Complete Unit 3 Blog

Class 20

Andrew and I's ultra fail...

Today we "learned" about the structure and uses of a DNA strand. Unfortunately our paper cutting activity of creating a DNA model ended in a disaster, and to be honest we did not learn much today. I had to supplement my knowledge through wikipedia that night...

What we wished ours would closely resemble...

What it actually looked like...

Class 21-22

The Results of the PGlo Lab:
During last class, we did a lab called PGlo where we observed the growth of bacteria colonies in 4 different petri dish samples. The purpose of such an experiment is to discover how viruses infect bacteria cells and change their genetic code. We injected pGlo viruses along with E.Coli into our samples, some with antibiotics and some without. The pGlO contains virus gives the bacteria immunity to antibiotics.
During this class, we collected our results and discovered that bacteria colonies grew in petri dishes with PGlo, and failed to grow in ones without, thus proving that PGlo gives antibiotic resistance. However, some PGLO dishes did not glow in the dark, only the positive ones with arabinose...therefore we have seen a new characteristic of genetics, the operon system.

Clear picture describing our results

The rest of the class was spent on learning about DNA replication using our paper models, but since Andrew and I quite literally destroyed our model, we didn't completely understand everything...Back to self-learning for me!

Day 23

We came into the class today quite well informed about protein synthesis, well those of us who watched the video that is. Anyway, on the board was a quite intimidating drawing of protein synthesis' whole process (without labels)...

I went up first to explain the transcription process inside the nucleus...Even though i knew the process quite well, I was overwhelmed by the prying eyes and taunting by Mr. Quick, therefore I jittered and made quite a fool of myself until Missy decided to step up and save my day. It was quite heroic of her. But in the end, we went through protein synthesis and everyone had a great understanding of the subject.

We also did a worksheet explaining codons and their translation into pep-tides.To be honest it wasn't that difficult.

Class 24

With the impending test coming we had a review day of most of the concepts including a more in depth view of the operon system: a control/on-off switch for our cells. We discovered that this had something to do with our +PGLO dishes which are slowly diminishing in glow, the arabinose has been used up.

Our test is next day, and I find no better way than to explain all my knowledge of this unit through a long Mr.Quick like video that I have made to explain this unit fron DNA structure, DNA replication, Protein Synthesis, and the Operon system.

The video can be found on this link: https://sites.google.com/site/seanyangworkhardlabharder/hon-bio-dna

The Inner Fish Chapter 3

Scientists attempt to discover the type of cells responsible for making each of our body characteristics appear different. By purposefully tampering with an embryo's development scientists hope that they can gain insight on the nature of genes by looking at the resulting mutation. Obviously, human embryos were out of the question, so scientists decided to use chicken.

Randy Dahn decided to use sharks for his experiment because shark were the first animals with skeletons and also having a fin. In their embryonic stage, they also show striking similarity to a humans'. Due to the difficulty of obtaining shark embryos (possibly due to animal activists), skates embryos are used instead. The hedgehog gene in these embryos were found in a patch of tissue in the back end of the animal's fin, and mirror image duplication also occurred when Dahn treated the embryos with vitamin A.

Scientists have discovered and confirmed the existence of these hedgehog genes which are responsible for making our body look the way it is, and create limbs.

Survival Of the Sickest Chapter 6

Every human being starts of as 1 single cell, and it contains every single genetic instruction to construct that human being. These instructions are in 3 billion pairs of nucleotides (DNA base pairs),there are also around 30000 genes, organized in 23 pairs of chromosomes for a total of forty six. One set of chromosomes will come from the mother, and another set from the father.Chromosomes contain information that determines us as a person. As for traits, the dominant traits are always more influential than recessive.

Scientists first discovered that only 3 percent of our DNA contains instructions for building cells, and decided to call the rest as junk DNA, DNA which doesn't help nor hinder our lives. However, later studies have discovered that these DNA are actually traces of past viruses or bacteria that have been in our body. They are now called non-coding DNA.

For a long time scientists also believed that genetic mutations which occurred in ones genes were only from accidents. Such as exposure to radiation or sunspots. However, Barbara McClintock discovered otherwise, she found jumping genes in corn and discovered that their whole sequence of DNA moves from one place to another, and has erratic behavior.This also explained why scientists thought that there were once more than 100000 genes in a human body, one for each specific job/trait, now it is only estimated to be around 30000, since McClintock discovered that through the shuffling of these genes, they can do a huge amount of different things.

Scientists also conclude that genes can adapt to its environment. John Cairns once fed only lactose to a E. Coli bacteria (a food digesting bacteria), and discovered that the bacteria underwent mutations to become lactose tolerant.This shows that genes can determine and choose whether or not they want to mutate.

The best example of these shifting and jumping genes would be the human immune system. Why is it that after contracting chicken pox for the first time, it is near impossible to get it another time in your life? This is because the human body has genes which create antibodies to fight foreign invaders such as viruses and bacteria, and genes adapts to fight against new types of viruses by creating different antibodies.

