CHE 211 Study Guide - Midterm Guide: Diethyl Ether, Meat Tenderizer, Toothpick

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13 May 2018

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Experiment Notes (Final)

Isolation of DNA

As you now know, in the cells of all living things are molecules called nucleic acids that provide all the

information needed for cellular replication and growth by directing protein synthesis. There are two types of

nucleic acids; DNA, which carries the genetic code to each new generation of cells, and RNA, which carries the

instructions for a protein to the ribosomes where proteins are synthesized.

Every living organism contains DNA that provides the directions to make proteins for the characteristics of that

organism. The DNA in an onion has a set of instructions to make an onion, just like the DNA in a strawberry or

in a banana contains the instructions to make a strawberry or a banana. Each daughter cell is just like the

parent cell because DNA is duplicated in every cell division.

The procedure is designed to extract only the DNA and leave all the other components of the cell behind. If

you consider the number and types of proteins and lipids found in the cell, it is pretty surprising and quite

interesting that DNA is relatively easy to isolate. The DNA will be isolated by first disrupting the cell walls with

a mixture of shampoo and salt. The salt helps to break open the cell by osmosis. This process is aided by the

presence of the shampoo, which dissolves the outside layer of the cell. Remember the cell membrane is

largely comprised of lipids, which will be washed away just like grease and dirt. Next meat tenderizer will be

added to the mixture. Meat tenderizer is needed to remove up the proteins, which hold the DNA tightly coiled

inside the cell and destroys the enzymes, which break DNA into small pieces. We want the DNA to be long

stringy strands so it will wrap around a toothpick or chopstick. When the DNA leaks out of the broken cell, it

can be precipitated out of the mixture by adding rubbing alcohol. The DNA is not soluble in the alcohol.

Because DNA molecules are long polymer chains, they tend to bind together when they are precipitated and

will resemble eggs whites. The isolated strands of DNA can be wrapped around a toothpick or chopstick.

Alcohol Fermentation

◼ The starting reagents are Acetaldehyde, Diethyl Ether and Sodium Borohydride (catalyst)

◼ The starting time is 6:45pm; The first sign of the product is after 1 minute; all the starting material is gone after

around 52 minutes; +1 minutes, +10, +10, +10, +10, +10 and 1+ minutes

◼ After all the starting product is gone; we are then going to extract it with water; the diethyl ether organic layer is

at the top and the aqueous layer is at the bottom containing ethanol and water

◼ The temperature on the distillation apparatus read 25 degrees Celsius before the distilling process

◼ The distillation process started at 10:35pm; after 1 minute, temperature reads 35.6 degrees; after 2 minutes, it

reads 46.2 degrees; after 3 minutes, it reads 51.5 degrees; 4 minutes = 67.4 degrees; after 5 minutes, it reads

72.7 degrees; 6 minutes = 78 degrees

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◼ After 6 minutes is when I first see the distillate in the collection flask; it takes about 35 minutes for the entire

product to be distilled

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Document Summary

As you now know, in the cells of all living things are molecules called nucleic acids that provide all the information needed for cellular replication and growth by directing protein synthesis. There are two types of nucleic acids; dna, which carries the genetic code to each new generation of cells, and rna, which carries the instructions for a protein to the ribosomes where proteins are synthesized. Every living organism contains dna that provides the directions to make proteins for the characteristics of that organism. The dna in an onion has a set of instructions to make an onion, just like the dna in a strawberry or in a banana contains the instructions to make a strawberry or a banana. Each daughter cell is just like the parent cell because dna is duplicated in every cell division. The procedure is designed to extract only the dna and leave all the other components of the cell behind.

Related Questions

Biochemistry Review Questions

What is the classification of the compound shown here?

