Protein Evolution Introducing the use of Biology Workbench as a Bioinformatics Tool

What is Bioinformatics? The application of computer technology to the management of biological information It involves the development of computer databases and algorithms that facilitate more efficient biological research, particularly in relation to comparing gene and protein sequences within and between organisms

To begin with let’s review a few basics

Central Dogma of Genetics DNA encodes information about how amino acids will be linked to form proteins. Information is encoded in the sequence of adenine, guanine, cytosine and thymine nucleotides in DNA This information is copied into an mRNA molecules in the process of transcription This information is then used at the ribosomes during the process of translation to dictate the order in which amino acids are assembled to form polypeptides.

So To Summarize Transcription Translation DNA PROTEINS mRNA

About Proteins All proteins are made of amino acids which have been linked in particular sequences Each protein has a particular 3 Dimensional structure which suits it to the function it performs The importance of different proteins varies within an organism; some proteins are produced in all cells of the organism and are essential to the survival of the organism Some proteins are the same or very similar in different organisms however; not all organisms produce the same proteins

Amino Acids There are 20 Different Amino Acids Each has a three letter code, which is often simply the first three letters of its name - there are some exceptions to this though Each amino acid also has a one letter code which makes it easier for scientists to work with, particularly when comparisons need to be made between lengthy proteins The following slide outlines the triple and single letter codes for each amino acid

Amino Acid Codes Amino Acid Triple letter code Single letter Code AlanineAla A ArginineArg R AsparagineAsn N Aspartic AcidAsp D CysteineCys C Glutamic AcidGlu E GlutamineGln Q GlycineGly G HistidineHis H IsoleucineIle I Amino Acid Triple letter code Single letter Code LeucineLeu L LysineLys K MethionineMet M PhenylalaninePhe F ProlinePro P SerineSer S ThreonineThr T TryptophanTrp W TyrosineTyr Y ValineVal V

HOMOLOGUES Proteins that share a common Ancestry They are coded for by genes that have been derived from a shared ancestry One type of homologous proteins are called ORTHOLOGUES Orthologues are: Essentially the “same” proteins in different species Due to passing of “same” gene from a common ancestor when new species diverge from their shared ancestor e.g insulin is present in many species of mammals Common Ancestor (insulin) Species A (Insulin variant 1’) Species B (Insulin variant 2’)

Phylogenetic Trees Phylogeny: Evolutionary relationships between any set of species Phylogeny can be represented as a tree These trees are called phylogenetic tree There are many different way that such trees can be drawn Species that extend from the same branch of the tree share a common ancestor and are more closely related by evolutionary descent than those on different branches of the tree

Aims of this Activity To examine homologous proteins and study an example of an orthologue To become familiar with and use the Biology WorkBench as a Bioinformatics Tool To use the Biology WorkBench to comparing Cytochrome C from a variety of different mammal species To use use Biology WorkBench to create non rooted and rooted phylogenetic trees and to analyse these To apply genetic understanding to explain how different orthologous proteins can arise

Cytochrome c: an Orthologue Cytochrome c is an ancient protein, developed early in the evolution of life It is found in all organisms including eukaryotes and prokaryotes This essential protein performs a key step in the production of cellular energy Inside mitochondria it shuttles electrons along electron transport chains to where they are needed. It has changed little in millions of years of evolution Yeast cells, plant cells or human cells all have a very similar form of cytochrome c

Cytochrome c The amino acid sequence in human cytochrome c, using the single letter code is: MGDVEKGKKIFIMKSQCHTVEKGGKHKTGPLHG LFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYL ENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATN Cytochrome C

Molecular Comparison of Cytochrome c in various species YOUR TASK: To use the Biology WorkBench to compare the amino acid sequences of cytochrome c from a variety of species and draw conclusions about their relatedness based upon this Before you begin this activity you will need to open the cytochrome c data file and save it onto your desk top. To open the file you will need to click on the button at the bottom of this page, but first read the dot point below carefully. After you have opened the document click on file then scroll down and click on Save as and save onto the desktop. Don’t change the name of the file. Now click here to open the file

Molecular Comparison of Cytochrome c in various species To proceed with the activity you will need a copy of: The Instruction For Using the Biology WorkBench handout The Data Sheet The BioInformatics and Protein Evolution Worksheet To access the Biology WorkBench click here

YOU HAVE FINISHED WELL DONE! WELCOME TO OUR NEW WORLD OF BIOINFORMATIC