Enzyme Lab and Graphs

I think the week we did the Enzyme Lab was the most confused I have ever been in Biology. I have been putting this blog off for awhile but I know my grade depends on getting it done, so here it is.


Our group had a simple setup. (or so Michael said, didn't seem that simple to me) We mixed 3 ml of water with 3 ml of hydrogen peroxide. We added the enzyme yeast to make a chemical reaction that would make oxygen. The yeast, our enzyme, breaks the oxygen from the hydrogen peroxide and releases the oxygen into the air. Using a pressure probe we measured the pressure coming from the chemical reaction. We did our experiment three different ways. In the first we changed the amount of enzyme we put in. In the second we changed the temperature of the solution that we put the enzyme in to make the reaction. In the third experiment we changed the water in the solution to a pH solution. We did each experiment 3 times so we could calculate accurate data for each experiment.

Here are the different graphs we used to collect our data from the experiment.

In this graph we changed the amount of enzyme that we added to the solution. Or a simpler way to say it!...We changed the amount of drops we added to the mixture in the test tube. (10, 20, 30, or 40 drops.) The graph has a constant slope. I'm going to say what this means in two ways.
SIMPLE WAY: The more enzyme thats in the solution the more pressure there is.
SMART WAY: The speed at which the reaction occurs is a direct result of the ratio of the enzyme to the solution. (thank you Michael for helping me come up with that! =])

In this graph we changed the temperature of the solution where the reaction is taking place. The simple explanation....We changed the temperature of the stuff in the test tube. (0, 25, 38, or 80 degrees Celsius.) We kept the yeast at 25 drops every time.
From this graph we noted that freezing the solution at 0 degrees Celsius and heating it up to 80 degrees Celsius was not good on the reaction. When the temperature got to hot the graph decreased rapidly. This is because when there is to much heat is causes the enzymes to become denatured. (FUN FACT: Denatured means the shape changed...you know you can learn a lot looking at other peoples blogs.) We found out the best temperature for making oxygen was between 25 and 38 degrees Celsius. This is where the highest rate of reaction occurred.



Ok this was the part in the experiment that I was really confused. So I decided to look at my fellow group members blogs( Michael and Kyle H) to try and understand what went on better. Well....that made me more confused. Kyle said that the graph was messed up because Sierra(She was also in our group) couldn't measure out drops right....So there was one thing they had in common so I am going to talk about that.

In this graph we changed the 3ml of water in the solution to 3 ml of different pH solutions. (4, 7, and 10). So I think the graph kind of shows this but we found that the most oxygen was produced at the pH level 7. (FUN FACT: which is normal by the way!) It produced less oxygen at the pH levels 4 and 10.



In my research on enzymes this is something interesting I learned:  Superoxide Dismutase, or SOD, is a metalloenzyme. SOD plays an extremely important role in the protection of all life-systems. The enzyme superoxide dismutase, or SOD, catalyzes into oxygen and hydrogen peroxide. SOD is present in essentially every cell in the body. The two major forms of superoxide dismutase (SOD) in humans are the mitochondrial manganese SOD and the cytosolic copper/zinc SOD. When organisms cause serious disease, it takes the body a very long time to recover, and depending on the strength of the patient the bacteria may win. The ability of the enzyme to provide some protection to organisms is shown by the existence of a motor neuron disease in individuals who have point mutations in SOD.  The absence of SOD may lead to a form of anemia. A number of tumour cells have been found to be deficient in SOD. The absence of SOD activity seems to support cancer. In addition, SOD mops up the superoxide. Amyotophic Lateral Sclerosis (ALS), or Lou Gehrig’s Disease, is a crippling neuromuscular disease that usually attacks people between the ages of fifty and sixty. Strong evidence links ALS to mutations in the SOD1 gene. When the SOD gene is mutated, the enzyme is also mutated. The mutated enzyme loses its anti-oxidant effect. Inhibiting this enzyme could slow or stop the degeneration of nerve cells, which leads to the disruption of muscle control in ALS patients. As an enzyme, SOD has particular value as an antioxidant that can help to protect against cell destruction. It has the ability to neutralize superoxide, one of the most damaging free radical substances in nature. Like so many other protective compounds which naturally occur in the body, it decreases with age, making cells much more vulnerable to the oxidants which cause aging and disease. It occurs naturally in broccoli, Brussels's sprouts, wheat grass and in the majority of green plants.



