BIOL1060 Lab 3-4: Photosynthesis and Cellular Respiration Lab

Lab 3-4: Photosynthesis and Cellular Respiration

Please copy this page into your word processing software to make a template. Submit this with your responses and images in the template to the appropriate dropbox in the Canvas. You are responsible for filling in responses wherever there is an arrow followed by bold text. If you prefer, you can submit only these items aggregated. I aggregated those prompts at the bottom of this page. 

Learning Outcomes

  • Describe how organisms assimilate and process energy.
  • Investigate the biochemical pathways common to all living organisms.

Materials:

Complete this survey if you haven’t already: BIOL1060 Lab Supply Pick-up RSVP FA19

If you can pick up your supplies, arrange to meet me at office hours as soon as I post that the supplies are here on campus.

If you plan to order your supplies because you are unable to come to campus, please reference the Syllabus for the materials list

Supplies needed
Test tube rack
6 test tubes
bromothymol blue indicator solution
Elodea aquatic plant

Common household items
tin foil
a lamp for a light source
a straw
water
cleaning supplies to clean up your lab area
a way to record time
a camera

Overview

Firstly, to be alive, matter must be composed of cells, so there is that. All organisms have DNA and furthermore, this DNA is composed of the same alphabet- A, T, C, and G, ie adenine, thymine, cytosine, and guanine.

Prokaryotes have no organelles, but they still have DNA in their cytoplasm. All eukaryotes have even more in common. They all have the same organelles, with a few specialized organelles for autotrophs, ie primary producers, that harness energy for all living organisms.

prokaryotic cell

prokaryote photo credit: https://upload.wikimedia.org/wikipedia/commons/thumb/c/c5/Prokaryote_cell.svg/914px-Prokaryote_cell.svg.png 

Eukaryotic DNA is protected in a double membrane nucleus offering two layers for protection. RNA help shuttle the information contained in DNA beyond the nucleus, but the DNA can never leave the nucleus. This is truly amazing. The most important biological material is protected from damage in a fortress called the nucleus.

eukaryotic plant cell

eukaryote photo credit: https://upload.wikimedia.org/wikipedia/commons/0/08/Plant_cell_structure.png 

Throughout evolutionary history, speciation has occurred but these tenets of cellular biology have not diverged. This is what common ancestor theory means. For those who struggle with the ape to man concept, remember that evolution occurs to populations. No ape turned into a man. Yes, we are related in many ways, but no amazing transformation occurred. Rather, it was a slow process in which organisms struggled to survive on the ever-changing planet Earth. Some genetic mutations became favorable and other ceased to exist. As a result, subsequent generations of individuals survived, exploiting different habitats and eventually becoming completely distinct and unique species after many, many generations. But what remains is the fact that on the inside, all species are remarkably similar.

The idea of the Domains Archaea, Bacteria and Eukarya comes in part from our increasing understanding of phylogenetics. The development of the electron microscope (mid 20th century) and genetic technologies afforded the opportunity to categorize organisms according to their evolutionary relatedness, rather than just according to their morphological similarities.

phylogenetic tree

phylogenetic tree photo credit: https://upload.wikimedia.org/wikipedia/commons/thumb/0/0b/PhylogeneticTree%2C_Woese_1990.PNG/1280px-PhylogeneticTree%2C_Woese_1990.PNG 

Woese, Kandler and Wheelis (1990) proposed this evolutionary model of phylogeny called the Three Domain System. It is based on variations in cells’ ribosomal RNA (rRNA), the cell’s membrane lipid structure, and its sensitivity to antibiotics. The variations studied were in the sequences of nucleotides in the rRNA. rRNA are useful to study because they do not change very much over time. Similarities in rRNA indicate relatedness. We will investigate a variety of organisms in this course.

If we can appreciate the great similarities across organisms on planet Earth, we can surely make the leap to understand how all organisms carry out similar chemical reactions to harness and utilize energy. In this lab, we will study photosynthesis and cellular respiration, the chemical processes that harness the energy of the Sun and make it useful to living organisms for growth, repair, metabolism, movement, and reproduction.

