Tuesday, May 20, 2014

Dissection Post


External Organs:

First Dorsal Fin- helps fish swim, provides stability 
Second Dorsal Fin- helps fish swim, provides stability 

Internal Organs: 

Gills- allow water to flow freely with oxygen and ammonium as it goes in and out of the fish
Muscle Segment- helps fish move efficiently 
Anus- fecal matter is ejected from the body 
Stomach- receives food to be digested 
Swim Bladder- allows fish to remain buoyant at specific depths 
Intestine- absorption of nutrients is carried out and waste is transformed into fecal matter 
Spleen- impurities in blood destroyed here 
Urinary Bladder- urine from kidney gathers here before being evacuated through urogenital aperture 
Urogenital aperture- opening to genital/urinary tracts allowing evacuation of gametes and urine 
Pyloric Caecum- digestive tract where part of digestion mainly occurs. Fermentation sometimes occurs here too. 
Kidney- eliminates metabolic waste and maintains pressure of initial fluids 
Liver- secretes bile and other substances 

Link to dissection video: http://youtu.be/uCVIQx5MN1Y


External Anatomy:
The crayfish is made up of 2 parts
The cephalothorax is made up of the head and thoracic 
The abdomen is the lower part of the crayfish.
Antenna: they use this to gather sensory information. (touch, taste, and smell)
Antennule: they use for balance and gathering sensory information (touch and taste) 
Cheliped: These are their large front claws. They help capture prey and can be used for defense. 
Walking legs:  Used for moving.
Swimmerets: They help create water currents and assist in reproduction 

External Anatomy cont.
Telson: its job is to hold the anus. 
Uropod: it is a segment of the cray fish and it contains the telson.
Telson + Uropod = makes the tail fan. This helps propel the crayfish backwards because cray swims  backwards. 
How to tell if it is boy or girl
This can be identified in the walking limbs. Using magnifying glass look at  the base of the leg. 
If you see a crescent shape slit it is a girl 
On the 4th walking leg there is a slit for the sperm duct opening, that means it is a boy

Internal Anatomy
Flexor muscle: It helps move the abdomen. It lines a majority of the abdomen. It is a powerful force when the cray fish needs to move backwards 
Gills: The gills are used to let carbon dioxide and oxygen to exchange, gills help them breath.
Green Gland: they accept waste from cellular waste, they then excrete the waste though the antennas pores. 
Brain: used for maintaining  homeostasis and other processing functions. 
Digestive gland: They make digestive juices and in these gland nutrients absorption takes places. 
Intestine: undigested nutrients goes to here. 
Tail muscles: this muscle is to help propel the crayfish

Link for dissection video: http://www.youtube.com/watch?v=siRSnEbFeyQ



Anterior and posterior ends of the clam- muscles that pulls the valves together 
Umbo- bump at the end of the anterior end which shields the clam. This is the oldest part of a clam (where it first started to grow)
Growth rings- tell how old a clam is by how many rings it has
Hinge ligament- keeps the clam together when it opens up
Ventral- the shell that protects the clam's soft body inside by surrounding around the outside


Gills- essential for almost all sea life in order to breathe. It is one of the clam's respiratory organs
Posterior & Anterior Adductor- by relaxing and contracting these muscles, it allows for movement of the clam 
Exhalant siphon- expels water and waste out of the clam
Inhalant siphon- brings in oxygen, food, and water into the clam

Mantle- forms outer wall of clam, and it encloses it's internal organs
Tooth- allows for the breakdown of a clam's food 

Incision Guide
Not many places you need to cut, all you really have to do it open it!!
A scalpel is ideal for cutting, you will need to cut through the clam's muscles along the side a little bit. Clams can be very stubborn, don't strain yourself because of its strong seal! Ask a teacher for assistance if you are unable to open it.

