Introduction to Bioinformatics - Department of Computer Science


2 Οκτ 2013 (πριν από 3 χρόνια και 6 μήνες)

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Introduction to Bioinformatics

What is Bioinformatics

Easy Answer

Using computers to solve molecular biology
problems; Intersection of molecular biology and
computer science

Hard Answer

Computational techniques (e.g. algorithms, artificial
intelligence, databases) for management and
analysis of biological data and knowledge


Bioinformatics = Biology + Information

Biology is becoming an information science

Computation methods are necessary to
analyze the massive amount of information
that coming out of the genome projects

Bioinformatics is Another
Revolution in Biology

Three concepts, which remain
central to Bioinformatics

Data representation

A complex, dynamic, three
dimensional molecule a simple
string of characters

Three concepts, which remain
central to Bioinformatics

The concept of similarity

Evolution has operated on every sequence

In biomolecular sequences (DNA, RNA or amino acid
sequences). High sequence similarity usually implies
significant functional or structural similarity.

The opposite is not true

Algorithms for comparing sequences and finding
similar regions are at the heart of bioinformatics

Three concepts, which remain
central to Bioinformatics

Bioinformatics is not a theoretical science; it is
driven by the data, which in turn is driven by the
needs of biology.


Microarray technologies

GenBank Growth

Moore’s Law

What do you need to know?

It all depends on your background

Are you a …?

Biologist with some computer knowledge, or

Computer scientist with some biology

Few do both well


Biology for Computer Scientists

Computer Science for Biologists

Biological Information Flow



Gene Sequence

Protein Sequence

Protein Functions

Protein Structure

Cellular Pathways

attempts to model
this pathway

Living Things

Entropy (the tendency to disorder) always

Living organisms have low entropy
compared with things like soil

They are relatively orderly…

The most critical task is to maintain the
distinction between inside and outside

Living Things

In order to maintain low entropy, living organisms
must expend energy to keep things orderly.

They figured out how to do this 4 billion years ago

The functions of life, therefore, are meant to
facilitate the acquisition and orderly expenditure
of energy

Living Things

The compartments with low entropy are
separated from “the world.”

Cells are the smallest unit of such

Bacteria are single
cell organisms

Humans are multi
cell organisms

The “living things” have the
following tasks:

Gather energy from environment

Use energy to maintain inside/outside distinction

Use extra energy to reproduce

Develop strategies for being successful and
efficient at the above tasks

Develop ways to move around

Develop signal transduction capabilities (e.g. vision)

Develop methods for efficient energy capture (e.g.

Develop ways to reproduce effectively

How to accomplish…?

Living compartments on earth have
developed three basic technologies

Ability to separate inside from outside (lipids)

Ability to build three
dimensional molecules
that assist in the critical functions of life
(Protein, RNA)

Ability to compress the information about how
(and when) to build these molecules in linear
code (DNA)

Bioinformatics Schematic of a


Made of hydrophilic (water loving) molecular
fragment connected to hydrophobic fragments

Spontaneously form sheets (lipid membranes) in
which all the hydrophilic ends align on the
outside, and hydrophobic ends align on the inside

Creates a very stable separation, not easy to pass
through except for water and a few other small

What is Nucleotide?

Pentose, base, phosphate group

Pentose: RNA and DNA


Adenine (A),
Cytosine (C),
Guanine (G),
Thymine (T),

Uracil (U).

Nucleic Acid Chain

Condensation reaction


From 5’ to 3’

In DNA or RNA, a nucleic
acid chain is called “Strand”

DNA: double

RNA: a single strand

The number of bases

Base pair (bp) in DNA

DNA Structure

DNA Structure

DNA Structure

RNA Structure and Function

The major role of RNA is to participate in protein

Messenger RNA (mRNA)

Transfer RNA (tRNA)

Ribosomal RNA (rRNA)


The Genetic Code

What is gene?

A gene includes the entire nucleic acid
sequence necessary for the expression of its

Such sequence may be divided into

Regulatory region

Transcriptional region: exons and introns

Exons encode a peptide or functional RNA

Introns will be removed after transcription



The total genetic information of an

For most organisms, it is the complete DNA

For RNA viruses, the genome is the
complete RNA sequence

Genes and Control

Human genome has 3,000,000,000 bps divided into 23
liner segments (chromosome)

A gene has an average 1340 DNA bps, thus specifying a
protein of about

(how many) amino acids

Humans have about 35,000 genes = 40,000,000 DNA bps
= 3% of total DNA in genome

Human have another 2,960,000,000 bps for control
information. (e.g. when, where, how long, etc…)

Gene Expression

An organism may contain many types of cells,
each with distinct shape and function

However, they all have the same genome

The genes in a genome do not have any effect on
cellular functions until they are “expressed”

Different types of cells express different sets of
genes, thereby exhibiting various shapes and

Gene Expression

The production of a protein or a functional
RNA from its gene

Several steps are required


RNA processing

Nuclear transport

Protein synthesis

Gene Expression

Central Dogma




Next …

Protein Structure and Function

An Amino Acid

An amino acid is defined as the molecule
containing an amino group (NH2), a
carboxyl group (COOH) and an R group.


The R group differs among various amino acids.

In a protein, the R group is also call a sidechain.

An Amino Acid

The Twenty Amino Acids of

The Twenty Amino Acids of


― a chain of amino acids linked
together by peptide bonds.

Polypeptides ― long peptides

Oligopeptides ― short peptides (< 10
amino acids)

Protein are made up of one or more
polypeptides with more than 50 amino acids

Protein Structure

Primary Structure

Refers to its amino acid sequence

Secondary structure

Regular, repeated
patterns of folding of
the protein backbone.

Two most common
folding patterns

Alpha helix

Beta sheet

Tertiary Structure

The overall folding of the entire polypeptide
chain into a specific 3D shape

Quaternary Structure

Many proteins are formed more than one
polypeptide chain

Describe the way in which the different
subunits are packed together to form the
overall structure of the protein

Hemoglobin molecule

Quaternary Structure


― rare events, sometimes single base
changes, sometimes larger events

Recombination ― how your genome was
constructed as a mixture of your two parents

Through Natural Selection

Homology (similarity): different species are
assumed to have common ancestors

The genetic variation between different people is

(surprisingly ..)