From Atoms To Traits

1. Mendel conducted an experiment with many different types of peas. He cross-bred these different species of peas with each other and discovered that their offspring would have traits resembling one of their parents. As more peas are cross-bred, more traits of different peas appeared significantly in future offspring. The pea experiment by Mendal divided heritable traits into 2 categories, one being blendable and ephemeral and the other heritable and lasting for a long period of time.
    2. The structure of the DNA was discovered by James Watson and Francis Crick. It is in the shape of a double-helix

3. Variations causing mutation can be caused by: a single letter replaced in the DNA strand, a string of letters gone, duplication or addition of new letters, and transformation of the originial letters.

4. Evo-devo: The study of the effects of mutation in developing genes and its role in the process of evolution.

5. A child born from parents that does not drink milk after their infancy does not have the lactase enzyme to digest milk through adulthood, therefore they are lactose intolerant. However, a child from a family that does drink milk after infancy will be lactose tolerant.

Origin of Man: The Out-Of-Africa Theory

Over twenty years ago, studies made by geneticists hinted at an incredible and unbelievable explanation for the origin of man kind. By tracing the trails of DNA left behind in multiple regions in the world, gathering samples from various different races and isolated indigenous tribes, scientists came up with a theory that all races of humans we know today originated from one location in mid-south Africa. Only after extensive research, and numerous DNA samples, have scientists been able to confidently publish their new founding. This new theory, as irrational as it sounds, after numerous experiments conducted was found to be more plausible and reasonable than the old theory of many different species of homosapiens in different areas and interbreeding.

Gathering such extensive data was difficult. It is an arduous task to travel to remote regions of earth and meet with indigenous tribes that have little to none outside contact. Many tribes even refused to cooperate, as they were suspicious with why scientists were drawing blood samples from and gathering DNA samples from their saliva with a cotton swab.

The long standing opposing theory to the “out-of-Africa” theory is called the Multiregional theory. To this day, many scientists still believe that homosapiens developed in different regions, adapted to their surroundings, and interbreed to preserve their race and create many different features of early humans. People argued that a large percent of the population is a result of this interbreeding, not from a single stemmed African species. The debate continues onwards, however, more and more genealogical evidence has been discovered to support the out-of Africa theory.

Perhaps the one obstacle that has troubled scientists most is the lack of physical evidence. A DNA trail clearly shows that traces of DNA and microorganisms were left behind during the migration out of Africa. However, there hasn’t been any fossils/prehistoric tools found on these trails, leading many scientists to question the validity of this theory. However, fossils are usually incredibly difficult to find, and many scientists argue that fossils or physical evidence is inapplicable in this particular research.

New Topic: Evolution & Fossils

Today in class we have started a new topic on evolution. I have always believed evolution and anything to do with fossils are a part of paleontology; apparently, I was wrong as we focused a lot on how genes and DNA affects on organism's adaptations and development over time.

Formation Of A Fossil:

1. Organism dies, bones must remain
2. Bones buried within sedimentary rocks
3. Bones/shells are preserved,sometimes through crystallization
4. After movement of rocks over a long period of time,old fossils are buried deeper whilst newer ones from above
5. Fossils can be discovered through weathering, erosion and other natural means.
Or just paleontologists digging.

Oldest rocks at bottom, newest at top

The Theory of Evolution

With the discovery of fossils Charles Darwin formulated a theory of evolution.
Before class, we watched a video describing the definition of a theory. A theory is formed
by a hypothesis, observation, evidence, and conclusion. Homology is a term used to describe
the similar structures of different organisms in order to determine any common ancestries.
Organisms mutate through millions of years in order to adapt to the ever-changing living
environments. When the structure of 2 different animals show qualities of similarity, they
are called analogous structures. An example could be the dragonfly and a bird, which both have wings but possess vastly different skeletons.

                                    

We also learned about how to prove the theory of evolution. We learned and read about the Tiktaalik,
a fish that was also amphibian. The Tiktaalik served as a missling link between the transition
of sea-living organisms to land-dwellers. It shared common characteristics of fish and early
amphibians. For example, it had a limbs that resembled a fish's fin, however they allowed
the titaalik to swim in shallow water and also move on land. Soon becoming an amphibian.

                                       

                                                                  The Titaalik
                           

We also did an activity in class where we analyzed the biomedical evidence of different organisms,
such as DNA and protein. Finally we have reached the biology part of evolution. By comparing a
chemical named cytochrome C in different organisms, we can construct a detailed graph and cladogram
to determine which organisms are closely related to each other. The less differences, the more similar
2 organisms are, and thereby proving that the 2 organisms have a common ancestor.

                             

                                 We spent a long time compiling a list like this, determining the differences

                                 between strands of cytochrome c from different animals.

Quiz for Evolution

Access the quiz at: https://docs.google.com/file/d/0B_nnOJLj_iJAaFVCUWxHelRvM1E/edit?usp=sharing

Question 1 Answer:

The whole picture shows the evolution of a species of whales.
Mesonychid: mammal that lived on land, with 4 limbs to move and search for food.
Ambulocetus: Evolved from Mesonychid. It has a flatter head with a slightly longer and more sharp-triangular mouth. Its limbs adapted to amphibian like arms and legs, allowing it to traverse both on land and water to search for food. A closer inspection also reveals that the Ambulocetus has eyes which are closer to the sides of its head, this allowed the species to have better vision in water.
Rodhocetus: Evolved from Ambulocetus. The most significant change was the whole structure of the Rodhocetus is more water dynamic, along with the change of limbs to fins (limbs were not needed in water), and the splitting of the tail into 2 (gives balance when swimming),
Basilosaurus: Evolved from Rodhocetus. The body evolved even more water dynamic, its fins grew smaller as it had a long and huge tail which would propel it through water.