Link for video on how to dissect: http://youtu.be/50U8o_661-g




spinal cord: (not pictured) component of the nervous system made up of a soft fatty substance


heart: muscular organ helping blood to circulate.


gallbladder: small reservoir in which bile secreted by the liver collects before being discharged into the intestine during digestion.


liver: gland secreting bile that contributes to digestion.


pancreas: digestive gland connected to the intestine that produces secretions and hormones.


stomach: dilated section of the digestive tract before the intestine; it receives food to be digested.


small intestine: long thin portion of the digestive tract behind the stomach in which most of the digestion and food absorption take place.


large intestine: short wide portion of the digestive tract beforethe cloaca in which a small part of digestion and elimination of waste take place.


urinary bladder: (not pictured) reservoir where urine from the kidneys collects before being evacuated by the cloaca.


cloaca: (not pictured) orifice common to the intestine and the genital and urinary tracts; it is located at the end of the digestive tract.


spleen: (not pictured) organ of the circulatory system where impurities in the blood are destroyed.


kidney: (not pictured) organ secreting urine; it eliminates toxic substances from the body.


testis: (not pictured) male genital gland producing sperm.


lung: respiratory organ made of an extensible tissue; it forms a sac into which air inhaled through the nostrils is carried. A frog also breathes through its skin.


brain: (not pictured) main organ of the nervous system consisting of nerve centers; it is located in the upper portion of the head.


esophagus: (not pictured) canal of the anterior portion of the digestive tract; it carries food to the stomach.


tongue: (not pictured) movable mouthpart having gustatory and prehensile functions.



hind limb: long powerful articulated member attached to the terminal end of the trunk; it has five webbed toes used for walking, jumping and swimming.

webbed foot: each of the digits of the foot, connected by membranes; when spread, they make swimming easier.

web: fine membrane of skin connecting the digits of the foot; it stretches when the frog swims.

digit: terminal end of the limbs formed of various articulated bones; it has neither nails nor claws.

forelimb: short articulated member located behind the head; it has four digits and is used for walking.

lower eyelid: thin muscular membrane that is translucent and movable; it rises from the lower edge of the eye to protect and cleanse it.

mouth: anterior cavity of the digestive tract located on the ventral surface that allows food to be ingested.

nostril: external orifice of the nasal cavity located above the mouth and having olfactory and respiratory functions.

snout: anterior round protruding portion of the head that forms the mouth and the nostrils.

eyeball: protruding organ of sight contained in the bony cavity at the top of the head used to perceive light intensity, motion and shapes.

tympanum: thin strong elastic membrane connected to the inner ear to capture acoustic vibrations.

upper eyelid: thick fixed membrane.

trunk: bony portion of the body to which the head and limbs are attached.

Link for dissection video: http://youtu.be/FrDbIR-GU0k


Internal organs:

ring canal : circular canal where filtered water enters through the madreporite and flows into the radiated canals.

rectal cecum: waste is stored here before it goes through the anus.

stomach : receives food to be digested.

gonad : produces gametes (spermatozoids or ovules) depending on the sex of the starfish

pyloric cecum : radiated duct of the digestive tract produces digestive enzymes and allowed digested food to be stored.

gonopore :where gametes are expelled into the water to be fertilized.

intestine : where absorption of nutrients is carried out and waste is transformed into fecal matter.

radial canal : receives water from the annular canal, which then passed into the tube feet.

ampulla : contracts to let water enter the tube foot, allowing it to extend; when it dilates, the foot retracts.

esophagus : allows food to reach the stomach.

External organs:

Arms or rays - project from disc

Central disc - the center of the starfish 

Oral surface  - where the mouth is

Aboral surface - the top of the starfish

Madreporite - small white circular area, off-center on aboral surface of disc

anus - small centered aborally on disc, allows waste to be ejected

Spines - many short, rough, limy, in patterns over aboral surface

Eyespot - small, pigmented on one end of each arm

Ambulacral grooves - one along oral surface of each ray

Oral Spines - surround the mouth

Tube feet - soft, slender, with expanded tips; 2 or 4 rows in each groove

Mouth - on oral surface in center, allows food to be digested 

Link for dissection video: http://youtu.be/uh6MdVdMxe0






Monday, March 17, 2014

pGLO Lab

pGLO Lab


Genetic transformation is an alteration within genes that is a direct result of exogenous DNA. One can insert a specific gene into an organism in order to change its trait. In this lab, we transformed bacteria into a gene that codes for GFP, or Green Fluorescent Protein. This specific protein allows for a glowing of bright green under a ultraviolet light. In this experiment, the pGLO is resistant to the antibiotic ampicillin in the plasmid DNA. Transformed cells will only grow on the dishes with LB/amp and will not show on those without it 


The purpose of this pGLO lab was to insert a plasmid into the DNA of a bacteria. Dependent on the presence or absence of the sugar, arabinose, determined whether the bacteria glowed or not. We transformed this bacteria into a gene that codes for Green Fluorescent Protein. This protein is what makes the certain ecoli glow under the ultraviolet light.  We then compared the absence/presence of the pGlo and sugars.