A) an aldohexose B) a ketohexose C) an aldopentose D) a ketopentose

2. In a disaccharide, the CâO bond that joins the two rings together is called _____.

A) a hemiacetal B) a glycosidic linkage C) an alditol D) an anomer

3. What is the structure of amylopectin?

A) unbranched skeleton of glucose molecules joined by 1ï®4-ï¡-glycoside linkages

B) branched skeleton of glucose molecules joined by 1ï®4-ï¡-glycoside linkages

C) unbranched skeleton of glucose molecules joined by 1ï®4-ï¢-glycoside linkages

D) branched skeleton of glucose molecules joined by 1ï®4-ï¢-glycoside linkages

4. In a disaccharide, the CâO bond that joins the two rings together is called _____.

A) a hemiacetal B) a glycosidic linkage C) an alditol D) an anomer

5. Which type of linkage between the two rings is in the structure shown?

A) 1Â®4-b-glycoside linkage D) 1Â®1-a-glycoside linkage

B) 1Â®4-a-glycoside linkage E) 1Â®2-b-glycoside linkage

C) 1Â®1-b-glycoside linkage

6. What is the structure of cellulose?

A) unbranched skeleton of glucose molecules joined by 1Â®4-a-glycoside linkages

B) branched skeleton of glucose molecules joined by 1Â®4-a-glycoside linkages

C) unbranched skeleton of glucose molecules joined by 1Â®4-b-glycoside linkages

D) branched skeleton of glucose molecules joined by 1Â®4-b-glycoside linkages

7. Which amino acid is a basic amino acid?

A) serine B) arginine C) cysteine D) alanine E) valine

8. What monosaccharide is found in cellulose, starch, and glycogen?

A) glucose

B) galactose

C) N-acetyl-D-glucosamine

D) fructose

E) More than one of the monosaccharides above is found in cellulose, starch, and glycogen.

9. Which is not a reducing sugar?

A) glucose B) fructose C) sucrose D) galactose E) an aldopentose

10. Sucrose contains one _____ unit and one _____ unit.

11. What is the particular sequence of amino acids of a protein that are joined together by peptide bonds called?

A) the primary structure of a protein C) the tertiary structure of a protein

B) the secondary structure of a protein D) the quaternary structure of a protein

12. What is the charge on an amino acid at a pH below its pI?

A) positive

B) neutral

C) negative

D) The charge or lack of charge varies depending on the amino acid.

13. What is the C-terminal amino acid in the tetrapeptide glycylalanyisoleucylmethionine?

A) alanine B) glycine C) methionine D) isoleucine

14. How many different dipeptides can be formed when one valine reacts with one glycine?

A) 1 B) 2 C) 3 D) 4

15. What is the process of altering the shape of a protein without breaking the amide bonds that form the primary structure?

A) hydrolysis B) competitive inhibition C) denaturation D) oxidation

16. Which of the following compounds is an enzyme?

A) glucose C) N-acetyl-D-glucosamine

B) triosephosphate isomerase D) dihydrofolate

17. What is a zymogen?

A) an amino acid with a neutral charge

B) inactive precursor of an enzyme

C) a molecule that causes an enzyme to lose activity

D) a nonprotein organic molecule needed for an enzyme-catalyzed reaction to occur

18. Which of the following will the cause the rate of enzyme activity to first increase and then level off?

increasing the enzyme concentration

increasing the temperature

increasing the substrate concentration

increasing the pH

19. Which of the following make up a nucleoside?

base + sugar

base + phosphate + sugar

base + phosphate

phosphate + sugar

20. Transcription corresponds to which of the following?

the separation of the two strands of DNA to enable the formation of two identical DNA molecules

the transfer of genetic information from DNA to RNA

the transfer of genetic information from RNA to DNA

the use of genetic information to synthesize a specific protein

21. Each individual tRNA contains _____

A) a base sequence that is identical to the informational strand of DNA.

B) the sequence of codons that determines the order of amino acids in the protein.

C) an anticodon of three nucleotides that is complementary to the codon in mRNA and identifies individual amino acids.

D) an anticodon complementary to any of the three stop codons.