Question 2 Answer:

E

Question 3 Answer:

All of the three animals have wings, and can fly. Bats are different in that they have finger bones; Birds have one single limb; whilst dragon flys have none. Birds also have strong feet, which allow them to stand. The dragonfly is the only animal out of the three that has a long tail, which it uses for balancing in flight. Birds and bats do not need a tail.

Question 4 Answer:

Differences between the strand of cytochrome C between different species show their similarity. As creatures mutate over time, the more different 2 creatures are from each other the more different their DNAs will change, thus the more differences there will be in the sequences of cytochrome C. Humans and chimpanzees have only 1 difference in their cytochrome C amino acid strands...they are very closely related.

Question 5 Answer:

Titaaliks and fishes, modern day whales and the Rodhocetus all share common ancestors. Homology shows the relationship between the 2 species' structures and genes.

Class 4 & 5: Diffusion and Osmosis

In classes 4 to 5 we did a large lab on demonstrating diffusion and osmosis. First we went through all of the important terms and background information.

Definitions:

Diffusion: Molecules travel from an area of high concentration to low concentration, such as perfume spreading through the air.

Osmosis: Transfer of water molecules from area of high concentration to low concentration through a semi-permeable membrane like a cell. Stopping when equilibrium is reached.

Hypertonic: A solution that where there are more solvent than solute

Hypotonic: Opposite of hypertonic, where a solution has more solute than solvent

Isotonic: Equal amount of solute and solvent

LAB:

Part 1: Starch diffusion through a cell (fake cell made with dialysis tubing)

Part 2: Osmosis of 6 different concentration fake cells

Part 3: Determining the solute % of 4 different potatoes through osmosis of its cells

Part 4: Determining the solute % of 4 different energy drinks (same as above basically)

Extra Part 5: Diffusion of benedict's solution into a NaCl cell. Calculate percent diffusion

For a complete formal lab report with data visit:

https://sites.google.com/site/seanyangworkhardlabharder/

Pictures of the lab:

Potatoes!

6 Different concentration solutions!

6 fake cells!

More potatoes!

Cell after osmosis

Class 3: Water, Surface Tension, and Coins

Class 3

Our homework before coming to class today was to listen to a slightly funny sounding video made by Mr. Quick on the properties of water. In class, we went over all the different characteristics of water, such as its molecular shape, polarity, cohesion/adhesion, and surface tension.
In order to demonstrate cohesion and adhesion, we did a small experiment involving coins.

We would slowly drip drops of water onto the coin so that it forms a groovy dome-like, hemispherical body of water over the coin. Mr. Quick told us that water forms a dome shape when its molecules cohere with each other because a water molecule's molecular shape is bent, therefore showing that when water is filled to the brim in a cup, there is a small smooth hump over the lip of the cup.

We then proceeded to dip a toothpick covered with dish soap into the water covered coin. The water spread itself out all over the table immediately. This phenomenon happens because dish soap breaks the surface tension of the water; the cohesion bonds between each molecule. From this experiment, we also learned why a water-strider can run across water; Their thin legs are light enough so that it does not break the bonds of the water.

Class 1 and 2: Milk Experiment and Molecular Structure Review

Class 1: Milk lab Experiment and Doing Labs In General

After watching a video showing whole milk, food coloring, and dish soap mix in a bizarre matter, we were tasked with forming a hypothesis about why such a phenomenon would happen and create a useful experiment in order to test our hypothesis.

Hypothesis: 

Dish soap has the ability to attract fat molecules and break them apart, thus creating a chaotic mess. The food coloring is in the mixture simply to show the dish soap breaking apart milk’s fat.

In order to test our hypothesis, we used the following equipment and decided to test many different solutions copying the same method used in the video.

Procedure:

1.     Pour whole milk into a circular dish

2.     Dab 2-3 drops of water coloring in the circular dish

3.     Dip toothpick into dish soap, and then dip toothpick into solution

4.     Observe chemical reaction of the solution

5.     Repeat above process with different solutions using same dish soap

Though our experiment is far from perfect and contained numerous human errors, we discovered that solutions that contained the most amounts of fat (whole milk) reacted most vigorously when dabbed with dish soap whilst solutions which had less fat (skim milk) or no fat at all (coffee/orange juice) did not react much at all.

Equipment used

Solutions

Important notes

After our first experiment, Mr. Quick went over some key aspects on doing effective experiments in general. Hopefully next time when my team and I are given an experiment, we can complete it in a more efficient and professional way.

Class 2

In our second class we simply went over some basic chemistry topics from Chem last year. We mainly focused on molecular shapes and did a worksheet on different molecules. We had a brief review of the octet rule and different bonds also.