First we had 2 test tubes, we labeled one +PGLO and the other one -PGLO. We also labeled the 4 LB agar plates. The first plate was LB/AMP/+PGLO. The second one was LB/AMP/ARA/+PGLO. The third plate was LB/AMP/-PGLO. The last plate was LB/-PGLO. AMP was the antibiotic and the ARA was sugar. Then we used a sterilized pipet and put 250 micro liters of transformation solution in both test tubes labeled PGLO + and -. Both tubes were then placed on ice. A single colony of bacteria put in the +PGLO. We do this by taking a sterile loop and putting it in the bacterial colony and the placing the sterile loop in the test tube. We swirl the loop in the tube to make sure the bacteria colony is completely immersed in the PGLO. This was repeated for -PGLO. Then we added a DNA plasmid in the +PGLO and not the -PGLO. We added the plasmid by using another sterile loop and taking the plasmid for a DNA stock tube, after we did that we swirled the loop in the +PGLO. Next we put both test tubes in a foam rake on ice for 10 minutes. After the 10 minutes we needed to heat shock the test tube. We did this by transfer the test tubes in the foam rake into a water bath that was 42 degrees Celsius for 50 seconds, and then putting the test tubes back on ice for 2 minutes. After the heat shock we used a sterile pipet to but 250 micro-liters of LB broth into both test tubes (+PGLO and -PGLO). The next thing we did was incubate the test tubes at room temperature for 10 minutes. We tapped the test tube with our fingers to make sure the LB was spreading out. Our next step was to pipet 100 micro liters of +PGLO  suspension to plate the nutrient plate 1 and 2. Then we pipeted 100 micro liters of -PGLO suspension  was added to plate 3 and 4. For each plate a new sterilized pipet was used. Next we used a sterile loop at spread the suspension around the plate. We did this by rubbing the loop all over the plate but we couldn't press too hard on the agar. We repeated this step for all 4 plates using new loops each time. We then flipped the plates upside down and stacked them to let the plates incubate in a 37 degree Celsius for the night. The next day we unflipped the plates to check the growth. Then we used a UV to check the plate LB/AMP/ARA/+PGLO to see if any of the bacteria were glowing. We took pictures of all the plates, to record the growth.


After letting the E.coli incubate over night, we were able to determine our results the next day. The Petrie dish with LB and -pGlo grew a big amount compared to all the other dishes. This happened because the dish only had LB (a type of broth) and -pGlo. This -pGlo did not have an effect on the cells. The bacteria grew like normal bacteria would. We made this dish even though we knew it would not glow in UV light to show that our bacteria did grow normally; it showed that the bacteria worked essentially. The next tray had LB/ AMP and -pGlo. This tray had the broth (LB) and an antibiotic (AMP). This tray did not experience any growth at all because it had the antibiotic and was missing the plasmid,+pGlo, which prevented it from growing. Another tray contained +pGlo, LB, and AMP. This had the broth and antibiotic as well as the plasmid, +pGlo. The dish grew approximately six colonies of DNA. It was able to grow because it had the antibiotic and plasmid. This tray did not glow in the UV light because it did not have the sugar, ARA, present that makes it glow. This dish acted as our control for the experiment. The last dish had the plasmid, +pGlo, the LB broth, the antibiotic, AMP, and lastly the sugar, ARA. The ARA sugar in this dish separated it from all the other ones. This tray glowed and grew about five colonies of bacteria. This tray glowed in the UV light because of the ARA sugar, plasmid, and antibiotic AMP. 
After seeing the growth in the different dishes, our group calculated the transformation efficiency of our experiment. The transformation efficiency is the extent to which we genetically transformed the bacteria (in this case, E.coli). When doing an experiment, of course, the more cells you genetically transform the better, so the higher the transformation efficiency the better as well. In this experiment's case, the transformation efficiency represents the total number of bacterial cells that express the green protein, divided by the amount of DNA used in the experiment. This then tells us the total number of bacterial cells transformed by one microgram of DNA. The formula used is: 

Transformation efficiency = total number of cells growing on the agar plate
                                             Amount of DNA spread on the agar plate 

Our transformation efficiency was 14.16 which is very off of the standard amount. Standard amounts are usually way higher, around about 8.0 x 10^2. Clearly, we did not genetically transform many of the DNA cells.  


