biogeno.us

Dear Diary,

          Today I learned many wonderful things.  For example, did you know that carbon is the second most important thing for life after water?  About 25% of cells is composed of carbon compounds.  The reason carbon is so prevalent is due to its versatility, which is a result of it being capable of forming 4 stable covalent bonds.

          Organic Chemistry is the study of these carbon compounds, such as hydrocarbons.  These combinations of carbon and hydrogen are non-polar, hydrophobic, and are gas at room temperature.

          Isomers are molecules that have different structures yet the same molecular formula.  Their different structures gives them different properties and functions.  An example of this is alanine.  One form of alanine, L-alanine is used in proteins, while the other, D-alanine, is unusable.

Look at all the diversity!

The diversity of all the different combinations of atoms or groups around the carbon is numerous.  What accounts for this diversity are the functional groups, which are the parts of organic molecules that are involved in chemical reactions.  These functional groups interact with different targets in the body and cause different effects.  These include hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate.

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Chemistry, surprisingly enough, plays a large role in the study of Biology. That is why Chapters 2 and 3 of our Biology textbook are devoted to a review of the smallest building blocks of our world. Today in class, our minds were refreshed on the basics of chemistry, particularly atoms and how they bond together.

Unlike our unfortunate rivals in Chem II, us Biology kids do not need to memorize all the elements on the Periodic Table. While about 25 elements are essential for life, the majority of life is made up of carbon, hydrogen, oxygen, and nitrogen. Trace amounts of calcium, potassium, sulfur and phosphorous also exist.

These elements, as well as all the others, bond together based on their electrons. The amount of electrons in the valence shell of the atom determines its chemical behavior. Atoms want to either complete a partially filled valence shell of empty a partially filled valence shell, depending on the number of electrons in that shell. When this happens, bonds between atoms result.

There are both weak bonds and strong bonds in the chemical world. Hydrogen bonds, an attraction between positive and negative ends of molecules, is an example of a weak bond. These bonds only occur between Oxygen and Hydrogen, Nitrogen and Hydrogen and Fluorine and Hydrogen.

Hydrogen Bonding Video (user: mtchemers)

Hydrophilic and hydrophobic interactions also occur between water and another element. The final types of weak bonds are Van derWaals forces and ionic bonds, but we did not discuss them any further in our class today.

Covalent bonds are the strongest bonds in chemistry. These bonds result when two atoms share a pair of electrons between them. This results in the formation of a molecule. Multiple covalent bonds, like double or triple bonds also can result, depending on the number of electron pairs being shared. There are both polar and nonpolar covalent bonds which depend whether of not the electron pair (or pairs) are shared equally between the two atoms. If the electronegativity of one atom is significantly larger than the other, a polar bond occurs.

Finally, hydrogen bonding, like discussed earlier, occurs with water molecules as well. The irregularity of the water molecule gives water some of its unique characteristics. That is the subject of our next chapter, and the next blog as well.

Class was very interesting and brought back some feelings of nostalgia for us, if it is possible to have nostalgic feelings about chemistry.

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There are various factors that influence seed germination, some of which include: sunlight, water, natural causes, predators, fertilization, etc. However, the main ones are sunlight, water, and “food”. These produce the whole sprouting case to occur. In order to begin the lab of seed germination, you need to have a factor (variable), predicted effect, and explanation for prediction. From this logic process, your hypothesis is formed.

The whole point of an experiment is designed so that it is controlled. In this case, the designed experiment is to see whether or not “Miracle Gro” speeds up the seed germination process. For an experiment you need your independent and dependent variable, so “Miracle Gro” would be your independent variable and the rate at which the seed will germinate is your dependent variable.

The materials needed are:

• seeds
• 50mL 5% “Miracle Gro”
• 5  plastic bags
• 5  paper towels
• 10mL graduated cylinder

The experiment is started by putting the seeds in a plastic bag, also known as your germination bag; soil will not be used. To make a germination bag, you place 1 folded paper towel in the plastic bag and lay the seeds in a line, so they are exposed for the germination process. Next add 10 mL of solution to the bag, for dilution ask teacher for ratio. To help keep track of each individual germination process, label your bags, for example 1%, 2%, 3%, etc. When completed with all 5 bags, seal tightly with little air as possible and tape them to a door. As days continue, collect your data and record in a data table including your variables. The number of trial completed should be 5.