We learned a bit about plants is the first lab. To continue that understanding, photosynthesis is a chemical process in which light energy excites electrons in chloroplasts. Chloroplasts are organelles specific to autotrophs including plants and cyanobacteria.  Packets of light energy called photons strike the chloroplasts organelles within autotrophic organisms. Chloroplasts have thylakoids, which are membranous disks stacked together called grana.

photosynthesis diagram

A big take-away here should be preponderance of membranes. If chemicals are not proximity, they can not react. Membranes mediate the passage of chemicals into and out of a cell.

Chemistry Review

Getting back to the photons, they strike these chloroplast membranes and knock electrons out of place. Electrons are negatively charged subatomic particles of atoms, the smallest individual particles of an element. Electrons are the currency of chemical reactions. Relatively speaking, they are extremely small and far away from the nucleus of an atom where the protons and neutrons exist.

Note: We are talking about atoms here, not cells. Cells contains a multitude of atoms. An atom contains protons, neutrons, and electrons, collectively called subatomic particles. Protons give the identity of a element as described in the Periodic Table. If the protons are knocked out of place with energy, this is a nuclear reaction. A photon of light does not contain the energy required to induce nuclear reactions. Therefore we are discussing chemical reactions involving electron interactions.

atom diagram

atom photo credit and for more information: https://www.universetoday.com/wp-content/uploads/2010/02/c-atom_e1-1280×720.gif 

Back to photosynthesis…

When photons dislodge electrons, they induce an anabolic reaction in which carbon dioxide and water, small molecules, are assembled into larger molecules including glucose and other nitrogenous biological macromolecules when nitrogen is added in further chemical processing.

photosynthesis reacton

photosynthesis photo credit: https://upload.wikimedia.org/wikipedia/commons/a/a3/Figure_08_01_04.jpg

Autotrophs capable of harnessing the Sun’s photon energy provide ALL of the energy available to heterotrophs like animals, fungi and protists. Plants evolved first on planet Earth. Photosynthetic reactions are responsible for the oxygen-rich atmosphere that supports other kingdoms of life that consume oxygen.

Cellular Respiration

When a heterotroph inhales oxygen, oxygen’s electrons facilitate the complimentary reaction in all biological organisms- cellular respiration.

Oxygen energizes photosynthetic products like glucose in catabolic reactions that break down molecules. When molecules are broken into smaller molecules, the energy of the broken bonds becomes available and consumed to proceed cellular processes like metabolism, growth, repair, reproduction, and movement. All of these processes are mediated by chemical reactions involving electrons.

cellular respiration

photosynthesis photo credit: https://upload.wikimedia.org/wikipedia/commons/a/a3/Figure_08_01_04.jpg with my own drawing

Chemoautotrophs

In 1984, scientists found chemoautotrophs that evolved near geothermal vents at the bottom of the ocean. In this anoxic environment, oxygen could not possibly facilitate cellular respiration. Therefore, scientists discovered a whole new branch of biological organisms that, like all other organisms, contain cells and DNA and exhibit cellular respiration, but that use an alternate electron receptor instead of oxygen. The chemoautotrophs closest to us live in hot springs. The Archaea of Yellowstone National Park’s geothermal features are subjects of extensive scientific research.

yellowstone pic

photo credit: Speer and Waggoner, 2001

Lab Procedures – Setting up the Experiment

In this lab, you will create an experiment to detect photosynthetic activity in plant material. We will use Elodea, an aquatic plant, as the biological material. Remember that the biological specimen of interest is the dependent variable in experiments and these data are depicted on the y-axis of a graph.