From these results, we can come to two conclusions. E Coli can only grow in the presence of an anitbiotic when it has been treated with pGLO which causes the bacteria to become antibiotic resistant. The glowing characteristic of the pGLO, however, is only activated in the presence of a sugar. We know this is true because the bacteria only treated with pGLO and anitbiotic was able to grow but not glow but the bacteria treated with both grew and glowed.  

Friday, December 20, 2013

Cell Communication Lab: Yeast Cells

For this lab, we focused on cellular communication. Cell communication happens between unicellular organisms and inside multicellular organisms. To communicate with their neighbors, cells secrete chemicals to other cells to "switch on" the cell. Organisms communicate via chemical signals to coordinate functions and to respond to the stimuli in their environment. A molecular signal reaches it receptor on the cell, and a series of reactions occur. Cells can communicate by direct contact, local signaling, or long-distance signaling. Yeast cells are unicellular fungi, that can reproduce sexually or asexually. Yeast can be cultured on solid or liquid media. If cells are streaked over a solid medium, they grow in colonies on top of one another while yeast cells that are mixed into a liquid medium grow evenly throughout it. During this experiment we observed yeast cells and their responses in both solid and liquid mediums.

The purpose of this lab was to determine how cells, like yeast cells, communicate with one another. Yeast cells do not have legs and cannot swim to other cells to mate with them, so we wanted to see exactly how that would happen. We were also testing to see how much the yeast cells would reproduce during the time increments we set for them. We counted the different types of cells after 0 minutes, 24 hours, 24 hours and 30 minutes, and 48 hours. The independent variable is the amount of time that the cells had to reproduce. The dependent variable is the percent of the total of the cell that a certain type of cell was, like a single haploid cell. 

First, we labeled each agar plate and corresponding culture tubes "a-type," "alpha-type," and "mixed type". We added about 2ml of water using a pipet to each culture, then used a toothpick swab to pick up a colony from each plate (using a different pick each time). Following this, our lab group observed each yeast Petri dish under the microscope: once at the start, after 24 hours, 24 hours and 30 minutes, and again after 48. We counted to the best of our abilities the cells we observed under the microscope. 
During this lab we were instructed to practice the "sterile technique," meaning handling tools without contamination. By doing so, we did not allow our tools of this lab to touch anywhere that's not a "clean zone". We never used a pipet, swab, or spreader more than one time. If we did, who knows what kind of bacterial growth we would see. We were sure not to let our skin touch the yeast either. 


          Alpha culture after 24 hours 

                         Mixed culture after 48 hours 
            Alpha type after zero minutes 

In this experiment we wanted to test the communication in different strands of yeast. We tested  A type, Alpha type, and mixed type. The  key difference between these types are the different genes in Alpha and A type.. These A and alpha type can combine to make a mixed cell via single transduction pathway. The mixed cells are a combination of A type and Alpha type, these cells can become a haploid, budding haploid, zygote, budding zygote, or a shmoo. A haploid is a single cell. A budding haploid is a single cell with a growth on the side. A zygote is two cells that look like an infinity sign. The budding zygote is 2 cells that are like infinity signs with a growth that looks like a dot. A schmoo looks like a pear, and it the two cells combining together. The mixed type can have shmoos, both haploids, and both zygotes. The A factor and alpha type only have budding haploids and haploids, this is because the A type and Alpha type had nothing to mate with. Single transduction pathways use several steps to produce a cellular response.  The yeast cells use G- protein receptors system to mate. G protein receptors are also single transduction pathway. G proteins consist of a signaling molecule, a g protein, G protein coupled receptors and an enzyme.  The signaling comes to bind to the G protein on the extracellular side. This causes the G protein coupled receptor to change shape on the cytoplasmic side. When the receptor changes shapes a G protein to bind to it. This activates G protein to make a GTP and get ride of the GDP the protein currently was holding. Then the active G protein combines with the enzyme to active the enzyme, to trigger a cellular response. Once the enzyme is activated, the G protein acts like a GTPase enzyme. GTPase use hydrolysis to get ride of the third phosphate. To make the protein inactive and ready for reuse. This yeast cells are able to do this by commicating with secret messages. These secret messages are called pherenomes. In the graphs you can see that the for the first 30 minutes on the A type of Alpha type the number were very high at first but as time progressed to 24 hours the number of haploid and budding haploid started to decreases. This happened because the cells had no one to mate to so they started to die off as time went on.  For the mixed type the numbers increased as time went on. This is because the Alpha and A type were able to mate, and create more yeast cells. 