This is my last blog for the semester because now it is time for Christmas Break. Even though this was the most challenging thing in Biology for me this year I think I understand enzymes pretty well now.
MERRY CHRISTMAS!
and
HAPPY NEW YEAR!
SEE ALL OF MY BIOLOGY FRIENDS NEXT YEAR IN 2011!

PKU Webquest

Phenylketonuria is a long word! In my blog whenever I mean to say Phenylketonuria I am going to say PKU. To help understand this diesese we were given some questions and websites to look at. There was so much information on the websites that I couldn't put it all down, but I got as much as I could. Here are the links to the sites that Mr. Ludwig gave us.

Your Genes, Your Health: Phenylketonuria

http://www.ygyh.org

NSPKU Home Page

http://www.nspku.org

Texas Department of Health Genetic Disorders

http://www.dshs.state.tx.us/newborn

Phenylketonuria - The Genetics

http://willroberts.com/pku/

PKU is a condition where phenylalanine builds up in the body. It is a very rare disease and is inherited. Phenylalanine is a building block of protein and is a natural substance. Mostly all babies get tested for PKU when they are just born. The test used is a heel prick test.

To help us understand PKU better we were given questions to try and answer. They are kind of hard to understand at first but once you get to reading the sites it is easier.

1. What enzyme is most commonly defective in people with phenylketonuria?

The most enzyme that is most commonly defective in people with phenylketonuria is the PAH Enzyme.

2. What reaction does this enzyme catalyze? (What is the substrate and what product is produced?)

A person infected with PKU can get dangerously high phenylalanine in the brain. This can cause mental retardation and epilepsy.

3. Describe the symptoms of phenylketonuria?

The symptoms in children that have undetected PKU  are smaller then normal head, lighter skin and hair then unaffected family members, Epilepsy, and Mental Retardation.

4. What causes the symptoms of PKU, the lack of a substance or the buildup of one?

The symptoms of PKU are caused by the lack of the enzyme to break down the amino acid which builds it up. The build up of the amino acid causes the symptoms. The state of high levels of phenylalanine is called Hyperphenylalaninaemia. (long word I know!)  Hyperphenylalaninaemia can cause brain damage.
 

5. How common is phenylketonuria? How is it treated?
PKU is found in about 1 in 10,000 births in Caucasians and East Asians. There are some ethnic groups that have higher rates. For example PKU is extremely rare in Africans. 
As soon as children are diagnosed they must keep a low- protein diet and stay on the diet as long as they possibly can. Most experts recommend that people infected with PKU diet for life. Phenylalanine is found in the protein part of food. This is why the treatment is to keep a low protein diet. Foods that are not in this diet are meat, cheese, poultry, eggs, and milk.

Photosynthesis, Cellular Respiration, and Energy

Sierra, Sidney, and I all worked on a glogster together. This was my first time using glogster and I really liked it. There will probably be future glogsters on my blog in the future. =) But for now here is our glogster on Photosynthesis, Cellular Respiration, and Energy.

Photosynthesis "Dry Lab"

So instead of doing an experiment and writing down the observations, this week we went backwards. We were given a set of observations and we had to write the procedure that went along with this experiment. It was kind of hard for me at first but then I looked at other peoples blogs and that helped me understand. So here is my Photosynthesis "Dry Lab."



Materials

•           Distilled Water
•           Bromothymol Blue (BTB)
•           Aquarium Snail
•           Elodea
•           Large test tubes
•           Light
•           Dark space

        

Procedure

1. Put 15 ml of water and 15 drops of  BTB in a large test tube and let it sit for 3 hours under light. Record your observations.
2. Put 15 ml of water, 15 drops of BTB, and an aquarium snail in a large test tube and let it sit for 3 hours under light. Record your observations.
3. Put 15 ml of water, 15 drops of BTB, and a elodea (funny plant) in a large test tube and let it sit for 3 hours under light. Record your observations.
4. Put 15ml of water, 15 drops of BTB, an aquarium snail, and an elodea in a large test tube in the light for 3 hours. Record your observations.
5. Repeat Step 4 procedure but put it in the dark for three hours and let it sit. Record your observations.

