BIO181 Transcription Translation Worksheet2

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BIO181 Transcription Translation Worksheet If any questions are unanswered, you will receive a score of 0. The extension questions are required . Name: Michael Pasek Class Time: 10:30 Part 1: Transcription ______________________________________________________________________________________ READ THIS : DNA is often referred to as a genetic blueprint. In the same way that blueprints contain the instructions for construction of a building, the DNA found inside the nuclei of cells contains the instructions for assembling a living organism. The DNA blueprint carries its instructions in the form of genes. In most cases the genes direct the production of a polypeptide, from which other more complex proteins, such as enzymes or hormones, may be constructed. These polypeptides and other molecules run the organism’s metabolism and, in multicellular organisms, dictate what each cell’s job is. So, what is the language of these instructions and how are they read and decoded by the cellular organelles? This activity will focus on the decoding of genes in eukaryotes. ______________________________________________________________________________________ Note - These are the same images. The image on the left is provided as a Google drawing. To edit it, draw on it, add circles or labels to it, double click the image while in Google Docs. Add in what you need to, then hit “Save and Close”. The image on the right is clearer but cannot be edited. 1. Refer to Model 1. a. What is the base-pair rule for a DNA strand matching an RNA strand? C to G T to A A (DNA) to U (RNA) b. Compare this base-pair rule with that of two DNA strands. DNA does not contain uracil, to T matches to A and A matches to T in DNA. However in DNA/RNA match, T bonds with A and A bonds with U 1

2. Which strand of the DNA contains the “blueprint” for the pre-mRNA? Template strand 3. Consider Model 1 a. In which direction is the DNA template strand read? 3’ to 5’ b. The DNA template strand and pre-mRNA strand are anti-parallel. With this in mind label the 3ʹ and 5ʹ ends of the pre-mRNA strand in Model 1. TCAGCCAUUACAUGGAU c. In which direction is the pre-mRNA molecule constructed? On which end are new bases added? 5’ to 3’ _______________________________________________________________________________________ READ THIS: In eukaryotes the enzyme RNA polymerase joins with several transcription factor proteins at the promoter, which is a special sequence of base pairs on the DNA template strand that signals the beginning of a gene. The transcription factor proteins, along with the RNA polymerase, is called the transcription initiation complex . This moves along the DNA template strand at about 40 base pairs per second producing pre-mRNA. When the RNA polymerase reaches the terminator sequence of base pairs on the DNA template strand, it completes the production of pre-mRNA and releases it into the nucleoplasm. _______________________________________________________________________________________ 4. Where on the DNA strand does the transcription initiation complex form? It forms on the promoter 5. Imagine the diversity of functions in which your cells participate. a. Do you think that the cells in your big toe contain the same DNA as the neurons in your brain? Yes all the cells in your big toe contain the same DNA as the neurons in our brain b. Will an individual cell transcribe every, or almost every, gene in its genome? Explain. No, cells only transcribe genes as they are needed to make specific proteins. No certain genes will be switched on in specific cells and switched off in others depending on the location and function of the cell its coding for. 2

Note - These are the same images. The image on the left is provided as a Google drawing. To edit it, draw on it, add circles or labels to it, double click the image while in Google Docs. Add in what you need to, then hit “Save and Close”. The image on the right is clearer but cannot be edited. 6. Compare the pre-mRNA to the mRNA leaving the nucleus in Model 1. a. What has been removed from the pre-mRNA to make it into mRNA? The introns have been removed b. What has been added to the mRNA that was not present in the pre-mRNA, and where on the mRNA strand are the additional items located? A methyl cap has been added to the 5’ end of the mRNA and a poly-A tail has been added to the 3’ end of the mRNA 7. Can mRNA diffuse through a membrane? Why or why not? mRNA can diffuse through a membrane through membrane nanotubes and not by diffusion. 3