This experiment can be fixed by wearing gloves. Maybe if we wore gloves it could decrease on contamination. The lab was very sterile but if we had gloves we could make it even more  sterile. This could help prevent other types of bacteria from growing. Also, our lab group was not very accurate when we were counting the different types of cells. The next time we do this lab, we would work on counting them more accurately to get better data. 

Cell communication is required in many different biological functions (sexual reproduction included). In this lab, we observed cells signaling each other in two strains of the yeast Saccharimyces cerevisiae. In the A and Alpha type cultures, we examined the life cycle and mating routines in the yeast and in the mixed cultures, tons of bacteria were living throughout. 

Friday, December 6, 2013

Photosynthesis and Chromatography Lab


     Photosynthesis is a process that converts light energy into chemical energy that can be used to fuel the organisms. Below is the formula for photosynthesis.
                                       6H20 + 6CO2   -->  C6H12O6 + 6O2
         Photosynthesis has two parts, the light dependent reactions (light reactions) and the light independent reactions (dark reactions). The light reaction happens in the thylakoid and convert light energy into chemical energy. This chemical reaction must take place in the light. The dark reaction takes place in the stroma within the chloroplast, and converts CO2 to sugar. Although called dark reactions this reaction needs the energy  produced in the light reactions in order to trigger the reaction. Organisms that carry out photosynthesis and make their own organic molecules are called autotrophs.
         Chloroplasts are organelles in plants that conduct photosynthesis.  Chloroplasts capture light energy from the sun to produce the energy stored in ATP and NADPH photosynthesis.  Under certain circumstances the proteins in chloroplasts can be denatured or unable to conduct photosynthesis, such as high temperature or lack of light.  In this experiment we will test these circumstances and see for ourselves the affects that can harm photosynthesis.
         This experiment tests the light reactions. The light reactions are the first step of photosynthesis. The light reaction have 2 photosystems. There is photosystem I and II, they can be abbreviated PS I and PS II . PS II comes before PS I. PS II is also called P680, because it absorbed a wavelength of 680 nm the best. PS I is also called  P700, because it absorbs a wavelength of 700 nam the best.In PS II light enters it and stimulates the electrons. Water also enters it and excites the electrons by splitting water, H+ remains in PS II and O2 leaves the photosystem. The electrons bounce around till they reach the chlorophyll a molecule. The electrons are then sent to the primary electron acceptor and makes them 680+. 
          After the electrons are sent to an electron transport chain. Electron transport chains help lower the energy in electrons. It also helps drive chemiosmosis  to make ATP.  Some of the electrons that are in the transport chain get sent to the chlorophyll a molecules of PS I. PS I electrons come from light and the electrons from PS II. PS I  is similar to PS II, in having the chlorophyll a molecules pushing electrons to the primary electrons acceptor. The difference is in the end. Instead of going to an electron transport chain to make ATP,  P700+ goes through the electron transport chain to be reduced by the enzyme, NADP+ reeducase to make NADPH. Both of these process are meant to make ATP and NADPH for the Calvin cycle. 
The purpose of this experiment was to test how enzymes (in this experiment the enzyme was DPIP) would effect how much is transmitted. We wanted to see what would happen if we used boiled and unboiled chloroplast. We would see if the boiled maybe decreased the prcent transmitted.  Also we wanted to see the effect of having the curettes being placed in the light and dark. We could test if curettes kept in the dark would lower the percent transmitted.  In this experiment the independent variable was the DPIP and the dependent was the precent transmitted.
       First we set up the 5 different test tubes. The first test tube was a blank. It had 1 mL of phosphate buffer, 4 mL of distilled H2O, no DPIP, and 3 drops of unboiled chloroplast. The second test tube 1 mL of phosphate buffer, 3 mL distilled H2O, 1 mL of DPIP, and 3 drops of unboiled chloroplast. The third test tube had 1 mL of phosphate buffer, 3 mL of of distilled H2O, 1 mL of DPIP, and 3 drops of unboiled chloroplast. The fourth test tube had 1 mL of phosphate buffer, 1 mL of DPIP, and 3 drops of boiled chloroplast.  The fifth test tube was 1 mL of phosphate buffer, 3 mL of distilled H2O, 1 mL of DPIP, and no chloroplast. When the test tube was ready to be measured in the spectrophotometer the contents in the test tube would be put in to a cuvette. For each test tube the chloroplast was not added until it was put into a cuvette. After we got all the test tubes ready, we filled up a big beaker of water and behind the beaker of water was a huge floodlight. The first test tube was a blank that was used to calibrate the spectrophotometer. After it was used to calibrate it was kept in the light. Because we ran out of time we measured all the test tubes at the same time. We would put test tube 2 in the spectrophotometer then get it's reading. Then we would take the test tube out and put it in the light for 5 minutes. But the 2nd test tube is covered in foil to prevent the light from getting in. Right after that we would put in test tube 3, get a reading on the spectrophotometer and then put it in the light for 5 minutes. This same thing happened to test tube 4 and 5. After every 5 minutes we would take the test tube out of the light and measured in in the spectrophotometer we would go up to 15 minutes. We would take measure if the test tubes in the order of 2,3,4,5.
We repeated this experiment again. This time the experiment was slightly changed. The content that was put in each test tube was the same except that for every 1 drop of chloroplast we would add 3 drops of water  to try to dilute the chloroplast. This took place in test tubes 1-4. It did not happen in test tube 5 because it had no chloroplast in it. Everything else in the experiment was the same like the process of measuring with the spectrophotometer. 

