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Presenter: Sandra Porter
 

Preparation:  

Get Cn3D here:  http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml  and install it on your computer.

Schedule:  

Part I.  Get Cn3D going

A.  Download 1NAJ.cn3

• Turn structures

• Move structures without turning

• Make structures bigger / smaller

• Change rendering style

• Change coloring style

• Show and hide parts of a structure

• Make color key

B.  Become familiar with Cytochrome Oxidase C

• Look at chains - how many?
  • try different coloring styles - what do you see?

• Look at active site
  • rendering style tubes, coloring style element
  • heme by a copper

• Look at metal bonds
  • select copper at the active site
  • Select by distance - 5 angstroms
  • Show selected
  • change rendering style to Ball n Stick
  • Clear highlights

Part II.  Talk about Bio-ITEST bioinformatics curriculum for high school students

NSF ITEST grant to NWABR, Digital World Biology, EdLab Group, in collaboration with Shoreline Community College

Combines career education with bioinformatics & DNA barcoding & bioethics

• Beginner strand:  Using Bioinformatics:  Genetic Testing
  • breast cancer,
  • genetic testing,
  • bioethics
  • comparing sequences
  • breast cancer protein structure

• Advanced strand:  Using Bioinformatics:  Genetic Research
  • Compare sequences,
  • make phylogenetic trees,
  • look at Cytochrome Oxidase & Murder,
  • isolating DNA and sequencing
  • DNA barcoding

• Exploring Careers

Part III.  Solve the mystery

• Divide into groups & get your structure - these are normal & mystery structures superimposed with VAST

• Structure A

• Structure B

• Structure C

• Structure D

• Structure E

• Structure F

• Work with your group to solve the mystery

• Present your results and theory to the class