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______________________________________________________________________________________ READ THIS: Introns are sections of pre-mRNA that are noncoding. That is, they don’t provide useful information for the production of the polypeptide being synthesized. There is evidence that suggests these introns allow certain sections of DNA to code for different polypeptides when different sections are removed. The removal of specific sections is triggered by a signal response in the cell. The portions of the pre-mRNA that remain are called exons . The methyl cap (sometimes called the GTP cap or 5ʹ cap) helps the mRNA molecule move through the nuclear pore and attach to a ribosome, its final destination. mRNA is a short lived molecule. Once in the cytoplasm the mRNA will be subject to exonucleases that immediately start removing individual nucleotides from the 3ʹ end of a nucleic acid. The individual mRNA nucleotides will then be free to be used again during the process of transcription. ______________________________________________________________________________________ 8. The human genome contains about 25,000 genes and yet produces about 100,000 different polypeptides. Propose an explanation of how this is possible. A single sequence of pre-mRNA can produce different mRNA sequences depending on what introns are removed 9. Using the information in Read This section , develop a hypothesis to explain the advantage of the poly-A tail added to the 3’ end of the mRNA. The advantage of the poly-A tail added to the 3’ end of the mRNA is that it prevents the information-carrying part of mRNA from being destroyed by the exonuclease before a polypeptide can be formed. 10.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. An mrna with at short tail will have a shorter lifespand. If mRNA has a longer tail it will have a longer lifespan. Proteins that are needed over long periods of time might come long-tail mRNA’s where proteins that are only needed briefly can come from short tailed mRNA. 11.Summarize the steps of transcription. Pre-mRNA is made from the template strand of DNA starting at the promoter by the transcription initiation complex. When the RNA polymerase reaches the terminator, the pre-mRNA is released. Introns are removed and the methyle cap and poly-A tail are added to make mRNA. Part 2: Translation 4

_______________________________________________________________________________________ READ THIS : The message in your DNA of who you are and how your body works is carried out by cells through gene expression. In most cases this means synthesizing a specific protein to do a specific job. First, mRNA is transcribed from the DNA code. Then, the mRNA sequence is translated into a polypeptide sequence. _______________________________________________________________________________________ Note - These are the same images. The image on the left is provided as a Google drawing. To edit it, draw on it, add circles or labels to it, double click the image while in Google Docs. Add in what you need to, then hit “Save and Close”. The image on the right is clearer but cannot be edited. 12.Model 1 defines the code scientists have discovered that relates the nucleotide sequence of mRNA to the amino acid sequence of polypeptides. The language of mRNA is often described as a “triplet code.” Explain the significance of this reference. Its called the triple code due to the fact that their at triplet code because each group of three bases in mRNA constitutes a codon. Then each codon specifies for a particular amino acid. 13.If an mRNA molecule had 300 nucleotides in the coding region of the strand, how many amino acids would be in the polypeptide that was synthesized? Show mathematical work to support your answer. 300/3= 100 14.Consider the information in Model 1. a. Compare all of the codons for Proline. What are the similarities and differences? All the proline codons are the same starting with CC. The difference is the third base. b. Considering that mistakes can occur during transcription and DNA replication, what advantage is there for an organism to have multiple mRNA sequences code for the same amino acid? In case one codon makes a mistake/ fails the mRNA will still translate properly into the amino acid 15.Use the mRNA codon chart in Model 1 to complete the table below: 5

5’ or 3’? (for mRNA) 1 st position 2 nd position 3 rd position 4 th position 5 th position 6 th position 5’ or 3’ (for mRNA) DNA 3’ TAC CTT CGG ATG GTC ACT 5’ mRNA 5’ AUG GAA GCC UAC CAG UGA 3’ peptid e N- terminus MET GLU ALA TYR GLU Stop C-terminus 16.According to the table in Model 1, what amino acid is at the beginning of every polypeptide? Methionine Note - These are the same images. The image on the left is provided as a Google drawing. To edit it, draw on it, add circles or labels to it, double click the image while in Google Docs. Add in what you need to, then hit “Save and Close”. The image on the right is clearer but cannot be edited. 17.Describe why the 3 stages of translation are named as they are. ( Hint: What do these terms mean in standard English? ) Initiation, elongation, termination 18.According to Model 2, when the mRNA leaves the nucleus, to which cellular complex does it attach? 6