                                                    Zero minute mark 

                                                      Five minute Mark 

                                                Ten minute Mark 
                                                    Fifteen minute mark 
                   Test tubes with Solutions 
             Cuvettes Sitting in the Light 

Our group had to perform the experiment twice because of inaccurate data. The first time we ran the experiment, the percent transmittance jumped well past 100% for several cuvettes at the 0 minute mark, which is clearly inaccurate. After having the chloroplast added to the rest of the solution for less than a minute, there shouldn't be that strong of the ratio of intensity of the light that has passed through the sample to the intensity of the light when it entered the sample. This led us to believe that our data was not correct. We believe that the solutions were using up the chloroplast too fast, causing the unreliable data. However, after performing the experiment a second time, we received more accurate data, especially since we deluded the chloroplast with one drop of water per one drop of chloroplast. In cuvette one there was no DPIP added. The data stayed at zero the whole time. Photosynthesis was not able to take place then because there was nothing to act as an electron acceptor, similar to how DPIP would have done. In cuvette two, unboiled chloroplast was added and the cuvette was wrapped in tinfoil, leaving it in the dark. Photosynthesis was not able to occur because the light reactions of photosynthesis need light to take place, but since the cuvette was wrapped in tinfoil, there was no light to provide light energy for the reaction. No electrons were made, and the color didn't change. The transmittance at each 5 minute mark stayed within a three percent range of one another for this particular cuvette for these reasons. In cuvette three, unboiled chloroplast was added, and it was placed in front of the light. The cuvette was placed in front of the light so this provided light energy for the light reaction to take place. This is why the transmittance of this cuvette went up by a total of about 9% throughout the experiment, the most by far of any cuvette in the experiment. In cuvette four, boiled chloroplast was added, and the cuvette had been placed in front of the light. It was hard for photosynthesis to occur in this cuvette because since the chloroplast was boiled, this denatures it. Photosynthesis is not able to take place with unliving chloroplast. This is why the percent transmittance for this cuvette went down. No reaction was able to take place at all. In cuvette five, there was no chloroplast added and the cuvette was not placed in front of the light, however, it was not wrapped in tin foil in the dark either. The percent transmittance stayed the same for this cuvette since there was an absence of chloroplast and light to get photosynthesis going. 
           Since we ran the experiment twice there were two conclusions. As shown in the methods and discussion, The first time we ran the experiment the percent transmittance was over 100 for the cuvettes, which was not what was supposed to occur. We came to the conclusion that we needed to delude the solution in order for the usage of chloroplasts to slow down. In the second experiment we changed the procedure by adding an extra drop of water with every drop of chloroplast. After this slight change the data showed that the percent transmittance was no longer sky rocketing but a gradual increase. The adding of water to delude the chloroplast definitely made an impact on our results and made significantly more accurate. Yay go chloroplasts!