(If your water doesn't turn blue after 15 drops of BTB keep putting drops in until it turns blue)


Observations:
Water plus BTB is blue-green.
         Water is neutral. It changes to the color of the substance that is put in it.


Water plus BTB and an Aquarium Snail is yellow in light.
          Animals respire (breath) and they let Carbon Dioxide out. Carbon dioxide in water produces carbonic acid. When there is acid in BTB and water it turns to yellow.


Water plus BTB plus elodea is blue-green in light.
          Green plants respire. Then they photosynthesize and use the Carbon Dioxide. The plant keeps the water from acid it stays a neutral at the blue green color.


Water plus BTB plus a snail plus elodea is blue-green in light.
          The plant and snail respire. But the plant photosynthesizes and uses the Carbon Dioxide so it turns to blue green and there is no carbonic acid.

Water plus BTB plus a snail plus elodea is yellow in dark.
          The snail and plant respire. Since there is no light the plant can't photosynthesize. The carbon dioxide is still in the water so it stays an acid and the color stays yellow.


Conclusion:
When BTB is added to water it turns yellow because Carbon Dioxide and water mixed together make a carbonic acid. It stays blue with just water because water is a neutral.

Cell Structure-Plants and Animals

To teach you about cell structure I tried the site bubbl.us. I DO NOT RECOMMEND TRYING IT. I got so frustrated trying to organize all my bubbles. I think I got it organized enough to where you could read it.
I went to a site where I found out a lot about animal cells. There was a lot of information that I could not get on my web so I am posting the site here.

Site with information about Animal Cells

I also went to a website to find out information about plant cells. I learned a lot! Here is the link to the site.

Information bout Plant Cells

And here is my huge web about cell structure:

Microscope Week

This week in Biology we have been working with microscopes. It's amazing how small something can be and how much is involved in it. Microscopes can see the smallest things that human eyes can't see. We have looked at onions, different kinds of pond water, human saliva, and many many other things. My group got to use like a camera type thing. This camera hooks up to the microscope and then pugs into the computer. We get a clearer view of everything and we got to take cool pictures.
I think my favorite thing so far has been one kind of pond water. There was so much in it! We saw a little guy that sucked up everything in its area and it kept getting bigger and bigger. It was amazing to see.

In class the plan is going to keep learning about cells. Hopefully we get to keep using the microscopes! I want to get better at using it! :-)

Carbohydrates- The book is used!

So it took me awhile to get Carbohydrates down. I did about half a lab(I missed the other half because I was sick), took a quiz.....twice (I bombed the first time and got a B the second time....I would have aced it but I mixed two sugars up even though I knew what they were! I'm still mad at myself for that!), and now I am doing this blog post. I learned a little from each activity I did but most of the learning came out of yes......reading the book. I'm starting to think our Biology book is useful in this class. I still think I can learn a lot more about carbohydrates. I may understand them now but I still see myself studying a lot before that final comes. But for now here is all the information I read about last night and learned the past few weeks in class.


The three elements in all carbohydrates are carbon, hydrogen, and oxygen. Most of the carbohydrates have a carbon to hydrogen to oxygen ratio of 1:2:1(fact from the book!). There are two times the number of hydrogen atoms then oxygen atoms. The word carbohydrate has single sugar molecules and also sugar chains. The length of the chains can go anywhere from a few sugars to hundreds of sugars. The long chains are called polymers.

Carbohydrates are made up of saccharides. There are three type of saccharides: mono, di, and poly. Two of the most common examples of monosaccharides are glucose and fructose. (FUN FACT: Glucose is a hexagon of carbon elements and fructose is a pentagon of carbons.) Some examples of disaccharides are sucrose and lactose. Some examples of polysaccharides are starch and cellulose.

Monosaccharides have only a single sugar molecule. They are called simple sugars. The molecular formula for a monosaccharide is some multiple of CH(2)O. This suggests that every carbon is bonded to an H and an -OH. That is not strictly correct. (In the above line the 2 is supposed to be a small 2 near the bottom of the H but I did not know how to do that on the computer.) Sugars have a lot of hydroxyl groups and because of this polar functional group they are soluble in water. (another fact from the book! see how useful it is?!)