22. Where does energy production occur in animal cells?

A) cell membrane B) cytoplasm C) mitochondria D) nucleus

23. How many molecules of CO2 are produced for each turn of the citric acid cycle?

A) 0 B) 1 C) 2 D) 3 E) 4

25. Which is not a reaction found in stage [2] of catabolism?

A) fatty acid oxidation C) oxidative phosphorylation

B) glycolysis D) amino acid catabolism

26. What is the classification of the reaction shown?

A) oxidation D) hydrolysis

B) reduction E) isomerization

C) decarboxylation

27. Synthesis of glucose from amino acids is called

A) Glycolysis C) Gluconeogensis

B) Glycogenesis D) Hydrolysis

28. The synthesis of large molecules from smaller ones in the body is referred to as

A) catabolism C) Ketogenesis

B) anabolism D)glycolysis

29. The nucleic acid base found in the mRNA but not in DNA is

A) Adenine C) Uracil

B) Guanine D) Cytosine

30. DNA rich in A-T base pairs have

A) 1 hydrogen bond C) 2 hydrogen bonds

B) 3 hydrogen bonds D) 4 hydrogen bonds

31. Where does the energy production occur in the cell?

A) Ribosome C) Mitochondria

B) Nucleus D) Cytoplasm

32. Where does the protein synthesis occur in the cell?

A) Ribosome C) Mitochondria

B) Nucleus D) Cytoplasm

33. In the process of transcription, the flow of genetic information is from

A) DNA to DNA C) DNA to protein

B) RNA to protein D) DNA to RNA

34. Ammonium ions are converted to non-toxic nitrogen containing compounds through

A) Amino acid metabolism C) Urea cycle

B) Citric acid cycle D) transamination

35. In protein structure, B-pleated cheats are examples of

A) Primary structure C) Secondary structure

B) Tertiary structure D) Quaternary structure

36. Lactose is a disaccharide formed of

A) Glucose + fructose C) Glucose + galactose

B) Glucose + glucose D) Fructose + galactose

37. Saponification is

A) Hydrolysis of fats by strong base

B) Hydrolysis of glycerol by lipases

C) Esterification

D) Oxidation reaction

38. The connection between amino acid residues in molecules of protein is

A) glycosidic linkage C) peptide linakge

C) ether linkage D) phosphodiester linkage

39. Polyunsaturated fatty acids are generally

A) Oil at room temperature C) Solid at room temperature

B) Semisolid at room temperature D) All of the above

40. Maximum energy is produced by

A) Carbohydrates C) Lipids

B) Proteins D) Nucleic acids

41. A polynucleotide contains _____

A) one free phosphate group at the 5' end.

B) a backbone of alternating sugar and base groups.

C) one free phosphate group at the 1' end.

D) one free OH group at the 5' end.

42. How many molecules of CO2 are produced for each turn of the citric acid cycle?

A) 0 B) 1 C) 2 D) 3 E) 4

43. How many molecules of GTP are produced for each turn of the citric acid cycle?

A) 0 B) 1 C) 2 D) 3 E) 4

44. Which is the enzyme that hydrolyzes triacylglycerols?

A) acetyl CoA D) lipase

B) protease pepsin E) succinate dehydrogenase

C) amylase

Creat Testable Question?

Not all questions are testable!!

A testable question asks. . .

"What is the effect of the Independent Variable on the Dependent Variable?"

Creat a Hypothesis?

A hypothesis is a prediction of the outcome of the lab. Your prediction is based on your understanding of the scientific concept.

It answers your testable question. Use the following pattern:

IF the (IV- how it is changing), then the DV- how you think it will change), BECAUSE (why do you think this is happening.

Example- If the IV increases, then the DV will decrease because....

6.Creat a Procedures ?

Procedures are a list of materials used in the experiment and the steps in performing the experimental part. Procedures are the recipe you follow in order to perform the experiment. Write these in order, in paragraph form, and using your own words. Do not simply copy and paste from the student lab guide.

7. Creat Data Table ?

Data is recorded during the procedures. You need to a data collection table for your experiment. Below is an example Data collection table. you need your own collection table using labels with the names of your variables and the correct units you are measuring.

{Insert name of Independent Variable} (insert units)

{Insert name of Dependent Variable} (insert units)

Average { Insert name of Dependent Variable }(insert units)

Trial 1 *

Trial 2 *

Trial 3*

Control

{Insert Treatment 1 Name}

{Insert Treatment 2 Name}

{Insert Treatment 3 Name}

Project Guide

Introduction from Vernier

Almost all chemical reactions that occur in living organisms are catalyzed by enzymes. Enzymes are globular proteins, responsible for most of the chemical activities of living organisms. They act as catalysts, substances that reduce activation energy, or the energy it takes to get a reaction started. Enzymes are not destroyed or altered during the process. They are extremely efficient and may be used over and over again. One enzyme may catalyze thousands of reactions every second. Many factors in a cell's environment, like temperature, pH, concentration and salinity, affect the action of an enzyme. Changes in these conditions may change the shape of the enzyme making it useless, a process called denaturation. In this investigation, you will conduct an experiment to determine the effect of a variable on an enzyme catalyzed reaction.

