pH and Yeast. uh oh

Abstract: 

In this experiment, my partner, Chris Jung, and I explored the effects that pH had on the cell respiration of yeast. We altered the pH of 3 different yeast/water/glucose solutions, while keeping a control solution. Thus, we ended up with one acidic solution with a pH of 1-2, our control at a pH of 7, and two basic solutions with a pH of 8 and 9. We measured the rate of cell respiration by the amount of CO₂ created. The results showed that the optimum pH for the cellular respiration of yeast is more acidic than basic, and is closer to 7 than 1 or 2.

Background:

            Cellular Respiration is a process that is essential to all life. Through cell respiration, ATP is captured from the chemical energy released after digesting foods like carbohydrates, fats, and proteins.

The process of Cellular Respiration uses the fuel of glucose/fructose/galactose and oxygen to create carbon dioxide, water, and 36-38 ATP, which is then used to normal bodily functions. This can be seen in the chemical formula, C6H12O6 +6O2 → 6CO2 + 6H2O + 36-38 ATP.

            There are three parts to Cellular Respiration: Glycolysis, Krebs cycle, and oxidative phosphorylation. In glycolysis, which occurs in the cytosol of the cell, the 6 carbon (glucose/fructose/galactose) is broken down, through the investment of 2 ATP, into 2 three carbon chains a.k.a pyruvate. The pyruvate molecules are then oxidized and both lose one Carbon in the form of Carbon Dioxide. These 2 two carbon chains, acetyl coA, are then taken into the matrix of the mitochondria to participate in the krebs cycle. Here, NADH and FADH₂ are formed and carry electrons off to the Christae and Electron Transport Chain. In this last phase of Cellular respiration, the electrons are transferred through carriers from one protein to another, with oxygen being the final acceptor. Each time, hydrogen is attracted and led out the membrane. Eventually, a higher concentration of Hydrogen is formed on the outside compared the inside. This group of protons goes through chemiosmosis, and is pumped through the membrane by the ATP synthase. Once pumped through, the hydrogen join oxygen to create water. The energy released during this process is used to form ATP.

            However, we know that because yeast is unable to go through aerobic respiration, it goes through fermentation a form of anaerobic respiration. In fermentation,

C6H12O6 (glucose) → 2 C2H5OH (ethanol) + 2 CO2 (carbon dioxide),

Glucose is changed into energy, with ethanol and carbon dioxide as the waste products. In yeast, there the enzyme zymase is responsible for breaking glucose anaerobically to ethanol and CO2.

Hypothesis: 

Because yeast is able to go through cellular respiration in solutions with plain water, the farther away the pH in a yeast solution is from 7 the slower the rate of cellular respiration will be. Out of all our experiments, our control will have the best results.

Materials:

·         4 test tubes

·         Salt

·         Glucose

·         Yeast

·         Warm water

·         4 test tube stoppers with holes and pipes in them

·         4 syringes that connect to the test tubes pipes

·         Timer

·         Test tube rack

·         HCL

·         NaOH

Procedure:

1.      Before you start, collect the 3 solutions that your teacher so kindly created for you, because you were too slow. These solutions should then be labeled with their appropriate pH levels: 1-2, 8, and 9. These solutions were created by a mixture of water and HCL or NaOH.

2.      Collect 4 test tubes and label them, 1, 2, 3, and 4.

3.      Fill each test tube with 1 gram of yeast and 1 gram of salt each.

4.      Fill test tube # 1 with 35 mL of warm water

5.      Fill test tube #2, with 35 ml of the solution with a pH of 1-2, test tube #3 with 35mL of the solution with a pH of 8, and test tube 4 with 35 mL of the solution with a pH of 9.

6.      Connect each test tube with a stopper, tube, and a syringe.

7.      Make sure each syringe is starting around 2.0 ml

8.      Wait 5 minutes for the process of cell respiration/fermentation to begin.

9.      After the 5 minutes, every minute measure the amount of CO2 produced.

a.       To measure how much CO2 is being released, push down the syringe, then wait for it to rise, and read the new number.

10.  Do this for 10 minutes, or as long as you can to get some clear results.

Results:

Time (min) \ pH	7 (control)	1-2	8	9
1	2.3	2.4	2.0	2.1
2	2.4	2.2	2.2	2.4
3	2.4	2.0	2.4	2.4
4	2.5	1.9	2.5	2.4
5	2.6	1.2	2.6	2.4
6	2.8	0	2.6	2.4
7	2.9	0	2.8	2.6

All four lines should have started 2.0 and should have continued to 7 minutes. There were some technical difficulties.
The Title of this chart is effects of pH on production of CO2

Conclusion:

            In this experiment, the pH of the environment of the yeast was changed. The results matched my hypothesis. Because of fact that yeast can release carbon dioxide normally with simple tap water already, it was hypothesized that the amount of co2 produced would be greatest the closer to the pH of 7, like our control.