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The ribosome 19.The mRNA attaches to the complex at the sequence AUG. What is the significance of this sequence of nucleotides? The AUG is the start codon 20.Describe the movement of the ribosome as translation occurs. The ribosome moves along the mRNA chain from 5 to 3 _______________________________________________________________________________________ READ THIS : The ribosome is a large complex of ribosomal RNA (rRNA) and proteins. It consists of two subunits. The smaller subunit binds to the mRNA strand and the larger subunit holds the tRNA molecules in place while the covalent peptide bond is formed between the amino acids. Several ribosomes can attach to an mRNA molecule simultaneously. This allows for many polypeptide chains to be synthesized at once. _______________________________________________________________________________________ 21.The tRNA molecules in a cell are short sequences of nucleotides (about 80 bases) that contain an anticodon and carry a specific amino acid. a. Find the tRNA in Model 2 that is carrying the Histidine (His). What sequence of nucleotides makes the anticodon on this tRNA molecule? GUA b. What codon on mRNA would match this anticodon? CAU c. Verify that the codon you wrote in part b codes to Histidine by looking at the table in Model 1. Verified d. What anticodon would be found on a tRNA molecule carrying Glycine (Gly)? ( Note: There are several correct answers here.) CCA CCU CCG CCC 22.The “t” in tRNAs is short for transfer. In a complete sentence, explain why this molecule is called transfer It transfers the correct amino acid in the correct sequence to the ribosome to produce the functional protein 23.Describe two things that occur during termination as illustrated in Model 2. A release factor binds to the last codon which stops the process of adding more amino acids to the polypeptide. A water molecule is added to the end of the amino acid chain. 7

Part 3: Extension Questions- Must be complete to earn credit 24.Consider the hypothetical protein represented by triple letter amino acid designations: N terminus Met‐Asn‐His‐Glu‐Pro‐Ser‐Tyr C-terminus a. Propose one RNA sequence that could encode this sequence (be sure to include start and stop codons and indicate 5’ and 3’ ends). 5’ AUG AAU CAU GAA CCU AGU UAU UGA 3’ b. Propose the Template DNA strand sequence that could be transcribed into your RNA sequence (be sure to include start and stop codons and indicate 5’ and 3’ ends). 3’ ATC TTA GTA CTT GGA TCA 5’ 25.Here is the beginning of a protein‐encoding gene sequence. Assume the bottom strand is the template strand. 5’-ATGAAGTTTGGCACTTAA-3’ 3’-TACTTCAAACCGTGAATT-5’ a. Give the RNA transcript that would be transcribed from this DNA sequence. 5’ AUG AAG UUU GGC ACU UAA 3’ b. Translate the mRNA sequence into a protein sequence. Met-Lys-Phe-Gly-Thr c. What would be the effect on the final protein product if a mutation caused the following single base‐pair insertion: 5’-ATGAAGATTTGGCACTTAA-3’ 3’-TACTTCTAAACCGTGAATT-5’ The entire final protein would change and become something completely different d. What would be the effect on the final protein product if a mutation caused the following single base‐pair substitution: 5’-ATGAAGTTCGGCACTTAA-3’ 3’-TACTTCAAGCCGTGAATT-5’ An arginine replaces a glycine, this will change the structure and stability of a protein 8

e. What would be the effect on the final protein product if a mutation caused the following single base‐pair substitution: 5’-ATGAAGTTTCGCACTTAA-3’ 3’-TACTTCAAAGCGTGAATT-5’ No change f. What would be the effect on the final protein product if a mutation caused the following single base‐pair substitution: 5’-ATGTAGTTTGGCACTTAA-3’ 3’-TACATCAAACCGTGAATT-5’ This mutation will change the second codon into a stop codon g. Using your knowledge from Bio 282, predict which of the above mutation(s) you would expect to be the most severe in terms of the overall effect on the person carrying such a mutation? Justify your answer. The reading frame changes and you get a completely different codon 26.A mutation is a change in the DNA sequence which can then propagate to the mRNA and protein. 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. Original – TAC AAA CCC GGA Mutated-TAC AAG CCC CCA 9

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BIO181 Transcription Translation Worksheet2

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