Paper chromatography is used to separate and identify pigments and other molecules in a solution that contain many complex molecules. The paper creates stronger and weaker bonds with certain solutes (molecules). How strong the bond is depends on the solubility of the solute in the solvent. The further a pigment (or molecule) travels up the paper, the more soluble that solute is in the specified solvent and forms weaker hydrogen bonds with the paper itself. 
Carotene forms no hydrogen bonds with cellulose; therefore, it is very soluble in the solvent. Xanthophyll forms hydrogen bonds with cellulose which slows down its progress up the the chromatography paper because it is less soluble.  Chlorophyll contains oxygen and nitrogen which causes it to form stronger bonds with the paper and move up more slowly.
The distance the pigment moved divided by the distance the solvent moved is called the Rf constant. It illustrates the relationship between the two factors.

This lab tries to show how many different pigments are present in a plant through paper chromatography. This allows all the pigments to separate due to their solubility and bonding.  When we calculate the Rf constant we can more easily compare which pigments are more soluble and form certain type of bonds because the distance the solvent moved is already calculated in as a comparison. 

Many materials were used in this experiment, such as filter paper, solvent, cylinder, a coin, and a spinach leaf. As instructed, we cut a 1.5 cm point on the tip of the filter paper and crushed a spinach leaf with a penny in order to extract pigments of the leaf cells. By doing so, a green line of spinach particles appeared near the end of the paper. We then placed the paper into a graduated cylinder, and let it sit until the pigments traveled almost to the top. We removed the filter paper right away and marked the furthest migration with a pencil, then all the others. The Rf was thus calculated from the distance of the pigment of which it traveled.


       Measurement of Migration of Pigments 

      Measuring the Migration of Pigments 

        Spinach Leaf Pigments in Solvent 

In the lab we found that xanthophyll moved the furthest up the paper. Also, it had an Rf constant of one. This shows that this pigment was the most soluble and most polar because it was able to easily travel up the paper with the water.  Carotene was next. It had an Rf factor of .547. Then, chlorophyll A with an Rf of .444. Finally, chlorophyll B with an Rf of .282. We can observe that the closer the Rf factor is to one the more soluble and polar it is because the distance the pigment traveled is closet to that of the distance traveled by the solvent. The separation of pigments in chromatography allows us to examine the different colored pigments present in plants. We can from this predict which light and wavelengths of light will be most absorbed by this plant because the plant will reflect the colors present in the leaf and not absorb as much of them, This means that green, yellow, and orange light will be reflected in some way or form in the spinach leaf. The other from least absorbance to greater absorbance is in the respective order.

         By performing this lab and analyzing its results, our lab group found that the many pigments found in chloroplast take part in the process of absorption of energy from the sun. The filter paper and its color spectrum showed each pigment's solubility from which we measured each pigment's migration


Monday, November 18, 2013

Cellular Respiration Lab

Purpose- The purpose of this experiment is to determine whether germinated or non-germinated seeds had a higher respiration.  We did this by determining the rate of respiration for the non-germinated seeds and then with the germinated seeds before and after having sat in cold water. We used temperature as variable to see if the results would differ.  We also tested glass beads to determine a control between the two.  This lab helped us to understand the process of respiration and what can potentially slow down this process.

