Download Bioinformatics Powerpoint - Heredity

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
DNA
Transcription
mRNA
Translation
PROTEINS
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
Alanine
Ala
A
Arginine
Arg
Asparagine
Amino
Acid
Triple letter
code
Single
letter
Code
Leucine
Leu
L
R
Lysine
Lys
K
Asn
N
Methionine
Met
M
Aspartic Acid
Asp
D
Phenylalanine
Phe
F
Cysteine
Cys
C
Proline
Pro
P
Glutamic Acid
Glu
E
Serine
Ser
S
Glutamine
Gln
Q
Threonine
Thr
T
Glycine
Gly
G
Tryptophan
Trp
W
Histidine
His
H
Tyrosine
Tyr
Y
Isoleucine
Ile
I
Valine
Val
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:
Cytochrome C
MGDVEKGKKIFIMKSQCHTVEKGGKHKTGPLHG
LFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYL
ENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATN
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