In conclusion, the rate at which the seed germinated the best tells you what the dilution of “Miracle Gro” should be for the seed to germinate.

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The major themes in biology are science as a process of inquiry, evolution, energy transfer, continuity and change, the relationship of structure to function, regulation, interdependence in nature, and science and technology in society. The hypothesis in all experiments is the process of inquiry. A scientists makes an educated guess at what he think will be the outcome of the experiment. At the end of the experiment, his “inquiry,” or hypothesis is either proven right or wrong. To ensure that the results of all the variables are correct, it is best that the scientist repeats the process. Evolution is the core theme of biology. It states that all life adapted and slowly evolved onto what it is today through the process of natural selection. Basically, there would be no life or purpose to biology without the process of evolution. It explains the unity of life in their biochemistry and physiology because according to the theory, every living thing has a common ancestor. It also explains the differences, because through the process of natural selection, adaptations have allowed animals with advantageous traits to thrive in particular areas. Energy transfer is related to life, because life is an open system that requires constant input of energy, energy to flow through it, and energy to exit. This continually recycles nutrients through the different organisms. The reason for the continuity of life is found in DNA. DNA is the genetic material which carries traits and biological information through generations. Another major theme is the fact that in all levels of biology, form is related to function. Simply put, from the smallest organelles to the largest organisms, everything in biology is put together in a form that allows it to serve a function that helps preserve the life of itself, as well as other living things in its ecosystem. Organisms regulate themselves to maintain homeostasis. Even when they are surrounded by changing conditions, they have positive and negative feedback loops that allow for the proper response. That way body temperature, pain, etc…can be regulated and kept within a good range. The theme of interdependence in biology says that no organism stands alone, it needs other living creatures, or possibly sunlight to survive. All living things on Earth have some sort of a symbiotic relationship. The last theme in biology is how it relates to science, technology and society. There are moral and ethical dilemmas preventing the further expansion of science. In the field of biology, scientists no longer question if certain things such as cloning are possible. They question if they should do it. By studying the themes of biology, a near infinite mass of information can be generalized, so that one person can have an understanding of all of its aspects.

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Today we zealously rushed through notes even though everyone was rather sluggish due to a weekend filled with homecoming festivities. Our teacher lectured the class on the oxidation of pyruvate, the Krebs cycle, and the beginning of the electron transport chain.

The following will be a summary of the main points of the topics touched upon in class:

The oxidation of pyruvate takes place after glycolysis and occurs in the membrane of the mitochondria. This second stage in cellular respiration converts two molecules of pyruvate into two molecules of acetyl CoA. Also, two ATP and 2 NADH molecules are produced. The next stage in cellular respiration is the Krebs cycle, sometimes called the citric acid cycle.  The krebs cycle takes place in the mitochondrial matrix. During this stage, 2 molecules of acetyl CoA are converted to 8 NADH and 2 FADH2, as well as 2 ATP. Carbon dioxide is released (CO2 is fully oxidized).  The final stage in cellular respiration is the electron transport chain, which occurs in the mitochondria. The electron carriers, NADH and FADH2 give their electrons to membrane proteins. These proteins in return uses the energy to pump H+ into the intermembrane space creating a concentration gradient. H+ flows through the concentration gradient and into ATP synthase to produce ATP. All in all, 36 ATP are produced (minus the first two that were used to begin glycolysis) in order to power cellular work.

Don’t  forget—NADH and FADH2 are reduced coenzymes that store energy. They play a huge role in producing ATP in the electron transport stage of cellular respiration.

Now for some outside thinking: why do cells produce ATP? In order to do work. The cells that produce the most ATP are muscle and nerve cells, the ones that perform the most work.
What would happen if a cell did not have oxygen to utilize the stages of cellular respiration past glycolysis. Not  much. The cell could produce some trivial amounts of ATP, but not enough. For example when muscles work they need energy. When there is a lack of oxygen, and thus a lack of energy, the muscle becomes fatigued and soreness from the accumulation of lactic acid sets in (due to lactic acid fermentation).

photo courtesy Meredith Snookums on flickr.com

Here is a good website link to supplement your studying of cellular respiration–http://www.phschool.com/science/biology_place/biocoach/cellresp/intro.html

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Class started off with a dress count. Eight out of the nine students participated in “New York Pride Day” where students were allowed to wear anything that was related to New York.

