Minutes 20100920 Moffatt TA Meeting BIOL 208

From SnOwy - Ed's Wiki Notebook

Holdover from last week

• issues regarding comprehension of Template Strand and Coding Strand last week follow
• would be good to emphasize the following points:
  • it is not usual for a template and coding sequence to reverse on its own in nature -- for this to happen, human scientists need to create an artificial gene

Questions from the floor

• how is the grade for our tutorial section composed?
  • i.e. does attendance factor into the grade, or is it completely quiz answer based?
  • marks are only allotted for quizzes
• when are tutorial questions to be taken up?
  • i.e. do we take them up in the same class or on the following week?
  • they aren't actively taken up however, the solutions are discussed on the discussion board so far

This week

• would be good to demonstrate NCBI BLAST suite of tools
• I understand that holding the students' hand through the process isn't very instructive
• instead, we need to insure they understand what they're doing
• possibly go over two examples with them
• Questions and answers: the questions are numbered 1~7 while the answers are numbered 1~4, 6~8

Question 5 ...

• http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=190415
• "Describe the mRNAs that are produced"
• does a student basically look at the output and indicate:
  • the number of mRNAs produced
  • the offset into the transcription start (+1) position where each mRNA is found
  • the exons that are found in each mRNA (given by their start and stop offsets)
  • the total length of the mRNA produced
• some intelligible composition of the above data
• -- "this gene alternatively spliced" looks sufficient :)

P.44: Exons include 3'UTR and 5'UTR?

• I don't agree!
• why would NCBI decide that sequence that 'isn't translated' gets to be part of a translated unit?
  • reasoning: UTRs make it into the mRNA -- is an exon
  • reasoning: UTRs do not make it into the protein -- not an exon
• we need to explain that it's inconsistent, thus we'll be clear when we discuss it for examination

P.42: Text 15~16: What is a gene?

• I don't think that students are troubled with memorizing a definition
• in reality, the lack of a definition is far more detrimental to morale;
  • therefore, I propose we create a concise unified definition that students of this course would be comfortable with
  • OR that we not examine students on such a vague idea.
• what is the answer that is satisfactory for this course?
  • the sequence from the start to the stop codon?
  • any sequence of DNA that has meaning?
  • that which codes for peptides or have structural roles in holding DNA conformation?
• clearly understanding how this information is examined is key to happiness.

p.33: Stacking Energy

• call this "hydrophobic interaction" for students

The chart on p.49

• a chart that needs to be filled in.
• size of E. coli genome: 4e6bp +genes: 4k +transcripts per cell: 1.5k +polypeptide: 2.5k +average size of protein: 30-50kDa
• size of Human genome: 3.3e9bp +genes: 22~25k +transcripts per cell: 40k* +polypeptide: 10~20k +average size of protein: 30-50 kDa
  • we call all the multisplice products of a single transcript a single locus
  • -- *colorectal cell line

Intergenic Region

• what's the official ruling on this definition? Is it ...
  • the region between the stop codon of one gene and the start codon of the next
• do we include regulatory elements?

Week 1 Holdovers

• transformation -- wasn't defined
• "knock-out" -- wasn't defined

Week 2

• we're not releasing the tutorial questions.
• this week's quizzes.
• teach Genbank
• conciseness for the comparison questions
  • emphasize short sentence answers
• point out the past midterms
• don't worry about denaturation, renaturation, hybridization etc.,
• fish for exam questions -- ask about key points / skeleton

Questions from Kunal

• Is the Stop Codon included in the ORF?
• The distinction between ORF and CDS.
  • CDS does not include the 5'UTR
  • ORF includes the 5'UTR
• What proportion of quizzes are counted toward the final grade?
  • Best eight.
• Denaturation with formaldehyde

Disambiguation

• The start codon is allowed to be within the first exon rather than at the very end of it.
  • The first exon is the one after the 5'UTR in the above statement (Although some consider the first exon to BE the 5'UTR)
• Open Reading Frame: Does not include include the introns -- refers to translatable mRNA.
• Coding Sequence: Does not include introns -- this is a concatenation of exons only.
• Coding Region: Allowed to include introns -- in the case of prokarya, there are no introns.

Questions from the floor

• When drawing a diagram, do we want the DNA, primary transcript or the mRNA?
  • As long as it's known what is a primary transcript is vs a mRNA, then that's OK.
• Which strand is "being transcribed"? Enzyme mechanical action vs. sequence information duplication?
  • The coding strand