Monosaccharides often do not stay mono. Monosaccharides bond together and make disaccharides. This happens during a dehydration reaction. For example glucose and fructose make sucrose. Or two glucoses can combine and make maltose.  (okay so just for a little funny story...I learned the underlined facts when Mr. Ludwig and Michael were arguing about it after school!) Sucrose is another name for table sugar.  It is a disaccharide of special interest because sucrose is the form in which sugar is transported in plants. (FUN FACT: Sucrose is the sugar used to sweeten our food)

Polysaccharides are polymers of monosaccharides or many monosaccharides combined together. Another way to describe them is complex carbohydrates. There are some types of polysaccharides that function as short- term energy storing molecules. These have to be storage molecules because they are not as soluble in water and they are much larger than a normal sugar. Also, because they are bigger they cannot easily pass through the plasma membrane. The polysaccahride is broken down to release sugar molecules when an organism needs energy. Starch is often found in plants and glycogen is used in animals. The complex carbohydrate cellulose is used in plants to form a cell wall.

I hope dear reader(I'm pretty positive this is Mr. Ludwig, but for anyone else too) that you learned a few things about carbohydrates today. But even a little more I hoped you learn that you can learn things from anywhere. Any resource you have use it! It can be an experiment, a quiz, an article on the computer, the book, or even a conversation between your teacher and a really smart kid!

Fruit Loops-Protein Molecules and Collagens

In class we did an activity where we stringed fruit loops together on a string. Can you guess what this is supposed to represent? Protein Molecules!! This was probably the best way Mr. Ludwig could of taught protein molecules to me because I love fruit loops! (one of my favorite parts was eating them afterwords)

This is what I learned:

Protein Molecules have 20 different amino acids. (we didn't have 20 different colors to represent them but that's where a highschoolers imagination comes to play). Amino acids are molecules. They are composed of an amino group and an acidic group. There is a third group known as the R group. (this group has  everything else that comes in and joins the protein). This group is what gives the proteins different characteristics.

When you combine amino acids you get peptides. Peptides are a covalent bond between the acid group of one amino acid and an amino group of another amino acid. When you combine peptides you get polypeptides.

Proteins can have many different functions. For example they can be enzymes, provide support, transport substances, defend the body, and regulate metabolism.

After we made strands of protein molecules we combined with other people to make different kinds of proteins. Sierra, Sidney, and I braided ours together and made an example of collagen. This was not the only way you could combine them. Other groups in class combined theirs to make globular protein. You can tell the difference between them because a collagen is a strand and a globular protein is a huge glob.

Collagen is a type of protein. It is made of fibers and it connects and supports body tissues. Tissues it connects are skin, bone, tendons, muscles, and cartilage. Collagen is present supporting internal body organs and is can be found in teeth. Actually there are 25 types of collagen in the human body. Some people say it is the glue that holds the human body together. If a body didn't have collagen we would fall apart! (but the collagen in our body isn't made of fruit loops! :-) ) Collagen is very strong and is different from many other proteins.
Collagen can be found inside and outside the cell walls. It's fibers play a major part in the external structure of cells. Collagen plays a major part in the body and can be used in medicine. The organ collagen is mainly associated with is the skin. It helps provide skin with flexibility, strength, and resilience. Collagen loses its structure when it is heated.

There are several types of collagen.
Type 1: is the long, simple chain we made in class. It has three polypeptide chains. It can weave together and make fibrils. Fibrils are the space between cells.

Type 4: This is pretty much like type 1. You add a head on one end and a tail on the other end. When you get four type 4's together the heads come together in the middle and the tails spread out in like the shape of an X. They form a dense mat of them.

I only know about these two types of collagen because the guy that taught it to me only knew about these two. ;-)

Fluid Mosaic Model

Last week in class we drew Fluid Mosaic Models. In class we split into groups and each drew our own. I am not very artistic but I really enjoyed working in groups off the computer. And even though I am not very artistic I still enjoyed drawing!

I learned so much while doing this poster. There are many parts in a membrane. On our poster we had the transmembrane protein, cytoplasm, glycoprotein, and many other parts! One thing I learned while researching cells was that Glyco means sugar. So anything that has glyco attached to it means it has sugar on it. For example a glycolipid is a lipid with sugar attached. It is the same with a glycoprotein.