We then took the Ch 8 quiz which was a tough one. Everyone in the class did not receive good grades on it so our instructor let us take it home in order to correct our mistakes. He strongly supports this method of learning since fixing our mistakes will allow us to learn the information that we did not know. It helped me tremendously since I learned the information and since our instructor awarded us a half of a point for every corrected answer on our first unit test. The corrected quiz is due on 10/16 because seniors have no school on 10/15 while everybody else does which really sucks for them who have to take standardized tests.

After our quiz we took notes for the rest of the class period. The first part of chapter nine was about cell respiration and glycolysis. All organisms are endergonic systems which means they absorb energy from outside souces. The obtained energy is then used through Exergonic (catabolic) reactions to fuel Endergonic (anabolic) reactions. They use this energy coupling for synthesizing biomolecules, reproducing, moving, regulating temperature (Endothermic organisms only), and using active transport within cell membranes.

Adenine Triphosphate (ATP) is a modified nucleotide which is composed of a Ribose base with an Adenine and three Phosphate groups. Each Phosphate group is covalently bonded with either the Ribose base or with another Phosphate group which means the bonds store huge amounts of energy. The bond between the 2nd and 3rd P_i molecules holds the most amount of energy. It is very unstable since it is bonding two negative Phosphate groups and it is easily able to release energy like a spring-loaded mechanism.  The negative aspect of ATP is that it can’t be stored for a long period of time because it is too reactive and releases the P_i easily. When ATP loses the third Phosphate group, it is converted into ADP and the Phosphate group is transferred to other molecules which makes those molecules unstable. This process, called Phosphorylation, is used when the cell is building polymers from monomers and it is seen in the first steps of respiration.

The ATP Cycle. Photo found at http://io.uwinnipeg.ca/~simmons/Enzymes/img013.jpg

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Today in AP biology we finished our notes by talking about how salinity concentration plays a role in the reaction rate of enzymes.  We learned that the more salt concentration there is the more cations and anions there are. This leads to a disruption in the attraction between the charged amino acids. This in return denatures the proteins that can be found. In conclusion to salinity, we learned that enzymes are very intolerant of extreme salinity.

Then after our notes we got to have fun with an interactive activity that allowed us to see enzymes and how they work in a new and interesting way. In the activity our hands were supposed to represent enzymes called toothpicks. In the first part of the activity each person with their lab partner had to count and keep track of how many toothpicks could be broken over ten second intervals of time. By using our hands one lab partner counted while the other broke the toothpicks apart, acting like enzymes bonding with substrates. When finished, we concluded that overall the number of toothpicks broken practically remained the same but then started to decrease at the end. This is because the more toothpicks that were broken, the longer it took to distinguish between the whole ones and the broken ones.

After the first step of our activity we had to mix in twenty paper clips with the toothpicks. We were then supposed to repeat what we did in step one by keeping track of how many toothpicks were broken within ten second intervals. But in this case the number of toothpicks that had been broken continually decreased because the different substance (paperclips) got in the way and took up time as did the already broken toothpicks.

In doing our last experience however, we had to see how temperature would effect how the enzymes (our hands). We first had to break ten toothpicks and see how long it took us to break them at room temperature. Then a person in our lab had to place there hands in ice cold water and then see how long it would take to break the same amount of toothpicks as we did before at room temperature. With the hands being cold and the temperature affected it took twice as long for a person in our lab to break all the toothpicks.

After finishing the activity we then had to graph the data that we had found in step one and two. We then had to draw a trend line in order to show were the average of the two steps were at. Then we were asked a series of questions that pertained to our activity that would further help us understand what we learned as well as how and why by changing thing could effect the accuracy and quickness of an enzyme.

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courtesy of divyawe from flickr

Before we started our lesson for today, John and Kyle discussed their blogs that they recently posted. Both of their posts talked about the subject of viruses such as HIV/AIDS and the eternal question of whether a virus is a living organism or not. Today, our class quickly reviewed the concept of synthesis and decomposition. Then we moved on to discuss the factors that affected enzymes.

The teacher explained the relation of substrates and enzymes. As each factor increases, the rate of the experiment significantly increases also. The rate increases greatly for period until it will level off. Through an activity, the class was able to depict the scenario of the substrates attaching to enzymes. As the concentration of substrates increase, it becomes the limiting factor.  We also discussed how the enzymes would “tag” the substrates. If there are more substrates, it will collide with the enzymes more often. This reaction would also level off. All the enzymes have the active sites engaged and the enzyme is saturated.

