Protein Synthesis and ProcessingHow do cell synthesis polypeptides and convert them to functional proteins?

Why?DNA is often referred to as the genetic blueprint. In the same way blueprints produced by an architect contain the instructions for construction of a building, the DNA found inside the nucleus of cells contains the instructions for assembling a living organism. In an architect’s blueprint, the written instructions tell the construction company what materials are needed and in what quantities; the DNA blueprint carries its instructions in the form of genes. Each gene directs the production of a polypeptide, from which other more complex proteins, such as enzymes or hormones, may be constructed. So, what is the language of these instructions and how are they read and decoded by the cellular organelles?

Model 1 – Structure of Chromosomes and Genes

1. What are the instructions on a chromosome called?

2. Within each gene there are two types of regions. What are they called?

3. Which regions do not contain any coding material?

4. With your group develop a hypothesis to explain the function of these non-coding regions.

5. Each chromosome is made from what biological molecule? 1

6. What are the four types of nitrogenous bases found in a strand of DNA?

7. What type of biological molecule will be produced using these instructions?

Model 2 – Transcription (Reading and Copying the Genetic Code)

Note: Outside the cell are organelles in the cytoplasm ie.g. ribosomes and mitochondria

8. Where in the cell is the DNA found?

9. Where in the cell is the pre-mRNA produced?

10. What monomers are used to construct the pre-mRNA and where are they found?

11. What is the base found in pre-mRNA that is not present in DNA?

12. What is the base pair rule for making pre mRNA from DNA?

13. Which strand of the DNA is “read” to produce pre-mRNA?

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14. What molecule other than DNA is involved in the production of pre-mRNA, and what type of biological molecule is it?

15. In which direction is the DNA molecule read?

16. When you pply to college they usually request a copy of your transcript. What exactly are they asking for when they request a transcript and how does this relate to the process of transcription in the nucleus of a cell?

Read This!

17. Will a cell transcribe all the genes within its nucleus simultaneously? Justify your answer using complete sentences.

18. Considering the many types of cells and their different functions, will all cells transcribe all genes at some point in time? Justify your answer using complete sentences.

Model 3: mRNA Processing (in Eukaryotes only)

Nearly all cells contain identical DNA, and each DNA strand may contain hundreds or thousands of individual sections, or genes. Each gene usually contains the code for one polypeptide strand, however some genes may code

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19. What has been removed from the pre-mRNA to make it into mRNA?

20. Thinking back to Model 1 and the hypothesis you developed in question 4, why do you think these regions have been removed?

21. What three bases makes up the start codon?

22. What has been added to the mRNA before the start codon and to which end of the molecule was it added?

23. There are 18 nucleotides and 6 condons in this mRNA strand. Given that information define a codon using complete sentences.

24. What has been added to the other end of the mRNA, after the last codon?

25. Through which structure is the mRNA leaving the nucleus?

26. The “m” in mRNA is short for messenger. Why is this molecule called messenger RNA?

Read This!

27. What type of biological molecule is an exonuclease?

28. Using the information in the Read This! box, develop a hypothesis to explain why a poly-A tail is added to one end of the mRNA.

29. Different mRNA molecules can have poly-A tails of different lengths. Considering the purpose of adding the poly-A tail (from the previous question),

mRNA is a short-lived molecule which will eventually be degraded by exonucleases. Exonucleases can only remove individual nucleotides from the 3’ end of a nucleic acid. The individual mRNA nucleotides will then be free to be used again during the process of transcription.

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why are some tails longer than others? Justify your answer using complete sentences.

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Structure of tRNA strand in detail. The tRNA may be “charged” (carrying an amino acid) or “uncharged” (with no amino acid).

Initiation complex

Model 4 – Translation (Protein Synthesis, uses peptide bonds between amino acids to form a polypeptide)

Initiation Elongation

P-Site A site

Elongation Termination

Start and Stop Codons in the mRNA are used in protein synthesis

anticodon

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30. What are the three components of the initiation complex?

31. What is attached to one of the free ends of the charged tRNA molecule?

32. What are the 3 bases on the tRNA called that are complementary to the codon on the mRNA?

33. What is the relationship between the anticodon, mRNA codon, DNA code and amino acid?

34. What are the three stages of translation?

35. To which site on the ribosome does the start codon bind?

36. Into which site on the ribosome are the new amino acids brought?

37. From which site does the tRNA molecule exit the ribosome?

38. What will happen to the unattached tRNA once it has delivered its amino acid?

39. The “t” in tRNA is short for transfer. In a complete sentence, explain why this molecule is called transfer RNA.

40. During elongation a series of amino acids are delivered to the ribosome and connected to form a polypeptide. What type of bond connects each amino acid to the next?

