Spring 2010

Cellular Energetics- Photosynthesis, Cellular Respiration and Fermentation

Given Thursday, April 15, 2010 in class

You and a partner will be given a opportunity to make a poster showing the biochemical pathway of photosynthesis or cell respiration with

fermenation (humans) You should be prepared for either pathway and you will find out your partner at the beginning of class.

Assignment: You and an assigned partner should quickly prepare a detailed, colorful display that shows the complete pathway of either

photosynthesis or cell respiration/ fermentation. You should attempt to include as many terms and diagrams of the concepts from the list given below.

Photosynthesis- Overall structure of the leaf, stomata, layers, gas exchange, Overall structure of the chloroplast- stroma, thylakoid,  The complete light

reaction including the photosystems that harvest light, ETC, H+ gradient, ATP Synthase and NAPD+ and NADPH. You should show the structure of the

thylakoid membrane. The complete connection between the products of the light reaction and the dark reaction. The Dark Reaction- carbon fixation,

rubisco, glucose, intermediates. You will need to show the summary reaction for photosynthesis. You should include small paragraphs of text to

explain major concepts. Your diagrams should be clear, easy to follow and well layed out and

colorful.

Cellular Respiration- Summary reaction of Cellular Respiration, All three phases of cellular respiration- Glycolysis, Krebs, and ETC Chain including where

they occur. You do not need to include all the intermediates for any reaction but be sure that the begining and end molecules are present and labeled.

You should include text for each and the label where the reactions occur in the cell. Your diagrams should be clear, easy to follow and well layed out and

colorful.

You will not be allowed to bring any materials to the actual test

Cell Parts, Membrane Dynamics, Enerygy, and Enzymes

Essay Test Monday March 8, 2010

1. Membranes are important structural features of cells and vital for the process of cellular respiration and

photosynthesis. The proteins embedded in membrane as well as the properties of selectively permeable

are of considerable importance to the processes of cellular energetics. Thoroughly describe the role of

membranes in the synthesis of ATP in either cellular respiration or photosynthesis.

2. Describe the fluid-mosaic model of a plasma membrane. Discuss the role of the membrane in the

movement of materials through by each of the following processes. a. Active Transport b. Passive Transport c. Facilitated diffusion.

You should have at least one example of each type of transport.

3. A laboratory assistant prepared solutions of 80 g/L, 60 g/L, 40g/L, and 20 g/L sucrose, but forgot to label them.

After realizing the error, the assistant randomly labeled the flasks containing these four unknown solutions

as flask A, flask B, flask C, and flask D.

Design an experiment that the assistant could use to determine which of the flasks contains each of the four

unknown solutions. Include in your answer

                    (a) a description of how you would set up and perform the experiment;

                    (b) the results you would expect from your experiment

                    (c) an explanation of those results based on the principles involved.

5. Plant and animal cells are very similar; however, there are several key differences. Yet these cells are

very different from prokaryotic (archea and eubacteria- or regular bacteria) cells. Explain how all cells are

basically structurally related and how they are related to each other through evolution. Contrast the prokaryote

cell model to the eukaryotic cell model and finally discuss the divergence of plant and animal cells structure

and function.

Friday January 29 2010

Biochemistry Essay/ Hands on Portion

You and your partner (to be assigned the day before the test) will be responsible for creating a model of the structure assigned to you.

The molecule will be assigned randomly the day of the "test"

The molecules will be chosen from the following list.

1. one molecule of chitin

2. aspartame (a dipeptide)

3. Sucralose ( a chemically modified sucrose)

4. an alpha glucose and a beta glucose

You and your partner will need to (rapidly) build the structure and answer several questions on the structure you have been asked to build.

You are welcome to bring in any supporting material that you feel necessary to help you build the structures but remember you will not know your

group's assigned structure ahead of the class designated for building the model. You will need to research ALL of the above structures ahead of class.

You are encourage to share and discuss your questions with all bio students ahead of Build day.

Some possible questions on your molecule may include:

  Draw a bond line structure of your molecule

  What is the biological significance of your structure? 

  Is your structure derived from naturally occuring structure? How is your molecule altered?

  What catagory of Macromolecule is your structure a member of? or derived from?

10 points can be earned for the correct model

10 points can be earned for the correct answers on handout.

Semester Exam

June 2009

PartI -group work with mutiple choice

Part II - group work with mutiple choice

Part III- Teacher Individualized Portion of the Exam/ Short Answer

Directions- I will be choosing 4 of the following questions for the individual portion of the final exam. Similar to the tests given this

year you will NOT be permitted to use notes or materials during the test.

1. Traditional cancer chemotheraphy agents (chemicals/drugs used to kill cancerous cell) such as Taxol also have detrimental effects on healthy cells

in the body. These drugs especially have a profound side-effect on epithelial cells lining the gastrointestinal tract such as the esophagus and intestines.

Why would cancer chemotherapy agents have these side-effects on healthy epithelial cells? Explain based on your understanding of the mechanisms

and functions of cell division.

