. The picture below illustrates
an example:

For this class, we reviewed basic concepts of diffusion and osmosis, and went through key words such as water potential, molecular motion, hypertonic, hypotonic, isotonic etc. After, we started on 2 labs relating to osmosis. For our first lab, we put different solutes of various molarities into semi- permeable membrane and we massed and put them in a beaker with water outside of the membrane. After 30 minutes,  we massed them again and determined the mass change thus allowing us to know the molarity of each of the solutes.
Link of results: https://docs.google.com/spreadsheet/ccc?key=0AvnnOJLj_iJAdFZQSlo0QjdONVBRQ2ZMcExvSVdkZEE#gid=0

After, we started our second lab and we soaked the potatoes inside the solutes this time and the results will be determined and posted soon.

Dihydrogen Monoxide

Water is essential to all living things and it is imperative for us to have a true understanding of this substance. In class, we went through different problems relating to water and explained why water is so simple yet is so vital for life and interesting.

Interesting facts
- Water covers 70% of Earth's surface
- Only 3% of water on Earth's surface is freshwater

Properties of Water:
-Cohesive behavior
- Expansion as freezing
- Versatility as solvent
- Moderate temperature

Water Cycle:
-Evaporation: Liquid water changes into water vapor
-Sublimation: Snow or ice turning directly into water vapor
- Transpiration: Liquid given off by plants evaporating
- Condensation: Water vapor turning into liquid water
- Precipitation: Water in clouds drop to Earth's surface


















Cohesion/ Adhesion

- Water molecules forms hydrogen bonds with other water molecules / surface

Expansion as freezing

- Water = bent structure (120 degrees)
- When frozen = forms crystalline structure (more space) = expansion

Moderate Temperature

- Water takes 30 times more energy to heat than gold
- Able to break and recreate hydrogen bonds quickly
- Ability to insulate (Ice above water = keep water warm)

Solvent

- Molecules with different polarities
- Water molecules comes
- Hydrogen bonds surround the molecule
- Forms hydration cell



How plants transfer water form roots to leaves?
- Water goes through Xylem
- Uses both adhesion and cohesion
- Adhesion = water sticking onto the xylems
- Cohesion = water sticking to water itself
Video:
http://www.phschool.com/science/biology_place/labbench/lab9/images/xylem.gif

Basic Chemistry.... In Preparation for Biology

Biology is the study of living things, and all living things are made out of atom. Therefore for us to understand. Biology, we must first grasp basic concepts of chemistry. From having the knowledge of atoms to how chemical bonds together.

Important Terms

Elements: matter combined with same atoms with same proton numbers

Compound: mixture of elements

Atom: "the undivisible", smallest division of anything

Proton: part of the nucleus of an atom, with a positive +1 charge and weighing 1 Dalton

Neutron: other part of the nucleus of an atom, with no charge, also weighing 1 Dalton

Electron: particles that surround the nucleus, with a negative -1 charge, with a negligible weight

Isotope: When an atom has different number of neutrons-

Atoms

Atoms are the basic material of everything, and it can be divided into 3 sub-atomic particles: protons, electrons, and neutrons. Below is a diagram of the carbon atom

As seen in the diagram, electrons are found on the outer energy level of the nucleus while protons and neutrons are found inside the nucleus.

Particle	Location	Relative mass	Charge
Proton	Nucleus	1	+1
Neutron	Nucleus	1	0
Electron	Outside the nucleus	1/1840	-1

Electrons are arranged according to their energy level. This is called the electronic structure orelectronic configuration of the atom. Shown Below:



 

Elements 

Elements are substances made out of atoms with the same number of protons. They are the most basic substance. 

Each element has its own:

• name and chemical symbol
• characteristic physical properties, e.g. density, electrical conductivity, melting point and boiling point
• characteristic chemical properties, e.g. reactions with water, oxygen, acids and other chemical

Different number of neutrons = an isotope

Different number of electrons = an ion

Different number of protons = different element

Compounds

Compounds are formed by combining elements through chemical reactions. However, elements can only bond according to the number of valence electrons they have, and they always try to to get 8 valence electrons, aka the octet rule.