            The results show that our control, the yeast solution made with only water (pH of 7), had the greatest amount of carbon dioxide emission. Solution 3 and 4 had the next greatest amounts of CO2 emission, in that order. This makes sense seeing as how solution 3 (pH of 8), which is closer to solution 1 in terms of pH instead of solution 4, had a greater emission than solution 4. Solution 2, with a pH of 1, had the lowest amount of emission; in fact, there was absorption of CO2 apparently. This, however, may have been a result of a leak. Still, if it was intentional, it makes sense, for the enzymes in the yeast, zymase, was denatured, and forced into a habitat  far from its optimal level.

            After some research, I found that the optimal pH level for zymase is 6 (5-7), proving the results of my experiment. Though there were many small errors in my lab report, like not capping the test tubes immediately, the results were still able to be conclusive, and accurate.

            For future experiments, I would hope to use more solutions, one for the pH levels of 1-14. I would also like to take measurements every 10 minutes, for I had run out of time during this experiment. 

Forensics Quiz

Situation: A twenty -year old man was found supine on Thompson Creak Trail (really nice. in Claremont) with a bullet wound. The entrance of the wound was on the left lateral side 1 cm above the third rib. The exit wound was 5 cm above the belly button in the umbilical region. while tracing the bullet path you notice at the entrance the bullet travels in the frontal plane with a 45- degree downward angle. On inspection of the right side of the rib cage by x-ray you observe the 8th rib fractured. Fragments of the bullets are then traced to the final exit wound. What is the leading differential diagnosis (and why) and what are three plausible alternatives and how would you rule them out?

Leading Differential Diagnosis: The man was killed due to internal bleeding and extensive damage to  the heart, which was punctured by the bullet as it bounced off the 8th rib and exited out above the belly button.

Alternatives:

1. The bullet punctured both lungs creating a hole in both. This causes air to enter the body through the entrance wound, causing a change in pressure, and thus the lung collapsing. New air is not allowed to enter the lungs, causing shortness of breath and eventually death. You could rule this out because of the fact that the bullet exited 5 cm above the belly button, meaning it would be improbably that they bullet punctured both lungs.

2. The bullet punctured the stomach and small intestines, causing a serious infection from fecal matter leaking out into the body. Also death from extensive bleeding.

3. The bullet hit the 8th rib, bounced to the spinal chord, broke it, and then back out through the belly button. The man then continued to bleed internally and externally.



                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          

Animals (Monohybrid and Dihybrid) Crossing

A Monohybrid Cross is a cross between  two parents that involves only one trait.
For example lets take a cross between a heterozygous mother and father for the height trait.
 Tall = T short = t

In the end you would use a punnet square, and cross the genotypes.
You would end up with a 25% chance for a genotype offspring of TT, 50% chance for a genotype offspring of Tt, and 25% chance of a genotype offspring of tt.
You would have 75% chance of having a phenotype/appearance of a tall kid, and 25% for a shortie, like me.

DiHybrid Cross is when you cross two parents and you are mixing two traits.
For example you are mixing a mother who is heterozygous round and heterozygous yellow. (RrYy) and a father who is the same.
R=round seed, r=wrinkled seed, Y= yellow, y= green

First you would have to come up with all possible combinations in the genotypes of each parent.
Eg. RrYy, if you chose two letters at random, could be RY, rY, Ry, or ry.
so you match those 4 options with the 4 you get from the father and you end up with a possibility from 16 offspring.
In this case the resulting genotype ist 9/16 RRYY, 3/16 RRyy, 3/16 rrYY, and 1/16 rryy
for genotype its 9 yellow round, 3 green round, 3 wrnikled yellow, and 1 wrinkled green.

Thats Monohybrid and DiHibrid Crossing.

Operon System

An Operon System can either be repressible or inducible.

Inducible Operon System

Repressible Operon System

DNA Reptile. (Replication)

DNA replication is a process where DNA replicates itself.
There are many enzymes that help in this process.

Helicase- The scissors in the group.
Starting from the Origin of Replication (the starting point) Helicase, (In class we used a yellow triangle to represent Helicase. You can do this if you need some visual aids) breaks down the Hydrogen bonds that connect the two bases.
It does this to unwind the double helix, and prepare a single stranded DNA replication.

Then RNA primase comes on and places rna pairings to the single stranded dna. For example, if you had a strand that read CTAG, the RNA paired with it would be, GAUC, with the Thymine being replaced with Uracil. 