In every cell of the body, hydrogen peroxide, H₂O₂, is produced as a waste product. However, hydrogen peroxide kills living cells. Although H₂O₂ is toxic to most living organisms, many organisms are capable of enzymatically destroying the H₂O₂ before it can do much damage. H₂O₂ can be converted to oxygen and water, as follows.

2H₂O₂ â 2H₂O + O₂

Because your liver is responsible for detoxifying your blood, your liver cells contain a lot of catalase to break down H₂O₂ into harmless H₂O and O₂. Yeast cells also contain catalase, so we will use them as an easy and inexpensive source of catalase in this lab.

When the H₂O₂ encounters the yeast catalase, it bubbles, as the gaseous O₂ escapes. We will measure the amount of O₂ being produced using a gas pressure sensor. The more O₂ that is produced, the greater the pressure in the tube will become. An increase in pressure tells us that the catalase is effective at breaking down the H₂O₂.

The results of your experiment will be shared in an experiment report due week 15. This lab gives you hands on practice with the Vernier sensors. Use of the sensors will be required in other courses for the Natural Sciences Degree Program. The hands on procedure is detailed step by step below.

After reading through the direction make sure to watch the video showing the procedure in action.

Safety Precautions

Make sure to wear safety goggles. Keep a close eye on your pressures and make sure your gas sensor does not get wet (this will ruin the sensor)

Lab Materials

1 Vernier LabQuest

1 Vernier Gas pressure sensor w/ tubing set

1 Vernier Logger Pro (installed on computer)

1 Lab goggle (from HOL kit)

10 mL graduated cylinder (from HOL kit)

200 mL beaker (from HOL kit)

Tap water

4 cups (any kind)

1 Bottle FRESH 3% H₂O₂ (hydrogen peroxide)

3 18 x 150mm test tubes)

1 Test tube rack (create using cardboard, legos etc.)

1 packet of yeast

3 pipets (from HOL kit)

1 Thermometer (any kitchen or medical thermometer will work)

IMPORTANT NOTES:

You must use fresh hydrogen peroxide and yeast for this lab to yield decent results. Yeast can be bought at any grocery store (look at the expiration date closely) and hydrogen peroxide can be bought at any pharmacy or grocery store. You should buy a couple of packs of yeast in case you make an error in preparing the yeast solution If peroxide is kept in the refrigerator, it must be brought to room temperature before the lab.

Set out a large container of water so the water equilibrates to room temperature overnight.

Make sure you are using metric units on your thermometer. You can always run conversions from Fahrenheit to Celsius.

You must run a test on the catalase (yeast) to make sure that the yeast suspension is at the right concentration/activity before testing it with your independent variable. You should prepare the solution when you are ready to test your independent variable. The solution will serve as your control in the experiment

To make yeast suspension as seen in the included video, add the following into a cup :

100 ml warm water (37-40C, but no hotter or the yeast will die or enzymes will denature).

1 packet of yeast (approx 7g)

1 packet of sugar (the little packets they give at restaurants) (or make a 2% sugar solution by adding 4 g sugar to 250 ml water, then add a packet of yeast to 100 ml of this solution. You can use your scale provided in the HOL kit to weigh the sugar)

Let the solution sit for 10 minutes before testing.

Follow lab procedure steps 1 & 2. Add 2 drops of the yeast suspension and measure following lab procedure steps 4-9. (Make sure to read the lab steps before adding the yeast suspension. It is time sensitive and must be measured quickly after being dropped in the test tube.)

The room temperature reaction with two drops of suspension should produce around 130 kPa (1.3 atm) in 40-60 seconds. Pressures above 130 kPA will cause the stoppers to pop off. Pressures above 210 kPA may damage the sensor so keep a close eye on your numbers!

If your numbers are too high, add more warm water, to dilute the suspension. Start by adding a small increment of water (10 mL) and repeat the test. Continue adding water until you reach 130kPa in 40-60 seconds.