2. Skeletal muscle cells are multi-nucleated. In your own words, describe what processes must go on inside a cell for it to become multi-nucleated.

(Hint: each nuclei is complete and contains the normal number of chromosomes) Think about what processes must be going on and what processes

must NOT be going on. Your answer should include relevant terms and concepts discussed in class.

3. Slight heating is often enough to render many proteins nonfunctional. But a polysaccharide such as starch must literally be boiled in acid before

it is significantly affected. Explain why.

4. You learned in your textbook that cells have an effective “maximum size” because as the size of the cell increases, the ratio of surface area to volume

decreases. (1) Why is a low surface area to volume ratio a disadvantage for a cell. Explain in your own words. (2) We talked about the unique structure

of the inner membrane of the mitochondria. This structural advantage is related to the first part of this question. Explain.

Why is this “structure” an advantage?

5. You place 10g of glucose, 3 grams of yeast, and 200mL of water into a flask and cover the top with an airlock attached to a rubber stopper.

Yeast is capable of metabolizing glucose. You produce three such setups and incubate them at three different temperatures: 4°C (the temperature

of a refrigerator), 22°C (room temperature), and 37°C (body temperature). You count the number of bubbles being generated per minute after an in

initial 10 minute incubation which was repeated two more times at 20 and 30 minutes. Describe what you expect to see under these conditions.

Explain your reasoning for your description.

6. We discussed in class how UV radiation can affect the structure of DNA so that enzymes would not be able to recognize the nucleotide sequence properly.

What is a possible consequence to replication if DNA damaged by UV radiation goes unfixed? In your answer, make sure you describe the specific enzyme(s)

that might be affected. Make sure that your answer provides specific details... “UV radiation can cause cancer” is NOT acceptable.

Directions:

You will be be completing a few of the following as part of a future essay test in class.

Please review the questions carefully and plan your answer using your notes and

additional resources.You are encouraged to do all of the essays with solid answers

before the test. You are welcome to discuss the answers with your classmates.  You

will not be permitted to bring in any of your prepared work to the exam.

Essay Test #3

1. Creating concept maps is a very effective method to conceptually and visually organize the

relationship between multiple concepts and ideas.  Concepts maps connect individual ideas

with each other, highlighting its relationship and connections.  See the example below: 

Create a concept map using the following set of key concepts discussed in class. 

The descriptions should be limited to a SINGLE sentence connecting the two concepts. 

There can be multiple arrows pointing to each concept, but ALL listed concepts should

be tied together into a single map. Diagrams are not appropriate answers for this question. The terms

below are NOT listed in any particular order and can be arranged in any order for your answer.

            DNA, nucleus, chromosome, mRNA, tRNA, rRNA, transcription,

      ribosome, promoter, codon, translation.

2.   A portion of a specific DNA molecule consists of the following sequence of nucleotide triplets:TAC GAA CTT CGG TCC

What is the polypeptide that is coded for by this amino acid chain. Describe the steps in the synthesis of this polypeptide.

What would be the effect of a deletion or an addition in one of the DNA nucleotides?What would be the effect of a

substitution in one of the nucleotides?

3.   You and your colleagues have recently identified a protein that when found in a mutated form may cause cancer.

You have been able to successfully determine the primary structure of the protein (the * is the end of the protein corresponding

with the stop codon)

              1 mmnvnavyae kcvtpdeavt litsgshlsm gmfaaeppal lnalakrakr geindlrvyc

         61 yetasiagnt ifryelsdyi hlysmvspmd kygyfnfgig ndystriart akklivevnk

        121 ymprvhgega aihiseidai venhvpliel pirtavaedi aisqiiaslv pdgaclqmgv

        181 galpelicna l*

After determining the protein’s primary structure, your colleagues suggested that they would be able to determine the

entire and continuous DNA sequence that encodes the protein.  You quickly point out that this would probably be

very difficult or even impossible for two different reasons.  What are they?

As you continue your research, you find a protein that functions very similarly in two other tissue samples. 

Interested to see if these proteins are similar in structure or not, you quickly determine their primary sequences as well:

You carefully analyze and compare the primary structures of the three proteins and notice obvious similarities

but you find that they are not identical. 

         1 mmnvnavyae kcvtpdeavt litsgshlsm gmfaafitgi eralirqgie ssgrkivnyv              

       61 psnfhqatrl laddigidtf ihtvspmdky gyfnfgignd ystriartak klivevnkym

      121 prvhgegaai hiseidaive nhvplielpi rtavaediai sqiiaslvpd gaclqmgvga

      181 lpelicnal*

        1 mmnvnavyae kcvtpdeavt litsgshlsm gmfaaeppal lnalakrakr geindlrvyc

       61 yetasiagnt ifryelsdyi hlysmfitgi eralirqgie ssgrkivnyv psnfhqatrl

      121 laddigidtf ihthiseida ivenhvplie lpirtavaed iaisqiiasl vpdgaclqmg

      181 vgalpelicn al*

You report your findings to your colleagues.  They immediately suggest that the three proteins must be encoded

by three separate genes that belong to a single gene family (a closely related set of genes with similar structure

and function).  They suggest that some mechanism regulates these genes so that just one version is expressed in the

different types of tissues you analyzed. 