Introduction- Cellular respiration is a multi- step metabolic process that produces energy by the oxidation of organic molecules. Humans and animals go though this process. This process is aerobic and anaerobic. Aerobic means it has oxygen and anaerobic means without oxygen. The reason it is anaerobic and aerobic is because one step is anaerobic and the other steps are aerobic.  The process starts with an organic molecule and oxygen and ends with carbon dioxide, water, and energy. An example of this is glucose going through cellular respiration C6H12O2 + 6O2 -> 6 CO2 + 6 H2O + Energy. This is also called a redox reaction. Redox reactions are the transferring of electrons. The name redox comes from a mixture of the 2 things happening in a redox reaction.  One substance in being reduced (gains electrons) and oxidation (losing an electron). The electrons are transferred with coenzymes. NAD+ is the oxidized state and NADH is the reduced state.  Cellular respiration  goes through 3 steps. The first step is glycolysis which is an anaerobic process. Glycolysis end products are 2 ATP and 2 NADH and 2 pyruvate. The 2 pyruvate are oxidized to become 2 acetyl CoA . The next step is called the Krebs or Citric Acid cycle. The Krebs cycle is named after the scientist who discovered it Hans Krebs. This cycle uses the 2 acetyl CoA. This means that this cycle is repeated. After the 2 times the end products are 6 NADH and 2 FAD2.The last step is oxidation phosphorylation it consists of the electron transport chain and chemiosmosis. The electron transport chamber helps gradually decreases the free energy. During this time H+ are being pumped across the membrane and it creates a H+ gradient. In chemiosmosis the flow of H+ helps power  ATP synthesis.Oxidation phosphorylation   creates 26- 28 ATP. After all the steps are complete  it should result in about 30-32 ATPs. In this experiment we will use these concepts to help us understand the CO2 release.

                                                        Glass beads 

                                                 Germinating barley seeds 
                                           Non germinating barley seeds 
                                               Cold germinating barley seeds 
             Germinating barley seeds 
                      Barley seeds

   CO2 chamber- calculated amount of CO2 being produced by seeds and glass beads. 

Methods- We picked out 25 glass beads and 25 barley seeds that were germinated and 25 seeds that were not germinated. The 25 glass beads were used for a control group. We then put 25 glass beads in the respiration chamber. We let the beads the glass beads sit for 10 minutes. After the ten minutes was up we started to take measurements of CO2, with a device that measures CO2 contents.  We recorded the data on our Vernier Lab quest . Next we performed the same steps from the glass beads to the germinating Barley seeds, non germinating barley seeds. Except the  germinating barley seeds that have been placed in a cold ice bath for ten minutes. 

Discussion- Germination causes a higher rate of respiration than the non-germinating peas. This is because a seed needs to have optimal conditions in order for it to germinate. These conditions are met through cellular respiration which provide the correct amount of energy for these reactions to occur. Non-germinating seeds are "dormant" and their energy is stored (this is why nuts and seeds have so many calories); therefore, they don't need as much energy to perform vital processes. The beads served as a control group because no cell respiration occurred. This allowed for certain factors such as pressure to be accounted for without having to directly control it.

Lower temperature slows down the respiration process. The rate at which a reaction occurs, increases with higher temperatures. The higher the temperature of a solution, the faster the molecules are moving in solution. There are more collisions between reacting molecules, and more of those collisions have the necessary kinetic energy required to break bonds and perform necessary function. Respiration is a chemical reaction that breaks down glucose into carbon dioxide and water, so it works in the same way. The higher the temperature, the more kinetic energy because of the molecules moving around, the more cellular respiration can occur.

Not maintaining a constant temperature in the water bath could have caused inaccurate results. Keeping the cold, germinating seeds at a constant temperature would've made the experiment more accurate. Putting the respiration chamber in an ice bath would be a good idea. 

Conclusion- We concluded from the lab that germinating peas that have been at room temperature or in a cold ice bath have a higher rate of cellular respiration. This is because when plants germinate, they are coming out of the seeds as sprouts and beginning to grow, thus needing to use up more oxygen. Seeds that are not germinating do not need as much oxygen because they are not beginning to grow. The germinating seeds that were placed in the cold ice bath had a slightly slower rate of cellular respiration than the germinating seeds at room temperature because the cold temperature slowed it down. The rate of respiration is faster in warmer temperatures. 

References- References- http://en.wikipedia.org/wiki/Germination