The Process Learning Objectives: Course Objective: Apply past knowledge to new problems Unit Objectives: Students should be able to: 1)Explain and give examples of why proteins are essential to cell function. 2)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. 3)Describe the four levels of protein structure, and give examples of each. 4)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. 5)Explain what mutations are, understand how they occur, and know the role of mutations on protein function. Higher Level Objectives 1) Explain and give examples of why proteins are essential to cell function. 2) Apply knowledge of protein structures to predict structure of novel amino acid sequences 3) Compare proteins across organisms. 4) Be able to use and compare available databases. In-class activities/assessments • "Clicker" questions will be included in the lectures, with a minimum of 4 questions per lecture (L1-5) • "Name that structure" (L2,5 and H 2) -students are given an a.a. sequence and asked to identify alpha helix or beta pleated sheets. Out-class activities/assessments • BlackBoard quiz that reviews material from lecture.(L1-5) • Pre-Lab BlackBoard quiz to make sure that students understand what they are doing in lab and how it relates to information we covered in class.(L1-5) • "Name that Protein" assignment (L1,3,5,6 and H1-4) Example Assignment - Out of Class 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 common you think your proteins are and what taxonomic groups have them (just bacteria, just vertebrates etc.) 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? Please send summaries of your results and your conclusions and discussions to [email protected] Please include sufficient output from your analyses (copy and paste or screen dumps) to support each of your answers/conclusions. It is the conclusions that are the most important. Short answers are not appropriate. Please respond with full sentences and paragraphs on each topic above.