41. Using the diagrams above, explain how the cell terminates the process of translation.

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First Base

Second Base

Third Base

42. To translate usually means to change from one language into another. Explain how the term translation applies to the synthesis of proteins from DNA instructions.

Read This!

Model 5: Triplet Code for Amino Acids

43. Using the mRNA codon chart above, complete the following:

DNA TAC CTT CGG ATG GTC ACT

mRNA ____ ____ ____ ____ ____ ___

The codons in mRNA are nucleotide bases read in sets of 3 (a triplet code). An mRNA codon chart is used to translate the language of the mRNA code into the language of amino acids.

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polypeptide sequence ____ ____ ____ ____ ____ ____

Extension Questions44. There are 64 possible codons, with 61 of the 64 actually coding for amino

acids and the other three serving as stop signals. There are only 20 known amino acids. Why is it beneficial to living organisms to have multiple codons that code for the same amino acid?

45. A silent mutation is one that does not affect protein structure. Write a code for an original DNA strand containing at least 12 bases, and then mutate the original DNA so that the final protein is unaffected.

46. In prokaryotic cells, translation begins before transcription is finished. Give 2 reasons why this would not be possible in eukaryotic cells.

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Teacher’s Guide & Answer KeyLearning Objectives:

After completing the activity students should be able to

1. Explain the relationship among DNA, RNA and amino acids.

2. List the steps and events of transcription and translation (protein synthesis)

3. Transcribe and translate a DNA sequence into a polypeptide sequence

Prerequisites:

1. Prior knowledge of polymers and monomers is necessary, specifically nucleotides as the monomers of nucleic acids and amino acids as the monomers of proteins. Some basic knowledge of enzymes is also required.

2. Students need to recognize cell organelles, including the nucleus and ribosome and their functions.

3. Knowledge of DNA structure.

Evaluation Questions

1. A possible sequence of nucleotides in DNA that would code for the polypeptide sequence phe-leu-ile-val would be

a. 3’ AAA-AAT-ATA-ACA 5’b. 5’ TTG-CTA-CAG-TAG 3’c. 3’ AAA-GAA-TAA-CAA 5’d. 3’ AAC-GAC-GUC-AUA 5’e. 5’ AUG-CTG-CAG-TAT 3’

2. The processing of pre-m RNA involvesa. the removal of introns and the splicing together of exonsb. The removal of exons and the splicing together of introns.c. The addition of a sulfur cap and poly(A) taild. The attachment of introns to mRNAe. Both A and C

3. Explain what a silent mutation is and how the genetic code helps to minimize functional mutations. A mutation that does not affect the polypeptide sequence. Because multiple codons code for the same amino acid many mutations are silent.

Additional materials:

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There is a great variation of the traditional codon chart that is much easier to use. An online version is at http://ingsscience.com/.

Target Responses

1. What are the instructions on a chromosome called? genes

2. Within each gene there are two types of regions. What are they called? Introns/non-coding & exons/coding.

3. Which regions do not contain any coding material? introns

4. With your group develop a hypothesis to explain the function of these non-coding regions. Answers may vary but should include ideas such as spacers between coding sections, or remnants of past mutated portions of the DNA. (They also allow different cells to splice the pre-mRNA in different ways so that different cells can use the same gene to make slightly different end proteins, but students are not expected to know this).

5. Each chromosome is made from what biological molecule? DNA

6. What are the four types of nitrogenous base found in a strand of DNA? Adenine, Thymine, Cytosine & Guanine

7. What type of biological molecule will be produced using these instructions? Proteins or polypeptides

8. Where in the cell is the DNA found? In the nucleus

9. Where in the cell is the pre-mRNA produced? In the nucleus

10. What monomers are used to construct pre-mRNA and where are they found? Free RNA nucleotides found within the nucleus (or nucleoplasm).

11. What is the base found in pre-mRNA that is not present in DNA? Uracil

12. What is the base pair rule for making pre-mRNA from DNA?) A-U; U-A; C-G; G-C

13. Which strand of the DNA is “read” to produce pre-mRNA? The template strand or coding strand

14. What molecule other than DNA is involved in the production of pre-mRNA, and what type of biological molecule is it? RNA polymerase; an enzyme/protein

15. In which direction is the DNA molecule read? 3’ to 5’

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16. When you apply to college they usually request a copy of your transcript. What exactly are they asking for when they request a transcript and how does this relate to the process of transcription in the nucleus of a cell? Transcripts are a copy of a student’s information from their time in school, such as grades, discipline etc. Transcription in the nucleus is taking a copy of the information from the DNA.

17. Will a cell transcribe all the genes within its nucleus simultaneously? Justify your answer using complete sentences. No, cells only transcribe genes as they are needed to make specific proteins. Use an analogy such as turning all the lights on in your house when you are only using one room.