Usually you would try to derive the empirical formula from the molecular formula. The empirical formula is the same thing as the molecular formula except you take the L.C.M of the formula and simplify it. In other words, the molecular formula gives you exact number of atoms while empirical formula only gives you the ratio. Example Problem:

Chemical Bonds

Chemical bonds are something that atoms form with each other when combining with each other. There are 2 kinds of chemical bonds, the Ionic Bond, and the Molecular Bond (Covelant Bond).

Ionic Bonds

Electrons are transferred in ionic bonds. Ionic bonds form when metals bond with non metals. Salts are examples. Like other ionic compounds, many salts are soluble in water. In water, the giant 3-D lattice breaks up into ions which move around relatively freely in solution. Each ion is surrounded by a cluster of water molecules (we say they are hydrated). This can be shown by an equation:

NaCl (s) + aq    Na⁺ (aq) and Cl^- (aq)

Covalent Bonds (Molecular Bonds)

Electrons are transferred in covelant bonds. Covalent bonds form when when non metals bond with non metals. 

Reference: http://www.rsc.org/Education/Teachers/Resources/cfb/basicchemistry.htm

http://www.universetoday.com/82128/parts-of-an-atom/

http://preparatorychemistry.com/images/molecular_formula_trioxane_.gif

For our second class of honors biology, we went through some worksheets of basic chemistry, in preparation for our topic on biochemistry. The above information gives a general idea of what I learnt/ reviewed in the class. In addition to that, we reviewed on how to correctly draw lewis-dot structures for ionic bonds and covelant bonds respectively.

Spectral Dancing Milk Experiment

With a drop of your magic potion, aka dish soap, you can create a spectacular performance with food coloring and your daily drink, milk. The secret lies behind the chemicals in dish soap mixing with the fat and protein in the milk. Let's take a look at how that "magic" works.

Hypothesis: Since dish soap contains water (polar) and other chemicals (non-polar), when added to milk with food coloring, which also contains water (polar) and other vitamins/ chemicals (non-polar), the water that are polar bonds together and other chemicals of the dish soap bonds with non-polar chemicals such as fat and protein, then creating the swirling reaction that we see.

Materials:
-Whole milk,2% milk orange juicr, Palmolive dish soap, phone (stopwatch), pan, toothpicks, graduated cylinder, water, and food coloring (blue and red)

Procedure: 1) Measure 10 mL of the liquid with graduated cylinder
2) Pour the liquid in the graduated cylinder into the pan
3) Add a few drops of red/ blue food coloring in the liquid
4) Add a drop of dish soap into the pan with a toothpick
5) Record the time needed for the full reaction
6) Repeat steps 1-5 with different liquids
7) Repeat the experiment with all the liquids at least 3 times

Results of Experiment:

Whole Milk:                                 Time: 37 seconds

 2% milk:                                     Time: 1:20                          

 Orange Juice:                              Time: N/A

Water:                                         Time:N/A

After adding the dish soap to the relative liquids, some of the food coloring started to swirl around, indicating there is a reaction going on. Liquids like water and milk have a characteristic called surface tension, the cohesive force of the liquid's molecules. We assume that the dish soap as a surfactant reduced the surface tension of the milk, thus creating free flow on the surface of the milk, allowing the reaction to take place. The dish soap reacted vigorously with both of the milks, and barely reacted with the orange juice, also having no reaction with water.The experiment clearly showed that liquids with more fat and protein in it reacted more with the dish soap, and didn't react when there's no fat or protein in the liquid (water). Also, we know that there are more fat in whole milk than 2% milk, and also the fact that it took whole milk to complete the reaction quicker than 2% milk. Since we got the identical results all three times we repeated the reactions, therefore we can conclude that the more fat in the liquid, the faster the reaction will take place.