Elodea aquatic plant

Elodea photo credit: https://upload.wikimedia.org/wikipedia/commons/e/ec/Elodea_canadensis.jpeg

The experimental habitat for this lab is a series of test tubes. Set up your test tube rack with six test tubes, each containing a sprig of Elodea, water to fill the test tube, and 5ml of bromothymol blue.

pH Indicator – Bromothymol Blue

Bromothymol blue is an indicator used in experiments where limited range pH detection is required. When carbon dioxide is exhaled from your body into the straw and into the test tubes, it dissolves in the aqueous solution, which becomes  carbonic acid. This chemical reaction releases H+ cations into solution thereby reducing the pH of the solution. In acidic solutions, bromothymol blue turns yellow. In basic solutions it is blue and in neutral solutions it is green.

bromothymol blue

test tube photo credit: https://commons.wikimedia.org/wiki/File:Bromothymol_blue_colors.jpg

Review of pH

pH stands for parts hydrogen. A cup of water at equilibrium is actually a solution of hydroxide anions (OH), H20, and hydronium ions (H3O+) because water auto-dissociates in solution. At equilibrium, pure water has a pH of 7, meaning essentially that all of the ion charges are balanced in solution.

beaker of water

beaker photo credit: https://storage.needpix.com/rsynced_images/lab-309424_1280.png with my writing on it 

The introduction of other molecules to an aqueous solution can affect the pH of the solution. To introduce carbon dioxide, the carbon source with which photosynthetic products are produced, you will exhale through a straw into some of the test tubes.  When you exhale carbon dioxide into the water, the carbon dislodges hydrogen atoms from water molecules in a chemical reaction involving carbon dioxide and water to produce carbonic acid. The addition of free radical hydrogen cations to the solution shift the pH lower. Solutions of pH lower than 7 are acidic solutions. You will know that you have added sufficient quantities of carbon dioxide to the environment (the test tube) when the solution turns yellow. When/if the solution changes color during the experimental observation period, this will be a qualitative indication of carbon dioxide consumed during photosynthetic reactions.

Lab Procedures – Levels of the Experimental Treatment

The biological material is the dependent variable and the components of your experiment are the independent variables, depicted on the x-axis in a graph and usually abiotic. They can be biotic, but I will reserve that explanation for the ecology lab.

The experimental treatment always has at least two levels- the do something treatment (the experimental variables) and the do nothing treatment (the control).

One test tube will be a control, containing only water, Elodea, and the indicator bromothymol blue. Remember that a control is one level of your experimental treatment for which you change no environmental parameters.

The other five test tubes will represent an experiment you design. The fixed points for the experiment include:

1) the control

2) the environmental habitat of test tubes with water/carbonic acid and Elodea

3) you have to blow through the straw until the solution turns yellow to introduce a carbon source by making carbonic acid

4) the two hour observation period

You design the rest. To get your mind working, here are some ideas. You can use one or two of these ideas or come up with your own. Keep in mind that you have only five test tubes for experimental levels. You can not test more than two variables because you have to be able to cross two variables to complete the experimental design. I hope my examples explain that concept.

Ideas for experimental design- choose or design your own

1) Alter the light availability across test tubes. One test tube must get the same light regime at the control. Light availability can be determined by intensity, duration, color, etc. If you want to separate your test tube rack for two light regimes, use cardboard to divide the environments.

2) Alter the carbon dioxide regime. You don’t have to use carbonic acid solution (the solution containing your exhaled carbon dioxide) for every test tube.

Note: if you alter the carbon availability and the light, you need to have levels of your treatment that cross these variables. For example, light/carbonic acid, dark/carbonic acid, light/water, dark/water.

Don’t overthink it! We already know that light and carbon dioxide are required for photosynthesis to proceed. You can’t really do more than two levels/variables without running sequential experiments to test out each treatment level. Be creative, but focus on writing up a descriptive and professional summary of your experiment in the form of a lab report (read more on this below).

Lab Procedures – Data Collection

One fixed point of this lab is the two hour observation time. Whatever experiment you design should be observed for two hours. The observation time and the color change of the solution are the important factors to measure in your data collection effort. Decide:

Will you observe the color change only at the end of the experiment or at interval in between?
How will you quantify the color change?
Will you take pictures?
Will you use a diagram that relates color to pH range?
Will you have a dark/water and light/water control or just a light/water control? Why?