The next subject we elaborated upon was how temperature would affect the rate of enzymes. This can be represented with a bell graph. For example, with the enzymes in humans, the optimum temperature is about 37 degrees celsius. Anything above or below the optimum range would hinder the rate of the enzymes. When the temperature increase, denaturization occurs, which causes the substrates and enzymes to lose their structure. In colder temperatures, the molecules move at a much slower rate and this decreases the collisions of the enzymes and substrates. As a result, endotherms are able to have very stable rates of enzymes as the temperature increases. In contrast, ectotherms are able to survive drastic temperature changes and still have functioning enzymes. This is because ectotherms can operate even low temperatures because they have four to ten different enzyme systems that have the ability to function at different temperatures. This occurs because ectotherms also have much more complex metabolisms.

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Today was something i like to call rapid-fire information day.

After an intense test last class, we started off today with a new chapter, Chapter 8. This chapter is about cell metabolism and enzymes plus the flow of energy. Life is built upon chemical reactions and energy transfers from one form to another. All energy ultimately comes from the sun and plants are the only things that can take sunlight and convert it to energy. (this is the part where the teacher showed the class a picture of a lion eating a giraffe)
With metabolism there are two different chemical reactions, forming bonds(anabolic) and breaking bonds(catatonic). Some Chemical reactions release energy, such as Exergonic reactions, like in digestion. Other chemical reactions requite input of energy like Endergonic reactions, and dehydration synthesis.
To Activate energy, Catalysts are used to reduce the amount of energy to start the reactions. Enzymes are used to reduce the activation of energy. THe enzyme substrate is a reactant the binds to enzymes, the product is the end of the reaction. The  Enzymes active site is a catalytic site where the substrate sits into the active site.
Enzymes are Reaction specific where they each work with specific substrate, with a special chemical fit between the two of them. The enzymes are unique by the fact that a single one can catalyze thousands of reactions but the enzymes themselves aren’t affected at all. The only way they are affected by cellular conditions that affect protein structure, such as the temperature, pH. or salinity.
Naming the enzymes is easy. For example:
Lipases break down lipids and Proteases break down proteins.
Lock and Key model is a vague way of showing how the enzymes react. The more accurate is the Induced fit model. This substrate binding causes the enzyme to alter its shape to create a tighter fit. (the conformational change brings chemical groups into positions for catalystic reactions.)

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Today, October 2, 2008, in AP Biology we took notes on the cell cycle. We focused mainly on the phases of cell division. I took my notes on a laptop in order to inject some much needed technology into my otherwise old school day. The class got through all of the phases of cell division, with minimal delays from the slower note takers. The phases of cell division are broken down into two main sections: interphase and mitotic phase. Interphase consists of a first growth phase, a synthesis phase (where the cell duplicates its DNA), and a second growth phase (the cell prepares for division). The mitotic phase consists of prophase, metaphase, anaphase, and telophase. During prophase, the chromatin condenses and appears as sister chromatids. The nuclear envelope breaks down and the centrioles move to opposite poles. The nucleus disappears and the next transitional step, prometaphase, occurs. Prometaphase consists of the mitotic spindle, made of microtubules, attaching to a structure at the centromere of each chromosome called the kintochore.

**A sketch of cell division by falsestartjunkyard on flickr.com

During metaphase the replicated chromosomes line up on the metaphase plate, or the middle line of the cell. The next step is anaphase, in which the sister chromatids separate. The sister chromatids then move to opposite poles of the spindle. The cell begins to lengthen. The next phase of cell division is telophase. The chromosomes go to opposite poles, the daughter nuclei form, and the chromosomes spread out. At that point, the cell division processes are no longer visible under the light microscope. The next step is cytokinesis in which microfilaments condense in the center of the lengthened cell. Cleavage furrows form and the cell splits in two.

What happens when cell division doesn’t work like its supposed to? Malignant cancer cells spread throughout the body because their cell division is unregulated. Cancer cells continue to divide, forming abnormal cells. Cancer is an example of what happens when cell division goes wrong.

cancer cells invading a mouse's cells by mearse on flickr.com

the-cell-cycle-notes-pdf

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