1. in-class activities Sat and Sun Tuesday Thursday Wednesday Friday Monday out-of-class activities Protein Module * ** * * -- !! -- / * = clicker questions ** = tie in of lab to lecture / = in-class assignmment (week 1) -- = on-line questions for out-of-class assessment !! = out of class assignment (week 2)

2. Course Objective– Students will apply past knowledge to new problems use theories and models as way to predict future events Course Objective– Students will apply past knowledge to new problems use theories and models as way to predict future events

3. Higher Level Unit Objective - Students will Explain and give examples of why proteins are essential to cell function. Apply knowledge of protein structures to predict structure of novel amino acid sequences Compare proteins across organisms Be able to use and compare available databases Higher Level Unit Objective - Students will Explain and give examples of why proteins are essential to cell function. Apply knowledge of protein structures to predict structure of novel amino acid sequences Compare proteins across organisms Be able to use and compare available databases

4. Low Level Unit Objective - Students will Explain and give examples of why proteins are essential to cell function. Sketch the basic structure of an amino acid, and describe why and how the side chains affect the function and structure of each amino acid. Describe the four levels of protein structure, and give examples of each. Explain what an enzyme is, understand why enzymes are needed to help chemical reactions proceed in living cells, and know the role of the active site. Explain what mutations are, understand how they occur, and know the role of mutations on protein function. Low Level Unit Objective - Students will Explain and give examples of why proteins are essential to cell function. Sketch the basic structure of an amino acid, and describe why and how the side chains affect the function and structure of each amino acid. Describe the four levels of protein structure, and give examples of each. Explain what an enzyme is, understand why enzymes are needed to help chemical reactions proceed in living cells, and know the role of the active site. Explain what mutations are, understand how they occur, and know the role of mutations on protein function.

5. Review information on transcription and translation

6. What kind of protein structure involves hydrogen bonding along the backbone to form an a-helix? A. primary protein structure B. secondary protein structure C. tertiary protein structure D. quaternary protein structure In-Class Assessment

7. A short segment of a mRNA molecule is shown below. The polypeptide it codes for is also shown: 5'-AUGGUGCUGAAG : methionine-valine-leucine-lysine Assume that a mutation in the DNA occurs so that the fourth base (counting from the 5' end) of the messenger RNA now reads A rather than G. What sequence of amino acids will the mRNA now code for? (You do not need a copy of the genetic code to answer the question.) A. methionine-valine-leucine-lysine B. methionine-lysine-leucine-lysine C. methionine-valine-methionine-lysine D. methionine-methionine-leucine-lysine E. methionine-leucine-leucine-lysine Out-of-class BlackBoard Questions

8. in-class activities in-class activities "Name that structure" You have just discovered a new protein called, topoisomerase. This protein functions as an enzyme that unwinds the DNA double helix, so it can be copied during S phase of the cell cycle. The amino acid sequence of this enzyme is shown below. Cells that contain defective versions of topoisomerase cannot divide because the cell never exits S phase. VAL-PRO-ILE-MET-VAL-ser-GLY-GLY-TRP-PHE-gln-asn-tyr-ser-lys-glu-leu-CYS-tyr-asp-asp-ILE-VAL-PRO-TRP- PHE-VAL-ALA-VAL-PRO (hydrophobic amino acids are in CAPS) What is the shape of topoisomerase? -apply past knowledge to new problems -use theories and models as way to predict future events -apply past knowledge to new problems -use theories and models as way to predict future events

9. Out-of-Class Formative Assessment Name That Protein The purpose of this assignment is to help you understand the importance of a protein of your choosing. You will also research the form and function of your particular protein and how mutations might change the function. 1. Please choose a protein of interest to you from the human genome and give its GeneID as a link to its Entrez entry like this: http://www.ncbi.nlm.nih.gov/gene/5111 2. Briefly discuss what the protein does and why you chose it. 3. How many homologous proteins are known in other organisms. Use both homologene http://www.ncbi.nlm.nih.gov/homologene and ENSEMBL http://useast.ensembl.org/index.html databases. Describe the results in both databases, how they differ. Mention how commo n you think your proteins are and what taxonomic groups have them (just bacteria, just vertebrates etc.) How many transcripts and how many alternative splice forms are known for this protein? Are any of the alternative spliced forms expressed ? Do they have alternative functions? Again look at both data from Evidence database in NCBI and the Transcripts from ENSEMBL. How do the number of alternatively spliced differ between the two databases and which do you feel is more accurate and why. Briefly discuss which cellular component your protein is a part, which biological process(es) does it participate in and which molecular function does it mediate if any? You will find the relevant gene ontology terms in both NCBI Gene and in the UniProt database. Briefly discuss which specific structures or pathways your protein participate in?