Describe ALL of these details. I am looking for a strong accounting of the process. I am not looking for originality or complexity in the experimental design. no extra credit for extravagant experiments!

You will be most successful if you design your data collection table before you begin your experiment. A simple table might look much like the test tube rack itself:

test tube 1 2 3 4 5 6
control
light
carbonic acid

You could have two tables very similar to this one. The first could describe the experimental levels and the second could organize the data collected. Ask yourself:

–>What goes in the spreadsheet cells if you are describing the design of the experiment? Word, numbers, check marks?

–>What goes into the cells if you are collecting data? Are those data words or numbers? If words, what words will you use for this lab? If numbers, what numbers will you use for this lab? 

–> Copy your data table here.

After you set up your experiment, take a picture with you and your test tube rack set-up. You need to submit at least one photo with each lab to authenticate that you did your own lab work. It’s a selfie. Please include a note card with your name and the date in the photograph. Submit the photograph in your lab report document.

While you wait two hours, observing your experiment along the way, let’s practice writing a lab report and being efficient. A lab report is a simple five paragraph paper that summarizes a scientific experiment. You will need to write a formal lab report at least once this semester about any lab we have completed. For this lab, just keep working through this document and submit only this document.

Answer the following questions:

–> What role does photosynthesis play in supporting life on planet Earth?

–> Do ALL organisms exhibit cellular respiration? Explain. 

–> Write one sentence describing the purpose of your experiment. 

The answers to these two questions plus the purpose statement would suffice in supporting the Introduction (paragraph 1) of a lab report.

Now, describe your methods in as much detail as you can. Use at least enough detail that someone else could complete your experiment after reading only your methods section (paragraph 2 of the lab report).

–> Methods:

Lab Procedures – Data Analysis

At this point, two hours later, your data table should be filled out and you should have some pictures of the process. Now it is time to transform that data into a meaningful summary of the results. We have not employed replicates here, but ideally, your whole experiment would be executed at least three times so you could average the results. An average or mean is a simple mathematical computation that lends reliability to your data. If you repeat the same experiment over and over and get similar results, your data is reliable.

In other words, we can count on the same result occurring over and over again.  In this experiment, we are relying on the fact that we know from countless trials and investigations done by other scientists that 1) photosynthesis occurs and that 2) the chemical reaction requires light energy, water and carbon dioxide. The experiments we design here are validations of these scientific “facts.” I caution against the use of this word “fact”, but I am most certain that photosynthesis occurs exactly as we understand it chemically because at least a century of research confirms it. So in this case, I think we are talking scientific facts.

Other factors not measured

Of course there are many other factors we are ignoring here like nutrition and light frequency, but as you will see throughout the semester, I am most interested in you understanding how to use your mind to construct unbiased experiments of all life’s questions. The experimental process and your reporting of it drive your success in this course. It’s okay if the experiment doesn’t go as planned. Mistakes, unexpected results and stumbling blocks usually result in more learning and understanding in the long run.

Lab Procedures – Make a graph

In the simplest terms, a graph shows two variables. The x-axis depicts the experimental design and the y-axis depicts the biological response. Please make a digital graph that represents your experimental results. It should include

1) a title

2) axes labels

3) an indication of the units employed, for example, time is depicted in seconds (s)

4) data, in the form of bar graphs since each test tube is a unique, disconnected environment from the other test tube environments. These are categorical data. Your bar labels should indicate the conditions in the test tube. The y-axis should indicate pH, as depicted by a color change. So if the solution is green, the bar for that solution should be the height of the “7” on the y-axis. Remember that the pH change is the biological response measurement. We assume that the removal of carbon dioxide from the experimental environment indicates the forward progression of photosynthetic reactions.

–> Copy your graph here: 

Check your understanding with this question:

–> Where did the carbon dioxide go?