It does this to allow DNA Polymerse III the ability to read the strands, because it places rna which has a 3' OH base, which DNA polymerse III can read. 

DNA polymerse III then comes in and reads the strand of RNA and creates the complementary nucleotides. Each new base forms phosphodeister bonds. 

DNA Polymerse I then replaces the rna with the newly created bases. 

Ligase glues all the okazaki fragments together. 

DNA Structure

According to Wikipedia, Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. 
Basically, DNA is our human code. It makes us, us. Every cell in our body has the same DNA in it. 

DNA is usually in a shape of a double helix, and has two strands running in opposite directions. (5' - 3', and 3' - 5')

There are 4 bases, Adenine, Thymine, Guanine, and Cytosine. A goes with T and G goes with C to form base pairs. Each base is connected to the sugar phosphate backbone. 

Day 18 DNA!!

1. Explain the significance of Mendel. 
Gregor Mendel's experiment of breeding pea plants showed that traits from parents are present in the offspring. His tests supported Darwin's theory of "blending inheritance." It was later proved that the changes in the pea plants were due to the changes in the DNA through generations.

2. Draw the structure of DNA and who discovered this structure.

James D. Watson and Francis Crick discovered the structure of a double helix. 

3. Explain each of the five examples of variations that occur to DNA and give an example of each.
 a. Point Mutation - a single base pair change. the mutation inactivates a gene for a signaling molecule.
ex. Dogs are moderately more muscular when only one copy of the gene is disabled. 

b. Insertion- when multiple base-pair sequences are inserted into a gene. 
ex. when 800 base-pair sequences are inserted into a pea produces peas that are wrinkled rather then smooth. The intruding DNA disables a a gene necessary for starch synthesis, affecting the sugar and water content. 

c. Gene-Copy number- When you copy errors during cell division to duplicate entire genes.
ex. where the enzyme salivary amylase  is copied 10x more in humans than chimpanzees, making humans the better starch digestors.

4. What is evo-devo?
Evo-devo is a subspeciality in evolutionary biology that concentrates on studying the effects of changes in important developmental genes and the role they play in evolution. 

5. Make a connection between human migration and the mutation of lactose intolerance.

Day 17- Traces of a Distant Past

Traces of a Distant Past is all about how DNA gives us a clearer picture of the multimillennial trek from Africa all the way to the tip of South America. It goes on to explain the multiple studies over the differences of human genome from person to person. Almost all DNA, at least 99.9 percent of it, is the same from person to person, but by studying the differences in the last .1 percent, scientists are hoping to uncover clues about the journey our ancestors ventured on from continent to continent. 

Only recently have scientists began widening their focus range from only a few isolated stretches of DNA to study hundreds of thousands of nucleotides scattered throughout the genome instead of just the comparisons between let's say East Africans and Native Americans. Scientists are able to follow the breadcrumbs that were left behind by our ancestors. 

From the video, "Journey of Man", we learned that Y chromosome gives us an opportunity to follow our migratory heritage back to "Adam," just as earlier work in mitochondrial DNA allowed the identification of Eve the mother of all homo sapiens. 

In our Y Chromosomes and our Mitochondrial DNA, scieintists are constantly looking for genetic markers - characteristic patterns of nucleotides - and how they differ from population group to population group. 

After piecing this information together, Scientists are then able to piece together a map of the travels our ancestors took to spread throughout the world. 

(below) 

The difficulties with DNA are that unlike Fossils, the rate of mutation can differ from one strand to another, causing inconsistencies. Yet, fossil remains are too rare, and often incomplete. 

To fill in the missing blanks that DNA and fossils can't clearly fill, Scientists use more DNA from microbes that hitch rides on humans. (ie. lice, bacteria, and viruses) 

Using this information, Scientists have formulated the Out-of-Africa theory. From 50,000 to 60,000 years ago, our ancestors traveled out of Africa, and eventually overtook the Homo Erectus species and converged into once species. Through interbreeding, the species were able to remain one and the same, making us part Neanderthal.

Then there's the multi-regional theory, which states that over the past 1.8 million years ago, that our ancestors evolved from Asia, Europe, and Africa, and eventually emerged as Homo Sapiens. 

The Occasional interbreeding made sure we didn't evolve into multiple species. 

There is evidence that supports interbreeding from both theories, many fossilized skeletons of H. Sapiens have features reminiscent of earlier hominids. Scientists estimate that the two genomes are 99.5 percent alike. Yet studies have shown that the Y chromosones in Neanderthals differed from ours.

Scientist would like to use this information and these theories to claim that there is no race. We are all brothers to each other, there is no genetic differences, only geographic gradients.