Another part of the cell is the transmembrane protein. When I first tried to Google this I came up very confused. The definition I found did not help me understand at all. Then Mr. Ludwig said to break down the word into parts and figure out each part and then I will be able to understand the word as a whole. Well I know trans means across, like the trans continental is a train that goes across the country. Across being the key word. So a transmembrane protein is a protein that goes across the membrane.

So I wrote the first part of my blog and got to thinking this is all I know! I only know the parts of the membrane and what glyco and trans means. So this kind of scared me but thankfully today in class Mr. Ludwig said that was the point. Last week we were learning the parts of the membrane and this week we are learning the functions of everything. So stayed tuned for a continuing blog! 

Biology- It's not easy

So I have spent almost a quarter now in Biology. One thing I really understand now is Acids and Bases. All I had to do was focus and actually work on it instead of cruising facebook. I also really understand Water Properties and how they work now. I'm thinking it just takes me a little bit longer to understand science then at the pace we were going at. I just have to make sure I don't get distracted on my computer doing something else that I shouldn't be doing. Something I really need to work on is carbohydrates and sugars. I'm having a hard time understanding them. But I know if I stay more focused in class I can keep up and understand things better.

Acids and Bases.....Uhh

What makes an acid an acid?
Acids make things taste sour. Vinegar and lemon juice are both sour because they are acids. Acids are corrosive to metals, change litmus red, and become less acidic when they are mixed with acids. They also taste sour. A scientist named Arrhenius suggested that acids are compounds that contain hydrogen and can dissolve in water to release hydrogen ions into solution. Arrhenius's suggestion can explain why acids have similar properties to each other.

What makes a base a base?
Bases are different from acids. Bases feel slippery and change litmus blue instead of red. They also bacome less basic when they are mixed with acids. Arrhenius said that bases are substances that dissolve in water to release hydroxide ions into solution. An example of a base is sodium hydroxide. All bases are similar in their properties and they all release OH-.

Neautralization is the idea that acids and bases counteract each other. The idea is that a base makes an acid weaker and an acid makes a base weaker.


Why is water neutral?
Water is neutral becauase the hydrogen negative and OH positive are the same amount.

 How do antacids work? 
Antacids work by increasing the PH level of stomach acid. They work by neutralizing acid and coating the stomach. The opposite of an acid is a base and that is what an antacid is. Antacids can treat symptoms like heartburn and gastritis.

Properties of Water Review "Dead Simple"

The article I read "Dead Simple"(http://www.futurity.org/science-technology/dead-simple-way-to-see-atomic-structure/)  was about how scientists are trying to find new ways to see atomic structure. They were using many different ideas to obtain the first direct images of how water coats surfaces at room temperature.
One way they tried actually happened on accident. A guy named Heath accidentally figured out a technique how to pin down moving molecules under room temperature conditions.
Graphene is composed of a one-atom thick layer of carbon atoms in a honey comb like lattitce. Graphene should be completely flat but while experimenting Heath found some nanoscale island-shaped structures trapped between the graphene and something called mica that they didn't expect to see. Heath likes to call this experiment a happy accident. There were many different ways this team found that you couls study molecular structure.
Next this team hopes to improve the resolution of the technique so it can be used to image the atomic structure of biomolecules like antibodies. This science team is making a lot of progress.

Water Properties

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Generic Brands vs. Name Brands

Clinical Trials- Alzheimer's Disease

This week in Biology we learned about Clinical Trials. More specifically: double- blind trials. In double- blind trials the subjects that are in the trial don't know whether they are taking the control drug or the experimental drug. The personnel giving the subjects their drugs don't know either. In the clinical trial I looked at for Alzheimer's Disease the experimental drug was called Dimebon and the control was called Placebo. That is the thing I don't like about double-blind trials. The people that have the sickness don't know whether they are taking the treatment pill or the control. The opposite side, however, is that the treatment pill could be killing people and the control is safe.  In "A Phase 3 Study To Evaluate The Safety And Tolerability Of Dimebon Patients With Mild To Moderate Alzheimer's Disease" there were two study cohorts. In Cohort 1 the patients got either Dimebon 20 mg or Placebo TID for 26 weeks. In Cohort 2 AD patients got Dimebon 20 mg or Placebo TID for 12 weeks. I think they did two Cohorts because they wanted to make sure they got accurate results. In this study you could only participate  if you were 50 years or older and had Alzheimer's. I think that double-blind trials can be effective but I don't like them very much.