Download Protein Synthesis and Processing

Protein Synthesis and Processing
How 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?
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?
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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?
14. What molecule other than DNA is involved in the production of pre-mRNA, and what type of
biological molecule is it?
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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!
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 for more than one polypeptide.
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)
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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!
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.
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), why are some tails longer than others? Justify your
answer using complete sentences.
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Model 4 – Translation (Protein Synthesis, uses peptide bonds between amino
acids to form a polypeptide)
Structure of tRNA strand in detail.
The tRNA may be “charged”
(carrying an amino acid) or
“uncharged” (with no amino acid).
anticodon
Initiation
Elongation
Initiation complex
P-Site
Elongation
A site
Termination
Start and Stop Codons in the mRNA are used in protein synthesis
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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.
42. To translate usually means to change from one language into another. Explain how the
translation applies to the synthesis of proteins from DNA instructions.
term
Read This!
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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Model 5: Triplet Code for Amino Acids
Second Base
Third Base
First Base
43. Using the mRNA codon chart above, complete the following:
DNA 
TAC
CTT
CGG ATG GTC ACT
mRNA
____
____
____
____
____
___
polypeptide sequence 
____
____
____
____
____
____
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Extension Questions
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 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 Key
Learning 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-ileval 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 involves
a. the removal of introns and the splicing together of exons
b.
c.
d.
e.
The removal of exons and the splicing together of introns.
The addition of a sulfur cap and poly(A) tail
The attachment of introns to mRNA
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:
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
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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’
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.
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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)
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
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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.
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
(start)
Ala
Tyr
Gln
[Stop]
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:
DNA
mRNA
Amino acid
original
TACAAACCCGGA
AUGUUUGGGCCU
Met-Phe-Gly-Pro
mutated
TACAAGCCCGGA
AUGUUCGGGCCU
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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