Bio 310L

Henrik Kibak

California State University Monterey Bay
BIO 310L - Cytochrome C

   
In this lab we will investigate Cytochrome C: gene sequence, coding sequence, amino acid sequence, secondary structure, and tertiary structure.
 
 

Search the NCBI Structure Database for "Cytochrome C Bos"

 

 NCBI
 
Nucleotide sequences are translated into amino acid sequences by ribosomes and tRNAs using a triplet-based code. We can do this ourselves by hand or "in-silico" using a table of the genetic code. Genetic Code
 
Cut and paste the Cytochrome C nucleotide sequence in FASTA format into this program and look at what happens when you translate the DNA into Protein in all six reading frames. ORF Finder
 
When you have translated the coding sequence for Cytochrome C into amino acids, format the translation into FASTA format and search the protein database for similar sequences. Blast (Protein - Protein)
 
Your instructor will show you how to prepare files for multiple alignments. Prepare a multiple alignment of Cytochrome C from a variety of species and see if you can determine the sections of the protein that don't seem to change during evolution. Web versions of Clustal - Japan Europe

Using Cn3D and the Bos taurus Cytochrome C crystal structure, highlight the conserved regions of Cytochrome C and save the image to your website.

Go through this same exercise on your own using "human myoglobin."

Prepare a webpage (Use WORD if you want) titled "Homework #1" and link to it from your index page.

 Cn3D
Homework #1 should contain two multiple alignments, one for Cytochrome C and the other for Myoglobin. It should also contain the two highlighted images.