If the solution isn't strong enough, add 1 more drop to the test tube (3 drops instead of 2 for example). Continue to increase the number of drops until you get results near 130 kPA after 1 minute. Record the number of drops needed and use that number of drops as the control for the experiment. *With the exception of enzyme concentration, that will be the number needed for each test tube. If you are doing your experiment on enzyme concentration and it for example it takes 4 drops instead of 2 you will need to double the number of drops for all of your concentrations.

Variables:

You can modify this lab to test the effect of enzyme concentration, temperature, sugar source, enzyme source or salinity. Choose 1 independent variable to test. Below are lists of variables and some ideas on how to test them:

Enzyme: With 3ml H₂O₂ and 3ml H₂O in each tube, add 1 drop of enzyme suspension. Repeat with different numbers of drops. Make sure none of the enzyme solution touches the sides of the test tube and mix before measuring. These must be measured quickly after the drops have been added.

Temperature: With 3ml H₂O₂ and 3ml H₂O in each tube, add 2 drops of enzyme suspension. Fill cups with water of different temperatures. Set each test tube in the water for 5 minutes before recording data.

Salinity: With 3ml H₂O₂ and 3ml H₂O in each tube, add 2 drops of enzyme suspension. Add drops of 1M NaCl. To make 1M NaCL, dissolve 58.44grams of table salt in 1 liter of water. Repeat with different numbers of drops. These will also need to be measure quickly after the enzyme and NaCL solution are added.

Sugar source: Make the yeast suspensions with various types of sugars (brown sugar, granulated, powdered, glucose, fructose, lactose, etc). Measure quickly after yeast suspension is added to test tubes.

If you have an idea for another variable not on this list that you would like to test, please send me a message for pre-approval.

Procedure

Place test tubes in a rack and label them 1, 2, 3 etc. You can improvise a rack by cutting holes in a cardboard box. You just need something that will keep the test tubes vertical and easy to distinguish.

Add 3 mL of 3.0% H2O₂ and 3 mL of tap water to each test tube (Use a plastic pipet/dropper to easily dispense the water and H2O₂âdon't mix up the pipets!).

Conduct your experiment according to which variable you have chosen to test. Make sure to follow the time guidance for each variable as directed on page 3. For example if you were testing temperature you would place your tubes in water of different temperatures (pictured below), for salinity you would add drops of saline solution etc. If you have questions about how to test your chosen variable please send me a message.

To collect data connect the plastic tubing to the valve on the gas pressure sensor.

Connect the sensor to CH1 on the LabQuest.

Connect your Lab Quest to your computer. (You can conduct this experiment just using the Lab Quest but it is nice to use Logger Pro because you can easily export the graphs and tables for use in your report. ) Turn on Logger Pro (cd included with Vernier equipment, very easy to install on your computer and generates great graphics for your report)

In Logger Pro click Open â Experiments â Biology w Vernier â(Pressure)Enzyme.cmbl

Once Logger Pro is open to the Pressure Enzyme lab you should have all the lab settings pre-set so that the sensor will collect for the correct duration of time.

Turn the LabQuest on.

For your control, add 2 drops (or more depending on calibration) of the enzyme solution and put the stopper on the tube and GENTLY swirl the tube to mix the contents.

Start data collection by pressing the green play icon on your computer screen. The test will run for 180 seconds.

Disconnect the stopper from the test tube. Rinse out the test tube and leave it to dry.

Processing the DATA

There are several options for processing the Data. I recommend running through the steps listed in the experiment procedure on the Lab Quest. You can also follow the steps below to analyze the slope. The slope, m, tells us the pressure generated every minute, so the units would be kPa per minute, or kPa/min. Kilopascals, or kPa, are just a unit of pressure; you may have heard of other units of pressure like pounds per square inch (PSI) in car tires or atmospheres (atm) or millimeters of mercury (mmHG) for weather pressure. For example, if m is 0.00376 our rate of gas production is 0.00376 kPa/min. The larger the slope, the more oxygen is generated and the more active the enzyme is at those conditions.

Choose Curve Fit from the Analyze menu. Check mark Pressure.

Choose Linear Fit to get an equation in the form y=mx+b

Record the slope of the line, m, in your data table. Select OK.

Store the data from the first run.

Repeat steps 2-16 for each of your treatments.

Tap Run 3. Select All Runs. All three runs will now be on the same graph.

CHE 211 Study Guide - Midterm Guide: Diethyl Ether, Meat Tenderizer, Toothpick

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