You quickly provide another explanation based on your understanding of gene regulation in eukaryotic organisms. 

What is this alternate explanation?  Describe the possible relationship between these three proteins by highlighting

their similarities leading to your conclusion.  Draw a simple schematic of the gene(s) encoding these proteins

to support your answer.

4. Given the following results from your transformation plates:

Plate 1 (LB only/+ plasmid)- lawn growth

Plate 2 (LB only/- plasmid- lawn growth

Plate 3 (LB/AMP/+ plasmid)- no growth

Plate 4 (LB/Amp/-plasmid)-no growth

Plate 5 (LB/AMP/ARA/+ plasmid)- colony growth

Plate 6 (LB/Amp/ARA/- plasmid- no growth

Draw a plasmid that would work given the above results. Label the regions of your plasmid carefully and include

text to explain what different areas on your plasmid represent.

Essay Test #2 - Cell Structure, Cell Dynamics, Cellular Respiration Friday, March 13

1. Membranes are important structural features of cells and vital for the process of cellular respiration and

photosynthesis. The proteins embedded in membrane as well as the properties of selectively permeable

are of considerable importance to the processes of cellular energetics. Thoroughly describe the role of

membranes in the synthesis of ATP in either cellular respiration or photosynthesis.

2. The results below are measurements of cumulative oxygen consumption by germinating peas in different temperatures.

Time (minutes)                                   0      10       20       30       40

22o C Germinating Seeds                  0.0     8.8     16.0     23.7    32.0

10o C Germinating Seeds                  0.0     2.9     6.2       9.4      12.5

                     a. Plot the results for the germinating seeds at 22o C and 10o C. Construct your graph carefully.

                     b. Calculate the rate of oxygen consumption for the germinating seeds at 22o C, using the time interval

                         between 10 and 20 minutes.

                     c. Explain the difference in oxgen consumption between the peas in different environment 1) germinating

                         seeds at 22o C and at 10o C.

3. Describe the fluid-mosaic model of a plasma membrane. Discuss the role of the membrane in the

movement of materials through by each of the following processes. a. Active Transport b. Passive Transport c. facilitated diffusion

4. A laboratory assistant prepared solutions of 0.8 M, 0.6 M, 0.4 M, and 0.2 M sucrose, but forgot to label them.

After realizing the error, the assistant randomly labeled the flasks containing these four unknown solutions

as flask A, flask B, flask C, and flask D.

Design an experiment that the assistant could use to determine which of the flasks contains each of the four

unknown solutions. Include in your answer

                    (a) a description of how you would set up and perform the experiment;

                    (b) the results you would expect from your experiment

                    (c) an explanation of those results based on the principles involved.

5. Plant and animal cells are very similar; however, there are several key differences. Yet these cells are

very different from prokaryotic (archea and eubacteria- or regular bacteria) cells. Explain how all cells are

basically structurally related and how they are related to each other through evolution. Contrast the prokaryote

cell model to the eukaryotic cell model and finally discuss the divergence of plant and animal cells structure

and function.

Essay Test #1- Biochemistry given Wednesday January, 28th

1. You have overheard your parents discussing your Dad's high cholesterol. His doctor has recommended that he go on the drug Lipitor to help

manage the cholesterol. You walked in to the kitchen as your you hear your father say "I don't understand what it means when the doctor says

I have have I high cholesterol. I eat right and excersise. I wish someone would explain to me what it really means when my doctors tell me I

have high cholesterol and explain exactly how Lipitor works to control it!"  You chime in that you can!

Explain what cholesterol is, it's role in the body, and what are the possible causes of high cholesterol. (life style and dietary).

What are the health concerns for someone with "high cholesterol'? Research Lipitor and try to discover is mechanism of action.

2. The following diagram shows the active site of an enzyme (G-Protein) with a molecule of GDP in it. Notice the exposed sidechains in the enzyme’s active site.

Imagine that you can induce mutations (change the amino acids) in the binding pocket of the G-protein shown above, and hence change the sidechains that line the active site.

 If Asp is mutated to a Proline, the result is a G protein that cannot bind its substrate, GDP.  Explain why. (Hint: You many need the amino acid sheet.)

 Include in your discussion how all levels of protein structure may be changed by this mutation.

 3. Macromolecules- monomers to polymers to function. Discuss the biological importance of each of the following organic compounds in relation

 to cellular structure and its function in cellular metabolism. Include example of how their structure is related to their role and function.

     a. Carbohydrates

     b. Proteins

     c. Lipids

Essay Test #2

1. The Lock-and-Key Model of enzyme-substrate interaction is a fairly strong analogy to describe how enzymes interact with their substrates.

Explain this model using a specific enzymatic reaction discussed in class. Discuss examples of how the following may effect the enzyme substrate

interactions.        

  a. pH shifts                                  

  b. Temperature shifts                                  

  c. Non-competitive inhibition