17.2: Exercise

Part 1: DNA to Protein Exercise

The following DNA sequence is part of the gene that controls dimples. Decode the DNA message into mRNA, tRNA and finally amino acids. Use the genetic code chart to fill in the table below.

Note

The genetic code is based on mRNA (not DNA or tRNA). When you have finished this, you will be able to determine the phenotype of the person the DNA came from. (If arginine is the 3rd amino acid, the person will have dimples.)

Data Table for Codons, Anticodons, and Amino Acids

DNA	mRNA Codon	tRNA Anticodon	Amino Acid
C G A
G T C
G C A
T A A

1. Does the person with the sequence above have dimples?

2. What two great tasks are carried out by our genetic machinery?

3. What name do we call a three-nucleotide sequences of mRNA?

4. How many DNA bases does it take to code for an RNA codon?

5. How many amino acids does an RNA codon code for?

6. What brings amino acids to the ribosome?

7. What is the difference between transcription and translation?

8. True or false: Most of the DNA in the human genome codes for proteins.

Part 2: Protein Synthesis Exercise

DNA: 3′ A G C C G T A G A A T T 5′

1. Using this strand of DNA as a template, draw a picture of the complete DNA molecule. Include all parts of the DNA molecule. You do not need to draw your molecule with atomic accuracy.

2. Now draw a complete picture of the mRNA strand that will be made from this DNA. Label the 5′ and 3′ ends of your mRNA strand. (Use the given DNA strand at the top of this page as your template . . .)

3. Carefully indicate the codons present in the mRNA strand from question 2.

4. Draw a complete picture of all the tRNA molecules that will match up with the codons from the previous question. Include all appropriate amino acids in your picture, and do not mix up their order!

5. Draw a picture of the completed protein coded for by this strand of DNA (abbreviations are fine). Show the amino acids in the same order they would be observed in the finished protein.

Part 3: Protein Synthesis Bingo

Fill in the boxes with 16 of the 20 amino acids. Every bingo square will be unique. Then listen as random nucleotide sequences are pulled from the hat. Listen carefully to what kind of sequence is called! Use the mRNA codon chart on the previous page to determine the amino acid associated with each sequence. (Printable version here.)

Table of Amino Acids

alanine—ala—A	cysteine—cys—C	histidine—his—H	methionine—met—M	threonine—thr—T
arginine—arg—R	glutamine—gln—Q	isoleucine—ile—I	phenylalanine—phe—F	tryptophan—trp—W
asparagine—asn—N	glutamic acid—glu—E	leucine—leu—L	proline—pro—P	tyrosine—tyr—Y
aspartic acid—asp—D	glycine—gly—G	lysine—lys—K	serine—ser—S	valine—val—V

Data Table for Codons and AAs

	Sequence Called	DNA? mRNA? tRNA?	Codon	AA
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

Part 4: Wheat Germ Extraction

Wheat germ is the sprouting embryo contained within a wheat kernel (the wheat seed). The remainder of the wheat kernel is called the endosperm, and is the food storage site for the developing embryo. Our task today is to break down the cells within the wheat germ and remove the DNA.

Materials:

• Raw, Untoasted Wheat Germ (2 g.)
• Adolph’s Natural Meat Tenderizer (unseasoned)
• Liquid Dishwashing Detergent (Palmolive) (3 mL.)
• 1M Sodium Bicarbonate—NaHCO₃ (5 mL.)
• Ice Cold 95% Ethanol (20 mL.)
• Tap Water
• Water Bath (55° C)
• 250 mL. Beaker
• Thermometer
• Graduated Cylinder (10 mL.)
• Serological Pipette, 10 mL.
• Glass Stirring Rod
• Glass DNA Hook
• Ice Bath

Procedure:

1. Measure 45 mL. of tap water into your beaker using the graduated cylinder, and place it in the warm water bath (55°C). Allow it a few minutes to warm up. Do not allow the temperature of the bath to exceed 60° C!
2. Sprinkle in 2 g of wheat germ into the beaker and gently stir in 3 mL. of detergent. Incubate this mixture in the warm water bath for 5 minutes.
   1. Detergents dissolve lipids and proteins that form the cell membranes found in the wheat germ by disrupting the chemical bonds that hold the membrane together. This releases the cell’s contents, including the DNA held within the nucleus, into the solution.
   2. The warm water bath denatures enzymes that might otherwise damage the DNA, and it also helps the detergent work more effectively. If your water bath is too hot, then your DNA will become damaged.
3. After 5 minutes, gently stir in 2 g of meat tenderizer and 5 mL. of the 1M sodium bicarbonate solution. Incubate this mixture at 55° C for an additional 15–20 minutes.
   1. Eventually, even at 55° C, the DNA would be damaged, so this additional incubation period must not exceed 15–20 minutes.
   2. The sodium bicarbonate acts as a buffer that maintains a near-neutral pH in the solution. This ensures the DNA remains stable, and it also enables the enzyme found in the meat tenderizer to be most effective.
   3. The meat tenderizer contains a proteolytic enzyme that degrades the proteins found in the nuclear membrane, ultimately freeing the DNA into solution.
4. Transfer the beaker containing the wheat germ mixture to an ice bath for a few minutes to quickly cool it to room temperature. Gently stir during this time.
   1. The ice bath cools down the mixture so that the DNA is not damaged by the heat!
5. Using the serological pipet, carefully layer 10 mL of ice-cold alcohol over the wheat germ solution in the beaker. Allow the alcohol to flow from the pipet with the pipet tip held against the inside surface of the beaker, just above the liquid level. If the DNA does not appear, repeat this step.
   1. When the dissolved DNA makes contact with the very cold alcohol, the alcohol effectively dehydrates the DNA and it precipitates from the solution. This is because DNA is insoluble in the alcohol (and this is especially true of ice COLD alcohol).
   2. If carried out accurately, long strands of DNA will form at the interface between the alcohol and the original solution. These can be physically spooled using the glass DNA hook.
6. Using the DNA hook, attempt to spool the DNA using slow, twirling motion.

Show your DNA to your instructor for credit!

Licenses and Attributions

CC licensed content, Original

• Biology Labs. Authored by: Wendy Riggs. Provided by: College of the Redwoods. Located at: http://www.redwoods.edu. License: CC BY: Attribution

CC licensed content, Shared previously

• 0322 DNA Nucleotides. Provided by: OpenStax. Located at: http://cnx.org/content/col11496/1.6. License: CC BY: Attribution
• Central Dogma of Molecular Biochemistry with Enzymes. Authored by: Dhorspool. Located at: https://commons.wikimedia.org/wiki/File:Central_Dogma_of_Molecular_Biochemistry_with_Enzymes.jpg. License: CC BY-SA: Attribution-ShareAlike

Public domain content

• The completed chart of the genetic code. Provided by: National Institutes of Health. Located at: http://history.nih.gov/exhibits/nirenberg/HS5_cracked.htm. License: Public Domain: No Known Copyright