Bio 206 Week 6 Tutorial PDF

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Translation Worksheet - TA

BIO206H5 | Introduction to Cell & Molecular Biology University of Toronto Mississauga

Worksheet - TA Translation

Page 1 of 4

Due to the amount of material covered in these worksheets, students are expected to complete all exercises prior to attending tutorials. The goal of tutorial class time is to address material in the worksheet that the students find challenging. It is up to the TA’s discretion to volunteer covering material that might be relevant but not directly asked by students. 1.

Which amino acids’ codon(s), if altered, would most likely lead to premature termination of translation? Please explain your answer. Any codon one base off from Stop codons (UAA UAG UGA).

2.

One of the tRNA genes for tyrosine has a mutation in its anticodon sequence. a. What might be the possible consequences of this change? Tyrosine has 2 codons. This implies that ~50% of tyr a.a. would not be incorporated. May be lethal. This also implies that Tyr will be inserted elsewhere, in competition with another tRNA. b. How would you determine which tRNA-Tyr anticodon was altered? One option is to Sequence tRNA genes. Another is to create the synthetic peptides UAUUAUUAU and UACUACUAC since Tyrosine’s codons are UAU UAC. Then see which one is made/not made.

3.

What would be the effect of truncating the 3’end of the 16S rRNA of a prokaryote? No or improper ribosomal alignment (binding inefficiency or inaccuracy in recognition) with Shine-Dalgarno sequence of mRNA. This implies no, delayed, or inaccurate protein synthesis. May be lethal.

4.

List instances in which GTP plays a role in protein synthesis. Students can easily list instances of GTP involvement while studying. However, this is a good exercise that highlights the importance of absorbing the course material in a manner that allows them to go through the steps of processes in their mind and scan for information such as GTP involvement. One example is 

5.

Does RNA have catalytic abilities? RNA enzymes (ribozymes) have catalytic activity. Examples include RNA in the ribosome catalyzing protein synthesis and ribozymes that can undergo self-cleavage.

6.

Which of the following mutations would most likely have the severest consequences: Explain your reasoning. a. A change in amino acid recognition of an aminoacyl-tRNA synthetase b. A frame shift mutation at the end of the coding sequence of a gene c. A mutation at a splice junction Scenario a. implies that almost every single protein produced in the cell will be affected. Odds are very high that at least one affected protein will cause lethality. Scenario b. involves products of one gene only (or maybe more depending on how many genes are read from that stretch of DNA). In the worst cases, the consequences might also be lethal. However, odds are definitely lower than situation a. Same logic applies to Scenario c. Case a. is definitely the most severe.

7.

List a few similarities between prokaryotic and eukaryotic translation (i.e. protein synthesis). Initiator factors, elongation factors, initial tRNA is methionine, ribosome has 2 subunits, small subunit aligns, large subunit catalytically active, same codon usage, termination, GTP energy source, 1 aa added at a time etc.

8.

List a few differences between prokaryotic and eukaryotic translation. Different Ribosome binding sequences (Shine Dalgarno vs Kozak), location of ribosome binding sequences relative to the start codons (Kozak sequence contains AUG whereas Shine Dalgarno is upstream of AUG), 5’ cap is first recognized in eukaryotes etc. Consider the processes in Error: Reference source not foundFig 2 and Fig 1 below Arrange the letters in the appropriate order. TAs : Fig 1 and 2 have been deleted in the answers key, but are present in the student version of the worksheet. Figure 1: D-F-A-C-E-B Figure 2: D-A-B-C

9.

BIO206H5 | Introduction to Cell & Molecular Biology

University of Toronto Mississauga

Page 2 of 4

Worksheet - TA Translation

Omit for 2020 - Exploring NCBI The National Center for Biotechnology Information (NCBI), located in the United States, houses a variety of databases and computing tools as well as provides links to other external databases and computing tools relevant to cell and molecular biology. NCBI is a leadmember of an international consortium whose goals are to create central ‘hubs’ from which a variety of biological information can be publically accessed, in order to further our understanding of genes and their products in health and disease. NCBI is the central repository for all known nucleotide and amino acid sequence data obtained from all types of biological organisms and is a key resource for all molecular biologists. During the coming weeks we will explore this website and some of its capabilities. -

Go to the NCBI website http://www.ncbi.nlm.nih.gov/ Type in the term ‘insulin homo sapiens’ in the search bar. Choose Gene as the database of interest. Click Search. Filter results to those found in Homo sapiens. Click on the INS gene (ID: 3630) Read the summary provided under the Summary heading. Scroll down to the Genomic regions, transcripts, and products section. Click on the sequence representing insulin. Blue and red rectangles and lines now appear below it.

1.

What does the green structure represent? DNA

2.

What do the blue structures immediately below the green structures represent? The different mRNA splice variants

3.

What process results in the production of the blue structures? Transcription

4.

What is the difference between the different blue structures belonging to insulin? Each represents a differently spliced mRNA – The first exon is the main difference.

5.

What do the red structures represent? Protein primary structure

6.

What process results in the production of the red structures? Translation

7.

What do the lines represent in the red structures? Regions not translated into the primary transcript

8.

Do the red lines exist in reality? No

9.

What is the difference between the different red structures? None other than originating from different splice variants

10. What are the 1st 6 bases read in each of the blue structures? Hint: The zooming tool will allow you to explore the sequence and retrieve this information. AGCCCU 11. The 1st amino acid incorporated in a protein is always the same. Why do none of those bases in the previous question code for this amino acid?

BIO206H5 | Introduction to Cell & Molecular Biology

University of Toronto Mississauga

Page 3 of 4

Worksheet - TA Translation

This is the 5’UTR. This region is not translated. 12. Where can the bases that code for this amino acid be found. Can you navigate your way through the graphical panel to find these bases? What is the location number of the 1st of the 3 bases relative to the chromosome? Hint: The zooming tool will allow you to retrieve this information. The 3 start codon bases (AUG coded by ATG) can be found right above the beginning of the primary sequence. The number of the 1st base of the start codon is 2,160,969. 13. Are these bases encoded by the top or bottom line of grey letters? (The 2 grey lines of letters can be found at the top of the Genomic regions, transcripts, and products section if you zoom in enough). These bases are encoded by the top line (template strand) 3’ to 5’ to make RNA, which in turn is read 5’ to 3’ to make a protein. 14. Provide 3 names to each of the 2 different lines of letters. Top strand: template, non-coding, anti-sense. Bottom strand: non-template, coding, sense 15. Towards the end of the gene, it is visible that some of the blue structures do not have corresponding red structures below them. Why is this the case? This is the 3’UTR. 16. What are the beginning and end of the red structures called? N & C- terminus

BIO206H5 | Introduction to Cell & Molecular Biology

University of Toronto Mississauga...