18. Will all cells transcribe all genes at some point in time? Justify your answer using complete sentences. No, certain genes will be switched on in specific cells and switched off in others depending on the location and function of the cell.

19. What has been removed from the pre-mRNA to make it into mRNA? introns

20. Thinking back to Model 1 and the hypothesis you developed in question 4, why do you think these regions have been removed? Because they are non-coding regions so they don’t need to be read.

21. What three bases makes up the start codon? AUG

22. What has been added to the mRNA before the start codon and to which end of the molecule was it added?A methyl cap at the 5’ end.

23. There are 18 codons in this mRNA strand. Given that information define a codon using complete sentences. A set of 3 mRNA nucleotides.

24. What has been added to the other end of the mRNA, after the last codon? A poly A tail

25. Through which structure is the mRNA leaving the nucleus? Nuclear pore

26. The “m” in mRNA is short for messenger. Why is this molecule called messenger RNA? It is acting as a messenger and relaying a message from the DNA to the ribosome.

27. What type of biological molecule is an exonuclease? Enzyme (protein)

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28. Using the information in the Read This! box, develop a hypothesis to explain why a poly-A tail is added to one end of the mRNA. It prevents the information-carrying part of the mRNA from being degraded too quickly by the exonucleases

29. Different mRNA molecules can have poly-A tails of different lengths. Considering the purpose of adding the poly-A tail (from the previous question) why are some tails longer than others? Justify your answer using complete sentences. An mRNA with a short tail will have a shorter lifespan. Proteins that are needed over long periods of time might come from long-tail mRNAs whereas proteins that are only needed briefly may come from short-tailed mRNAs

30. What are the three components of the initiation complex? mRNA; charged tRNA; ribosome

31. What is attached to one of the free ends of the charged tRNA molecule? An amino acid

32. What are the 3 bases on the tRNA called that are complementary to the codon on the mRNA? An anticodon

33. What is the relationship between the anticodon, codon, DNA code and amino acid? The anticodon of the tRNA is complementary to the codon of the mRNA. The 3 bases on the tRNA’s anticodon determine the amino acid that it carries. The codon is complementary to the DNA code, so the DNA code actually relates to the amino acid needed.

34. What are the three stages of translation? Initiation, elongation and termination

35. To which site on the ribosome does the start codon bind? P site

36. Into which site on the ribosome are the new amino acids brought? A site

37. From which site does the tRNA molecule exit the ribosome? P site

38. What will happen to the unattached tRNA once it has delivered its amino acid? It is released from the ribosome and is free to pick up and carry another amino acid.

39. The “t” in tRNA is short for transfer. In a complete sentence explain why this molecule is called transfer RNA. It is transferring the correct amino acids in the correct sequence to the ribosome to produce the functional protein.

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40. During elongation a series of amino acids are delivered to the ribosome and connected to form a polypeptide. What type of bond connects each amino acid to the next? Peptide bond (a type of covalent bond)

41. Using the diagrams above, explain how the cell terminates the process of translation. A release factor binds to the last codon, which causes a water molecule to bind to the last amino acid in the polypeptide chain. This stops the process of adding more amino acids to the polypeptide.

42. To translate usually means to change from one language into another. Explain how the term translation applies to the synthesis of proteins from DNA instructions. The language of DNA, in the form of nitrogen bases read in sets of 3 called codons is being translated into amino acids.

43. Using the mRNA code box above, complete the following:

DNA TAC CTT CGG ATG GTC ACT

mRNA AUG GAA GCC UAC CAG UGA

polypeptide sequence Met Glu Ala Tyr Gln [Stop](start)

44. There are 64 possible codons, with 61 of the 64 actually coding for amino acids and the other three serving as stop signals. There are only 20 known amino acids. Why is it beneficial to living organisms to have multiple codons that all code for the same amino acid? If more than one codon can code for the same amino acid then many mutations will have no effect as they will still code for the same functional protein.

45. A silent mutation is one that does not affect protein structure. Write a code for an original DNA strand containing at least 12 bases, and then mutate the original DNA so that the final protein is unaffected. Accept any answer that shows the student understands the concept of silent mutations, such as the one below:

original mutated DNA TACAAACCCGGA TACAAGCCCGGAmRNA AUGUUUGGGCCU AUGUUCGGGCCUAmino acid Met-Phe-Gly-Pro Meg-Phe-Gly-Pro

46. In prokaryotic cells, translation begins before transcription is finished. Give 2 reasons why this would not be possible in eukaryotic cells. Eukaryotic cells have a nucleus and transcription takes place in the nucleus and translation takes place on the ribosome in the cytoplasm of the cell.

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Eukaryotic cells have introns that need to be removed from the pre-mRNA before translation can happen.

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