Data is reported in the Results section of a lab report. The results section includes tables, figures, and written sentences that describe whatever is in the data and analysis. Your response to this question “Where did the carbon dioxide go?” would initiate your final lab report sections, the Discussion and Conclusion. In these sections, you interpret the meaning of the data results. Finally, you summarize and remind your reader of why you did this experiment. You might also write about how the procedures could be improved, or present ideas for future research.

More on Cellular Respiration

All organisms, including photosynthetic autotrophs use cellular respiration to unlock the energy stored in biological macromolecules assembled by photosynthesis. Cellular respiration is required for the body to do work. Thinking back to physics, matter can never be created or destroyed. The carbon dioxide that was fixed into glucose through photosynthesis is consumed inside of your body to facilitate all the processes that define what is means to be alive- growth, repair, reproduction, metabolism, and movement.

We called oxygen the electron receptor in cellular respiration but what this means in practical terms is that heterotrophic organisms use oxygen to do work in the body. We can re-use our experimental set-up here to look a bit deeper into the production of carbon dioxide as a by-product of cellular respiration.

Lab Procedures – Set up the Cellular Respiration Lab

Once you have your test tubes clean and your Elodea safely stored back in its little aquarium (the Erlenmeyer flask with water) or in your fish tank or returned to me for safe keeping, set out your 6 test tubes once again. Fill them with water and 5 ml of bromothymol blue.

Now you are the biological specimen. You will blow through the straw into the test tubes while at rest (the control), and then immediately after a series of increasingly vigorous levels of an exercise treatment. You design the treatment, just like you did above.

–> Describe your cellular respiration experiment here. Draw a table in which you will collect data.

After each level of the treatment, exhale through the straw into a test tube. Record how long it takes for the solution to turn completely yellow. Do the control first, and work up to the most vigorous level of exercise so you don’t confound the results by having to wonder how long it takes to get back to a resting state.

–> Describe the results of your experiment here. Did your body produce more carbon dioxide immediately after exercise?

–> The amount of carbon dioxide your body produces is a direct indication of what biological process?

Clean up your test tubes one last time and store them for future use.

–> Write 100+ words of reflection about your learning experience in this lab (free-write):

–> Include at least one photo of your experimental set-up or results. The photo is a selfie. It should have your face, evidence of your work, and an index card with your name, the date, and the lab name. 

Do yourself a favor- Now read the next lab …. and if you are really ambitious, you will go right ahead a read (and participate!) in the next discussion. Knowing what you have to do and how you will be assessed is your first step to success. 🙂

References

Speer, B.R. and Waggoner, B. 2001. Introduction to the Archaea: Life’s extremists. UC Berkeley. Retrieved from http://www.ucmp.berkeley.edu/archaea/archaea.html

Woese, C. R., Kandler, O., & Wheelis, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences, 87(12), 4576-4579. http://www.pnas.org/content/87/12/4576.full.pdf?&$NMW_TRANS$=ext

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Aggregated responses. You could copy and submit only this section if you prefer:

Ask yourself:

–>What goes in the spreadsheet cells if you are describing the design of the experiment? Word, numbers, check marks?

–>What goes into the cells if you are collecting data? Are those data words or numbers? If words, what words will you use for this lab? If numbers, what numbers will you use for this lab? 

–> Copy your data table here.

Answer the following questions:

–> What role does photosynthesis play in supporting life on planet Earth?

–> Do ALL organisms exhibit cellular respiration? Explain. 

–> Write one sentence describing the purpose of your experiment. 

–> Methods:

–> Copy your graph here: 

Check your understanding with this question:

–> Where did the carbon dioxide go?

–> Describe your cellular respiration experiment here. Draw a table in which you will collect data.

–> Describe the results of your experiment here. Did your body produce more carbon dioxide immediately after exercise?

–> The amount of carbon dioxide your body produces is a direct indication of what biological process?

–> Write 100+ words of reflection about your learning experience in this lab (free-write):

–> Include at least one photo of your experimental set-up or results. The photo is a selfie. It should have your face, evidence of your work, and an index card with your name, the date, and the lab name.