Bioinformatics and Molecular Biology Background
 
DNA makes RNA makes Protein
  • DNA contains Information coded in a linear sequence of dA's, dT's, dC's and dG's
  • DNA is Double-Stranded
  • DNA can be copied
 
  • RNA is a linear chain of of A's, U's, C's, and G's
  • RNA is Functional, can have important Structure, and can carry Information
  • The Genetic Code relates the Information in DNA to the Structure of Proteins through RNA
 
  • Proteins are linear chains of 20 different amino acids
  • Amino acids have unique characteristics based on their specific side chain
  • The structure of a protein is based on the specific sequence of amino acids along the chain
 
Evolution by Natural Selection
 
  • Organisms have their Genetic Information coded in the DNA of their Chromosomes.
  • The organization of Chromosomal DNA is very different for Eukaryotes and Prokaryotes.
  • Genetic Information changes through mutation and the change can be passed on to subsequent generations
  • The probability of the change being passed to subsequent generations is increased if the change is beneficial
  • The sequence of dA's, dT's, dC's and dG's is more similar in closely related organisms and less similar in distantly related organisms.
 

In this course we use all of these concepts to examine the relatedness of a taxonomic group of intertidal mussels, and investigate the invasion of a cryptic species in this group.  The markers we will use for this investigation are nuclear (eukaryotic) DNA encoding Lysin (a sexually selected protein), and mitochondrial (prokaryotic) DNA encoding Cytochrome c Oxidase (a respiratory chain protein).
 

Using Computers for Bioinformatics MLML Computer Lab Instructions
DNA Structure  
DNA Replication  
Polymerase Chain Reaction
The Polymerase Chain Reaction (PCR): Simple Flash Animation then look at the details (excellent!).

Primer Matching
 

PDF of Primer Matching Activity (Word Doc)
Cloning
  		 
DNA Sequencing
  		DNA sequencing: Sanger - Old School - New School
Reading DNA sequence data file using Chromas

Checking the results of sequencing your PCR products.

Reading DNA Sequences (Chromas to FASTA)
National Center for Biotechnology Information (NCBI)
  		Using NCBI
Searching the NCBI nucleotide database using BLAST
  		Using Blast
Cleaning up your sequence data
  		 
Nucleotide Alignments
  		Help with ClustalX
Finding Open Reading Frames

Genetic Code: DNA version - RNA version

PDF of Open Reading Frames (ORFs) Exercise (Word Doc)

Using ORF Finder and Non-standard Genetic Codes
Amino acid chemistry is important for preparing alignments
  		Amino Acid Explorer (NCBI)
Protein Alignments

Protein Alignment by Hand (problem set)
Answers to problem set here

Protein Alignment using ClustalX
Nucleotide/Protein Alignments using Codon Align
  		 
Preparing Trees using Phylip
 

First you need ClustalX output.

Then you need a postscript plotting program.
Looking at Protein Stucture

Using Cn3D to Compare Sequences to Known Structures

Using Protein Explorer