Writing in Biology

Question 1: The fossil needed to support the phylogeny is a common ancestor of both the hippo and the whale and would have characteristics of both.  Specifically it would have the pulley shaped astragalus. The common ancestor of the whale and hippo diverged and created 2 seperate species, hippo and whale, and did this by the hippo keeping its pulley shaped astragalus and the whale losing the pulley shape.  The common ancestor is some sort of combination that contains the pulley shaped astragalus but also some characteristics of the whale. The requirement for the pulley shape is because it would be near impossible for the common ancestor to evolve from a pulley shaped astragalus ancestor and then lose that trait only to gain it back in the hippo but not in the whale.  It makes much more sense to say the common ancestor contained the pulley shaped astragalus.

Question 2: The definition of homology is a characteristics that is shared or very similar among different species shared by their one common ancestor.  The definition of homoplasy which is, shared characteristics between species that wasn’t present in the common ancestor, is shown in the phylogeny when both the monotremes and the Therians both develop the unattached bone even though their common ancestor had the bone attached to the jaw.  This is a basic example of homoplasy and is likely due to living in similar conditions and having somewhat similar behaviors that benefited having an unattached bone. The phylogeny shows homology with the evolution of the 3 inner ear bones. Up until the Morganucodon the species all have the same inner ear and have it attached and to the lower jaw bone.  This shows homology because the ancestor is passing on its genes and the species has the same inner ear as their ancestor. One specific example is how the red bone keeps getting smaller, it happens to all the common ancestors as the time goes on and when the therians and monotremes both have very small red bones and a very similar shaped green bone which are both derived from their common ancestor meaning those traits are homology traits.

Antibodies are part of the body’s defense against foreign invaders. They are proteins produced by a type of white blood cell, called B cells, and like any proteins, their structure determines their function. Antibodies have a variable region that is different for each antibody that binds to a different antigen. An antigen is anything that the body does not recognize as “self” and can range from pieces of virus capsids to pieces of bacterial surface proteins. The antibody is structured in a “Y” shape and has light and heavy chains that are held together by disulfide bonds. The top of the “Y” is where there is a variable antigen binding region. The constant region of the antibody allows for consistency of response and the variable top allows for different identification of foreign bodies. The antibody gene allows for the randomization of the antigen binding amino acid structure which is what creates the variability in the region. The randomized antibody gene is created by V(D)J recombination. It is non-template directed and done by tdt polymerase which is a form of DNA polymerase.

Organic Molecules are everywhere around us. That human walking her dog across the street, made up of organic molecules. The dog she is walking, made up of organic molecules. The dictionary defines the word “organic” as “of or relating to living matter.” What should jump out from this definition is the word “living”. All living things are organic, which means they are made up of some combination of Carbon, Hydrogen, Nitrogen, and Oxygen. These combinations generally form the four macromolecules that are found in living organisms known as, proteins, carbohydrates, lipids, and nucleic acids. In the following experiment we set out to find out what different foods were, using a variety of tests, such as the lipid test, simple sugar test, and the protein test. These tests allowed us to find out what the different types of unknown substances were.

Kinetics governs how quickly a chemical reaction occurs. Chemical reactions may be exergonic or endergonic. During an exergonic reaction, molecules with high free energy, become molecules with low free energy. These reactions generally release energy and thus have a negative delta G value, are favorable and spontaneous. Endergonic reactions do the opposite, turning molecules with low free energy into molecules with a high free energy. Therefore, exergonic reactions require energy, which is stored within the bonds of the molecules. This also means the reaction has a positive delta G, is unfavorable and not spontaneous.

In order to make a chemical reaction occur more quickly, enzymes are used. The mechanism by which enzymes work is described by an induced fit concept. This means that the enzyme orientates molecules in such a way to favor the transition state of a reaction. In other words, the delta G of the transition state is decreased, decreasing the activation energy of the reaction. It is important to note that the delta G of the reaction of as a whole, the difference between products and reactants, does not change.

Materials: The materials used in this experiment are as follows: 4x4 in. Brown paper, Drop of Oil, Drop of water, drop of five unknowns (for the Lipid Test); 500ml of the following (glucose solution, distilled water, unknowns 1-5), test tubes, 1 ml of Benedict’s reagent (for the Simple Sugar Test). Seven Test tubes, 1 mL of starch, 1 mL of distilled water, 1 mL of each unknown 1-4, two drops of Lugol’s iodine reagent (for each tube) (for the Starch Test). 2 mL of each unknown (1-5), 2 mL of 2.5% NaOH, 3 drops of Biuret reagent (for each tube) (Protein Test)

    Methods: The method for the experiments in this lab are as follows:

Part 1 Identifying Lipids. To identify which unknowns are lipids, obtain a small square of brown paper, divide into seven sections. Label them, Water, Oil, Unknown #1, Unknown #2, Unknown #3,Unknown #4,Unknown #5. Put a small drop of each substance on each section of the brown paper and rub it in gently with your fingertip. Allow the substances to dry (approximately one hour), then record your results.

    Part 2 Identifying Carbohydrates. To identify carbohydrates in the unknown, two tests are done. The simple sugar test, in which you start by making a boiling bath of water. Obtain seven test tubes and label them #1-7. Put 500 mL of 0.01 M glucose in tube #1. Put 500 mL of distilled water in tube #2. In tubes #3-7, put 500 mL of the unknown substances in the tubes, each tube with only one substance. Add 1 mL of Benedict’s reagent to each tube. Place the tubes in the boiling bath for 5 minutes. After 5 minutes, remove the tubes from the water bath using tongs. Place in tube rack to cool for a 2 minutes. Record observations. The second test, Testing for Starch, goes as follows. Obtain seven tubes and label them #1-7. Put 1 mL of 1% starch solution in tube 1. Put 1 mL of distilled water in tube 2. Put 1 mL of unknowns in each of the remaining tubes. Add 2 drops of Lugol’s iodine reagent to each tube. Record your observations.

    Part 3 Identifying Proteins. To identify a protein in solution, Biuret Reagent. Obtain 7 test tubes and label them #1-7. Add 2 mL of each material to the appropriate tube. Add 2 mL of 2.5 NaOH to each tube. Add 3 drops of Biuret reagent to each tube, mix thoroughly. Hold the tubes against a white piece of paper for better contrast. Record Changes.

The Paddlefish is classified into Actinopterygii, or ray finned fishes. More specifically, it is placed in the Acipensiformes order. This fish has an elongated snout, supported by a matrix of tiny thin bones. While individually the bones are very fragile, together they form a sturdy yet lightweight structure. This long snout contains electroreceptors, a trait previously lost in bony fishes, and allows the paddlefish to detect plankton in its direct pathway. Once a large enough group of plankton is detected, the paddlefish will open its mouth, drawing in the water and engulfing the plankton. Water will flow through the gills and gill rakers, which filter out the plankton to be directed into the Paddlefishes stomach. Water safely passes through the gill slits as is normal, exchanging gases extraordinarily efficiently.

Modern sharks, rays and skates are united under the Chondrichthyes class. All Chondrichthians have cartilaginous skeletons. The males have intromittent organs called claspers, which are derived from the pelvic fins of the fish. All fertilization occurs internally and females my be either oviparous or viviparous. All Chondrichthians have no swim bladder. Sharks in particular rely on their large pectoral fins and oily livers to maintain bouncy. This also comes with the benefit of being able to traverse a variety of depths without expanding or compressing as much as a fish with a swim bladder would. Another interesting characteristic of Chondrichthians is the presence of placoid scales, teeth like structures which produce a sand-paper like skin.

A subclass of Chondrichthyes is the Elasmobranchs, which means plated gills. This class may be further seperated into Selachians, the sharks, or Batoids, the rays and skates. Seleachians have their plated gills on the side of their head while the gills of Batoids are located ventrally. A Batoids pectoral fins will be fused to the side of the head, in place of the gills location. Rays and skates differ by their means of reproduction. A ray is viviparous, giving live birth, while a skate is oviparous and will lay eggs.

I believe that both reserves, 1 and 2, were designed equally efficient in promoting heterozygosity and conservation of population alleles. Although the two reserves differ slightly, they had similar outcomes. Reserve 1 had a lower heterozygosity than Reserve 2, yet preserved more alleles. This was due to the presence of subpopulations. The subpopulations restrict the interactions between the ferrets, decreasing the heterozygosity. The conservation of alleles was due to the subpopulation dynamic. The subpopulations decrease the negative effect of the loss of an allele on the entire population due to the sectional divisions. Reserve 2 had higher heterozygosity than Reserve 1, yet lost more alleles. This was due to the single unit design of the reserve. The single unit allowed for more ferrets to interact and breed, increasing heterozygosity. Yet, the single unit was affected more when an allele was loss, due to the lack of division in the reserve.

The “Yeast Mutation and Analysis” lab protocol served as a guideline for the first day of our Yeast Mutagenesis experiment. On day one we performed a serial dilution of ~107to ~104yeast cells using a pipette, sterile test tubes, and vortexer. From the105dilution, we pipetted 100µL onto a YED plate and repeated with a second YED plate.  We then exposed both plates to UV radiation for 5 seconds. We made a control plate that we did not expose to UV radiation and incubated all three plates for 3-5 days.  After that time, the lab professor removed them from the incubator.

The “Yeast Mutation and Analysis” lab protocol served as a guideline for the first day of our Yeast Mutagenesis experiment. During the first day, we performed a serial dilution of ~107to ~104yeast cells using a pipette, sterile test tubes, and vortexer. From the105dilution, we pipetted 100µL onto a YED plate and repeated with a second YED plate.  We then exposed both plates to UV radiation for 5 seconds. We made a control plate that we did not expose to UV radiation and incubated all three plates for 3-5 days.  After that time, the lab professor removed them from the incubator. During the next lab period on September 26th, we observed the plates. Since we had no mutants, mutated yeast cells were provided to us.  We designed an experiment to test what gene the mutants were mutated in. We decided to cross the 4 unknown types of mutants we were given with 4 known types of mutants to see which mutants complemented and which mutants had mutations in the same genes. During the same lab period, we streaked the 4 unknown mutants and the 4 known mutant parent groups onto a YED plate and left them to incubate for two days. The streaks contained 1a, 2a, aMw, and aMx on the horizontal axis and 1ɑ, 2ɑ, ɑMy, and ɑMz on the vertical axis.  On September 28th, two days after streaking and incubation, we mated the UV mutants. A small sample of each of the corresponding parent colonies was put where the two parent groups would intersect and mixed with each other. We allowed 2 days of incubation after mating before replica plating onto an MV plate. On October 2nd, the YED plate was replica plated onto an MV plate and an MV+Ade plate. We left the replica MV plates in the incubator until the following lab period.